From 261cb04f9472aa56ea07c05f5453b10867a09f82 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 26 Jan 2025 18:43:50 +0100 Subject: [PATCH 01/75] Modifications to register exemplar IVAS/APSuite concepts for the atom probe app, we have edited these here, despite there is currently an active NIAC-feature branch fairmat-2024-apm that is in the process of negotiation with NIAC. To move forward we still work with the old fairmat branch, knowing that the example will need refactoring and reprocessing ones NXapm has been accepted as an official appdef in NeXus by the NIAC, likely end of Q1 2025 --- contributed_definitions/nyaml/NXapm.yaml | 42 +- .../nyaml/NXapm_hit_finding.yaml | 5 + contributed_definitions/nyaml/NXapm_msr.yaml | 35 +- .../nyaml/NXapm_reconstruction.yaml | 57 ++ .../nyaml/NXapm_volt_and_bowl.yaml | 4 + .../nyaml/NXpositioner_sts.yaml | 552 ++++++++++++++++++ .../nyaml/NXpulser_apm.yaml | 2 +- 7 files changed, 676 insertions(+), 21 deletions(-) create mode 100644 contributed_definitions/nyaml/NXpositioner_sts.yaml diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 4b497fd048..3a5f0945d9 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -78,6 +78,7 @@ NXapm(NXobject): We follow this habit of most atom probe groups. Such interrupted runs should be stored as individual :ref:`NXentry` instances in one NeXus file. experiment_alias(NX_CHAR): + exists: recommended doc: | Either an identifier or an alias that is human-friendly so that scientists find that experiment again. For experiments usually this is the run_number but for simulation typically no run_numbers are issued. @@ -124,6 +125,10 @@ NXapm(NXobject): doc: | ISO 8601 time code with local time zone offset to UTC included when the atom probe session ended. + elapsed_time(NX_FLOAT): + doc: | + TODO + unit: NX_TIME (NXcite): exists: [min, 0, max, infty] doi(NX_CHAR): @@ -373,6 +378,7 @@ NXapm(NXobject): unit: NX_ANGLE # describing the geometry of the specimen coordinate_system_set(NXcoordinate_system_set): + exists: recommended # should be made required doc: | Set to hold different coordinate systems conventions. Inspect the description of the :ref:`NXcoordinate_system_set` @@ -432,11 +438,18 @@ NXapm(NXobject): measurement(NXapm_msr): exists: optional instrument(NXinstrument): + identifier_name(NX_UINT): + doc: | + TODO instrument_name(NX_CHAR): exists: optional fabrication(NXfabrication): vendor(NX_CHAR): model(NX_CHAR): + serial_number(NX_UINT): + doc: | + TODO + unit: NX_UNITLESS identifier(NXidentifier): exists: recommended reflectron(NXreflectron): @@ -476,22 +489,21 @@ NXapm(NXobject): The wavelength of the radiation emitted by the source. unit: NX_WAVELENGTH # use NXbeam in the future - # stage_lab(NXstage_lab): - analysis_chamber(NXchamber): + stage(NXstage_lab): exists: recommended - flight_path(NX_FLOAT): - exists: recommended + specimen_temperature(NX_FLOAT): doc: | - The space inside the atom probe along which ions pass nominally - when they leave the specimen and travel to the detector. - unit: NX_LENGTH + TODO + unit: NX_TEMPERATURE + analysis_chamber(NXchamber): + exists: recommended # atmosphere(NXcollection): # buffer_chamber(NXchamber): # load_lock_chamber(NXchamber): # getter_pump(NXpump): # roughening_pump(NXpump): # turbomolecular_pump(NXpump): - status(NX_CHAR): + status(NX_CHAR): event_data_apm_set(NXevent_data_apm_set): exists: optional # the case of allowing to not have event_data but only the above-mentioned instrument @@ -554,10 +566,8 @@ NXapm(NXobject): # getter_pump(NXpump): # roughening_pump(NXpump): # turbomolecular_pump(NXpump): - simulation(NXapm_sim): exists: optional - atom_probe(NXroi): exists: recommended # [min, 0, max, infty] doc: | @@ -607,8 +617,9 @@ NXapm(NXobject): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): + exists: optional algorithm(NX_CHAR): - + exists: optional hit_finding(NXapm_hit_finding): exists: recommended # we careful how we go about doing this here, we recommended to make some details of the hit_finding @@ -636,6 +647,8 @@ NXapm(NXobject): # results of the hit_finding algorithm hit_quality_types(NX_CHAR): exists: optional + total_hit_quality(NX_UINT): + exists: optional hit_quality_identifier(NX_UINT): exists: optional hit_positions(NX_NUMBER): @@ -734,8 +747,10 @@ NXapm(NXobject): dim: (n,) # result calibrated_tof(NX_FLOAT): + exists: recommended # make required dim: (n,) - + tof_zero_estimate(NX_FLOAT): + exists: optional mass_to_charge_conversion(NXprocess): exists: recommended sequence_index(NX_POSINT): @@ -847,7 +862,6 @@ NXapm(NXobject): algorithm(NX_CHAR): # number_of_ion_types(NX_UINT): maximum_number_of_atoms_per_molecular_ion(NX_UINT): - mass_to_charge_distribution(NXprocess): exists: recommended sequence_index(NX_POSINT): @@ -870,7 +884,6 @@ NXapm(NXobject): axis_mass_to_charge(NX_FLOAT): dim: (n_bins,) \@long_name(NX_CHAR): - background_quantification(NXprocess): exists: recommended sequence_index(NX_POSINT): @@ -932,7 +945,6 @@ NXapm(NXobject): position(NX_NUMBER): # peak deconvolution(NXprocess): - peak_identification(NXprocess): # aka specify ranging definitions i.e. mqmin, mqmax intervals (ranges) and (molecular) ion candidates exists: recommended sequence_index(NX_POSINT): diff --git a/contributed_definitions/nyaml/NXapm_hit_finding.yaml b/contributed_definitions/nyaml/NXapm_hit_finding.yaml index d71e671939..948db910d1 100644 --- a/contributed_definitions/nyaml/NXapm_hit_finding.yaml +++ b/contributed_definitions/nyaml/NXapm_hit_finding.yaml @@ -60,6 +60,11 @@ NXapm_hit_finding(NXprocess): # when evolving these ideas further inherit from Identifier have to be within hit_quality_identifier. unit: NX_UNITLESS dim: (p,) + total_hit_quality(NX_UINT): + doc: | + Individual total how many hits of specific quality were found. + In the order of hit_quality_types. + dim: (n_ht,) hit_multiplicity(NX_UINT): doc: | This processing yields for each ion with how many others it evaporated diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml index c9a15fd480..984402984a 100644 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ b/contributed_definitions/nyaml/NXapm_msr.yaml @@ -101,6 +101,10 @@ NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_met doc: | A local electrode guiding the ion flight path. Also called counter or extraction electrode. + voltage(NX_FLOAT): + doc: | + Acceleration voltage + unit: NX_VOLTAGE # but the local_electrode does not really on purpose create a magnetic field, # specific for an electro-magnetic lens is the symmetry of its field # NEW ISSUE: for now keep that we have what is an NXlens_em @@ -110,18 +114,39 @@ NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_met ion_detector(NXdetector): doc: | Detector for taking raw time-of-flight and ion/hit impact positions data. + mcp_efficiency(NX_FLOAT): + doc: | + TODO + unit: NX_DIMENSIONLESS + mesh_efficiency(NX_FLOAT): + doc: | + TODO + unit: NX_DIMENSIONLESS # model, serial_number, manufacturer_name all inherited from NXdetector base class pulser(NXpulser_apm): - stage_lab(NXstage_lab): + stage(NXstage_lab): # NEW ISSUE: add NXapm_energy_analyzer, a voltage grid like done in Rouen/GPM analysis_chamber(NXchamber): + flight_path(NX_FLOAT): + exists: recommended + doc: | + The space inside the atom probe along which ions pass nominally + when they leave the specimen and travel to the detector. + unit: NX_LENGTH + pressure(NX_FLOAT): + doc: | + TODO + unit: NX_PRESSURE buffer_chamber(NXchamber): load_lock_chamber(NXchamber): getter_pump(NXpump): roughening_pump(NXpump): turbomolecular_pump(NXpump): - status(NX_CHAR): + comments(NX_CHAR): doc: | - A statement whether the measurement was successful or failed prematurely. - enumeration: [success, failure, unknown] - (NXevent_data_apm_set): + TODO + status(NX_CHAR): + doc: | + A statement whether the measurement was successful or failed prematurely. + enumeration: [success, failure, unknown] + (NXevent_data_apm_set): diff --git a/contributed_definitions/nyaml/NXapm_reconstruction.yaml b/contributed_definitions/nyaml/NXapm_reconstruction.yaml index 5529442a0c..4f1ee772d1 100644 --- a/contributed_definitions/nyaml/NXapm_reconstruction.yaml +++ b/contributed_definitions/nyaml/NXapm_reconstruction.yaml @@ -30,6 +30,63 @@ NXapm_reconstruction(NXprocess): in this free-text field to guide how to parameterize this better in the future. For LEAP systems and reconstructions performed with IVAS/APSuite see `T. Blum et al. `_ (page 371). + quality(NX_CHAR): + doc: | + TODO + primary_element(NX_CHAR): + doc: | + TODO + efficiency(NX_FLOAT): + doc: | + TODO + unit: NX_DIMENSIONLESS + evaporation_field(NX_FLOAT): + doc: | + TODO + unit: NX_ANY + image_compression(NX_FLOAT): + doc: | + Image compression factor (ICF) + unit: NX_UNITLESS + kfactor(NX_FLOAT): + doc: | + k factor + unit: NX_UNITLESS + volume(NX_FLOAT): + doc: | + Volume of the reconstruction + unit: NX_VOLUME + shank_angle(NX_FLOAT): + doc: | + Shank angle + unit: NX_ANGLE + obb(NXobject): # NXcg_polyhedron + doc: | + Tight, axis-aligned bounding box about the point cloud of the reconstruction. + xmin(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH + xmax(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH + ymin(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH + ymax(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH + zmin(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH + zmax(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH protocol_name(NX_CHAR): doc: | Qualitative statement about which reconstruction protocol was used. diff --git a/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml b/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml index 5a52bd765c..ac7a478728 100644 --- a/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml +++ b/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml @@ -33,3 +33,7 @@ NXapm_volt_and_bowl(NXprocess): # when evolving these ideas further inherit fro Calibrated time-of-flight. unit: NX_TIME dim: (n,) + tof_zero_estimate(NX_FLOAT): + doc: | + TODO + unit: NX_TIME diff --git a/contributed_definitions/nyaml/NXpositioner_sts.yaml b/contributed_definitions/nyaml/NXpositioner_sts.yaml new file mode 100644 index 0000000000..729a270bc2 --- /dev/null +++ b/contributed_definitions/nyaml/NXpositioner_sts.yaml @@ -0,0 +1,552 @@ +category: base +doc: | + A generic positioner such as a motor or piezo-electric transducer. +type: group +NXpositioner_sts(NXobject): + name: + doc: | + symbolic or mnemonic name (one word) + description: + doc: | + description of positioner + value(NX_NUMBER): + unit: NX_ANY + doc: | + best known value of positioner - need [n] as may be scanned + dimensions: + rank: 1 + dim: [[1, n]] + raw_value(NX_NUMBER): + unit: NX_ANY + doc: | + raw value of positioner - need [n] as may be scanned + dimensions: + rank: 1 + dim: [[1, n]] + target_value(NX_NUMBER): + unit: NX_ANY + doc: | + targeted (commanded) value of positioner - need [n] as may be scanned + dimensions: + rank: 1 + dim: [[1, n]] + tolerance(NX_NUMBER): + unit: NX_ANY + doc: | + maximum allowable difference between target_value and value + dimensions: + rank: 1 + dim: [[1, n]] + soft_limit_min(NX_NUMBER): + unit: NX_ANY + doc: | + minimum allowed limit to set value + soft_limit_max(NX_NUMBER): + unit: NX_ANY + doc: | + maximum allowed limit to set value + velocity(NX_NUMBER): + unit: NX_ANY + doc: | + velocity of the positioner (distance moved per unit time) + acceleration_time(NX_NUMBER): + unit: NX_ANY + doc: | + time to ramp the velocity up to full speed + controller_record: + doc: | + Hardware device record, e.g. EPICS process variable, taco/tango ... + \@default: + doc: | + .. index:: plotting + + Declares which child group contains a path leading + to a :ref:`NXdata` group. + + It is recommended (as of NIAC2014) to use this attribute + to help define the path to the default dataset to be plotted. + See https://www.nexusformat.org/2014_How_to_find_default_data.html + for a summary of the discussion. + depends_on(NX_CHAR): + doc: | + NeXus positions components by applying a set of translations and rotations + to apply to the component starting from 0, 0, 0. The order of these operations + is critical and forms what NeXus calls a dependency chain. The depends_on + field defines the path to the top most operation of the dependency chain or the + string "." if located in the origin. Usually these operations are stored in a + NXtransformations group. But NeXus allows them to be stored anywhere. + + .. todo:: + Add a definition for the reference point of a positioner. + (NXtransformations): + doc: | + This is the group recommended for holding the chain of translation + and rotation operations necessary to position the component within + the instrument. The dependency chain may however traverse similar groups in + other component groups. + position(NXtransformations): + doc: | + To clarify the frame laboratory frame. The scanning area in x, y, and z position in the + frame. + z_contronller(NX_NUMBER): + doc: | + This controllers task is to continuously adjust the Z position of the stm tip in order + to keep the selected control signal as close as possible to the Set Point. Different control + signals lead to different contronller beahvior. + z_offset(NX_NUMBER): + unit: NX_LENGTH + doc: | + Offset added to the initial averaged position Zaver before starting to swepp. + tip_position_z(NX_NUMBER): + unit: NX_LENGTH + doc: | + Indicate the tip position Z between tip and sample. The tip position can also be varied when + the controller is not running. + controller_name(NX_CHAR): + doc: | + Controller name. This name which will be displayed at places where you can select a + controller. + setpoint(NX_NUMBER): + unit: NX_CURRENT + doc: | + Set Point is the desired value of the control signal. It can be set by editing the number + or using the slider bar. Click the "Set" button above the input field to use the actual + value as Set Point. The slider shows the Set Point as well as the current value. + tip_lift(NX_NUMBER): + unit: NX_LENGTH + doc: | + Lifts the tip by the specified amount when then controller is switched off. This can be + a positive or a negative number, i.e. the tip can also be moved towards the sample. Be + careful with sign and value when using this feature. + switch_off_delay(NX_NUMBER): + unit: NX_TIME + doc: | + Use this parameter for a reproducible position when switching off the Z-controller. + When >0 and the Z-controller is switched off, it doesn't switch off immediately but continues + to run for the specified time and averages the Z position. + z_controller_hold(NX_BOOLEAN): + doc: | + (In bias spectroscopy) Select whether to set the Z-Controller on hold (i.e. disabled) during + the sweep. It is selected by default. When deselected, Z-offset and Z control time parameters + are disabled. + final_z(NX_NUMBER): + unit: NX_LENGTH + doc: | + The final z-position during the bias spectroscopy scan. The availability of values is + related to the mode of scanning. + + # scan_control(NXcollection): + # doc: | + # To control the tip and various scan operations. + scanfield(NX_NUMBER): + unit: NX_LENGTH + doc: | + Configure the scan frame like x position; y position; width; height. + pixels_line(NX_NUMBER): + unit: NX_COUNT + doc: | + Scan resolution by setting the Lines equal to Pixels. + lines(NX_NUMBER): + unit: NX_ANY + doc: | + Define the image resolution. + speed_forw(NX_NUMBER): + unit: NX_ANY + doc: | + Define the scan forward speed in the forward direction. + speed_backw(NX_NUMBER): + unit: NX_ANY + doc: | + Define the scan backward speed in the forward direction. + piezo_calibration: + doc: | + Piezo calibration module is used to define the X Y Z piezos calibration. + active_calib(NX_CHAR): + doc: | + The name of calibration type. + calib_N(NX_NUMBER): + + # z_contronller(NXcollection): + # name: + # doc: | + # This controllers task is to continuously adjust the Z position of the stm tip in order to keep the selected control signal as close as possible to the Set Point. Different contro; signals lead to different contronller beahvior. + # z_offset(NX_NUMBER): + # doc: Offset added to the initial averaged position Zaver before starting to swepp. + # unit: NX_LENGTH + # tip_position_z(NX_NUMBER): + # doc: Indicate the tip position Z between tip and sample. The tip position can also be varied when the controller is not running. + # unit: NX_LENGTH + # controller_name: + # doc: Controller name. This name which will be displayed at places where you can select a controller. + # setpoint(NX_NUMBER): + # doc: Set Point is the desired value of the control signal. It can be set by editing the number or using the slider bar. Click the "Set" button above the input field to use the actual value as Set Point. The slider shows the Set Point as well as the current value. + # unit: NX_CUTTENT + # setpoint_unit: + # doc: The unit of setpoint during the scanning. + p_gain(NX_NUMBER): + unit: NX_UNITLESS + doc: | + The Type switches controller parameters between :math:`P/I` (proportional gain/integral gain) and :math:`P/T` + (proportional gain/time constant). The formula for the controller in the frequency domain is: + :math:`G(s) = P + I/s = P(1 + 1/(Ts))`. + The integral gain and time constant are related as follows: :math:`I = P/T`. + i_gain(NX_NUMBER): + unit: NX_UNITLESS + doc: | + The Type switches controller parameters between :math:`P/I` (proportional gain/integral gain) and + P/T (proportional gain/time constant). The formula for the controller in the frequency + domain is: :math:`G(s) = P + I/s = P(1 + 1/(Ts))`. The integral gain and time constant are related + as follows: `:math:I = P/T`. + time_const(NX_NUMBER): + unit: NX_TIME + doc: | + The Type switches controller parameters between :math:`P/I` (proportional gain/integral gain) and + :math:`P/T` (proportional gain/time constant). The formula for the controller in the frequency + domain is: :math:`G(s) = P + I/s = P(1 + 1/(Ts))`. The integral gain and time constant are related + as follows: :math:`I = P/T`. + + # tip_lift(NX_NUMBER): + # doc: | + # Lifts the tip by the specified amount when then controller is switched off. This + # can be a positive or a negative number, i.e. the tip can also be moved towards the sample. + # Be careful with sign and value when using this feature. + # unit: NX_LENGTH + # switch_off_delay(NX_NUMBER): + # doc: | + # Use this parameter for a reproducible position when switching off the Z-controller. + # When >0 and the Z-controller is switched off, it doesn't switch off immediately but + # continues to run for the specified time and averages the Z position. + # unit: NX_TIME + # z_controller_hold(NX_CHAR): + # doc: | + # (In biase spectroscopy) Select whether to set the Z-Controller on hold (i.e. disabled) + # during the sweep. It is selected by default. When deselected, Z-offset and Z control time + # parameters are disabled. + scan_contronller(NX_NUMBER): + doc: | + There are 2 parameters in X and Y directions. If you know them, you can enter the 2nd order + piezo characteristics to compensate for it. The following equation shows the interpretation + of the 2nd order correction parameter: For the X-piezo: + :math:`Ux = 1/cx · X + cxx · X2`; with units: :math:`[V] = [V/m] · [m] + [V/m2] · [m2]` + where cx is the calibration of the piezo X and cxx is the 2nd order correction. :math:`(V/m^2)` + drift(NX_NUMBER): + unit: NX_ANY + doc: | + There are 2 parameters in X and Y directions. Define the drift speed for all three axes. + When the compensation is on, the piezos will start to move at that speed. + drift_correction_status(NX_CHAR): + doc: | + Use the button to turn on/off the drift compensation. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# c283fbd6a2f31ecac078679a845a38ab1b6a4da57e37453198e1cfacdd04e0e2 +# +# +# +# +# +# A generic positioner such as a motor or piezo-electric transducer. +# +# +# +# symbolic or mnemonic name (one word) +# +# +# +# +# description of positioner +# +# +# +# +# best known value of positioner - need [n] as may be scanned +# +# +# +# +# +# +# +# raw value of positioner - need [n] as may be scanned +# +# +# +# +# +# +# +# targeted (commanded) value of positioner - need [n] as may be scanned +# +# +# +# +# +# +# +# maximum allowable difference between target_value and value +# +# +# +# +# +# +# +# minimum allowed limit to set value +# +# +# +# +# maximum allowed limit to set value +# +# +# +# +# velocity of the positioner (distance moved per unit time) +# +# +# +# +# time to ramp the velocity up to full speed +# +# +# +# +# Hardware device record, e.g. EPICS process variable, taco/tango ... +# +# +# +# +# .. index:: plotting +# +# Declares which child group contains a path leading +# to a :ref:`NXdata` group. +# +# It is recommended (as of NIAC2014) to use this attribute +# to help define the path to the default dataset to be plotted. +# See https://www.nexusformat.org/2014_How_to_find_default_data.html +# for a summary of the discussion. +# +# +# +# +# NeXus positions components by applying a set of translations and rotations +# to apply to the component starting from 0, 0, 0. The order of these operations +# is critical and forms what NeXus calls a dependency chain. The depends_on +# field defines the path to the top most operation of the dependency chain or the +# string "." if located in the origin. Usually these operations are stored in a +# NXtransformations group. But NeXus allows them to be stored anywhere. +# +# .. todo:: +# Add a definition for the reference point of a positioner. +# +# +# +# +# This is the group recommended for holding the chain of translation +# and rotation operations necessary to position the component within +# the instrument. The dependency chain may however traverse similar groups in +# other component groups. +# +# +# +# +# To clarify the frame laboratory frame. The scanning area in x, y, and z position in the +# frame. +# +# +# +# +# This controllers task is to continuously adjust the Z position of the stm tip in order +# to keep the selected control signal as close as possible to the Set Point. Different control +# signals lead to different contronller beahvior. +# +# +# +# +# Offset added to the initial averaged position Zaver before starting to swepp. +# +# +# +# +# Indicate the tip position Z between tip and sample. The tip position can also be varied when +# the controller is not running. +# +# +# +# +# Controller name. This name which will be displayed at places where you can select a +# controller. +# +# +# +# +# Set Point is the desired value of the control signal. It can be set by editing the number +# or using the slider bar. Click the "Set" button above the input field to use the actual +# value as Set Point. The slider shows the Set Point as well as the current value. +# +# +# +# +# Lifts the tip by the specified amount when then controller is switched off. This can be +# a positive or a negative number, i.e. the tip can also be moved towards the sample. Be +# careful with sign and value when using this feature. +# +# +# +# +# Use this parameter for a reproducible position when switching off the Z-controller. +# When >0 and the Z-controller is switched off, it doesn't switch off immediately but continues +# to run for the specified time and averages the Z position. +# +# +# +# +# (In bias spectroscopy) Select whether to set the Z-Controller on hold (i.e. disabled) during +# the sweep. It is selected by default. When deselected, Z-offset and Z control time parameters +# are disabled. +# +# +# +# +# The final z-position during the bias spectroscopy scan. The availability of values is +# related to the mode of scanning. +# +# +# +# +# +# Configure the scan frame like x position; y position; width; height. +# +# +# +# +# Scan resolution by setting the Lines equal to Pixels. +# +# +# +# +# Define the image resolution. +# +# +# +# +# Define the scan forward speed in the forward direction. +# +# +# +# +# Define the scan backward speed in the forward direction. +# +# +# +# +# Piezo calibration module is used to define the X Y Z piezos calibration. +# +# +# +# +# The name of calibration type. +# +# +# +# +# +# +# The Type switches controller parameters between :math:`P/I` (proportional gain/integral gain) and :math:`P/T` +# (proportional gain/time constant). The formula for the controller in the frequency domain is: +# :math:`G(s) = P + I/s = P(1 + 1/(Ts))`. +# The integral gain and time constant are related as follows: :math:`I = P/T`. +# +# +# +# +# The Type switches controller parameters between :math:`P/I` (proportional gain/integral gain) and +# P/T (proportional gain/time constant). The formula for the controller in the frequency +# domain is: :math:`G(s) = P + I/s = P(1 + 1/(Ts))`. The integral gain and time constant are related +# as follows: `:math:I = P/T`. +# +# +# +# +# The Type switches controller parameters between :math:`P/I` (proportional gain/integral gain) and +# :math:`P/T` (proportional gain/time constant). The formula for the controller in the frequency +# domain is: :math:`G(s) = P + I/s = P(1 + 1/(Ts))`. The integral gain and time constant are related +# as follows: :math:`I = P/T`. +# +# +# +# +# +# There are 2 parameters in X and Y directions. If you know them, you can enter the 2nd order +# piezo characteristics to compensate for it. The following equation shows the interpretation +# of the 2nd order correction parameter: For the X-piezo: +# :math:`Ux = 1/cx · X + cxx · X2`; with units: :math:`[V] = [V/m] · [m] + [V/m2] · [m2]` +# where cx is the calibration of the piezo X and cxx is the 2nd order correction. :math:`(V/m^2)` +# +# +# +# +# There are 2 parameters in X and Y directions. Define the drift speed for all three axes. +# When the compensation is on, the piezos will start to move at that speed. +# +# +# +# +# Use the button to turn on/off the drift compensation. +# +# +# diff --git a/contributed_definitions/nyaml/NXpulser_apm.yaml b/contributed_definitions/nyaml/NXpulser_apm.yaml index fbb3a8cf4c..7b5d93cae3 100644 --- a/contributed_definitions/nyaml/NXpulser_apm.yaml +++ b/contributed_definitions/nyaml/NXpulser_apm.yaml @@ -74,7 +74,7 @@ NXpulser_apm(NXobject): name(NX_CHAR): doc: | Given name/alias. - (NXfabrication): + fabrication(NXfabrication): wavelength(NX_FLOAT): doc: | Nominal wavelength of the laser radiation. From 8cfc492c1f56c4682390941faf5dfc73d9ba1cdb Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 26 Jan 2025 22:07:51 +0100 Subject: [PATCH 02/75] make nxdl causing many changes because change of year and changes in nyaml addressing proper handling of copyright dates as discussed in e.g. #1303 on the niac side --- applications/NXarpes.nxdl.xml | 2 +- base_classes/NXbeam.nxdl.xml | 2 +- base_classes/NXdata.nxdl.xml | 2 +- base_classes/NXdetector.nxdl.xml | 2 +- base_classes/NXentry.nxdl.xml | 2 +- base_classes/NXenvironment.nxdl.xml | 2 +- base_classes/NXinstrument.nxdl.xml | 2 +- base_classes/NXmonochromator.nxdl.xml | 2 +- base_classes/NXroot.nxdl.xml | 2 +- base_classes/NXsample.nxdl.xml | 2 +- base_classes/NXsample_component.nxdl.xml | 2 +- base_classes/NXsensor.nxdl.xml | 2 +- base_classes/NXsubentry.nxdl.xml | 2 +- base_classes/NXtransformations.nxdl.xml | 2 +- base_classes/NXuser.nxdl.xml | 2 +- contributed_definitions/NXaberration.nxdl.xml | 2 +- contributed_definitions/NXactuator.nxdl.xml | 2 +- contributed_definitions/NXapm.nxdl.xml | 46 +++++++---- .../NXapm_charge_state_analysis.nxdl.xml | 2 +- .../NXapm_compositionspace_config.nxdl.xml | 2 +- .../NXapm_compositionspace_results.nxdl.xml | 2 +- .../NXapm_hit_finding.nxdl.xml | 11 ++- contributed_definitions/NXapm_msr.nxdl.xml | 54 ++++++++++--- .../NXapm_paraprobe_clusterer_config.nxdl.xml | 2 +- ...NXapm_paraprobe_clusterer_results.nxdl.xml | 2 +- .../NXapm_paraprobe_distancer_config.nxdl.xml | 2 +- ...NXapm_paraprobe_distancer_results.nxdl.xml | 2 +- ...Xapm_paraprobe_intersector_config.nxdl.xml | 2 +- ...apm_paraprobe_intersector_results.nxdl.xml | 2 +- .../NXapm_paraprobe_nanochem_config.nxdl.xml | 2 +- .../NXapm_paraprobe_nanochem_results.nxdl.xml | 2 +- .../NXapm_paraprobe_ranger_config.nxdl.xml | 2 +- .../NXapm_paraprobe_ranger_results.nxdl.xml | 2 +- .../NXapm_paraprobe_selector_config.nxdl.xml | 2 +- .../NXapm_paraprobe_selector_results.nxdl.xml | 2 +- .../NXapm_paraprobe_spatstat_config.nxdl.xml | 2 +- .../NXapm_paraprobe_spatstat_results.nxdl.xml | 2 +- .../NXapm_paraprobe_surfacer_config.nxdl.xml | 2 +- .../NXapm_paraprobe_surfacer_results.nxdl.xml | 2 +- ...Xapm_paraprobe_tessellator_config.nxdl.xml | 2 +- ...apm_paraprobe_tessellator_results.nxdl.xml | 2 +- .../NXapm_paraprobe_tool_common.nxdl.xml | 2 +- .../NXapm_paraprobe_tool_config.nxdl.xml | 2 +- .../NXapm_paraprobe_tool_results.nxdl.xml | 2 +- ...NXapm_paraprobe_transcoder_config.nxdl.xml | 2 +- ...Xapm_paraprobe_transcoder_results.nxdl.xml | 2 +- .../NXapm_ranging.nxdl.xml | 2 +- .../NXapm_reconstruction.nxdl.xml | 77 ++++++++++++++++++- contributed_definitions/NXapm_sim.nxdl.xml | 2 +- .../NXapm_volt_and_bowl.nxdl.xml | 7 +- contributed_definitions/NXatom_set.nxdl.xml | 2 +- .../NXbeam_device.nxdl.xml | 2 +- .../NXbeam_transfer_matrix_table.nxdl.xml | 2 +- .../NXcg_alpha_complex.nxdl.xml | 2 +- .../NXcg_cylinder_set.nxdl.xml | 2 +- .../NXcg_ellipsoid_set.nxdl.xml | 2 +- .../NXcg_face_list_data_structure.nxdl.xml | 2 +- .../NXcg_geodesic_mesh.nxdl.xml | 2 +- contributed_definitions/NXcg_grid.nxdl.xml | 2 +- .../NXcg_half_edge_data_structure.nxdl.xml | 2 +- .../NXcg_hexahedron_set.nxdl.xml | 2 +- .../NXcg_marching_cubes.nxdl.xml | 2 +- .../NXcg_parallelogram_set.nxdl.xml | 2 +- .../NXcg_point_set.nxdl.xml | 2 +- .../NXcg_polygon_set.nxdl.xml | 2 +- .../NXcg_polyhedron_set.nxdl.xml | 2 +- .../NXcg_polyline_set.nxdl.xml | 2 +- .../NXcg_primitive_set.nxdl.xml | 2 +- contributed_definitions/NXcg_roi_set.nxdl.xml | 2 +- .../NXcg_sphere_set.nxdl.xml | 2 +- .../NXcg_tetrahedron_set.nxdl.xml | 2 +- .../NXcg_triangle_set.nxdl.xml | 2 +- .../NXcg_triangulated_surface_mesh.nxdl.xml | 2 +- .../NXcg_unit_normal_set.nxdl.xml | 2 +- contributed_definitions/NXchamber.nxdl.xml | 2 +- .../NXcollectioncolumn.nxdl.xml | 2 +- contributed_definitions/NXcomponent.nxdl.xml | 2 +- .../NXcoordinate_system.nxdl.xml | 2 +- .../NXcoordinate_system_set.nxdl.xml | 2 +- .../NXcorrector_cs.nxdl.xml | 2 +- .../NXcrystal_structure.nxdl.xml | 2 +- .../NXcs_computer.nxdl.xml | 2 +- .../NXcs_filter_boolean_mask.nxdl.xml | 2 +- contributed_definitions/NXcs_prng.nxdl.xml | 2 +- .../NXcs_profiling.nxdl.xml | 2 +- .../NXcs_profiling_event.nxdl.xml | 2 +- contributed_definitions/NXdata_mpes.nxdl.xml | 2 +- .../NXdata_mpes_detector.nxdl.xml | 2 +- contributed_definitions/NXdeflector.nxdl.xml | 2 +- .../NXdelocalization.nxdl.xml | 2 +- .../NXebeam_column.nxdl.xml | 2 +- .../NXelectron_level.nxdl.xml | 2 +- .../NXelectronanalyser.nxdl.xml | 2 +- .../NXellipsometry.nxdl.xml | 2 +- contributed_definitions/NXem.nxdl.xml | 2 +- .../NXem_calorimetry.nxdl.xml | 2 +- .../NXem_correlation.nxdl.xml | 2 +- contributed_definitions/NXem_ebsd.nxdl.xml | 2 +- contributed_definitions/NXem_eds.nxdl.xml | 2 +- contributed_definitions/NXem_eels.nxdl.xml | 2 +- contributed_definitions/NXem_img.nxdl.xml | 2 +- contributed_definitions/NXem_method.nxdl.xml | 2 +- contributed_definitions/NXem_msr.nxdl.xml | 2 +- contributed_definitions/NXem_sim.nxdl.xml | 2 +- .../NXenergydispersion.nxdl.xml | 2 +- .../NXevent_data_apm.nxdl.xml | 2 +- .../NXevent_data_apm_set.nxdl.xml | 2 +- .../NXevent_data_em.nxdl.xml | 2 +- .../NXevent_data_em_set.nxdl.xml | 2 +- contributed_definitions/NXfit.nxdl.xml | 2 +- .../NXfit_background.nxdl.xml | 2 +- .../NXfit_function.nxdl.xml | 2 +- .../NXfit_parameter.nxdl.xml | 2 +- .../NXgraph_edge_set.nxdl.xml | 2 +- .../NXgraph_node_set.nxdl.xml | 2 +- contributed_definitions/NXgraph_root.nxdl.xml | 2 +- contributed_definitions/NXhistory.nxdl.xml | 2 +- .../NXibeam_column.nxdl.xml | 2 +- contributed_definitions/NXidentifier.nxdl.xml | 2 +- contributed_definitions/NXimage_set.nxdl.xml | 2 +- .../NXinteraction_vol_em.nxdl.xml | 2 +- contributed_definitions/NXion.nxdl.xml | 2 +- contributed_definitions/NXisocontour.nxdl.xml | 2 +- ...ctro_chemo_mechanical_preparation.nxdl.xml | 2 +- .../NXlab_sample_mounting.nxdl.xml | 2 +- contributed_definitions/NXlens_em.nxdl.xml | 2 +- contributed_definitions/NXlens_opt.nxdl.xml | 2 +- .../NXmanipulator.nxdl.xml | 2 +- .../NXmatch_filter.nxdl.xml | 2 +- .../NXmicrostructure.nxdl.xml | 2 +- .../NXmicrostructure_gragles_config.nxdl.xml | 2 +- .../NXmicrostructure_gragles_results.nxdl.xml | 2 +- .../NXmicrostructure_imm_config.nxdl.xml | 2 +- .../NXmicrostructure_imm_results.nxdl.xml | 2 +- .../NXmicrostructure_ipf.nxdl.xml | 2 +- .../NXmicrostructure_kanapy_results.nxdl.xml | 2 +- .../NXmicrostructure_mtex_config.nxdl.xml | 2 +- .../NXmicrostructure_odf.nxdl.xml | 2 +- .../NXmicrostructure_pf.nxdl.xml | 2 +- .../NXmicrostructure_score_config.nxdl.xml | 2 +- .../NXmicrostructure_score_results.nxdl.xml | 2 +- .../NXmicrostructure_slip_system.nxdl.xml | 2 +- contributed_definitions/NXmpes.nxdl.xml | 2 +- contributed_definitions/NXmpes_arpes.nxdl.xml | 2 +- contributed_definitions/NXopt_window.nxdl.xml | 2 +- .../NXoptical_system_em.nxdl.xml | 2 +- contributed_definitions/NXpeak.nxdl.xml | 2 +- contributed_definitions/NXpid.nxdl.xml | 2 +- .../NXprocess_mpes.nxdl.xml | 2 +- contributed_definitions/NXpulser_apm.nxdl.xml | 4 +- contributed_definitions/NXpump.nxdl.xml | 2 +- contributed_definitions/NXraman.nxdl.xml | 2 +- contributed_definitions/NXreflectron.nxdl.xml | 2 +- contributed_definitions/NXresolution.nxdl.xml | 2 +- contributed_definitions/NXroi.nxdl.xml | 2 +- .../NXrotation_set.nxdl.xml | 2 +- contributed_definitions/NXscanbox_em.nxdl.xml | 2 +- contributed_definitions/NXserialized.nxdl.xml | 2 +- .../NXsimilarity_grouping.nxdl.xml | 2 +- .../NXspatial_filter.nxdl.xml | 2 +- .../NXspectrum_set.nxdl.xml | 2 +- contributed_definitions/NXstage_lab.nxdl.xml | 2 +- .../NXsubsampling_filter.nxdl.xml | 2 +- contributed_definitions/NXsubstance.nxdl.xml | 2 +- .../NXtransmission.nxdl.xml | 2 +- contributed_definitions/NXunit_cell.nxdl.xml | 2 +- contributed_definitions/NXwaveplate.nxdl.xml | 2 +- contributed_definitions/NXxps.nxdl.xml | 2 +- 168 files changed, 330 insertions(+), 193 deletions(-) diff --git a/applications/NXarpes.nxdl.xml b/applications/NXarpes.nxdl.xml index 8d17472ad3..e506cd3d29 100644 --- a/applications/NXarpes.nxdl.xml +++ b/applications/NXarpes.nxdl.xml @@ -3,7 +3,7 @@ - + Set to hold different coordinate systems conventions. Inspect the description of the :ref:`NXcoordinate_system_set` @@ -514,10 +519,20 @@ schema for heat treatment + + + TODO + + + + + TODO + + @@ -560,24 +575,23 @@ schema for heat treatment - - - + + + - The space inside the atom probe along which ions pass nominally - when they leave the specimen and travel to the detector. + TODO - - - + @@ -701,8 +715,8 @@ a time series of the specimen shape evolution--> - - + + @@ -728,6 +742,7 @@ we can only make recommendations--> + @@ -835,11 +850,12 @@ Relevant for ranging are the calibrated data, thats why only these - + + diff --git a/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml b/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml index e0adb79803..3b6b342a0a 100644 --- a/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml +++ b/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml @@ -3,7 +3,7 @@ A local electrode guiding the ion flight path. Also called counter or extraction electrode. + + + Acceleration voltage + + Detector for taking raw time-of-flight and ion/hit impact positions data. + + + TODO + + + + + TODO + + - + - + + + + The space inside the atom probe along which ions pass nominally + when they leave the specimen and travel to the detector. + + + + + TODO + + + - + - A statement whether the measurement was successful or failed prematurely. + TODO - - - - - - + + + A statement whether the measurement was successful or failed prematurely. + + + + + + + + diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml index 21897a43b9..d8b35b2d46 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml @@ -3,7 +3,7 @@ + + + TODO + + diff --git a/contributed_definitions/NXatom_set.nxdl.xml b/contributed_definitions/NXatom_set.nxdl.xml index 0a1e208560..c3e2cae5d4 100644 --- a/contributed_definitions/NXatom_set.nxdl.xml +++ b/contributed_definitions/NXatom_set.nxdl.xml @@ -3,7 +3,7 @@ - + diff --git a/contributed_definitions/NXapm_reconstruction.nxdl.xml b/contributed_definitions/NXapm_reconstruction.nxdl.xml index fd2282f600..6fe7e6060e 100644 --- a/contributed_definitions/NXapm_reconstruction.nxdl.xml +++ b/contributed_definitions/NXapm_reconstruction.nxdl.xml @@ -74,6 +74,11 @@ TODO + + + TODO + + TODO diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 3a5f0945d9..7db715bebf 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -810,6 +810,7 @@ NXapm(NXobject): algorithm(NX_CHAR): # config/input parameter(NX_CHAR): + exists: recommended protocol_name(NX_CHAR): exists: recommended crystallographic_calibration(NX_CHAR): diff --git a/contributed_definitions/nyaml/NXapm_reconstruction.yaml b/contributed_definitions/nyaml/NXapm_reconstruction.yaml index 4f1ee772d1..3a80adeb15 100644 --- a/contributed_definitions/nyaml/NXapm_reconstruction.yaml +++ b/contributed_definitions/nyaml/NXapm_reconstruction.yaml @@ -40,6 +40,10 @@ NXapm_reconstruction(NXprocess): doc: | TODO unit: NX_DIMENSIONLESS + flight_path(NX_FLOAT): + doc: | + TODO + unit: NX_LENGTH evaporation_field(NX_FLOAT): doc: | TODO From e0648fec27df7583215b344cb297d4a5c9c6e888 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Tue, 28 Jan 2025 10:22:16 +0100 Subject: [PATCH 04/75] Edits in reply to issues spotted when using cameca examples in NOMAD --- contributed_definitions/NXapm.nxdl.xml | 22 +++++++---- contributed_definitions/NXapm_msr.nxdl.xml | 13 +++---- .../NXapm_reconstruction.nxdl.xml | 38 ++++++++++++++----- .../NXfabrication.nxdl.xml | 8 +++- contributed_definitions/nyaml/NXapm.yaml | 12 ++++-- contributed_definitions/nyaml/NXapm_msr.yaml | 8 ++-- .../nyaml/NXapm_reconstruction.yaml | 33 ++++++++++++---- .../nyaml/NXfabrication.yaml | 4 ++ 8 files changed, 95 insertions(+), 43 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index b3bcdcd458..a7f3bbeee6 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -528,11 +528,7 @@ schema for heat treatment - - - TODO - - + @@ -584,14 +580,24 @@ schema for heat treatment - - - + + + Free text field for additional comments. + + + + + + + CAnalysis.CResults.fQuality + + diff --git a/contributed_definitions/NXapm_msr.nxdl.xml b/contributed_definitions/NXapm_msr.nxdl.xml index 6e4d828d85..846ae339ed 100644 --- a/contributed_definitions/NXapm_msr.nxdl.xml +++ b/contributed_definitions/NXapm_msr.nxdl.xml @@ -176,7 +176,7 @@ NEW ISSUE: local electrode, baking strategies, storage--> - TODO + CRunHeader.CLasHeader.fAnalysisPressure @@ -185,9 +185,9 @@ NEW ISSUE: local electrode, baking strategies, storage--> - + - TODO + Free text field for additional comments. @@ -195,11 +195,8 @@ NEW ISSUE: local electrode, baking strategies, storage--> A statement whether the measurement was successful or failed prematurely. - - - - - + + diff --git a/contributed_definitions/NXapm_reconstruction.nxdl.xml b/contributed_definitions/NXapm_reconstruction.nxdl.xml index 6fe7e6060e..afd2360c07 100644 --- a/contributed_definitions/NXapm_reconstruction.nxdl.xml +++ b/contributed_definitions/NXapm_reconstruction.nxdl.xml @@ -59,51 +59,69 @@ see `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_ (page 371). - - - TODO - - - TODO + CAnalysis.CSpatial.fPrimaryElement - TODO + CAnalysis.CSpatial.fEfficiency - TODO + CAnalysis.CSpatial.fFlightPath - TODO + CAnalysis.CSpatial.fEvaporationField + CAnalysis.CSpatial.fImageCompression + Image compression factor (ICF) + CAnalysis.CSpatial.fKfactor + k factor - Volume of the reconstruction + CAnalysis.CSpatial.fRecoVolume + + Sum of ion volumes + CAnalysis.CSpatial.fShankAngle + Shank angle + + + CAnalysis.CSpatial.fTipRadius + + + + + CAnalysis.CSpatial.fTipRadius0 + + + + + CAnalysis.CSpatial.fVoltage0 + + Tight, axis-aligned bounding box about the point cloud of the reconstruction. diff --git a/contributed_definitions/NXfabrication.nxdl.xml b/contributed_definitions/NXfabrication.nxdl.xml index 7c22f6d812..ba89274df2 100644 --- a/contributed_definitions/NXfabrication.nxdl.xml +++ b/contributed_definitions/NXfabrication.nxdl.xml @@ -3,7 +3,7 @@ - - - TODO - - + - + + + + + @@ -993,7 +998,7 @@ results--> - + diff --git a/contributed_definitions/NXapm_msr.nxdl.xml b/contributed_definitions/NXapm_msr.nxdl.xml index 846ae339ed..27f57c996e 100644 --- a/contributed_definitions/NXapm_msr.nxdl.xml +++ b/contributed_definitions/NXapm_msr.nxdl.xml @@ -165,7 +165,13 @@ NEW ISSUE: local electrode, baking strategies, storage--> - + + + + CRunHeader.CAnalysis.fSpecimenTemperature + + + diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 462c706d4e..56704a5563 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -9,6 +9,8 @@ symbols: instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of ions included in the reconstructed volume if the application definition is used to store results of an already reconstructed datasets. + n_ht: | + Number of hit qualities (hit types) distinguished. n: | Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. @@ -489,9 +491,7 @@ NXapm(NXobject): stage(NXstage_lab): exists: recommended specimen_temperature(NX_FLOAT): - doc: | - TODO - unit: NX_TEMPERATURE + exists: recommended analysis_chamber(NXchamber): exists: recommended # atmosphere(NXcollection): @@ -653,6 +653,7 @@ NXapm(NXobject): exists: optional total_hit_quality(NX_UINT): exists: optional + dim: (n_ht,) hit_quality_identifier(NX_UINT): exists: optional hit_positions(NX_NUMBER): @@ -865,7 +866,7 @@ NXapm(NXobject): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - # number_of_ion_types(NX_UINT): + number_of_ion_types(NX_UINT): maximum_number_of_atoms_per_molecular_ion(NX_UINT): mass_to_charge_distribution(NXprocess): exists: recommended diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml index 0b2535d9cf..38becc8290 100644 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ b/contributed_definitions/nyaml/NXapm_msr.yaml @@ -125,6 +125,10 @@ NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_met # model, serial_number, manufacturer_name all inherited from NXdetector base class pulser(NXpulser_apm): stage(NXstage_lab): + specimen_temperature(NX_FLOAT): + doc: | + CRunHeader.CAnalysis.fSpecimenTemperature + unit: NX_TEMPERATURE # NEW ISSUE: add NXapm_energy_analyzer, a voltage grid like done in Rouen/GPM analysis_chamber(NXchamber): flight_path(NX_FLOAT): From 3b983b6b203f0621de957a35cfd4204d9692b276 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Tue, 28 Jan 2025 19:13:28 +0100 Subject: [PATCH 06/75] Moved location of number of ions --- contributed_definitions/NXapm.nxdl.xml | 4 +-- .../NXapm_ranging.nxdl.xml | 30 +++++++++---------- contributed_definitions/nyaml/NXapm.yaml | 4 +-- .../nyaml/NXapm_ranging.yaml | 27 ++++++++--------- 4 files changed, 32 insertions(+), 33 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 53f8d2f886..3a13211de7 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -998,8 +998,6 @@ results--> - - @@ -1102,6 +1100,8 @@ in an e.g. work of A. London et al.--> + + diff --git a/contributed_definitions/NXapm_ranging.nxdl.xml b/contributed_definitions/NXapm_ranging.nxdl.xml index 2fc3de39d9..8382de58f9 100644 --- a/contributed_definitions/NXapm_ranging.nxdl.xml +++ b/contributed_definitions/NXapm_ranging.nxdl.xml @@ -37,21 +37,6 @@ - - - How many ion types are distinguished. If no ranging was performed, each - ion is of the special unknown type. The iontype ID of this unknown type - is 0 representing a reserve value. Consequently, - iontypes start counting from 1. - - - - - Assumed maximum value that suffices to store all relevant - molecular ions, even the most complicated ones. - Currently, a value of 32 is used (see M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). - - Specifies the mass-to-charge-state-ratio histogram. @@ -106,6 +91,21 @@ eventually processed via deconvolution methods--> error models, were interpreted as ion types or not. + + + How many ion types are distinguished. If no ranging was performed, each + ion is of the special unknown type. The iontype ID of this unknown type + is 0 representing a reserve value. Consequently, + iontypes start counting from 1. + + + + + Assumed maximum value that suffices to store all relevant + molecular ions, even the most complicated ones. + Currently, a value of 32 is used (see `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). + + diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 56704a5563..360ecb0345 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -866,8 +866,6 @@ NXapm(NXobject): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - number_of_ion_types(NX_UINT): - maximum_number_of_atoms_per_molecular_ion(NX_UINT): mass_to_charge_distribution(NXprocess): exists: recommended sequence_index(NX_POSINT): @@ -959,6 +957,8 @@ NXapm(NXobject): exists: [min, 1, max, infty] program(NX_CHAR): \@version(NX_CHAR): + number_of_ion_types(NX_UINT): + maximum_number_of_atoms_per_molecular_ion(NX_UINT): ionID(NXion): exists: [min, 1, max, 256] nuclide_hash(NX_UINT): diff --git a/contributed_definitions/nyaml/NXapm_ranging.yaml b/contributed_definitions/nyaml/NXapm_ranging.yaml index 335a878ab3..ea5199a8b3 100644 --- a/contributed_definitions/nyaml/NXapm_ranging.yaml +++ b/contributed_definitions/nyaml/NXapm_ranging.yaml @@ -16,20 +16,6 @@ type: group NXapm_ranging(NXprocess): # when evolving these ideas further inherit from NXapm_method instead (NXprogram): (NXserialized): - number_of_ion_types(NX_UINT): - doc: | - How many ion types are distinguished. If no ranging was performed, each - ion is of the special unknown type. The iontype ID of this unknown type - is 0 representing a reserve value. Consequently, - iontypes start counting from 1. - unit: NX_UNITLESS - maximum_number_of_atoms_per_molecular_ion(NX_UINT): - doc: | - Assumed maximum value that suffices to store all relevant - molecular ions, even the most complicated ones. - Currently, a value of 32 is used (see M. Kühbach et al. `_). - unit: NX_UNITLESS - mass_to_charge_distribution(NXprocess): doc: | Specifies the mass-to-charge-state-ratio histogram. @@ -72,4 +58,17 @@ NXapm_ranging(NXprocess): # when evolving these ideas further inherit from NXap Details about how peaks, with taking into account error models, were interpreted as ion types or not. (NXprogram): + number_of_ion_types(NX_UINT): + doc: | + How many ion types are distinguished. If no ranging was performed, each + ion is of the special unknown type. The iontype ID of this unknown type + is 0 representing a reserve value. Consequently, + iontypes start counting from 1. + unit: NX_UNITLESS + maximum_number_of_atoms_per_molecular_ion(NX_UINT): + doc: | + Assumed maximum value that suffices to store all relevant + molecular ions, even the most complicated ones. + Currently, a value of 32 is used (see `M. Kühbach et al. `_). + unit: NX_UNITLESS (NXion): From bd675f4be068c0495876e951fc904631ea31958d Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Thu, 30 Jan 2025 12:14:51 +0100 Subject: [PATCH 07/75] Refactored storing of event types --- contributed_definitions/NXapm.nxdl.xml | 12 ------ .../NXapm_hit_finding.nxdl.xml | 41 +++++++++++-------- contributed_definitions/nyaml/NXapm.yaml | 10 ----- .../nyaml/NXapm_hit_finding.yaml | 30 +++++++++----- 4 files changed, 45 insertions(+), 48 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 3a13211de7..872bd0db25 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -748,24 +748,12 @@ we can only make recommendations--> - - - - - - - - - - - - diff --git a/contributed_definitions/NXapm_hit_finding.nxdl.xml b/contributed_definitions/NXapm_hit_finding.nxdl.xml index 50add08de1..df5ab465fd 100644 --- a/contributed_definitions/NXapm_hit_finding.nxdl.xml +++ b/contributed_definitions/NXapm_hit_finding.nxdl.xml @@ -98,21 +98,39 @@ - + - Name of the hit_qualities distinguished. - AMETEK/Cameca uses e.g. golden, multiple, partial, - irrecoverable, and multi-first and multi-late. + CRunHeader.fTotalEventGolden + + + + + CRunHeader.fTotalEventIncomplete + + + + + CRunHeader.fTotalEventMultiple + + + + + CRunHeader.fTotalEventPartials + + + + + CRunHeader.fTotalEventRecords - - - Identifier used for each hit_quality type. Following the order of hit_quality_types. + + + @@ -123,15 +141,6 @@ - - - Individual total how many hits of specific quality were found. - In the order of hit_quality_types. - - - - - This processing yields for each ion with how many others it evaporated diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 360ecb0345..019eb6e44c 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -649,19 +649,9 @@ NXapm(NXobject): arrival_time_pairs(NX_NUMBER): exists: optional # results of the hit_finding algorithm - hit_quality_types(NX_CHAR): - exists: optional - total_hit_quality(NX_UINT): - exists: optional - dim: (n_ht,) - hit_quality_identifier(NX_UINT): - exists: optional hit_positions(NX_NUMBER): exists: recommended dim: (i, 2) - hit_quality(NX_UINT): - exists: optional - dim: (i,) hit_multiplicity(NX_UINT): exists: recommended dim: (i,) diff --git a/contributed_definitions/nyaml/NXapm_hit_finding.yaml b/contributed_definitions/nyaml/NXapm_hit_finding.yaml index 948db910d1..24da55ae3c 100644 --- a/contributed_definitions/nyaml/NXapm_hit_finding.yaml +++ b/contributed_definitions/nyaml/NXapm_hit_finding.yaml @@ -44,27 +44,37 @@ NXapm_hit_finding(NXprocess): # when evolving these ideas further inherit from \@depends_on(NX_CHAR): doc: | Defines in which reference frame the positions are defined. - hit_quality_types(NX_CHAR): + total_event_golden(NX_UINT): doc: | - Name of the hit_qualities distinguished. - AMETEK/Cameca uses e.g. golden, multiple, partial, - irrecoverable, and multi-first and multi-late. - dim: (n_ht,) + CRunHeader.fTotalEventGolden + unit: NX_UNITLESS + total_event_incomplete(NX_UINT): + doc: | + CRunHeader.fTotalEventIncomplete + unit: NX_UNITLESS + total_event_multiple(NX_UINT): + doc: | + CRunHeader.fTotalEventMultiple + unit: NX_UNITLESS + total_event_partial(NX_UINT): + doc: | + CRunHeader.fTotalEventPartials + unit: NX_UNITLESS + total_event_record(NX_UINT): + doc: | + CRunHeader.fTotalEventRecords + unit: NX_UNITLESS hit_quality_identifier(NX_UINT): doc: | Identifier used for each hit_quality type. Following the order of hit_quality_types. + dim: (n_ht,) hit_quality(NX_UINT): doc: | Hit quality identifier for each pulse. Identifier have to be within hit_quality_identifier. unit: NX_UNITLESS dim: (p,) - total_hit_quality(NX_UINT): - doc: | - Individual total how many hits of specific quality were found. - In the order of hit_quality_types. - dim: (n_ht,) hit_multiplicity(NX_UINT): doc: | This processing yields for each ion with how many others it evaporated From f6e55a9ce5248218aca59e58599e70e647aa8712 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Thu, 30 Jan 2025 17:40:07 +0100 Subject: [PATCH 08/75] Added instrument types --- contributed_definitions/NXapm.nxdl.xml | 33 ++++++++++++++++++- contributed_definitions/NXpulser_apm.nxdl.xml | 2 ++ contributed_definitions/nyaml/NXapm.yaml | 7 ++-- .../nyaml/NXpulser_apm.yaml | 2 +- 4 files changed, 40 insertions(+), 4 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 872bd0db25..a534b7516c 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -529,7 +529,38 @@ schema for heat treatment TODO - + + + Which type of instrument. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/contributed_definitions/NXpulser_apm.nxdl.xml b/contributed_definitions/NXpulser_apm.nxdl.xml index dc6559ea8a..11ae8bec97 100644 --- a/contributed_definitions/NXpulser_apm.nxdl.xml +++ b/contributed_definitions/NXpulser_apm.nxdl.xml @@ -46,6 +46,8 @@ + + - + + + Device which reduces ToF differences of ions in ToF experiments. + + For atom probe the reflectron can be considered an energy compensation device. + Such a device can be realized technically for example with a Poschenrieder lens. + + Consult the following U.S. patents for further details: + + * 3863068 and 6740872 for the reflectron + * 8134119 for the curved reflectron + + + + Presence and status of the reflectron. + + + + + + + + + Given name/alias. + + + + + Free-text field to specify further details about the reflectron. + The field can be used to inform e. g. if the reflectron is flat or curved. + + + + + The maximum voltage applied to the reflectron, relative to system ground. + + + + + Manufacturer metadata that inform about the reflectron + + + + + Affine transformation(s) which detail where the reflectron is located + relative to e.g. the origin of the specimen space reference coordinate + system. This group can also be used for specifying how the reflectron + is rotated relative to a given axis in the instrument. + + + A counter electrode of the LEAP 6000 series atom probes. diff --git a/contributed_definitions/NXevent_data_apm.nxdl.xml b/contributed_definitions/NXevent_data_apm.nxdl.xml index c47cbf484a..d194467538 100644 --- a/contributed_definitions/NXevent_data_apm.nxdl.xml +++ b/contributed_definitions/NXevent_data_apm.nxdl.xml @@ -170,7 +170,23 @@ - + + + + Presence and status of the reflectron. + + + + + + + + + + The maximum voltage applied to the reflectron, relative to system ground. + + + diff --git a/contributed_definitions/NXreflectron.nxdl.xml b/contributed_definitions/NXreflectron.nxdl.xml deleted file mode 100644 index 3211ba5700..0000000000 --- a/contributed_definitions/NXreflectron.nxdl.xml +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. - - - - - Base class for a device which reduces ToF differences of ions in ToF experiments. - - For atom probe the reflectron can be considered an energy compensation device. - Such a device can be realized technically for example with a Poschenrieder lens. - - Consult the following U.S. patents for further details: - - * 3863068 and 6740872 for the reflectron - * 8134119 for the curved reflectron - - - - Status of eventual existence and potential usage of this reflectron. - - - - - - - - - - Given name/alias. - - - - - - Free-text field to specify further details about the reflectron. - The field can be used to inform e. g. if the reflectron is flat or curved. - - - - - The maximum voltage applied to the reflectron, relative to system ground. - - - - - - Affine transformation(s) which detail where the reflectron is located - relative to e.g. the origin of the specimen space reference coordinate - system. This group can also be used for specifying how the reflectron - is rotated relative to a given axis in the instrument. - - - - diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 05de1cba67..5be03f9d5f 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -454,7 +454,8 @@ NXapm(NXobject): serial_number(NX_CHAR): identifier(NXidentifier): exists: recommended - reflectron(NXreflectron): + reflectron(NXobject): + exists: optional status(NX_CHAR): fabrication(NXfabrication): exists: recommended diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml index 38becc8290..c7cf038d1c 100644 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ b/contributed_definitions/nyaml/NXapm_msr.yaml @@ -90,7 +90,42 @@ NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_met Location of the lab or place where the instrument is installed. Using GEOREF is preferred. (NXfabrication): - (NXreflectron): + reflectron(NXobject): # NXcomponent at soonish + doc: | + Device which reduces ToF differences of ions in ToF experiments. + + For atom probe the reflectron can be considered an energy compensation device. + Such a device can be realized technically for example with a Poschenrieder lens. + + Consult the following U.S. patents for further details: + + * 3863068 and 6740872 for the reflectron + * 8134119 for the curved reflectron + + status(NX_CHAR): + doc: | + Presence and status of the reflectron. + enumeration: [present, used] + name(NX_CHAR): + doc: | + Given name/alias. + description(NX_CHAR): + doc: | + Free-text field to specify further details about the reflectron. + The field can be used to inform e. g. if the reflectron is flat or curved. + voltage(NX_FLOAT): + doc: | + The maximum voltage applied to the reflectron, relative to system ground. + unit: NX_VOLTAGE + fabrication(NXfabrication): + doc: | + Manufacturer metadata that inform about the reflectron + (NXtransformations): + doc: | + Affine transformation(s) which detail where the reflectron is located + relative to e.g. the origin of the specimen space reference coordinate + system. This group can also be used for specifying how the reflectron + is rotated relative to a given axis in the instrument. decelerate_electrode(NXlens_em): doc: | A counter electrode of the LEAP 6000 series atom probes. diff --git a/contributed_definitions/nyaml/NXevent_data_apm.yaml b/contributed_definitions/nyaml/NXevent_data_apm.yaml index 819669d5a3..6e11162002 100644 --- a/contributed_definitions/nyaml/NXevent_data_apm.yaml +++ b/contributed_definitions/nyaml/NXevent_data_apm.yaml @@ -126,7 +126,15 @@ NXevent_data_apm(NXobject): enumeration: [detection_rate] target_detection_rate(NX_FLOAT): unit: NX_ANY # ions/pulse - (NXreflectron): + reflectron(NXobject): + status(NX_CHAR): + doc: | + Presence and status of the reflectron. + enumeration: [none, present, used] + voltage(NX_FLOAT): + doc: | + The maximum voltage applied to the reflectron, relative to system ground. + unit: NX_VOLTAGE local_electrode(NXlens_em): ion_detector(NXdetector): signal_amplitude(NX_FLOAT): diff --git a/contributed_definitions/nyaml/NXreflectron.yaml b/contributed_definitions/nyaml/NXreflectron.yaml deleted file mode 100644 index bb8eb03b54..0000000000 --- a/contributed_definitions/nyaml/NXreflectron.yaml +++ /dev/null @@ -1,46 +0,0 @@ -category: base -doc: | - Base class for a device which reduces ToF differences of ions in ToF experiments. - - For atom probe the reflectron can be considered an energy compensation device. - Such a device can be realized technically for example with a Poschenrieder lens. - - Consult the following U.S. patents for further details: - - * 3863068 and 6740872 for the reflectron - * 8134119 for the curved reflectron - -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - p: | - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. -type: group -NXreflectron(NXobject): - status(NX_CHAR): - doc: | - Status of eventual existence and potential usage of this reflectron. - enumeration: [none, present, used] - name(NX_CHAR): - doc: | - Given name/alias. - (NXfabrication): - description(NX_CHAR): - doc: | - Free-text field to specify further details about the reflectron. - The field can be used to inform e. g. if the reflectron is flat or curved. - voltage(NX_FLOAT): - doc: | - The maximum voltage applied to the reflectron, relative to system ground. - unit: NX_VOLTAGE - # dim: (p,) - (NXtransformations): - doc: | - Affine transformation(s) which detail where the reflectron is located - relative to e.g. the origin of the specimen space reference coordinate - system. This group can also be used for specifying how the reflectron - is rotated relative to a given axis in the instrument. - # The purpose of these more detailed instrument descriptions - # is to support the creation of a digital twin of the instrument - # for computational science. From f87c859cb67f9738c99fdf18663a4142ed1b0edb Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 14:32:47 +0100 Subject: [PATCH 10/75] Refactoring to remove the base class NXapm_volt_and_bowl as that will likely be used only in atom probe and thus may not warrant to become proposed towards NIAC --- .../NXapm_volt_and_bowl.nxdl.xml | 74 ------------------- contributed_definitions/nyaml/NXapm.yaml | 26 ++++--- .../nyaml/NXapm_volt_and_bowl.yaml | 15 +--- 3 files changed, 18 insertions(+), 97 deletions(-) delete mode 100644 contributed_definitions/NXapm_volt_and_bowl.nxdl.xml diff --git a/contributed_definitions/NXapm_volt_and_bowl.nxdl.xml b/contributed_definitions/NXapm_volt_and_bowl.nxdl.xml deleted file mode 100644 index 430f0e5fae..0000000000 --- a/contributed_definitions/NXapm_volt_and_bowl.nxdl.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of ions spatially filtered from results of the hit_finding algorithm - :ref:`NXapm_hit_finding` from which an instance of a reconstructed volume - has been generated. These ions get new identifier assigned in the process - - the so-called evaporation_identifier, which must not be confused with - the pulse_identifier! - - - - - Base class for the configuration and results from a voltage-and-bowl ToF correction algorithm. - - The voltage-and-bowl correction is a ata post-processing step to correct for ion impact position - flight path differences, detector biases, and nonlinearities. - - - - - - - Raw time-of-flight data without corrections. - - - - - - - - Calibrated time-of-flight. - - - - - - - - TODO - - - diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 5be03f9d5f..ea0e2ca70b 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -722,8 +722,13 @@ NXapm(NXobject): identifier(NX_INT): # at this point the original set of events p has been filtered down to n - voltage_and_bowl(NXapm_volt_and_bowl): + voltage_and_bowl(NXprocess): exists: recommended + doc: | + Configuration of and results obtained from a voltage-and-bowl ToF correction algorithm. + + The voltage-and-bowl correction is a data post-processing step to correct ion impact positions + for flight path differences, detector biases, and nonlinearities. sequence_index(NX_POSINT): exists: recommended programID(NXprogram): @@ -736,20 +741,23 @@ NXapm(NXobject): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - # config/input to the algorithm - # NEW ISSUE: realistic is that currently scientists can pull always a calibrated time-of-flight - # but not necessarily unprocessed timing data from the detector (unless individuals built the instrument). - # Relevant for ranging are the calibrated data, thats why only these - # (as an intermediate/compromise solution) are required in this version of the application definition raw_tof(NX_FLOAT): + # currently cannot be made required because of being a quantity measured by proprietary hardware with proprietary semantics exists: recommended + doc: | + Raw time-of-flight data without corrections. dim: (n,) # result - calibrated_tof(NX_FLOAT): - exists: recommended # make required - dim: (n,) tof_zero_estimate(NX_FLOAT): exists: optional + doc: | + The parameter :math:`t_0` CAnalysis.CCalibMass.fT0Estimate + unit: NX_TIME + calibrated_tof(NX_FLOAT): + exists: recommended + doc: | + Calibrated time-of-flight. + dim: (n,) mass_to_charge_conversion(NXprocess): exists: recommended sequence_index(NX_POSINT): diff --git a/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml b/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml index ac7a478728..562a17467f 100644 --- a/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml +++ b/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml @@ -23,17 +23,4 @@ NXapm_volt_and_bowl(NXprocess): # when evolving these ideas further inherit fro # Relevant for ranging are the calibrated data, thats why only these # (as an intermediate/compromise solution) are required in this version of the application definition # result - raw_tof(NX_FLOAT): - doc: | - Raw time-of-flight data without corrections. - unit: NX_TIME - dim: (n,) - calibrated_tof(NX_FLOAT): - doc: | - Calibrated time-of-flight. - unit: NX_TIME - dim: (n,) - tof_zero_estimate(NX_FLOAT): - doc: | - TODO - unit: NX_TIME + From e58b66e7f3cf3a54497710f0fab43b69b098de89 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 14:53:07 +0100 Subject: [PATCH 11/75] Refactoring to remove the base class NXapm_sim as that was not detailed strong enough and thus may not warrant to become proposed towards NIAC --- contributed_definitions/NXapm_sim.nxdl.xml | 32 --------- contributed_definitions/nyaml/NXapm.yaml | 4 +- contributed_definitions/nyaml/NXapm_msr.yaml | 70 ++++++++++---------- contributed_definitions/nyaml/NXapm_sim.yaml | 7 -- 4 files changed, 38 insertions(+), 75 deletions(-) delete mode 100644 contributed_definitions/NXapm_sim.nxdl.xml delete mode 100644 contributed_definitions/nyaml/NXapm_sim.yaml diff --git a/contributed_definitions/NXapm_sim.nxdl.xml b/contributed_definitions/NXapm_sim.nxdl.xml deleted file mode 100644 index a30fa497cb..0000000000 --- a/contributed_definitions/NXapm_sim.nxdl.xml +++ /dev/null @@ -1,32 +0,0 @@ - - - - - - - Base class for simulating ion extraction from matter via laser and/or voltage - pulsing. - - - diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index ea0e2ca70b..f8ed6fc3b4 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -574,8 +574,10 @@ NXapm(NXobject): # getter_pump(NXpump): # roughening_pump(NXpump): # turbomolecular_pump(NXpump): - simulation(NXapm_sim): + simulation(NXobject): exists: optional + doc: | + Simulation of ion extraction from matter via laser and/or voltage pulsing. atom_probe(NXroi): exists: recommended # [min, 0, max, infty] doc: | diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml index c7cf038d1c..998914a706 100644 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ b/contributed_definitions/nyaml/NXapm_msr.yaml @@ -2,13 +2,12 @@ category: base doc: | Base class for collecting a session with a real atom probe or field-ion microscope. - Ideally, we would like to describe the workflow of experiments and simulations of atom probe and - field-evaporation simulation research in more detail and contextualize better descriptions of - experiments and computer simulations for atom probe research. - - The main motivation for this is the ongoing development and tighter becoming connection between atom probe - and other material characterization techniques foremost electron microscopy (see `T. Kelly et al. `_, `C. Fleischmann et al. `_, and `W. Windl et al. `_ or `C. Freysoldt et al. `_ to mention but a few). - To arrive at a design of base classes and an application definition which can be used for both real and simulated atom probe experiments, it is worthwhile to recall concepts that are related to events and (molecular) ions: + Workflows used during experiments or simulations of atom probe and related field-evaporation + research should be documented in more detail and be better contextualized not only because of + ongoing developments and the tighter becoming connection between atom probe and other + methods for material characterization foremost electron microscopy (see `T. Kelly et al. `_, `C. Fleischmann et al. `_, `W. Windl et al. `_, `C. Freysoldt et al. `_, or `G. da Costa et al. `_ to mention but a few). + To arrive at a design of base classes and an application definition which can be used for both real and simulated atom probe experiments, + it is worthwhile to recall concepts that are related to events and (molecular) ions: * Pulsing events which are used to trigger ion extraction events. * Physical events and corresponding signal triggered by an ion hitting the detector. @@ -19,17 +18,20 @@ doc: | * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually selected (molecular) ions based on which an instance of a reconstruction is created. * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values - and charge states of the (molecular) ions to substantiate that some of these ions are can be considered - as rangable ions and hence an iontype can be associated by running peak finding algorithms and labeling - i.e. algorithms for defining ranging definitions. + and charge states of the (molecular) ions to substantiate that some of these ions can be considered + as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms + and subsequent peak labeling. In the field of atom probe this these peak identification methods + are known as ranging definitions. Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts are well distinguished. However, the algorithms used to transform correlations between pulses and physical events - into actual events (detector hits) ions is a proprietary one. Due to this practical inaccessibility of details, - virtually all atom probe studies currently use a reporting scheme where the course of the specimen evaporation - is documented such that quantities are a function of evaporation identifier i.e. actual event/ion, i.e. after having - the hits finding algorithm and correlations applied. That is evaporation_identifier values take the role of an implicit - time and course of the experiment given that ion extraction is a sequential physical process. + into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme + where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier + i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is evaporation_identifier values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. There is a number of research groups who build own instruments and share different aspects of their technical specifications and approaches how they apply data processing (e.g. `M. Monajem et al. `_, `P. Stender et al. `_ , or `I. Dimkou et al. `_ to name but a few). @@ -39,33 +41,31 @@ doc: | Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which - scientific conclusions about the characterized material volume are made. + scientific conclusions about the characterized material volume are made. Also here a reconstruction is + point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. - By contrast, simulations of field-evaporation have the luxury to document the flight path and allow following the - whereabouts of each ion evaporated if needed. This level of detail is currently not characterizable in experiment. + By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all + the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. We argue that this divide can be bridged with realizing the above-mentioned context and the realization that - similar concepts are used in both research realms with many concepts not only being similar but exactly the same. + similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment - and its reconstructions. In both cases, the recorded simulated physical events of simulated ions hitting a simulated detector - is not the end of the research workflow but typically the input to apply addition algorithms such as (spatial) filtering - and reconstruction algorithms. Only the practical need for making ranging definitions is (at least as of now) not as much needed - in field-evaporation simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. - Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. - Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. - Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation are simplified - because of otherwise too high computing resource demands and knowledge gaps in how to deal with some complexities. - Molecular ion dissociation upon flight is one such complexity. Also the complexity of simulation setups is simpler e.g. the assumption of a straight flight path - instrument is used or details are ignored such as local electrodes or physical obstacles and electric fields (controlled or stray fields). + and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting + a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as + (spatial) filtering and reconstruction algorithms. - To conclude, we thus propose two base classes :ref:`NXapm_msr` and :ref:`NXapm_sim` where the second one may become - obsolete in the future as people realize that a simulated atom probe is maybe equivalent in design and function to a - real atom probe if considering that the simulation is just stripped of many components. -# noteworthy the situation is similar to electron microscopy especially transmission electron microscopy where factually -# interpretation without simulations is pointless. The only difference is that in electron microscopy there is a large availability -# of documentation and open-source tools for performing such simulations. + Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation simulations + than it is in real world measurements because each ion has a prescribed iontype in the simulation. Be it a specifically charged + nuclid or a molecular ion whose flight path the simulation resolves. + Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. + Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require + simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps + in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. + Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) + than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path + such as local electrodes or physical obstacles and electric fields (controlled or stray fields). symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. diff --git a/contributed_definitions/nyaml/NXapm_sim.yaml b/contributed_definitions/nyaml/NXapm_sim.yaml deleted file mode 100644 index bf95b17664..0000000000 --- a/contributed_definitions/nyaml/NXapm_sim.yaml +++ /dev/null @@ -1,7 +0,0 @@ -category: base -doc: | - Base class for simulating ion extraction from matter via laser and/or voltage pulsing. -# mirroring the design of NXem_msr/NXem_sim, NXem can be used for experiment and simulation -type: group -NXapm_sim(NXobject): - (NXprogram): From 0c5228dff7fe239612ee987c75fb7e11a9ad93cb Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 14:54:33 +0100 Subject: [PATCH 12/75] Remove accidentally recreated NXapm_volt_and_bowl.yaml --- .../nyaml/NXapm_volt_and_bowl.yaml | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml diff --git a/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml b/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml deleted file mode 100644 index 562a17467f..0000000000 --- a/contributed_definitions/nyaml/NXapm_volt_and_bowl.yaml +++ /dev/null @@ -1,26 +0,0 @@ -category: base -doc: | - Base class for the configuration and results from a voltage-and-bowl ToF correction algorithm. - - The voltage-and-bowl correction is a ata post-processing step to correct for ion impact position - flight path differences, detector biases, and nonlinearities. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n: | - Number of ions spatially filtered from results of the hit_finding algorithm - :ref:`NXapm_hit_finding` from which an instance of a reconstructed volume - has been generated. These ions get new identifier assigned in the process - - the so-called evaporation_identifier, which must not be confused with - the pulse_identifier! -type: group -NXapm_volt_and_bowl(NXprocess): # when evolving these ideas further inherit from NXapm_method instead - (NXprogram): - (NXserialized): - # config/input to the algorithm - # NEW ISSUE: realistic is that currently scientists can pull always a calibrated time-of-flight - # but not necessarily unprocessed timing data from the detector (unless individuals built the instrument). - # Relevant for ranging are the calibrated data, thats why only these - # (as an intermediate/compromise solution) are required in this version of the application definition - # result - From 77979ed8b36d72e2f543a00a82ec920098c04255 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 15:14:57 +0100 Subject: [PATCH 13/75] Refactoring to remove the base class NXapm_hit_finding that detailed strong enough but used in the end only by NXapm thus we thought it is better to move it into the appdef directly, also because NXapm can cover now use cases of measurements and is envisioned to cover also simulations of APT and FIM so no more need to warrant another appdef that would then use NXapm_hit_finding, cameca could inherit from NXapm as base class inheritance has already been accepted by the NIAC as a result of the Autumn NIAC 2024 hackathon --- contributed_definitions/NXapm.nxdl.xml | 168 +++++++++++++++--- .../NXapm_hit_finding.nxdl.xml | 165 ----------------- contributed_definitions/NXapm_msr.nxdl.xml | 70 ++++---- .../NXapm_reconstruction.nxdl.xml | 7 +- contributed_definitions/nyaml/NXapm.yaml | 106 ++++++++--- .../nyaml/NXapm_hit_finding.yaml | 95 ---------- .../nyaml/NXapm_reconstruction.yaml | 7 +- 7 files changed, 268 insertions(+), 350 deletions(-) delete mode 100644 contributed_definitions/NXapm_hit_finding.nxdl.xml delete mode 100644 contributed_definitions/nyaml/NXapm_hit_finding.yaml diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index b7efe83b02..1af05e88a2 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -34,11 +34,21 @@ to store results of an already reconstructed datasets. + + + Number of pulses returned by the hit finding algorithm. Not necessarily p or n. + + Number of hit qualities (hit types) distinguished. + + + Number of delay-line wires of the detector. + + Number of ions spatially filtered from results of the hit_finding algorithm @@ -701,7 +711,11 @@ load_lock_chamber(NXchamber): getter_pump(NXpump): roughening_pump(NXpump): turbomolecular_pump(NXpump):--> - + + + Simulation of ion extraction from matter via laser and/or voltage pulsing. + + A region-of-interest analyzed either during or after the session for which @@ -757,7 +771,10 @@ a time series of the specimen shape evolution--> - + + + Configuration of and results obtained from a hit finding algorithm. + - - + + + The number of wires in the detector. + + + + + + + + + + Alias tuple (begin, end) of each DLD wire of the detector. + Order follows arrival_time_pairs. + + + + + + + + + Raw readings from the analog-to-digital-converter + timing circuits of the detector wires. + + + + + + + - + + + Evaluated ion impact coordinates on the detector. + Use the depends_on field to specify which reference + frame the positions are defined. + - + + + + Defines in which reference frame the positions are defined. + + + + + + CRunHeader.fTotalEventGolden + - + + + CRunHeader.fTotalEventIncomplete + + + + + CRunHeader.fTotalEventMultiple + + + + + CRunHeader.fTotalEventPartials + + + + + CRunHeader.fTotalEventRecords + + + + + Identifier used for each hit_quality type. + Following the order of hit_quality_types. + + + + + + + + Hit quality identifier for each pulse. + Identifier have to be within hit_quality_identifier. + - + + + + + + This processing yields for each ion with how many others it evaporated + if these were collected on the same pulse. Extraction of multiple ions + on one pulse on different or even the same pixel of the detector are possible. + + Multiplicity must not be confused with how many atoms of the same element + a molecular ion contains. + + + - + dim: (n,) +pulse_identifier(NX_INT): + dim: (n,)--> @@ -856,7 +955,13 @@ i number of hits after hits finding but prior calibrations--> - + + + Configuration of and results obtained from a voltage-and-bowl ToF correction algorithm. + + The voltage-and-bowl correction is a data post-processing step to correct ion impact positions + for flight path differences, detector biases, and nonlinearities. + @@ -869,23 +974,32 @@ i number of hits after hits finding but prior calibrations--> - + + + Raw time-of-flight data without corrections. + + + + The parameter :math:`t_0` CAnalysis.CCalibMass.fT0Estimate + + + + Calibrated time-of-flight. + - diff --git a/contributed_definitions/NXapm_hit_finding.nxdl.xml b/contributed_definitions/NXapm_hit_finding.nxdl.xml deleted file mode 100644 index df5ab465fd..0000000000 --- a/contributed_definitions/NXapm_hit_finding.nxdl.xml +++ /dev/null @@ -1,165 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of delay-line wires of the detector. - - - - - Number of hit qualities (hit types) distinguished. - - - - - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. If this is not defined, - p is the number of ions included in the reconstructed volume if an application - definition is used to store results of already reconstructed datasets. - - - - - Base class for the configuration and results from a hit finding algorithm. - - - - - - - The number of wires in the detector. - - - - - - - - - - Alias tuple (begin, end) of each DLD wire of the detector. - Order follows arrival_time_pairs. - - - - - - - - - Raw readings from the analog-to-digital-converter - timing circuits of the detector wires. - - - - - - - - - - - Evaluated ion impact coordinates on the detector. - Use the depends_on field to spec - - - - - - - - Defines in which reference frame the positions are defined. - - - - - - CRunHeader.fTotalEventGolden - - - - - CRunHeader.fTotalEventIncomplete - - - - - CRunHeader.fTotalEventMultiple - - - - - CRunHeader.fTotalEventPartials - - - - - CRunHeader.fTotalEventRecords - - - - - Identifier used for each hit_quality type. - Following the order of hit_quality_types. - - - - - - - - Hit quality identifier for each pulse. - Identifier have to be within hit_quality_identifier. - - - - - - - - This processing yields for each ion with how many others it evaporated - if these were collected on the same pulse. Extraction of multiple ions - on one pulse on different or even the same pixel of the detector are possible. - - Multiplicity must not be confused with how many atoms of the same element - a molecular ion contains (which is instead encoded with the - isotope_vector field of each :ref:`NXion` instance). - - - - - - - diff --git a/contributed_definitions/NXapm_msr.nxdl.xml b/contributed_definitions/NXapm_msr.nxdl.xml index df4d035649..3dca438261 100644 --- a/contributed_definitions/NXapm_msr.nxdl.xml +++ b/contributed_definitions/NXapm_msr.nxdl.xml @@ -22,9 +22,6 @@ # For further information, see http://www.nexusformat.org --> - The symbols used in the schema to specify e.g. dimensions of arrays. @@ -39,13 +36,12 @@ of documentation and open-source tools for performing such simulations.--> Base class for collecting a session with a real atom probe or field-ion microscope. - Ideally, we would like to describe the workflow of experiments and simulations of atom probe and - field-evaporation simulation research in more detail and contextualize better descriptions of - experiments and computer simulations for atom probe research. - - The main motivation for this is the ongoing development and tighter becoming connection between atom probe - and other material characterization techniques foremost electron microscopy (see `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_, `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_, and `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ or `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ to mention but a few). - To arrive at a design of base classes and an application definition which can be used for both real and simulated atom probe experiments, it is worthwhile to recall concepts that are related to events and (molecular) ions: + Workflows used during experiments or simulations of atom probe and related field-evaporation + research should be documented in more detail and be better contextualized not only because of + ongoing developments and the tighter becoming connection between atom probe and other + methods for material characterization foremost electron microscopy (see `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_, `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_, `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_, `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_, or `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ to mention but a few). + To arrive at a design of base classes and an application definition which can be used for both real and simulated atom probe experiments, + it is worthwhile to recall concepts that are related to events and (molecular) ions: * Pulsing events which are used to trigger ion extraction events. * Physical events and corresponding signal triggered by an ion hitting the detector. @@ -56,17 +52,20 @@ of documentation and open-source tools for performing such simulations.--> * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually selected (molecular) ions based on which an instance of a reconstruction is created. * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values - and charge states of the (molecular) ions to substantiate that some of these ions are can be considered - as rangable ions and hence an iontype can be associated by running peak finding algorithms and labeling - i.e. algorithms for defining ranging definitions. + and charge states of the (molecular) ions to substantiate that some of these ions can be considered + as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms + and subsequent peak labeling. In the field of atom probe this these peak identification methods + are known as ranging definitions. Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts are well distinguished. However, the algorithms used to transform correlations between pulses and physical events - into actual events (detector hits) ions is a proprietary one. Due to this practical inaccessibility of details, - virtually all atom probe studies currently use a reporting scheme where the course of the specimen evaporation - is documented such that quantities are a function of evaporation identifier i.e. actual event/ion, i.e. after having - the hits finding algorithm and correlations applied. That is evaporation_identifier values take the role of an implicit - time and course of the experiment given that ion extraction is a sequential physical process. + into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme + where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier + i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is evaporation_identifier values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. There is a number of research groups who build own instruments and share different aspects of their technical specifications and approaches how they apply data processing (e.g. `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_, `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ , or `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ to name but a few). @@ -76,30 +75,31 @@ of documentation and open-source tools for performing such simulations.--> Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which - scientific conclusions about the characterized material volume are made. + scientific conclusions about the characterized material volume are made. Also here a reconstruction is + point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. - By contrast, simulations of field-evaporation have the luxury to document the flight path and allow following the - whereabouts of each ion evaporated if needed. This level of detail is currently not characterizable in experiment. + By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all + the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. We argue that this divide can be bridged with realizing the above-mentioned context and the realization that - similar concepts are used in both research realms with many concepts not only being similar but exactly the same. + similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment - and its reconstructions. In both cases, the recorded simulated physical events of simulated ions hitting a simulated detector - is not the end of the research workflow but typically the input to apply addition algorithms such as (spatial) filtering - and reconstruction algorithms. Only the practical need for making ranging definitions is (at least as of now) not as much needed - in field-evaporation simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. - Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. - Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. - Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation are simplified - because of otherwise too high computing resource demands and knowledge gaps in how to deal with some complexities. - Molecular ion dissociation upon flight is one such complexity. Also the complexity of simulation setups is simpler e.g. the assumption of a straight flight path - instrument is used or details are ignored such as local electrodes or physical obstacles and electric fields (controlled or stray fields). + and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting + a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as + (spatial) filtering and reconstruction algorithms. - To conclude, we thus propose two base classes :ref:`NXapm_msr` and :ref:`NXapm_sim` where the second one may become - obsolete in the future as people realize that a simulated atom probe is maybe equivalent in design and function to a - real atom probe if considering that the simulation is just stripped of many components. + Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation simulations + than it is in real world measurements because each ion has a prescribed iontype in the simulation. Be it a specifically charged + nuclid or a molecular ion whose flight path the simulation resolves. + Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. + Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require + simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps + in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. + Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) + than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path + such as local electrodes or physical obstacles and electric fields (controlled or stray fields). diff --git a/contributed_definitions/NXapm_reconstruction.nxdl.xml b/contributed_definitions/NXapm_reconstruction.nxdl.xml index afd2360c07..ab97a90d79 100644 --- a/contributed_definitions/NXapm_reconstruction.nxdl.xml +++ b/contributed_definitions/NXapm_reconstruction.nxdl.xml @@ -29,10 +29,9 @@ Number of ions spatially filtered from results of the hit_finding algorithm - :ref:`NXapm_hit_finding` from which an instance of a reconstructed volume - has been generated. These ions get new identifier assigned in the process - - the so-called evaporation_identifier, which must not be confused with - the pulse_identifier! + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process - the so-called + evaporation_identifier, which must not be confused with the pulse_identifier! diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index f8ed6fc3b4..9aab4c909e 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -9,8 +9,12 @@ symbols: instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of ions included in the reconstructed volume if the application definition is used to store results of an already reconstructed datasets. + p_out: | + Number of pulses returned by the hit finding algorithm. Not necessarily p or n. n_ht: | Number of hit qualities (hit types) distinguished. + n_dld: | + Number of delay-line wires of the detector. n: | Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. @@ -630,8 +634,10 @@ NXapm(NXobject): exists: optional algorithm(NX_CHAR): exists: optional - hit_finding(NXapm_hit_finding): + hit_finding(NXprocess): exists: recommended + doc: | + Configuration of and results obtained from a hit finding algorithm. # we careful how we go about doing this here, we recommended to make some details of the hit_finding # algorithm open namely the input and the output what the black box then does by AMETEK/Cameca # does not have to be exposed (although this clearly is against FAIR principles but the scientific community @@ -652,31 +658,91 @@ NXapm(NXobject): algorithm(NX_CHAR): number_of_dld_wires(NX_UINT): exists: recommended + doc: | + The number of wires in the detector. + unit: NX_UNITLESS + enumeration: [1, 2, 3] + dld_wire_names(NX_CHAR): + exists: optional + doc: | + Alias tuple (begin, end) of each DLD wire of the detector. + Order follows arrival_time_pairs. + dim: (n_dld, 2) arrival_time_pairs(NX_NUMBER): exists: optional + doc: | + Raw readings from the analog-to-digital-converter + timing circuits of the detector wires. + unit: NX_TIME + dim: (p, n_dld, 2) # results of the hit_finding algorithm hit_positions(NX_NUMBER): exists: recommended - dim: (i, 2) + doc: | + Evaluated ion impact coordinates on the detector. + Use the depends_on field to specify which reference + frame the positions are defined. + unit: NX_LENGTH + dim: (p_out, 2) + \@depends_on(NX_CHAR): + doc: | + Defines in which reference frame the positions are defined. + total_event_golden(NX_UINT): + exists: optional + doc: | + CRunHeader.fTotalEventGolden + unit: NX_UNITLESS + total_event_incomplete(NX_UINT): + exists: optional + doc: | + CRunHeader.fTotalEventIncomplete + unit: NX_UNITLESS + total_event_multiple(NX_UINT): + exists: optional + doc: | + CRunHeader.fTotalEventMultiple + unit: NX_UNITLESS + total_event_partial(NX_UINT): + exists: optional + doc: | + CRunHeader.fTotalEventPartials + unit: NX_UNITLESS + total_event_record(NX_UINT): + exists: optional + doc: | + CRunHeader.fTotalEventRecords + unit: NX_UNITLESS + hit_quality_identifier(NX_UINT): + exists: optional + doc: | + Identifier used for each hit_quality type. + Following the order of hit_quality_types. + dim: (n_ht,) + hit_quality(NX_UINT): + exists: optional + doc: | + Hit quality identifier for each pulse. + Identifier have to be within hit_quality_identifier. + unit: NX_UNITLESS + dim: (p_out,) hit_multiplicity(NX_UINT): - exists: recommended - dim: (i,) - # statistics(NXprocess): - # multiples(NX_FLOAT): - # doc: | - # Fraction of multiple hits. - # unit: NX_DIMENSIONLESS - # the following two quantities are relicts from ePOS files used to give some - # insight into the results of the hit_finding algorithm of IVAS/APSuite but typically - # used only in the context to learn about the multiplicity of an ion. - # pulses_since_last_ion(NX_UINT): - # exists: optional - # dim: (i,) - # pulse_identifier(NX_INT): # this is the pulse on which they came - # exists: optional - # dim: (i,) - # i number of hits after hits finding but prior calibrations - + exists: optional + doc: | + This processing yields for each ion with how many others it evaporated + if these were collected on the same pulse. Extraction of multiple ions + on one pulse on different or even the same pixel of the detector are possible. + + Multiplicity must not be confused with how many atoms of the same element + a molecular ion contains. + unit: NX_UNITLESS + dim: (p_out,) + # the following two quantities are relicts from ePOS files used to give some + # insight into the results of the hit_finding algorithm of IVAS/APSuite but typically + # used only in the context to learn about the multiplicity of an ion. + # pulses_since_last_ion(NX_UINT): + # dim: (n,) + # pulse_identifier(NX_INT): + # dim: (n,) hit_spatial_filtering(NXprocess): exists: recommended sequence_index(NX_POSINT): diff --git a/contributed_definitions/nyaml/NXapm_hit_finding.yaml b/contributed_definitions/nyaml/NXapm_hit_finding.yaml deleted file mode 100644 index 24da55ae3c..0000000000 --- a/contributed_definitions/nyaml/NXapm_hit_finding.yaml +++ /dev/null @@ -1,95 +0,0 @@ -category: base -doc: | - Base class for the configuration and results from a hit finding algorithm. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_dld: | - Number of delay-line wires of the detector. - n_ht: | - Number of hit qualities (hit types) distinguished. - p: | - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. If this is not defined, - p is the number of ions included in the reconstructed volume if an application - definition is used to store results of already reconstructed datasets. -type: group -NXapm_hit_finding(NXprocess): # when evolving these ideas further inherit from NXapm_method instead - (NXprogram): - (NXserialized): - # config/input - number_of_dld_wires(NX_UINT): - doc: | - The number of wires in the detector. - unit: NX_UNITLESS - enumeration: [1, 2, 3] - dld_wire_names(NX_CHAR): - doc: | - Alias tuple (begin, end) of each DLD wire of the detector. - Order follows arrival_time_pairs. - dim: (n_dld, 2) - arrival_time_pairs(NX_NUMBER): - doc: | - Raw readings from the analog-to-digital-converter - timing circuits of the detector wires. - unit: NX_TIME - dim: (p, n_dld, 2) - # results of the hit_finding algorithm - hit_positions(NX_NUMBER): - doc: | - Evaluated ion impact coordinates on the detector. - Use the depends_on field to spec - unit: NX_LENGTH - dim: (p, 2) - \@depends_on(NX_CHAR): - doc: | - Defines in which reference frame the positions are defined. - total_event_golden(NX_UINT): - doc: | - CRunHeader.fTotalEventGolden - unit: NX_UNITLESS - total_event_incomplete(NX_UINT): - doc: | - CRunHeader.fTotalEventIncomplete - unit: NX_UNITLESS - total_event_multiple(NX_UINT): - doc: | - CRunHeader.fTotalEventMultiple - unit: NX_UNITLESS - total_event_partial(NX_UINT): - doc: | - CRunHeader.fTotalEventPartials - unit: NX_UNITLESS - total_event_record(NX_UINT): - doc: | - CRunHeader.fTotalEventRecords - unit: NX_UNITLESS - hit_quality_identifier(NX_UINT): - doc: | - Identifier used for each hit_quality type. - Following the order of hit_quality_types. - dim: (n_ht,) - hit_quality(NX_UINT): - doc: | - Hit quality identifier for each pulse. - Identifier have to be within hit_quality_identifier. - unit: NX_UNITLESS - dim: (p,) - hit_multiplicity(NX_UINT): - doc: | - This processing yields for each ion with how many others it evaporated - if these were collected on the same pulse. Extraction of multiple ions - on one pulse on different or even the same pixel of the detector are possible. - - Multiplicity must not be confused with how many atoms of the same element - a molecular ion contains (which is instead encoded with the - isotope_vector field of each :ref:`NXion` instance). - unit: NX_UNITLESS - dim: (p,) - # the following two quantities are relicts from ePOS files used to give some - # insight into the results of the hit_finding algorithm of IVAS/APSuite but typically - # used only in the context to learn about the multiplicity of an ion. - # pulses_since_last_ion(NX_UINT): - # dim: (n,) - # pulse_identifier(NX_INT): - # dim: (n,) diff --git a/contributed_definitions/nyaml/NXapm_reconstruction.yaml b/contributed_definitions/nyaml/NXapm_reconstruction.yaml index 71767ce31e..bf606b03b7 100644 --- a/contributed_definitions/nyaml/NXapm_reconstruction.yaml +++ b/contributed_definitions/nyaml/NXapm_reconstruction.yaml @@ -11,10 +11,9 @@ symbols: The symbols used in the schema to specify e.g. dimensions of arrays. n: | Number of ions spatially filtered from results of the hit_finding algorithm - :ref:`NXapm_hit_finding` from which an instance of a reconstructed volume - has been generated. These ions get new identifier assigned in the process - - the so-called evaporation_identifier, which must not be confused with - the pulse_identifier! + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process - the so-called + evaporation_identifier, which must not be confused with the pulse_identifier! type: group NXapm_reconstruction(NXprocess): # when evolving these ideas further inherit from NXapm_method instead From a8602870f13f04b8befc902efb345afe650d8dd3 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 15:29:38 +0100 Subject: [PATCH 14/75] Refactoring to remove the base class NXevent_data_apm_set as it was only a container to store instances of NXevent_data_em, reorganized via defining these concepts directly in NXapm_msr --- contributed_definitions/NXapm.nxdl.xml | 11 ++--- contributed_definitions/NXapm_msr.nxdl.xml | 23 ++++++++- .../NXevent_data_apm_set.nxdl.xml | 48 ------------------- contributed_definitions/nyaml/NXapm.yaml | 15 +++--- contributed_definitions/nyaml/NXapm_msr.yaml | 20 +++++++- .../nyaml/NXevent_data_apm_set.yaml | 25 ---------- 6 files changed, 52 insertions(+), 90 deletions(-) delete mode 100644 contributed_definitions/NXevent_data_apm_set.nxdl.xml delete mode 100644 contributed_definitions/nyaml/NXevent_data_apm_set.yaml diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 1af05e88a2..a36beb1f2f 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -640,10 +640,10 @@ turbomolecular_pump(NXpump):--> CAnalysis.CResults.fQuality - + - + dim: (p,)--> - + @@ -693,9 +693,8 @@ dim: (p,)--> - - + + diff --git a/contributed_definitions/NXapm_msr.nxdl.xml b/contributed_definitions/NXapm_msr.nxdl.xml index 3dca438261..0648a9672c 100644 --- a/contributed_definitions/NXapm_msr.nxdl.xml +++ b/contributed_definitions/NXapm_msr.nxdl.xml @@ -253,6 +253,25 @@ NEW ISSUE: local electrode, baking strategies, storage--> - - + + + Group to hold instances of :ref:`NXevent_data_apm`. + + Which temporal granularity is adequate depends on the situation and research + question. Using a model which enables a collection of events offers the most + flexible way to cater for both atom probe experiments or simulation. + + To monitor the course of an ion extraction experiment (or simulation) + it makes sense to track time explicitly via time stamps or implicitly + via e.g. a clock inside the instrument, such as the clock of the pulser + and respective pulsing event identifier. + + As set and measured quantities typically change over time and we do not + yet know during the measurement which of the events have associated + (molecular) ions that will end up in the reconstructed volume, we must not + document quantities as a function of the evaporated_identifier but as a + function of the (pulsing) event_identifier. + + + diff --git a/contributed_definitions/NXevent_data_apm_set.nxdl.xml b/contributed_definitions/NXevent_data_apm_set.nxdl.xml deleted file mode 100644 index a6c469a178..0000000000 --- a/contributed_definitions/NXevent_data_apm_set.nxdl.xml +++ /dev/null @@ -1,48 +0,0 @@ - - - - - - Base class for a set of :ref:`NXevent_data_apm` instances. - - Members of the set are instances of :ref:`NXevent_data_apm`. - These have an associated time interval during which the conditions - of the instrument were considered stable and fit enough for purpose. - - Which temporal granularity is adequate depends on the situation and research - question. Using a model which enables a collection of events offers the most - flexible way to cater for both atom probe experiments or simulation. - - To monitor the course of an ion extraction experiment (or simulation) - it makes sense to track time explicitly via time stamps or implicitly - via e.g. a clock inside the instrument, such as the clock of the pulser - and respective pulsing event identifier. - - As set and measured quantities typically change over time and we do not - yet know during the measurement which of the events have associated - (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the evaporated_identifier but as a - function of the (pulsing) event_identifier. - - - diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 9aab4c909e..08812ae1d2 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -516,12 +516,12 @@ NXapm(NXobject): quality(NX_CHAR): doc: | CAnalysis.CResults.fQuality - event_data_apm_set(NXevent_data_apm_set): + event_data(NXobject): exists: optional # the case of allowing to not have event_data but only the above-mentioned instrument # details can be useful to convey details about an atom probe instrument in general - event_data_apm(NXevent_data_apm): - exists: recommended + eventID(NXevent_data_apm): + exists: [min, 0, max, infty] # all these cannot be made required because for LEAP only stored in RHIT/HITS # but for M-TAP and Oxcart these pieces of information are available. # start_time(NX_DATE_TIME): @@ -550,25 +550,24 @@ NXapm(NXobject): # unit: NX_DIMENSIONLESS # dim: (p,) \@logged_against(NX_CHAR): - pulse_voltage(NX_FLOAT): # pulsed voltage + pulse_voltage(NX_FLOAT): # ePOS, APT pulsed voltage exists: recommended # not required for voltage pulsing # unit: NX_VOLTAGE # dim: (p,) \@logged_against(NX_CHAR): # pulse_number(NX_UINT): - standing_voltage(NX_FLOAT): + standing_voltage(NX_FLOAT): # ePOS, APT standing voltage # unit: NX_VOLTAGE # dim: (p,) \@logged_against(NX_CHAR): - (NXsource): + sourceID(NXsource): exists: [min, 0, max, 2] # not required for voltage pulsing pulse_energy(NX_FLOAT): # unit: NX_ENERGY # dim: (p,) \@logged_against(NX_CHAR): # laser geometry at the moment has no example nor any feedback from the community - # but NXpulser_apm base class shows how this could be done, plus examples for NXmpes - stage_lab(NXstage_lab): + stage(NXstage_lab): # setpoint_temperature(NX_FLOAT): base_temperature(NX_FLOAT): analysis_chamber(NXchamber): diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml index 998914a706..dd275d8228 100644 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ b/contributed_definitions/nyaml/NXapm_msr.yaml @@ -188,4 +188,22 @@ NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_met doc: | A statement whether the measurement was successful or failed prematurely. # enumeration: [success, failure, unknown] - (NXevent_data_apm_set): + event_data(NXobject): + doc: | + Group to hold instances of :ref:`NXevent_data_apm`. + + Which temporal granularity is adequate depends on the situation and research + question. Using a model which enables a collection of events offers the most + flexible way to cater for both atom probe experiments or simulation. + + To monitor the course of an ion extraction experiment (or simulation) + it makes sense to track time explicitly via time stamps or implicitly + via e.g. a clock inside the instrument, such as the clock of the pulser + and respective pulsing event identifier. + + As set and measured quantities typically change over time and we do not + yet know during the measurement which of the events have associated + (molecular) ions that will end up in the reconstructed volume, we must not + document quantities as a function of the evaporated_identifier but as a + function of the (pulsing) event_identifier. + (NXevent_data_apm): diff --git a/contributed_definitions/nyaml/NXevent_data_apm_set.yaml b/contributed_definitions/nyaml/NXevent_data_apm_set.yaml deleted file mode 100644 index cf5c26323a..0000000000 --- a/contributed_definitions/nyaml/NXevent_data_apm_set.yaml +++ /dev/null @@ -1,25 +0,0 @@ -category: base -doc: | - Base class for a set of :ref:`NXevent_data_apm` instances. - - Members of the set are instances of :ref:`NXevent_data_apm`. - These have an associated time interval during which the conditions - of the instrument were considered stable and fit enough for purpose. - - Which temporal granularity is adequate depends on the situation and research - question. Using a model which enables a collection of events offers the most - flexible way to cater for both atom probe experiments or simulation. - - To monitor the course of an ion extraction experiment (or simulation) - it makes sense to track time explicitly via time stamps or implicitly - via e.g. a clock inside the instrument, such as the clock of the pulser - and respective pulsing event identifier. - - As set and measured quantities typically change over time and we do not - yet know during the measurement which of the events have associated - (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the evaporated_identifier but as a - function of the (pulsing) event_identifier. -type: group -NXevent_data_apm_set(NXobject): - (NXevent_data_apm): From 8846f36679b608b230fa020e9d91cb1fc3df021b Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 15:59:41 +0100 Subject: [PATCH 15/75] BREAKING REFACTORING, resolve the error-prone repetition of concepts definition below instrument that was required with the previous design. The key idea always was to have one group where static props of the instrument are stored and another group (event_data) where dynamic values are stored, so far the implementation for this recreated all concepts of the instrument on the one hand in NXapm_msr and on the other hand in NXevent_data_apm. However, now with base class inheritance supported and accepted by the NIAC, it would be much better to refactor NXapm_msr towards a base class called NXinstrument_apm that offers a dictionary for the concepts for static and typically quantities with more dynamic i.e. frequently changing values. Thereby measurement and NXevent_data_apm can just inherit NXinstrument_apm and thus the description of the NXevent_data_apm base class becomes much slimmer, less prone to making manual errors like copy-paste, the appdef will then just constrain for which concepts inherited from either NXinstrument_apm will be required, then possibly one may even remove NXevent_data_apm altogether via eventID(NXobject) with a child NXinstrument_apm --- contributed_definitions/nyaml/NXapm.yaml | 117 +++++++++++++++--- contributed_definitions/nyaml/NXapm_msr.yaml | 4 - .../nyaml/NXevent_data_apm.yaml | 3 - 3 files changed, 97 insertions(+), 27 deletions(-) diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 08812ae1d2..7f95dfe27a 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -441,9 +441,94 @@ NXapm(NXobject): y_direction(NX_CHAR): z_direction(NX_CHAR): - measurement(NXapm_msr): + measurement(NXobject): exists: optional - instrument(NXinstrument): + # docstring currently with NXapm_msr + doc: | + Base class for collecting a session with a real atom probe or field-ion microscope. + + Workflows used during experiments or simulations of atom probe and related field-evaporation + research should be documented in more detail and be better contextualized not only because of + ongoing developments and the tighter becoming connection between atom probe and other + methods for material characterization foremost electron microscopy see e.g.: + + * `T. Kelly et al. `_ + * `C. Fleischmann et al. `_ + * `W. Windl et al. `_ + * `C. Freysoldt et al. `_ + * `G. da Costa et al. `_ + + to mention but a few. + + To arrive at a design of base classes and an application definition that can be used + for both real and simulated atom probe experiments it is worthwhile to recall concepts that are + related to events and (molecular) ions: + + * Pulsing events which are used to trigger ion extraction events. + * Physical events and corresponding signal triggered by an ion hitting the detector. + Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. + * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input + and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are + wortwhile to be considered further and eventually included in the reconstructed volume. + * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually + selected (molecular) ions based on which an instance of a reconstruction is created. + * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values + and charge states of the (molecular) ions to substantiate that some of these ions can be considered + as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms + and subsequent peak labeling. In the field of atom probe this these peak identification methods + are known as ranging definitions. + + Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts + are well distinguished. However, the algorithms used to transform correlations between pulses and physical events + into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme + where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier + i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is evaporation_identifier values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. + + There is a number of research groups who build own instruments and share different aspects of their technical + specifications and approaches how they apply data processing e.g.: + + * `M. Monajem et al. `_ + * `P. Stender et al. `_ + * `I. Dimkou et al. `_ + + to name but a few. + + Despite some of these activities embrace practices of open-source development, they use essentially the same + workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface + software is used to explore and thus analyze reconstructed atom probe datasets. + + Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. + Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which + scientific conclusions about the characterized material volume are made. Also here a reconstruction is + point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. + + By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all + the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. + Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. + We argue that this divide can be bridged with realizing the above-mentioned context and the realization that + similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. + + A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed + datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment + and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting + a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as + (spatial) filtering and reconstruction algorithms. + + Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation + simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. + Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. + Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. + Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require + simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps + in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. + Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) + than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path + such as local electrodes or physical obstacles and electric fields (controlled or stray fields). + instrument(NXinstrument_apm): identifier_name(NX_UINT): doc: | TODO @@ -513,10 +598,13 @@ NXapm(NXobject): Free text field for additional comments. status(NX_CHAR): exists: recommended + doc: | + A statement whether the measurement was successful or failed prematurely. quality(NX_CHAR): + exists: recommended doc: | CAnalysis.CResults.fQuality - event_data(NXobject): + events(NXobject): exists: optional # the case of allowing to not have event_data but only the above-mentioned instrument # details can be useful to convey details about an atom probe instrument in general @@ -529,7 +617,7 @@ NXapm(NXobject): # delta_time(NX_NUMBER): # pulse_identifier_offset(NX_INT): # pulse_identifier(NX_INT): - instrument(NXinstrument): + instrument(NXinstrument_apm): exists: recommended control(NXcollection): evaporation_control(NX_CHAR): @@ -581,27 +669,18 @@ NXapm(NXobject): exists: optional doc: | Simulation of ion extraction from matter via laser and/or voltage pulsing. + # future possibility to reuse concepts from NXinstrument_apm again without + # the need for defining them again atom_probe(NXroi): exists: recommended # [min, 0, max, infty] doc: | A region-of-interest analyzed either during or after the session for which specific processed data of the measured or simulated data are available. - # add a default plot V = f(time/evaporation_id), essentially for each quantity - # NEW ISSUE: check also here the PYCCAPT pipeline from P. Felfer's group - # all other details are instances of NXprocess as steps along the pipeline - - # NEW ISSUE: hit_quality table - # NEW ISSUE: pyccapt - # NEW ISSUE: add section for propagation_delay(NXprocess) ? - # NEW ISSUE: make recon an own subentry NXapm_reconstruction - # NEW ISSUE: different algorithms used one could create a class for each reconstruction method - # NEW ISSUE: make this rather an own subentry NXapm_ranging - + # earlier comments here https://github.com/FAIRmat-NFDI/nexus_definitions/commit/a8602870f13f04b8befc902efb345afe650d8dd3 initial_specimen(NXimage_set): exists: recommended doc: | - SEM or TEM image of the initial specimen i.e. - ideally taken prior to the data acquisition. + SEM or TEM image of the initial specimen (ideally taken prior data acquisition). image_2d(NXdata): \@signal(NX_CHAR): \@axes(NX_CHAR): @@ -613,9 +692,7 @@ NXapm(NXobject): axis_i(NX_NUMBER): dim: (n_i,) \@long_name(NX_CHAR): - # one could use a stack_3d(NXdata) to record - # a time series of the specimen shape evolution - + # could use a stack_3d(NXdata) to record time series of specimen shape evolution raw_data(NXprocess): exists: recommended sequence_index(NX_POSINT): diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml index dd275d8228..6c5570eca1 100644 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ b/contributed_definitions/nyaml/NXapm_msr.yaml @@ -184,10 +184,6 @@ NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_met comment(NX_CHAR): doc: | Free text field for additional comments. - status(NX_CHAR): - doc: | - A statement whether the measurement was successful or failed prematurely. - # enumeration: [success, failure, unknown] event_data(NXobject): doc: | Group to hold instances of :ref:`NXevent_data_apm`. diff --git a/contributed_definitions/nyaml/NXevent_data_apm.yaml b/contributed_definitions/nyaml/NXevent_data_apm.yaml index 6e11162002..9eb21a8f57 100644 --- a/contributed_definitions/nyaml/NXevent_data_apm.yaml +++ b/contributed_definitions/nyaml/NXevent_data_apm.yaml @@ -146,9 +146,6 @@ NXevent_data_apm(NXobject): atom probe groups of the GPM in Rouen, France. unit: NX_CURRENT dim: (p,) - # does p only specific the length or does it also convey a logical correlation - # conceptually to another vector which happens to have the same dimensions - # I clear say NO ! pulser(NXpulser_apm): stage_lab(NXstage_lab): setpoint_temperature(NX_FLOAT): From 44c3eda0bb3b5588a674adc6d10c16e9cb4d64ba Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 16:52:25 +0100 Subject: [PATCH 16/75] Implementation of the afore-mentioned BREAKING REFACTORING for NXapm_msr refactored into NXinstrument_apm, next and last step, check that relevant groups of NXinstrument_apm are defined and constrained properly in the NXapm appdef to complete the BREAKING REFACTORING --- contributed_definitions/NXapm.nxdl.xml | 147 +++++-- contributed_definitions/NXapm_msr.nxdl.xml | 277 ------------- .../NXevent_data_apm.nxdl.xml | 3 - .../NXinstrument_apm.nxdl.xml | 369 ++++++++++++++++++ contributed_definitions/NXpulser_apm.nxdl.xml | 240 ------------ contributed_definitions/nyaml/NXapm.yaml | 21 +- contributed_definitions/nyaml/NXapm_msr.yaml | 205 ---------- .../nyaml/NXinstrument_apm.yaml | 252 ++++++++++++ .../nyaml/NXpulser_apm.yaml | 134 ------- 9 files changed, 760 insertions(+), 888 deletions(-) delete mode 100644 contributed_definitions/NXapm_msr.nxdl.xml create mode 100644 contributed_definitions/NXinstrument_apm.nxdl.xml delete mode 100644 contributed_definitions/NXpulser_apm.nxdl.xml delete mode 100644 contributed_definitions/nyaml/NXapm_msr.yaml create mode 100644 contributed_definitions/nyaml/NXinstrument_apm.yaml delete mode 100644 contributed_definitions/nyaml/NXpulser_apm.yaml diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index a36beb1f2f..254bacd9f8 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -532,8 +532,93 @@ schema for heat treatment - - + + + Base class for collecting a session with a real atom probe or field-ion microscope. + + Workflows used during experiments or simulations of atom probe and related field-evaporation + research should be documented in more detail and be better contextualized not only because of + ongoing developments and the tighter becoming connection between atom probe and other + methods for material characterization foremost electron microscopy see e.g.: + + * `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ + * `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_ + * `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ + * `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ + * `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ + + to mention but a few. + + To arrive at a design of base classes and an application definition that can be used + for both real and simulated atom probe experiments it is worthwhile to recall concepts that are + related to events and (molecular) ions: + + * Pulsing events which are used to trigger ion extraction events. + * Physical events and corresponding signal triggered by an ion hitting the detector. + Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. + * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input + and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are + wortwhile to be considered further and eventually included in the reconstructed volume. + * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually + selected (molecular) ions based on which an instance of a reconstruction is created. + * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values + and charge states of the (molecular) ions to substantiate that some of these ions can be considered + as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms + and subsequent peak labeling. In the field of atom probe this these peak identification methods + are known as ranging definitions. + + Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts + are well distinguished. However, the algorithms used to transform correlations between pulses and physical events + into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme + where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier + i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is evaporation_identifier values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. + + There is a number of research groups who build own instruments and share different aspects of their technical + specifications and approaches how they apply data processing e.g.: + + * `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_ + * `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ + * `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ + + to name but a few. + + Despite some of these activities embrace practices of open-source development, they use essentially the same + workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface + software is used to explore and thus analyze reconstructed atom probe datasets. + + Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. + Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which + scientific conclusions about the characterized material volume are made. Also here a reconstruction is + point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. + + By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all + the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. + Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. + We argue that this divide can be bridged with realizing the above-mentioned context and the realization that + similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. + + A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed + datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment + and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting + a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as + (spatial) filtering and reconstruction algorithms. + + Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation + simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. + Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. + Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. + Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require + simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps + in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. + Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) + than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path + such as local electrodes or physical obstacles and electric fields (controlled or stray fields). + + TODO @@ -634,15 +719,39 @@ turbomolecular_pump(NXpump):--> - - + + + A statement whether the measurement was successful or failed prematurely. + + + CAnalysis.CResults.fQuality - - + + + + Group to hold instances of :ref:`NXevent_data_apm`. + + Which temporal granularity is adequate depends on the situation and research + question. Using a model which enables a collection of events offers the most + flexible way to cater for both atom probe experiments or simulation. + + To monitor the course of an ion extraction experiment (or simulation) + it makes sense to track time explicitly via time stamps or implicitly + via e.g. a clock inside the instrument, such as the clock of the pulser + and respective pulsing event identifier. + + As set and measured quantities typically change over time and we do not + yet know during the measurement which of the events have associated + (molecular) ions that will end up in the reconstructed volume, we must not + document quantities as a function of the evaporated_identifier but as a + function of the (pulsing) event_identifier. + - - - - - + Simulation of ion extraction from matter via laser and/or voltage pulsing. + A region-of-interest analyzed either during or after the session for which specific processed data of the measured or simulated data are available. - - + - SEM or TEM image of the initial specimen i.e. - ideally taken prior to the data acquisition. + SEM or TEM image of the initial specimen (ideally taken prior data acquisition). @@ -753,8 +851,7 @@ NEW ISSUE: make this rather an own subentry NXapm_ranging--> - + diff --git a/contributed_definitions/NXapm_msr.nxdl.xml b/contributed_definitions/NXapm_msr.nxdl.xml deleted file mode 100644 index 0648a9672c..0000000000 --- a/contributed_definitions/NXapm_msr.nxdl.xml +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. - - - - - Base class for collecting a session with a real atom probe or field-ion microscope. - - Workflows used during experiments or simulations of atom probe and related field-evaporation - research should be documented in more detail and be better contextualized not only because of - ongoing developments and the tighter becoming connection between atom probe and other - methods for material characterization foremost electron microscopy (see `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_, `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_, `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_, `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_, or `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ to mention but a few). - To arrive at a design of base classes and an application definition which can be used for both real and simulated atom probe experiments, - it is worthwhile to recall concepts that are related to events and (molecular) ions: - - * Pulsing events which are used to trigger ion extraction events. - * Physical events and corresponding signal triggered by an ion hitting the detector. - Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. - * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input - and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are - wortwhile to be considered further and eventually included in the reconstructed volume. - * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually - selected (molecular) ions based on which an instance of a reconstruction is created. - * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values - and charge states of the (molecular) ions to substantiate that some of these ions can be considered - as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms - and subsequent peak labeling. In the field of atom probe this these peak identification methods - are known as ranging definitions. - - Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts - are well distinguished. However, the algorithms used to transform correlations between pulses and physical events - into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. - - Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme - where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier - i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. - That is evaporation_identifier values take the role of an implicit time and course of the experiment given that - ion extraction physically is a sequential process. - - There is a number of research groups who build own instruments and share different aspects of their technical - specifications and approaches how they apply data processing (e.g. `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_, `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ , or `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ to name but a few). - Despite some of these activities embrace practices of open-source development, they use essentially the same - workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface - software is used to explore and thus analyze reconstructed atom probe datasets. - - Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. - Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which - scientific conclusions about the characterized material volume are made. Also here a reconstruction is - point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. - - By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all - the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. - Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. - We argue that this divide can be bridged with realizing the above-mentioned context and the realization that - similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. - - A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed - datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment - and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting - a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as - (spatial) filtering and reconstruction algorithms. - - Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation simulations - than it is in real world measurements because each ion has a prescribed iontype in the simulation. Be it a specifically charged - nuclid or a molecular ion whose flight path the simulation resolves. - Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. - Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require - simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps - in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. - Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) - than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path - such as local electrodes or physical obstacles and electric fields (controlled or stray fields). - - - - Metadata of the atom probe or field-ion microscope instrument, henceforth called - microscope or instrument, and the lab in which it stands. - - - - - Given name of the microscope as defined by the hosting lab. This is an alias. - Examples could be LEAP6000, Raptor, Oxcart, one atom at a time, etc. - - - - - Location of the lab or place where the instrument is installed. - Using GEOREF is preferred. - - - - - - Device which reduces ToF differences of ions in ToF experiments. - - For atom probe the reflectron can be considered an energy compensation device. - Such a device can be realized technically for example with a Poschenrieder lens. - - Consult the following U.S. patents for further details: - - * 3863068 and 6740872 for the reflectron - * 8134119 for the curved reflectron - - - - Presence and status of the reflectron. - - - - - - - - - Given name/alias. - - - - - Free-text field to specify further details about the reflectron. - The field can be used to inform e. g. if the reflectron is flat or curved. - - - - - The maximum voltage applied to the reflectron, relative to system ground. - - - - - Manufacturer metadata that inform about the reflectron - - - - - Affine transformation(s) which detail where the reflectron is located - relative to e.g. the origin of the specimen space reference coordinate - system. This group can also be used for specifying how the reflectron - is rotated relative to a given axis in the instrument. - - - - - - A counter electrode of the LEAP 6000 series atom probes. - - - - - - A local electrode guiding the ion flight path. - Also called counter or extraction electrode. - - - - Acceleration voltage - - - - - - - Detector for taking raw time-of-flight and ion/hit impact positions data. - - - - TODO - - - - - TODO - - - - - - - - - CRunHeader.CAnalysis.fSpecimenTemperature - - - - - - - - The space inside the atom probe along which ions pass nominally - when they leave the specimen and travel to the detector. - - - - - CRunHeader.CLasHeader.fAnalysisPressure - - - - - - - - - - - Free text field for additional comments. - - - - - - A statement whether the measurement was successful or failed prematurely. - - - - - - Group to hold instances of :ref:`NXevent_data_apm`. - - Which temporal granularity is adequate depends on the situation and research - question. Using a model which enables a collection of events offers the most - flexible way to cater for both atom probe experiments or simulation. - - To monitor the course of an ion extraction experiment (or simulation) - it makes sense to track time explicitly via time stamps or implicitly - via e.g. a clock inside the instrument, such as the clock of the pulser - and respective pulsing event identifier. - - As set and measured quantities typically change over time and we do not - yet know during the measurement which of the events have associated - (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the evaporated_identifier but as a - function of the (pulsing) event_identifier. - - - - diff --git a/contributed_definitions/NXevent_data_apm.nxdl.xml b/contributed_definitions/NXevent_data_apm.nxdl.xml index d194467538..65111ada8d 100644 --- a/contributed_definitions/NXevent_data_apm.nxdl.xml +++ b/contributed_definitions/NXevent_data_apm.nxdl.xml @@ -202,9 +202,6 @@ - diff --git a/contributed_definitions/NXinstrument_apm.nxdl.xml b/contributed_definitions/NXinstrument_apm.nxdl.xml new file mode 100644 index 0000000000..1d6e45a22c --- /dev/null +++ b/contributed_definitions/NXinstrument_apm.nxdl.xml @@ -0,0 +1,369 @@ + + + + + + + Base class to document an instrument used for atom probe microscopy. + + Inheriting from NXinstrument, this base class is designed to offer the same concepts about + instrument-centric metadata to be used in two places inside NXapm without demanding that + the application definition needs to define the concepts in two places as maintaining this is + prone to errors. This base class implements the key design idea behind the NXapm application + definition in that we would like to offer a design where all (meta)data which over the course + of a measurement remain static can be stored only once and without polluting the application + definition with another group with concepts that should be used for storing (meta)data about + the instrument during events that happen during the course of the measurement. + + This design was inspired by NXem and electron microscopy where typically the instrument is + used in sessions and dozens of logical sets of data are collected under not necessarily always + the same instrument conditions. We do not want to repeat therefore the static (meta)data, as + this is redundant storage by virtue of design. The typical example is an electron microscope + where hundreds of images are taken and all static instrument data stored with each image. + This makes sense in cases when the image is used as a digital artifact that is exchanged across + different software applications or research data management systems but as in NeXus there + is either all information bundled into one artifact or there is a coordinating master artifact + that references related artifacts there is no point to store hundreds of times that always the + same microscope with the same lens setup was used to collect these images. + + + + + Location of the lab or place where the instrument is installed. Using GEOREF is + preferred. + + + + + Device which reduces ToF differences of ions in ToF experiments. + + For atom probe the reflectron can be considered an energy compensation device. + Such a device can be realized technically for example with a Poschenrieder lens. + + Consult the following U.S. patents for further details: + + * 3863068 and 6740872 for the reflectron + * 8134119 for the curved reflectron + + + + Presence and status of the reflectron. + + + + + + + + + Given name/alias. + + + + + Free-text field to specify further details about the reflectron. + The field can be used to inform e. g. if the reflectron is flat or curved. + + + + + The maximum voltage applied to the reflectron, relative to system ground. + + + + + + Affine transformation(s) which detail where the reflectron is located + relative to e.g. the origin of the specimen space reference coordinate + system. This group can also be used for specifying how the reflectron + is rotated relative to a given axis in the instrument. + + + + + + A counter electrode of the LEAP 6000 series atom probes. + + + + + + A local electrode guiding the ion flight path. + Also called counter or extraction electrode. + + + + Acceleration voltage + + + + + + + Detector for taking raw time-of-flight and ion/hit impact positions data. + + + + CRunHeader.fMcpEfficiency + + + + + CRunHeader.fMeshEfficiency + + + + + + + Laser- and/or voltage-pulsing device to trigger ion removal. + + + + + + Detail whereby ion extraction is triggered methodologically. + + + + + + + + + + + + + Frequency with which the pulser fire(s). + + + + Path to pulse_identifier + + + + + + Fraction of the pulse_voltage that is applied in addition + to the standing_voltage at peak voltage of a pulse. + + If a standing voltage is applied, this gives nominal pulse fraction + (as a function of standing voltage). Otherwise, this field should + not be present. + + + + Path to pulse_identifier + + + + + + + Pulsed voltage, in laser pulsing mode this field can be omitted. + + + + Path to pulse_identifier + + + + + + Absolute number of pulses starting from the beginning of the experiment. + + + + Path to pulse_identifier + + + + + + + Direct current voltage between the specimen and the (local electrode) in + the case of local electrode atom probe (LEAP) instrument. Otherwise, the + standing voltage applied to the sample, relative to system ground. + + + + Path to pulse_identifier + + + + + + Atom probe microscopes use controlled laser, voltage, or a combination of + pulsing strategies to trigger ion extraction via exciting and eventual field evaporation + field emission of ion at the specimen surface. + + + + + Nominal wavelength of the laser radiation. + + + + + Nominal power of the laser source while illuminating the specimen. + + + + + Average energy of the laser at peak of each pulse. + + + + Path to pulse_identifier + + + + + + Details about specific positions along the laser beam + which illuminates the (atom probe) specimen. + + + + Track time-dependent settings over the course of the measurement + how the laser beam shines on the specimen, i.e. the mean vector + is parallel to the laser propagation direction. + + + + Path to pulse_identifier + + + + + + Track time-dependent settings over the course of the measurement + where the laser beam exits the focusing optics. + + + + Path to pulse_identifier + + + + + + Track time-dependent settings over the course of the + measurement where the laser hits the specimen. + + + + Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. + + + + + + + Affine transformations which describe the geometry how the + laser focusing optics/pinhole-attached coordinate system is + defined, how it has to be transformed so that it aligns with + the specimen coordinate system. + + + + + + + + CRunHeader.CAnalysis.fSpecimenTemperature + + + + + + + + The space inside the atom probe along which ions pass nominally + when they leave the specimen and travel to the detector. + + + + + CRunHeader.CLasHeader.fAnalysisPressure + + + + + + + + + + + Free-text field for additional comments. + + + + + TODO + + + + Parameter set typically in the GUI of the control software which + defines the rules and control loops whereby the pulser and other + components of the instrument are controlled during evaporation. + + + + + Control parameter set typically in the GUI relevant to assure that + the instrument internally controls its settings such to assure a + significant yet not too high ion influx on the detector to avoid + detection losses. + + + + diff --git a/contributed_definitions/NXpulser_apm.nxdl.xml b/contributed_definitions/NXpulser_apm.nxdl.xml deleted file mode 100644 index 11ae8bec97..0000000000 --- a/contributed_definitions/NXpulser_apm.nxdl.xml +++ /dev/null @@ -1,240 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. - - - - - Base class for a laser- and/or voltage-pulsing device used in atom probe - microscopy. - - - - - Detail whereby ion extraction is triggered methodologically. - - - - - - - - - - - - - Frequency with which the pulser fire(s). - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - Fraction of the pulse_voltage that is applied in addition - to the standing_voltage at peak voltage of a pulse. - - If a standing voltage is applied, this gives nominal pulse fraction - (as a function of standing voltage). Otherwise, this field should - not be present. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - - Pulsed voltage, in laser pulsing mode this field can be omitted. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - Absolute number of pulses starting from the beginning of the experiment. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - - Direct current voltage between the specimen and the (local electrode) in - the case of local electrode atom probe (LEAP) instrument. Otherwise, the - standing voltage applied to the sample, relative to system ground. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - Atom probe microscopes use controlled laser, voltage, or a combination of - pulsing strategies to trigger ion extraction via exciting and eventual field evaporation - field emission of ion at the specimen surface. - - - - Given name/alias. - - - - - - Nominal wavelength of the laser radiation. - - - - - Nominal power of the laser source while illuminating the specimen. - - - - - Average energy of the laser at peak of each pulse. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - Details about specific positions along the laser beam - which illuminates the (atom probe) specimen. - - - - Track time-dependent settings over the course of the measurement - how the laser beam shines on the specimen, i.e. the mean vector - is parallel to the laser propagation direction. - - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - Track time-dependent settings over the course of the measurement - where the laser beam exits the focusing optics. - - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - Track time-dependent settings over the course of the - measurement where the laser hits the specimen. - - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - - Affine transformations which describe the geometry how the - laser focusing optics/pinhole-attached coordinate system is - defined, how it has to be transformed so that it aligns with - the specimen coordinate system. - - - - - diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 7f95dfe27a..f652395dc6 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -443,7 +443,6 @@ NXapm(NXobject): measurement(NXobject): exists: optional - # docstring currently with NXapm_msr doc: | Base class for collecting a session with a real atom probe or field-ion microscope. @@ -608,6 +607,23 @@ NXapm(NXobject): exists: optional # the case of allowing to not have event_data but only the above-mentioned instrument # details can be useful to convey details about an atom probe instrument in general + doc: | + Group to hold instances of :ref:`NXevent_data_apm`. + + Which temporal granularity is adequate depends on the situation and research + question. Using a model which enables a collection of events offers the most + flexible way to cater for both atom probe experiments or simulation. + + To monitor the course of an ion extraction experiment (or simulation) + it makes sense to track time explicitly via time stamps or implicitly + via e.g. a clock inside the instrument, such as the clock of the pulser + and respective pulsing event identifier. + + As set and measured quantities typically change over time and we do not + yet know during the measurement which of the events have associated + (molecular) ions that will end up in the reconstructed volume, we must not + document quantities as a function of the evaporated_identifier but as a + function of the (pulsing) event_identifier. eventID(NXevent_data_apm): exists: [min, 0, max, infty] # all these cannot be made required because for LEAP only stored in RHIT/HITS @@ -619,9 +635,6 @@ NXapm(NXobject): # pulse_identifier(NX_INT): instrument(NXinstrument_apm): exists: recommended - control(NXcollection): - evaporation_control(NX_CHAR): - target_detection_rate(NX_FLOAT): # optional groups can always be added but they will not be annotated eventually properly by pynxtools # reflectron(NXreflectron): # decelerate_electrode(NXlens_em): diff --git a/contributed_definitions/nyaml/NXapm_msr.yaml b/contributed_definitions/nyaml/NXapm_msr.yaml deleted file mode 100644 index 6c5570eca1..0000000000 --- a/contributed_definitions/nyaml/NXapm_msr.yaml +++ /dev/null @@ -1,205 +0,0 @@ -category: base -doc: | - Base class for collecting a session with a real atom probe or field-ion microscope. - - Workflows used during experiments or simulations of atom probe and related field-evaporation - research should be documented in more detail and be better contextualized not only because of - ongoing developments and the tighter becoming connection between atom probe and other - methods for material characterization foremost electron microscopy (see `T. Kelly et al. `_, `C. Fleischmann et al. `_, `W. Windl et al. `_, `C. Freysoldt et al. `_, or `G. da Costa et al. `_ to mention but a few). - To arrive at a design of base classes and an application definition which can be used for both real and simulated atom probe experiments, - it is worthwhile to recall concepts that are related to events and (molecular) ions: - - * Pulsing events which are used to trigger ion extraction events. - * Physical events and corresponding signal triggered by an ion hitting the detector. - Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. - * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input - and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are - wortwhile to be considered further and eventually included in the reconstructed volume. - * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually - selected (molecular) ions based on which an instance of a reconstruction is created. - * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values - and charge states of the (molecular) ions to substantiate that some of these ions can be considered - as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms - and subsequent peak labeling. In the field of atom probe this these peak identification methods - are known as ranging definitions. - - Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts - are well distinguished. However, the algorithms used to transform correlations between pulses and physical events - into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. - - Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme - where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier - i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. - That is evaporation_identifier values take the role of an implicit time and course of the experiment given that - ion extraction physically is a sequential process. - - There is a number of research groups who build own instruments and share different aspects of their technical - specifications and approaches how they apply data processing (e.g. `M. Monajem et al. `_, `P. Stender et al. `_ , or `I. Dimkou et al. `_ to name but a few). - Despite some of these activities embrace practices of open-source development, they use essentially the same - workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface - software is used to explore and thus analyze reconstructed atom probe datasets. - - Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. - Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which - scientific conclusions about the characterized material volume are made. Also here a reconstruction is - point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. - - By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all - the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. - Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. - We argue that this divide can be bridged with realizing the above-mentioned context and the realization that - similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. - - A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed - datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment - and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting - a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as - (spatial) filtering and reconstruction algorithms. - - Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation simulations - than it is in real world measurements because each ion has a prescribed iontype in the simulation. Be it a specifically charged - nuclid or a molecular ion whose flight path the simulation resolves. - Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. - Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require - simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps - in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. - Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) - than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path - such as local electrodes or physical obstacles and electric fields (controlled or stray fields). -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - p: | - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. -type: group -NXapm_msr(NXobject): # when evolving these ideas further inherit from NXapm_method instead - instrument(NXinstrument): - doc: | - Metadata of the atom probe or field-ion microscope instrument, henceforth called - microscope or instrument, and the lab in which it stands. - # (NXcsg): - # doc: | - # Possibility to include a detailed computational geometry description of the instrument. - instrument_name(NX_CHAR): - doc: | - Given name of the microscope as defined by the hosting lab. This is an alias. - Examples could be LEAP6000, Raptor, Oxcart, one atom at a time, etc. - location(NX_CHAR): - doc: | - Location of the lab or place where the instrument is installed. - Using GEOREF is preferred. - (NXfabrication): - reflectron(NXobject): # NXcomponent at soonish - doc: | - Device which reduces ToF differences of ions in ToF experiments. - - For atom probe the reflectron can be considered an energy compensation device. - Such a device can be realized technically for example with a Poschenrieder lens. - - Consult the following U.S. patents for further details: - - * 3863068 and 6740872 for the reflectron - * 8134119 for the curved reflectron - - status(NX_CHAR): - doc: | - Presence and status of the reflectron. - enumeration: [present, used] - name(NX_CHAR): - doc: | - Given name/alias. - description(NX_CHAR): - doc: | - Free-text field to specify further details about the reflectron. - The field can be used to inform e. g. if the reflectron is flat or curved. - voltage(NX_FLOAT): - doc: | - The maximum voltage applied to the reflectron, relative to system ground. - unit: NX_VOLTAGE - fabrication(NXfabrication): - doc: | - Manufacturer metadata that inform about the reflectron - (NXtransformations): - doc: | - Affine transformation(s) which detail where the reflectron is located - relative to e.g. the origin of the specimen space reference coordinate - system. This group can also be used for specifying how the reflectron - is rotated relative to a given axis in the instrument. - decelerate_electrode(NXlens_em): - doc: | - A counter electrode of the LEAP 6000 series atom probes. - # counter_electrodes being optional WO2016171675A1 - # see https://en.wikipedia.org/wiki/Einzel_lens for details double einzel lens in the invizo 6000 - # according to A. Breen (UNSW) - local_electrode(NXlens_em): - doc: | - A local electrode guiding the ion flight path. - Also called counter or extraction electrode. - voltage(NX_FLOAT): - doc: | - Acceleration voltage - unit: NX_VOLTAGE - # but the local_electrode does not really on purpose create a magnetic field, - # specific for an electro-magnetic lens is the symmetry of its field - # NEW ISSUE: for now keep that we have what is an NXlens_em - # NEW ISSUE: APEX MONITOR / LEAP distance monitoring - # NEW ISSUE: the definition of flat test data should be included and documented - # NEW ISSUE: local electrode, baking strategies, storage - ion_detector(NXdetector): - doc: | - Detector for taking raw time-of-flight and ion/hit impact positions data. - mcp_efficiency(NX_FLOAT): - doc: | - TODO - unit: NX_DIMENSIONLESS - mesh_efficiency(NX_FLOAT): - doc: | - TODO - unit: NX_DIMENSIONLESS - # model, serial_number, manufacturer_name all inherited from NXdetector base class - pulser(NXpulser_apm): - stage(NXstage_lab): - specimen_temperature(NX_FLOAT): - doc: | - CRunHeader.CAnalysis.fSpecimenTemperature - unit: NX_TEMPERATURE - # NEW ISSUE: add NXapm_energy_analyzer, a voltage grid like done in Rouen/GPM - analysis_chamber(NXchamber): - flight_path(NX_FLOAT): - exists: recommended - doc: | - The space inside the atom probe along which ions pass nominally - when they leave the specimen and travel to the detector. - unit: NX_LENGTH - pressure(NX_FLOAT): - doc: | - CRunHeader.CLasHeader.fAnalysisPressure - unit: NX_PRESSURE - buffer_chamber(NXchamber): - load_lock_chamber(NXchamber): - getter_pump(NXpump): - roughening_pump(NXpump): - turbomolecular_pump(NXpump): - comment(NX_CHAR): - doc: | - Free text field for additional comments. - event_data(NXobject): - doc: | - Group to hold instances of :ref:`NXevent_data_apm`. - - Which temporal granularity is adequate depends on the situation and research - question. Using a model which enables a collection of events offers the most - flexible way to cater for both atom probe experiments or simulation. - - To monitor the course of an ion extraction experiment (or simulation) - it makes sense to track time explicitly via time stamps or implicitly - via e.g. a clock inside the instrument, such as the clock of the pulser - and respective pulsing event identifier. - - As set and measured quantities typically change over time and we do not - yet know during the measurement which of the events have associated - (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the evaporated_identifier but as a - function of the (pulsing) event_identifier. - (NXevent_data_apm): diff --git a/contributed_definitions/nyaml/NXinstrument_apm.yaml b/contributed_definitions/nyaml/NXinstrument_apm.yaml new file mode 100644 index 0000000000..9e243ad0f9 --- /dev/null +++ b/contributed_definitions/nyaml/NXinstrument_apm.yaml @@ -0,0 +1,252 @@ +category: base +doc: | + Base class to document an instrument used for atom probe microscopy. + + Inheriting from NXinstrument, this base class is designed to offer the same concepts about + instrument-centric metadata to be used in two places inside NXapm without demanding that + the application definition needs to define the concepts in two places as maintaining this is + prone to errors. This base class implements the key design idea behind the NXapm application + definition in that we would like to offer a design where all (meta)data which over the course + of a measurement remain static can be stored only once and without polluting the application + definition with another group with concepts that should be used for storing (meta)data about + the instrument during events that happen during the course of the measurement. + + This design was inspired by NXem and electron microscopy where typically the instrument is + used in sessions and dozens of logical sets of data are collected under not necessarily always + the same instrument conditions. We do not want to repeat therefore the static (meta)data, as + this is redundant storage by virtue of design. The typical example is an electron microscope + where hundreds of images are taken and all static instrument data stored with each image. + This makes sense in cases when the image is used as a digital artifact that is exchanged across + different software applications or research data management systems but as in NeXus there + is either all information bundled into one artifact or there is a coordinating master artifact + that references related artifacts there is no point to store hundreds of times that always the + same microscope with the same lens setup was used to collect these images. +# One could use an NXnote or reference to another NeXus file where these static (meta)data +# are stored but then referencing this in an application definition would demand to make such +# file required, while NXinstrument_apm can be used directly for the static and the dynamic +# or volatile (meta)data. +type: group +NXinstrument_apm(NXinstrument): + # (NXcsg): + # doc: | + # Possibility to include a detailed computational geometry description of the instrument. + location(NX_CHAR): + doc: | + Location of the lab or place where the instrument is installed. Using GEOREF is preferred. + reflectron(NXobject): # NXcomponent soonish + doc: | + Device which reduces ToF differences of ions in ToF experiments. + + For atom probe the reflectron can be considered an energy compensation device. + Such a device can be realized technically for example with a Poschenrieder lens. + + Consult the following U.S. patents for further details: + + * 3863068 and 6740872 for the reflectron + * 8134119 for the curved reflectron + + status(NX_CHAR): + doc: | + Presence and status of the reflectron. + enumeration: [present, used] + name(NX_CHAR): + doc: | + Given name/alias. + description(NX_CHAR): + doc: | + Free-text field to specify further details about the reflectron. + The field can be used to inform e. g. if the reflectron is flat or curved. + voltage(NX_FLOAT): + doc: | + The maximum voltage applied to the reflectron, relative to system ground. + unit: NX_VOLTAGE + fabrication(NXfabrication): + (NXtransformations): + doc: | + Affine transformation(s) which detail where the reflectron is located + relative to e.g. the origin of the specimen space reference coordinate + system. This group can also be used for specifying how the reflectron + is rotated relative to a given axis in the instrument. + decelerate_electrode(NXlens_em): + doc: | + A counter electrode of the LEAP 6000 series atom probes. + # counter_electrodes being optional WO2016171675A1 + # see https://en.wikipedia.org/wiki/Einzel_lens for details double einzel lens in the invizo 6000 + # according to A. Breen (UNSW) + local_electrode(NXlens_em): + doc: | + A local electrode guiding the ion flight path. + Also called counter or extraction electrode. + voltage(NX_FLOAT): + doc: | + Acceleration voltage + unit: NX_VOLTAGE + # but the local_electrode does not really on purpose create a magnetic field, + # specific for an electro-magnetic lens is the symmetry of its field + # NEW ISSUE: for now keep that we have what is an NXlens_em + # NEW ISSUE: APEX MONITOR / LEAP distance monitoring + # NEW ISSUE: the definition of flat test data should be included and documented + # NEW ISSUE: local electrode, baking strategies, storage + ion_detector(NXdetector): + doc: | + Detector for taking raw time-of-flight and ion/hit impact positions data. + mcp_efficiency(NX_FLOAT): + doc: | + CRunHeader.fMcpEfficiency + unit: NX_DIMENSIONLESS + mesh_efficiency(NX_FLOAT): + doc: | + CRunHeader.fMeshEfficiency + unit: NX_DIMENSIONLESS + # model, serial_number, manufacturer_name all inherited from NXdetector base class + pulser(NXobject): + doc: | + Laser- and/or voltage-pulsing device to trigger ion removal. + # technical design + fabrication(NXfabrication): + pulse_mode(NX_CHAR): + doc: | + Detail whereby ion extraction is triggered methodologically. + enumeration: [laser, voltage, laser_and_voltage, other, unknown] + pulse_frequency(NX_FLOAT): + doc: | + Frequency with which the pulser fire(s). + # the example of how the IFES APT TC's HDF format deals with such data conceptually, concepts are mixed into superconcepts interleaved tuple with different units: "PulseFrequency : Real array, 2xn (Hz) This is the frequency of the high voltage or laser pulser. first entry : first pulse number where the spacing between this and all subsequent pulses are considered to be at the selected frequency. Each first entry must be strictly increasing in value. The second entry contains the frequency value" as data can be compressed in this case very efficiently we go for with an array of length 1xn_ions + unit: NX_FREQUENCY + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pulse_fraction(NX_FLOAT): + doc: | + Fraction of the pulse_voltage that is applied in addition + to the standing_voltage at peak voltage of a pulse. + + If a standing voltage is applied, this gives nominal pulse fraction + (as a function of standing voltage). Otherwise, this field should + not be present. + unit: NX_DIMENSIONLESS + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pulse_voltage(NX_FLOAT): + doc: | + Pulsed voltage, in laser pulsing mode this field can be omitted. + # example of a conditional requirement that can be dealt with igorously by OWL but not by NeXus! + # as either pulse_voltage is required in an appdef but then that + # existence constraint is independent of other values. + unit: NX_VOLTAGE + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pulse_number(NX_UINT): + doc: | + Absolute number of pulses starting from the beginning of the experiment. + unit: NX_UNITLESS + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + # eventually equivalent to pulse_identifier within NXevent_data_apm + standing_voltage(NX_FLOAT): + doc: | + Direct current voltage between the specimen and the (local electrode) in + the case of local electrode atom probe (LEAP) instrument. Otherwise, the + standing voltage applied to the sample, relative to system ground. + unit: NX_VOLTAGE + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + sourceID(NXsource): + doc: | + Atom probe microscopes use controlled laser, voltage, or a combination of + pulsing strategies to trigger ion extraction via exciting and eventual field evaporation + field emission of ion at the specimen surface. + fabrication(NXfabrication): + wavelength(NX_FLOAT): + doc: | + Nominal wavelength of the laser radiation. + unit: NX_WAVELENGTH + power(NX_FLOAT): + doc: | + Nominal power of the laser source while illuminating the specimen. + unit: NX_POWER + pulse_energy(NX_FLOAT): + doc: | + Average energy of the laser at peak of each pulse. + unit: NX_ENERGY + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + (NXbeam): + doc: | + Details about specific positions along the laser beam + which illuminates the (atom probe) specimen. + incidence_vector(NX_NUMBER): + doc: | + Track time-dependent settings over the course of the measurement + how the laser beam shines on the specimen, i.e. the mean vector + is parallel to the laser propagation direction. + unit: NX_LENGTH + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pinhole_position(NX_NUMBER): + doc: | + Track time-dependent settings over the course of the measurement + where the laser beam exits the focusing optics. + unit: NX_LENGTH + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + spot_position(NX_NUMBER): + doc: | + Track time-dependent settings over the course of the + measurement where the laser hits the specimen. + unit: NX_LENGTH + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. + (NXtransformations): + doc: | + Affine transformations which describe the geometry how the + laser focusing optics/pinhole-attached coordinate system is + defined, how it has to be transformed so that it aligns with + the specimen coordinate system. + stage(NXstage_lab): + specimen_temperature(NX_FLOAT): + doc: | + CRunHeader.CAnalysis.fSpecimenTemperature + unit: NX_TEMPERATURE + # NEW ISSUE: add NXapm_energy_analyzer, a voltage grid like done in Rouen/GPM + analysis_chamber(NXchamber): + flight_path(NX_FLOAT): + doc: | + The space inside the atom probe along which ions pass nominally + when they leave the specimen and travel to the detector. + unit: NX_LENGTH + pressure(NX_FLOAT): + doc: | + CRunHeader.CLasHeader.fAnalysisPressure + unit: NX_PRESSURE + buffer_chamber(NXchamber): + load_lock_chamber(NXchamber): + getter_pump(NXpump): + roughening_pump(NXpump): + turbomolecular_pump(NXpump): + comment(NX_CHAR): + doc: | + Free-text field for additional comments. + control(NXcollection): + doc: | + TODO + evaporation_control(NX_CHAR): + doc: | + Parameter set typically in the GUI of the control software which + defines the rules and control loops whereby the pulser and other + components of the instrument are controlled during evaporation. + target_detection_rate(NX_NUMBER): + doc: | + Control parameter set typically in the GUI relevant to assure that + the instrument internally controls its settings such to assure a + significant yet not too high ion influx on the detector to avoid + detection losses. + unit: NX_ANY # ions/pulse diff --git a/contributed_definitions/nyaml/NXpulser_apm.yaml b/contributed_definitions/nyaml/NXpulser_apm.yaml deleted file mode 100644 index 1af0a47f87..0000000000 --- a/contributed_definitions/nyaml/NXpulser_apm.yaml +++ /dev/null @@ -1,134 +0,0 @@ -category: base -doc: | - Base class for a laser- and/or voltage-pulsing device used in atom probe microscopy. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - p: | - Number of pulses collected in between start_time and end_time - resolved by an instance of :ref:`NXevent_data_apm`. -type: group -NXpulser_apm(NXobject): - (NXfabrication): - pulse_mode(NX_CHAR): - doc: | - Detail whereby ion extraction is triggered methodologically. - enumeration: [laser, voltage, laser_and_voltage, other, unknown] - pulse_frequency(NX_FLOAT): - doc: | - Frequency with which the pulser fire(s). - # the example of how the IFES APT TC's HDF format deals with such data conceptually, concepts are mixed into superconcepts interleaved tuple with different units: "PulseFrequency : Real array, 2xn (Hz) This is the frequency of the high voltage or laser pulser. first entry : first pulse number where the spacing between this and all subsequent pulses are considered to be at the selected frequency. Each first entry must be strictly increasing in value. The second entry contains the frequency value" as data can be compressed in this case very efficiently we go for with an array of length 1xn_ions - unit: NX_FREQUENCY - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - pulse_fraction(NX_FLOAT): - doc: | - Fraction of the pulse_voltage that is applied in addition - to the standing_voltage at peak voltage of a pulse. - - If a standing voltage is applied, this gives nominal pulse fraction - (as a function of standing voltage). Otherwise, this field should - not be present. - unit: NX_DIMENSIONLESS - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - pulse_voltage(NX_FLOAT): - doc: | - Pulsed voltage, in laser pulsing mode this field can be omitted. - # example of a conditional requirement that can be dealt with igorously by OWL but not by NeXus! - # as either pulse_voltage is required in an appdef but then that - # existence constraint is independent of other values. - unit: NX_VOLTAGE - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - pulse_number(NX_UINT): - doc: | - Absolute number of pulses starting from the beginning of the experiment. - unit: NX_UNITLESS - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - # eventually equivalent to pulse_identifier within NXevent_data_apm - standing_voltage(NX_FLOAT): - doc: | - Direct current voltage between the specimen and the (local electrode) in - the case of local electrode atom probe (LEAP) instrument. Otherwise, the - standing voltage applied to the sample, relative to system ground. - unit: NX_VOLTAGE - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - (NXsource): - doc: | - Atom probe microscopes use controlled laser, voltage, or a combination of - pulsing strategies to trigger ion extraction via exciting and eventual field evaporation - field emission of ion at the specimen surface. - name(NX_CHAR): - doc: | - Given name/alias. - fabrication(NXfabrication): - wavelength(NX_FLOAT): - doc: | - Nominal wavelength of the laser radiation. - unit: NX_WAVELENGTH - power(NX_FLOAT): - doc: | - Nominal power of the laser source while illuminating the specimen. - unit: NX_POWER - pulse_energy(NX_FLOAT): - doc: | - Average energy of the laser at peak of each pulse. - unit: NX_ENERGY - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - (NXbeam): - doc: | - Details about specific positions along the laser beam - which illuminates the (atom probe) specimen. - incidence_vector(NX_NUMBER): - doc: | - Track time-dependent settings over the course of the measurement - how the laser beam shines on the specimen, i.e. the mean vector - is parallel to the laser propagation direction. - unit: NX_LENGTH - dim: (p, 3) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - pinhole_position(NX_NUMBER): - doc: | - Track time-dependent settings over the course of the measurement - where the laser beam exits the focusing optics. - unit: NX_LENGTH - dim: (p, 3) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - spot_position(NX_NUMBER): - doc: | - Track time-dependent settings over the course of the - measurement where the laser hits the specimen. - unit: NX_LENGTH - dim: (p, 3) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - (NXtransformations): - doc: | - Affine transformations which describe the geometry how the - laser focusing optics/pinhole-attached coordinate system is - defined, how it has to be transformed so that it aligns with - the specimen coordinate system. - # A right-handed Cartesian coordinate system, the so-called laser space, - # should be assumed, whose positive z-axis points - # into the direction of the propagating laser beam. From ef786b723226c62ba6c4c886b0fe986a48edde2d Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 23:25:26 +0100 Subject: [PATCH 17/75] Finished refactoring of NXapm --- contributed_definitions/NXapm.nxdl.xml | 248 ++++++++---------- .../NXinstrument_apm.nxdl.xml | 35 ++- contributed_definitions/nyaml/NXapm.yaml | 182 ++++++------- .../nyaml/NXapm_ranging.yaml | 2 +- .../nyaml/NXinstrument_apm.yaml | 7 +- 5 files changed, 227 insertions(+), 247 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 254bacd9f8..87a310bd12 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -26,27 +26,33 @@ The symbols used in the schema to specify e.g. dimensions of arrays. - + - Number of pulses collected in between start_time and end_time resolved by an - instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of - ions included in the reconstructed volume if the application definition is used - to store results of an already reconstructed datasets. + Number of hit qualities (hit types) distinguished. - + - Number of pulses returned by the hit finding algorithm. Not necessarily p or n. + Number of delay-line wires of the detector. - + - Number of hit qualities (hit types) distinguished. + Number of bins used in the mass-to-charge-state-ratio spectrum. - + - Number of delay-line wires of the detector. + Number of pulses collected in between start_time and end_time resolved by an + instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of + ions included in the reconstructed volume if the application definition is used + to store results of an already reconstructed datasets. + + + + + Number of pulses returned by the hit finding algorithm. + Neither necessarily equal to p nor to n. @@ -55,7 +61,7 @@ from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process (the so-called evaporation_identifier). This identifier must not be confused with - the pulse_identifier. + the pulse_identifier. Typically smaller than both p_out and p_out. @@ -619,100 +625,43 @@ schema for heat treatment such as local electrodes or physical obstacles and electric fields (controlled or stray fields). - - - TODO - - - - - Which type of instrument. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - + - + - + - - + + + - - - The wavelength of the radiation emitted by the source. - - - - - - - - + Free text field for additional comments. @@ -754,67 +703,68 @@ details can be useful to convey details about an atom probe instrument in genera + + + - - + + + + + + + + + - - - - + + + + - - - + + + + + + + + + + - + + + - + - - + - + - Simulation of ion extraction from matter via laser and/or voltage pulsing. @@ -853,6 +803,15 @@ the need for defining them again--> + + For almost atom probe instruments (meta)data about raw data follow proprietary semantics. + Therefore, this group can currently be used only to point to these digital artifacts + in an effort to document all step of an analysis workflow. + + The physical quantities measured in an atom probe experiment are time-of-flight and + tuples of arrival_time_pairs as a function of the event chain on the pulser. + From these tuples hits are computed in a process called hit_finding. + @@ -866,29 +825,7 @@ the need for defining them again--> - - - - Configuration of and results obtained from a hit finding algorithm. - - - - - - - - - - - - - - - + The number of wires in the detector. @@ -920,6 +857,29 @@ we can only make recommendations--> + + + + Configuration of and results obtained from a hit finding algorithm. + + + + + + + + + + + + + + + @@ -1000,7 +960,8 @@ used only in the context to learn about the multiplicity of an ion. pulses_since_last_ion(NX_UINT): dim: (n,) pulse_identifier(NX_INT): - dim: (n,)--> + dim: (n,) +at this point the original set of events p has been filtered down to p_out--> @@ -1050,13 +1011,13 @@ pulse_identifier(NX_INT): - + - Configuration of and results obtained from a voltage-and-bowl ToF correction algorithm. + Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. - The voltage-and-bowl correction is a data post-processing step to correct ion impact positions - for flight path differences, detector biases, and nonlinearities. + The voltage-and-bowl correction is a data post-processing step to correct ion impact + positions for flight path differences, detector biases, and nonlinearities. @@ -1071,8 +1032,8 @@ pulse_identifier(NX_INT): @@ -1085,7 +1046,7 @@ proprietary hardware with proprietary semantics - The parameter :math:`t_0` CAnalysis.CCalibMass.fT0Estimate + The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate @@ -1235,7 +1196,6 @@ results--> - diff --git a/contributed_definitions/NXinstrument_apm.nxdl.xml b/contributed_definitions/NXinstrument_apm.nxdl.xml index 1d6e45a22c..4cdce88940 100644 --- a/contributed_definitions/NXinstrument_apm.nxdl.xml +++ b/contributed_definitions/NXinstrument_apm.nxdl.xml @@ -50,6 +50,39 @@ or volatile (meta)data.--> that references related artifacts there is no point to store hundreds of times that always the same microscope with the same lens setup was used to collect these images. + + + Which type of instrument. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -247,7 +280,7 @@ existence constraint is independent of other values. - Nominal wavelength of the laser radiation. + The wavelength of the radiation emitted by the source. diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index f652395dc6..17e7d1b6fd 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -4,23 +4,26 @@ doc: | symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. + n_ht: | + Number of hit qualities (hit types) distinguished. + n_dld: | + Number of delay-line wires of the detector. + n_bins: | + Number of bins used in the mass-to-charge-state-ratio spectrum. p: | Number of pulses collected in between start_time and end_time resolved by an instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of ions included in the reconstructed volume if the application definition is used to store results of an already reconstructed datasets. p_out: | - Number of pulses returned by the hit finding algorithm. Not necessarily p or n. - n_ht: | - Number of hit qualities (hit types) distinguished. - n_dld: | - Number of delay-line wires of the detector. + Number of pulses returned by the hit finding algorithm. + Neither necessarily equal to p nor to n. n: | Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process (the so-called evaporation_identifier). This identifier must not be confused with - the pulse_identifier. + the pulse_identifier. Typically smaller than both p_out and p_out. type: group NXapm(NXobject): (NXentry): # entryID @@ -528,70 +531,45 @@ NXapm(NXobject): than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path such as local electrodes or physical obstacles and electric fields (controlled or stray fields). instrument(NXinstrument_apm): - identifier_name(NX_UINT): - doc: | - TODO type(NX_CHAR): exists: recommended - doc: | - Which type of instrument. - enumeration: [Inspico, 3DAP, LAWATAP, LEAP 3000 Si, LEAP 3000X Si, LEAP 3000 HR, LEAP 3000X HR, LEAP 4000 Si, LEAP 4000X Si, LEAP 4000 HR, LEAP 4000X HR, LEAP 5000 XS, LEAP 5000 XR, LEAP 5000 R, EIKOS, EIKOS-UV, LEAP 6000 XR, LEAP INVIZO, Photonic AP, TeraSAT, TAPHR, Modular AP, Titanium APT, Extreme UV APT, unknown] fabrication(NXfabrication): + exists: recommended vendor(NX_CHAR): model(NX_CHAR): serial_number(NX_CHAR): - identifier(NXidentifier): - exists: recommended reflectron(NXobject): exists: optional status(NX_CHAR): - fabrication(NXfabrication): - exists: recommended - vendor(NX_CHAR): - model(NX_CHAR): - # decelerate_electrode(NXlens_em): local_electrode(NXlens_em): - # add flat test status + exists: recommended name(NX_CHAR): fabrication(NXfabrication): - exists: recommended + exists: optional vendor(NX_CHAR): model(NX_CHAR): ion_detector(NXdetector): exists: recommended fabrication(NXfabrication): - exists: recommended # for LEAP systems they come shipped configured + exists: optional vendor(NX_CHAR): model(NX_CHAR): - pulser(NXpulser_apm): + pulser(NXobject): + exists: recommended fabrication(NXfabrication): - exists: recommended + exists: optional vendor(NX_CHAR): model(NX_CHAR): pulse_mode(NX_CHAR): + pulse_frequency(NX_FLOAT): + exists: recommended sourceID(NXsource): - exists: [min, 0, max, 2] # conditionally required if pulse_mode is not voltage! + exists: [min, 0, max, 2] # conditionally required, sourceID only if pulse_mode is not voltage! fabrication(NXfabrication): exists: recommended vendor(NX_CHAR): model(NX_CHAR): - wavelength(NX_FLOAT): - doc: | - The wavelength of the radiation emitted by the source. - unit: NX_WAVELENGTH - # use NXbeam in the future - stage(NXstage_lab): - exists: recommended - specimen_temperature(NX_FLOAT): - exists: recommended - analysis_chamber(NXchamber): - exists: recommended - # atmosphere(NXcollection): - # buffer_chamber(NXchamber): - # load_lock_chamber(NXchamber): - # getter_pump(NXpump): - # roughening_pump(NXpump): - # turbomolecular_pump(NXpump): + # wavelength and pulse_energy as dynamic/volatile quantities stored in event data part comment(NX_CHAR): doc: | Free text field for additional comments. @@ -628,56 +606,53 @@ NXapm(NXobject): exists: [min, 0, max, infty] # all these cannot be made required because for LEAP only stored in RHIT/HITS # but for M-TAP and Oxcart these pieces of information are available. - # start_time(NX_DATE_TIME): - # end_time(NX_DATE_TIME): + start_time(NX_DATE_TIME): + exists: recommended + end_time(NX_DATE_TIME): + exists: recommended # delta_time(NX_NUMBER): # pulse_identifier_offset(NX_INT): # pulse_identifier(NX_INT): instrument(NXinstrument_apm): exists: recommended - # optional groups can always be added but they will not be annotated eventually properly by pynxtools - # reflectron(NXreflectron): + reflectron(NXobject): + exists: recommended + voltage(NX_FLOAT): # decelerate_electrode(NXlens_em): - # local_electrode(NXlens_em): + local_electrode(NXlens_em): + exists: recommended + voltage(NX_FLOAT): # ion_detector(NXdetector): - # exists: optional - # signal_amplitude(NX_FLOAT): - pulser(NXpulser_apm): + pulser(NXobject): + exists: recommended pulse_frequency(NX_FLOAT): - # unit: NX_FREQUENCY - # dim: (p,) \@logged_against(NX_CHAR): pulse_fraction(NX_FLOAT): - # unit: NX_DIMENSIONLESS - # dim: (p,) \@logged_against(NX_CHAR): pulse_voltage(NX_FLOAT): # ePOS, APT pulsed voltage - exists: recommended # not required for voltage pulsing - # unit: NX_VOLTAGE - # dim: (p,) + exists: optional # not required for voltage pulsing + dim: (n,) + \@logged_against(NX_CHAR): + pulse_number(NX_UINT): + exists: optional + dim: (n,) \@logged_against(NX_CHAR): - # pulse_number(NX_UINT): standing_voltage(NX_FLOAT): # ePOS, APT standing voltage - # unit: NX_VOLTAGE - # dim: (p,) + exists: optional + dim: (n,) \@logged_against(NX_CHAR): sourceID(NXsource): exists: [min, 0, max, 2] # not required for voltage pulsing pulse_energy(NX_FLOAT): - # unit: NX_ENERGY - # dim: (p,) + dim: (n,) \@logged_against(NX_CHAR): - # laser geometry at the moment has no example nor any feedback from the community + # laser geometry at the moment has neither a worked out example + # nor any feedback from the community despite the work from B. Gault + # on laser atom probe was granted a Leibnitz award stage(NXstage_lab): - # setpoint_temperature(NX_FLOAT): - base_temperature(NX_FLOAT): + specimen_temperature(NX_FLOAT): analysis_chamber(NXchamber): - chamber_pressure(NX_FLOAT): - # buffer_chamber(NXchamber): - # load_lock_chamber(NXchamber): - # getter_pump(NXpump): - # roughening_pump(NXpump): - # turbomolecular_pump(NXpump): + analysis_pressure(NX_FLOAT): simulation(NXobject): exists: optional doc: | @@ -708,6 +683,14 @@ NXapm(NXobject): # could use a stack_3d(NXdata) to record time series of specimen shape evolution raw_data(NXprocess): exists: recommended + doc: | + For almost atom probe instruments (meta)data about raw data follow proprietary semantics. + Therefore, this group can currently be used only to point to these digital artifacts + in an effort to document all step of an analysis workflow. + + The physical quantities measured in an atom probe experiment are time-of-flight and + tuples of arrival_time_pairs as a function of the event chain on the pulser. + From these tuples hits are computed in a process called hit_finding. sequence_index(NX_POSINT): exists: recommended programID(NXprogram): @@ -723,6 +706,26 @@ NXapm(NXobject): exists: optional algorithm(NX_CHAR): exists: optional + # technical details of data the ion_detector collects + number_of_dld_wires(NX_UINT): + exists: recommended + doc: | + The number of wires in the detector. + unit: NX_UNITLESS + enumeration: [1, 2, 3] + dld_wire_names(NX_CHAR): + exists: optional + doc: | + Alias tuple (begin, end) of each DLD wire of the detector. + Order follows arrival_time_pairs. + dim: (n_dld, 2) + arrival_time_pairs(NX_NUMBER): + exists: optional + doc: | + Raw readings from the analog-to-digital-converter + timing circuits of the detector wires. + unit: NX_TIME + dim: (p, n_dld, 2) hit_finding(NXprocess): exists: recommended doc: | @@ -745,25 +748,6 @@ NXapm(NXobject): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - number_of_dld_wires(NX_UINT): - exists: recommended - doc: | - The number of wires in the detector. - unit: NX_UNITLESS - enumeration: [1, 2, 3] - dld_wire_names(NX_CHAR): - exists: optional - doc: | - Alias tuple (begin, end) of each DLD wire of the detector. - Order follows arrival_time_pairs. - dim: (n_dld, 2) - arrival_time_pairs(NX_NUMBER): - exists: optional - doc: | - Raw readings from the analog-to-digital-converter - timing circuits of the detector wires. - unit: NX_TIME - dim: (p, n_dld, 2) # results of the hit_finding algorithm hit_positions(NX_NUMBER): exists: recommended @@ -832,6 +816,7 @@ NXapm(NXobject): # dim: (n,) # pulse_identifier(NX_INT): # dim: (n,) + # at this point the original set of events p has been filtered down to p_out hit_spatial_filtering(NXprocess): exists: recommended sequence_index(NX_POSINT): @@ -877,15 +862,14 @@ NXapm(NXobject): bitdepth(NX_UINT): mask(NX_UINT): identifier(NX_INT): - - # at this point the original set of events p has been filtered down to n + # at this point the set of events p_out has been filtered down to n voltage_and_bowl(NXprocess): exists: recommended doc: | - Configuration of and results obtained from a voltage-and-bowl ToF correction algorithm. + Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. - The voltage-and-bowl correction is a data post-processing step to correct ion impact positions - for flight path differences, detector biases, and nonlinearities. + The voltage-and-bowl correction is a data post-processing step to correct ion impact + positions for flight path differences, detector biases, and nonlinearities. sequence_index(NX_POSINT): exists: recommended programID(NXprogram): @@ -899,7 +883,8 @@ NXapm(NXobject): checksum(NX_CHAR): algorithm(NX_CHAR): raw_tof(NX_FLOAT): - # currently cannot be made required because of being a quantity measured by proprietary hardware with proprietary semantics + # currently cannot be made required because of being a quantity measured + # by proprietary hardware with proprietary semantics exists: recommended doc: | Raw time-of-flight data without corrections. @@ -908,7 +893,7 @@ NXapm(NXobject): tof_zero_estimate(NX_FLOAT): exists: optional doc: | - The parameter :math:`t_0` CAnalysis.CCalibMass.fT0Estimate + The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate unit: NX_TIME calibrated_tof(NX_FLOAT): exists: recommended @@ -933,7 +918,6 @@ NXapm(NXobject): # results mass_to_charge(NX_FLOAT): dim: (n,) - reconstruction(NXapm_reconstruction): exists: recommended sequence_index(NX_POSINT): @@ -1008,7 +992,6 @@ NXapm(NXobject): axis_x(NX_FLOAT): dim: (n_x,) \@long_name(NX_CHAR): - ranging(NXapm_ranging): exists: recommended sequence_index(NX_POSINT): @@ -1034,7 +1017,6 @@ NXapm(NXobject): program(NX_CHAR): \@version(NX_CHAR): min_incr_max(NX_FLOAT): - # dim: (3,) # u mass_spectrum(NXdata): \@signal(NX_CHAR): \@axes(NX_CHAR): diff --git a/contributed_definitions/nyaml/NXapm_ranging.yaml b/contributed_definitions/nyaml/NXapm_ranging.yaml index ea5199a8b3..1246600c98 100644 --- a/contributed_definitions/nyaml/NXapm_ranging.yaml +++ b/contributed_definitions/nyaml/NXapm_ranging.yaml @@ -23,7 +23,7 @@ NXapm_ranging(NXprocess): # when evolving these ideas further inherit from NXap min_incr_max(NX_FLOAT): doc: | Smallest, increment, and largest mass-to-charge-state ratio value. - unit: NX_ANY # u + unit: NX_ANY # Da dim: (3,) mass_spectrum(NXdata): doc: | diff --git a/contributed_definitions/nyaml/NXinstrument_apm.yaml b/contributed_definitions/nyaml/NXinstrument_apm.yaml index 9e243ad0f9..535abaa0d5 100644 --- a/contributed_definitions/nyaml/NXinstrument_apm.yaml +++ b/contributed_definitions/nyaml/NXinstrument_apm.yaml @@ -27,6 +27,11 @@ doc: | # or volatile (meta)data. type: group NXinstrument_apm(NXinstrument): + type(NX_CHAR): + doc: | + Which type of instrument. + enumeration: [Inspico, 3DAP, LAWATAP, LEAP 3000 Si, LEAP 3000X Si, LEAP 3000 HR, LEAP 3000X HR, LEAP 4000 Si, LEAP 4000X Si, LEAP 4000 HR, LEAP 4000X HR, LEAP 5000 XS, LEAP 5000 XR, LEAP 5000 R, EIKOS, EIKOS-UV, LEAP 6000 XR, LEAP INVIZO, Photonic AP, TeraSAT, TAPHR, Modular AP, Titanium APT, Extreme UV APT, unknown] + fabrication(NXfabrication): # (NXcsg): # doc: | # Possibility to include a detailed computational geometry description of the instrument. @@ -163,7 +168,7 @@ NXinstrument_apm(NXinstrument): fabrication(NXfabrication): wavelength(NX_FLOAT): doc: | - Nominal wavelength of the laser radiation. + The wavelength of the radiation emitted by the source. unit: NX_WAVELENGTH power(NX_FLOAT): doc: | From 65cec2975d0f53be9d7e0a2c98d5cd8254f8731c Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 31 Jan 2025 23:46:13 +0100 Subject: [PATCH 18/75] Cleaning the APM landing page of the documentation and tests --- contributed_definitions/NXapm.nxdl.xml | 7 +- .../NXevent_data_apm.nxdl.xml | 146 +----------------- .../NXinstrument_apm.nxdl.xml | 15 +- contributed_definitions/nyaml/NXapm.yaml | 8 +- .../nyaml/NXevent_data_apm.yaml | 100 +----------- .../nyaml/NXinstrument_apm.yaml | 12 +- .../contributed_definitions/apm-structure.rst | 38 +---- 7 files changed, 52 insertions(+), 274 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 87a310bd12..822c8741ae 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -652,8 +652,6 @@ schema for heat treatment - - @@ -719,6 +717,7 @@ pulse_identifier(NX_INT):--> + @@ -761,6 +760,10 @@ on laser atom probe was granted a Leibnitz award--> + + + + diff --git a/contributed_definitions/NXevent_data_apm.nxdl.xml b/contributed_definitions/NXevent_data_apm.nxdl.xml index 65111ada8d..bad1c9eda7 100644 --- a/contributed_definitions/NXevent_data_apm.nxdl.xml +++ b/contributed_definitions/NXevent_data_apm.nxdl.xml @@ -35,7 +35,9 @@ Base class to store state and (meta)data of events over the course of an atom probe experiment. - This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs + Having at least one instance for an instance of NXapm is recommended. + + This base class applies the concept of the NXevent_data_em base class to the specific needs of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication of information. Specifically, the time interval considered is the entire time starting at start_time until end_time during which we assume the pulser triggered named pulses. @@ -128,8 +130,7 @@ instrument follows a sequence of pulses to trigger field evaporation. The pulse_identifier is used to associate thus an information about time - when the quantities documented in this NXpulser_apm base class have been - collected via sampling. + when quantities have been collected via sampling. In virtually all cases the pulser is a blackbox. Depending on how the instrument is configured during a measurement the target @@ -153,142 +154,5 @@ - - - (Meta)data of the dynamics and changes of the microscope over the course of - pulsing. - - - - Relevant quantities during a measurement with a LEAP system as suggested by - `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_. - - - - - - - - - - - - Presence and status of the reflectron. - - - - - - - - - - The maximum voltage applied to the reflectron, relative to system ground. - - - - - - - - Amplitude of the signal detected on the multi-channel plate (MCP). - - This field should be used for storing the signal amplitude quantity - within ATO files. The ATO file format is used primarily by the - atom probe groups of the GPM in Rouen, France. - - - - - - - - - - - Set point temperature to achieve during the measurement. - - - - - Average temperature (at the specimen base) during the measurement. - - - - - - The best estimate, at experiment time, for the temperature at the - sample base (furthest point along sample apex and holding assembly - that is removable from the sample stage). - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - - - Average pressure in the analysis chamber during the measurement. - - - - - Pressure in the analysis chamber. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - - - Pressure in the analysis chamber. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - - - Pressure in the analysis chamber. - - - - - - - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - - - - - - + diff --git a/contributed_definitions/NXinstrument_apm.nxdl.xml b/contributed_definitions/NXinstrument_apm.nxdl.xml index 4cdce88940..ff6d4b5ccb 100644 --- a/contributed_definitions/NXinstrument_apm.nxdl.xml +++ b/contributed_definitions/NXinstrument_apm.nxdl.xml @@ -168,6 +168,18 @@ NEW ISSUE: local electrode, baking strategies, storage--> Detector for taking raw time-of-flight and ion/hit impact positions data. + + + Amplitude of the signal detected on the multi-channel plate (MCP). + + This field should be used for storing the signal amplitude quantity + within ATO files. The ATO file format is used primarily by the + atom probe groups of the GPM in Rouen, France. + + + + + CRunHeader.fMcpEfficiency @@ -381,7 +393,8 @@ existence constraint is independent of other values. - TODO + Relevant quantities during a measurement with a LEAP system as were + suggested by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_. diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 17e7d1b6fd..ab6f76d611 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -560,9 +560,6 @@ NXapm(NXobject): exists: optional vendor(NX_CHAR): model(NX_CHAR): - pulse_mode(NX_CHAR): - pulse_frequency(NX_FLOAT): - exists: recommended sourceID(NXsource): exists: [min, 0, max, 2] # conditionally required, sourceID only if pulse_mode is not voltage! fabrication(NXfabrication): @@ -625,6 +622,7 @@ NXapm(NXobject): # ion_detector(NXdetector): pulser(NXobject): exists: recommended + pulse_mode(NX_CHAR): pulse_frequency(NX_FLOAT): \@logged_against(NX_CHAR): pulse_fraction(NX_FLOAT): @@ -653,6 +651,10 @@ NXapm(NXobject): specimen_temperature(NX_FLOAT): analysis_chamber(NXchamber): analysis_pressure(NX_FLOAT): + control(NXcollection): + exists: recommended + evaporation_control(NX_CHAR): + target_detection_rate(NX_NUMBER): simulation(NXobject): exists: optional doc: | diff --git a/contributed_definitions/nyaml/NXevent_data_apm.yaml b/contributed_definitions/nyaml/NXevent_data_apm.yaml index 9eb21a8f57..54ea678c16 100644 --- a/contributed_definitions/nyaml/NXevent_data_apm.yaml +++ b/contributed_definitions/nyaml/NXevent_data_apm.yaml @@ -2,7 +2,9 @@ category: base doc: | Base class to store state and (meta)data of events over the course of an atom probe experiment. - This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs + Having at least one instance for an instance of NXapm is recommended. + + This base class applies the concept of the NXevent_data_em base class to the specific needs of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication of information. Specifically, the time interval considered is the entire time starting at start_time until end_time during which we assume the pulser triggered named pulses. @@ -93,8 +95,7 @@ NXevent_data_apm(NXobject): instrument follows a sequence of pulses to trigger field evaporation. The pulse_identifier is used to associate thus an information about time - when the quantities documented in this NXpulser_apm base class have been - collected via sampling. + when quantities have been collected via sampling. In virtually all cases the pulser is a blackbox. Depending on how the instrument is configured during a measurement the target @@ -115,95 +116,4 @@ NXevent_data_apm(NXobject): pulse onwards. The values of pulse_identifier are then [0, 99999] respectively. unit: NX_UNITLESS dim: (p,) - instrument(NXinstrument): - doc: | - (Meta)data of the dynamics and changes of the microscope over the course of pulsing. - control(NXcollection): - doc: | - Relevant quantities during a measurement with a LEAP system as suggested by - `T. Blum et al. `_. - evaporation_control(NX_CHAR): - enumeration: [detection_rate] - target_detection_rate(NX_FLOAT): - unit: NX_ANY # ions/pulse - reflectron(NXobject): - status(NX_CHAR): - doc: | - Presence and status of the reflectron. - enumeration: [none, present, used] - voltage(NX_FLOAT): - doc: | - The maximum voltage applied to the reflectron, relative to system ground. - unit: NX_VOLTAGE - local_electrode(NXlens_em): - ion_detector(NXdetector): - signal_amplitude(NX_FLOAT): - doc: | - Amplitude of the signal detected on the multi-channel plate (MCP). - - This field should be used for storing the signal amplitude quantity - within ATO files. The ATO file format is used primarily by the - atom probe groups of the GPM in Rouen, France. - unit: NX_CURRENT - dim: (p,) - pulser(NXpulser_apm): - stage_lab(NXstage_lab): - setpoint_temperature(NX_FLOAT): - doc: | - Set point temperature to achieve during the measurement. - unit: NX_TEMPERATURE - base_temperature(NX_FLOAT): - doc: | - Average temperature (at the specimen base) during the measurement. - unit: NX_TEMPERATURE - # normally one would use NXsensor/NXlog but point is that the temperature - # is logged against the pulse_identifier as even in the proprietary file format from - # AMETEK/Cameca nowhere there is the actual time when the pulse was triggered - # just the sampling frequency and I guess but am not 100percent sure which quantity - # from Cameca this is also the time when the first pulse was triggered - # using NXlog does make sense when individual NXsensors have different timing - # but for atom probe if at all the pulse-based implicit time is available - temperature(NX_FLOAT): - doc: | - The best estimate, at experiment time, for the temperature at the - sample base (furthest point along sample apex and holding assembly - that is removable from the sample stage). - unit: NX_TEMPERATURE - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - analysis_chamber(NXchamber): - chamber_pressure(NX_FLOAT): - doc: | - Average pressure in the analysis chamber during the measurement. - unit: NX_PRESSURE - pressure(NX_FLOAT): - doc: | - Pressure in the analysis chamber. - unit: NX_PRESSURE - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - buffer_chamber(NXchamber): - pressure(NX_FLOAT): - doc: | - Pressure in the analysis chamber. - unit: NX_PRESSURE - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - load_lock_chamber(NXchamber): - pressure(NX_FLOAT): - doc: | - Pressure in the analysis chamber. - unit: NX_PRESSURE - dim: (p,) - \@logged_against(NX_CHAR): - doc: | - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. - # getter_pump(NXpump): - # roughening_pump(NXpump): - # turbomolecular_pump(NXpump): + instrument(NXinstrument_apm): diff --git a/contributed_definitions/nyaml/NXinstrument_apm.yaml b/contributed_definitions/nyaml/NXinstrument_apm.yaml index 535abaa0d5..8ae49e09d0 100644 --- a/contributed_definitions/nyaml/NXinstrument_apm.yaml +++ b/contributed_definitions/nyaml/NXinstrument_apm.yaml @@ -95,6 +95,15 @@ NXinstrument_apm(NXinstrument): ion_detector(NXdetector): doc: | Detector for taking raw time-of-flight and ion/hit impact positions data. + signal_amplitude(NX_FLOAT): + doc: | + Amplitude of the signal detected on the multi-channel plate (MCP). + + This field should be used for storing the signal amplitude quantity + within ATO files. The ATO file format is used primarily by the + atom probe groups of the GPM in Rouen, France. + unit: NX_CURRENT + dim: (p,) mcp_efficiency(NX_FLOAT): doc: | CRunHeader.fMcpEfficiency @@ -242,7 +251,8 @@ NXinstrument_apm(NXinstrument): Free-text field for additional comments. control(NXcollection): doc: | - TODO + Relevant quantities during a measurement with a LEAP system as were + suggested by `T. Blum et al. `_. evaporation_control(NX_CHAR): doc: | Parameter set typically in the GUI of the control software which diff --git a/manual/source/classes/contributed_definitions/apm-structure.rst b/manual/source/classes/contributed_definitions/apm-structure.rst index 2cbeaae4a3..2e4beb8df8 100644 --- a/manual/source/classes/contributed_definitions/apm-structure.rst +++ b/manual/source/classes/contributed_definitions/apm-structure.rst @@ -47,7 +47,7 @@ The following base classes are proposed to support modularizing the storage of p Base classes to describe different coordinate systems used and/or to be harmonized or transformed into one another when interpreting the dataset. - :ref:`NXion`: (about to become replaced by :ref:`NXatom_set`) + :ref:`NXion`: (about to become replaced by NXatom) A base class to describe molecular ions with an adjustable number of atoms/isotopes building each ion. For the usage in atom probe research the maximum number of atoms supported building a molecular ion is currently set to a maximum of 32. Suggestions made in reference `DOI: 10.1017/S1431927621012241 `_ are used to map isotope to hash values with @@ -65,13 +65,6 @@ The following base classes are proposed to support modularizing the storage of p :ref:`NXpump`: A base class to describe details about pump(s) used as components of an instrument. - :ref:`NXpulser_apm`: - A base class to describe the high-voltage and/or laser pulsing capabilities. - - :ref:`NXreflectron`: - A base class to describe a kinetic-energy-sensitive filtering device - for time-of-flight (ToF) mass spectrometry. - :ref:`NXstage_lab`: A base class to describe the specimen fixture including the cryo-head. Nowadays, stages of microscopes represent small-scale laboratory platforms. @@ -84,29 +77,12 @@ Microscopy experiments, not only taking into account those performed on commerci data processing steps. Some of them are frequently applied on-the-fly. For now we represent these steps with specifically named instances of the :ref:`NXprocess` base class. -Several base classes were defined to document processing of atom probe data with established algorithms: - - :ref:`NXapm_hit_finding`: - A base class to describe hit finding algorithm. - - :ref:`NXapm_volt_and_bowl`: - A base class to describe the voltage-and-bowl correction. - - :ref:`NXapm_charge_state_analysis`: - A base class to document the resolving of the charge_state. - - :ref:`NXapm_reconstruction`: - A base class to document the tomographic reconstruction algorithm. - - :ref:`NXapm_ranging`: - A base class to document the ranging process. - - :ref:`NXapm_msr`, :ref:`NXapm_sim`: - Respective base classes that serve as templates to compose the :ref:`NXapm` application definition from. - -These base classes are examples that substantiate that data processing steps are essential to transform atom probe measurements or simulations into knowledge. Therefore, these steps should be documented -to enable reproducible research, if possible even numerical reproducibility of the results, -and learn how pieces of information are connected. In what follows, an example is presented how an +Several instances of NXprocess were defined in NXapm to document processing of atom probe data +including hit finding, voltage-and-bowl correction, combinatorial recovery of charge states, reconstruction, +and ranging definitions. These base classes are examples that substantiate that data processing steps are +essential when transforming atom probe measurements or simulations into knowledge. Consequently, these +steps should be documented to enable reproducible research, if possible even numerical reproducibility +of the results, and to learn better the workflow. In what follows, an example is presented how an open-source community software can be modified to use descriptions of these computational steps. A detailed inspection of spatial and other type of filters frequently used in analysis of atom probe From b74acd892db5df7f6883ac3f8868b9d64d530fbb Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sat, 1 Feb 2025 20:05:45 +0100 Subject: [PATCH 19/75] Fixes of NOMAD APM example --- contributed_definitions/NXapm.nxdl.xml | 26 +++++++++++------------- contributed_definitions/nyaml/NXapm.yaml | 17 ++++++++-------- 2 files changed, 21 insertions(+), 22 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 822c8741ae..ae9a52de50 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -188,9 +188,9 @@ the appdef definition here is nothing else then the documentation of this for a when the atom probe session ended. - + - TODO + How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime @@ -718,47 +718,45 @@ pulse_identifier(NX_INT):--> - - - - - - + + + + - + - + - + - - - + diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index ab6f76d611..5377de8229 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -135,8 +135,9 @@ NXapm(NXobject): ISO 8601 time code with local time zone offset to UTC included when the atom probe session ended. elapsed_time(NX_FLOAT): + exists: recommended doc: | - TODO + How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime unit: NX_TIME (NXcite): exists: [min, 0, max, infty] @@ -624,33 +625,33 @@ NXapm(NXobject): exists: recommended pulse_mode(NX_CHAR): pulse_frequency(NX_FLOAT): - \@logged_against(NX_CHAR): + # \@logged_against(NX_CHAR): pulse_fraction(NX_FLOAT): - \@logged_against(NX_CHAR): + # \@logged_against(NX_CHAR): pulse_voltage(NX_FLOAT): # ePOS, APT pulsed voltage exists: optional # not required for voltage pulsing dim: (n,) - \@logged_against(NX_CHAR): + # \@logged_against(NX_CHAR): pulse_number(NX_UINT): exists: optional dim: (n,) - \@logged_against(NX_CHAR): + # \@logged_against(NX_CHAR): standing_voltage(NX_FLOAT): # ePOS, APT standing voltage exists: optional dim: (n,) - \@logged_against(NX_CHAR): + # \@logged_against(NX_CHAR): sourceID(NXsource): exists: [min, 0, max, 2] # not required for voltage pulsing pulse_energy(NX_FLOAT): dim: (n,) - \@logged_against(NX_CHAR): + # \@logged_against(NX_CHAR): # laser geometry at the moment has neither a worked out example # nor any feedback from the community despite the work from B. Gault # on laser atom probe was granted a Leibnitz award stage(NXstage_lab): specimen_temperature(NX_FLOAT): analysis_chamber(NXchamber): - analysis_pressure(NX_FLOAT): + pressure(NX_FLOAT): control(NXcollection): exists: recommended evaporation_control(NX_CHAR): From cc3dc402e8fa1b21d47ff419b1b1cf3f16056ea7 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 2 Feb 2025 00:20:09 +0100 Subject: [PATCH 20/75] run_number now NX_UINT --- contributed_definitions/NXapm.nxdl.xml | 2 +- contributed_definitions/nyaml/NXapm.yaml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index ae9a52de50..e175f33f5a 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -109,7 +109,7 @@ - + diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 5377de8229..c708d221ff 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -63,7 +63,7 @@ NXapm(NXobject): service(NX_CHAR): identifier(NX_CHAR): is_persistent(NX_BOOLEAN): - run_number(NX_CHAR): + run_number(NX_UINT): exists: recommended # cannot be made required as for simulations you do not have a run number! doc: | @@ -86,6 +86,7 @@ NXapm(NXobject): needs to be distinguished with different run numbers. We follow this habit of most atom probe groups. Such interrupted runs should be stored as individual :ref:`NXentry` instances in one NeXus file. + unit: NX_UNITLESS experiment_alias(NX_CHAR): exists: recommended doc: | From d93f5b5c4a6ca60f333a292f1b5cb3a66d847218 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 7 Feb 2025 16:12:39 +0100 Subject: [PATCH 21/75] Implementing additions for bugfixes when parsing config and results files from CompositionSpace (NFDI-MatWerk) or paraprobe-toolbox (FAIRmat) into NOMAD for the apmapp developments --- .../NXapm_compositionspace_config.nxdl.xml | 4 +- .../NXapm_compositionspace_results.nxdl.xml | 79 +++++++++++++------ .../NXapm_paraprobe_nanochem_config.nxdl.xml | 54 ++++++++++--- .../nyaml/NXapm_compositionspace_config.yaml | 2 +- .../nyaml/NXapm_compositionspace_results.yaml | 27 +++++-- .../NXapm_paraprobe_nanochem_config.yaml | 18 +++++ 6 files changed, 139 insertions(+), 45 deletions(-) diff --git a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml index ae78d4ad08..df6028cf7d 100644 --- a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml @@ -3,7 +3,7 @@ diff --git a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml index 8e9921e0e4..3173fcdfea 100644 --- a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml @@ -3,7 +3,7 @@ + + + Contextualize back to the specimen from which the + dataset was collected that was here analyzed with + CompositionSpace tool. + + + + A qualifier whether the specimen is a real one or a virtual one. + + + + + + + + + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. + + + Step during which the point cloud is discretized to compute element-specific composition fields. @@ -89,7 +118,7 @@ for if desired all the dependencies and libraries--> Using a discretization grid that is larger than the average distance between reconstructed ion positions reduces computational costs. This is the key idea of the CompositionSpace tool compared to other methods - used in atom probe for characterizing microstructural features using the ion position data directly. + used in atom probe for characterizing microstructural features that use the ion position data directly. @@ -97,14 +126,14 @@ for if desired all the dependencies and libraries--> - + - - - + + + @@ -113,13 +142,13 @@ for if desired all the dependencies and libraries--> - - + + - - + + @@ -128,7 +157,7 @@ for if desired all the dependencies and libraries--> Position of each cell in Euclidean space. - + @@ -137,7 +166,7 @@ for if desired all the dependencies and libraries--> Discrete coordinate of each voxel. - + @@ -147,7 +176,7 @@ for if desired all the dependencies and libraries--> For each ion, the identifier of the voxel into which the ion binned. - + @@ -157,7 +186,7 @@ for if desired all the dependencies and libraries--> Total number of weight (counts for discretization with a rectangular transfer function) for the occupancy of each voxel with atoms. - + @@ -172,7 +201,7 @@ for if desired all the dependencies and libraries--> Element-specific weight (counts for discretization with a rectangular transfer function) for the occupancy of each voxel with atoms of this element. - + @@ -197,7 +226,7 @@ for if desired all the dependencies and libraries--> Element identifier stored sorted in descending order of feature importance. - + @@ -211,7 +240,7 @@ for if desired all the dependencies and libraries--> Element relative feature importance stored sorted in descending order of feature importance. - + @@ -246,7 +275,7 @@ for if desired all the dependencies and libraries--> Explained variance values - + @@ -255,7 +284,7 @@ for if desired all the dependencies and libraries--> Elements identifier matching those from ENTRY/voxelization/elementID as the principal component analysis. - + @@ -284,7 +313,7 @@ for if desired all the dependencies and libraries--> y_pred return values of the computation. - + @@ -301,7 +330,7 @@ for if desired all the dependencies and libraries--> Akaike information criterion values - + @@ -309,7 +338,7 @@ for if desired all the dependencies and libraries--> Bayes information criterion values - + @@ -317,7 +346,7 @@ for if desired all the dependencies and libraries--> Actual n_ic_cluster values used - + @@ -358,7 +387,7 @@ for if desired all the dependencies and libraries--> Raw label return values - + @@ -369,7 +398,7 @@ for if desired all the dependencies and libraries--> Using these identifiers correlated element-wise with the values in the label array specifies for which voxel in the grid clusters from this process were found. - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml index 8f86ddbd50..7a5ad37189 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -3,7 +3,7 @@ + + + Configuration for the algorithm that defines how the multiplicity of all + those ions are computed that are considered in the delocalization. + + + + TODO + + + + + + + + + + + + + + TODO + + + + + + TODO + + + + @@ -250,7 +282,7 @@ identifier(NX_UINT):--> Unused values in each row of the matrix are nullified. Nuclides are identified as hashed nuclide (see :ref:`NXion`) for further details. - + @@ -261,7 +293,7 @@ identifier(NX_UINT):--> on a cuboidal 3D grid (:ref:`NXcg_grid`). The tool performs as many delocalization computations as values are specified in grid_resolution. - + @@ -279,7 +311,7 @@ identifier(NX_UINT):--> The tool performs as many delocalization computations as values are specified in kernel_variance. - + @@ -707,7 +739,7 @@ identifier(NX_UINT):--> Array of nuclide iontypes to filter. - + @@ -724,7 +756,7 @@ identifier(NX_UINT):--> which specify how the initial triangles of the mesh should be iteratively refined by edge splitting and related mesh refinement operations. - + @@ -739,7 +771,7 @@ identifier(NX_UINT):--> self-intersections may occur. The tool detects these and stops in a controlled manner so that the user can repeat the analyses with using a different parameterization. - + @@ -752,7 +784,7 @@ identifier(NX_UINT):--> parameter values to be used in the first DCOM iteration. The first entry of each array those for the second DCOM iteration and so on and so forth. - + @@ -971,19 +1003,19 @@ identifier(NX_UINT):--> cardinality(NX_POSINT):--> - + - + - + diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml index 843c1803fe..0a68afcc9b 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml @@ -6,7 +6,7 @@ doc: | This is an application definition for the common NFDI-MatWerk/FAIRmat infrastructure use case IUC09 that explores how to improve the organization and results storage of the - CompositionSpace software using NeXus. + CompositionSpace tool by using the NeXus data model and semantics. type: group NXapm_compositionspace_config(NXobject): # by default for appdefs the value of the exists keyword is required unless it is explicitly specified differently diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml index 145fc6bfbf..9659ad99a7 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml @@ -51,6 +51,26 @@ NXapm_compositionspace_results(NXobject): # results (NXuser): exists: optional + specimen(NXsample): + doc: | + Contextualize back to the specimen from which the + dataset was collected that was here analyzed with + CompositionSpace tool. + type(NX_CHAR): + doc: | + A qualifier whether the specimen is a real one or a virtual one. + enumeration: [experiment, simulation] + atom_types(NX_CHAR): + doc: | + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. voxelization(NXprocess): exists: [min, 0, max, 1] doc: | @@ -60,25 +80,20 @@ NXapm_compositionspace_results(NXobject): Using a discretization grid that is larger than the average distance between reconstructed ion positions reduces computational costs. This is the key idea of the CompositionSpace tool compared to other methods - used in atom probe for characterizing microstructural features using the ion position data directly. + used in atom probe for characterizing microstructural features that use the ion position data directly. sequence_index(NX_POSINT): enumeration: [1] cg_grid(NXcg_grid): dimensionality(NX_POSINT): - unit: NX_UNITLESS enumeration: [3] cardinality(NX_POSINT): - unit: NX_UNITLESS origin(NX_NUMBER): - unit: NX_LENGTH dim: (grid_dim,) symmetry: enumeration: [cubic] cell_dimensions(NX_NUMBER): - unit: NX_LENGTH dim: (grid_dim,) extent(NX_POSINT): - unit: NX_UNITLESS dim: (grid_dim,) identifier_offset(NX_INT): unit: NX_UNITLESS diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml index 793c0c7114..dd240194fd 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml @@ -128,6 +128,24 @@ NXapm_paraprobe_nanochem_config(NXobject): evaporation_id_filter(NXsubsampling_filter): exists: optional min_incr_max(NX_INT): + decomposition(NXmatch_filter): + doc: | + Configuration for the algorithm that defines how the multiplicity of all + those ions are computed that are considered in the delocalization. + method(NX_CHAR): + doc: | + TODO + enumeration: [resolve_unknown, resolve_point, resolve_atom, resolve_element, resolve_element_charge, resolve_isotope, resolve_isotope_charge] + nuclide_whitelist(NX_UINT): + doc: | + TODO + unit: NX_UNITLESS + # dim: ??? + charge_state_whitelist(NX_INT): + doc: | + TODO + unit: NX_DIMENSIONLESS + # dim: ??? iontype_filter(NXmatch_filter): exists: optional method(NX_CHAR): From a79703bcabdb56ebdcf897bc1bafce6cd2f9d352 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sat, 15 Feb 2025 02:43:37 +0100 Subject: [PATCH 22/75] Updated NXmicrostructure_score_config appdef, next step, update results and generate NXDL files --- .../nyaml/NXmicrostructure_odf.yaml | 1 + .../nyaml/NXmicrostructure_score_config.yaml | 876 ++++++------------ 2 files changed, 274 insertions(+), 603 deletions(-) diff --git a/contributed_definitions/nyaml/NXmicrostructure_odf.yaml b/contributed_definitions/nyaml/NXmicrostructure_odf.yaml index 119dc6b691..93510d5379 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_odf.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_odf.yaml @@ -44,6 +44,7 @@ NXmicrostructure_odf(NXprocess): kth_extrema(NXobject): doc: | Group to store descriptors and summary statistics for extrema of the ODF. + # name like in NXmicrostructure_score_config extrema(NX_CHAR): doc: | Minima or maxima, if extrema is set to minima values for location and volume_fraction diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index 6e480e6046..b5a6a969ad 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -10,6 +10,8 @@ symbols: Number of Bunge-Euler angle triplets for deformed grains. n_rx_ori: | Number of Bunge-Euler angle triplets for recrystallization nuclei. + n_ori: | + Number of texture components to analyze. n_drag: | Number of support points for the linearized drag profile. n_temp: | @@ -20,142 +22,187 @@ symbols: Number of entries when to collect snapshots of the evolving microstructure. n_su: | Number of solitary unit domains to export. + d: | + Dimensionality of the simulation. type: group NXmicrostructure_score_config(NXobject): (NXentry): definition(NX_CHAR): enumeration: [NXmicrostructure_score_config] - simulation_identifier(NX_UINT): + identifier_simulation(NX_UINT): doc: | - Simulation ID as an alias to refer to this simulation. + An alias to refer to this simulation. description(NX_CHAR): + exists: optional doc: | Discouraged free-text field to add further details to the computation. start_time(NX_DATE_TIME): - end_time(NX_DATE_TIME): - exists: recommended + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the configuration file was created. + # end_time(NX_DATE_TIME): + # exists: optional profiling(NXcs_profiling): exists: optional - (NXuser): + userID(NXuser): exists: [min, 0, max, infty] + sample(NXsample): + exists: recommended + dimensionality(NX_UINT): + doc: | + Dimensionality of the simulation. + enumeration: [3] + type(NX_CHAR): + doc: | + A qualifier whether the sample is a real one or a virtual one. + enumeration: [experiment, simulation] + atom_types(NX_CHAR): + doc: | + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. program1(NXprogram): - program_name: - \@version: - \@url: - exists: recommended + exists: recommended + doc: | + Name of the program whereby this config file was created. + program(NX_CHAR): + \@version(NX_CHAR): environment(NXobject): - exists: optional + exists: recommended doc: | Programs and libraries representing the computational environment programID(NXprogram): exists: [min, 1, max, infty] program(NX_CHAR): \@version(NX_CHAR): - discretization(NXmicrostructure): + material(NXobject): doc: | - Relevant data to instantiate a starting configuration that is typically - a microstructure in deformed conditions where stored (elastic) energy - is stored in the form of crystal defects, which in the SCORE model are - is considered as mean-field dislocation content. - grid(NXcg_grid): - extent(NX_UINT): - doc: | - Extend of each CA domain in voxel along the x, y, and z direction. - Deformation of sheet material is assumed. - The x axis is assumed pointing along the rolling direction. - The y axis is assumed pointing along the transverse direction. - The z axis is assumed pointing along the normal direction. - cell_dimensions(NX_NUMBER): + (Mechanical) properties of the material which scale the + amount of stored (elastic) energy in the system and + thus mainly affect recrystallization kinetics. + shear_modulus(NX_FLOAT): + doc: | + Reference shear modulus at zero Kelvin. + unit: NX_PRESSURE + burgers_vector(NX_FLOAT): + doc: | + Magnitude of the Burgers vector at zero Kelvin. + unit: NX_LENGTH + # firstOrderdG0dT + # alloyConstantThermalExpCoeff + # FirstOrderThermalExpCoeff + # SecondOrderThermalExpCoeff + melting_temperature(NX_FLOAT): + doc: | + Melting temperature in degrees Celsius. + unit: NX_TEMPERATURE + deformation(NXobject): doc: | - Details how the deformed grains should be modelled. - model: + Details about the geometry and properties of the polycrystal that represents the + starting configuration (typically a deformed microstructure) for the simulation. + model(NX_CHAR): doc: | Which model should be used to generate a starting microstructure. + + * cuboidal, a regular array of equally shaped cuboidal grains + * poisson_voronoi, a discretized poisson voronoi + * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map + * damask, the result of a simulation from `DAMASK -# -# -# -# -# -# -# Number of Bunge-Euler angle triplets for deformed grains. -# -# -# -# -# Number of Bunge-Euler angle triplets for recrystallization nuclei. -# -# -# -# -# Number of solitary unit domains to export. -# -# -# -# -# Application definition to control a simulation with the SCORE model. -# -# -# -# -# Version specifier of this application definition. -# -# -# -# -# Official NeXus NXDL schema with which this file was written. -# -# -# -# -# -# -# -# -# -# -# -# -# Ideally, a (globally persistent) unique identifier for referring -# to this analysis. -# -# -# -# -# Possibility for leaving a free-text description about this analysis. -# -# -# -# -# Path to the directory where the tool should store NeXus/HDF5 results -# of this analysis. If not specified results will be stored in the -# current working directory. -# -# -# -# -# ISO 8601 formatted time code with local time zone offset to UTC -# information included when this configuration file was created. -# -# -# -# -# Relevant data to instantiate a starting configuration that is typically -# a microstructure in deformed conditions where stored (elastic) energy -# is stored in the form of crystal defects, which in the SCORE model are -# is considered as mean-field dislocation content. -# -# -# -# Which model should be used to generate a starting microstructure. -# -# -# -# -# -# -# -# -# -# -# Edge length of the cubic cells of each CA domain. -# -# -# -# -# Extend of each CA domain in voxel along the x, y, and z direction. -# Deformation of sheet material is assumed. -# The x axis is assumed pointing along the rolling direction. -# The y axis is assumed pointing along the transverse direction. -# The z axis is assumed pointing along the normal direction. -# -# -# -# -# -# -# -# Extent of each deformed grain along the x, y, and z direction when type is -# cuboidal. -# -# -# -# -# -# -# -# Average spherical diameter when type is poisson_voronoi. -# -# -# -# -# Set of Bunge-Euler angles to sample orientations randomly from. -# -# -# -# -# -# -# -# -# The EBSD dataset from which the initial microstructure is instantiated -# if initial_microstructure/type has value ebsd. -# -# -# -# Path and name of the EBSD dataset from which to generate the starting -# microstructure. -# -# -# -# SHA256 checksum of the file which contains the EBSD dataset. -# -# -# -# -# -# Size of the EBSD. The EBSD orientation mapping has to be on a -# regular grid of square-shaped pixels. -# -# -# -# -# -# -# -# -# -# Phenomenological model according to which it nuclei are placed -# into the domain and assumed growing. -# -# -# -# According to which model will the nuclei become distributed spatially. -# CSR means complete spatial randomness. -# Custom is implementation specific. -# GB places nuclei at grain boundaries. -# -# -# -# -# -# -# -# -# -# According to which model will the nuclei start to grow. -# -# -# -# -# -# -# -# According to which model will the nuclei get their orientation assigned. -# -# -# -# -# -# -# -# Set of Bunge-Euler angles to sample orientations of nuclei randomly from. -# -# -# -# -# -# -# -# -# -# (Mechanical) properties of the material which scale the amount -# of stored (elastic) energy in the ROI/system. -# -# -# -# Shear modulus at zero Kelvin. -# -# -# -# -# Magnitude at the Burgers vector at zero Kelvin. -# -# -# -# -# -# Melting temperature in degrees Celsius. -# -# -# -# -# -# Model for the assumed mobility of grain boundaries with different -# disorientation. -# -# -# -# Which type of fundamental model for the grain boundary mobility: -# For the Sebald-Gottstein model the following equation is used. -# For the Rollett-Holm model the following equation is used. -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Simulated evolution of the dislocation density as the stored -# (elastic) energy assumed stored in each grain. -# -# -# -# Which type of recovery model. -# -# -# -# -# -# -# -# -# Simulated reduction of the grain boundary speed due to -# the presence of dispersoids through which the total grain boundary -# area of the recrystallization front can be reduced. -# -# -# -# Which type of drag model. -# -# -# -# -# -# -# -# -# -# -# -# Support point of the linearized curve of simulated time matching -# a specific support point of the average dispersoid radius. -# -# -# -# -# -# -# -# Support point of the linearized curve of the average dispersoid radius. -# -# -# -# -# -# -# -# -# -# Simulated time temperature profile -# -# -# -# Support point of the linearized curve of simulated time matching -# a specific support point of the temperature. -# -# -# -# -# -# -# -# Support point of the linearized curve of the temperature. -# -# -# -# -# -# -# -# -# Criteria which enable to stop the simulation in a controlled manner. -# Whichever criterion is fulfilled first stops the simulation. -# -# -# -# Maximum recrystallized volume fraction. -# -# -# -# -# Maximum simulated physical time. -# -# -# -# -# Maximum number of iteration steps. -# -# -# -# -# -# Settings relevant for stable numerical integration. -# -# -# -# Maximum fraction equivalent to the migration of the -# fastest grain boundary in the system how much a cell -# may be consumed in a single iteration. -# -# -# -# -# Fraction of the total number of cells in the CA which -# should initially be allocated for offering cells in the -# recrystallization front. -# -# -# -# -# By how much more times should the already allocated memory -# be is increased to offer space for storing states of cells -# in the recrystallization front. -# -# -# -# -# Should the cache for cells in the recrystallization front -# be defragmented on-the-fly. -# -# -# -# -# Heuristic recrystallized volume target values at which -# the cache for cells in the recrystallization front -# will be defragmented on-the-fly. -# -# -# -# -# -# -# -# List of recrystallized volume target values at which a -# snapshot of the CA state should be exported for. -# -# -# -# -# -# -# -# -# -# Perform a statistical analyses of the results as it was -# proposed by M. Kühbach (solitary unit model ensemble approach). -# -# -# -# -# How many independent cellular automaton domains -# should be instantiated. -# -# -# -# -# Into how many time steps should the real time interval be discretized upon -# during post-processing the results with the solitary unit modeling approach. -# -# -# -# -# List of identifier for those domain which should be rendered. -# Identifier start from 0. -# -# -# -# -# -# -# -# -# -# -# + # identifier_domain(NX_UINT): + # doc: | + # List of identifier for those CAs domains which should be sampled. + # Identifier start from 1. + # unit: NX_UNITLESS + # dim: (n_su,) From 417519adeffdddc08358e57e3beafab27e3e079f Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 16 Feb 2025 00:35:23 +0100 Subject: [PATCH 23/75] Updated score_results and microstructure --- .../nyaml/NXmicrostructure.yaml | 44 ++-- .../nyaml/NXmicrostructure_score_results.yaml | 229 +++++++++--------- 2 files changed, 140 insertions(+), 133 deletions(-) diff --git a/contributed_definitions/nyaml/NXmicrostructure.yaml b/contributed_definitions/nyaml/NXmicrostructure.yaml index 88af25f7f5..0bb671c863 100644 --- a/contributed_definitions/nyaml/NXmicrostructure.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure.yaml @@ -145,7 +145,7 @@ NXmicrostructure(NXobject): # (NXcsg): # (NXcontinuous_function): # examples for specific frequently discussed microstructural features - crystal(NXobject): + crystals(NXobject): doc: | One- or two-dimensional projections, or three-dimensional representations of crystals. @@ -181,20 +181,20 @@ NXmicrostructure(NXobject): Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. unit: NX_UNITLESS - crystal_identifier_offset(NX_INT): + identifier_offset_crystal(NX_INT): doc: | First identifier whereby to identify crystals implicitly. unit: NX_UNITLESS - crystal_identifier(NX_INT): + identifier_crystal(NX_INT): doc: | Identifier whereby to identify each crystal explicitly. unit: NX_UNITLESS dim: (i,) # with i = n_c_one or n_c_two or n_c_three - phase_identifier_offset(NX_INT): + identifier_offset_phase(NX_INT): doc: | First identifier whereby to identify phases implicitly. unit: NX_UNITLESS - phase_identifier(NX_INT): + identifier_phase(NX_INT): doc: | Identifier whereby to identify phase for each crystal explicitly. unit: NX_UNITLESS @@ -226,7 +226,7 @@ NXmicrostructure(NXobject): Volume of each crystal unit: NX_VOLUME # m^3 dim: (i,) - interface(NXobject): + interfaces(NXobject): doc: | One- or two-dimensional projections or three-dimensional representation of interfaces between crystals as topological entities equivalent to dual_junctions. @@ -258,26 +258,26 @@ NXmicrostructure(NXobject): unit: NX_UNITLESS dim: (i,) # with i == n_i_one or n_i_two or n_i_three for all fields of group interface # topological view, interface specification through the the pair of crystals sharing an interface - crystal_identifier(NX_INT): + identifier_crystal(NX_INT): doc: | - Set of pairs of crystal_identifier for each interface. + Set of pairs of identifier_crystal for each interface. unit: NX_UNITLESS dim: (i, 2) \@use_these(NX_CHAR): doc: | The specific identifiers whereby to resolve ambiguities. - phase_identifier(NX_INT): + identifier_phase(NX_INT): doc: | - Set of pairs of phase_identifier for each interface. + Set of pairs of identifier_phase for each interface. unit: NX_UNITLESS dim: (i, 2) \@use_these(NX_CHAR): doc: | The specific identifiers whereby to resolve ambiguities. # topological view, interface specification through the pair of triple line projections (i.e. triple points) adjoining the interface - triple_junction_identifier(NX_INT): + identifier_triple_junction(NX_INT): doc: | - Set of pairs of triple_junction_identifier for each interface. + Set of pairs of identifier_triple_junction for each interface. unit: NX_UNITLESS dim: (i, 2) # with i == n_i_two but junctions can be points or lines! \@use_these(NX_CHAR): @@ -311,7 +311,7 @@ NXmicrostructure(NXobject): The surface area of all interfaces. unit: NX_AREA dim: (i,) - triple_junction(NXobject): + triple_junctions(NXobject): doc: | Projections or representations of junctions at which three interfaces meet. @@ -358,13 +358,13 @@ NXmicrostructure(NXobject): Explicit positions. unit: NX_LENGTH dim: (i, d) - crystal_identifier(NX_INT): + identifier_crystal(NX_INT): doc: | Set of tuples of identifier of crystals connected to the junction for each triple junction. unit: NX_UNITLESS dim: (i, 3) # example ii) three interfaces (maybe projections of them) meet at a triple junction - interface_identifier(NX_INT): + identifier_interface(NX_INT): doc: | Set of tuples of identifier of interfaces connected to the junction for each triple junction. unit: NX_UNITLESS @@ -373,14 +373,14 @@ NXmicrostructure(NXobject): doc: | The specific interface identifiers whereby to resolve ambiguities. # example iii) three polyline segments meet at a triple junction, polyline segments of discretized interface segments - polyline_identifier(NX_INT): + identifier_polyline(NX_INT): doc: | Set of tuples of identifier for polyline segments connected to the junction for each triple junction. unit: NX_UNITLESS dim: (i, 3) \@use_these(NX_CHAR): doc: | - The specific polyline identifiers whereby to resolve ambiguities. + The specific identifier_polyline whereby to resolve ambiguities. # example iv) e.g. crystals of three different phases meet at a triple junction # EXAMPLES FOR DESCRIPTOR VALUES boundary_contact(NX_BOOLEAN): @@ -410,7 +410,7 @@ NXmicrostructure(NXobject): The volume of the each triple junction unit: NX_VOLUME dim: (i,) - quadruple_junction(NXobject): + quadruple_junctions(NXobject): doc: | Quadruple junctions as a region where four crystals meet. @@ -451,7 +451,7 @@ NXmicrostructure(NXobject): unit: NX_LENGTH dim: (i, 3) # example ii) four crystals meet at a quadruple junction - crystal_identifier(NX_INT): + identifier_crystal(NX_INT): doc: | Set of tuples of identifier of crystals connected to the junction for each junction. unit: NX_UNITLESS @@ -459,7 +459,7 @@ NXmicrostructure(NXobject): \@use_these(NX_CHAR): doc: | The specific identifier to instances of crystal identifiers whereby to resolve ambiguities. - interface_identifier(NX_INT): + identifier_interface(NX_INT): doc: | Set of tuples of identifier of interfaces connected to the junction for each junction. unit: NX_UNITLESS @@ -468,7 +468,7 @@ NXmicrostructure(NXobject): doc: | The specific identifier to instances of interface identifiers whereby to resolve ambiguities. # example iii) e.g. three triple lines meet at a quadruple junction - triple_junction_identifier(NX_INT): + identifier_triple_junction(NX_INT): doc: | Set of tuples of identifier for triple junctions connected to the junction for each quadruple junction. unit: NX_UNITLESS @@ -477,7 +477,7 @@ NXmicrostructure(NXobject): doc: | The specific identifier to instances of triple junction identifiers whereby to resolve ambiguities. # example iv) crystals of eventually four different phases meet at a quadruple junction - phase_identifier(NX_INT): + identifier_phase(NX_INT): doc: | Set of tuples of identifier for phases of crystals connected to the junction for each quadruple junction. unit: NX_UNITLESS diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml index 0013926e25..0183b31fd8 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml @@ -1,14 +1,14 @@ category: application doc: | - Application definition for storing results of the SCORE cellular automaton. + Application definition for storing results of the SCORE cellular automata model. - The SCORE cellular automaton model for primary recrystallization is an - example of typical materials engineering applications used within the field - of so-called Integral Computational Materials Engineering (ICME) whereby - one can simulate the evolution of microstructures. + The SCORE cellular automata model for primary recrystallization is an example + of a typical materials engineering application used within the field of so-called + Integral Computational Materials Engineering (ICME) whereby one can simulate + the evolution of microstructures. - Specifically the SCORE model can be used to simulate the growth of static - recrystallization nuclei. The model is described in the literature: + Specifically the SCORE model can be used to simulate the growth of nuclei during + static recrystallization. The model is described in the literature: * `M. Kühbach et al. `_ * `C. Haase et al. `_ @@ -16,45 +16,52 @@ doc: | symbols: doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays n_summary_stats: | - The total number of summary statistic log entries. + The total number of summary statistic log entries n_b: | - Number of boundaries of the bounding box or primitive to domain. + Number of boundaries of the bounding box or primitive about the computational domain n_p: | - Number of parameter required for chosen orientation parameterization. + Number of parameter required for chosen orientation parameterization n_tex: | - Number of texture components identified. + Number of texture components identified d: | - Dimensionality. + Dimensionality c: | - Cardinality. + Cardinality n_front: | - Number of active cells in the (recrystallization) front. + Number of active cells in the (recrystallization) front n_grains: | - Number of grains in the computer simulation. + Number of grains in the computer simulation # inspect comments behind NXmicrostructure type: group NXmicrostructure_score_results(NXobject): (NXentry): definition(NX_CHAR): enumeration: [NXmicrostructure_score_results] - simulation_identifier(NX_UINT): + identifier_simulation(NX_UINT): doc: | Simulation ID as an alias to refer to this simulation. description(NX_CHAR): + exists: optional doc: | Discouraged free-text field to add further details to the computation. start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the simulation was started. end_time(NX_DATE_TIME): exists: recommended - (NXuser): - exists: [min, 0, max, infty] + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the simulation ended. + profiling(NXcs_profiling): + exists: optional program1(NXprogram): - program_name: + doc: | + Name of the program with which the simulation was performed. + program(NX_CHAR): \@version: - \@url: - exists: recommended environment(NXobject): exists: optional doc: | @@ -63,38 +70,38 @@ NXmicrostructure_score_results(NXobject): exists: [min, 1, max, infty] program(NX_CHAR): \@version(NX_CHAR): - coordinate_system_set(NXcoordinate_system_set): - rotation_handedness: - rotation_convention: - euler_angle_convention: - axis_angle_convention: - sign_convention: - sample_reference_frame(NXcoordinate_system): - type: - enumeration: [cartesian] - handedness: - enumeration: [right_handed] - origin: - enumeration: [front_bottom_left] - x_alias: - enumeration: [rolling_direction] - x_direction: - enumeration: [east] - y_alias: - enumeration: [transverse_direction] - y_direction: - enumeration: [in] - z_alias: - enumeration: [normal direction] - z_direction: - enumeration: [north] + rotation_conventions(NXrotation_conventions): + rotation_handedness(NX_CHAR): + rotation_convention(NX_CHAR): + euler_angle_convention(NX_CHAR): + axis_angle_convention(NX_CHAR): + sign_convention(NX_CHAR): + sample_reference_frame(NXcoordinate_system): + type: + enumeration: [cartesian] + handedness: + enumeration: [right_handed] + origin: + enumeration: [front_bottom_left] + x_alias: + enumeration: [rolling_direction] + x_direction: + enumeration: [east] + y_alias: + enumeration: [transverse_direction] + y_direction: + enumeration: [in] + z_alias: + enumeration: [normal direction] + z_direction: + enumeration: [north] discretization(NXmicrostructure): exists: [min, 1, max, 1] grid(NXcg_grid): dimensionality(NX_POSINT): cardinality(NX_POSINT): origin(NX_NUMBER): - symmetry: + symmetry(NX_CHAR): cell_dimensions(NX_NUMBER): extent(NX_UINT): identifier_offset(NX_INT): @@ -127,21 +134,31 @@ NXmicrostructure_score_results(NXobject): The field must have as many entries as there are number_of_boundaries. dim: (6,) spatiotemporalID(NXobject): - exists: [min, 1, max, infty] # max 1 in case of classical CA simulation, i.e. without solitary units + exists: [min, 1, max, infty] # max 1 in case of a single classical CA simulation, i.e. without solitary units doc: | - Documentation of the spatiotemporal evolution + Documentation of the spatiotemporal evolution for each CA domain. # static quantities for which no change is modelled # the typical lean summary statistics flattened - summary_statistics(NXobject): + summary_statistics(NXprocess): doc: | Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening in for practical reasons though in while - running the simulation. Place used for storing descriptors from continuum mechanics + (averaging, integrating, interpolating) happening for practical and performance reasons + during the simulation. Place used for storing descriptors from continuum mechanics and thermodynamics at the scale of the entire ROI. - kinetics(NXprocess): - exists: optional + kinetics(NXdata): + exists: recommended doc: | Evolution of the recrystallized volume fraction over time. + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@time_indices(NX_UINT): + \@iteration_indices(NX_UINT): + exists: optional + \@temperature_indices(NX_UINT): + exists: optional + \@x_indices(NX_UINT): + title(NX_CHAR): + exists: recommended time(NX_NUMBER): doc: | Evolution of the physical time not to be confused with wall-clock time or profiling data. @@ -151,33 +168,34 @@ NXmicrostructure_score_results(NXobject): doc: | Iteration or increment counter. unit: NX_UNITLESS + dim: (n_summary_stats,) temperature(NX_FLOAT): doc: | Evolution of the simulated temperature over time. unit: NX_TEMPERATURE dim: (n_summary_stats,) - recrystallized_volume_fraction(NX_FLOAT): + x(NX_FLOAT): doc: | Recrystallized volume fraction. unit: NX_DIMENSIONLESS dim: (n_summary_stats,) - stress(NXprocess): + stress(NXdata): exists: optional - type: + type(NX_CHAR): doc: | Which type of stress. enumeration: [cauchy] - stress(NX_FLOAT): + tensor(NX_FLOAT): doc: | Applied external stress tensor on the ROI. unit: NX_ANY dim: (n_summary_stats, 3, 3) - strain(NXprocess): + strain(NXdata): exists: optional - type: + type(NX_CHAR): doc: | Which type of strain. - strain(NX_FLOAT): + tensor(NX_FLOAT): doc: | Applied external strain tensor on the ROI. unit: NX_ANY @@ -188,68 +206,70 @@ NXmicrostructure_score_results(NXobject): doc: | Which type of deformation gradient. enumeration: [piola] - value(NX_FLOAT): + tensor(NX_FLOAT): doc: | Applied deformation gradient tensor on the ROI. unit: NX_ANY dim: (n_summary_stats, 3, 3) - magnetic_field(NXprocess): - exists: optional - strength(NX_FLOAT): - doc: | - Applied external magnetic field on the ROI. - unit: NX_ANY - dim: (n_summary_stats, 3, 3) - electrical_field(NXprocess): - exists: optional - # specify type of field - strength(NX_FLOAT): - doc: | - Applied external electrical field on the ROI. - unit: NX_ANY - dim: (n_summary_stats, 3, 3) - # the typically storage-costlier snapshot data + # magnetic_field(NXprocess): + # exists: optional + # strength(NX_FLOAT): + # doc: | + # Applied external magnetic field on the ROI. + # unit: NX_ANY + # dim: (n_summary_stats, 3, 3) + # electrical_field(NXprocess): + # exists: optional + # strength(NX_FLOAT): + # doc: | + # Applied external electrical field on the ROI. + # unit: NX_ANY + # dim: (n_summary_stats, 3, 3) + # the typically storage-costlier snapshot data microstructureID(NXmicrostructure): - exists: [min, 1, max, infty] # always storing starting configuration + exists: [min, 1, max, infty] # always storing the starting configuration time(NX_NUMBER): - iteration(NX_INT): + iteration(NX_UINT): + doc: | + Iteration or increment counter. + unit: NX_UNITLESS temperature(NX_FLOAT): doc: | Simulated temperature for this snapshot. unit: NX_TEMPERATURE - x_value(NX_FLOAT): + x(NX_FLOAT): doc: | Current recrystallized volume fraction (taking fractional infections into account). unit: NX_DIMENSIONLESS - x_target(NX_NUMBER): + x_set(NX_NUMBER): doc: | Target value for which a snapshot was requested for the recrystallized volume fraction. unit: NX_DIMENSIONLESS # optional places to store the grid for instance if it changes grid(NXcg_grid): exists: recommended - grain_identifier(NX_UINT): + identifier_grain(NX_UINT): exists: recommended doc: | Grain identifier for each cell. unit: NX_UNITLESS dim: (n_x, n_y, n_z) - thread_identifier(NX_UINT): + identifier_thread(NX_UINT): exists: optional doc: | Identifier of the OpenMP thread which processed this part of the grid. unit: NX_UNITLESS dim: (n_x, n_y, n_z) - crystal(NXobject): + crystals(NXobject): representation: exists: recommended number_of_crystals(NX_UINT): number_of_phases(NX_UINT): - crystal_identifier_offset(NX_INT): - crystal_identifier(NX_INT): + identifier_offset_crystal(NX_INT): + identifier_crystal(NX_INT): dim: (n_grains,) - phase_identifier_offset(NX_INT): - phase_identifier(NX_INT): + identifier_offset_phase(NX_INT): + identifier_phase(NX_INT): dim: (n_grains,) volume(NX_NUMBER): doc: | @@ -265,8 +285,8 @@ NXmicrostructure_score_results(NXobject): dislocation_density(NX_FLOAT): exists: recommended doc: | - Current value for the dislocation density as a measure of the remaining stored energy - in assumed crystal defects inside each grain. + Current value for the dislocation density as a measure of the remaining + stored energy in assumed crystal defects inside each grain. unit: NX_ANY # 1/m^2 dim: (n_grains,) is_deformed(NX_BOOLEAN): @@ -292,9 +312,9 @@ NXmicrostructure_score_results(NXobject): mobility_weight(NX_FLOAT): exists: recommended doc: | - So-called mobility weight which is a scaling factor to - control the mobility of the grain boundary which is assumed - to sweep currently this volume. + So-called mobility weight which is a scaling factor to control the + mobility of the grain boundary that is modelled sweeping cells that + make the discrete recrystallization front. unit: NX_UNITLESS dim: (n_front,) coordinate(NX_NUMBER): @@ -303,19 +323,19 @@ NXmicrostructure_score_results(NXobject): The x, y, z grid coordinates of each cell in the recrystallization front. unit: NX_UNITLESS dim: (n_front, 3) - deformed_grain_identifier(NX_UINT): + identifier_deformed_grain(NX_UINT): exists: recommended doc: | Grain identifier assigned to each cell in the recrystallization front. unit: NX_UNITLESS dim: (n_front,) - recrystallized_grain_identifier(NX_UINT): + identifier_recrystallized_grain(NX_UINT): exists: recommended doc: | Grain identifier assigned to each nucleus which affected that cell in the recrystallization front. unit: NX_UNITLESS dim: (n_front,) - thread_identifier(NX_UINT): + identifier_thread(NX_UINT): exists: optional doc: | Identifier of the OpenMP thread processing each cell in the recrystallization front. @@ -327,16 +347,3 @@ NXmicrostructure_score_results(NXobject): Hint about the direction from which the cell was infected. unit: NX_UNITLESS dim: (n_front,) - # performance(NXcs_profiling): - # exists: optional - # current_working_directory: - # command_line_call: - # exists: optional - # start_time(NX_DATE_TIME): - # exists: recommended - # end_time(NX_DATE_TIME): - # exists: recommended - # total_elapsed_time(NX_NUMBER): - # number_of_processes(NX_POSINT): - # number_of_threads(NX_POSINT): - # number_of_gpus(NX_POSINT): From 536e271993ea2d3fe69651fe691410caf60979d5 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 16 Feb 2025 00:49:49 +0100 Subject: [PATCH 24/75] Generated NXDL files --- .../NXmicrostructure.nxdl.xml | 120 ++-- .../NXmicrostructure_score_config.nxdl.xml | 535 ++++++++++++------ .../NXmicrostructure_score_results.nxdl.xml | 346 +++++------ .../nyaml/NXmicrostructure_score_config.yaml | 6 +- .../nyaml/NXmicrostructure_score_results.yaml | 12 +- 5 files changed, 592 insertions(+), 427 deletions(-) diff --git a/contributed_definitions/NXmicrostructure.nxdl.xml b/contributed_definitions/NXmicrostructure.nxdl.xml index f55411184e..54ddddb2d9 100644 --- a/contributed_definitions/NXmicrostructure.nxdl.xml +++ b/contributed_definitions/NXmicrostructure.nxdl.xml @@ -3,7 +3,7 @@ - + One- or two-dimensional projections, or three-dimensional representations of crystals. @@ -268,29 +268,29 @@ examples for specific frequently discussed microstructural features--> Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. - + First identifier whereby to identify crystals implicitly. - + Identifier whereby to identify each crystal explicitly. - + - + First identifier whereby to identify phases implicitly. - + Identifier whereby to identify phase for each crystal explicitly. - + @@ -300,7 +300,7 @@ examples for specific frequently discussed microstructural features--> True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - + @@ -310,7 +310,7 @@ examples for specific frequently discussed microstructural features--> of that crystal evaluated as a summary statistic for all probed positions vs the average disorientation of that crystal. - + @@ -318,7 +318,7 @@ examples for specific frequently discussed microstructural features--> Length of each crystal - + @@ -326,7 +326,7 @@ examples for specific frequently discussed microstructural features--> Area of each crystal. - + @@ -334,12 +334,12 @@ examples for specific frequently discussed microstructural features--> Volume of each crystal - + - + One- or two-dimensional projections or three-dimensional representation of interfaces between crystals as topological entities equivalent to dual_junctions. @@ -374,16 +374,16 @@ examples for specific frequently discussed microstructural features--> Identifier whereby to identify each interface explicitly. - + - + - Set of pairs of crystal_identifier for each interface. + Set of pairs of identifier_crystal for each interface. - + @@ -393,11 +393,11 @@ examples for specific frequently discussed microstructural features--> - + - Set of pairs of phase_identifier for each interface. + Set of pairs of identifier_phase for each interface. - + @@ -408,11 +408,11 @@ examples for specific frequently discussed microstructural features--> - + - Set of pairs of triple_junction_identifier for each interface. + Set of pairs of identifier_triple_junction for each interface. - + @@ -428,7 +428,7 @@ examples for specific frequently discussed microstructural features--> True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - + @@ -436,7 +436,7 @@ examples for specific frequently discussed microstructural features--> Gibbs free surface energy for each interface. - + @@ -444,7 +444,7 @@ examples for specific frequently discussed microstructural features--> Non-intrinsic mobility of each interface. - + @@ -455,7 +455,7 @@ examples for specific frequently discussed microstructural features--> This is not necessarily the same as the length of the individual polyline segments whereby the interface is discretized. - + @@ -463,12 +463,12 @@ examples for specific frequently discussed microstructural features--> The surface area of all interfaces. - + - + Projections or representations of junctions at which three interfaces meet. @@ -504,7 +504,7 @@ examples for specific frequently discussed microstructural features--> Identifier to identify each triple junction explicitly. - + @@ -515,7 +515,7 @@ example i) triple points as projections of triple lines have locations--> Set of identifier for positions whereby to identify the location of each junction. - + @@ -528,28 +528,28 @@ example i) triple points as projections of triple lines have locations--> Explicit positions. - + - + Set of tuples of identifier of crystals connected to the junction for each triple junction. - + - + Set of tuples of identifier of interfaces connected to the junction for each triple junction. - + @@ -560,18 +560,18 @@ example i) triple points as projections of triple lines have locations--> - + Set of tuples of identifier for polyline segments connected to the junction for each triple junction. - + - The specific polyline identifiers whereby to resolve ambiguities. + The specific identifier_polyline whereby to resolve ambiguities. @@ -582,7 +582,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - + @@ -590,7 +590,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Specific line energy of each triple junction - + @@ -598,7 +598,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Non-intrinsic mobility of each triple junction. - + @@ -609,7 +609,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> This is not necessarily the same as the length of the individual polyline segments whereby the junction is discretized. - + @@ -617,12 +617,12 @@ EXAMPLES FOR DESCRIPTOR VALUES--> The volume of the each triple junction - + - + Quadruple junctions as a region where four crystals meet. @@ -650,7 +650,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Identifier to identify each quadruple junction explicitly. - + @@ -661,7 +661,7 @@ example i) quadruple point locations explicitly--> Set of identifier for positions whereby to identify the location of each junction. - + @@ -674,18 +674,18 @@ example i) quadruple point locations explicitly--> Explicit positions. - + - + Set of tuples of identifier of crystals connected to the junction for each junction. - + @@ -696,12 +696,12 @@ example i) quadruple point locations explicitly--> - + Set of tuples of identifier of interfaces connected to the junction for each junction. - + @@ -713,12 +713,12 @@ example i) quadruple point locations explicitly--> - + Set of tuples of identifier for triple junctions connected to the junction for each quadruple junction. - + @@ -730,12 +730,12 @@ example i) quadruple point locations explicitly--> - + Set of tuples of identifier for phases of crystals connected to the junction for each quadruple junction. - + @@ -752,7 +752,7 @@ example i) quadruple point locations explicitly--> True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - + @@ -760,7 +760,7 @@ example i) quadruple point locations explicitly--> Energy of the quadruple_junction as a defect. - + @@ -768,7 +768,7 @@ example i) quadruple point locations explicitly--> Non-intrinsic mobility of each quadruple_junction. - + diff --git a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml index 7d09f7ff0d..834999265b 100644 --- a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -3,7 +3,7 @@ - - - - - + + + + + Dimensionality of the simulation. + + + + + + + + A qualifier whether the sample is a real one or a virtual one. + + + + + + + + + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. + + + + + + Name of the program whereby this config file was created. + + + - + Programs and libraries representing the computational environment @@ -102,33 +152,45 @@ - + - Relevant data to instantiate a starting configuration that is typically - a microstructure in deformed conditions where stored (elastic) energy - is stored in the form of crystal defects, which in the SCORE model are - is considered as mean-field dislocation content. + (Mechanical) properties of the material which scale the + amount of stored (elastic) energy in the system and + thus mainly affect recrystallization kinetics. - - - - Extend of each CA domain in voxel along the x, y, and z direction. - Deformation of sheet material is assumed. - The x axis is assumed pointing along the rolling direction. - The y axis is assumed pointing along the transverse direction. - The z axis is assumed pointing along the normal direction. - - - - + + + Reference shear modulus at zero Kelvin. + + + + + Magnitude of the Burgers vector at zero Kelvin. + + + + + + Melting temperature in degrees Celsius. + + - Details how the deformed grains should be modelled. + Details about the geometry and properties of the polycrystal that represents the + starting configuration (typically a deformed microstructure) for the simulation. - + Which model should be used to generate a starting microstructure. + + * cuboidal, a regular array of equally shaped cuboidal grains + * poisson_voronoi, a discretized poisson voronoi + * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map + * damask, the result of a simulation from `DAMASK <https://damask-multiphysics.org>`_. @@ -138,45 +200,63 @@ + Extent of each deformed grain in voxel along the - x, y, and z direction when type is cuboidal. + x, y, and z direction when model is cuboidal. - + - Average spherical diameter when type is poisson_voronoi. + Average spherical diameter when model is poisson_voronoi. - + + - Set of Bunge-Euler angles ( :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) - to sample orientations of deformed grains randomly from. + Settings for instantiating properties of deformed grains when model is cuboidal + or poisson. - - - - - + + + Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) + out of which the orientations of deformed grains are sampled. + + + + + + + + + Set of stored elastic energy quantified as a dislocation density which is assigned + to deformed grains with orientations from bunge_euler with index queries matching + for the bunge_euler and stored_energy fields. + + + + + + The EBSD dataset from which the initial microstructure is instantiated if model is ebsd. - - - - + + + + - Extent of the pixel of the EBSD orientation mapping assuming square-shaped - pixels. + Extent of the pixel of the EBSD orientation mapping assuming square-shaped pixels + or cube-shaped voxels respectively. - - + + @@ -184,14 +264,14 @@ Phenomenological model according to which recrystallization nuclei - are placed into the domain and assumed growing. + are placed into the domain whose growth is studied with the simulation. - + According to which model will the nuclei become distributed spatially: - * csr, complete spatial randomness. - * custom, implementation specific. + * csr, complete spatial randomness + * custom, implementation-specific * gb, nuclei placed at grain boundaries @@ -200,7 +280,7 @@ - + According to which model will the nuclei start to grow. @@ -208,7 +288,7 @@ - + According to which model will the nuclei get their orientation assigned. @@ -216,50 +296,39 @@ - + + - Set of Bunge-Euler angles ( :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) - to sample orientations of nuclei randomly from. + Settings for instantiating properties of nuclei for recrystallizing grains. - - - - - - - - - (Mechanical) properties of the material which scale - the amount of stored (elastic) energy in the system and - thus mainly affect recrystallization kinetics. - - - - Shear modulus at zero Kelvin. - - - - - Magnitude at the Burgers vector at zero Kelvin. - - - - - - Melting temperature in degrees Celsius. - - + + + Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) + out of which the orientations of nuclei/recrystallized grains are sampled. + + + + + + + + + Incubation time which is assigned to deformed grains with orientations from bunge_euler + with index queries matching for the bunge_euler and stored_energy fields. + + + + + + Model for the assumed mobility of grain boundaries with different disorientation - essentially implementing variations of Turnbull's model for - thermally-activated migration. + implemented as parameterized Turnbull's model for thermally-activated + grain boundary migration. - + Which type of fundamental model for the grain boundary mobility. @@ -277,12 +346,14 @@ TODO: add equation for the Rollett-Holm model the following equation--> Parameter of the Sebald-Gottstein migration model. - - - At which disorientation angle are grain boundary considered as high-angle grain - boundaries. - - + Pre-exponential factor for low-angle grain boundaries. @@ -305,12 +376,16 @@ TODO: add equation for the Rollett-Holm model the following equation--> - Pre-exponential factor for particularly mobile boundaries. + Pre-exponential factor for high-angle grain boundaries which in + bicrystal or other tailored experiments showed a particular high + mobility. - Migration activation enthalpy for particularly mobile boundaries. + Migration activation enthalpy for high-angle grain boundaries which in + bicrystal or other tailored experiments showed a particular high + mobility. @@ -321,13 +396,12 @@ TODO: add equation for the Rollett-Holm model the following equation--> - The assumed mobility :math:`m_0` of the fastest grain boundary in the system at the assumed - temperature. GraGLeS was developed for modelling isothermal annealing. + The assumed mobility :math:`m_0` of the fastest grain boundary in the system. - Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not one. + Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. @@ -344,9 +418,9 @@ TODO: add equation for the Rollett-Holm model the following equation--> - Time-dependent reduction of the stored (elastic) energy to account for recovery. + Time-dependent reduction of the stored energy to account for recovery effects. - + Which type of recovery model. @@ -358,9 +432,10 @@ TODO: add equation for the Rollett-Holm model the following equation--> Reduction of the grain boundary migration speed due to the presence of dispersoids - through which the total grain boundary area of the recrystallization front can be reduced. + through which the total grain boundary area of the recrystallization front can be reduced + while the boundary is arrested at the dispersoids. - + Which type of drag model. @@ -369,73 +444,160 @@ TODO: add equation for the Rollett-Holm model the following equation--> - + + - Parameter of the Zener-Smith drag model. + Parameter of the Zener-Smith drag model when model is zener_smith. - + Configuration-dependent constant which factorizes the drag pressure. - + Average surface energy of the grain-boundary-dispersoid-surface configuration which factorizes the drag pressure. - + + - Support point of the linearized curve of simulated time matching - a specific support point of the average dispersoid radius. + Assumed dispersoid mean radius-time profile - - - - - - - Support point of the linearized curve of the average dispersoid radius. - - - - - + + + + + + + + Support point of the linearized curve of simulated time matching + a specific support point of the average dispersoid radius. + + + + + + + + + Support point of the linearized curve of the average dispersoid radius. + + + + + + + - + + + + Given name of a texture component. + + + + + + + + Bunge-Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the + of texture components in sequence of the name field. + + + + + + + + + Integration radius that constraints the theta angular region of the orientation space (SO3) + about each central location (obeying symmetries) as specified by bunge_euler indexed in + the same sequence as the bunge_euler and name fields. + + + + + + + Desired simulated time-temperature profile + + + + + Support point of the linearized curve of simulated time matching a specific support point of the temperature. - + + Support point of the linearized curve of the temperature. - + + - + + + Relevant data to instantiate a starting configuration that is typically + a microstructure in deformed conditions where (elastic) energy is stored + in the form of crystal defects (mostly dislocations). The SCORE model + does not resolve individual dislocations but works with one + homogenized mean-field density per grain. For simulations that are + instantiated from EBSD datasets or crystal plasticity simulations + individual values are available for each voxel that may be used as is + for each voxel or may need a pre-processing of the data to coarse-grain + material point-specific values to values averaged per deformed grain. + + + + + Extend of each CA domain in voxel along the x, y, and z direction. + Deformation of sheet material is assumed. + The x axis is assumed pointing along the rolling direction. + The y axis is assumed pointing along the transverse direction. + The z axis is assumed pointing along the normal direction. + + + + + Edge length of the material point (single cell of the cellular automata). + + + + + + + + Criteria which enable to stop the simulation in a controlled manner. Whichever criterion is fulfilled first stops the simulation. + Furthermore, numerical configuration required to achieve + a stable numerical integration. Maximum recrystallized volume fraction. - + Maximum simulated physical time. @@ -445,11 +607,6 @@ TODO: add equation for the Rollett-Holm model the following equation--> Maximum number of iteration steps. - - - - Settings relevant for stable numerical integration. - Maximum fraction equivalent to the migration of the @@ -457,54 +614,63 @@ TODO: add equation for the Rollett-Holm model the following equation--> may be consumed in a single iteration. - - - Fraction of the total number of cells in the CA which - should initially be allocated for offering cells in the - recrystallization front. - - - - - By how much more times should the already allocated memory - be increased to offer space for storing states of cells - in the recrystallization front. - - - - - Should the cache for cells in the recrystallization front - be defragmented on-the-fly. - - - + + - Heuristic recrystallized volume target values at which - the cache for cells in the recrystallization front - will be defragmented on-the-fly. + Parameter which control the memory management + of cells in the recrystallization front. - - - - + + + Fraction of the total number of cells in the CA which + should initially be allocated for offering storage for + cells making up the recrystallization front. + + + + + By how much more times should the already allocated memory + be increased to offer space for storing states of cells + in the recrystallization front. + + + + + Should the cache for cells in the recrystallization front + be defragmented on-the-fly or not. + + + + + Target values at which recrystallized volume fraction the cache + for cells in the recrystallization front will be defragmented + on-the-fly. Defragmentation packs active cells closer into + main memory to reduce cache misses in subsequent evaluations + of the recrystallization front. + + + + + + - List of recrystallized volume target values at which a - snapshot of the CA state should be stored. - - The code documents summary statistics like recrystallized volume fraction - for each iteration. However, snapshots of the microstructure can take much - space as SCORE is able to evolve automata with up to :math:`1600^3` cells. - Snapshot data document the current microstructure which includes the grain - assigned to each of these cells plus the state of the recrystallization front. + List of target values at which recrystallized volume fractions the state + of the CA is evaluated and stored. The code documents summary statistics + like recrystallized volume fraction for each iteration and the volume of each + grain. Furthermore, snapshots of the microstructure are stored. + These can take much disk space though because SCORE is able to evolve CA + with up to :math:`1600^3` cells. Snapshot data document the current microstructure + including the assignment of grains and cells surplus the state of the + recrystallization front. Despite these front data make up for approximately one order of magnitude less cells than represented in the domain, more numerical data have to be - collected each cell in the front than just a grain identifier. + collected for each cell in the front than just a grain identifier. - + @@ -512,8 +678,8 @@ TODO: add equation for the Rollett-Holm model the following equation--> - Perform a statistical analyses of the results as it was - proposed by M. Kühbach (solitary unit model ensemble approach). + Perform a statistical analyses of the results as it was proposed + by M. Kühbach (solitary unit model ensemble approach). @@ -528,15 +694,12 @@ TODO: add equation for the Rollett-Holm model the following equation--> during post-processing the results with the solitary unit modeling approach. - - - List of identifier for those domain which should be rendered. - Identifier start from 0. - - - - - + diff --git a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml index 1d7a46e47b..39623718f8 100644 --- a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -3,7 +3,7 @@ - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays - The total number of summary statistic log entries. + The total number of summary statistic log entries - Number of boundaries of the bounding box or primitive to domain. + Number of boundaries of the bounding box or primitive about the computational + domain - Number of parameter required for chosen orientation parameterization. + Number of parameter required for chosen orientation parameterization - Number of texture components identified. + Number of texture components identified - Dimensionality. + Dimensionality - Cardinality. + Cardinality - Number of active cells in the (recrystallization) front. + Number of active cells in the (recrystallization) front - Number of grains in the computer simulation. + Number of grains in the computer simulation - Application definition for storing results of the SCORE cellular automaton. + Application definition for storing results of the SCORE cellular automata model. - The SCORE cellular automaton model for primary recrystallization is an - example of typical materials engineering applications used within the field - of so-called Integral Computational Materials Engineering (ICME) whereby - one can simulate the evolution of microstructures. + The SCORE cellular automata model for primary recrystallization is an example + of a typical materials engineering application used within the field of so-called + Integral Computational Materials Engineering (ICME) whereby one can simulate + the evolution of microstructures. - Specifically the SCORE model can be used to simulate the growth of static - recrystallization nuclei. The model is described in the literature: + Specifically the SCORE model can be used to simulate the growth of nuclei during + static recrystallization. The model is described in the literature: * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ * `C. Haase et al. <https://doi.org/10.1016/j.actamat.2015.08.057>`_ @@ -90,23 +91,35 @@ inspect comments behind NXmicrostructure--> - + Simulation ID as an alias to refer to this simulation. - + Discouraged free-text field to add further details to the computation. - - - + + + ISO 8601 time code with local time zone offset to UTC information + included when the simulation was started. + + + + + ISO 8601 time code with local time zone offset to UTC information + included when the simulation ended. + + + - + + Name of the program with which the simulation was performed. + + - @@ -119,66 +132,65 @@ inspect comments behind NXmicrostructure--> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + @@ -207,7 +219,7 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele 4 - von Neumann 5 - Dirichlet - + @@ -216,7 +228,7 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele Name of the boundaries. Left, right, front, back, bottom, top, The field must have as many entries as there are number_of_boundaries. - + @@ -224,27 +236,34 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele - Documentation of the spatiotemporal evolution + Documentation of the spatiotemporal evolution for each CA domain. - + Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening in for practical reasons though in while - running the simulation. Place used for storing descriptors from continuum mechanics + (averaging, integrating, interpolating) happening for practical and performance reasons + during the simulation. Place used for storing descriptors from continuum mechanics and thermodynamics at the scale of the entire ROI. - + Evolution of the recrystallized volume fraction over time. + + + + + + + Evolution of the physical time not to be confused with wall-clock time or profiling data. - + @@ -252,26 +271,29 @@ the typical lean summary statistics flattened--> Iteration or increment counter. + + + Evolution of the simulated temperature over time. - + - + Recrystallized volume fraction. - + - - + + Which type of stress. @@ -279,28 +301,28 @@ the typical lean summary statistics flattened--> - + Applied external stress tensor on the ROI. - + - - + + Which type of strain. - + Applied external strain tensor on the ROI. - + @@ -316,36 +338,11 @@ the typical lean summary statistics flattened--> - + Applied deformation gradient tensor on the ROI. - - - - - - - - - - - Applied external magnetic field on the ROI. - - - - - - - - - - - - - Applied external electrical field on the ROI. - - + @@ -353,22 +350,40 @@ the typical lean summary statistics flattened--> - + - + + + Iteration or increment counter. + + Simulated temperature for this snapshot. - + Current recrystallized volume fraction (taking fractional infections into account). - + Target value for which a snapshot was requested for the recrystallized volume fraction. @@ -376,40 +391,40 @@ the typical lean summary statistics flattened--> - + Grain identifier for each cell. - + - + Identifier of the OpenMP thread which processed this part of the grid. - + - + - - - + + + - - - + + + @@ -417,7 +432,7 @@ the typical lean summary statistics flattened--> Volume of each grain accounting also for partially transformed cells. - + @@ -426,17 +441,17 @@ the typical lean summary statistics flattened--> Bunge-Euler angle triplets for each grain. - + - Current value for the dislocation density as a measure of the remaining stored energy - in assumed crystal defects inside each grain. + Current value for the dislocation density as a measure of the remaining + stored energy in assumed crystal defects inside each grain. - + @@ -444,7 +459,7 @@ the typical lean summary statistics flattened--> Is the grain deformed. - + @@ -452,7 +467,7 @@ the typical lean summary statistics flattened--> Is the grain recrystallized. - + @@ -466,17 +481,17 @@ the typical lean summary statistics flattened--> Which cells are currently in a halo region of threads. - + - So-called mobility weight which is a scaling factor to - control the mobility of the grain boundary which is assumed - to sweep currently this volume. + So-called mobility weight which is a scaling factor to control the + mobility of the grain boundary that is modelled sweeping cells that + make the discrete recrystallization front. - + @@ -484,34 +499,34 @@ the typical lean summary statistics flattened--> The x, y, z grid coordinates of each cell in the recrystallization front. - + - + Grain identifier assigned to each cell in the recrystallization front. - + - + Grain identifier assigned to each nucleus which affected that cell in the recrystallization front. - + - + Identifier of the OpenMP thread processing each cell in the recrystallization front. - + @@ -519,7 +534,7 @@ the typical lean summary statistics flattened--> Hint about the direction from which the cell was infected. - + @@ -527,17 +542,4 @@ the typical lean summary statistics flattened--> - diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index b5a6a969ad..6c0792f4d6 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -114,7 +114,7 @@ NXmicrostructure_score_config(NXobject): * cuboidal, a regular array of equally shaped cuboidal grains * poisson_voronoi, a discretized poisson voronoi * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map - * damask, the result of a simulation from `DAMASK `_. enumeration: [cuboidal, poisson_voronoi, ebsd, damask] extent(NX_FLOAT): @@ -283,7 +283,7 @@ NXmicrostructure_score_config(NXobject): Reduction of the grain boundary migration speed due to the presence of dispersoids through which the total grain boundary area of the recrystallization front can be reduced while the boundary is arrested at the dispersoids. - model: + model(NX_CHAR): doc: | Which type of drag model. enumeration: [none, zener_smith] @@ -299,7 +299,7 @@ NXmicrostructure_score_config(NXobject): doc: | Average surface energy of the grain-boundary-dispersoid-surface configuration which factorizes the drag pressure. - unit: NX_ANY # J/m^2 + unit: NX_ANY # J/m^2 radius_evolution(NXdata): # required when model is zener_smith # decorators to make the config file immediately useful diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml index 0183b31fd8..33ac04996e 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml @@ -70,12 +70,12 @@ NXmicrostructure_score_results(NXobject): exists: [min, 1, max, infty] program(NX_CHAR): \@version(NX_CHAR): - rotation_conventions(NXrotation_conventions): - rotation_handedness(NX_CHAR): - rotation_convention(NX_CHAR): - euler_angle_convention(NX_CHAR): - axis_angle_convention(NX_CHAR): - sign_convention(NX_CHAR): + # rotation_conventions(NXrotation_conventions): + # rotation_handedness(NX_CHAR): + # rotation_convention(NX_CHAR): + # euler_angle_convention(NX_CHAR): + # axis_angle_convention(NX_CHAR): + # sign_convention(NX_CHAR): sample_reference_frame(NXcoordinate_system): type: enumeration: [cartesian] From 36ba122a7646638951602275cde8f151ef1ff471 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 16 Feb 2025 01:40:25 +0100 Subject: [PATCH 25/75] Minor edits score config --- .../NXmicrostructure_score_config.nxdl.xml | 70 ++++++++++--------- .../nyaml/NXmicrostructure_score_config.yaml | 57 ++++++++------- 2 files changed, 68 insertions(+), 59 deletions(-) diff --git a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml index 834999265b..54ae3a441a 100644 --- a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -394,22 +394,27 @@ lagb_to_hagb_cut(NX_FLOAT): Parameter of the Rollett-Holm migration model. - + - The assumed mobility :math:`m_0` of the fastest grain boundary in the system. + Pre-exponential factor for the fastest grain boundary in the system. - + + + Migration activation enthalpy for the fastest grain boundary in the system. + + + Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. - + Mobility scaling factor :math:`c_2`. Typically 5. - + Mobility scaling factor :math:`c_3`. Typically 9. @@ -566,7 +571,7 @@ like showing a r(t) plot--> material point-specific values to values averaged per deformed grain. - + Extend of each CA domain in voxel along the x, y, and z direction. Deformation of sheet material is assumed. @@ -574,17 +579,19 @@ like showing a r(t) plot--> The y axis is assumed pointing along the transverse direction. The z axis is assumed pointing along the normal direction. + + + - + - Edge length of the material point (single cell of the cellular automata). + Edge length of the material point that in SCORE + is discretized via equisized cubic voxels. - - - + Criteria which enable to stop the simulation in a controlled manner. @@ -614,7 +621,25 @@ like showing a r(t) plot--> may be consumed in a single iteration. - + + + List of target values at which recrystallized volume fractions the state + of the CA is evaluated and stored. The code documents summary statistics + like recrystallized volume fraction for each iteration and the volume of each + grain. Furthermore, snapshots of the microstructure are stored. + These can take much disk space though because SCORE is able to evolve CA + with up to :math:`1600^3` cells. Snapshot data document the current microstructure + including the assignment of grains and cells surplus the state of the + recrystallization front. + + Despite these front data make up for approximately one order of magnitude + less cells than represented in the domain, more numerical data have to be + collected for each cell in the front than just a grain identifier. + + + + + Parameter which control the memory management @@ -654,27 +679,6 @@ like showing a r(t) plot--> - - - - List of target values at which recrystallized volume fractions the state - of the CA is evaluated and stored. The code documents summary statistics - like recrystallized volume fraction for each iteration and the volume of each - grain. Furthermore, snapshots of the microstructure are stored. - These can take much disk space though because SCORE is able to evolve CA - with up to :math:`1600^3` cells. Snapshot data document the current microstructure - including the assignment of grains and cells surplus the state of the - recrystallization front. - - Despite these front data make up for approximately one order of magnitude - less cells than represented in the domain, more numerical data have to be - collected for each cell in the front than just a grain identifier. - - - - - - diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index 6c0792f4d6..348e7d5363 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -255,19 +255,23 @@ NXmicrostructure_score_config(NXobject): doc: | Parameter of the Rollett-Holm migration model. # For rollett_holm :math:`m(\Theta) = m_0 \cdot (1 - c_1 * exp(-c_2 \cdot \frac{\Theta}{15}^{c_3}))`. - m_null(NX_FLOAT): + pre_factor(NX_FLOAT): doc: | - The assumed mobility :math:`m_0` of the fastest grain boundary in the system. + Pre-exponential factor for the fastest grain boundary in the system. unit: NX_ANY # m^4/Js - c_one(NX_FLOAT): + enthalpy(NX_FLOAT): + doc: | + Migration activation enthalpy for the fastest grain boundary in the system. + unit: NX_ANY # eV + c1(NX_FLOAT): doc: | Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. unit: NX_DIMENSIONLESS - c_two(NX_FLOAT): + c2(NX_FLOAT): doc: | Mobility scaling factor :math:`c_2`. Typically 5. unit: NX_UNITLESS - c_three(NX_FLOAT): + c3(NX_FLOAT): doc: | Mobility scaling factor :math:`c_3`. Typically 9. unit: NX_UNITLESS @@ -382,11 +386,14 @@ NXmicrostructure_score_config(NXobject): The x axis is assumed pointing along the rolling direction. The y axis is assumed pointing along the transverse direction. The z axis is assumed pointing along the normal direction. - cell_dimensions(NX_NUMBER): + unit: NX_UNITLESS + dim: (3,) # (d,) + cell_dimensions(NX_FLOAT): doc: | - Edge length of the material point (single cell of the cellular automata). + Edge length of the material point that in SCORE + is discretized via equisized cubic voxels. unit: NX_LENGTH - dim: (d,) + # dim: (d,) numerics(NXobject): doc: | Criteria which enable to stop the simulation in a controlled manner. @@ -411,7 +418,22 @@ NXmicrostructure_score_config(NXobject): fastest grain boundary in the system how much a cell may be consumed in a single iteration. unit: NX_DIMENSIONLESS - ##################################### + x_set(NX_FLOAT): + doc: | + List of target values at which recrystallized volume fractions the state + of the CA is evaluated and stored. The code documents summary statistics + like recrystallized volume fraction for each iteration and the volume of each + grain. Furthermore, snapshots of the microstructure are stored. + These can take much disk space though because SCORE is able to evolve CA + with up to :math:`1600^3` cells. Snapshot data document the current microstructure + including the assignment of grains and cells surplus the state of the + recrystallization front. + + Despite these front data make up for approximately one order of magnitude + less cells than represented in the domain, more numerical data have to be + collected for each cell in the front than just a grain identifier. + unit: NX_DIMENSIONLESS + dim: (n_snapshot,) cell_cache(NXobject): doc: | Parameter which control the memory management @@ -441,23 +463,6 @@ NXmicrostructure_score_config(NXobject): of the recrystallization front. unit: NX_DIMENSIONLESS dim: (n_defrag,) - sampling(NXobject): - x(NX_FLOAT): - doc: | - List of target values at which recrystallized volume fractions the state - of the CA is evaluated and stored. The code documents summary statistics - like recrystallized volume fraction for each iteration and the volume of each - grain. Furthermore, snapshots of the microstructure are stored. - These can take much disk space though because SCORE is able to evolve CA - with up to :math:`1600^3` cells. Snapshot data document the current microstructure - including the assignment of grains and cells surplus the state of the - recrystallization front. - - Despite these front data make up for approximately one order of magnitude - less cells than represented in the domain, more numerical data have to be - collected for each cell in the front than just a grain identifier. - unit: NX_DIMENSIONLESS - dim: (n_snapshot,) solitary_unit(NXobject): apply(NX_BOOLEAN): doc: | From c274ae549b0a28122add4b3cea2df1c67d3d2a52 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 24 Feb 2025 12:41:53 +0100 Subject: [PATCH 26/75] Finalizing NXmicrostructure_score using newest nyaml --- .../NXmicrostructure_score_config.nxdl.xml | 441 +++++++++--------- .../NXmicrostructure_score_results.nxdl.xml | 279 +++++------ .../nyaml/NXmicrostructure_score_config.yaml | 39 +- .../nyaml/NXmicrostructure_score_results.yaml | 51 +- 4 files changed, 443 insertions(+), 367 deletions(-) diff --git a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml index 54ae3a441a..26d38bc32b 100644 --- a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -25,56 +25,56 @@ - Number of Bunge-Euler angle triplets for deformed grains. + Number of Bunge-Euler angle triplets for deformed grains. - Number of Bunge-Euler angle triplets for recrystallization nuclei. + Number of Bunge-Euler angle triplets for recrystallization nuclei. - Number of texture components to analyze. + Number of texture components to analyze. - Number of support points for the linearized drag profile. + Number of support points for the linearized drag profile. - Number of suport points for the desired time-temperature profile. + Number of suport points for the desired time-temperature profile. - Number of entries when to defragment i.e. garbage collect the memory holding - state information for recrystallized cells. + Number of entries when to defragment i.e. garbage collect the memory holding + state information for recrystallized cells. - Number of entries when to collect snapshots of the evolving microstructure. + Number of entries when to collect snapshots of the evolving microstructure. - Number of solitary unit domains to export. + Number of solitary unit domains to export. - Dimensionality of the simulation. + Dimensionality of the simulation. - Application definition to configure a simulation with the SCORE model. - - * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ - * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ + Application definition to configure a simulation with the SCORE model. + + * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ + * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ @@ -84,28 +84,28 @@ - An alias to refer to this simulation. + An alias to refer to this simulation. - Discouraged free-text field to add further details to the computation. + Discouraged free-text field to add further details to the computation. - ISO 8601 time code with local time zone offset to UTC information - included when the configuration file was created. + ISO 8601 time code with local time zone offset to UTC information + included when the configuration file was created. - + - Dimensionality of the simulation. + Dimensionality of the simulation. @@ -113,7 +113,7 @@ - A qualifier whether the sample is a real one or a virtual one. + A qualifier whether the sample is a real one or a virtual one. @@ -122,21 +122,21 @@ - List of comma-separated elements from the periodic table that are - contained in the specimen. If the specimen substance has multiple - components, all elements from each component must be included in - `atom_types`. - - The purpose of the field is to offer research data management systems an - opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by parent_identifier or walk through - eventually deeply nested groups in data instances. + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. - Name of the program whereby this config file was created. + Name of the program whereby this config file was created. @@ -144,9 +144,9 @@ - Programs and libraries representing the computational environment + Programs and libraries representing the computational environment - + @@ -154,18 +154,18 @@ - (Mechanical) properties of the material which scale the - amount of stored (elastic) energy in the system and - thus mainly affect recrystallization kinetics. + (Mechanical) properties of the material which scale the + amount of stored (elastic) energy in the system and + thus mainly affect recrystallization kinetics. - Reference shear modulus at zero Kelvin. + Reference shear modulus at zero Kelvin. - Magnitude of the Burgers vector at zero Kelvin. + Magnitude of the Burgers vector at zero Kelvin. - Melting temperature in degrees Celsius. + Melting temperature - Details about the geometry and properties of the polycrystal that represents the - starting configuration (typically a deformed microstructure) for the simulation. + Details about the geometry and properties of the polycrystal that represents the + starting configuration (typically a deformed microstructure) for the simulation. - Which model should be used to generate a starting microstructure. - - * cuboidal, a regular array of equally shaped cuboidal grains - * poisson_voronoi, a discretized poisson voronoi - * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map - * damask, the result of a simulation from `DAMASK <https://damask-multiphysics.org>`_. + Which model should be used to generate a starting microstructure. + + * cuboidal, a regular array of equally shaped cuboidal grains + * poisson_voronoi, a discretized poisson voronoi + * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map + * damask, the result of a simulation from `DAMASK <https://damask-multiphysics.org>`_. @@ -202,87 +202,106 @@ SecondOrderThermalExpCoeff--> - Extent of each deformed grain in voxel along the - x, y, and z direction when model is cuboidal. + Extent of each deformed grain in voxel along the + x, y, and z direction when model is cuboidal. - + - Average spherical diameter when model is poisson_voronoi. + Average spherical diameter when model is poisson_voronoi. - - + - Settings for instantiating properties of deformed grains when model is cuboidal - or poisson. + Settings for instantiating properties of deformed grains when model is cuboidal + or poisson. - Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) - out of which the orientations of deformed grains are sampled. + Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) + out of which the orientations of deformed grains are sampled. - + - Set of stored elastic energy quantified as a dislocation density which is assigned - to deformed grains with orientations from bunge_euler with index queries matching - for the bunge_euler and stored_energy fields. + Set of stored elastic energy quantified as a dislocation density which is assigned + to deformed grains with orientations from bunge_euler with index queries matching + for the bunge_euler and stored_energy fields. - + - + - The EBSD dataset from which the initial microstructure is - instantiated if model is ebsd. + Settings for instantiating properties of deformed grains from an + EBSD orientation map when model is cuboidal or poisson. - - - + + + + + + - Extent of the pixel of the EBSD orientation mapping assuming square-shaped pixels - or cube-shaped voxels respectively. + Extent of the pixel of the EBSD orientation mapping assuming square-shaped pixels + or cube-shaped voxels respectively. - + + + + Settings for instantiating properties of deformed grains and nuclei when model + is damask. + + + + Name of the DREAM.3D HDF5 file that was instantiated from the + a previously performed DAMASK simulation. + + + + + + + + + - Phenomenological model according to which recrystallization nuclei - are placed into the domain whose growth is studied with the simulation. + Phenomenological model according to which recrystallization nuclei + are placed into the domain whose growth is studied with the simulation. - According to which model will the nuclei become distributed spatially: - - * csr, complete spatial randomness - * custom, implementation-specific - * gb, nuclei placed at grain boundaries + According to which model will the nuclei become distributed spatially: + + * csr, complete spatial randomness + * custom, implementation-specific + * gb, nuclei placed at grain boundaries - - + - According to which model will the nuclei start to grow. + According to which model will the nuclei start to grow. @@ -290,33 +309,39 @@ SecondOrderThermalExpCoeff--> - According to which model will the nuclei get their orientation assigned. + According to which model will the nuclei get their orientation assigned: + + * ensemble, picking randomly one from ensemble/bunge_euler + * random, picking randomly on the SO3 + * damask, picking based on information provided in deformation/damask - + + + - Settings for instantiating properties of nuclei for recrystallizing grains. + Settings for instantiating properties of nuclei for recrystallizing grains. - Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) - out of which the orientations of nuclei/recrystallized grains are sampled. + Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) + out of which the orientations of nuclei/recrystallized grains are sampled. - + - Incubation time which is assigned to deformed grains with orientations from bunge_euler - with index queries matching for the bunge_euler and stored_energy fields. + Incubation time which is assigned to deformed grains with orientations from bunge_euler + with index queries matching for the bunge_euler and stored_energy fields. - + @@ -324,16 +349,16 @@ SecondOrderThermalExpCoeff--> - Model for the assumed mobility of grain boundaries with different disorientation - implemented as parameterized Turnbull's model for thermally-activated - grain boundary migration. + Model for the assumed mobility of grain boundaries with different disorientation + implemented as parameterized Turnbull's model for thermally-activated + grain boundary migration. - Which type of fundamental model for the grain boundary mobility. - - Grain boundaries with disorientation angle smaller than 15 degree are considered - as low-angle grain boundaries. Other grain boundaries are high-angle boundaries. + Which type of fundamental model for the grain boundary mobility. + + Grain boundaries with disorientation angle smaller than 15 degree are considered + as low-angle grain boundaries. Other grain boundaries are high-angle boundaries. @@ -344,7 +369,7 @@ TODO: add equation for the Rollett-Holm model the following equation--> - Parameter of the Sebald-Gottstein migration model. + Parameter of the Sebald-Gottstein migration model. - Pre-exponential factor for low-angle grain boundaries. + Pre-exponential factor for low-angle grain boundaries. - Migration activation enthalpy for low-angle grain boundaries. + Migration activation enthalpy for low-angle grain boundaries. - Pre-exponential factor for high-angle grain boundaries. + Pre-exponential factor for high-angle grain boundaries. - Migration activation enthalpy for high-angle grain boundaries. + Migration activation enthalpy for high-angle grain boundaries. - Pre-exponential factor for high-angle grain boundaries which in - bicrystal or other tailored experiments showed a particular high - mobility. + Pre-exponential factor for high-angle grain boundaries which in + bicrystal or other tailored experiments showed a particular high + mobility. - Migration activation enthalpy for high-angle grain boundaries which in - bicrystal or other tailored experiments showed a particular high - mobility. + Migration activation enthalpy for high-angle grain boundaries which in + bicrystal or other tailored experiments showed a particular high + mobility. - Parameter of the Rollett-Holm migration model. + Parameter of the Rollett-Holm migration model. - Pre-exponential factor for the fastest grain boundary in the system. + Pre-exponential factor for the fastest grain boundary in the system. - Migration activation enthalpy for the fastest grain boundary in the system. + Migration activation enthalpy for the fastest grain boundary in the system. - Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. + Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. - Mobility scaling factor :math:`c_2`. Typically 5. + Mobility scaling factor :math:`c_2`. Typically 5. - Mobility scaling factor :math:`c_3`. Typically 9. + Mobility scaling factor :math:`c_3`. Typically 9. - Time-dependent reduction of the stored energy to account for recovery effects. + Time-dependent reduction of the stored energy to account for recovery effects. - Which type of recovery model. + Which type of recovery model. @@ -436,13 +461,13 @@ lagb_to_hagb_cut(NX_FLOAT): - Reduction of the grain boundary migration speed due to the presence of dispersoids - through which the total grain boundary area of the recrystallization front can be reduced - while the boundary is arrested at the dispersoids. + Reduction of the grain boundary migration speed due to the presence of dispersoids + through which the total grain boundary area of the recrystallization front can be reduced + while the boundary is arrested at the dispersoids. - Which type of drag model. + Which type of drag model. @@ -452,17 +477,17 @@ lagb_to_hagb_cut(NX_FLOAT): - Parameter of the Zener-Smith drag model when model is zener_smith. + Parameter of the Zener-Smith drag model when model is zener_smith. - Configuration-dependent constant which factorizes the drag pressure. + Configuration-dependent constant which factorizes the drag pressure. - Average surface energy of the grain-boundary-dispersoid-surface configuration - which factorizes the drag pressure. + Average surface energy of the grain-boundary-dispersoid-surface configuration + which factorizes the drag pressure. @@ -470,7 +495,7 @@ lagb_to_hagb_cut(NX_FLOAT): decorators to make the config file immediately useful like showing a r(t) plot--> - Assumed dispersoid mean radius-time profile + Assumed dispersoid mean radius-time profile @@ -479,19 +504,19 @@ like showing a r(t) plot--> - Support point of the linearized curve of simulated time matching - a specific support point of the average dispersoid radius. + Support point of the linearized curve of simulated time matching + a specific support point of the average dispersoid radius. - + - Support point of the linearized curve of the average dispersoid radius. + Support point of the linearized curve of the average dispersoid radius. - + @@ -502,36 +527,36 @@ like showing a r(t) plot--> - Given name of a texture component. + Given name of a texture component. - + - Bunge-Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the - of texture components in sequence of the name field. + Bunge-Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the + of texture components in sequence of the name field. - + - Integration radius that constraints the theta angular region of the orientation space (SO3) - about each central location (obeying symmetries) as specified by bunge_euler indexed in - the same sequence as the bunge_euler and name fields. + Integration radius that constraints the theta angular region of the orientation space (SO3) + about each central location (obeying symmetries) as specified by bunge_euler indexed in + the same sequence as the bunge_euler and name fields. - + - Desired simulated time-temperature profile + Desired simulated time-temperature profile @@ -540,19 +565,19 @@ like showing a r(t) plot--> - Support point of the linearized curve of simulated time matching - a specific support point of the temperature. + Support point of the linearized curve of simulated time matching + a specific support point of the temperature. - + - Support point of the linearized curve of the temperature. + Support point of the linearized curve of the temperature. - + @@ -560,33 +585,33 @@ like showing a r(t) plot--> - Relevant data to instantiate a starting configuration that is typically - a microstructure in deformed conditions where (elastic) energy is stored - in the form of crystal defects (mostly dislocations). The SCORE model - does not resolve individual dislocations but works with one - homogenized mean-field density per grain. For simulations that are - instantiated from EBSD datasets or crystal plasticity simulations - individual values are available for each voxel that may be used as is - for each voxel or may need a pre-processing of the data to coarse-grain - material point-specific values to values averaged per deformed grain. + Relevant data to instantiate a starting configuration that is typically + a microstructure in deformed conditions where (elastic) energy is stored + in the form of crystal defects (mostly dislocations). The SCORE model + does not resolve individual dislocations but works with one + homogenized mean-field density per grain. For simulations that are + instantiated from EBSD datasets or crystal plasticity simulations + individual values are available for each voxel that may be used as is + for each voxel or may need a pre-processing of the data to coarse-grain + material point-specific values to values averaged per deformed grain. - Extend of each CA domain in voxel along the x, y, and z direction. - Deformation of sheet material is assumed. - The x axis is assumed pointing along the rolling direction. - The y axis is assumed pointing along the transverse direction. - The z axis is assumed pointing along the normal direction. + Extend of each CA domain in voxel along the x, y, and z direction. + Deformation of sheet material is assumed. + The x axis is assumed pointing along the rolling direction. + The y axis is assumed pointing along the transverse direction. + The z axis is assumed pointing along the normal direction. - + - Edge length of the material point that in SCORE - is discretized via equisized cubic voxels. + Edge length of the material point that in SCORE + is discretized via equisized cubic voxels. @@ -594,86 +619,86 @@ like showing a r(t) plot--> - Criteria which enable to stop the simulation in a controlled manner. - Whichever criterion is fulfilled first stops the simulation. - Furthermore, numerical configuration required to achieve - a stable numerical integration. + Criteria which enable to stop the simulation in a controlled manner. + Whichever criterion is fulfilled first stops the simulation. + Furthermore, numerical configuration required to achieve + a stable numerical integration. - Maximum recrystallized volume fraction. + Maximum recrystallized volume fraction. - Maximum simulated physical time. + Maximum simulated physical time. - Maximum number of iteration steps. + Maximum number of iteration steps. - Maximum fraction equivalent to the migration of the - fastest grain boundary in the system how much a cell - may be consumed in a single iteration. + Maximum fraction equivalent to the migration of the + fastest grain boundary in the system how much a cell + may be consumed in a single iteration. - List of target values at which recrystallized volume fractions the state - of the CA is evaluated and stored. The code documents summary statistics - like recrystallized volume fraction for each iteration and the volume of each - grain. Furthermore, snapshots of the microstructure are stored. - These can take much disk space though because SCORE is able to evolve CA - with up to :math:`1600^3` cells. Snapshot data document the current microstructure - including the assignment of grains and cells surplus the state of the - recrystallization front. - - Despite these front data make up for approximately one order of magnitude - less cells than represented in the domain, more numerical data have to be - collected for each cell in the front than just a grain identifier. - - + List of target values at which recrystallized volume fractions the state + of the CA is evaluated and stored. The code documents summary statistics + like recrystallized volume fraction for each iteration and the volume of each + grain. Furthermore, snapshots of the microstructure are stored. + These can take much disk space though because SCORE is able to evolve CA + with up to :math:`1600^3` cells. Snapshot data document the current microstructure + including the assignment of grains and cells surplus the state of the + recrystallization front. + + Despite these front data make up for approximately one order of magnitude + less cells than represented in the domain, more numerical data have to be + collected for each cell in the front than just a grain identifier. + + - Parameter which control the memory management - of cells in the recrystallization front. + Parameter which control the memory management + of cells in the recrystallization front. - Fraction of the total number of cells in the CA which - should initially be allocated for offering storage for - cells making up the recrystallization front. + Fraction of the total number of cells in the CA which + should initially be allocated for offering storage for + cells making up the recrystallization front. - By how much more times should the already allocated memory - be increased to offer space for storing states of cells - in the recrystallization front. + By how much more times should the already allocated memory + be increased to offer space for storing states of cells + in the recrystallization front. - Should the cache for cells in the recrystallization front - be defragmented on-the-fly or not. + Should the cache for cells in the recrystallization front + be defragmented on-the-fly or not. - Target values at which recrystallized volume fraction the cache - for cells in the recrystallization front will be defragmented - on-the-fly. Defragmentation packs active cells closer into - main memory to reduce cache misses in subsequent evaluations - of the recrystallization front. + Target values at which recrystallized volume fraction the cache + for cells in the recrystallization front will be defragmented + on-the-fly. Defragmentation packs active cells closer into + main memory to reduce cache misses in subsequent evaluations + of the recrystallization front. - + @@ -682,20 +707,20 @@ like showing a r(t) plot--> - Perform a statistical analyses of the results as it was proposed - by M. Kühbach (solitary unit model ensemble approach). + Perform a statistical analyses of the results as it was proposed + by M. Kühbach (solitary unit model ensemble approach). - How many independent cellular automaton domains - should be instantiated. + How many independent cellular automaton domains + should be instantiated. - Into how many time steps should the real time interval be discretized upon - during post-processing the results with the solitary unit modeling approach. + Into how many time steps should the real time interval be discretized upon + during post-processing the results with the solitary unit modeling approach. diff --git a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml index 39623718f8..2ee6fe2f72 100644 --- a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -26,64 +26,64 @@ inspect comments behind NXmicrostructure--> - The symbols used in the schema to specify e.g. dimensions of arrays + The symbols used in the schema to specify e.g. dimensions of arrays - The total number of summary statistic log entries + The total number of summary statistic log entries - Number of boundaries of the bounding box or primitive about the computational - domain + Number of boundaries of the bounding box or primitive about the computational + domain - Number of parameter required for chosen orientation parameterization + Number of parameter required for chosen orientation parameterization - Number of texture components identified + Number of texture components identified - Dimensionality + Dimensionality - Cardinality + Cardinality - Number of active cells in the (recrystallization) front + Number of active cells in the (recrystallization) front - Number of grains in the computer simulation + Number of grains in the computer simulation - Application definition for storing results of the SCORE cellular automata model. - - The SCORE cellular automata model for primary recrystallization is an example - of a typical materials engineering application used within the field of so-called - Integral Computational Materials Engineering (ICME) whereby one can simulate - the evolution of microstructures. - - Specifically the SCORE model can be used to simulate the growth of nuclei during - static recrystallization. The model is described in the literature: - - * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ - * `C. Haase et al. <https://doi.org/10.1016/j.actamat.2015.08.057>`_ - * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ + Application definition for storing results of the SCORE cellular automata model. + + The SCORE cellular automata model for primary recrystallization is an example + of a typical materials engineering application used within the field of so-called + Integral Computational Materials Engineering (ICME) whereby one can simulate + the evolution of microstructures. + + Specifically the SCORE model can be used to simulate the growth of nuclei during + static recrystallization. The model is described in the literature: + + * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ + * `C. Haase et al. <https://doi.org/10.1016/j.actamat.2015.08.057>`_ + * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ @@ -93,30 +93,40 @@ inspect comments behind NXmicrostructure--> - Simulation ID as an alias to refer to this simulation. + Simulation ID as an alias to refer to this simulation. + + + Configuration file with the parameterization of the + SCORE model that was used for this simulation. + + + + + - Discouraged free-text field to add further details to the computation. + Discouraged free-text field to add further details to the computation. - ISO 8601 time code with local time zone offset to UTC information - included when the simulation was started. + ISO 8601 time code with local time zone offset to UTC information + included when the simulation was started. - ISO 8601 time code with local time zone offset to UTC information - included when the simulation ended. + ISO 8601 time code with local time zone offset to UTC information + included when the simulation ended. + - Name of the program with which the simulation was performed. + Name of the program with which the simulation was performed. @@ -124,9 +134,9 @@ inspect comments behind NXmicrostructure--> - Programs and libraries representing the computational environment + Programs and libraries representing the computational environment - + @@ -195,61 +205,64 @@ inspect comments behind NXmicrostructure--> - + - A tight bounding box or sphere or bounding primitive about the grid. + A tight bounding box or sphere or bounding primitive about the grid. +https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron_set because a parallelepiped--> - How many distinct boundaries are distinguished? - Most grids discretize a cubic or cuboidal region. In this case - six sides can be distinguished, each making an own boundary. + How many distinct boundaries are distinguished? + Most grids discretize a cubic or cuboidal region. In this case + six sides can be distinguished, each making an own boundary. - The boundary conditions for each boundary: - - 0 - undefined - 1 - open - 2 - periodic - 3 - mirror - 4 - von Neumann - 5 - Dirichlet + The boundary conditions for each boundary: + + * 0 - undefined + * 1 - open + * 2 - periodic + * 3 - mirror + * 4 - von Neumann + * 5 - Dirichlet - + - Name of the boundaries. Left, right, front, back, bottom, top, - The field must have as many entries as there are number_of_boundaries. + Name of the boundaries. Left, right, front, back, bottom, top, + The field must have as many entries as there are number_of_boundaries. - + - + - Documentation of the spatiotemporal evolution for each CA domain. + Documentation of the spatiotemporal evolution for each CA domain. + + SCORE is a hybrid parallelized code that can evolve multiple replicas + in parallel. The set of replicas is distributed across MPI processes. + Each such replica is then evolved via OpenMP multi-threading. - + - Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening for practical and performance reasons - during the simulation. Place used for storing descriptors from continuum mechanics - and thermodynamics at the scale of the entire ROI. + Summary quantities which are the result of some post-processing of the snapshot data + (averaging, integrating, interpolating) happening for practical and performance reasons + during the simulation. Place used for storing descriptors from continuum mechanics + and thermodynamics at the scale of the entire ROI. - Evolution of the recrystallized volume fraction over time. + Evolution of the recrystallized volume fraction over time. @@ -258,36 +271,36 @@ the typical lean summary statistics flattened--> - + - Evolution of the physical time not to be confused with wall-clock time or - profiling data. + Evolution of the physical time not to be confused with wall-clock time or + profiling data. - + - Iteration or increment counter. + Iteration or increment counter. - + - Evolution of the simulated temperature over time. + Evolution of the simulated temperature over time. - + - Recrystallized volume fraction. + Recrystallized volume fraction. - + @@ -295,7 +308,7 @@ the typical lean summary statistics flattened--> - Which type of stress. + Which type of stress. @@ -303,9 +316,9 @@ the typical lean summary statistics flattened--> - Applied external stress tensor on the ROI. + Applied external stress tensor on the ROI. - + @@ -315,14 +328,14 @@ the typical lean summary statistics flattened--> - Which type of strain. + Which type of strain. - Applied external strain tensor on the ROI. + Applied external strain tensor on the ROI. - + @@ -332,7 +345,7 @@ the typical lean summary statistics flattened--> - Which type of deformation gradient. + Which type of deformation gradient. @@ -340,9 +353,9 @@ the typical lean summary statistics flattened--> - Applied deformation gradient tensor on the ROI. + Applied deformation gradient tensor on the ROI. - + @@ -365,37 +378,37 @@ electrical_field(NXprocess): unit: NX_ANY dim: (n_summary_stats, 3, 3) the typically storage-costlier snapshot data--> - - + + - Iteration or increment counter. + Iteration or increment counter. - Simulated temperature for this snapshot. + Simulated temperature for this snapshot. - Current recrystallized volume fraction (taking fractional infections into - account). + Current recrystallized volume fraction (taking fractional infections into + account). - + - Target value for which a snapshot was requested for the recrystallized volume - fraction. + Target value for which a snapshot was requested for the recrystallized volume + fraction. - + - Grain identifier for each cell. + Grain identifier for each cell. - + @@ -403,9 +416,9 @@ the typically storage-costlier snapshot data--> - Identifier of the OpenMP thread which processed this part of the grid. + Identifier of the OpenMP thread which processed this part of the grid. - + @@ -413,128 +426,128 @@ the typically storage-costlier snapshot data--> - - - - - - + + + + + + - - - + + + - + - Volume of each grain accounting also for partially transformed cells. + Volume of each grain accounting also for partially transformed cells. - + - Bunge-Euler angle triplets for each grain. + Bunge-Euler angle triplets for each grain. - + - Current value for the dislocation density as a measure of the remaining - stored energy in assumed crystal defects inside each grain. + Current value for the dislocation density as a measure of the remaining + stored energy in assumed crystal defects inside each grain. - + - Is the grain deformed. + Is the grain deformed. - + - Is the grain recrystallized. + Is the grain recrystallized. - + - Details about those cells which in this time step represent the discrete - recrystallization front. + Details about those cells which in this time step represent the discrete + recrystallization front. - Which cells are currently in a halo region of threads. + Which cells are currently in a halo region of threads. - + - So-called mobility weight which is a scaling factor to control the - mobility of the grain boundary that is modelled sweeping cells that - make the discrete recrystallization front. + So-called mobility weight which is a scaling factor to control the + mobility of the grain boundary that is modelled sweeping cells that + make the discrete recrystallization front. - + - The x, y, z grid coordinates of each cell in the recrystallization front. + The x, y, z grid coordinates of each cell in the recrystallization front. - + - Grain identifier assigned to each cell in the recrystallization front. + Grain identifier assigned to each cell in the recrystallization front. - + - Grain identifier assigned to each nucleus which affected that cell in the - recrystallization front. + Grain identifier assigned to each nucleus which affected that cell in the + recrystallization front. - + - Identifier of the OpenMP thread processing each cell in the recrystallization - front. + Identifier of the OpenMP thread processing each cell in the recrystallization + front. - + - Hint about the direction from which the cell was infected. + Hint about the direction from which the cell was infected. - + diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index 348e7d5363..387c5857a1 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -46,6 +46,7 @@ NXmicrostructure_score_config(NXobject): exists: optional userID(NXuser): exists: [min, 0, max, infty] + nameType: partial sample(NXsample): exists: recommended dimensionality(NX_UINT): @@ -79,6 +80,7 @@ NXmicrostructure_score_config(NXobject): Programs and libraries representing the computational environment programID(NXprogram): exists: [min, 1, max, infty] + nameType: partial program(NX_CHAR): \@version(NX_CHAR): material(NXobject): @@ -100,9 +102,8 @@ NXmicrostructure_score_config(NXobject): # SecondOrderThermalExpCoeff melting_temperature(NX_FLOAT): doc: | - Melting temperature in degrees Celsius. + Melting temperature unit: NX_TEMPERATURE - deformation(NXobject): doc: | Details about the geometry and properties of the polycrystal that represents the @@ -129,7 +130,7 @@ NXmicrostructure_score_config(NXobject): Average spherical diameter when model is poisson_voronoi. unit: NX_LENGTH ensemble(NXobject): - # required for cuboidal, poisson + exists: optional doc: | Settings for instantiating properties of deformed grains when model is cuboidal or poisson. bunge_euler(NX_FLOAT): @@ -145,14 +146,14 @@ NXmicrostructure_score_config(NXobject): for the bunge_euler and stored_energy fields. unit: NX_ANY dim: (n_dg_ori,) - ebsd(NXserialized): + ebsd(NXnote): exists: optional doc: | - The EBSD dataset from which the initial microstructure is - instantiated if model is ebsd. - type(NX_CHAR): - path(NX_CHAR): + Settings for instantiating properties of deformed grains from an + EBSD orientation map when model is cuboidal or poisson. + file_name(NX_CHAR): algorithm(NX_CHAR): + enumeration: [sha256] checksum(NX_CHAR): stepsize(NX_FLOAT): doc: | @@ -160,6 +161,17 @@ NXmicrostructure_score_config(NXobject): or cube-shaped voxels respectively. unit: NX_LENGTH dim: (d,) + damask(NXnote): + exists: optional + doc: | + Settings for instantiating properties of deformed grains and nuclei when model is damask. + file_name(NX_CHAR): + doc: | + Name of the DREAM.3D HDF5 file that was instantiated from the + a previously performed DAMASK simulation. + algorithm(NX_CHAR): + enumeration: [sha256] + checksum(NX_CHAR): nucleation(NXobject): doc: | Phenomenological model according to which recrystallization nuclei @@ -172,15 +184,20 @@ NXmicrostructure_score_config(NXobject): * custom, implementation-specific * gb, nuclei placed at grain boundaries - enumeration: [csr, custom, gb] + enumeration: [csr, damask] incubation_time(NX_CHAR): doc: | According to which model will the nuclei start to grow. enumeration: [site_saturation] orientation(NX_CHAR): doc: | - According to which model will the nuclei get their orientation assigned. - enumeration: [sample_from_nucleus_euler] + According to which model will the nuclei get their orientation assigned: + + * ensemble, picking randomly one from ensemble/bunge_euler + * random, picking randomly on the SO3 + * damask, picking based on information provided in deformation/damask + + enumeration: [ensemble, random, damask] ensemble(NXobject): # required unless custom nucleation model doc: | diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml index 33ac04996e..1040112333 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml @@ -42,6 +42,13 @@ NXmicrostructure_score_results(NXobject): identifier_simulation(NX_UINT): doc: | Simulation ID as an alias to refer to this simulation. + config(NXnote): + doc: | + Configuration file with the parameterization of the + SCORE model that was used for this simulation. + file_name(NX_CHAR): + algorithm(NX_CHAR): + checksum(NX_CHAR): description(NX_CHAR): exists: optional doc: | @@ -57,6 +64,7 @@ NXmicrostructure_score_results(NXobject): included when the simulation ended. profiling(NXcs_profiling): exists: optional + # consider integrating content that is currently stored in ThreadProfiling.csv program1(NXprogram): doc: | Name of the program with which the simulation was performed. @@ -68,6 +76,7 @@ NXmicrostructure_score_results(NXobject): Programs and libraries representing the computational environment programID(NXprogram): exists: [min, 1, max, infty] + nameType: partial program(NX_CHAR): \@version(NX_CHAR): # rotation_conventions(NXrotation_conventions): @@ -105,11 +114,11 @@ NXmicrostructure_score_results(NXobject): cell_dimensions(NX_NUMBER): extent(NX_UINT): identifier_offset(NX_INT): - boundary(NXcg_polyhedron_set): + boundary(NXcg_hexahedron_set): doc: | A tight bounding box or sphere or bounding primitive about the grid. # a good example for a general bounding box description for such a grids of triclinic cells - # https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallelepiped + # https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron_set because a parallelepiped number_of_boundaries(NX_POSINT): unit: NX_UNITLESS doc: | @@ -121,12 +130,13 @@ NXmicrostructure_score_results(NXobject): doc: | The boundary conditions for each boundary: - 0 - undefined - 1 - open - 2 - periodic - 3 - mirror - 4 - von Neumann - 5 - Dirichlet + * 0 - undefined + * 1 - open + * 2 - periodic + * 3 - mirror + * 4 - von Neumann + * 5 - Dirichlet + dim: (6,) boundaries: doc: | @@ -135,9 +145,13 @@ NXmicrostructure_score_results(NXobject): dim: (6,) spatiotemporalID(NXobject): exists: [min, 1, max, infty] # max 1 in case of a single classical CA simulation, i.e. without solitary units + nameType: partial doc: | Documentation of the spatiotemporal evolution for each CA domain. - # static quantities for which no change is modelled + + SCORE is a hybrid parallelized code that can evolve multiple replicas + in parallel. The set of replicas is distributed across MPI processes. + Each such replica is then evolved via OpenMP multi-threading. # the typical lean summary statistics flattened summary_statistics(NXprocess): doc: | @@ -159,7 +173,7 @@ NXmicrostructure_score_results(NXobject): \@x_indices(NX_UINT): title(NX_CHAR): exists: recommended - time(NX_NUMBER): + time(NX_FLOAT): doc: | Evolution of the physical time not to be confused with wall-clock time or profiling data. unit: NX_TIME @@ -228,7 +242,8 @@ NXmicrostructure_score_results(NXobject): # the typically storage-costlier snapshot data microstructureID(NXmicrostructure): exists: [min, 1, max, infty] # always storing the starting configuration - time(NX_NUMBER): + nameType: partial + time(NX_FLOAT): iteration(NX_UINT): doc: | Iteration or increment counter. @@ -241,14 +256,14 @@ NXmicrostructure_score_results(NXobject): doc: | Current recrystallized volume fraction (taking fractional infections into account). unit: NX_DIMENSIONLESS - x_set(NX_NUMBER): + x_set(NX_FLOAT): doc: | Target value for which a snapshot was requested for the recrystallized volume fraction. unit: NX_DIMENSIONLESS # optional places to store the grid for instance if it changes grid(NXcg_grid): exists: recommended - identifier_grain(NX_UINT): + identifier_crystal(NX_UINT): exists: recommended doc: | Grain identifier for each cell. @@ -261,17 +276,23 @@ NXmicrostructure_score_results(NXobject): unit: NX_UNITLESS dim: (n_x, n_y, n_z) crystals(NXobject): - representation: + representation(NX_CHAR): exists: recommended number_of_crystals(NX_UINT): + exists: recommended number_of_phases(NX_UINT): + exists: recommended identifier_offset_crystal(NX_INT): + exists: recommended identifier_crystal(NX_INT): + exists: recommended dim: (n_grains,) identifier_offset_phase(NX_INT): + exists: recommended identifier_phase(NX_INT): + exists: recommended dim: (n_grains,) - volume(NX_NUMBER): + volume(NX_FLOAT): doc: | Volume of each grain accounting also for partially transformed cells. unit: NX_VOLUME From dc331be1c6d65970c025168dd7b60b059c0d25e1 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 24 Feb 2025 13:14:21 +0100 Subject: [PATCH 27/75] Updated NXem_calorimetry based on NIAC changes --- .../NXem_calorimetry.nxdl.xml | 320 ++++++++---------- .../nyaml/NXem_calorimetry.yaml | 263 +++++++------- 2 files changed, 269 insertions(+), 314 deletions(-) diff --git a/contributed_definitions/NXem_calorimetry.nxdl.xml b/contributed_definitions/NXem_calorimetry.nxdl.xml index 70b0ac3efa..b0b7d011df 100644 --- a/contributed_definitions/NXem_calorimetry.nxdl.xml +++ b/contributed_definitions/NXem_calorimetry.nxdl.xml @@ -3,7 +3,7 @@ - + - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - - Number of pattern + Number of diffraction pattern. - Number of azimuthal integration bins + Number of radial integration bins. - Number of coordinates along i axis. + Number of coordinates along i axis. - Number of coordinates along j axis. + Number of coordinates along j axis. - Application definition for minimal example in-situ calorimetry. - - What is the technique about. - - General context. - - Literature references. + Application definition for minimal example in-situ calorimetry. + + TODO: + + * What is the technique about. + * General context. + * Literature references. - - - - - - - - - - + + + Details about performance, profiling, etc. + + + + + + + + Name of the program whereby this config file was created. + + + + + + + + Programs and libraries representing the computational environment + + + + + + + + + + + + A qualifier whether the sample is a real one or a virtual one. + + + + + + + + + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. + + + + - - - + + + + Reference to the resource which stores acquired pattern from the + experiment or simulation that are analyzed in this workflow. + + Can refer to the original EMD or MRC files or the parsed NXem + in RDM e.g. NOMAD OASIS. + + + + - - + - Reference to the resource which stores acquired pattern from the experiment. - - Can refer to the original EMD or MRC files or the parsed NXem in RDM e.g. NOMAD OASIS. + Reference to the resource which stores actuator log file from the experiment. - - + - + - Reference to the resource which stores actuator log file from the experiment. + Configuration file that was used for parameterizing this analysis workflow. - - + - + - Assumptions and computations whereby timestamp data from the - detector used for collecting diffraction pattern and the actuator - (heating chip) were synchronized. + Assumptions and computations whereby timestamping data from + the detector and actuator (e.g. heating chip) were synchronized. - + - + + - Timestamp when pattern acquisition started. + Timestamp that is used for each diffraction pattern to correlate the results obtained from that pattern with associated actuator data. + ISO8601 with local time zone information if possible and as precise as practically possible. The indices follow the same order as + used for identifier_pattern. - + + + + Computation of the centre for each pattern using e.g. a Circular Hough + Transformation. + + + + - Timestamp when pattern acquisition ended. + Computed centre for each pattern. - + + - - - - - - - - - - - - - - + + Elliptical distortion correction as a step when computing the centre for + patterns. + - - - - - - - - - - - - - - - + + + + Computed centre for each pattern. + + + + + + - - + - Acquired diffraction pattern azimuthally integrated as a function of time. + Integrated diffraction pattern intensity as a function of radial distance from the centre + azimuthally integrated as a function of time. - - - - - - - + - - - - - - - - - - - - - - - - - - - - - Time since start of the in-situ experiment + Integrated intensity as a function of time and the radial distance from the + pattern centre. - - - - - - - - - - - - - - - - - - - - - Azimuthally integrated diffraction intensities corrected for background as a - function of time. - - - - - - - + + + identifier for each pattern. + - + + + Positions in reciprocal space. + - + - Time since start of the in-situ experiment + Time since start of the in-situ experiment @@ -280,20 +268,10 @@ no exists, i.e. assuming required - - - - - - + + - diff --git a/contributed_definitions/nyaml/NXem_calorimetry.yaml b/contributed_definitions/nyaml/NXem_calorimetry.yaml index b4f3deff57..5dd9ad2d92 100644 --- a/contributed_definitions/nyaml/NXem_calorimetry.yaml +++ b/contributed_definitions/nyaml/NXem_calorimetry.yaml @@ -2,11 +2,16 @@ category: application doc: | Application definition for minimal example in-situ calorimetry. - What is the technique about. + TODO: - General context. + * What is the technique about. + * General context. + * Literature references. - Literature references. +# intentionally axes are not named x, y, z to +# i) assure indices can be used for real and complex, +# ii) that people think hard about how their base vectors +# are aligned with what and how to name things symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -18,196 +23,168 @@ symbols: Number of coordinates along i axis. n_j: | Number of coordinates along j axis. -# intentionally axes are not named x, y, z to -# i) assure indices can be used for real and complex, -# ii) that people think hard about how their base vectors are aligned with what and how to name things - n_p: | - Number of pattern - n_f: | - Number of azimuthal integration bins type: group -# for a proper instance of a NeXus file also root level attributes should be set -# NeXus version, h5py version, again can be done later, we have tons of examples NXem_calorimetry(NXobject): - # by default for appdefs the value of the exists keyword is required unless it is explicitly specified differently (NXentry): exists: [min, 1, max, 1] definition(NX_CHAR): - \@version(NX_CHAR): - exists: optional enumeration: [NXem_calorimetry] - # take here inspiration from the dozens of example appdefs - # e.g. NXem, NXapm_paraprobe_* which shows how to add context - identifier(NXidentifier): - exists: optional - # a place whereby you can refer to your simulation run, etc - (NXuser): - exists: optional - # a place where you can give details about people who did it - (NXsample): + profiling(NXcs_profiling): exists: optional - # a place where you can tell e.g. based on which sample you build this simulation - (NXcite): + doc: | + Details about performance, profiling, etc. + start_time(NX_DATE_TIME): + exists: recommended + end_time(NX_DATE_TIME): + exists: recommended + total_elapsed_time(NX_NUMBER): + program1(NXprogram): + exists: recommended + doc: | + Name of the program whereby this config file was created. + program(NX_CHAR): + \@version(NX_CHAR): + environment(NXobject): + exists: recommended + doc: | + Programs and libraries representing the computational environment + programID(NXprogram): + exists: [min, 1, max, infty] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + userID(NXuser): exists: [min, 0, max, infty] + nameType: partial + sample(NXsample): + exists: recommended + type(NX_CHAR): + doc: | + A qualifier whether the sample is a real one or a virtual one. + enumeration: [experiment, simulation] + atom_types(NX_CHAR): + doc: | + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by parent_identifier or walk through + eventually deeply nested groups in data instances. + citeID(NXcite): + exists: [min, 0, max, infty] + nameType: partial # a place where to add citations for your work ... - (NXcoordinate_system_set): - diffraction_space(NXcoordinate_system): - (NXcoordinate_system): - exists: [min, 0, max, infty] - # a place where you can describe your coordinate system conventions - # hook-in NXem, alternatively inherit from NXem and just add - # add an actuator(NXactuator): - # doc: | - # DENSsolution heating chip. - # physical_quantity(NX_CHAR): - # # enumeration: [temperature] - # event_data for the actual sensor data - # alternatively - diffraction(NXsource): + diffraction_space(NXcoordinate_system): + exists: optional + diffraction(NXnote): doc: | - Reference to the resource which stores acquired pattern from the experiment. + Reference to the resource which stores acquired pattern from the + experiment or simulation that are analyzed in this workflow. - Can refer to the original EMD or MRC files or the parsed NXem in RDM e.g. NOMAD OASIS. - type(NX_CHAR): - path(NX_CHAR): + Can refer to the original EMD or MRC files or the parsed NXem + in RDM e.g. NOMAD OASIS. + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - actuator(NXserialized): + actuator(NXnote): doc: | Reference to the resource which stores actuator log file from the experiment. - type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + config(NXnote): + doc: | + Configuration file that was used for parameterizing this analysis workflow. + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - time_synchronization(NXprocess): + synchronization(NXprocess): doc: | - Assumptions and computations whereby timestamp data from the - detector used for collecting diffraction pattern and the actuator - (heating chip) were synchronized. + Assumptions and computations whereby timestamping data from + the detector and actuator (e.g. heating chip) were synchronized. sequence_index(NX_POSINT): - pattern_identifier(NX_UINT): + identifier_pattern(NX_UINT): dim: (n_p,) unit: NX_UNITLESS - start_time(NX_DATE_TIME): + # start_time(NX_DATE_TIME): + # doc: | + # Timestamp when pattern acquisition started. + # dim: (n_p,) + # end_time(NX_DATE_TIME): + # doc: | + # Timestamp when pattern acquisition ended. + # dim: (n_p,) + timestamp(NX_DATE_TIME): doc: | - Timestamp when pattern acquisition started. + Timestamp that is used for each diffraction pattern to correlate the results obtained from that pattern with associated actuator data. + ISO8601 with local time zone information if possible and as precise as practically possible. The indices follow the same order as + used for identifier_pattern. dim: (n_p,) - end_time(NX_DATE_TIME): - doc: | - Timestamp when pattern acquisition ended. - dim: (n_p,) - # alternatively only timestamp pattern_center(NXprocess): + doc: | + Computation of the centre for each pattern using e.g. a Circular Hough Transformation. sequence_index(NX_POSINT): - config(NXcollection): - result(NXcg_point_set): - # depends_on(NX_CHAR): - # doc: | - # Hint to help resolve in which coordinate system position values are defined. - position(NX_NUMBER): - unit: NX_LENGTH - dim: (n_p, 2) - #\@units: 1/nm + # NXcg_point + position(NX_FLOAT): + doc: | + Computed centre for each pattern. + unit: NX_LENGTH + dim: (n_p, 2) + #\@units: 1/nm distortion_correction(NXprocess): exists: optional + doc: | + Elliptical distortion correction as a step when computing the centre for patterns. sequence_index(NX_POSINT): - programID(NXprogram): - exists: optional - program(NX_CHAR): - \@version(NX_CHAR): - config(NXcollection): - result(NXcg_ellipsoid_set): - # depends_on(NX_CHAR): - center(NX_NUMBER): - unit: NX_LENGTH - dim: (n_p, 2) - #\@units: 1/nm - azimuthal_integration(NXprocess): - # no exists, i.e. assuming required + # TODO config(NXcollection): + # NXcg_ellipsoid + center(NX_NUMBER): + doc: | + Computed centre for each pattern. + unit: NX_LENGTH + dim: (n_p, 2) + #\@units: 1/nm + integration(NXprocess): doc: | - Acquired diffraction pattern azimuthally integrated as a function of time. + Integrated diffraction pattern intensity as a function of radial distance from the centre + azimuthally integrated as a function of time. sequence_index(NX_POSINT): - programID(NXprogram): - exists: optional - program(NX_CHAR): - \@version(NX_CHAR): - config(NXcollection): - # TODO integration parameter + # TODO config(NXcollection): result(NXdata): \@signal(NX_CHAR): - \@axes(NX_CHAR): # [axis_s] + \@axes(NX_CHAR): # [s] \@AXISNAME_indices(NX_CHAR): title(NX_CHAR): intensity(NX_FLOAT): - dim: (n_p, n_f) - unit: NX_UNITLESS - \@long_name(NX_CHAR): - axis_pattern_identifier(NX_UINT): - dim: (n_p,) - unit: NX_UNITLESS - \@long_name(NX_CHAR): - axis_s(NX_FLOAT): - dim: (n_f,) - unit: NX_ANY - #\@units: 1/nm - \@long_name(NX_CHAR): - axis_time(NX_FLOAT): doc: | - Time since start of the in-situ experiment - dim: (n_p,) - unit: NX_TIME - # \@units: s - background_subtraction(NXprocess): - exists: recommended - sequence_index(NX_POSINT): - programID(NXprogram): - program(NX_CHAR): - \@version(NX_CHAR): - config(NXcollection): - # TODO integration parameter - background(NXcollection): - # TODO e.g. could add parameter of functional forms for the background of each pattern - result(NXdata): - doc: | - Azimuthally integrated diffraction intensities corrected for background as a function of time. - \@signal(NX_CHAR): - \@axes(NX_CHAR): # [axis_time, axis_s] - \@AXISNAME_indices(NX_CHAR): - title(NX_CHAR): - intensity(NX_FLOAT): + Integrated intensity as a function of time and the radial distance from the pattern centre. dim: (n_p, n_f) unit: NX_UNITLESS \@long_name(NX_CHAR): - axis_pattern_identifier(NX_UINT): + identifier_pattern(NX_UINT): + doc: | + identifier for each pattern. dim: (n_p,) unit: NX_UNITLESS \@long_name(NX_CHAR): - axis_s(NX_FLOAT): + s(NX_FLOAT): + doc: | + Positions in reciprocal space. dim: (n_f,) unit: NX_ANY #\@units: 1/nm \@long_name(NX_CHAR): - axis_time(NX_FLOAT): + time(NX_FLOAT): doc: | Time since start of the in-situ experiment dim: (n_p,) unit: NX_TIME # \@units: s - # peak_fitting(NXpeak_fitting): - # exists: optional - # doc: | - # Background-corrected azimuthally integrated signals indexed for peaks. + # TODO e.g. could add parameter of functional forms for the background of each pattern # more NXprocess groups could follow only sky is the limit and your imagination and time devotion - profiling(NXcs_profiling): + background_subtraction(NXprocess): exists: optional - # possible place to store details about performance, profiling, etc. - current_working_directory(NX_CHAR): - exists: recommended - start_time(NX_DATE_TIME): - exists: recommended - end_time(NX_DATE_TIME): - exists: recommended - total_elapsed_time(NX_NUMBER): - # number_of_processes(NX_POSINT): - # number_of_threads(NX_POSINT): - # number_of_gpus(NX_POSINT): + sequence_index(NX_POSINT): From 724ad11f0da0bea8d0388655d8b5c0fc2f35fd56 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Wed, 26 Feb 2025 22:42:31 +0100 Subject: [PATCH 28/75] Edits on em_calorimetry --- .../NXem_calorimetry.nxdl.xml | 53 +++++++++++++------ .../nyaml/NXem_calorimetry.yaml | 52 +++++++++++++----- 2 files changed, 76 insertions(+), 29 deletions(-) diff --git a/contributed_definitions/NXem_calorimetry.nxdl.xml b/contributed_definitions/NXem_calorimetry.nxdl.xml index b0b7d011df..eea35eda2b 100644 --- a/contributed_definitions/NXem_calorimetry.nxdl.xml +++ b/contributed_definitions/NXem_calorimetry.nxdl.xml @@ -154,30 +154,47 @@ are aligned with what and how to name things--> the detector and actuator (e.g. heating chip) were synchronized. + + + ISO8601 with local time zone reference timestamp that tells + with which delta_time can be converted in timestamp. + The reference timestamp is defined as the time when the + actuator started acting on the sample. + + Time differences to this timestamp when correlated signals such + as diffraction pattern matching with a specific state of the sample + (e.g. obtained temperature via the actuator) are reported through + delta_time. + + - - + - Timestamp that is used for each diffraction pattern to correlate the results obtained from that pattern with associated actuator data. - ISO8601 with local time zone information if possible and as precise as practically possible. The indices follow the same order as - used for identifier_pattern. + Time difference to start_time. + + Collecting diffraction pattern also takes some time. + It is assumed that the acquisition time for each pattern is + substantial shorter than the time it takes the actuator to + cause a change in stimulus (e.g. temperature). + Computation of the centre for each pattern using e.g. a Circular Hough @@ -222,7 +239,13 @@ NXcg_ellipsoid--> - + + + The integrated intensities: + + * result_with_background + * result_without_background + @@ -238,9 +261,9 @@ NXcg_ellipsoid--> - + - identifier for each pattern. + Identifier for each pattern. diff --git a/contributed_definitions/nyaml/NXem_calorimetry.yaml b/contributed_definitions/nyaml/NXem_calorimetry.yaml index 5dd9ad2d92..752626534f 100644 --- a/contributed_definitions/nyaml/NXem_calorimetry.yaml +++ b/contributed_definitions/nyaml/NXem_calorimetry.yaml @@ -106,23 +106,39 @@ NXem_calorimetry(NXobject): Assumptions and computations whereby timestamping data from the detector and actuator (e.g. heating chip) were synchronized. sequence_index(NX_POSINT): + start_time(NX_DATE_TIME): + doc: | + ISO8601 with local time zone reference timestamp that tells + with which delta_time can be converted in timestamp. + The reference timestamp is defined as the time when the + actuator started acting on the sample. + + Time differences to this timestamp when correlated signals such + as diffraction pattern matching with a specific state of the sample + (e.g. obtained temperature via the actuator) are reported through + delta_time. identifier_pattern(NX_UINT): dim: (n_p,) unit: NX_UNITLESS - # start_time(NX_DATE_TIME): - # doc: | - # Timestamp when pattern acquisition started. - # dim: (n_p,) - # end_time(NX_DATE_TIME): - # doc: | - # Timestamp when pattern acquisition ended. - # dim: (n_p,) - timestamp(NX_DATE_TIME): + delta_time(NX_FLOAT): doc: | - Timestamp that is used for each diffraction pattern to correlate the results obtained from that pattern with associated actuator data. - ISO8601 with local time zone information if possible and as precise as practically possible. The indices follow the same order as - used for identifier_pattern. + Time difference to start_time. + + Collecting diffraction pattern also takes some time. + It is assumed that the acquisition time for each pattern is + substantial shorter than the time it takes the actuator to + cause a change in stimulus (e.g. temperature). + unit: NX_TIME dim: (n_p,) + # timestamp(NX_DATE_TIME): + # exists: optional + # doc: | + # Timestamp that is used for each diffraction pattern to correlate the results + # obtained from that pattern with associated actuator data. + # ISO8601 with local time zone information if possible and as precise as practically + # possible. The indices follow the same order as + # used for identifier_pattern. + # dim: (n_p,) pattern_center(NXprocess): doc: | Computation of the centre for each pattern using e.g. a Circular Hough Transformation. @@ -153,7 +169,14 @@ NXem_calorimetry(NXobject): azimuthally integrated as a function of time. sequence_index(NX_POSINT): # TODO config(NXcollection): - result(NXdata): + resultBACKGROUND(NXdata): + exists: [min, 0, max, 2] + doc: | + The integrated intensities: + + * result_with_background + * result_without_background + \@signal(NX_CHAR): \@axes(NX_CHAR): # [s] \@AXISNAME_indices(NX_CHAR): @@ -165,8 +188,9 @@ NXem_calorimetry(NXobject): unit: NX_UNITLESS \@long_name(NX_CHAR): identifier_pattern(NX_UINT): + exists: optional doc: | - identifier for each pattern. + Identifier for each pattern. dim: (n_p,) unit: NX_UNITLESS \@long_name(NX_CHAR): From 6277f774e33056ddb120d915f28c8e521a9c4c4d Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Fri, 7 Mar 2025 14:44:41 +0100 Subject: [PATCH 29/75] Reverting copyright end year back to 2024 --- applications/NXarpes.nxdl.xml | 2 +- base_classes/NXbeam.nxdl.xml | 2 +- base_classes/NXdata.nxdl.xml | 2 +- base_classes/NXdetector.nxdl.xml | 2 +- base_classes/NXentry.nxdl.xml | 2 +- base_classes/NXenvironment.nxdl.xml | 2 +- base_classes/NXinstrument.nxdl.xml | 2 +- base_classes/NXmonochromator.nxdl.xml | 2 +- base_classes/NXroot.nxdl.xml | 2 +- base_classes/NXsample.nxdl.xml | 2 +- base_classes/NXsample_component.nxdl.xml | 2 +- base_classes/NXsensor.nxdl.xml | 2 +- base_classes/NXsubentry.nxdl.xml | 2 +- base_classes/NXtransformations.nxdl.xml | 2 +- base_classes/NXuser.nxdl.xml | 2 +- 15 files changed, 15 insertions(+), 15 deletions(-) diff --git a/applications/NXarpes.nxdl.xml b/applications/NXarpes.nxdl.xml index e506cd3d29..8d17472ad3 100644 --- a/applications/NXarpes.nxdl.xml +++ b/applications/NXarpes.nxdl.xml @@ -3,7 +3,7 @@ - The geometries defined, made up of instances of :ref:`NXquadric` and :ref:`NXoff_geometry`. + The geometries defined, made up of e.g. instances of :ref:`NXquadric`, :ref:`NXoff_geometry`, + or instances of other base classes that define geometries. From 67b0adf5e502d72679e3155e36873ab3883133af Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 11:52:17 +0100 Subject: [PATCH 35/75] Syncing up with niac changes on fairmat PR #1422 which promotes apm to baseclasses and an accepted appdef in the standard --- .../NXapm.nxdl.xml | 0 .../NXapm_charge_state_analysis.nxdl.xml | 0 .../NXapm_ranging.nxdl.xml | 0 .../NXapm_reconstruction.nxdl.xml | 0 .../NXatom_set.nxdl.xml | 0 .../NXchemical_composition.nxdl.xml | 0 .../NXcircuit.nxdl.xml | 0 .../NXcoordinate_system.nxdl.xml | 0 .../NXcoordinate_system_set.nxdl.xml | 0 .../NXcs_computer.nxdl.xml | 0 .../NXcs_filter_boolean_mask.nxdl.xml | 0 .../NXcs_prng.nxdl.xml | 0 .../NXcs_profiling.nxdl.xml | 0 .../NXcs_profiling_event.nxdl.xml | 0 .../NXinstrument_apm.nxdl.xml | 0 .../NXion.nxdl.xml | 0 .../NXmanipulator.nxdl.xml | 0 .../NXpeak.nxdl.xml | 0 .../NXprogram.nxdl.xml | 0 .../NXpump.nxdl.xml | 0 .../NXrotation_set.nxdl.xml | 0 .../NXunit_cell.nxdl.xml | 0 contributed_definitions/NXstage_lab.nxdl.xml | 173 ------------------ 23 files changed, 173 deletions(-) rename {contributed_definitions => applications}/NXapm.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXapm_charge_state_analysis.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXapm_ranging.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXapm_reconstruction.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXatom_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXchemical_composition.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcircuit.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcoordinate_system.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcoordinate_system_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcs_computer.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcs_filter_boolean_mask.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcs_prng.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcs_profiling.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcs_profiling_event.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXinstrument_apm.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXion.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXmanipulator.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXpeak.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXprogram.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXpump.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXrotation_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXunit_cell.nxdl.xml (100%) delete mode 100644 contributed_definitions/NXstage_lab.nxdl.xml diff --git a/contributed_definitions/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml similarity index 100% rename from contributed_definitions/NXapm.nxdl.xml rename to applications/NXapm.nxdl.xml diff --git a/contributed_definitions/NXapm_charge_state_analysis.nxdl.xml b/base_classes/NXapm_charge_state_analysis.nxdl.xml similarity index 100% rename from contributed_definitions/NXapm_charge_state_analysis.nxdl.xml rename to base_classes/NXapm_charge_state_analysis.nxdl.xml diff --git a/contributed_definitions/NXapm_ranging.nxdl.xml b/base_classes/NXapm_ranging.nxdl.xml similarity index 100% rename from contributed_definitions/NXapm_ranging.nxdl.xml rename to base_classes/NXapm_ranging.nxdl.xml diff --git a/contributed_definitions/NXapm_reconstruction.nxdl.xml b/base_classes/NXapm_reconstruction.nxdl.xml similarity index 100% rename from contributed_definitions/NXapm_reconstruction.nxdl.xml rename to base_classes/NXapm_reconstruction.nxdl.xml diff --git a/contributed_definitions/NXatom_set.nxdl.xml b/base_classes/NXatom_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXatom_set.nxdl.xml rename to base_classes/NXatom_set.nxdl.xml diff --git a/contributed_definitions/NXchemical_composition.nxdl.xml b/base_classes/NXchemical_composition.nxdl.xml similarity index 100% rename from contributed_definitions/NXchemical_composition.nxdl.xml rename to base_classes/NXchemical_composition.nxdl.xml diff --git a/contributed_definitions/NXcircuit.nxdl.xml b/base_classes/NXcircuit.nxdl.xml similarity index 100% rename from contributed_definitions/NXcircuit.nxdl.xml rename to base_classes/NXcircuit.nxdl.xml diff --git a/contributed_definitions/NXcoordinate_system.nxdl.xml b/base_classes/NXcoordinate_system.nxdl.xml similarity index 100% rename from contributed_definitions/NXcoordinate_system.nxdl.xml rename to base_classes/NXcoordinate_system.nxdl.xml diff --git a/contributed_definitions/NXcoordinate_system_set.nxdl.xml b/base_classes/NXcoordinate_system_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcoordinate_system_set.nxdl.xml rename to base_classes/NXcoordinate_system_set.nxdl.xml diff --git a/contributed_definitions/NXcs_computer.nxdl.xml b/base_classes/NXcs_computer.nxdl.xml similarity index 100% rename from contributed_definitions/NXcs_computer.nxdl.xml rename to base_classes/NXcs_computer.nxdl.xml diff --git a/contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml b/base_classes/NXcs_filter_boolean_mask.nxdl.xml similarity index 100% rename from contributed_definitions/NXcs_filter_boolean_mask.nxdl.xml rename to base_classes/NXcs_filter_boolean_mask.nxdl.xml diff --git a/contributed_definitions/NXcs_prng.nxdl.xml b/base_classes/NXcs_prng.nxdl.xml similarity index 100% rename from contributed_definitions/NXcs_prng.nxdl.xml rename to base_classes/NXcs_prng.nxdl.xml diff --git a/contributed_definitions/NXcs_profiling.nxdl.xml b/base_classes/NXcs_profiling.nxdl.xml similarity index 100% rename from contributed_definitions/NXcs_profiling.nxdl.xml rename to base_classes/NXcs_profiling.nxdl.xml diff --git a/contributed_definitions/NXcs_profiling_event.nxdl.xml b/base_classes/NXcs_profiling_event.nxdl.xml similarity index 100% rename from contributed_definitions/NXcs_profiling_event.nxdl.xml rename to base_classes/NXcs_profiling_event.nxdl.xml diff --git a/contributed_definitions/NXinstrument_apm.nxdl.xml b/base_classes/NXinstrument_apm.nxdl.xml similarity index 100% rename from contributed_definitions/NXinstrument_apm.nxdl.xml rename to base_classes/NXinstrument_apm.nxdl.xml diff --git a/contributed_definitions/NXion.nxdl.xml b/base_classes/NXion.nxdl.xml similarity index 100% rename from contributed_definitions/NXion.nxdl.xml rename to base_classes/NXion.nxdl.xml diff --git a/contributed_definitions/NXmanipulator.nxdl.xml b/base_classes/NXmanipulator.nxdl.xml similarity index 100% rename from contributed_definitions/NXmanipulator.nxdl.xml rename to base_classes/NXmanipulator.nxdl.xml diff --git a/contributed_definitions/NXpeak.nxdl.xml b/base_classes/NXpeak.nxdl.xml similarity index 100% rename from contributed_definitions/NXpeak.nxdl.xml rename to base_classes/NXpeak.nxdl.xml diff --git a/contributed_definitions/NXprogram.nxdl.xml b/base_classes/NXprogram.nxdl.xml similarity index 100% rename from contributed_definitions/NXprogram.nxdl.xml rename to base_classes/NXprogram.nxdl.xml diff --git a/contributed_definitions/NXpump.nxdl.xml b/base_classes/NXpump.nxdl.xml similarity index 100% rename from contributed_definitions/NXpump.nxdl.xml rename to base_classes/NXpump.nxdl.xml diff --git a/contributed_definitions/NXrotation_set.nxdl.xml b/base_classes/NXrotation_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXrotation_set.nxdl.xml rename to base_classes/NXrotation_set.nxdl.xml diff --git a/contributed_definitions/NXunit_cell.nxdl.xml b/base_classes/NXunit_cell.nxdl.xml similarity index 100% rename from contributed_definitions/NXunit_cell.nxdl.xml rename to base_classes/NXunit_cell.nxdl.xml diff --git a/contributed_definitions/NXstage_lab.nxdl.xml b/contributed_definitions/NXstage_lab.nxdl.xml deleted file mode 100644 index 296db4ca7b..0000000000 --- a/contributed_definitions/NXstage_lab.nxdl.xml +++ /dev/null @@ -1,173 +0,0 @@ - - - - - - Base class for a stage (lab) used to hold, orient, and prepare a specimen. - - Modern stages are multi-functional devices. Stages provide a controlled - environment around the specimen. Stages enable experimentalists to apply - controlled external stimuli on the specimen. A stage_lab is a multi-purpose - /-functional tool that is constructed from multiple actuators, sensors, - and other components. - - With such stages comes the need for storing various (meta)data - that are generated while working and modifying the sample. - - Modern stages realize a hierarchy of components. Two examples are given to help - clarify how :ref:`NXstage_lab` instances should be used: Take a specimen that is - mounted on a multi-axial tilt rotation holder. This holder is fixed in the - support unit which connects the holder to the rest of the instrument. - Evidently different components are all considerable as to represent instances - of stages. - - In another example, taken from atom probe microscopy, researchers may work - with wire samples which are clipped into a larger fixing unit to enable - careful specimen handling. Alternatively, a microtip is a silicon post - upon which e.g. an atom probe specimen is mounted. - Multiple microtips are grouped into a microtip array to conveniently enable - loading of multiple specimens into the instrument with fewer operations. - That microtip array is fixed on a holder. Fixture units in atom probe are known - as stubs. Stubs in turn are positioned onto pucks. Pucks are then loaded onto - carousels. A carousel is a carrier unit with which eventually entire sets of - specimens can be moved in between parts of the microscope. All of these units - can be considered stage_lab instances. - - The :ref:`NXstage_lab` base class reflects this hierarchy. To cover for an as flexible - design of complex stages as possible, users should nest multiple instances of - :ref:`NXstage_lab` according to their needs to reflect the differences between what - they consider as the holder and what they consider is the stage. - The alias field can be used to specify the community jargon if necessary. - - However, a much clearer approach to reflect the hierarchy of all :ref:`NXstage_lab` - instances is postfix each instance named stage_lab with integers starting - from 1 as the top level unit. - In the microtip example one could thus use stage_lab1 for the microtip, - stage_lab2 for the microtip array, stage_lab3 holder, etc. - The depends_on keyword should be used to additional clarify the hierarchy - especially when users decide to not follow the above-mentioned postfixing - notation or when is not obvious from the postfixes which stage_lab is at - which level of the stage_lab hierarchy. - - Some examples for stage_labs in applications: - - * A nanoparticle on a copper grid. The copper grid is the holder. - The grid itself is fixed to a stage. - * An atom probe specimen fixed in a stub. In this case the stub can be - considered the holder, while the cryostat temperature control unit is - a component of the stage. - * Samples with arrays of specimens, like a microtip on a microtip array - is an example of an at least three-layer hierarchy commonly employed for - efficient sequential processing of atom probe experiments. - * With one entry of an application definition only one microtip should be - described. Therefore, the microtip is the specimen, - the array is the holder and the remaining mounting unit - that is attached to the cryo-controller is the stage. - * For in-situ experiments with e.g. chips with read-out electronics - as actuators, the chips are again placed in a larger unit. A typical - example are in-situ experiments using e.g. the tools of `Protochips <https://www.protochips.com>`_. - * Other examples are (quasi) in-situ experiments where experimentalists - anneal or deform the specimen via e.g. in-situ tensile testing machines - which are mounted on the specimen holder. - - For specific details and inspiration about stages in electron microscopes: - - * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ - * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ - * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ - * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) - * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) - * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) - * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ - - We are looking forward to suggestions from the scientists. - - - - Principal design of the stage. - - Exemplar terms could be side_entry, top_entry, - single_tilt, quick_change, multiple_specimen, - bulk_specimen, double_tilt, tilt_rotate, - heating_chip, atmosphere_chip, - electrical_biasing_chip, liquid_cell_chip - - - - - Free-text field to give a term how that a stage_lab at this level of the - stage_lab hierarchy is commonly referred to. Examples could be stub, - puck, carousel, microtip, clip, holder, etc. - - - - - The interpretation of this tilt should be specialized - and thus detailed via the application definition. - - - - - The interpretation of this tilt should be specialized - and thus detailed via the application definition. - - - - - The interpretation of this rotation should be specialized - and thus detailed via the application definition. - - - - - The interpretation of this position should be specialized - and thus detailed via the application definition. - - - - - - - - Voltage applied to the stage to decelerate electrons. - - - - - - - From b47ebd89791ab8ef06d68aabe89d6b80274ef961 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 12:30:31 +0100 Subject: [PATCH 36/75] Removal of classes for which the discussions with NIAC suggested their removal, and syncing of appdef NXapm with #1422 f719fe0e --- applications/NXapm.nxdl.xml | 172 +++++++++--------- contributed_definitions/NXchamber.nxdl.xml | 41 ----- .../NXchemical_process.nxdl.xml | 60 ------ contributed_definitions/NXidentifier.nxdl.xml | 49 ----- .../NXphysical_process.nxdl.xml | 61 ------- contributed_definitions/NXserialized.nxdl.xml | 74 -------- .../NXsingle_crystal.nxdl.xml | 72 -------- 7 files changed, 81 insertions(+), 448 deletions(-) delete mode 100644 contributed_definitions/NXchamber.nxdl.xml delete mode 100644 contributed_definitions/NXchemical_process.nxdl.xml delete mode 100644 contributed_definitions/NXidentifier.nxdl.xml delete mode 100644 contributed_definitions/NXphysical_process.nxdl.xml delete mode 100644 contributed_definitions/NXserialized.nxdl.xml delete mode 100644 contributed_definitions/NXsingle_crystal.nxdl.xml diff --git a/applications/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml index e175f33f5a..3c19739c01 100644 --- a/applications/NXapm.nxdl.xml +++ b/applications/NXapm.nxdl.xml @@ -81,7 +81,7 @@ which was used to generate this NeXus file instance. - + A collection of all programs and libraries which are considered relevant to understand with which software tools this NeXus file instance was @@ -104,11 +104,7 @@ - - - - - + @@ -708,7 +692,7 @@ but for M-TAP and Oxcart these pieces of information are available.--> pulse_identifier_offset(NX_INT): pulse_identifier(NX_INT):--> - + @@ -716,7 +700,7 @@ pulse_identifier(NX_INT):--> - + @@ -740,7 +724,7 @@ pulse_identifier(NX_INT):--> - + @@ -752,11 +736,17 @@ pulse_identifier(NX_INT):--> laser geometry at the moment has neither a worked out example nor any feedback from the community despite the work from B. Gault on laser atom probe was granted a Leibnitz award--> - - + + + + + - - + + + + + @@ -773,20 +763,20 @@ on laser atom probe was granted a Leibnitz award--> - + A region-of-interest analyzed either during or after the session for which specific processed data of the measured or simulated data are available. - + SEM or TEM image of the initial specimen (ideally taken prior data acquisition). - + @@ -814,17 +804,17 @@ the need for defining them again--> From these tuples hits are computed in a process called hit_finding. - + - + - - - + + + @@ -869,15 +859,15 @@ does not have to be exposed (although this clearly is against FAIR principles bu is does not have the authority to decide which portions of proprietary code have to be public we can only make recommendations--> - + - + - + @@ -965,14 +955,14 @@ pulse_identifier(NX_INT): at this point the original set of events p has been filtered down to p_out--> - + - + - + @@ -1021,14 +1011,14 @@ at this point the original set of events p has been filtered down to p_out--> positions for flight path differences, detector biases, and nonlinearities. - + - + - + @@ -1061,14 +1051,14 @@ by proprietary hardware with proprietary semantics - + - + - + @@ -1082,12 +1072,12 @@ results--> - + - + For LEAP and IVAS/APSuite-based analyses root file which stores the settings whereby an RHIT/HITS file can be used to regenerate the @@ -1097,11 +1087,11 @@ results--> group of the hit_finding section of this application definition. - + - + For LEAP and IVAS/APSuite-based analyses the resulting typically file with the reconstructed positions and (calibrated) mass-to-charge @@ -1115,7 +1105,7 @@ results--> management system. - + @@ -1131,7 +1121,7 @@ results--> - + @@ -1141,10 +1131,10 @@ results--> - + - + @@ -1175,23 +1165,23 @@ results--> - + - + The respective ranging definitions file RNG/RRNG/ENV/HDF5. - + - + @@ -1200,9 +1190,9 @@ results--> - + - + @@ -1219,7 +1209,7 @@ results--> - + @@ -1248,12 +1238,12 @@ NEW ISSUE: add parameters of the background model in an e.g. work of A. London et al.--> - + - + @@ -1285,14 +1275,14 @@ in an e.g. work of A. London et al.--> - + - + diff --git a/contributed_definitions/NXchamber.nxdl.xml b/contributed_definitions/NXchamber.nxdl.xml deleted file mode 100644 index f6cbac9137..0000000000 --- a/contributed_definitions/NXchamber.nxdl.xml +++ /dev/null @@ -1,41 +0,0 @@ - - - - - - Base class for a chamber in an instrument that stores real or simulated objects. - - - - Given name for the chamber of this component e.g. analysis chamber - or buffer chamber, load-lock chamber, microscope column, glove box. - - - - - Free-text field for describing details about the chamber. - For example out of which material was the chamber built. - - - - diff --git a/contributed_definitions/NXchemical_process.nxdl.xml b/contributed_definitions/NXchemical_process.nxdl.xml deleted file mode 100644 index 437fcf0b6a..0000000000 --- a/contributed_definitions/NXchemical_process.nxdl.xml +++ /dev/null @@ -1,60 +0,0 @@ - - - - - - A planned or unplanned process which results in chemical changes (i.e., changes in the chemical bonds) in a specified material. - - Examples include any chemical reactions (addition, subtraction, replacement, ...). - - - - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process started. - - - - - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process ended. - - - - - Short description of the chemical process. - - - - - Method by which this process was performed. - - - - - This can be any data or other descriptor acquired during the chemical process - (NXnote allows to add pictures, audio, movies). Alternatively, a - reference to the location or a unique identifier or other metadata file. In the - case these are not available, free-text description. - - - diff --git a/contributed_definitions/NXidentifier.nxdl.xml b/contributed_definitions/NXidentifier.nxdl.xml deleted file mode 100644 index ce05800f9e..0000000000 --- a/contributed_definitions/NXidentifier.nxdl.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - An identifier for a (persistent) resource, e.g., a DOI or orcid. - - - - The service by which the resource can be resolved. - - Examples: doi, urn, hdl, purl, orcid, iso, url - - - - - The unique code, IRI or hash to resolve this reference. - Typically, this is stated by the service which is considered a complete - identifier, e.g., for a DOI it's something of the form `10.1107/S1600576714027575` - or `https://doi.org/10.1107/S1600576714027575`, which are both resolvable. - - - - - True if the identifier is persistent (i.e., unique and available indefinitely), - False otherwise. - - - diff --git a/contributed_definitions/NXphysical_process.nxdl.xml b/contributed_definitions/NXphysical_process.nxdl.xml deleted file mode 100644 index d422e516c6..0000000000 --- a/contributed_definitions/NXphysical_process.nxdl.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - - - A planned or unplanned process which results in physical changes in a specified material. - - A physical change involve changes only in intermolecular forces, not in the chemical bonds. - Examples include sample preparation, material transformation, or (partially) destructive measurements. - - - - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process started. - - - - - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process ended. - - - - - Short description of the activity. - - - - - Method by which this process was performed. - - - - - This can be any data or other descriptor acquired during the physical process - (NXnote allows to add pictures, audio, movies). Alternatively, a - reference to the location or a unique identifier or other metadata file. In the - case these are not available, free-text description. - - - diff --git a/contributed_definitions/NXserialized.nxdl.xml b/contributed_definitions/NXserialized.nxdl.xml deleted file mode 100644 index fda0769482..0000000000 --- a/contributed_definitions/NXserialized.nxdl.xml +++ /dev/null @@ -1,74 +0,0 @@ - - - - - - Metadata to a set of pieces of information of a resource that has been serialized. - - A typical use case is the documentation of the source (file) or database (entry) - from which pieces of information have been extracted for consumption in e.g. a - research data management system (RDMS). This may be for reasons of enabling - services such as providing access to normalized information for which reading - again from the resource may not be desired, possibe, or feasible. - - Possible reasons could be the extraction of specific information for caching, - performance reasons, or re-evaluate given pieces of information based on other - views and interaction patterns with the data where information has been formatted - differently by tools than how these pieces of information were originally - serialized. - - - - Answers into what resource the information was serialized. - - - - - - - - - Path to the resource. - - E.g. the name of a file or its absolute or relative path, or the - identifier to a resource in another database. - - - - - Value of the hash that is obtained when running algorithm - on the content of the resource referred to by path. - - - - - Name of the algorithm whereby the checksum was computed. - - - - - - Extracted file containing the serialized information. - - - diff --git a/contributed_definitions/NXsingle_crystal.nxdl.xml b/contributed_definitions/NXsingle_crystal.nxdl.xml deleted file mode 100644 index 44f6e92c30..0000000000 --- a/contributed_definitions/NXsingle_crystal.nxdl.xml +++ /dev/null @@ -1,72 +0,0 @@ - - - - - - Description of a single crystal material or a single crystalline phase in a material. - - There is the option of using Busing-Levy convention (as orginally designed in NXsample) - or using a more detailed description with NXrotation_set. - - - - This will follow the Busing-Levy convention: - W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 - - - - - - - - Orientation matrix of single crystal sample using Busing-Levy convention: - W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 - - - - - - - - - UB matrix of single crystal sample using Busing-Levy convention: - W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464. This is - the multiplication of the orientation_matrix, given above, - with the :math:`B` matrix which can be derived from the lattice constants. - - - - - - - - - Detailed description of single crystal orientation and misorientation. - - - - - Unit cell of the single crystal. - - - From 3d550ac06e2ac2cab83a3f2393c90741e01c94c5 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 12:48:31 +0100 Subject: [PATCH 37/75] Syncing up base classes for apm with #1422 f719fe0e --- base_classes/NXapm_ranging.nxdl.xml | 4 +- base_classes/NXapm_reconstruction.nxdl.xml | 4 +- base_classes/NXatom.nxdl.xml | 133 ++++++++ base_classes/NXatom_set.nxdl.xml | 158 ---------- base_classes/NXchemical_composition.nxdl.xml | 4 +- base_classes/NXcircuit.nxdl.xml | 148 ++++----- base_classes/NXcoordinate_system_set.nxdl.xml | 287 +++++++++--------- 7 files changed, 341 insertions(+), 397 deletions(-) create mode 100644 base_classes/NXatom.nxdl.xml delete mode 100644 base_classes/NXatom_set.nxdl.xml diff --git a/base_classes/NXapm_ranging.nxdl.xml b/base_classes/NXapm_ranging.nxdl.xml index 8382de58f9..e57c5ae9fd 100644 --- a/base_classes/NXapm_ranging.nxdl.xml +++ b/base_classes/NXapm_ranging.nxdl.xml @@ -3,7 +3,7 @@ + + + Base class for documenting a set of atoms. + + Atoms in the set may be bonded. + The set may have a net charge to represent + an ion. Ions can be molecular ions. + + + + Given name for the set. + + This field could for example be used in the research field + of atom probe tomography for storing a standardized + human-readable name of the element or (molecular) ion + like such as Al +++ or 12C +. + + + + + Identifier used to refer to if the set of atoms represents a substance. + + + + + + + + Signed net (partial) charge of the (molecular) ion. + + Different methods for computing charge are in use. + Care needs to be exercised with respect to the integration. + `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. + + + + + Charge reported in multiples of the charge of an electron. + + For research using atom probe tomography the value should be set to + zero if the charge_state is unknown and irrecoverable. This can happen + when classical ranging definition files in formats like RNG, RRNG are used. + These file formats do not document the charge state explicitly but only + the number of atoms of each element per molecular ion surplus the + respective mass-to-charge-state-ratio interval. + + Details on ranging definition files in the literature are `M. K. Miller <https://doi.org/10.1002/sia.1719>`_. + + + + + Assumed volume affected by the set of atoms. + + Neither individual atoms nor a set of cluster of these have a volume + that is unique as a some cut-off criterion is required. + + + + + + Identifier for each atom at locations as detailed by position. + + + + + + + + Nuclide information for each atom at locations as detailed by position. + + One `approach <https://doi.org/10.1017/S1431927621012241>`_ for storing nuclide information efficiently + is via hashing with the following formula + + :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` + + the number of protons and :math:`N` the number of neutrons + of each nuclide given as 8-bit unsigned integer values. + + + + + + + + Position of each atom. + + + + + + + + Path to a reference frame in which positions are defined + to resolve ambiguity when the reference frame is different + to the NeXus default reference frame (McStas). + + + + + + Relative occupancy of the atom position. + + This field is useful for specifying the atomic motif in + instances of :ref:`NXunit_cell`. + + + + + + diff --git a/base_classes/NXatom_set.nxdl.xml b/base_classes/NXatom_set.nxdl.xml deleted file mode 100644 index c3e2cae5d4..0000000000 --- a/base_classes/NXatom_set.nxdl.xml +++ /dev/null @@ -1,158 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). - - - - - Number of mass-to-charge-state-ratio range intervals for ion type. - - - - - Base class for documenting a set of atoms. - - - - A unique identifier whereby such an ion can be referred to - via the service offered as described in identifier_type. - - - - - How can the identifier be resolved? - - - - - - - - Ion type (ion species) identifier. - - The identifier zero is reserved for the special unknown ion type. - - - - - Vector of nuclide hash values. - - Individual hash values :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - encode the number of protons :math:`Z` and the number of neutrons :math:`N` - of each nuclide respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - - The array is sorted in decreasing order. For the rationale behind this see `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. - The first column specifies the nuclide mass number, i.e. using the hashvalues - from the isotope_vector this is :math:`Z + N` or 0. The value 0 documents that no - isotope-specific information about the element encoded is relevant. - The second row specifies the number of protons :math:`Z` or 0. - The value 0 in this case documents a placeholder or that no element-specific - information is relevant. - Taking a carbon-14 nuclide as an example the mass number is 14. - That is encoded as a value pair (14, 6) as one row of the table. - - Therefore, this notation is the typical superscribed nuclide mass number - and subscripted number of protons element notation e.g. :math:`^{14}C`. - The array is stored matching the order of nuclide_hash. - - - - - - - - - - Assumed volume of the ion. - - In atom probe microscopy this field can be used to store the reconstructed - volume per ion (average) which is typically stored alongside ranging - definitions. - - - - - Charge of the ion. - - - - - Signed charge state if the atoms form an ion reported in multiples of electron charge. - - In the example of atom probe microscopy, only positive values will be measured - as the ions are accelerated by a negatively signed bias electric field. - In the case that the charge state is not explicitly recoverable, the value should - be set to zero. - - In atom probe microscopy this is for example the case when using - classical ranging definition files in formats like RNG, RRNG. - These file formats do not document the charge state explicitly - but the number of atoms of each element per molecular ion - surplus the mass-to-charge-state-ratio interval. - Details on ranging definition files can be found in the literature: - `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ - - - - - Human-readable name (e.g. Al +++) of the atom set, the atom group, or ion type. - The string should consists of UTF-8 characters, ideally using LaTeX - notation to specify the isotopes, ions, and charge state. - Examples are 12C + or Al +++. - - To ease automated parsing, isotope_vector should be the - preferred machine-readable information used. - - - - - Associated lower (mqmin) and upper (mqmax) bounds of the - mass-to-charge-state ratio interval(s) [mqmin, mqmax] - (boundaries inclusive). This field is primarily of interest - for documenting :ref:`NXprocess` steps of indexing a - ToF/mass-to-charge state histogram. - - - - - - - diff --git a/base_classes/NXchemical_composition.nxdl.xml b/base_classes/NXchemical_composition.nxdl.xml index fd92848709..c3962c9b7c 100644 --- a/base_classes/NXchemical_composition.nxdl.xml +++ b/base_classes/NXchemical_composition.nxdl.xml @@ -3,7 +3,7 @@ - - - - Constant to be used in the definition: the number of channels of the - circuit board. - - - - number of channels of the circuit board. - - - + - Application definition for circuit devices. - - Electronic circuits are hardware components connecting several electronic components to achieve - specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. + Base class for circuit devices. - Hardware where the circuit is implanted; includes information about the hardware manufacturers and - type (e.g. part number) - All the elements below may be single numbers of an array of values with length N_channel - describing multiple input and output channels. + Hardware type used in circuit, includes hardware manufacturers and type - - - List of components used in the circuit, e.g., resistors, capacitors, transistors or any - other complex components. - - - - - Description of how components are interconnected, including connection points - and wiring. - - - - - Details of the power source for the circuit, including voltage and current - ratings. - - - + - Type of signal (input signal) the circuit is designed to handle, e.g., analog, - digital, mixed-signal. + The tunneling current between tip and sample after application of bias voltage. - - + - The operating frequency of the circuit, see also bandwidth below, which is possibly - centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth - amplifier at low, audio frequencies 1 - 20,000 Hz) + Calibration of the current measurement (A/V). - - + - Input impedance of the circuit. + Offset of the current measurement. - + - Output impedance of the circuit. + Proportional relationship between the probe output voltage and the actual + tunneling current when measuring the tunneling current. - + - Gain of the circuit, if applicable, usually all instruments have a gain which might be - important or not. + The scan channels are selected by users (in scan contronaller). - + - RMS noise level (in current or voltage) in the circuit in voltage or current. + The bandwitdh of the Hardware and/or Software - + - The bandwidth of the frequency response of the circuit. + (Signals Periods) The Signals Period is the rate at which the signals are + transferred to the host computer running the control software. This is usually + lower by a factor of 10 than the sampling rate, because an internal oversampling + of the signal is done on the real time engine. You can reduce the oversampling + down to 1 in order to resolve higher frequencies in the Spectrum Analyzer. - + - Operating temperature range of the circuit. + Update rate for several processes like History Graph, Auto-Approach, and for + many Programming Interface functions. This is usually set to 20 ms. All + additional timings (7-9) can only be integer multiples of this value. They can + be set to different values, but the actual timing value will be coerced to a + multiple of the Acquisition Period. - - - Calibration data for the circuit. - - - + - Offset value for current or voltage. + Update rate of animated graphical indicators. These are e.g. some graphs & + sliders. A reasonable value is 40 ms (25 updates per second). Increase this + period to reduce the processor load for the graphical user interface, especially + on slow computers. This value is purely a user interface update rate and does + not affect measurements in any way. - + - Number of output channels collected to this circuit. Most probably N_channel. + Update rate of digital indicators, e.g. the numbers displayed besides each + slider. Here, 3 updates per second, or 300 ms is enough. This value is purely a + user interface update rate and does not affect measurements in any way. - + - Type of output signal, e.g., voltage, current, digital. + The Measurements period is the integration time for precise measurements + (averaging over specified period), mostly used in sweep modules. Examples are + recording of a force-distance curve or a resonance of a cantilever. For fast + measurements with small steps, a value of 40 ms may be reasonable. For normal + use, 300-500 ms is a good value, but for recording a resonance of a high-Q + cantilever, values of several seconds might be necessary. Usually this parameter + doesn’t need to be set from this module; the sweep modules will set this value + according to the sweep timings. - + - Power consumption of the circuit per unit time. + Number of output channels - + - Status indicators for the circuit, e.g., LEDs, display readouts. + The user output in each monitor mode. - + - Protection features built into the circuit, e.g., overvoltage protection, - thermal shutdown. + The values for each output channel. - + - Updated rate for several processes using the input signal, e.g., History Graph, the circuit - uses for any such process. + User outputs whose name can be modified in the corresponding module. - The rate at which the signal changes when ramping from the starting - value. + The rate at which the one of the signal changes when ramping to the starting + point. (V/s) diff --git a/base_classes/NXcoordinate_system_set.nxdl.xml b/base_classes/NXcoordinate_system_set.nxdl.xml index a842d257d2..4fd441238e 100644 --- a/base_classes/NXcoordinate_system_set.nxdl.xml +++ b/base_classes/NXcoordinate_system_set.nxdl.xml @@ -26,132 +26,129 @@ express conventions explicitly and understandable use depends_on field - not attribute - to point to conventions used--> - Base class to hold different coordinate systems and representation conversions. - - How many nodes of type :ref:`NXcoordinate_system_set` should be used in an application definition? - - * 0; if there is no instance of :ref:`NXcoordinate_system_set` and therein or elsewhere across - the application definition, an instance of NXcoordinate_system is defined, - the default NeXus `McStas <https://mailman2.mcstas.org/pipermail/mcstas-users/2021q2/001431.html>`_ - coordinate system is assumed. This makes :ref:`NXcoordinate_system_set` and - NXcoordinate_system base classes backwards compatible to older - NeXus conventions and classes. - * 1; if only one :ref:`NXcoordinate_system_set` is defined, it should be placed - as high up in the node hierarchy (ideally right below an instance of NXentry) - of the application definition tree as possible. - This :ref:`NXcoordinate_system_set` should define at least one NXcoordinate_system - instance. This shall be named such that it is clear how this coordinate system is - typically referred to in a community. For the NeXus `McStas coordinate system, it is - advised to call it mcstas for the sake of improved clarity. - Additional NXcoordinate_system instances should be specified if possible in that same - :ref:`NXcoordinate_system_set` instead of cluttering them across the tree. - - If this is the case, it is assumed that the NXcoordinate_system_members - overwrite the NeXus default McStas coordinate system, i.e. users can thereby - conveniently and explicitly specify the coordinate system(s) that - they wish to use. - - Users are encouraged to write also explicit and clean depends_on fields in - all groups that encode information about where the interpretation of coordinate - systems is relevant. If these depends_on hints are not provided, it is - automatically assumed that all children (to arbitrary depth) - of that branch and sub-branches below the one in which that - :ref:`NXcoordinate_system_set` is defined use either the only NXcoordinate_system_set - instance in that set or the application definition is considered - underconstrained which should at all costs be avoided and in which case - again McStas is assumed. - * 2 and more; as soon as more than one :ref:`NXcoordinate_system_set` is specified - somewhere in the tree, different interpretations are possible as to which - of these coordinate system sets and instances apply or take preference. - We realize that such ambiguities should at all costs be avoided. - However, the opportunity for multiple sets and their instances enables to - have branch-specific coordinate system conventions which could especially - be useful for deep classes where multiple scientific methods are combined or - cases where having a definition of global translation and conversion tables - how to convert between representations in different coordinate systems - is not desired or available for now. - We argue that having 2 or more :ref:`NXcoordinate_system_set` instances and respective - NXcoordinate_system instances makes the interpretation eventually unnecessary - complicated. Instead, developers of application definitions should always try - to work for clarity and thus use only one top-level coordinate system set. - - For these reasons we conclude that the option with one top-level - :ref:`NXcoordinate_system_set` instance is the preferred choice. - - McStas is used if neither an instance of :ref:`NXcoordinate_system_set` nor an instance - of NXcoordinate_system is specified. However, even in this case it is better - to be explicit like for every other coordinate system definition to support - users with interpreting the content and logic behind every instance of the tree. - - How to store coordinate systems inside :ref:`NXcoordinate_system_set`? - Individual coordinate systems should be specified as members of the - :ref:`NXcoordinate_system_set` instance using instances of NXcoordinate_system. - - How many individual instances of NXcoordinate_system to allow within one - instance of :ref:`NXcoordinate_system_set`? - - * 0; This case should be avoided for the sake of clarity but this case could - mean the authors of the definition meant that McStas is used. We conclude, - McStas is used in this case. - * 1; Like above-mentioned this case has the advantage that it is explicit - and faces no ambiguities. However, in reality typically multiple - coordinate systems have to be mastered especially for complex - multi-signal modality experiments. - * 2 or more; If this case is realized, the best practice is that in every - case where a coordinate system should be referred to the respective class - has a depends_on field which resolves the possible ambiguities which specific - coordinate systems is referred to. The benefit of this explicit and clear - specifying of the coordinate system used in every case is that especially - in combination with having coordinate systems inside deeper branches - makes up for a very versatile, backwards compatible, but powerful system - to express different types of coordinate systems using NeXus. In the case - of two or more instances of NXcoordinate_system in one :ref:`NXcoordinate_system_set`, - it is also advised to specify the relationship between the two coordinate systems by - using the (NXtransformations) group within NXcoordinate_system. - - In effect, 1 should be the preferred choice. However, if more than one coordinate - system is defined for practical purposes, explicit depends_on fields should - always guide the user for each group and field which of the coordinate system - one refers to. + Base class to hold different coordinate systems and representation conversions. + + How many nodes of type :ref:`NXcoordinate_system_set` should be used in an application definition? + + * 0; if there is no instance of :ref:`NXcoordinate_system_set` and therein or elsewhere across + the application definition, an instance of NXcoordinate_system is defined, + the default NeXus `McStas <https://mailman2.mcstas.org/pipermail/mcstas-users/2021q2/001431.html>`_ + coordinate system is assumed. This makes :ref:`NXcoordinate_system_set` and + NXcoordinate_system base classes backwards compatible to older + NeXus conventions and classes. + * 1; if only one :ref:`NXcoordinate_system_set` is defined, it should be placed + as high up in the node hierarchy (ideally right below an instance of NXentry) + of the application definition tree as possible. + This :ref:`NXcoordinate_system_set` should define at least one NXcoordinate_system + instance. This shall be named such that it is clear how this coordinate system is + typically referred to in a community. For the NeXus `McStas coordinate system, it is + advised to call it mcstas for the sake of improved clarity. + Additional NXcoordinate_system instances should be specified if possible in that same + :ref:`NXcoordinate_system_set` instead of cluttering them across the tree. + + If this is the case, it is assumed that the NXcoordinate_system_members + overwrite the NeXus default McStas coordinate system, i.e. users can thereby + conveniently and explicitly specify the coordinate system(s) that + they wish to use. + + Users are encouraged to write also explicit and clean depends_on fields in + all groups that encode information about where the interpretation of coordinate + systems is relevant. If these depends_on hints are not provided, it is + automatically assumed that all children (to arbitrary depth) + of that branch and sub-branches below the one in which that + :ref:`NXcoordinate_system_set` is defined use either the only NXcoordinate_system_set + instance in that set or the application definition is considered + underconstrained which should at all costs be avoided and in which case + again McStas is assumed. + * 2 and more; as soon as more than one :ref:`NXcoordinate_system_set` is specified + somewhere in the tree, different interpretations are possible as to which + of these coordinate system sets and instances apply or take preference. + We realize that such ambiguities should at all costs be avoided. + However, the opportunity for multiple sets and their instances enables to + have branch-specific coordinate system conventions which could especially + be useful for deep classes where multiple scientific methods are combined or + cases where having a definition of global translation and conversion tables + how to convert between representations in different coordinate systems + is not desired or available for now. + We argue that having 2 or more :ref:`NXcoordinate_system_set` instances and respective + NXcoordinate_system instances makes the interpretation eventually unnecessary + complicated. Instead, developers of application definitions should always try + to work for clarity and thus use only one top-level coordinate system set. + + For these reasons we conclude that the option with one top-level + :ref:`NXcoordinate_system_set` instance is the preferred choice. + + McStas is used if neither an instance of :ref:`NXcoordinate_system_set` nor an instance + of NXcoordinate_system is specified. However, even in this case it is better + to be explicit like for every other coordinate system definition to support + users with interpreting the content and logic behind every instance of the tree. + + How to store coordinate systems inside :ref:`NXcoordinate_system_set`? + Individual coordinate systems should be specified as members of the + :ref:`NXcoordinate_system_set` instance using instances of NXcoordinate_system. + + How many individual instances of NXcoordinate_system to allow within one + instance of :ref:`NXcoordinate_system_set`? + + * 0; This case should be avoided for the sake of clarity but this case could + mean the authors of the definition meant that McStas is used. We conclude, + McStas is used in this case. + * 1; Like above-mentioned this case has the advantage that it is explicit + and faces no ambiguities. However, in reality typically multiple + coordinate systems have to be mastered especially for complex + multi-signal modality experiments. + * 2 or more; If this case is realized, the best practice is that in every + case where a coordinate system should be referred to the respective class + has a depends_on field which resolves the possible ambiguities which specific + coordinate systems is referred to. The benefit of this explicit and clear + specifying of the coordinate system used in every case is that especially + in combination with having coordinate systems inside deeper branches + makes up for a very versatile, backwards compatible, but powerful system + to express different types of coordinate systems using NeXus. In the case + of two or more instances of NXcoordinate_system in one :ref:`NXcoordinate_system_set`, + it is also advised to specify the relationship between the two coordinate systems by + using the (NXtransformations) group within NXcoordinate_system. + + In effect, 1 should be the preferred choice. However, if more than one coordinate + system is defined for practical purposes, explicit depends_on fields should + always guide the user for each group and field which of the coordinate system + one refers to. - Convention how a positive rotation angle is defined when viewing - from the end of the rotation unit vector towards its origin, - i.e. in accordance with convention 2 of - DOI: 10.1088/0965-0393/23/8/083501. - Counter_clockwise is equivalent to a right-handed choice. - Clockwise is equivalent to a left-handed choice. + Convention how a positive rotation angle is defined when viewing + from the end of the rotation unit vector towards its origin, + i.e. in accordance with convention 2 of + DOI: 10.1088/0965-0393/23/8/083501. + Counter_clockwise is equivalent to a right-handed choice. + Clockwise is equivalent to a left-handed choice. - - How are rotations interpreted into an orientation - according to convention 3 of - DOI: 10.1088/0965-0393/23/8/083501. + How are rotations interpreted into an orientation + according to convention 3 of + DOI: 10.1088/0965-0393/23/8/083501. - - How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) - according to convention 4 of DOI: 10.1088/0965-0393/23/8/083501. - - The most frequently used convention is zxz, which is based on the work of H.-J. Bunge - but other conventions are possible. Apart from undefined, proper Euler angles - are distinguished from (improper) Tait-Bryan angles. + How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) + according to convention 4 of DOI: 10.1088/0965-0393/23/8/083501. + + The most frequently used convention is zxz, which is based on the work of H.-J. Bunge + but other conventions are possible. Apart from undefined, proper Euler angles + are distinguished from (improper) Tait-Bryan angles. - @@ -168,23 +165,21 @@ use depends_on field - not attribute - to point to conventions used--> - To which angular range is the rotation angle argument of an - axis-angle pair parameterization constrained according to - convention 5 of DOI: 10.1088/0965-0393/23/8/083501. + To which angular range is the rotation angle argument of an + axis-angle pair parameterization constrained according to + convention 5 of DOI: 10.1088/0965-0393/23/8/083501. - - Which sign convention is followed when converting orientations - between different parameterizations/representations according - to convention 6 of DOI: 10.1088/0965-0393/23/8/083501. + Which sign convention is followed when converting orientations + between different parameterizations/representations according + to convention 6 of DOI: 10.1088/0965-0393/23/8/083501. - @@ -195,46 +190,46 @@ use depends_on field - not attribute - to point to conventions used--> convention 1 of DOI: 10.1088/0965-0393/23/8/083501 is implemented by inheriting type from NXcoordinate_system--> - Details about eventually relevant named directions that may give reasons for anisotropies. - The classical example is mechanical processing where one has to specify which directions - (e.g. rolling, transverse, and normal direction) align how with the direction of the base - vectors of the sample_reference_frame. - - It is assumed that the configuration is inspected by looking towards the sample surface. - If a detector is involved, it is assumed that the configuration is inspected from a position - that is located behind this detector. - - If any of these assumptions is not met, the user is required to explicitly state this. - - Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the - base vectors of this coordinate system as Xp, Yp, Zp. + Details about eventually relevant named directions that may give reasons for anisotropies. + The classical example is mechanical processing where one has to specify which directions + (e.g. rolling, transverse, and normal direction) align how with the direction of the base + vectors of the sample_reference_frame. + + It is assumed that the configuration is inspected by looking towards the sample surface. + If a detector is involved, it is assumed that the configuration is inspected from a position + that is located behind this detector. + + If any of these assumptions is not met, the user is required to explicitly state this. + + Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the + base vectors of this coordinate system as Xp, Yp, Zp. - Details about the sample_reference_frame that is typically overlaid onto the surface of the sample. - - It is assumed that the configuration is inspected by looking towards the sample surface. - If a detector is involved, it is assumed that the configuration is inspected from a position - that is located behind this detector. - - If any of these assumptions is not met, the user is required to explicitly state this. - - Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the - base vectors of this coordinate system as Xs, Ys, Zs. + Details about the sample_reference_frame that is typically overlaid onto the surface of the sample. + + It is assumed that the configuration is inspected by looking towards the sample surface. + If a detector is involved, it is assumed that the configuration is inspected from a position + that is located behind this detector. + + If any of these assumptions is not met, the user is required to explicitly state this. + + Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the + base vectors of this coordinate system as Xs, Ys, Zs. - + - Details about the detector_reference_frame for a specific detector. - - Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the - base vectors of this coordinate system as Xd, Yd, Zd. - - It is assumed that the configuration is inspected by looking towards the sample surface - from a position that is located behind the detector. - - If any of these assumptions is not met, the user is required to explicitly state this. + Details about the detector_reference_frame for a specific detector. + + Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the + base vectors of this coordinate system as Xd, Yd, Zd. + + It is assumed that the configuration is inspected by looking towards the sample surface + from a position that is located behind the detector. + + If any of these assumptions is not met, the user is required to explicitly state this. From 86bb9238c61f309acff8f598e6a3cb9983aa97b2 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 12:53:29 +0100 Subject: [PATCH 38/75] Syncing up base classes for apm with #1422 f719fe0e, cs classes --- base_classes/NXcs_computer.nxdl.xml | 9 ++++----- base_classes/NXcs_filter_boolean_mask.nxdl.xml | 6 +++--- base_classes/NXcs_prng.nxdl.xml | 2 +- base_classes/NXcs_profiling.nxdl.xml | 2 +- base_classes/NXcs_profiling_event.nxdl.xml | 2 +- 5 files changed, 10 insertions(+), 11 deletions(-) diff --git a/base_classes/NXcs_computer.nxdl.xml b/base_classes/NXcs_computer.nxdl.xml index 6303eb3ae7..24be8abf88 100644 --- a/base_classes/NXcs_computer.nxdl.xml +++ b/base_classes/NXcs_computer.nxdl.xml @@ -2,9 +2,9 @@ + + + + + + Number of images in the stack, for stacks the slowest dimension. + + + + + Number of image points along the slow dimension (k equivalent to z). + + + + + Number of image points along the fast dimension (j equivalent to y). + + + + + Number of image points along the fastest dimension (i equivalent to x). + + + + + Base class for reporting a set of images. + + The most commonly used scanning methods are supported. That is one-, + two-, three-dimensional ROIs discretized using regular Euclidean tilings. + + Colloquially, an image is understood as a discretized representation of intensity distribution + detected or simulated for some ROI. When discretized with regular Euclidean tilings, the terms + pixel and voxel identify the smallest discretization unit. In this case, pixel and voxel are polygonal + or polyhedral unit cells respectively of the underlying tiling of the ROI within the reference space. + For all other tilings e.g. non-equispaced, the shape and size of pixel and voxel differs. Using the term + (image) point is eventually more appropriate when working with such tilings. + + Therefore, all docstrings in this base class refer to points (including pixel and voxel i.e. regular tilings). + + Point coordinates identify the location of the barycentre. + + For images in reciprocal space in practice, complex numbers are encoded via some formatted pair of real values. + Typically, fast algorithms for computing Fourier transformations (FFT) are used to encode + images in reciprocal (frequency) space. FFT libraries are used for implementing the key functionalities of + these mathematical operations. + + Different libraries use different representations and encoding of the images. + Details can be found in the respective sections of the typical FFT libraries documentations + + * `FFTW by M. Frigo and S. G. Johnson <https://www.fftw.org/fftw3_doc/Tutorial.html#Tutorial>`_ + * `Intel MKL by the Intel Co. <https://www.intel.com/content/www/us/en/docs/onemkl/developer-reference-c/2024-2/fourier-transform-functions.html>`_ + * `cuFFT by the NVidia Co. <https://docs.nvidia.com/cuda/cufft/index.html>`_ + * `NFFT by the TU Chemnitz group <https://www-user.tu-chemnitz.de/~potts/nfft/>`_ for non-equispaced computations + + Users are strongly advised to inspect carefully which specific conventions their library uses + to enable storing and modifying the implementation of their code such that the serialized + representations as they are detailed here for NeXus match. + + It is often the case that several images are combined using processing. In this case, + the number of images which are combined into collections is not necessarily the same + for each collection. The NXimage base class addresses this logical distinction + through the notation of identifier_image and identifier_group concepts. + That is identifier_image are always counting from offset in increments of one. + as each image is its own entity. By contrast, a group may contain no, or several images. + Consequently, identifier_group are not required to be contiguous. + + + + Details how NXdata instance were processed from detector readings/raw data. + + + + Resolvable data artifact (e.g. file) from which all values in the :ref:`NXdata` + instances in this :ref:`NXimage` were loaded during parsing. + + Possibility to document from which specific other serialized resource as the source + pieces of information were processed when using NeXus as a semantic file format + to serialize that information differently. + + The group in combination with an added field *absolute_path* therein adds context. + + + + Reference to a location inside the artifact that points to the specific group of values + that were processed if the artifacts contains several groups of values and thus + further resolving of ambiguities is required. + + + + + + Link or name of an :ref:`NXdetector` instance with which the data were + collected. + + + + + Program used for processing. + + + + + + One-dimensional image. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + Real part of the image intensity per point. + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Two-dimensional image. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + + Real part of the image intensity per point. + + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + + Point coordinate along the fast dimension. + + + + + + + Point coordinate along the fast dimension. + + + + + + Point coordinate along the fastest dimension. + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Three-dimensional image. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + + + Real part of the image intensity per point. + + + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + + + Point coordinate along the slow dimension. + + + + + + + Point coordinate along the slow dimension. + + + + + + Point coordinate along the fast dimension. + + + + + + + Point coordinate along the fast dimension. + + + + + + Point coordinate along the fastest dimension. + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Collection of one-dimesional images. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + + Real part of the image intensity per point. + + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + + Group identifier + + + + + + + Group identifier + + + + + + Image identifier + + + + + + + Image identifier + + + + + + Point coordinate along the fastest dimension. + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Collection of two-dimensional images. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + + + Real part of the image intensity per point. + + + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + + + Group identifier + + + + + + + Group identifier + + + + + + Image identifier + + + + + + + Image identifier. + + + + + + Point coordinate along the fast dimension. + + + + + + + Point coordinate along the fast dimension. + + + + + + Point coordinate along the fastest dimension. + + + + + + + Point coordinate along the fastest dimension. + + + + + + + Collection of three-dimensional images. + + + + Intensity for real-valued images as an alternative for real. + Magnitude of the image intensity for complex-valued data. + + + + + + + + + + + Real part of the image intensity per point. + + + + + + + + + + + Imaginary part of the image intensity per point. + + + + + + + + + + + Image intensity as a complex number as an alternative to real and + imag fields if values are stored as interleaved complex numbers. + + + + + + + + + + + Group identifier + + + + + + + Group identifier + + + + + + Image identifier + + + + + + + Image identifier + + + + + + Point coordinate along the slow dimension. + + + + + + + Point coordinate along the slow dimension. + + + + + + Point coordinate along the fast dimension. + + + + + + + Point coordinate along the fast dimension. + + + + + + Point coordinate along the fastest dimension. + + + + + + + Point coordinate along the fastest dimension. + + + + + diff --git a/base_classes/NXinstrument_apm.nxdl.xml b/base_classes/NXinstrument_apm.nxdl.xml index 9ed43e0471..86c7696717 100644 --- a/base_classes/NXinstrument_apm.nxdl.xml +++ b/base_classes/NXinstrument_apm.nxdl.xml @@ -3,7 +3,7 @@ Which type of instrument. - + @@ -79,7 +79,6 @@ or volatile (meta)data.--> - @@ -92,7 +91,7 @@ or volatile (meta)data.--> preferred. - + Device which reduces ToF differences of ions in ToF experiments. @@ -104,24 +103,9 @@ or volatile (meta)data.--> * 3863068 and 6740872 for the reflectron * 8134119 for the curved reflectron - + - Presence and status of the reflectron. - - - - - - - - - Given name/alias. - - - - - Free-text field to specify further details about the reflectron. - The field can be used to inform e. g. if the reflectron is flat or curved. + Was the reflectron used? @@ -129,15 +113,6 @@ or volatile (meta)data.--> The maximum voltage applied to the reflectron, relative to system ground. - - - - Affine transformation(s) which detail where the reflectron is located - relative to e.g. the origin of the specimen space reference coordinate - system. This group can also be used for specifying how the reflectron - is rotated relative to a given axis in the instrument. - - @@ -192,7 +167,7 @@ NEW ISSUE: local electrode, baking strategies, storage--> - + Laser- and/or voltage-pulsing device to trigger ion removal. @@ -202,12 +177,10 @@ NEW ISSUE: local electrode, baking strategies, storage--> Detail whereby ion extraction is triggered methodologically. - + - - - + - The space inside the atom probe along which ions pass nominally - when they leave the specimen and travel to the detector. - - - - - CRunHeader.CLasHeader.fAnalysisPressure + The space inside the atom probe along which ions pass nominally + when they leave the specimen and travel to the detector. + + + + + + + + + CRunHeader.CLasHeader.fAnalysisPressure + + + - - + + diff --git a/base_classes/NXion.nxdl.xml b/base_classes/NXion.nxdl.xml index 048eb5d336..ee278ead9e 100644 --- a/base_classes/NXion.nxdl.xml +++ b/base_classes/NXion.nxdl.xml @@ -2,9 +2,9 @@ - + Extension of NXpositioner to include fields to describe the use of manipulators in photoemission experiments. @@ -50,7 +50,7 @@ - + In case of a fixed or averaged cooling temperature, this is the scalar temperature setpoint. @@ -115,7 +115,7 @@ - + In case of a fixed or averaged temperature, this is the scalar temperature setpoint. @@ -165,7 +165,7 @@ - + In case of a fixed or averaged applied bias, this is the scalar voltage applied between @@ -208,13 +208,12 @@ - Any additional actuator on the manipulator used to control an external - condition. + Any additional actuators on the manipulator. - Any additional sensors on the manipulator used to monitor an external condition. + Any additional sensors on the manipulator. @@ -222,36 +221,4 @@ Class to describe the motors that are used in the manipulator - - - Refers to the last transformation specifying the positon of the manipulator in - the NXtransformations chain. - - - - - Collection of axis-based translations and rotations to describe the location and - geometry of the manipulator as a component in the instrument. Conventions from - the NXtransformations base class are used. In principle, the McStas coordinate - system is used. The first transformation has to point either to another - component of the system or . (for pointing to the reference frame) to relate it - relative to the experimental setup. Typically, the components of a system should - all be related relative to each other and only one component should relate to - the reference coordinate system. - - - - - .. index:: plotting - - Declares which child group contains a path leading - to a :ref:`NXdata` group. - - It is recommended (as of NIAC2014) to use this attribute - to help define the path to the default dataset to be plotted. - See https://www.nexusformat.org/2014_How_to_find_default_data.html - for a summary of the discussion. - - - diff --git a/base_classes/NXpeak.nxdl.xml b/base_classes/NXpeak.nxdl.xml index a5211a363f..4a030c6844 100644 --- a/base_classes/NXpeak.nxdl.xml +++ b/base_classes/NXpeak.nxdl.xml @@ -1,10 +1,10 @@ - + - + The symbols used in the schema to specify e.g. dimensions of arrays. - + - Rank of the dependent and independent data arrays (for - multidimensional/multivariate fit.) + Number of support points - Base class for describing a peak, its functional form, and support values - (i.e., the discretization (points) at which the function has been evaluated). + Description of peaks, their functional form or measured support. - + - Human-readable label which specifies which concept/entity + Human-readable identifier to specify which concept/entity the peak represents/identifies. - - - - Position values along one or more data dimensions (to hold the - values for the independent variable). - - - - The ``position`` field must have the same rank (``dimRank``) - as the ``intensity`` field. Each individual dimension of ``position`` - must have the same number of points as the corresponding dimension in - the ``intensity`` field. - - - - - - This array holds the intensity/count values of the fitted peak at each position. - - - - The ``intensity`` field must have the same rank (``dimRank``) - as the ``intensity`` field. Each individual dimension of ``position`` - must have the same number of points as the corresponding dimension in - the ``position`` field. - - - - - + + + Is the peak described analytically via a functional form + or is it empirically defined via measured/reported + intensity/counts as a function of an independent variable. + + If the functional form is not empirical or gaussian, users + should enter other for the peak_model and add relevant details + in the NXcollection. + + + + + + + + + - The functional form of the peak. This could be a Gaussian, Lorentzian, - Voigt, etc. + In the case of an empirical description of the peak and its shoulders, + this array holds the position values for the independent variable. - - + + + + + - Total area under the curve. + In the case of an empirical description of the peak and its shoulders, + this array holds the intensity/count values at each position. + + + - + - .. index:: plotting - - Declares which child group contains a path leading - to a :ref:`NXdata` group. - - It is recommended (as of NIAC2014) to use this attribute - to help define the path to the default dataset to be plotted. - See https://www.nexusformat.org/2014_How_to_find_default_data.html - for a summary of the discussion. + In the case of an analytical description (or if peak_model is other) this + collection holds parameter of (and eventually) the functional form. + For example in the case of Gaussians mu, sigma, cut-off values, + and background intensity are relevant parameter. - + diff --git a/base_classes/NXprogram.nxdl.xml b/base_classes/NXprogram.nxdl.xml index 2a2c10c03e..e92363efe8 100644 --- a/base_classes/NXprogram.nxdl.xml +++ b/base_classes/NXprogram.nxdl.xml @@ -3,7 +3,7 @@ - + Device to reduce an atmosphere (real or simulated) to a controlled pressure. diff --git a/base_classes/NXrotation_set.nxdl.xml b/base_classes/NXrotation_set.nxdl.xml index 3f47e3fb89..a304e3f47b 100644 --- a/base_classes/NXrotation_set.nxdl.xml +++ b/base_classes/NXrotation_set.nxdl.xml @@ -2,9 +2,9 @@ + + + + + + This interprets the ``name`` attribute as: + + * ``"specified"`` = Exactly this name. + Note that if no ``name`` and ``nameType`` are provided + for a group, ``nameType="any"`` becomes the default. + * ``"any"`` = Any name not already used in group. + * ``"partial"`` = The capital letters are substitutable + (empty string allowed) and the lower case letters + (and other allowed symbols, such as ``_``) are not. + + In each case, all names in a NeXus data file must + follow the naming :ref:`rules<Design-Naming>`. + + + + + + + + + + + + @@ -486,6 +517,7 @@ + @@ -660,9 +692,25 @@ String describing the engineering units. - The string should be appropriate for the value - and should conform to the NeXus rules for units. + The string should be appropriate for the value. + + * If a unit is not provided by the list of NeXus + unit categories, instead of providing a category, + a field element can include an example of the + units directly. + + * The example does not constrain the scale of the + units. For example, if the unit is ``eV/mm``, the + user could specify in a data file ``eV/cm``, or any + other unit that is convertible to the example given. + + It is recommended that users and application developers + check if their units and their unit examples adhere to + the UDUNITS standard. [#]_ + Conformance is not validated at this time. + + .. [#] https://www.unidata.ucar.edu/software/udunits/ @@ -913,21 +961,7 @@ - - - - This interprets the name attribute as: - * ``specified`` = use as specified - * ``any`` = can be any name not already used in group - - - - - - - - - + @@ -1006,6 +1040,7 @@ + @@ -1197,7 +1232,7 @@ (This data type is used internally in the NXDL schema to define elements and attributes to be used by users in NXDL specifications.) - + :: @@ -1209,6 +1244,20 @@ + Enumerations can be closed or open. A closed enumeration is one where the list of + values are the only ones allowed for a specification. An open enumeration is one + where the list of values is incomplete and additional values other than those listed + are allowed. Open enumerations should be used sparingly as the designer of the enumeration + should try to find all possible values for a given field/attribute. + + In case an open enumeration is used and the data provider wants to declare that the provided + value deliberately not from the given list of values, the data provider should, + + * for fields, set the attribute ``@custom=True``. + * for attributes, set an additional attribute ``@my_attribute_custom=True``, where + ``my_attribute`` is the name of the attribute with the open enumeration. + + Such attributes can be used deliberately to suppress warnings in NeXus validators. @@ -1244,6 +1293,14 @@ + + + + Is this an open enumeration? + An open enumeration allows additional values not listed. + + + diff --git a/nxdlTypes.xsd b/nxdlTypes.xsd index 8811142b90..b9c972571d 100644 --- a/nxdlTypes.xsd +++ b/nxdlTypes.xsd @@ -10,7 +10,7 @@ .. NeXus - Neutron and X-ray Common Data Format - Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC) + Copyright (C) 2008-2024 NeXus International Advisory Committee (NIAC) This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public @@ -44,6 +44,7 @@ They should describe valid units consistent with the manual section on NeXus units (based on UDUNITS). + Units are not validated by NeXus. @@ -81,6 +82,7 @@ nxdl:NX_VOLUME nxdl:NX_WAVELENGTH nxdl:NX_WAVENUMBER + xs:string " /> @@ -466,18 +468,14 @@ nxdl:NX_POSINT nxdl:NX_QUATERNION nxdl:NX_UINT + nxdl:NX_CHAR_OR_NUMBER "/> - The preferred string representation is :index:`UTF-8`. - Both fixed-length strings and variable-length strings are valid. - String arrays cannot be used where only a string is expected - (title, start_time, end_time, ``NX_class`` attribute,...). - Fields or attributes requiring the use of string arrays will be - clearly marked as such (like the ``NXdata`` attribute ``auxiliary_signals``). + A string of characters. The preferred string encoding is :index:`UTF-8`. This is the default field type. @@ -619,4 +617,14 @@ + + + Any valid character string or NeXus number representation + + + + diff --git a/requirements.txt b/requirements.txt index 74294d9b26..4b6ab51d58 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,18 +1,18 @@ # Prepare for Documentation -lxml>=4.9.1 +lxml pyyaml -nyaml==0.0.8 +nyaml # Documentation building sphinx>=5 sphinx-tabs sphinx-toolbox -sphinx_comments +chios # Testing pytest # Code style and auto-formatting -black>=24.1.1 +black>=22.3 flake8>=4 isort>=5.10 diff --git a/utils/create_release_notes.py b/utils/create_release_notes.py index 77a4d2c3b6..26ea3fc747 100755 --- a/utils/create_release_notes.py +++ b/utils/create_release_notes.py @@ -95,19 +95,23 @@ def get_release_info(token, base_tag_name, head_branch_name, milestone_name): logger.debug(f"repo: {repo}") # fmt: off - milestones = [ + all_milestones = tuple(repo.get_milestones(state="all")) + matching_milestones = tuple( m - for m in repo.get_milestones(state="all") + for m in all_milestones if m.title == milestone_name - ] + ) # fmt: on - if len(milestones) == 0: - msg = f"Could not find milestone: {milestone_name}" + if len(matching_milestones) == 0: + msg = f"Could not find milestone to match '{milestone_name}':" + for m in all_milestones: + msg += f"\n\t{m.title}" logger.error(msg) raise ValueError(msg) - milestone = milestones[0] + milestone = matching_milestones[0] logger.debug(f"milestone: {milestone}") + logger.debug(f"compare: {base_tag_name} -> {head_branch_name}") compare = repo.compare(base_tag_name, head_branch_name) logger.debug(f"compare: {compare}") @@ -124,9 +128,10 @@ def get_release_info(token, base_tag_name, head_branch_name, milestone_name): # t.commit == commit # t.commit.last_modified != commit.last_modified commit = repo.get_commit(t.commit.sha) - dt = str2time(commit.last_modified) + dt = commit.last_modified_datetime earliest = min(dt, earliest or dt) - logger.debug(f"# tags: {len(tags)}") + + logger.debug(f"# tags: {len(tags)} {earliest}") # fmt: off pulls = { @@ -191,18 +196,6 @@ def parse_command_line(): return parser.parse_args() -def str2time(time_string): - """convert date/time string to datetime object - - input string example: ``Tue, 20 Dec 2016 17:35:40 GMT`` - """ - if time_string is None: - msg = f"need valid date/time string, not: {time_string}" - logger.error(msg) - raise ValueError(msg) - return datetime.datetime.strptime(time_string, "%a, %d %b %Y %H:%M:%S %Z") - - def report(title, repo, milestone, tags, pulls, issues, commits): print(f"## {title}") print("") @@ -228,7 +221,7 @@ def report(title, repo, milestone, tags, pulls, issues, commits): print("-" * 5, " | ", "-" * 5, " | ", "-" * 5) for k, tag in sorted(tags.items()): commit = repo.get_commit(tag.commit.sha) - when = str2time(commit.last_modified).strftime("%Y-%m-%d") + when = commit.last_modified_datetime.strftime("%Y-%m-%d") print(f"[{tag.commit.sha[:7]}]({tag.commit.html_url}) | {when} | {k}") print("") print("### Pull Requests") @@ -240,7 +233,7 @@ def report(title, repo, milestone, tags, pulls, issues, commits): print("-" * 5, " | ", "-" * 5, " | ", "-" * 5, " | ", "-" * 5) for k, pull in sorted(pulls.items()): state = {True: "merged", False: "closed"}[pull.merged] - when = str2time(pull.last_modified).strftime("%Y-%m-%d") + when = pull.closed_at.strftime("%Y-%m-%d") # fmt: off print( f"[#{pull.number}]({pull.html_url})" @@ -307,7 +300,7 @@ def main(base=None, head=None, milestone=None, token=None, debug=False): # NeXus - Neutron and X-ray Common Data Format # -# Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC) +# Copyright (C) 2008-2024 NeXus International Advisory Committee (NIAC) # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Lesser General Public diff --git a/utils/update_copyright_date.py b/utils/update_copyright_date.py index 261b1933a3..c2aff310cb 100755 --- a/utils/update_copyright_date.py +++ b/utils/update_copyright_date.py @@ -12,12 +12,19 @@ import os, sys import mimetypes -from build_preparation import ROOT_DIR_EXPECTED_RESOURCES import datetime YEAR = datetime.datetime.now().year LEFT_SIDE_TEXT_MATCH = "Copyright (C) " RIGHT_SIDE_TEXT_MATCH = " NeXus International Advisory Committee (NIAC)" +ROOT_DIR_EXPECTED_RESOURCES = { + "files": """COPYING LGPL.txt Makefile NXDL_VERSION + nxdl.xsd nxdlTypes.xsd README.md + """.split(), + "subdirs": """applications base_classes contributed_definitions manual + package utils www impatient-guide + """.split(), +} def update(filename): @@ -170,7 +177,7 @@ def __developer_build_setup__(): # NeXus - Neutron and X-ray Common Data Format # -# Copyright (C) 2008-2022 NeXus International Advisory Committee (NIAC) +# Copyright (C) 2008-2024 NeXus International Advisory Committee (NIAC) # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Lesser General Public From 960890c27d45b4b501bcb1f4dacedda17bc9d4d3 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 14:12:56 +0100 Subject: [PATCH 42/75] Syncing up with niac changes on fairmat PR #1421 which promotes cg to baseclasses as accepted standard, first via a move of the files where most follow still the old pattern NXcg_something_set --- .../NXcg_alpha_complex.nxdl.xml | 0 .../NXcg_cylinder_set.nxdl.xml | 0 .../NXcg_ellipsoid_set.nxdl.xml | 0 .../NXcg_face_list_data_structure.nxdl.xml | 0 .../NXcg_geodesic_mesh.nxdl.xml | 0 {contributed_definitions => base_classes}/NXcg_grid.nxdl.xml | 0 .../NXcg_half_edge_data_structure.nxdl.xml | 0 .../NXcg_hexahedron_set.nxdl.xml | 0 .../NXcg_marching_cubes.nxdl.xml | 0 .../NXcg_parallelogram_set.nxdl.xml | 0 {contributed_definitions => base_classes}/NXcg_point_set.nxdl.xml | 0 .../NXcg_polygon_set.nxdl.xml | 0 .../NXcg_polyhedron_set.nxdl.xml | 0 .../NXcg_polyline_set.nxdl.xml | 0 .../NXcg_primitive_set.nxdl.xml | 0 {contributed_definitions => base_classes}/NXcg_roi_set.nxdl.xml | 0 .../NXcg_sphere_set.nxdl.xml | 0 .../NXcg_tetrahedron_set.nxdl.xml | 0 .../NXcg_triangle_set.nxdl.xml | 0 .../NXcg_triangulated_surface_mesh.nxdl.xml | 0 .../NXcg_unit_normal_set.nxdl.xml | 0 21 files changed, 0 insertions(+), 0 deletions(-) rename {contributed_definitions => base_classes}/NXcg_alpha_complex.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_cylinder_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_ellipsoid_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_face_list_data_structure.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_geodesic_mesh.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_grid.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_half_edge_data_structure.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_hexahedron_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_marching_cubes.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_parallelogram_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_point_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_polygon_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_polyhedron_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_polyline_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_primitive_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_roi_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_sphere_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_tetrahedron_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_triangle_set.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_triangulated_surface_mesh.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcg_unit_normal_set.nxdl.xml (100%) diff --git a/contributed_definitions/NXcg_alpha_complex.nxdl.xml b/base_classes/NXcg_alpha_complex.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_alpha_complex.nxdl.xml rename to base_classes/NXcg_alpha_complex.nxdl.xml diff --git a/contributed_definitions/NXcg_cylinder_set.nxdl.xml b/base_classes/NXcg_cylinder_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_cylinder_set.nxdl.xml rename to base_classes/NXcg_cylinder_set.nxdl.xml diff --git a/contributed_definitions/NXcg_ellipsoid_set.nxdl.xml b/base_classes/NXcg_ellipsoid_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_ellipsoid_set.nxdl.xml rename to base_classes/NXcg_ellipsoid_set.nxdl.xml diff --git a/contributed_definitions/NXcg_face_list_data_structure.nxdl.xml b/base_classes/NXcg_face_list_data_structure.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_face_list_data_structure.nxdl.xml rename to base_classes/NXcg_face_list_data_structure.nxdl.xml diff --git a/contributed_definitions/NXcg_geodesic_mesh.nxdl.xml b/base_classes/NXcg_geodesic_mesh.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_geodesic_mesh.nxdl.xml rename to base_classes/NXcg_geodesic_mesh.nxdl.xml diff --git a/contributed_definitions/NXcg_grid.nxdl.xml b/base_classes/NXcg_grid.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_grid.nxdl.xml rename to base_classes/NXcg_grid.nxdl.xml diff --git a/contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml b/base_classes/NXcg_half_edge_data_structure.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_half_edge_data_structure.nxdl.xml rename to base_classes/NXcg_half_edge_data_structure.nxdl.xml diff --git a/contributed_definitions/NXcg_hexahedron_set.nxdl.xml b/base_classes/NXcg_hexahedron_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_hexahedron_set.nxdl.xml rename to base_classes/NXcg_hexahedron_set.nxdl.xml diff --git a/contributed_definitions/NXcg_marching_cubes.nxdl.xml b/base_classes/NXcg_marching_cubes.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_marching_cubes.nxdl.xml rename to base_classes/NXcg_marching_cubes.nxdl.xml diff --git a/contributed_definitions/NXcg_parallelogram_set.nxdl.xml b/base_classes/NXcg_parallelogram_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_parallelogram_set.nxdl.xml rename to base_classes/NXcg_parallelogram_set.nxdl.xml diff --git a/contributed_definitions/NXcg_point_set.nxdl.xml b/base_classes/NXcg_point_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_point_set.nxdl.xml rename to base_classes/NXcg_point_set.nxdl.xml diff --git a/contributed_definitions/NXcg_polygon_set.nxdl.xml b/base_classes/NXcg_polygon_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_polygon_set.nxdl.xml rename to base_classes/NXcg_polygon_set.nxdl.xml diff --git a/contributed_definitions/NXcg_polyhedron_set.nxdl.xml b/base_classes/NXcg_polyhedron_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_polyhedron_set.nxdl.xml rename to base_classes/NXcg_polyhedron_set.nxdl.xml diff --git a/contributed_definitions/NXcg_polyline_set.nxdl.xml b/base_classes/NXcg_polyline_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_polyline_set.nxdl.xml rename to base_classes/NXcg_polyline_set.nxdl.xml diff --git a/contributed_definitions/NXcg_primitive_set.nxdl.xml b/base_classes/NXcg_primitive_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_primitive_set.nxdl.xml rename to base_classes/NXcg_primitive_set.nxdl.xml diff --git a/contributed_definitions/NXcg_roi_set.nxdl.xml b/base_classes/NXcg_roi_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_roi_set.nxdl.xml rename to base_classes/NXcg_roi_set.nxdl.xml diff --git a/contributed_definitions/NXcg_sphere_set.nxdl.xml b/base_classes/NXcg_sphere_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_sphere_set.nxdl.xml rename to base_classes/NXcg_sphere_set.nxdl.xml diff --git a/contributed_definitions/NXcg_tetrahedron_set.nxdl.xml b/base_classes/NXcg_tetrahedron_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_tetrahedron_set.nxdl.xml rename to base_classes/NXcg_tetrahedron_set.nxdl.xml diff --git a/contributed_definitions/NXcg_triangle_set.nxdl.xml b/base_classes/NXcg_triangle_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_triangle_set.nxdl.xml rename to base_classes/NXcg_triangle_set.nxdl.xml diff --git a/contributed_definitions/NXcg_triangulated_surface_mesh.nxdl.xml b/base_classes/NXcg_triangulated_surface_mesh.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_triangulated_surface_mesh.nxdl.xml rename to base_classes/NXcg_triangulated_surface_mesh.nxdl.xml diff --git a/contributed_definitions/NXcg_unit_normal_set.nxdl.xml b/base_classes/NXcg_unit_normal_set.nxdl.xml similarity index 100% rename from contributed_definitions/NXcg_unit_normal_set.nxdl.xml rename to base_classes/NXcg_unit_normal_set.nxdl.xml From 796f30b7a68e8e1dcf10c138a08483e22ca6308a Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 14:15:20 +0100 Subject: [PATCH 43/75] Syncing up with niac changes on fairmat PR #1421 which promotes cg to baseclasses as accepted standard, second via renaming those _set classes and removing those no longer propose or those that were refactored into other classes --- ...er_set.nxdl.xml => NXcg_cylinder.nxdl.xml} | 0 ...d_set.nxdl.xml => NXcg_ellipsoid.nxdl.xml} | 0 base_classes/NXcg_geodesic_mesh.nxdl.xml | 55 ----------------- ..._set.nxdl.xml => NXcg_hexahedron.nxdl.xml} | 0 base_classes/NXcg_marching_cubes.nxdl.xml | 58 ------------------ ...t.nxdl.xml => NXcg_parallelogram.nxdl.xml} | 0 ...point_set.nxdl.xml => NXcg_point.nxdl.xml} | 0 ...gon_set.nxdl.xml => NXcg_polygon.nxdl.xml} | 0 ..._set.nxdl.xml => NXcg_polyhedron.nxdl.xml} | 0 ...ne_set.nxdl.xml => NXcg_polyline.nxdl.xml} | 0 ...e_set.nxdl.xml => NXcg_primitive.nxdl.xml} | 0 ...Xcg_roi_set.nxdl.xml => NXcg_roi.nxdl.xml} | 0 base_classes/NXcg_sphere_set.nxdl.xml | 61 ------------------- ...set.nxdl.xml => NXcg_tetrahedron.nxdl.xml} | 0 ...le_set.nxdl.xml => NXcg_triangle.nxdl.xml} | 0 .../NXcg_triangulated_surface_mesh.nxdl.xml | 42 ------------- ...set.nxdl.xml => NXcg_unit_normal.nxdl.xml} | 0 17 files changed, 216 deletions(-) rename base_classes/{NXcg_cylinder_set.nxdl.xml => NXcg_cylinder.nxdl.xml} (100%) rename base_classes/{NXcg_ellipsoid_set.nxdl.xml => NXcg_ellipsoid.nxdl.xml} (100%) delete mode 100644 base_classes/NXcg_geodesic_mesh.nxdl.xml rename base_classes/{NXcg_hexahedron_set.nxdl.xml => NXcg_hexahedron.nxdl.xml} (100%) delete mode 100644 base_classes/NXcg_marching_cubes.nxdl.xml rename base_classes/{NXcg_parallelogram_set.nxdl.xml => NXcg_parallelogram.nxdl.xml} (100%) rename base_classes/{NXcg_point_set.nxdl.xml => NXcg_point.nxdl.xml} (100%) rename base_classes/{NXcg_polygon_set.nxdl.xml => NXcg_polygon.nxdl.xml} (100%) rename base_classes/{NXcg_polyhedron_set.nxdl.xml => NXcg_polyhedron.nxdl.xml} (100%) rename base_classes/{NXcg_polyline_set.nxdl.xml => NXcg_polyline.nxdl.xml} (100%) rename base_classes/{NXcg_primitive_set.nxdl.xml => NXcg_primitive.nxdl.xml} (100%) rename base_classes/{NXcg_roi_set.nxdl.xml => NXcg_roi.nxdl.xml} (100%) delete mode 100644 base_classes/NXcg_sphere_set.nxdl.xml rename base_classes/{NXcg_tetrahedron_set.nxdl.xml => NXcg_tetrahedron.nxdl.xml} (100%) rename base_classes/{NXcg_triangle_set.nxdl.xml => NXcg_triangle.nxdl.xml} (100%) delete mode 100644 base_classes/NXcg_triangulated_surface_mesh.nxdl.xml rename base_classes/{NXcg_unit_normal_set.nxdl.xml => NXcg_unit_normal.nxdl.xml} (100%) diff --git a/base_classes/NXcg_cylinder_set.nxdl.xml b/base_classes/NXcg_cylinder.nxdl.xml similarity index 100% rename from base_classes/NXcg_cylinder_set.nxdl.xml rename to base_classes/NXcg_cylinder.nxdl.xml diff --git a/base_classes/NXcg_ellipsoid_set.nxdl.xml b/base_classes/NXcg_ellipsoid.nxdl.xml similarity index 100% rename from base_classes/NXcg_ellipsoid_set.nxdl.xml rename to base_classes/NXcg_ellipsoid.nxdl.xml diff --git a/base_classes/NXcg_geodesic_mesh.nxdl.xml b/base_classes/NXcg_geodesic_mesh.nxdl.xml deleted file mode 100644 index 6314db3427..0000000000 --- a/base_classes/NXcg_geodesic_mesh.nxdl.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computational geometry description of a geodesic mesh. - - A geodesic surface mesh is a triangulated surface mesh with metadata which - can be used as an approximation to describe the surface of a sphere. - Triangulation of spheres are commonly used in Materials Science - for quantifying texture of materials, i.e. the relative rotation of - crystals to sample directions. - - For additional details or an introduction into the topic of geodesic meshes - see (from which specifically the section on subdivision schemes is relevant). - - * `E. S. Popko and C. J. Kitrick <https://doi.org/10.1201/9781003134114>`_ - - Earth scientists have specific demands and different views about what should - be included in such a base class, given that nested geodesic meshes are a key - component of climate modelling software. For now we propose to use this - base class as a container for organizing data related to geodesic meshes. - - Specifically an instance of this base class should detail the rule set how - e.g. a geodesic (surface) mesh was instantiated as there are many - possibilities to do so. - - - - diff --git a/base_classes/NXcg_hexahedron_set.nxdl.xml b/base_classes/NXcg_hexahedron.nxdl.xml similarity index 100% rename from base_classes/NXcg_hexahedron_set.nxdl.xml rename to base_classes/NXcg_hexahedron.nxdl.xml diff --git a/base_classes/NXcg_marching_cubes.nxdl.xml b/base_classes/NXcg_marching_cubes.nxdl.xml deleted file mode 100644 index b1f6310dd7..0000000000 --- a/base_classes/NXcg_marching_cubes.nxdl.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - Base class to detail the marching cubes (MC) algorithm. - - Documenting which specific version of MC was used helps with understanding - how robust the results are with respect to the topology of the triangulation. - - - - Metadata of the grid on which the here specified MC is operating. - - - - - Reference to the specific implementation of marching cubes used. - - See for example the following papers for details about specific - MC implementations: - - * `W. E. Lorensen <https://doi.org/10.1109/MCG.2020.2971284>`_ - * `T. S. Newman and H. Yi <https://doi.org/10.1016/j.cag.2006.07.021>`_ - - - - - Free text field in case a proper identifier is not available. - - - - - diff --git a/base_classes/NXcg_parallelogram_set.nxdl.xml b/base_classes/NXcg_parallelogram.nxdl.xml similarity index 100% rename from base_classes/NXcg_parallelogram_set.nxdl.xml rename to base_classes/NXcg_parallelogram.nxdl.xml diff --git a/base_classes/NXcg_point_set.nxdl.xml b/base_classes/NXcg_point.nxdl.xml similarity index 100% rename from base_classes/NXcg_point_set.nxdl.xml rename to base_classes/NXcg_point.nxdl.xml diff --git a/base_classes/NXcg_polygon_set.nxdl.xml b/base_classes/NXcg_polygon.nxdl.xml similarity index 100% rename from base_classes/NXcg_polygon_set.nxdl.xml rename to base_classes/NXcg_polygon.nxdl.xml diff --git a/base_classes/NXcg_polyhedron_set.nxdl.xml b/base_classes/NXcg_polyhedron.nxdl.xml similarity index 100% rename from base_classes/NXcg_polyhedron_set.nxdl.xml rename to base_classes/NXcg_polyhedron.nxdl.xml diff --git a/base_classes/NXcg_polyline_set.nxdl.xml b/base_classes/NXcg_polyline.nxdl.xml similarity index 100% rename from base_classes/NXcg_polyline_set.nxdl.xml rename to base_classes/NXcg_polyline.nxdl.xml diff --git a/base_classes/NXcg_primitive_set.nxdl.xml b/base_classes/NXcg_primitive.nxdl.xml similarity index 100% rename from base_classes/NXcg_primitive_set.nxdl.xml rename to base_classes/NXcg_primitive.nxdl.xml diff --git a/base_classes/NXcg_roi_set.nxdl.xml b/base_classes/NXcg_roi.nxdl.xml similarity index 100% rename from base_classes/NXcg_roi_set.nxdl.xml rename to base_classes/NXcg_roi.nxdl.xml diff --git a/base_classes/NXcg_sphere_set.nxdl.xml b/base_classes/NXcg_sphere_set.nxdl.xml deleted file mode 100644 index 8b12834749..0000000000 --- a/base_classes/NXcg_sphere_set.nxdl.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - The dimensionality, which has to be at least 2. - - - - - The cardinality of the set, i.e. the number of circles or spheres. - - - - - Computational geometry description of a set of spheres. - - Each sphere can have a different radius but all need to have finite volume. - - - - In the case that all spheres have the same radius. - - - - - In the case that spheres have different radius use this - instead of the radius field. - - - - - - diff --git a/base_classes/NXcg_tetrahedron_set.nxdl.xml b/base_classes/NXcg_tetrahedron.nxdl.xml similarity index 100% rename from base_classes/NXcg_tetrahedron_set.nxdl.xml rename to base_classes/NXcg_tetrahedron.nxdl.xml diff --git a/base_classes/NXcg_triangle_set.nxdl.xml b/base_classes/NXcg_triangle.nxdl.xml similarity index 100% rename from base_classes/NXcg_triangle_set.nxdl.xml rename to base_classes/NXcg_triangle.nxdl.xml diff --git a/base_classes/NXcg_triangulated_surface_mesh.nxdl.xml b/base_classes/NXcg_triangulated_surface_mesh.nxdl.xml deleted file mode 100644 index da55b25306..0000000000 --- a/base_classes/NXcg_triangulated_surface_mesh.nxdl.xml +++ /dev/null @@ -1,42 +0,0 @@ - - - - - - - The symbols used in the schema to specify e.g. dimensions of arrays. - - - - Computational geometry description of a mesh of triangles. - - The mesh may be self-intersecting and have holes but the - triangles used must not be degenerated. - - - - A graph-based approach to describe the mesh when it is also desired - to perform topological processing or analyses on the mesh. - - - diff --git a/base_classes/NXcg_unit_normal_set.nxdl.xml b/base_classes/NXcg_unit_normal.nxdl.xml similarity index 100% rename from base_classes/NXcg_unit_normal_set.nxdl.xml rename to base_classes/NXcg_unit_normal.nxdl.xml From 0ac8ed5028945a455f1dd94a88d7d8a757065d70 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 14:29:37 +0100 Subject: [PATCH 44/75] Syncing up with niac changes on fairmat PR #1421 which promotes cg to baseclasses as accepted standard, third, via cherry-picking all NXcg from the actual PR where they have been discussed with PeterChang --- base_classes/NXcg_alpha_complex.nxdl.xml | 83 +++++------- base_classes/NXcg_cylinder.nxdl.xml | 44 +++---- base_classes/NXcg_ellipsoid.nxdl.xml | 28 +++- .../NXcg_face_list_data_structure.nxdl.xml | 48 +++---- base_classes/NXcg_grid.nxdl.xml | 38 ++++-- .../NXcg_half_edge_data_structure.nxdl.xml | 39 +++--- base_classes/NXcg_hexahedron.nxdl.xml | 18 ++- base_classes/NXcg_parallelogram.nxdl.xml | 15 +-- base_classes/NXcg_point.nxdl.xml | 8 +- base_classes/NXcg_polygon.nxdl.xml | 23 ++-- base_classes/NXcg_polyhedron.nxdl.xml | 10 +- base_classes/NXcg_polyline.nxdl.xml | 30 +++-- base_classes/NXcg_primitive.nxdl.xml | 121 +++++++++++------- base_classes/NXcg_roi.nxdl.xml | 19 ++- base_classes/NXcg_tetrahedron.nxdl.xml | 22 +--- base_classes/NXcg_triangle.nxdl.xml | 11 +- base_classes/NXcg_unit_normal.nxdl.xml | 8 +- 17 files changed, 284 insertions(+), 281 deletions(-) diff --git a/base_classes/NXcg_alpha_complex.nxdl.xml b/base_classes/NXcg_alpha_complex.nxdl.xml index b6a466bc58..af58363ea8 100644 --- a/base_classes/NXcg_alpha_complex.nxdl.xml +++ b/base_classes/NXcg_alpha_complex.nxdl.xml @@ -3,7 +3,7 @@ - + - Computational geometry of alpha shapes or alpha wrappings about primitives. + Computational geometry of alpha complexes (alpha shapes or alpha wrappings) about primitives. For details see: * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, * https://dx.doi.org/10.1145/174462.156635 for 3D, * https://dl.acm.org/doi/10.5555/871114 for weighted, and - * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation - * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D wrappings + * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation of alpha shapes, and + * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D alpha wrappings - in CGAL, the Computational Geometry Algorithms Library. + in CGAL, the Computational Geometry Algorithms Library respectively. As a starting point, we follow the conventions of the CGAL library. + + In general, an alpha complex is a not necessarily connected or not necessarily pure complex, + i.e. singular faces may exist. The number of cells, faces, and edges depends on how a specific + alpha complex is filtered for lower-dimensional simplices. The fields is_regularized and + regularization can be used to provide details about regularization procedures. Type of alpha complex following the terminology used by CGAL for now. - Basic means (unweighted) alpha shapes. Alpha_wrapping means meshes - created using the alpha_wrapping algorithm. + Alpha_shape means meshes created using one of the alpha_shape algorithm. + Alpha_wrapping means meshes created using the alpha_wrapping algorithm. @@ -51,72 +56,46 @@ The so-called spectrum or sets of (weighted) alpha shapes includes the convex hu - + - Are singular faces removed, i.e. has the alpha complex - been regularized or not. + Human-readable description about regularization procedures. - - + - The alpha parameter, i.e. the radius of the alpha-sphere that - is used when computing the alpha complex. + Was the alpha complex regularized, i.e. have singular faces been removed, or not. + + + + + The alpha parameter, i.e. the squared radius of the alpha-sphere + that is used when computing the alpha complex. - The offset distance parameter used when computing alpha_wrappings. - - + - Point cloud for which the alpha shape or wrapping has been computed. + Point cloud serving as input for the computation of the alpha complex. - - + - Triangle soup for which the alpha wrapping has been computed. + Triangle soup serving as input for the computation of the alpha complex. - + - Triangle mesh representing the alpha complex. + Triangle mesh representing the output of the computation, i.e. the alpha complex. - - + - Set of tetrahedra representing the volume inside the alpha complex. + Tetrahedra representing an interior volume of the alpha complex (if such exists). - diff --git a/base_classes/NXcg_cylinder.nxdl.xml b/base_classes/NXcg_cylinder.nxdl.xml index e5bb83807a..36e3568d47 100644 --- a/base_classes/NXcg_cylinder.nxdl.xml +++ b/base_classes/NXcg_cylinder.nxdl.xml @@ -3,7 +3,7 @@ - - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -41,33 +38,30 @@ cylinder could be constructed, but NXcylinder is easier to understand--> - Computational geometry description of a set of cylinders. + Computational geometry description of a set of cylinders or (truncated) cones. + + The radius can either be defined in the radii field or by filling the upper_cap_radii + and lower_cap_radii fields respectively. The latter field case can + thus be used to represent (truncated) cones. - The radius can either be defined in the radii field or by filling both - the upper_cap_radii or lower_cap_radii field. The latter field case can - thus be used to represent truncated cones. + It is possible to define only one of the cap_radii fields + to represent half-open cylinder. A direction vector which is parallel to the cylinder/cone axis and whose magnitude is the height of the cylinder/cone. + + The upper_cap is assumed to represent the end while the + lower_cap is assumed to represent the start of the + respective cylinder instances when inspecting along the + direction vector. - Radius of the cylinder if all have the same radius. @@ -106,7 +100,7 @@ one should really better use NXquadric...--> - Lateral surface area + Lateral surface area of each cylinder. @@ -130,16 +124,10 @@ one should really better use NXquadric...--> - Sum of upper and lower cap areas and lateral surface area - of each cylinder. + Sum of upper and lower cap area and lateral surface area of each cylinder. - diff --git a/base_classes/NXcg_ellipsoid.nxdl.xml b/base_classes/NXcg_ellipsoid.nxdl.xml index e22a677c11..3913cf54dc 100644 --- a/base_classes/NXcg_ellipsoid.nxdl.xml +++ b/base_classes/NXcg_ellipsoid.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -42,9 +42,10 @@ redundant as there is NXcsg, and NXquadric but easier to understand--> Computational geometry description of a set of ellipsoids. - + - Radius of the half axes. + Length of the semi-axes (e.g. semi-major and semi-minor + respectively for an ellipse). Use if all ellipsoids in the set have the same half-axes. @@ -52,14 +53,29 @@ redundant as there is NXcsg, and NXquadric but easier to understand--> - + - Half-axes radii of each ellipsoid. + Length of the semi-axes if ellipsoids have individually different lengths. + + + + In the case that all ellipsoids are spheres. + + + + + In the case that all ellipsoids are spheres whose radii differ. + For a mixture of spheres use semi_axes_values. + + + + + diff --git a/base_classes/NXcg_face_list_data_structure.nxdl.xml b/base_classes/NXcg_face_list_data_structure.nxdl.xml index 081b928d5d..a808ce2011 100644 --- a/base_classes/NXcg_face_list_data_structure.nxdl.xml +++ b/base_classes/NXcg_face_list_data_structure.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -53,27 +53,21 @@ duplicate of an NXoff_geometry ?--> The total number of vertices of all faces. Faces are polygons. - - - The total number of Weinberg vector values of all faces. - - Computational geometry of primitives via a face-and-edge-list data structure. - Primitives must neither be degenerated nor self-intersect but can differ in - their properties. A face-and-edge-list-based description of primitives is + Primitives must neither be degenerated nor self-intersect but can have different + properties. A face-and-edge-list-based description of primitives is frequently used for triangles and polyhedra to store them on disk for visualization purposes (see OFF, PLY, VTK, or STL file formats). - Although this description is storage efficient it is not well suited for - topological analyses though. In this case, scientists may need a different - view on the primitives which is better represented with e.g. a - half_edge_data_structure. + Although this description is storage efficient, it is not well-suited for + topological analyses. In this case using a half-edge data structure is + an alternative. Having an own base class for the data structure how primitives are stored is - useful to embrace both users with small or very detailed specification demands. + useful to embrace both users with small or detailed specification demands. @@ -103,34 +97,34 @@ duplicate of an NXoff_geometry ?--> Number of faces of the primitives. - + Integer offset whereby the identifier of the first member of the vertices differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of NXcg_primitive_set for further details. + Inspect the definition of NXcg_primitive for further details. - + Integer offset whereby the identifier of the first member of the edges differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of NXcg_primitive_set for further details. + Inspect the definition of NXcg_primitive for further details. - + Integer offset whereby the identifier of the first member of the faces differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of NXcg_primitive_set for further details. + Inspect the definition of NXcg_primitive for further details. - + Integer identifier to distinguish all vertices explicitly. @@ -138,7 +132,7 @@ duplicate of an NXoff_geometry ?--> - + Integer used to distinguish all edges explicitly. @@ -146,7 +140,7 @@ duplicate of an NXoff_geometry ?--> - + Integer used to distinguish all faces explicitly. @@ -159,10 +153,10 @@ duplicate of an NXoff_geometry ?--> Positions of the vertices. Users are encouraged to reduce the vertices to a unique set as this may - result in a more efficient storage of the geometry data. - It is also possible though to store the vertex positions naively in which - case vertices_are_unique is likely False. Naively here means that each - vertex is stored even though many share the same positions. + result in more efficient storage. Alternatively, storing vertex positions naively + should be indicated with setting vertices_are_unique to False. + Naively means that each vertex is stored even though many vertices may + share the same positions. diff --git a/base_classes/NXcg_grid.nxdl.xml b/base_classes/NXcg_grid.nxdl.xml index c83d817d83..d79f46bd46 100644 --- a/base_classes/NXcg_grid.nxdl.xml +++ b/base_classes/NXcg_grid.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -46,15 +46,16 @@ Computational geometry description of a grid of Wigner-Seitz cells in Euclidean space. Three-dimensional grids with cubic cells are if not the most frequently used - example of such grids. Examples of numerical methods where grids are used - are spectral-solver based crystal plasticity or other stencil methods like - phase-field or cellular automata. + example of such grids. Numerical methods and models that use grids are used + in many cases in the natural sciences and engineering disciplines. Examples are + discretizations in space and time used for phase-field, cellular automata, or Monte Carlo + modeling. Location of the origin of the grid. - Use the depends_on field that is inherited from the :ref:`NXcg_primitive_set` + Use the depends_on field that is inherited from the :ref:`NXcg_primitive` class to specify the coordinate system in which the origin location is defined. @@ -77,7 +78,7 @@ - + Number of unit cells along each of the d unit vectors. @@ -112,7 +113,7 @@ should constraints on the grid be place here or not--> - + A tight bounding box about the grid. @@ -152,4 +153,25 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele + + + Details about the computational geometry method and implementation + used for discretizing internal surfaces as e.g. obtained with marching methods, + like marching squares or marching cubes. + + Documenting which specific version was used helps with understanding how + robust the results are with respect to the topology of the triangulation. + Reference to the specific implementation of marching cubes used. + + See for example the following papers for details about how to identify a + DOI which specifies the implementation used: + + * `W. E. Lorensen <https://doi.org/10.1109/MCG.2020.2971284>`_ + * `T. S. Newman and H. Yi <https://doi.org/10.1016/j.cag.2006.07.021>`_ + + The value placed here should ideally be an identifier of a program. + If not possible, an identifier for a paper, technical report, or free-text + description can be used instead. + + diff --git a/base_classes/NXcg_half_edge_data_structure.nxdl.xml b/base_classes/NXcg_half_edge_data_structure.nxdl.xml index 759e30943c..28a96999d8 100644 --- a/base_classes/NXcg_half_edge_data_structure.nxdl.xml +++ b/base_classes/NXcg_half_edge_data_structure.nxdl.xml @@ -3,7 +3,7 @@ - + @@ -52,8 +52,14 @@ Computational geeometry description of a half-edge data structure. Such a data structure can be used to efficiently circulate around faces - and iterate over vertices of a planar graph. + and iterate over vertices of a planar graph. The data structure is also + known as a doubly connected edge list. + + + Dimensionality of the primitives described. + + @@ -74,42 +80,37 @@ irrespectively whether edges are shared across faces or not. - + - - - Number of faces of the primitives. - - - + Integer offset whereby the identifier of the first member of the vertices differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of :ref:`NXcg_primitive_set` for further details. + Inspect the definition of :ref:`NXcg_primitive` for further details. - + Integer offset whereby the identifier of the first member of the edges differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of :ref:`NXcg_primitive_set` for further details. + Inspect the definition of :ref:`NXcg_primitive` for further details. - + Integer offset whereby the identifier of the first member of the faces differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of :ref:`NXcg_primitive_set` for further details. + Inspect the definition of :ref:`NXcg_primitive` for further details. - + The position of the vertices. @@ -176,7 +177,7 @@ - + Users are referred to the literature for the background of L. Weinberg's work about topological characterization of planar graphs: @@ -189,8 +190,4 @@ of microstructural objects like crystals/grains. - diff --git a/base_classes/NXcg_hexahedron.nxdl.xml b/base_classes/NXcg_hexahedron.nxdl.xml index 8ea85fb981..d424776bad 100644 --- a/base_classes/NXcg_hexahedron.nxdl.xml +++ b/base_classes/NXcg_hexahedron.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -65,7 +65,7 @@ from MarDI, for now let's assume we do not need polytopes for d > 3--> Hexahedra are important geometrical primitives, which are among the most frequently used elements in finite element meshing/modeling. - As a specialization of the :ref:`NXcg_primitive_set` base class hexahedra + As a specialization of the :ref:`NXcg_primitive` base class hexahedra are assumed non-degenerated, closed, and built of polygons that are not self-intersecting. @@ -169,23 +169,21 @@ from MarDI, for now let's assume we do not need polytopes for d > 3--> - - - - + + + Combined storage of all primitives of all hexahedra. - + Individual storage of each hexahedron. - + Individual storage of each hexahedron as a graph. diff --git a/base_classes/NXcg_parallelogram.nxdl.xml b/base_classes/NXcg_parallelogram.nxdl.xml index bfb868c47d..08b34c3065 100644 --- a/base_classes/NXcg_parallelogram.nxdl.xml +++ b/base_classes/NXcg_parallelogram.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -55,7 +55,7 @@ The term parallelogram will be used throughout this base class thus including the important special cases rectangle, square, 2D box, axis-aligned bounding box (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D - counterparts. See :ref:`NXcg_hexahedron_set` for the generalization in 3D. + counterparts. See :ref:`NXcg_hexahedron` for the generalization in 3D. An axis-aligned bounding box is a common data object in computational science and simulation codes to represent a rectangle whose edges are aligned with the @@ -89,18 +89,13 @@ - - Combined storage of all primitives of all parallelograms. + Combined storage of all parallelograms. - + Individual storage of each parallelogram. - diff --git a/base_classes/NXcg_point.nxdl.xml b/base_classes/NXcg_point.nxdl.xml index c2190590d0..95c981340b 100644 --- a/base_classes/NXcg_point.nxdl.xml +++ b/base_classes/NXcg_point.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -42,12 +42,12 @@ Points may have an associated time value. Users are advised though to store time data of point sets rather as instances of time events, where for each - point in time there is an :ref:`NXcg_point_set` instance which specifies the + point in time there is an :ref:`NXcg_point` instance which specifies the points' locations. This is a frequent situation in experiments and computer simulations, where positions of points are taken at the same point in time (real time or - simulated physical time). Thereby, the storage of redundant time stamp + simulated physical time). Thereby, the storage of redundant timestamp information per point is considered as obsolete. diff --git a/base_classes/NXcg_polygon.nxdl.xml b/base_classes/NXcg_polygon.nxdl.xml index 95c157ce1e..3021dc2302 100644 --- a/base_classes/NXcg_polygon.nxdl.xml +++ b/base_classes/NXcg_polygon.nxdl.xml @@ -3,7 +3,7 @@ - - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -46,9 +43,7 @@ descriptors.--> - + Computational geometry description of a set of polygons in Euclidean space. @@ -65,14 +60,14 @@ somewhat redundant as there is NXoff_geometry but easier to understand As three-dimensional objects, a set of polygons can be used to define the hull of what is effectively a polyhedron; however users are advised to use - the specific :ref:`NXcg_polyhedron_set` base class if they wish to describe closed + the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed polyhedra. Even more general complexes can be thought of. An example are the so-called piecewise-linear complexes used in the TetGen library. As these complexes can have holes though, polyhedra without holes are one - subclass of such complexes, users should rather design an own - base class e.g. NXcg_polytope_set to describe such even more - complex primitives instead of abusing this base class for such purposes. + subclass of such complexes, users should rather design an own base class + e.g. NXcg_polytope to describe such even more complex primitives instead + of abusing this base class for such purposes. @@ -85,12 +80,12 @@ somewhat redundant as there is NXoff_geometry but easier to understand Combined storage of all primitives of all polygons. - + Individual storage of the mesh of each polygon. - + Individual storage of each polygon as a graph. diff --git a/base_classes/NXcg_polyhedron.nxdl.xml b/base_classes/NXcg_polyhedron.nxdl.xml index b087b0c790..ab6decdb31 100644 --- a/base_classes/NXcg_polyhedron.nxdl.xml +++ b/base_classes/NXcg_polyhedron.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -61,7 +61,7 @@ for clean graph-based descriptions of polyhedra.--> For the description of more complicated manifolds and especially for polyhedra with holes, users are advised to check if their particular needs are described - by creating customized instances of an :ref:`NXcg_polygon_set`. + by creating customized instances of an :ref:`NXcg_polygon`. @@ -101,12 +101,12 @@ for clean graph-based descriptions of polyhedra.--> Combined storage of all primitives of all polyhedra. - + Individual storage of each polyhedron. - + Individual storage of each polygon as a graph. diff --git a/base_classes/NXcg_polyline.nxdl.xml b/base_classes/NXcg_polyline.nxdl.xml index f57d0c53f6..fc2d1b5cf8 100644 --- a/base_classes/NXcg_polyline.nxdl.xml +++ b/base_classes/NXcg_polyline.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -54,9 +54,16 @@ multiple vertices possible with the same point coordinates but different names.- Each polyline is built from a sequence of vertices (points with identifiers). Each polyline must have a start and an end point. - The sequence describes the positive traversal along the polyline when + The sequence describes the traversal along the polyline when walking from the first to the last vertex. + + + Reference to an instance of :ref:`NXcg_point` which defines the + location of the vertices that are referred to in this + NXcg_polyline instance. + + The total number of vertices that have different positions. @@ -71,8 +78,6 @@ multiple vertices possible with the same point coordinates but different names.- The total number of vertices of each polyline, irrespectively whether vertices are shared by vertices or not. - See the docstring for polylines for further details about how - a set with different polyline members should be stored. @@ -99,9 +104,6 @@ they share the same position in space but have different identifiers.--> - If true indicates that the vertices are all placed at different @@ -114,9 +116,9 @@ and then use--> Sequence of identifier for vertices how they build each polyline. A trivial example is a set with two polylines with three vertices each. - If the polylines meet in a junction, say the second vertex is shared - and marking the junction between the two polylines, it is possible that - there are only five unique positions. This suggests to store five + If the polylines meet at a vertex (assume for example that the second vertex + is shared and marking the junction between the two polylines), it is possible + that there are only five unique positions. This suggests to store five unique vertices. A non-trivial example is a set with several polylines. Assume that each @@ -127,9 +129,9 @@ and then use--> followed by the second vertex of the first polyline, until the last vertex of the first polyline. Thereafter, the first vertex of the second polyline, and so on and so forth. - Using the (cumulated) counts in number_of_vertices, the vertices of the - n-th polyline can be accessed on the following array index interval: - :math:`[\sum_{i=0}^{i=N-1}, \sum_{i=0}^{i=N}]`. + Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`), + the vertices of the N-th polyline can be accessed on the array + index interval :math:`[\sum_{i=0}^{i=N-1} n^v_i, \sum_{i=0}^{i=N} n^v_i]`. diff --git a/base_classes/NXcg_primitive.nxdl.xml b/base_classes/NXcg_primitive.nxdl.xml index 034216a3e0..efdbc40e78 100644 --- a/base_classes/NXcg_primitive.nxdl.xml +++ b/base_classes/NXcg_primitive.nxdl.xml @@ -3,7 +3,7 @@ - - + The symbols used in the schema to specify e.g. dimensions of arrays. - The dimensionality of the space. + The dimensionality of the embedding space. @@ -63,9 +43,6 @@ on your data...--> Primitives must neither be degenerated nor self-intersect. Individual primitives can differ in their properties (e.g. size, shape, rotation). - Reference to an instance of :ref:`NXcoordinate_system` in which these primitives @@ -74,9 +51,10 @@ to enable an instantiation of the actual geometric primitives--> - The dimensionality of the primitive set. + The dimensionality of the primitive set with value up to d. + @@ -84,7 +62,7 @@ to enable an instantiation of the actual geometric primitives--> - The cardinality of the primitive set. + The cardinality of the primitive set. Value should be equal to c. @@ -115,14 +93,13 @@ to enable an instantiation of the actual geometric primitives--> - The center of mass position of each primitive. + The center of each primitive - True if the center is a center of mass. @@ -133,7 +110,7 @@ to enable an instantiation of the actual geometric primitives--> - A qualitative description of the shape of each primitive. + Shape of each primitive @@ -142,9 +119,9 @@ to enable an instantiation of the actual geometric primitives--> - Qualifier for the length of characteristic features of the primitive. + Length of each primitive - Often the term length is associated with the assumption that one + Often the term is associated with the assumption that one edge is parallel to an axis of the coordinate system. @@ -153,8 +130,21 @@ to enable an instantiation of the actual geometric primitives--> - Qualifier often used to describe the length of one characteristic edge - within the coordinate system. + Width of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + + + + + + + + Height of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. @@ -168,11 +158,13 @@ to enable an instantiation of the actual geometric primitives--> - + Volume of each primitive. Set to NaN if does not apply for primitives for which is_closed is False. + Volume is an N-D concept for values of dimensionality larger than 1, + Area is an alias for the two-dimensional case. @@ -201,12 +193,53 @@ to enable an instantiation of the actual geometric primitives--> - - - - + + + Do the primitives define a mesh. + + + + + Do the primitives define a triangle mesh or not. + + + + + Do the primitives discretize the surface of an object or not. + + + + + Do the primitives define a geodesic mesh or not. + + A geodesic surface mesh is a triangulated surface mesh with metadata which + can be used as an approximation to describe the surface of a sphere. + Triangulation of spheres are commonly used in Materials Science + for quantifying texture of materials, i.e. the relative rotation of + crystals to sample directions. + + For additional details or an introduction into the topic of geodesic meshes + see (from which specifically the section on subdivision schemes is relevant). + + * `E. S. Popko and C. J. Kitrick <https://doi.org/10.1201/9781003134114>`_ + + Earth scientists have specific demands and different views about what should + be included in such a base class, given that nested geodesic meshes are a key + component of climate modelling software. For now we propose to use this + base class as a container for organizing data related to geodesic meshes. + + Specifically an instance of this base class should detail the rule set how + e.g. a geodesic (surface) mesh was instantiated as there are many + possibilities to do so. + + + + + Possibility to store details such as when primitives form a (specific) type + of mesh such as geodesic meshes. + + + + + diff --git a/base_classes/NXcg_roi.nxdl.xml b/base_classes/NXcg_roi.nxdl.xml index 69bc0042e5..b82fe7852a 100644 --- a/base_classes/NXcg_roi.nxdl.xml +++ b/base_classes/NXcg_roi.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. Use the depends_on fields of the respective specialized - :ref:`NXcg_primitive_set` base class surplus + :ref:`NXcg_primitive` base class surplus :ref:`NXcoordinate_system_set` with at least one instance of :ref:`NXcoordinate_system` to define explicitly the reference frame in which the primitives are defined. Alternatively, although @@ -46,12 +46,11 @@ eventually redundant NXsolid_geometry?--> region in space (and time) where an observation is made or for which a computer simulation is performed with given boundary conditions. - - - - - - + + + + + +see comment to NXcg_triangle roi--> diff --git a/base_classes/NXcg_tetrahedron.nxdl.xml b/base_classes/NXcg_tetrahedron.nxdl.xml index 509347c515..224f38de3a 100644 --- a/base_classes/NXcg_tetrahedron.nxdl.xml +++ b/base_classes/NXcg_tetrahedron.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -58,29 +58,19 @@ - Combined storage of all primitives of all tetrahedra. - + - Individual storage of each tetrahedron. + Individual storage of each tetrahedron. - + - Individual storage of each tetrahedron as a graph. + Individual storage of each tetrahedron as a graph. diff --git a/base_classes/NXcg_triangle.nxdl.xml b/base_classes/NXcg_triangle.nxdl.xml index 7d994eb3e9..03adf17d2b 100644 --- a/base_classes/NXcg_triangle.nxdl.xml +++ b/base_classes/NXcg_triangle.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -58,18 +58,13 @@ in file formats such as OFF, PLY, VTK, or STL. - + Individual storage of each triangle. Users are advised that using such individual storage of primitives may be less storage efficient than creating a combined storage. - Length of the edges of each triangle. diff --git a/base_classes/NXcg_unit_normal.nxdl.xml b/base_classes/NXcg_unit_normal.nxdl.xml index 21470b34f0..ea5bcb6792 100644 --- a/base_classes/NXcg_unit_normal.nxdl.xml +++ b/base_classes/NXcg_unit_normal.nxdl.xml @@ -3,7 +3,7 @@ - + @@ -46,7 +46,7 @@ rather make this a set of vectors, irrespective whether these are unit or not--> Computational geometry description of a set of (oriented) unit normal vectors. Store normal vector information as properties of primitives. - Use only only as a child of an instance of :ref:`NXcg_primitive_set` + Use only only as a child of an instance of :ref:`NXcg_primitive` so that this instance acts as the parent to define a context. @@ -60,7 +60,7 @@ rather make this a set of vectors, irrespective whether these are unit or not--> - Qualifier which details the orientation of each normal vector + An indicator which details the orientation of each normal vector in relation to its primitive, assuming the object is viewed from a position outside the object. From f39d3c5a7923c4aec3c016243e91b552b625fd68 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 14:52:58 +0100 Subject: [PATCH 45/75] Update docs to remove non-cg-related classes, which should be moved into an own modularized part for computer and microstructure --- .../cgms-structure.rst | 208 ++++-------------- 1 file changed, 47 insertions(+), 161 deletions(-) diff --git a/manual/source/classes/contributed_definitions/cgms-structure.rst b/manual/source/classes/contributed_definitions/cgms-structure.rst index 4fe1232c9a..af55e2ae59 100644 --- a/manual/source/classes/contributed_definitions/cgms-structure.rst +++ b/manual/source/classes/contributed_definitions/cgms-structure.rst @@ -1,207 +1,93 @@ .. _CgmsFeatures-Structure: -============================ -Geometry and microstructures -============================ +========================= +Geometry & Microstructure +========================= .. index:: - IntroductionCgms - PhysicsCgms - CgmsAppDef CgmsBC - -.. _IntroductionCgms: - -Introduction -############ - -The computational-geometry/microstructure-modeling-based part of the proposal -has the following aims: - -First, to contribute to efforts on standardizing a controlled vocabulary, definitions for terms, -and relations between terms, for computational-geometry-based descriptions of the structure of -materials and atomic configurations used when characterizing materials in experiments -and computer simulations. - -As far as NeXus is concerned, this proposed set of geometric primitives offer -a complementary alternative to the current set of base classes in NeXus for -constructive solid geometry (CSG) such as :ref:`NXcsg`, :ref:`NXoff_geometry`, or :ref:`NXquadric`. - -Second, to explore how terms which are frequently used by materials scientists in the field of -condensed-matter physics can be harmonized with definitions and terms offer by the NOMAD MetaInfo -description. NOMAD MetaInfo is the data schema of the NOMAD research data management system. - -Third, to yield a substantiated set of arguments and suggestions how descriptors for the structure -and the atomic architecture of materials can be harmonized. Especially this proposal reaches out to -other materials-science-related projects and consortia including the activities in the German NFDI -FAIRmat, NFDI-MatWerk, NFDI4Ing, NFDI4Chem, NFDI4Cat, MaRDI, and DAPHNE. - -.. _PhysicsCgms: - -Physics background -################## -Microstructural features or crystal defects are spatial arrangements of atoms. -Given their specific atomic arrangement and composition, such features have -specific constraints on the degrees of freedom. This causes these defects to have specific -properties (thermodynamic observables/descriptors). Provided well-defined coarse-graining procedures -are used and regions-of-interest and/or regions-of-applicability are defined, microstructural -features are often characterized and modelled to have associated thermodynamic descriptors. - -Another motivation for the proposal was the observation that frequently the design -of file formats for simulation software in the computational materials science especially -at the interface between condensed-matter physics and materials engineering are frequently -reimplementing the wheel when it comes to making decision how to store e.g. atom and feature positions -or how to document the shape of regions-of-interest, grids, crystals, grains, precipitates, and dislocations. -This generates a diversity of file formats and data schemas which hampers semantic interpretation -and interoperability. - -Maybe this is a historical burden given the large set of technical terms in place which then -motivated pragmatic solutions that have resulted in many research groups having developed -similar formats using similar descriptions. - -Defining crystal defects is a question of how to coarse-grain a given spatiotemporal set of atoms, -each having a nuclide type and position/trajectory. Different mathematical/geometrical methods exists -to determine how a point, a line, a surface, or a volumetric defect can be described and be spatiotemporally constrained through a geometrical model -with defined primitives and associated observables. - -The key motivation to such coarse-graining is to reduce the complexity of the description. -On the one hand to support visualization and scientific analyses - not only of crystal defect arrangements. -On the other hand it is the hope that using descriptors at a coarser level, i.e. nanometer, micrometer, and larger, -are still sufficiently accurate and precise to yield descriptors which avoid that one has -to account for the dynamics of each atom to predict or understand the properties -of defects and their dynamics. - -Experience has shown that computational-geometry-based descriptions -when combined with hierarchical clustering/labeling methods, applied on sets of -atoms and features turn out to yield useful descriptors. Examples include point, -line, surface defects, such as vacancies, solute cluster, dislocations, -disconnections, interfaces to name but a few. - .. _CgmsBC: Base Classes ############ -The following base classes are defined to incentivize the use of NeXus for using -computational-geometry-based descriptions. In what follows, base classes +The following base classes are defined to incentivize the use of NeXus for +using computational-geometry-based descriptions. In what follows, base classes for frequently used shapes and geometric primitives are proposed: - :ref:`NXcg_primitive_set`: - A base class to inherit from when defining base classes for specific primitives such as these: + :ref:`NXcg_ellipsoid`: + A description for a set of possibly dissimilar oriented ellipsoids. - :ref:`NXcg_sphere_set`: - A base class for a set of possibly dissimilar spheres. + :ref:`NXcg_cylinder`: + A description for a set of possibly dissimilar oriented cylinders. - :ref:`NXcg_ellipsoid_set`: - A base class for a set of possibly dissimilar rotated ellipsoids. + :ref:`NXcg_point`: + A collection of points with labels. - :ref:`NXcg_cylinder_set`: - A base class for a set of possibly dissimilar rotated cylinders. + :ref:`NXcg_polyline`: + A collection of lines and linear segments. - :ref:`NXcg_point_set`: - A base class for a collection of points with labels or mark data. + :ref:`NXcg_triangle`: + A collection of triangles. - :ref:`NXcg_polyline_set`: - A base class for a collection of lines and linearized segments. + :ref:`NXcg_parallelogram`: + A collection of possibly dissimilar parallelograms. - :ref:`NXcg_triangle_set`: - A base class for a collection (or soup) of triangles. + :ref:`NXcg_polygon`: + A collection of polygons. - :ref:`NXcg_parallelogram_set`: - A base class for a collection of possibly dissimilar parallelograms. + :ref:`NXcg_polyhedron`: + A collection of polyhedra. - :ref:`NXcg_triangulated_surface_mesh`: - A base class for a collection and/or mesh of triangles. - - :ref:`NXcg_polygon_set`: - A base class for a collection (or soup) of polygons. - - :ref:`NXcg_polyhedron_set`: - A base class for a collection (or soup) of polyhedra. - - :ref:`NXcg_roi_set`: + :ref:`NXcg_roi`: A container to host a number of different types of primitives. - :ref:`NXcg_tetrahedron_set`: - A base class for a collection (or soup) of tetrahedra. + :ref:`NXcg_tetrahedron`: + A collection of tetrahedra. - :ref:`NXcg_hexahedron_set`: - A base class for a collection (or soup) of hexahedra to represent - e.g. simpler (bounding) boxes for e.g. binary trees. + :ref:`NXcg_hexahedron`: + A collection of hexahedra with capabilities to represent + also simpler (bounding) boxes for e.g. binary trees. -These base classes make use of base classes which describe data structures: +These base classes describe data structures used for more complex geometries: :ref:`NXcg_face_list_data_structure`: - A base class to store the usual way how polygon/polyhedra data are reported: - Via a list of vertices and faces with identifiers and properties. + In essence, the usual way how polygon/polyhedra data are reported: + A list of vertices and faces with identifier and properties. :ref:`NXcg_half_edge_data_structure`: - A base class for more advanced but more efficiently traversable data structure: - A half-edge data structure is a useful complementary descriptor for - polygon/polyhedra which enables topological analyses and traversal of half-edges - about a topology of primitives. - - :ref:`NXcg_unit_normal_set`: - A base class for storing primitive unit normal vectors. + A half-edge data structure (also known as a doubly connected edge list) + is a useful complementary descriptor for polygon/polyhedra which enables + topological analyses and traversal of the graph of how polygons and + polyhedra are connected. - :ref:`NXcg_geodesic_mesh`: - Geodesic meshes are useful for all applications when meshing the surface of a sphere - with many applications in the analyses of diffraction data. + :ref:`NXcg_unit_normal`: + As an additional structuring element especially for meshes, well-documented + normal information is crucial for distance computations. :ref:`NXcg_alpha_complex`: Alpha shapes and alpha wrappings, specifically the special case of the convex hull, are frequently used geometrical models for describing a boundary or edge to a set of geometric primitives. -Furthermore, a few base classes are defined for documenting the working with -discretized representations of material (area or volume) which can be useful -not only for stencil-based methods: +Next, a few base classes are defined for documenting discretized representations +of material (area or volume) which can be useful not only for stencil-based methods: :ref:`NXcg_grid`: - A base class for a grid of cells discretizing e.g. a computational domain - or computation with models using representative volume elements (RVEs). + A grid of cells. :ref:`NXisocontour`: - A base class for isocontour descriptions. - - :ref:`NXcg_marching_cubes`: - A base class to store metadata of a specific implementation of - the Marching Cubes algorithm, whose sensitivity to specific topological - configurations is known to result in different triangle soups. - This is relevant e.g. for computations of isocontours. + A description for isocontour descriptions. :ref:`NXdelocalization`: - A base class to document procedures whereby a scalar field - is smoothened in a controlled manner (typically using kernel methods). + An approach to document procedures whereby a scalar field + is smoothed in a controlled manner. :ref:`NXsimilarity_grouping`: - A base class to describe clustering of objects (such as atoms or features). - - :ref:`NXrotation_set`: - A base class to describe the relative orientation or rotation members - of a set of features/objects. - - :ref:`NXchemical_composition`: - A base class to document (chemical) composition of a sample or a set of things. - -Finally, the following base classes allow data processing software to document its -input parameters and to summarize its performance statistics: - - :ref:`NXprogram`: - A base class for a specifically named and versioned program or library/component. - - :ref:`NXcs_filter_boolean_mask`: - A base class for a boolean mask. - - :ref:`NXcs_prng`: - A base class for settings of a pseudo-random number generator (PRNG) algorithm. - - :ref:`NXcs_profiling`: - A base class for holding a set of :ref:`NXcs_profiling_event` instances. + An alternative for NXclustering. - :ref:`NXcs_profiling_event`: - A base class for documenting profiling/benchmark for an algorithm or computational step. + :ref:`NXclustering`: + A description for clustering of objects (such as atoms or features). - :ref:`NXcs_computer`: - Base class for describing a computer and its components. +TODO CHECK THAT MICROSTRUCTURE PART IS COVERED IN ICME WHEN MICROSTRUCTURE PROPOSAL SYNCED UP From f441a9972da8abcf2c138900aa1c5a11afe5dc78 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Sun, 9 Mar 2025 15:03:30 +0100 Subject: [PATCH 46/75] Syncing up with niac changes on fairmat PR #1421, introducing concept name refactorings for the now dropped _set for all classes that refer to a NXcg class --- .../NXapm_paraprobe_clusterer_config.nxdl.xml | 8 ++--- .../NXapm_paraprobe_distancer_config.nxdl.xml | 8 ++--- ...Xapm_paraprobe_intersector_config.nxdl.xml | 2 +- .../NXapm_paraprobe_nanochem_config.nxdl.xml | 26 ++++++++-------- .../NXapm_paraprobe_nanochem_results.nxdl.xml | 18 +++++------ .../NXapm_paraprobe_ranger_config.nxdl.xml | 8 ++--- .../NXapm_paraprobe_selector_config.nxdl.xml | 8 ++--- .../NXapm_paraprobe_spatstat_config.nxdl.xml | 8 ++--- .../NXapm_paraprobe_surfacer_config.nxdl.xml | 8 ++--- .../NXapm_paraprobe_surfacer_results.nxdl.xml | 4 +-- ...Xapm_paraprobe_tessellator_config.nxdl.xml | 8 ++--- ...apm_paraprobe_tessellator_results.nxdl.xml | 4 +-- .../NXapm_paraprobe_tool_config.nxdl.xml | 2 +- .../NXcrystal_structure.nxdl.xml | 2 +- contributed_definitions/NXem_ebsd.nxdl.xml | 2 +- .../NXgraph_edge_set.nxdl.xml | 2 +- .../NXgraph_node_set.nxdl.xml | 2 +- .../NXlab_sample_mounting.nxdl.xml | 2 +- .../NXmicrostructure.nxdl.xml | 30 +++++++++---------- .../NXmicrostructure_score_results.nxdl.xml | 4 +-- .../NXoptical_system_em.nxdl.xml | 2 +- contributed_definitions/NXscanbox_em.nxdl.xml | 2 +- .../NXspatial_filter.nxdl.xml | 8 ++--- 23 files changed, 84 insertions(+), 84 deletions(-) diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml index 21897a43b9..f02c2064f2 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml @@ -141,7 +141,7 @@ doc: | - + @@ -149,7 +149,7 @@ doc: | - + @@ -157,7 +157,7 @@ doc: | - + @@ -165,7 +165,7 @@ doc: | - + diff --git a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml index e7d6d7917b..19b8ed4555 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml @@ -60,7 +60,7 @@ - + @@ -68,7 +68,7 @@ - + @@ -76,7 +76,7 @@ - + @@ -84,7 +84,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml index efdbdf9aeb..d7ed8a3284 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml @@ -155,7 +155,7 @@ Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the - members of the set as instances of NXcg_polyhedron_set. + members of the set as instances of NXcg_polyhedron. diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml index b97f85195f..e0fe160027 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -148,7 +148,7 @@ - + @@ -156,7 +156,7 @@ - + @@ -164,7 +164,7 @@ - + @@ -172,7 +172,7 @@ - + @@ -634,7 +634,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -642,7 +642,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -650,7 +650,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -658,7 +658,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> - + @@ -943,7 +943,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -951,7 +951,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -959,7 +959,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -967,7 +967,7 @@ from normals of neighboring facets, type of weighting schemes can affect results - + @@ -998,7 +998,7 @@ identifier(NX_UINT):--> for composition analyses via positioning and rotating them via a graphical user interface (such as in IVAS / AP Suite). - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml index 4b8e2d3a55..93c840320e 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml @@ -220,7 +220,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + A tight axis-aligned bounding box about the grid. @@ -527,7 +527,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + The resulting triangle soup computed via marching cubes. @@ -587,7 +587,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + Direction of each normal. @@ -611,9 +611,9 @@ The cardinality/total number of triangles in the triangle soup.--> - - + Direction of each normal. @@ -810,7 +810,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + An oriented bounding box (OBB) to each object. @@ -869,7 +869,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + - + The triangle surface mesh representing the interface model. Exported at state before or after the next DCOM step. @@ -1120,7 +1120,7 @@ face_identifier_offset(NX_UINT):--> - + The ROIs are defined as cylinders for the computations. To visualize these we discretize them into regular n-gons. Using for instance 360-gons, i.e. a regular n-gon with 360 edges, diff --git a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml index 3282c203db..e0c48c0d6f 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml @@ -72,7 +72,7 @@ - + @@ -80,7 +80,7 @@ - + @@ -88,7 +88,7 @@ - + @@ -96,7 +96,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml index 89484faa9f..7b3e5f70c5 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml @@ -60,7 +60,7 @@ - + @@ -68,7 +68,7 @@ - + @@ -76,7 +76,7 @@ - + @@ -84,7 +84,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml index 5f4b26836a..05819027e5 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml @@ -133,7 +133,7 @@ - + @@ -141,7 +141,7 @@ - + @@ -149,7 +149,7 @@ - + @@ -157,7 +157,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml index 3cb04dac60..03736cac90 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml @@ -70,7 +70,7 @@ - + @@ -78,7 +78,7 @@ - + @@ -86,7 +86,7 @@ - + @@ -94,7 +94,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml index fa2bbd8825..377b4c6c9f 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml @@ -149,7 +149,7 @@ for eventually performed preprocessing--> - + The set of triangles in the coordinate system paraprobe which discretizes the exterior surface of the alpha complex. @@ -196,7 +196,7 @@ for eventually performed preprocessing--> - + The set of tetrahedra which represent the interior volume of the complex if that is a closed two-manifold. diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml index bf91256517..bac46a1b36 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml @@ -67,7 +67,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + @@ -75,7 +75,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + @@ -83,7 +83,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + @@ -91,7 +91,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml index dbfa7dc94c..1348671608 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml @@ -73,7 +73,7 @@ - + The (tight) axis-aligned bounding box about the point cloud. @@ -96,7 +96,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml index c2169cc139..579eccb2b4 100644 --- a/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tool_config.nxdl.xml @@ -116,7 +116,7 @@ base class from which tool-specific appdefs inherit--> + an instance of :ref:`NXcg_triangle` is stored.--> Specification of the point-to-triangulated-surface-mesh distances to diff --git a/contributed_definitions/NXcrystal_structure.nxdl.xml b/contributed_definitions/NXcrystal_structure.nxdl.xml index e01993be3e..90cbb13f31 100644 --- a/contributed_definitions/NXcrystal_structure.nxdl.xml +++ b/contributed_definitions/NXcrystal_structure.nxdl.xml @@ -196,7 +196,7 @@ used algorithm. Dictionary-based alternatives are emerging.--> - + Atom positions. diff --git a/contributed_definitions/NXem_ebsd.nxdl.xml b/contributed_definitions/NXem_ebsd.nxdl.xml index a1926fef46..9fd2495181 100644 --- a/contributed_definitions/NXem_ebsd.nxdl.xml +++ b/contributed_definitions/NXem_ebsd.nxdl.xml @@ -608,7 +608,7 @@ we make this only required as people may not yet be so happy with having to walk a graph from measurement -> path -> NXevent_data_em -> em_lab/ebeam_deflector to retrieve the actual scan positions although this would be cleaner, also scan_point_positions could be -an instance of NXcg_point_set with a depends_on pointing +an instance of NXcg_point with a depends_on pointing to sample_reference_frame --> diff --git a/contributed_definitions/NXgraph_edge_set.nxdl.xml b/contributed_definitions/NXgraph_edge_set.nxdl.xml index da83632506..7ec795af3a 100644 --- a/contributed_definitions/NXgraph_edge_set.nxdl.xml +++ b/contributed_definitions/NXgraph_edge_set.nxdl.xml @@ -59,7 +59,7 @@ :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing use the field identifier. For implicit indexing, - consult :ref:`NXcg_primitive_set` to get guidance how to set identifier_offset. + consult :ref:`NXcg_primitive` to get guidance how to set identifier_offset. diff --git a/contributed_definitions/NXgraph_node_set.nxdl.xml b/contributed_definitions/NXgraph_node_set.nxdl.xml index 977f3d1120..65e6899311 100644 --- a/contributed_definitions/NXgraph_node_set.nxdl.xml +++ b/contributed_definitions/NXgraph_node_set.nxdl.xml @@ -84,7 +84,7 @@ :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing use the field identifier. For implicit indexing, - consult :ref:`NXcg_primitive_set` to get guidance how to set identifier_offset. + consult :ref:`NXcg_primitive` to get guidance how to set identifier_offset. diff --git a/contributed_definitions/NXlab_sample_mounting.nxdl.xml b/contributed_definitions/NXlab_sample_mounting.nxdl.xml index eeb34a01bc..a9ae2e097a 100644 --- a/contributed_definitions/NXlab_sample_mounting.nxdl.xml +++ b/contributed_definitions/NXlab_sample_mounting.nxdl.xml @@ -86,7 +86,7 @@ borrow from NXlab_thermo_mechanical_processing to document the external stimuli (eventually) applied during mounting temperature, mechanical, magnetic, electro-magnetic, are externally applied stimuli on the sample, can we use one master schema? -e.g. one can even store NXcg_polyhedron_set and NXcg_face_list_data_structure +e.g. one can even store NXcg_polyhedron and NXcg_face_list_data_structure instances to keep track of the geometry of specific instrument and how the samples were arranged in these key question is which steps has the sample experienced?--> diff --git a/contributed_definitions/NXmicrostructure.nxdl.xml b/contributed_definitions/NXmicrostructure.nxdl.xml index d839b72cfe..2d941e5af6 100644 --- a/contributed_definitions/NXmicrostructure.nxdl.xml +++ b/contributed_definitions/NXmicrostructure.nxdl.xml @@ -218,11 +218,11 @@ the idea is we may wish to run as many grain reconstructions as we want and add - - - - - + + + + + Reference to an instance of: - * :ref:`NXcg_polyline_set` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) - * :ref:`NXcg_polygon_set` for a two-dimensional representation as only a projection is available (like in most experiments) - * :ref:`NXcg_polyhedron_set` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions + * :ref:`NXcg_polyline` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) + * :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions (like in computer simulations or 3D experiments) which represent the geometrical entities of the discretization. @@ -352,8 +352,8 @@ examples for specific frequently discussed microstructural features--> Reference to an instance of: - * :ref:`NXcg_point_set` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) - * :ref:`NXcg_polyline_set` or :ref:`NXcg_polygon_set` for a two-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) + * :ref:`NXcg_polyline` or :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks (like in computer simulations or 3D experiments) @@ -480,11 +480,11 @@ examples for specific frequently discussed microstructural features--> Reference to an instance of: - * :ref:`NXcg_point_set` for a one-dimensional representation as only a projection is available (like in most experiments) - * :ref:`NXcg_polyline_set` for a two-dimensional representation as only a projection is available - * :ref:`NXcg_polygon_set` for a two-dimensional representation in the (seldom) case of sufficient spatial resolution + * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_polyline` for a two-dimensional representation as only a projection is available + * :ref:`NXcg_polygon` for a two-dimensional representation in the (seldom) case of sufficient spatial resolution and the line in the projection plane or cases where triple junction locations are approximated e.g. using a set of triangles - * :ref:`NXcg_polyhedron_set` for a three-dimensional representation via e.g. a representation of Voronoi cells about atoms + * :ref:`NXcg_polyhedron` for a three-dimensional representation via e.g. a representation of Voronoi cells about atoms * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks which represent the geometrical entities of the discretization. @@ -632,7 +632,7 @@ EXAMPLES FOR DESCRIPTOR VALUES--> Reference to an instance of: - * :ref:`NXcg_point_set` + * :ref:`NXcg_point` * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks diff --git a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml index 295b582891..deb666d28b 100644 --- a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -205,12 +205,12 @@ inspect comments behind NXmicrostructure--> - + A tight bounding box or sphere or bounding primitive about the grid. +https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallelepiped--> How many distinct boundaries are distinguished? diff --git a/contributed_definitions/NXoptical_system_em.nxdl.xml b/contributed_definitions/NXoptical_system_em.nxdl.xml index b0546c8c77..f38e6cff5a 100644 --- a/contributed_definitions/NXoptical_system_em.nxdl.xml +++ b/contributed_definitions/NXoptical_system_em.nxdl.xml @@ -81,7 +81,7 @@ the probe_current is equal to the beam_current only right at the surface where t inserting a Faraday cup in the beam path measures the beam_current (along a specific location on the beam before it enters the specimen but it is often assumed for the practical reason that measuring right at the surface that the beam current is the probe current.--> - + Geometry of the cross-section formed when the primary beam shines onto the specimen surface. diff --git a/contributed_definitions/NXscanbox_em.nxdl.xml b/contributed_definitions/NXscanbox_em.nxdl.xml index e0593714c1..a2ac1f2495 100644 --- a/contributed_definitions/NXscanbox_em.nxdl.xml +++ b/contributed_definitions/NXscanbox_em.nxdl.xml @@ -105,7 +105,7 @@ (NXlens_em):--> - diff --git a/contributed_definitions/NXspatial_filter.nxdl.xml b/contributed_definitions/NXspatial_filter.nxdl.xml index 7103ab86b8..1a3e685072 100644 --- a/contributed_definitions/NXspatial_filter.nxdl.xml +++ b/contributed_definitions/NXspatial_filter.nxdl.xml @@ -81,9 +81,9 @@ otherwise the filter falls back to entire dataset.--> - - - - + + + + From 8168db851e645f6159d8eb1cce9e6a8d96c612e6 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 10:09:55 +0100 Subject: [PATCH 47/75] Syncing up with NIAC changes on PR #1423 em, applications directory --- {contributed_definitions => applications}/NXem.nxdl.xml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {contributed_definitions => applications}/NXem.nxdl.xml (100%) diff --git a/contributed_definitions/NXem.nxdl.xml b/applications/NXem.nxdl.xml similarity index 100% rename from contributed_definitions/NXem.nxdl.xml rename to applications/NXem.nxdl.xml From 5458e8b3575f0b8c2fc311cc5a1cc6bab4ccaf74 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 10:10:23 +0100 Subject: [PATCH 48/75] Syncing up with NIAC changes on PR #1423 em, applications directory, em appdef changes --- applications/NXem.nxdl.xml | 1248 ++++++++++++++++-------------------- 1 file changed, 544 insertions(+), 704 deletions(-) diff --git a/applications/NXem.nxdl.xml b/applications/NXem.nxdl.xml index 5964f80b86..3478c40cdc 100644 --- a/applications/NXem.nxdl.xml +++ b/applications/NXem.nxdl.xml @@ -3,7 +3,7 @@ - Application definition for normalized representation of electron microscopy research. - - This application definition is a comprehensive example for a general description - with which to normalize specific pieces of information and data collected within - electron microscopy research. - - NXem is designed to be used for documenting experiments or computer simulations in which - controlled electron beams are used for studying electron-beam matter interaction to explore - physical mechanisms and phenomena, or to characterize materials with an electron microscope. + Application definition for normalized representation of electron microscopy research. + + This application definition is a comprehensive example for a general description + with which to normalize specific (meta)data collected from the research field + of electron microscopy + + NXem is designed to be used for documenting experiments or computer simulations in which + controlled electron beams are used for studying electron-beam matter interaction to explore + physical mechanisms and phenomena or to characterize materials with an electron microscope. - +but for practical purposes currently is interpretable only by human to provide them further contextualization +-| recommended: xref part ideally also as a list of triple (spec, term, url to uri)--> - - The configuration of the I/O writer software (e.g. `pynxtools <https://github.com/FAIRmat-NFDI/pynxtools>`_ or its plugins) - which was used to generate this NeXus file instance. + The configuration of the software that was used to generate this NeXus file. - + - A collection of all programs and libraries that are considered as relevant - to understand with which software tools this NeXus file instance was - generated. Ideally, to enable a binary recreation from the input data. - - Examples include the name and version of the libraries used to write the - instance. Ideally, the software which writes these NXprogram instances - also includes the version of the set of NeXus classes i.e. the specific - set of base classes, application definitions, and contributed definitions - with which the here described concepts can be resolved. - - For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ - which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ - research data management system, it makes sense to store e.g. the GitHub - repository commit and respective submodule references used. + A collection of all programs and libraries that are considered as relevant + to understand with which software tools this NeXus file instance was + generated. Ideally, to enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific set + of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ + which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + + Instances of programID can also be used to document the modules and + libraries that are offered by the computational environment such as those + parsed from conda or python virtualenv environments. - + - Ideally, a (globally) unique persistent identifier for referring to this experiment. - - An experiment should be understood in that this can be an experiment - in reality or a computer simulation because also the latter is an experiment - (see the Cambridge Dictionary experiment *a test done in order to find out - something, eg if an idea is correct*). - - The identifier is usually issued by the facility, laboratory, or the principle investigator. - The identifier enables to link experiments/simulations to e.g. proposals. + Ideally, a (globally) unique persistent identifier for referring to this experiment. + + An experiment should be understood in that this can be an experiment + in reality or a computer simulation because also the latter is an experiment + (see the Cambridge Dictionary experiment *a test done in order to find out + something, eg if an idea is correct*). + + The identifier is usually issued by the facility, laboratory, or the principle investigator. + The identifier enables to link experiments/simulations to e.g. proposals. - - - - - + + - Alias which scientists can easier identify this experiment by. + Alias (short name) which scientists can use to refer to this experiment. - Free-text description about the experiment. - - Users are strongly advised to parameterize the description of their experiment - by using respective groups and fields and base classes instead of writing prose - into the field. The reason is that such free-text field is difficult to machine-interpret. - The motivation behind keeping this field for now is to learn in how far the - current base classes need extension based on user feedback. + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into the field. The reason is that such free-text field is difficult to machine-interpret. + The motivation behind keeping this field for now is to learn in how far the + current base classes need extension based on user feedback. - ISO 8601 time code with local time zone offset to UTC information included - when the microscope session started. If the application demands that time - codes in this section of the application definition should only be used - for specifying when the experiment was performed - and the exact - duration is not relevant use this start_time field. - - Often though it is useful to specify a time interval via setting both a start_time - and an end_time because this enables software tools and users to collect a - more detailed bookkeeping of the experiment. - - Users should be aware though that even with having both time instances - specified, it may not be possible to infer how long the experiment took or - for how long data were acquired. - - More detailed timing data over the course of the experiment have - to be collected to compute this. These computations can take - advantage of individual time stamps start_time and end_time - in :ref:`NXevent_data_em` instances. + ISO 8601 time code with local time zone offset to UTC information included + when the microscope session started. If the application demands that time + codes in this section of the application definition should only be used + for specifying when the experiment was performed - and the exact + duration is not relevant - use this start_time field. + + Often though it is useful to specify a time interval via setting both a start_time + and an end_time because this enables software tools and users to collect a + more detailed bookkeeping of the experiment. + + Users should be aware though that even using only start_time and end_time + may not be sufficient to infer how long the experiment took or for how long + data were acquired. To bookkeep more fine-grained timestamps over the + course of the experiment is possible with start_time and end_time fields + of respective :ref:`NXevent_data_em` instances. - ISO 8601 time code with local time zone offset to UTC included when - the microscope session ended. - - See docstring of the start_time field to see how to use the - start_time and end_time together. + ISO 8601 time code with local time zone offset to UTC included when + the microscope session ended. + + See docstring of the start_time field to see how to use the + start_time and end_time together. - - + + - Possibility to store a collection of serialized resources associated with the - experiment. - - An example how to use this set could be to document from which files, which have been - e.g. generated by software of technology partners, the information in an instance of - NXem was filled with during parsing or transcoding between different formats. + Collection of serialized resources associated with the experiment. + + An example how to use this set is to document from which files in formatting + of technology partners, the (meta)data in an instance of NXem were filled with + during parsing to NeXus. - + - - + - Information about persons who performed or were involved in the microscope - session or simulation run. - - This can be the principle investigator who performed this experiment or the student who performed simulations. - Adding multiple users if relevant is recommended. + Information about persons who performed or were involved in the microscope + session or simulation run. + + Examples could be to put here the principle investigator who performed this + experiment or students who performed simulations to name but a few. + Adding multiple users if relevant is recommended. + + The protection of personal data by laws is in different stages of development + and strictness. For this reason no field of a userID instance is required. + + + - Given (first) name and surname. + Given (first) name and surname. - Name of the affiliation at the point in time when the experiment was performed. + Name of the affiliation at the point in time when the experiment was performed. - Postal address of the affiliation. + Postal address of the affiliation. - Email address at the point in time when the experiment was performed. - - Writing the most permanently used email is recommended. + Email address at the point in time when the experiment was performed. + + Writing the most permanently used email is recommended. - Telephone number at the point in time when the experiment was performed. + Telephone number at the point in time when the experiment was performed. - User role at the point in time when the experiment was performed. - - Examples are technician operating the microscope, student, postdoc, - principle investigator, or guest. + User role at the point in time when the experiment was performed. + + Examples are technician operating the microscope, student, postdoc, + principle investigator, or guest. - - - Identifier offered by a service to report the user other than by using its name. - - Examples could be an ORCID or social media account of the user. - - - - - - A physical entity which contains material intended to be investigated. - Sample and specimen are treated as de facto synonyms. Samples can be real or virtual ones. - - This concept is related to term `Specimen`_ of the EMglossary standard. - - .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 + A physical entity which contains material intended to be investigated. + Sample and specimen are treated as de facto synonyms. Samples can be real or virtual ones. + + This concept is related to term `Specimen`_ of the EMglossary standard. + + .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 - Qualifier whether the sample is a real or a virtual one. + Qualifier whether the sample is a real or a virtual one. - + - Ideally, (globally) unique persistent identifier which distinguishes the sample from all others - and especially the predecessor/origin from where that sample was cut. The terms sample - and specimen are here considered as exact synonyms. - - This field must not be used for an alias! Instead, use name. - - In cases where multiple specimens were loaded into the microscope, the identifier has to resolve - the specific sample, whose results are stored by this :ref:`NXentry` instance because a single - NXentry should be used for the characterization of a single specimen. - - Details about the specimen preparation should be stored in resources referring to parent_identifier. + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others + and especially the predecessor/origin from where that sample was cut. The terms sample + and specimen are here considered as exact synonyms. + + This field must not be used for an alias for the sample! Instead, use name. + + In cases where multiple specimens were loaded into the microscope, the identifier has to resolve + the specific sample, whose results are stored by this :ref:`NXentry` instance because a single + NXentry should be used for the characterization of a single specimen. + + Details about the specimen preparation should be stored in resources referring to identifier_parent. - - - - - + + + - Identifier of the sample from which the sample was cut or the string *None*. - - The purpose of this field is to support functionalities for tracking - sample provenance in a research data management system. + Identifier of the sample from which the sample was cut or the string *None*, + i.e. the parent to this sample. + + The purpose of this field is to support functionalities for tracking + sample provenance in a research data management system. - - - - + + - ISO 8601 time code with local time zone offset to UTC information - when the specimen was prepared. - - Ideally, report the end of the preparation, i.e. the last known timestamp when - the measured specimen surface was actively prepared. Ideally, this matches - the last timestamp that is mentioned in the digital resource pointed to by - parent_identifier. - - Knowing when the specimen was exposed to e.g. specific atmosphere is especially - required for environmentally sensitive material such as specimen charged with hydrogen - or experiments including tracers that have a short halflife. Additional time stamps - prior to preparation_date should better be placed in resources which describe but - which do not pollute the description here with prose. Resolving these connected - pieces of information is considered the responsibility of the - research data management system not of a NeXus file. + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known timestamp when + the measured specimen surface was actively prepared. Ideally, this matches + the last timestamp that is mentioned in the digital resource pointed to by + identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is especially + required for material that is sensitive to the environment such as specimens that were + charged with fast diffusing elements or short-lived radioactive tracers. + + Additional time stamps prior to preparation_date should better be placed in resources + which describe but do not pollute the description here with prose. Resolving these + connected metadata is considered as within the responsibility of the + research data management system and not the a NeXus file. - An alias used to refer to the specimen to please readability for humans. + An alias used to refer to the specimen to please readability for humans. - List of comma-separated elements from the periodic table that are contained in the sample. - If the sample substance has multiple components, all elements from each component - must be included in atom_types. - - The purpose of the field is to offer research data management systems an opportunity - to parse the relevant elements without having to interpret these from the resources - pointed to by parent_identifier or walk through eventually deeply nested groups in - individual data instances. + List of comma-separated elements from the periodic table that are contained in the sample. + If the sample substance has multiple components, all elements from each component + must be included in atom_types. + + The purpose of the field is to offer research data management systems an opportunity + to parse the relevant elements without having to interpret these from the resources + pointed to by identifier_parent or walk through eventually deeply nested groups in + individual data instances. - (Measured) sample thickness. - - The information is recorded to qualify if the beam used was likely - able to shine through the specimen. For scanning electron microscopy, - in many cases the specimen is typically thicker than what is - illuminatable by the electron beam. - - In this case the value should be set to the actual thickness of - the specimen viewed for an illumination situation where the nominal - surface normal of the specimen is parallel to the optical axis. + (Measured) sample thickness. + + The information is recorded to qualify if the beam used was likely + able to shine through the specimen. For scanning electron microscopy, + in many cases the specimen is typically thicker than what is + illuminatable by the electron beam. + + In this case the value should be set to the actual thickness of the specimen + viewed for an illumination situation where the nominal surface normal of the + specimen is parallel to the optical axis. - - (Measured) density of the specimen. - - For multi-layered specimens this field should only be used to describe - the density of the excited volume. For scanning electron microscopy - the usage of this field is discouraged and instead an instance of an - :ref:`NXinteraction_vol_em` within individual :ref:`NXevent_data_em` - instances can provide a cleaner description of the relevant details - why one may wish to store the density of the specimen. + (Measured) density of the specimen. + + For multi-layered specimens this field should only be used to describe + the density of the excited volume. For scanning electron microscopy + the usage of this field is discouraged and instead an instance of a region-of-interest within connection to individual :ref:`NXevent_data_em` + instances can provide a cleaner description of the relevant details + why one may wish to store the density of the specimen. - Discouraged free-text field to provide further detail although adding - parent_identifier and having a working research data management system - should provide this contextualization. + Discouraged free-text field to provide further detail. - Set to hold different coordinate systems conventions. - - Inspect the description of the :ref:`NXcoordinate_system_set` and :ref:`NXcoordinate_system` base classes - how to define coordinate systems in NeXus. + Set to hold different coordinate systems conventions. + + Inspect the description of the :ref:`NXcoordinate_system_set` and :ref:`NXcoordinate_system` base classes + how to define coordinate systems in NeXus. @@ -364,17 +327,16 @@ are the ibeam description capabilities not sufficient enough?--> - Location of the origin of the processing_reference_frame. - - It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. - Edges are interpreted by inspecting the direction of their outer unit normals - (which point either parallel or antiparallel) along respective base vector direction - of the reference frame. - - If any of these assumptions is not met, the user is required to explicitly state this. + Location of the origin of the processing_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. - @@ -387,11 +349,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing x-axis base vector of the - processing_reference_frame. + Direction of the positively pointing x-axis base vector of the + processing_reference_frame. - @@ -402,11 +363,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing y-axis base vector of the - processing_reference_frame. + Direction of the positively pointing y-axis base vector of the + processing_reference_frame. - @@ -417,11 +377,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing z-axis base vector of the - processing_reference_frame. + Direction of the positively pointing z-axis base vector of the + processing_reference_frame. - @@ -434,8 +393,8 @@ are the ibeam description capabilities not sufficient enough?--> - Reference to the specifically named :ref:`NXsample` instance(s) for - which these conventions apply (e.g. /entry1/sample1). + Reference to the specifically named :ref:`NXsample` instance(s) for + which these conventions apply (e.g. /entry1/sample1). @@ -443,17 +402,16 @@ are the ibeam description capabilities not sufficient enough?--> - Location of the origin of the sample_reference_frame. - - It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. - Edges are interpreted by inspecting the direction of their outer unit normals - (which point either parallel or antiparallel) along respective base vector direction - of the reference frame. - - If any of these assumptions is not met, the user is required to explicitly state this. + Location of the origin of the sample_reference_frame. + + It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. + Edges are interpreted by inspecting the direction of their outer unit normals + (which point either parallel or antiparallel) along respective base vector direction + of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. - @@ -466,11 +424,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing x-axis base vector of the - sample_reference_frame. + Direction of the positively pointing x-axis base vector of the + sample_reference_frame. - @@ -481,11 +438,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing y-axis base vector of the - sample_reference_frame. + Direction of the positively pointing y-axis base vector of the + sample_reference_frame. - @@ -496,11 +452,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing z-axis base vector of the - sample_reference_frame. + Direction of the positively pointing z-axis base vector of the + sample_reference_frame. - @@ -510,11 +465,11 @@ are the ibeam description capabilities not sufficient enough?--> - + - Reference to the specifically named :ref:`NXdetector` instance for - which these conventions apply (e.g. /entry1/instrument/detector1). + Reference to the specifically named :ref:`NXdetector` instance for + which these conventions apply (e.g. /entry1/instrument/detector1). @@ -522,16 +477,15 @@ are the ibeam description capabilities not sufficient enough?--> - Location of the origin of the detector_reference_frame. - - If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted - by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) - along respective base vector direction of the reference frame. - - If any of these assumptions is not met, the user is required to explicitly state this. + Location of the origin of the detector_reference_frame. + + If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted + by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) + along respective base vector direction of the reference frame. + + If any of these assumptions is not met, the user is required to explicitly state this. - @@ -544,11 +498,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing x-axis base vector of the - detector_reference_frame. + Direction of the positively pointing x-axis base vector of the + detector_reference_frame. - @@ -559,11 +512,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing y-axis base vector of the - detector_reference_frame. + Direction of the positively pointing y-axis base vector of the + detector_reference_frame. - @@ -574,11 +526,10 @@ are the ibeam description capabilities not sufficient enough?--> - Direction of the positively pointing z-axis base vector of the - detector_reference_frame. + Direction of the positively pointing z-axis base vector of the + detector_reference_frame. - @@ -589,263 +540,217 @@ are the ibeam description capabilities not sufficient enough?--> - - - - + + + + - + - + - + - Details about the control program used for operating the microscope. + Details about the control program used for operating the microscope. - - + - - - This concept is related to term `Source`_ of the EMglossary standard. - - .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 - + - + - - + + - + - + + - + - - - Device for improving energy resolution or reducing chromatic aberration. - - Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector - like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ - - - - - Qualitative type of the component. - - - - - - - - - - - + + - + - + - + - - Device reshaping an ellipse-shaped electron beam to a circular one. - - * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ - * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ - - Stigmator is an exact synonym. - - + - - - Electron biprism as it is used e.g. for electron holography. - - + + - + - - - - Device that causes a change in the phase of an electron wave. - - * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ - * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ - - - - Qualitative type - - - - - - - + + + - + - - + + + + - - + - + - + + + + + + + - + + - + - + + - + - - - Device for improving energy resolution or reducing chromatic aberration. - - Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector - like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ - - - - Qualitative type of the component. - - - - - - - - - - + - + - - + + + + - - + + + + - - + - + - - - - + + + + - + - - + + + + + + + + + + + + - + - + + This group should be used to store all event-related (meta)data, + which are typically measured datasets like images and spectra. + To avoid that static instrument-related metadata need to be stored + repetitively the NXem application definitions splits the storage of the + dynamic (meta)data that typically change for each image and spectrum + from the static one. + + - + - + - + - - + - - + + @@ -865,8 +770,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -889,8 +794,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -916,8 +821,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -930,10 +835,10 @@ lenses i.e. devices which can affect the pathes of beams - + - + @@ -943,8 +848,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -957,10 +862,10 @@ lenses i.e. devices which can affect the pathes of beams - + - + @@ -973,8 +878,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -987,10 +892,10 @@ lenses i.e. devices which can affect the pathes of beams - + - + @@ -1004,22 +909,21 @@ lenses i.e. devices which can affect the pathes of beams - + - + - + - - + - - + + @@ -1030,8 +934,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -1045,8 +949,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -1063,8 +967,8 @@ lenses i.e. devices which can affect the pathes of beams - - + + @@ -1084,12 +988,12 @@ lenses i.e. devices which can affect the pathes of beams - - + + - + @@ -1099,12 +1003,12 @@ lenses i.e. devices which can affect the pathes of beams - - + + - + @@ -1117,12 +1021,12 @@ lenses i.e. devices which can affect the pathes of beams - - + + - + @@ -1138,12 +1042,12 @@ lenses i.e. devices which can affect the pathes of beams - - + + - + @@ -1160,107 +1064,38 @@ lenses i.e. devices which can affect the pathes of beams - + - - - This concept is related to term `Source`_ of the EMglossary standard. - - .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 - - - - The potential difference between anode and cathode. - - This concept is related to term `Acceleration Voltage`_ of the EMglossary standard. - - .. _Acceleration Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 - - - - - Voltage which is utilised to create an electric field that draws particles from - the source. - - This concept is related to term `Extraction Voltage`_ of the EMglossary standard. - - .. _Extraction Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 - - - - - Electrical current which is released from the source. - - This concept is related to term `Emission Current`_ of the EMglossary standard. - - .. _Emission Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 - - - - - Electrical current which flows through the source. - - This concept is related to term `Filament Current`_ of the EMglossary standard. - - .. _Filament Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 - - + + + + + - - + + - - + + - Relevant value from the control software. - - This is not always just the diameter of the aperture (not even in the case) - of a circular aperture. Usually, it is a value that is set in the control - software whereby a specific configuration of an aperture is selected by the - software. - - The control software of commercial microscope typically offers the user - access at a high abstraction level because of which many details about - the actual settings of the electrical components are typically unknown. - - However, if more details are known or should be documented one should - use the description field for this. + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. - - - Device to improve energy resolution or chromatic aberration. - - Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector - like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ - - - - - Was the corrector used? - - - - - - Energy dispersion in e.g. µm/eV. - - - - - Corresponding voltage for that energy dispersion. - - + + + + - - + + + @@ -1384,143 +1219,143 @@ ceos--> - - Device reshaping an ellipse-shaped electron beam to a circular one. - - * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ - * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ - - Stigmator is an exact synonym. - - - - Was the corrector used? - - - - - Descriptor for the correction strength along the first direction when exact technical details - are unknown or not directly controllable as the control software of the microscope does not - enable or was not configured to display these values (for end users). - - - - - Descriptor for the correction strength along the second direction when exact technical details - are unknown or not directly controllable as the control software of the microscope does not - enable or was not configured to display these values (for end users). - - - - - - - - - - This concept is related to term `Electron Beam`_ of the EMglossary standard. - - .. _Electron Beam: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 - + + + + + + + + - + + - - + + - - + + - Relevant value from the control software. - - This is not always just the diameter of the aperture (not even in the case) - of a circular aperture. Usually, it is a value that is set in the control - software whereby a specific configuration of an aperture is selected by the - software. - - The control software of commercial microscope typically offers the user - access at a high abstraction level because of which many details about - the actual settings of the electrical components are typically unknown. - - However, if more details are known or should be documented one should - use the description field for this. + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. - + - - - + + + + - - + + + + Operation mode of the detector as displayed by the control software. + + - - - - - - Nominal current of the heater. - - - - - Nominal voltage of the heater. - - - - - Nominal power of the heater. - - - - + + + + + + + + + + + + Nominal current of the heater. + + + + + Nominal voltage of the heater. + + + + - - - + + + + Description of the volume of interaction between of particle-matter interaction. + + Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam + interaction simulations can be used to qualify and (or) quantify the shape of + the interaction volume. Results of such simulations can be summary statistics + or single-particle-resolved sets of trajectories. + + Explicit or implicit descriptions of the geometry of this + interaction volume are possible: + + * An implicit description is via a set of electron/specimen interactions + represented ideally as trajectory data from the computer simulation. + * An explicit description is via iso-contour surface using either + a simulation grid or a triangulated surface mesh of the approximated + iso-contour surface evaluated at specific threshold values. + Iso-contours could be computed from electron or particle flux through + an imaginary control surface (the iso-surface) or energy-levels + (e.g. the case of X-rays). Details depend on the model. + * Another explicit description is via theoretical models which may + be relevant e.g. for X-ray spectroscopy + + Further details on how the interaction volume can be quantified + is available in the literature for example: + + * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ + * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ + * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ + + + + + - +but normalized in its representation ready to be consumed for +research data management systems--> + - A region-of-interest analyzed either during or after the session - for which specific processed data are available. - - This concept is related to term `Region Of Interest`_ of the EMglossary standard. - - .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 + A region-of-interest analyzed either during or after the session + for which specific processed data are available. + + This concept is related to term `Region Of Interest`_ of the EMglossary standard. + + .. _Region Of Interest: https://purls.helmholtz-metadaten.de/emg/EMG_00000042 - - - - + + + - + - @@ -1538,7 +1373,7 @@ is required to provide such information in this way!--> - + @@ -1547,66 +1382,73 @@ is required to provide such information in this way!--> - + + - + - + + + - - - - - + + + + + - + - - + + + + + @@ -1622,22 +1464,22 @@ is required to provide such information in this way!--> - - + + - + - - + + @@ -1654,10 +1496,8 @@ is required to provide such information in this way!--> - - From abe07be5b25cb52dab9411bbc95c9a095b467264 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 10:16:00 +0100 Subject: [PATCH 49/75] Syncing up with NIAC changes on PR #1423 em, baseclasses, promoting from contributed to base classes --- {contributed_definitions => base_classes}/NXaberration.nxdl.xml | 0 {contributed_definitions => base_classes}/NXcorrector_cs.nxdl.xml | 0 {contributed_definitions => base_classes}/NXdeflector.nxdl.xml | 0 {contributed_definitions => base_classes}/NXebeam_column.nxdl.xml | 0 {contributed_definitions => base_classes}/NXem_ebsd.nxdl.xml | 0 {contributed_definitions => base_classes}/NXem_eds.nxdl.xml | 0 {contributed_definitions => base_classes}/NXem_eels.nxdl.xml | 0 {contributed_definitions => base_classes}/NXem_img.nxdl.xml | 0 .../NXevent_data_em.nxdl.xml | 0 {contributed_definitions => base_classes}/NXibeam_column.nxdl.xml | 0 {contributed_definitions => base_classes}/NXlens_em.nxdl.xml | 0 .../NXoptical_system_em.nxdl.xml | 0 .../NXspectrum_set.nxdl.xml => base_classes/NXspectrum.nxdl.xml | 0 13 files changed, 0 insertions(+), 0 deletions(-) rename {contributed_definitions => base_classes}/NXaberration.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcorrector_cs.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXdeflector.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXebeam_column.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXem_ebsd.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXem_eds.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXem_eels.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXem_img.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXevent_data_em.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXibeam_column.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXlens_em.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXoptical_system_em.nxdl.xml (100%) rename contributed_definitions/NXspectrum_set.nxdl.xml => base_classes/NXspectrum.nxdl.xml (100%) diff --git a/contributed_definitions/NXaberration.nxdl.xml b/base_classes/NXaberration.nxdl.xml similarity index 100% rename from contributed_definitions/NXaberration.nxdl.xml rename to base_classes/NXaberration.nxdl.xml diff --git a/contributed_definitions/NXcorrector_cs.nxdl.xml b/base_classes/NXcorrector_cs.nxdl.xml similarity index 100% rename from contributed_definitions/NXcorrector_cs.nxdl.xml rename to base_classes/NXcorrector_cs.nxdl.xml diff --git a/contributed_definitions/NXdeflector.nxdl.xml b/base_classes/NXdeflector.nxdl.xml similarity index 100% rename from contributed_definitions/NXdeflector.nxdl.xml rename to base_classes/NXdeflector.nxdl.xml diff --git a/contributed_definitions/NXebeam_column.nxdl.xml b/base_classes/NXebeam_column.nxdl.xml similarity index 100% rename from contributed_definitions/NXebeam_column.nxdl.xml rename to base_classes/NXebeam_column.nxdl.xml diff --git a/contributed_definitions/NXem_ebsd.nxdl.xml b/base_classes/NXem_ebsd.nxdl.xml similarity index 100% rename from contributed_definitions/NXem_ebsd.nxdl.xml rename to base_classes/NXem_ebsd.nxdl.xml diff --git a/contributed_definitions/NXem_eds.nxdl.xml b/base_classes/NXem_eds.nxdl.xml similarity index 100% rename from contributed_definitions/NXem_eds.nxdl.xml rename to base_classes/NXem_eds.nxdl.xml diff --git a/contributed_definitions/NXem_eels.nxdl.xml b/base_classes/NXem_eels.nxdl.xml similarity index 100% rename from contributed_definitions/NXem_eels.nxdl.xml rename to base_classes/NXem_eels.nxdl.xml diff --git a/contributed_definitions/NXem_img.nxdl.xml b/base_classes/NXem_img.nxdl.xml similarity index 100% rename from contributed_definitions/NXem_img.nxdl.xml rename to base_classes/NXem_img.nxdl.xml diff --git a/contributed_definitions/NXevent_data_em.nxdl.xml b/base_classes/NXevent_data_em.nxdl.xml similarity index 100% rename from contributed_definitions/NXevent_data_em.nxdl.xml rename to base_classes/NXevent_data_em.nxdl.xml diff --git a/contributed_definitions/NXibeam_column.nxdl.xml b/base_classes/NXibeam_column.nxdl.xml similarity index 100% rename from contributed_definitions/NXibeam_column.nxdl.xml rename to base_classes/NXibeam_column.nxdl.xml diff --git a/contributed_definitions/NXlens_em.nxdl.xml b/base_classes/NXlens_em.nxdl.xml similarity index 100% rename from contributed_definitions/NXlens_em.nxdl.xml rename to base_classes/NXlens_em.nxdl.xml diff --git a/contributed_definitions/NXoptical_system_em.nxdl.xml b/base_classes/NXoptical_system_em.nxdl.xml similarity index 100% rename from contributed_definitions/NXoptical_system_em.nxdl.xml rename to base_classes/NXoptical_system_em.nxdl.xml diff --git a/contributed_definitions/NXspectrum_set.nxdl.xml b/base_classes/NXspectrum.nxdl.xml similarity index 100% rename from contributed_definitions/NXspectrum_set.nxdl.xml rename to base_classes/NXspectrum.nxdl.xml From 7c604f2150c7c834abbede55c987b5bd0ebbfd5b Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 10:20:58 +0100 Subject: [PATCH 50/75] Syncing up with NIAC changes on PR #1423 non-em, generic classes that were in contributed but have now also been promoted to base classes mainly via other PRs --- {contributed_definitions => base_classes}/NXactivity.nxdl.xml | 0 {contributed_definitions => base_classes}/NXactuator.nxdl.xml | 0 {contributed_definitions => base_classes}/NXcalibration.nxdl.xml | 0 {contributed_definitions => base_classes}/NXcomponent.nxdl.xml | 0 {contributed_definitions => base_classes}/NXfabrication.nxdl.xml | 0 {contributed_definitions => base_classes}/NXhistory.nxdl.xml | 0 {contributed_definitions => base_classes}/NXregistration.nxdl.xml | 0 {contributed_definitions => base_classes}/NXresolution.nxdl.xml | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename {contributed_definitions => base_classes}/NXactivity.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXactuator.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcalibration.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXcomponent.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXfabrication.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXhistory.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXregistration.nxdl.xml (100%) rename {contributed_definitions => base_classes}/NXresolution.nxdl.xml (100%) diff --git a/contributed_definitions/NXactivity.nxdl.xml b/base_classes/NXactivity.nxdl.xml similarity index 100% rename from contributed_definitions/NXactivity.nxdl.xml rename to base_classes/NXactivity.nxdl.xml diff --git a/contributed_definitions/NXactuator.nxdl.xml b/base_classes/NXactuator.nxdl.xml similarity index 100% rename from contributed_definitions/NXactuator.nxdl.xml rename to base_classes/NXactuator.nxdl.xml diff --git a/contributed_definitions/NXcalibration.nxdl.xml b/base_classes/NXcalibration.nxdl.xml similarity index 100% rename from contributed_definitions/NXcalibration.nxdl.xml rename to base_classes/NXcalibration.nxdl.xml diff --git a/contributed_definitions/NXcomponent.nxdl.xml b/base_classes/NXcomponent.nxdl.xml similarity index 100% rename from contributed_definitions/NXcomponent.nxdl.xml rename to base_classes/NXcomponent.nxdl.xml diff --git a/contributed_definitions/NXfabrication.nxdl.xml b/base_classes/NXfabrication.nxdl.xml similarity index 100% rename from contributed_definitions/NXfabrication.nxdl.xml rename to base_classes/NXfabrication.nxdl.xml diff --git a/contributed_definitions/NXhistory.nxdl.xml b/base_classes/NXhistory.nxdl.xml similarity index 100% rename from contributed_definitions/NXhistory.nxdl.xml rename to base_classes/NXhistory.nxdl.xml diff --git a/contributed_definitions/NXregistration.nxdl.xml b/base_classes/NXregistration.nxdl.xml similarity index 100% rename from contributed_definitions/NXregistration.nxdl.xml rename to base_classes/NXregistration.nxdl.xml diff --git a/contributed_definitions/NXresolution.nxdl.xml b/base_classes/NXresolution.nxdl.xml similarity index 100% rename from contributed_definitions/NXresolution.nxdl.xml rename to base_classes/NXresolution.nxdl.xml From dbbcb7329c4a84461443a5ed2e75811b40b3f905 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 10:24:36 +0100 Subject: [PATCH 51/75] Syncing up with NIAC changes on PR #1423 em, removal of base classes that have been refactored based on NIAC feedback --- .../NXscanbox_em.nxdl.xml | 0 .../NXem_correlation.nxdl.xml | 245 ------- contributed_definitions/NXem_method.nxdl.xml | 45 -- contributed_definitions/NXem_msr.nxdl.xml | 98 --- contributed_definitions/NXem_sim.nxdl.xml | 59 -- .../NXevent_data_em_set.nxdl.xml | 49 -- contributed_definitions/NXimage_set.nxdl.xml | 652 ------------------ .../NXinteraction_vol_em.nxdl.xml | 57 -- 8 files changed, 1205 deletions(-) rename {contributed_definitions => base_classes}/NXscanbox_em.nxdl.xml (100%) delete mode 100644 contributed_definitions/NXem_correlation.nxdl.xml delete mode 100644 contributed_definitions/NXem_method.nxdl.xml delete mode 100644 contributed_definitions/NXem_msr.nxdl.xml delete mode 100644 contributed_definitions/NXem_sim.nxdl.xml delete mode 100644 contributed_definitions/NXevent_data_em_set.nxdl.xml delete mode 100644 contributed_definitions/NXimage_set.nxdl.xml delete mode 100644 contributed_definitions/NXinteraction_vol_em.nxdl.xml diff --git a/contributed_definitions/NXscanbox_em.nxdl.xml b/base_classes/NXscanbox_em.nxdl.xml similarity index 100% rename from contributed_definitions/NXscanbox_em.nxdl.xml rename to base_classes/NXscanbox_em.nxdl.xml diff --git a/contributed_definitions/NXem_correlation.nxdl.xml b/contributed_definitions/NXem_correlation.nxdl.xml deleted file mode 100644 index 14cf17914d..0000000000 --- a/contributed_definitions/NXem_correlation.nxdl.xml +++ /dev/null @@ -1,245 +0,0 @@ - - - - - - Base class to combine different method-specific data in electron microscopy. - - This base class represent a template for documenting correlations - (spatial, temporal) between different method-specific results. - - - - Details about processing steps. - - - - - - Details about correlated or logically connected EBSD datasets. - - One important class of such correlated experiments are the so-called - (quasi) in-situ experiments. In this case the same or nearly the same ROI - gets analyzed via a repetitive sequence of thermomechanical treatment, - sample preparation, measurement, on-the-fly-indexing. Phenomena - investigated are recrystallization, strain accumulation, material damage. - Post-processing is required to correlate and reidentify eventual - microstructural features or local ROIs across several orientation maps. - - Another important class of correlated experiments are the so-called - serial-sectioning experiments. Here the same sample is measured - repetitively after polishing each time, to create a stack of - orientation data which can be reconstructed to a - three-dimensional volume ROI. - - Data can be correlated in time, position (spatial), or both (spatiotemporal). - - Spatial correlations between repetitively characterized regions-of-interests - are typically correlated using image registration and alignment algorithms. - For this typically so-called landmarks are used. These can be grains with - a very large size or specific shape, i.e. grains which are qualitatively - different enough to be used as a guide how images are shifted relative to - one another. Other commonly used landmarks are fiducial marks which are - milled into the specimen surface using focus-ion beam milling and/or various - types of indentation methods. - - As far as the same physical region-of-interest is just measured several times, - the additional issue of the depth increment is not a concern. However, correct - assumptions for the depth increment, amount of material removed along the milling - direction is relevant for accurate and precise three-dimensional (serial-sectioning) - correlations. For these studies it can be tricky though to assume or estimate - useful depth increments. Different strategies have been proposed like - calibrations, wedged-shaped landmarks and computer simulation assisted - assumption making. - - Despite the use of landmarks, there are many practical issues which make the - processing of correlations imprecise and inaccurate. Among these are drift - and shift of the specimen, instabilities of the holder, the beam, irrespective - of the source of the drift, charging effects, here specifically causing local - image distortions and rotations which may require special processing algorithms - to reduce such imprecisions. - - Time correlations face all of the above-mentioned issues surplus the challenge - that specific experimental protocols have to be used to ensure the material state - is observed at specific physical time. The example of quasi in-situ characterization - of crystal growth phenomena, a common topic in engineering or modern catalysis research - makes it necessary to consider that e.g. the target value for the desired annealing - temperature is not just gauged based on macroscopic arguments but considers - that transient effects take place. Heating or quenching a sample might thus might - not have been executed under conditions in the interaction volume as they are - documented and/or assumed. - - These issue cause that correlations have an error margin as to how accurately - respective datasets were not only just synced based on the geometry of the - region-of-interests and the time markers but also to asssure which physical - conditions the specimen experienced over the course of the measurements. - - The fourth example of the em_om reference implementation explores the use of the - correlation group with a serial-sectioning datasets that was collected by the - classical Inconel 100 dataset collected by M. D. Uchic and colleagues - (M. Groeber M, Haley BK, Uchic MD, Dimiduk DM, Ghosh S 3d reconstruction and - characterization of polycrystalline microstructures using a fib-sem system data set. - Mater Charac 2006, 57 259–273. 10.1016/j.matchar.2006.01.019M). - - This dataset was specifically relevant in driving forward the implementation - of the DREAM.3D software. DREAM.3D is an open-source software project for - post-processing and reconstructing, i.e. correlating sets of orientation - microscopy data foremost spatially. One focus of the software is the - (post-)processing of EBSD datasets. Another cutting edge tool with similar - scope but a commercial solution by Bruker is QUBE which was developed by - P. Konijnenberg and coworkers. - - Conceptually, software like DREAM.3D supports users with creating linear - workflows of post-processing tasks. Workflows can be instructed via the - graphical user interface or via so-called pipeline processing via command line - calls. DREAM.3D is especially useful because its internal system documents all - input, output, and parameter of the processing steps. This makes DREAM.3D a - good candidate to interface with tools like em_om parser. Specifically, DREAM.3D - documents numerical results via a customized HDF5 file format called DREAM3D. - Workflow steps and settings are stored as nested dictionaries in JSON syntax - inside a supplementary JSON file or alongside the data in the DREAM3D file. - DREAM.3D has a few hundred algorithms implemented. These are called filters - in DREAM.3D terminology. - - Users configure a workflow which instructs DREAM.3D to send the data through - a chain of predefined and configured filters. Given that for each analysis - the filter is documented via its version tags surplus its parameter and setting - via a controlled vocabulary, interpreting the content of a DREAM3D HDF5 file - is possible in an automated manner using a parser. This makes DREAM.3D analyses - repeatable and self-descriptive. A key limitation though is that most frequently - the initial set of input data come from commercial files like ANG. - This missing link between the provenance of these input files, their associated - creation as electron microscope session, is also what NXem_ebsd solves. - - Nevertheless, as this can be solved with e.g. NXem_ebsd we are convinced that - the DREAM.3D and the em_om parser can work productively together to realize - RDMS-agnostic parsing of serial-section analyses. - - The internal documentation of the DREAM.3D workflow also simplifies the - provenance tracking represented by an instance of NXem_ebsd as not every - intermediate results has to be stored. Therefore, the fourth example - focuses on the key result obtained from DREAM.3D - the reconstructed - and aligned three-dimensional orientation map. - - Usually, this result is the starting point for further post-processing - and characterization of structural features. As here orientation microscopy - is insofar scale invariant using DREAM.3D, NXem_ebsd, and em_om should - be useful for different characterization methods, such as EBSD, Transmission - Kikuchi Diffraction (TKD), Automated Crystal Orientation Mapping (ACOM), - Nanobeam Electron Diffraction (using commercial systems like NanoMegas ASTAR) - or open-source implementations of these techniques (such as via pyxem/orix). - - The result of orientation microscopy methods are maps of local orientation - and thermodynamic phase (crystal structure) pieces of information. Virtually - all post-processing of such results for structural features includes again - a workflow of steps which are covered though by the NXmicrostructure partner application - definition. The respective source of the data in an instance of NXmicrostructure can - again be a link or reference to an instance of NXem_ebsd to complete the - chain of provenance. - - - - - - Descriptor representing the image contrast. - - - - - - Title of the default plot. - - - - - Descriptor values displaying the ROI. - - - - - - - - - - Descriptor values. - - - - - - Calibrated coordinate along the z-axis. - - - - - - - Label for the z axis - - - - - - Calibrated coordinate along the y-axis. - - - - - - - Label for the y axis - - - - - - Calibrated coordinate along the x-axis. - - - - - - - Label for the x axis - - - - - - - diff --git a/contributed_definitions/NXem_method.nxdl.xml b/contributed_definitions/NXem_method.nxdl.xml deleted file mode 100644 index 985183f35f..0000000000 --- a/contributed_definitions/NXem_method.nxdl.xml +++ /dev/null @@ -1,45 +0,0 @@ - - - - - - Base class to describe specific analysis methods in electron microscopy. - - This base class represent a template how specialized, deep, and method-specific - base classes can be defined with which an (NXem) application - definition gets equipped with specific groups to document method-specific - processing steps and report analyzed quantities. - - The template base class name :ref:`NXem_method` needs to be changed for - each method e.g. :ref:`NXem_ebsd`, :ref:`NXem_eels`, :ref:`NXem_eds`. - - - - Details about processing steps. - - - - - - - diff --git a/contributed_definitions/NXem_msr.nxdl.xml b/contributed_definitions/NXem_msr.nxdl.xml deleted file mode 100644 index d7d590456f..0000000000 --- a/contributed_definitions/NXem_msr.nxdl.xml +++ /dev/null @@ -1,98 +0,0 @@ - - - - - - Base class for collecting a session with a real electron microscope. - - For collecting data and experiments which are simulations of an - electron microscope use the :ref:`NXem_sim` base class. - - - - (Meta)data of the microscope and the lab in which it stands. - - This em_lab group differs from potential em_lab groups inside - :ref:`NXevent_data_em` instances in that here the more static descriptions - are kept while changing, i.e. time-dependent pieces of information are - logged, via the em_lab group inside the desired number of instances - of NXevent_data_em. - - While using an :ref:`NXevent_data_em` instance, users should store only those - settings about a component which are relevant to understand the current - state of the component. Here, current means for the time interval which - the event covers (as it is detailed via start_time and end_time) timestamps. - - For example it is not relevant to store in each :ref:`NXevent_data_em` - electron_source group again the details of the gun type and the manufacturer - but only the high-voltage value and that only if it is different from the value - that is specified in the em_lab section for the static settings. - - In effect, this defines an information inference hierarchy which starts - in an individual :ref:`NXevent_data_em` instance followed by a probing of the - static section. - - - - Given name of the microscope at the hosting institution. - This is an alias. Examples could be NionHermes, Titan, JEOL, - Gemini, etc. - - - - - Location of the lab or place where the instrument is installed. - Using GEOREF is preferred. - - - - - - - - - - - - Description of the type of the detector. - - Electron microscopes have typically multiple detectors. - Different technologies are in use like CCD, scintillator, - direct electron, CMOS, or image plate to name but a few. - - - - Instrument-specific alias/name - - - - - - - - - - diff --git a/contributed_definitions/NXem_sim.nxdl.xml b/contributed_definitions/NXem_sim.nxdl.xml deleted file mode 100644 index 610fe885c1..0000000000 --- a/contributed_definitions/NXem_sim.nxdl.xml +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - Base class for simulating electron microscopy relevant beam-matter interaction. - - The concept behind this base class is to keep it as generic as possible - that simulations of electron/ion beam interaction with matter can be - represented. This base class is envisioned as the twin of the :ref:`NXem_msr` - base class. - - It is an attempt to test the idea if at some point one might even use the - same base class template to describe measurements and computer simulations - of electron microscopy. This idea is attractive because the only practical - difference between a description of a measurement with a microscope and a - computer simulation is that the latter is typically a substantially simplified - representation of the real microscope surplus the focus of the research - in such cases on specific questions. - - Such simplification can be with respect to the optical setup, typically the - ignoring of the fact that the electron beam is produced by a complex setup - of lenses while in simulations often single Einzel lenses are considered. - Dynamics of the environment like temperature fluctuation in a lab, vibrations, - users, and multiple detectors are typically either ignored or reduced in - complexity and number and coming with idealizations to keep the simulations - focused on the specific reason questions and efficiently numerically executable. - - - - Details about the simulation. - - - - - - diff --git a/contributed_definitions/NXevent_data_em_set.nxdl.xml b/contributed_definitions/NXevent_data_em_set.nxdl.xml deleted file mode 100644 index 5d5a3a986c..0000000000 --- a/contributed_definitions/NXevent_data_em_set.nxdl.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - Base class for a set of :ref:`NXevent_data_em` instances. - - Members of the set are instances of :ref:`NXevent_data_em`. These have an associated - time interval during which the conditions were considered stable and - fit enough for purpose. - - Which temporal granularity is adequate depends on the situation and - research question. Using a model which enables a collection of events offers - the most flexible way to cater for both experiments with controlled electron - beams in a real microscope or the simulation of such experiments or - individual aspects of such experiments. - - - - - diff --git a/contributed_definitions/NXimage_set.nxdl.xml b/contributed_definitions/NXimage_set.nxdl.xml deleted file mode 100644 index c92a12d3ca..0000000000 --- a/contributed_definitions/NXimage_set.nxdl.xml +++ /dev/null @@ -1,652 +0,0 @@ - - - - - - - - - - Number of images in the stack, for stacks the slowest dimension. - - - - - Number of image points along the slow dimension (k equivalent to z). - - - - - Number of image points along the fast dimension (j equivalent to y). - - - - - Number of image points along the fastest dimension (i equivalent to x). - - - - - Base class for reporting a set of images. - - The mostly commonly used scanning methods are supported. That is one-, - two-, three-dimensional ROIs discretized using regular Euclidean tilings. - - Colloquially, an image is understood as a discretized representation of intensity distribution - that was detected or simulated for some ROI. When discretized with regular Euclidean tilings - the terms pixel and voxel identify the smallest discretization unit. Pixel and voxel are polygonal - or polyhedral unit cells respectively of the underlying tiling of the ROI within the reference space. - For all other tilings e.g. non-equispaced, the shape and size of pixel and voxel differs. Using the term - (image) point is eventually is more appropriate for such tilings. Therefore, all docstrings in this base class - refer to points (including pixel and voxel i.e. regular tilings). - - Point coordinates identify the location of the barycentre. - - For images in reciprocal space in practice, complex numbers are encoded via some - formatted pair of real values. Typically, fast algorithms for computing Fourier transformations - (FFT) are used to encode images in reciprocal (frequency) space. FFT libraries are used - for implementing the key functionalities of these mathematical operations. - - Different libraries use different representations and encoding of the images. - Details can be found in the respective sections of the typical FFT libraries documentations - - * `FFTW by M. Frigo and S. G. Johnson <https://www.fftw.org/fftw3_doc/Tutorial.html#Tutorial>`_ - * `Intel MKL by the Intel Co. <https://www.intel.com/content/www/us/en/docs/onemkl/developer-reference-c/2024-2/fourier-transform-functions.html>`_ - * `cuFFT by the NVidia Co. <https://docs.nvidia.com/cuda/cufft/index.html>`_ - * `NFFT by the Chemnitz group <https://www-user.tu-chemnitz.de/~potts/nfft/>`_ for non-equispaced computations - - Users are strongly advised to inspect carefully which specific conventions their library uses - to enable storing and modifying the implementation of their code such that the serialized - representations as they are detailed here for NeXus match. - - It is often the case that several images are combined using processing. In this case, - the number of images which are combined in a collection is not necessarily the same - for each collection. The NXimage_set base class addresses this logical distinction - through the notation of image_identifier and group_identifier concepts. - That is image_identifier are always counting from offset in increments of one. - as each image is its own entity. By contrast, a group may contain no, or several images. - Consequently, group_identifier are not required to be contiguous. - - - - Details how NXdata instance were processed from detector readings/raw data. - - - - Resolvable data artifact (e.g. file) from which all values in the :ref:`NXdata` - instances in this :ref:`NXimage_set` were loaded during parsing. - - Possibility to document from which specific other serialized resource as the source - pieces of information were processed when using NeXus as a semantic file format - to serialize that information differently. - - The group in combination with an added field *absolute_path* therein adds context. - - - - Reference to a location inside the artifact that points to the specific group of values - that were processed if the artifacts contains several groups of values and thus - further resolving of ambiguities is required. - - - - - - - Link or name of an :ref:`NXdetector` instance with which the data were - collected. - - - - - Program used for processing. - - - - - - - One-dimensional image. - - - - Intensity for real-valued images as an alternative for real. - Magnitude of the image intensity for complex-valued data. - - - - - - - - Real part of the image intensity per point. - - - - - - - - Imaginary part of the image intensity per point. - - - - - - - - Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. - - - - - - - - Point coordinate along the fastest dimension. - - - - - - - Point coordinate along the fastest dimension. - - - - - - - Two-dimensional image. - - - - Intensity for real-valued images as an alternative for real. - Magnitude of the image intensity for complex-valued data. - - - - - - - - - Real part of the image intensity per point. - - - - - - - - - Imaginary part of the image intensity per point. - - - - - - - - - Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. - - - - - - - - - Point coordinate along the fast dimension. - - - - - - - Point coordinate along the fast dimension. - - - - - - Point coordinate along the fastest dimension. - - - - - - - Point coordinate along the fastest dimension. - - - - - - - Three-dimensional image. - - - - Intensity for real-valued images as an alternative for real. - Magnitude of the image intensity for complex-valued data. - - - - - - - - - - Real part of the image intensity per point. - - - - - - - - - - Imaginary part of the image intensity per point. - - - - - - - - - - Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. - - - - - - - - - - Point coordinate along the slow dimension. - - - - - - - Point coordinate along the slow dimension. - - - - - - Point coordinate along the fast dimension. - - - - - - - Point coordinate along the fast dimension. - - - - - - Point coordinate along the fastest dimension. - - - - - - - Point coordinate along the fastest dimension. - - - - - - - Collection of image_1d. - - - - Intensity for real-valued images as an alternative for real. - Magnitude of the image intensity for complex-valued data. - - - - - - - - - Real part of the image intensity per point. - - - - - - - - - Imaginary part of the image intensity per point. - - - - - - - - - Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. - - - - - - - - - Group identifier - - - - - - - Group identifier - - - - - - Image identifier - - - - - - - Image identifier - - - - - - Point coordinate along the fastest dimension. - - - - - - - Point coordinate along the fastest dimension. - - - - - - - Collection of two-dimensional images. - - - - Intensity for real-valued images as an alternative for real. - Magnitude of the image intensity for complex-valued data. - - - - - - - - - - Real part of the image intensity per point. - - - - - - - - - - Imaginary part of the image intensity per point. - - - - - - - - - - Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. - - - - - - - - - - Group identifier - - - - - - - Group identifier - - - - - - Image identifier - - - - - - - Image identifier. - - - - - - Point coordinate along the fast dimension. - - - - - - - Point coordinate along the fast dimension. - - - - - - Point coordinate along the fastest dimension. - - - - - - - Point coordinate along the fastest dimension. - - - - - - - Collection of three-dimensional images. - - - - Intensity for real-valued images as an alternative for real. - Magnitude of the image intensity for complex-valued data. - - - - - - - - - - - Real part of the image intensity per point. - - - - - - - - - - - Imaginary part of the image intensity per point. - - - - - - - - - - - Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. - - - - - - - - - - - Group identifier - - - - - - - Group identifier - - - - - - Image identifier - - - - - - - Image identifier - - - - - - Point coordinate along the slow dimension. - - - - - - - Point coordinate along the slow dimension. - - - - - - Point coordinate along the fast dimension. - - - - - - - Point coordinate along the fast dimension. - - - - - - Point coordinate along the fastest dimension. - - - - - - - Point coordinate along the fastest dimension. - - - - - diff --git a/contributed_definitions/NXinteraction_vol_em.nxdl.xml b/contributed_definitions/NXinteraction_vol_em.nxdl.xml deleted file mode 100644 index f8d8a669f2..0000000000 --- a/contributed_definitions/NXinteraction_vol_em.nxdl.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - Base class for describing the interaction volume of particle-matter interaction. - - Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam - interaction simulations can be used to qualify and (or) quantify the shape of - the interaction volume. Results of such simulations can be summary statistics - or single-particle resolved sets of trajectories. - - Explicit or implicit descriptions are possible. - - * An implicit description is via a set of electron/specimen interactions - represented ideally as trajectory data from the computer simulation. - * An explicit description is via an iso-contour surface using either - a simulation grid or a triangulated surface mesh of the approximated - iso-contour surface evaluated at specific threshold values. - Iso-contours could be computed from electron or particle fluxes through - an imaginary control surface (the iso-surface). - Threshold values can be defined by particles passing through a unit control - volume (electrons) or energy-levels (e.g. the case of X-rays). - Details depend on the model. - * Another explicit description is via theoretical models which may - be relevant e.g. for X-ray spectroscopy - - Further details on how the interaction volume can be quantified - is available in the literature for example: - - * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ - * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ - * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ - - - - From b87254493a6be65ab567d254505b1fdb530dc196 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 10:33:24 +0100 Subject: [PATCH 52/75] Syncing up with NIAC changes on PR #1423 em, cherry-picking base classes from #1423 ee40f515 after comparison to current state as used in eventually apm, cg, ms 1 --- base_classes/NXaberration.nxdl.xml | 16 +-- base_classes/NXatom.nxdl.xml | 2 +- base_classes/NXchemical_composition.nxdl.xml | 18 ++-- base_classes/NXcircuit.nxdl.xml | 2 +- base_classes/NXcoordinate_system.nxdl.xml | 100 +++++++++---------- base_classes/NXcorrector_cs.nxdl.xml | 100 ++++++++----------- base_classes/NXcs_computer.nxdl.xml | 6 +- base_classes/NXcs_profiling.nxdl.xml | 2 +- base_classes/NXcs_profiling_event.nxdl.xml | 2 +- 9 files changed, 116 insertions(+), 132 deletions(-) diff --git a/base_classes/NXaberration.nxdl.xml b/base_classes/NXaberration.nxdl.xml index 44160b54fb..29427909a6 100644 --- a/base_classes/NXaberration.nxdl.xml +++ b/base_classes/NXaberration.nxdl.xml @@ -3,7 +3,7 @@ - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -37,8 +37,8 @@ +doc: | +IUPAC chemical formula--> Total based on which composition information is normalized. @@ -47,11 +47,11 @@ chemical_formula: - + Count or weight which, when divided by total yields the composition - of this element, isotope, molecule or ion. + for this element, isotope, molecule, or ion. diff --git a/base_classes/NXcircuit.nxdl.xml b/base_classes/NXcircuit.nxdl.xml index b0c6c56526..9648ae103a 100644 --- a/base_classes/NXcircuit.nxdl.xml +++ b/base_classes/NXcircuit.nxdl.xml @@ -3,7 +3,7 @@ - Base class to detail a coordinate system (CS). - - Whenever possible, an instance of :ref:`NXcoordinate_system` should be used as - a member in an :ref:`NXcoordinate_system_set` and the name of the instance - should be this alias. This may support a process whereby jargon when talking - about coordinate systems and conventions may become cleaner for users - because it is not evident for people outside a lab that terms like e.g. - tip space or specimen space refer to the same coordinate system. - This is an example of jargon used in e.g. the field of atom - probe tomography. + Base class to detail a coordinate system (CS). + + Whenever possible, an instance of :ref:`NXcoordinate_system` should be used as + a member in an :ref:`NXcoordinate_system_set` and the name of the instance + should be this alias. This may support a process whereby jargon when talking + about coordinate systems and conventions may become cleaner for users + because it is not evident for people outside a lab that terms like e.g. + tip space or specimen space refer to the same coordinate system. + This is an example of jargon used in e.g. the field of atom + probe tomography. - Human-readable field telling where the origin of this CS is. - Exemplar values could be *left corner of the lab bench*, *door-handle* - *pinhole through which the electron beam exists the pole piece*. - *barycenter of the triangle*, *center of mass of the stone*. + Human-readable field telling where the origin of this CS is. + Exemplar values could be *left corner of the lab bench*, *door-handle* + *pinhole through which the electron beam exists the pole piece*. + *barycenter of the triangle*, *center of mass of the stone*. - An alternative name given to that coordinate system. + An alternative name given to that coordinate system. - Coordinate system type. + Coordinate system type. - - Handedness of the coordinate system if it is a Cartesian. + Handedness of the coordinate system if it is a Cartesian. - - Possibility to define an alias for the name of the x-axis. + Possibility to define an alias for the name of the x-axis. - Human-readable field telling in which direction the x-axis points if that - instance of :ref:`NXcoordinate_system` has no reference to any parent and as such - is the mighty world reference frame. - - Exemplar values could be direction of gravity. + Human-readable field telling in which direction the x-axis points if that + instance of :ref:`NXcoordinate_system` has no reference to any parent + and as such is the world reference frame. + + Exemplar values could be direction of gravity. - + - Base unit vector along the first axis which spans the coordinate system. - This axis is frequently referred to as the x-axis in real space and - the i-axis in reciprocal space. + Base unit vector along the first axis which spans the coordinate system. + This axis is frequently referred to as the x-axis in real space and + the i-axis in reciprocal space. @@ -98,23 +96,23 @@ enumeration: [undefined, front_top_left, front_top_right, front_bottom_right, fr - Possibility to define an alias for the name of the y-axis. + Possibility to define an alias for the name of the y-axis. - Human-readable field telling in which direction the y-axis points if that - instance of :ref:`NXcoordinate_system` has no reference to any parent and as such - is the mighty world reference frame. - - See docstring of x_alias for further details. + Human-readable field telling in which direction the y-axis points if that + instance of :ref:`NXcoordinate_system` has no reference to any parent + and as such is the world reference frame. + + See docstring of x_alias for further details. - Base unit vector along the second axis which spans the coordinate system. - This axis is frequently referred to as the y-axis in real space and - the j-axis in reciprocal space. + Base unit vector along the second axis which spans the coordinate system. + This axis is frequently referred to as the y-axis in real space and + the j-axis in reciprocal space. @@ -122,23 +120,23 @@ enumeration: [undefined, front_top_left, front_top_right, front_bottom_right, fr - Possibility to define an alias for the name of the z-axis. + Possibility to define an alias for the name of the z-axis. - Human-readable field telling in which direction the z-axis points if that - instance of :ref:`NXcoordinate_system` has no reference to any parent and as such - is the mighty world reference frame. - - See docstring of x_alias for further details. + Human-readable field telling in which direction the z-axis points if that + instance of :ref:`NXcoordinate_system` has no reference to any parent + and as such is the world reference frame. + + See docstring of x_alias for further details. - Base unit vector along the third axis which spans the coordinate system. - This axis is frequently referred to as the z-axis in real space and - the k-axis in reciprocal space. + Base unit vector along the third axis which spans the coordinate system. + This axis is frequently referred to as the z-axis in real space and + the k-axis in reciprocal space. @@ -146,14 +144,14 @@ enumeration: [undefined, front_top_left, front_top_right, front_bottom_right, fr - This specificies the relation to another coordinate system by pointing to the last - transformation in the transformation chain in the NXtransformations group. + This specificies the relation to another coordinate system by pointing to the last + transformation in the transformation chain in the NXtransformations group. - Collection of axis-based translations and rotations to describe this coordinate system - with respect to another coordinate system. + Collection of axis-based translations and rotations to describe this coordinate system + with respect to another coordinate system. diff --git a/base_classes/NXcorrector_cs.nxdl.xml b/base_classes/NXcorrector_cs.nxdl.xml index a6f57819b6..211e7bb8b6 100644 --- a/base_classes/NXcorrector_cs.nxdl.xml +++ b/base_classes/NXcorrector_cs.nxdl.xml @@ -3,7 +3,7 @@ - The symbols used in the schema to specify e.g. dimensions of arrays. + The symbols used in the schema to specify e.g. dimensions of arrays. - Number of images taken, at least one. + Number of images taken, at least one. - Base class for a corrector reducing (spherical) aberrations in electron microscopy. - - Different technology partners use different naming schemes and - models for quantifying the aberration coefficients. - - The corrector in an electron microscope is composed of multiple lenses - and multipole stigmators with details specific for the technology partner - and microscope. Many of their technical details is proprietary knowledge. - - If functionalities for correcting multiple aberrations are included in - one :ref:`NXcomponent` `like it is reported here <https://www.ceos-gmbh.de/en/research/electrostat>`_ - use multiple groups: - - * :ref:`NXcorrector_cs` for spherical aberration - * :ref:`NXmonochromator` for energy filtering or chromatic aberration - * corrector_ax in :ref:`NXem` for axial astigmatism correction + Base class for a corrector reducing (spherical) aberrations in electron microscopy. + + Different technology partners use different conventions and + models for quantifying the aberration coefficients. + + The corrector in an electron microscope is composed of multiple lenses + and multipole stigmators with details that are specific for the technology partner + and microscope. Most technical details are proprietary knowledge. + + If one component corrects for multiple types of aberrations (like it is the case reported + here `CEOS <https://www.ceos-gmbh.de/en/research/electrostat>`_) follow this design: + + * Use :ref:`NXcorrector_cs` for spherical aberration + * Use :ref:`NXmonochromator` for energy filtering or chromatic aberration + * Use the group corrector_ax in :ref:`NXem` for axial astigmatism aberration - Was the corrector used? + Was the corrector used? - - + - Specific information about the alignment procedure that is a process during which - the corrector is configured to enable calibrated usage of the instrument. - - This :ref:`NXprocess` group should also be used when one describes in a computer - simulation the specific details about the modelled or assumed aberration - corrections. + Specific information about the alignment procedure that is a process during which + the corrector is configured to enable calibrated usage of the instrument. + + This :ref:`NXprocess` group should also be used when one describes in a computer + simulation the specific details about the modelled or assumed aberrations. - Discouraged free-text field to add further details about the alignment - procedure. + Discouraged free-text field to add further details about the alignment + procedure. - The outer tilt angle of the beam in tableau acquisition. - - TODO: The relevant axes which span the tilt_angle need a - cleaner description. + The outer tilt angle of the beam in tableau acquisition. + + TODO: The relevant axes which span the tilt_angle need a + cleaner description. @@ -87,7 +84,7 @@ https://doi.org/10.1017/9781316337455.022--> - The exposure time of single tilt images. + The exposure time of single tilt images. @@ -95,25 +92,26 @@ https://doi.org/10.1017/9781316337455.022--> - The factor of enlargement of the apparent size, - not the physical size, of an object. + The factor of enlargement of the apparent size, + not the physical size, of an object. - + - The images taken during the alignment procedure. + Image(s) taken during the alignment procedure - Place for storing measured or estimated aberrations (for each image or final). - - See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) - for different definitions available and further details. Table 7-2 of Ibid. publication (page 305ff) documents how - to convert from the Nion to the CEOS definitions. Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_. + Convention used for storing measured or estimated aberrations (for each image or final) + via fields c_1, a_1, c_1_0, c_1_2_a, and so on and so forth. + + See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) + for different definitions available and further details. Table 7-2 of Ibid. publication (page 305ff) documents how + to convert from the Nion to the CEOS definitions. Conversion tables are also summarized by `Y. Liao <https://www.globalsino.com/EM/page3740.html>`_. @@ -122,14 +120,10 @@ https://doi.org/10.1017/9781316337455.022--> - - - - @@ -154,8 +144,6 @@ https://doi.org/10.1017/9781316337455.022--> - @@ -167,8 +155,6 @@ https://doi.org/10.1017/9781316337455.022--> - @@ -217,5 +203,5 @@ parameter settings for the estimation oft the aberrations. technical design perspective--> - + diff --git a/base_classes/NXcs_computer.nxdl.xml b/base_classes/NXcs_computer.nxdl.xml index 24be8abf88..77bfa9c52d 100644 --- a/base_classes/NXcs_computer.nxdl.xml +++ b/base_classes/NXcs_computer.nxdl.xml @@ -2,9 +2,9 @@ - + Deflectors as they are used e.g. in an electron analyser. - + - Qualitative type of deflector with respect to the number of pole pieces. + Qualitative type of deflector with respect to the number of pole pieces @@ -39,20 +39,13 @@ Colloquial or short name for the deflector. For manufacturer names and - identifiers use respective manufacturer fields. - - - - - - Ideally an identifier, persistent link, or free text which gives - further details about the deflector. + identifiers use ``NXfabrication`` and ``identifierNAME``. - Excitation voltage of the deflector. For dipoles it is a single number. - For higher order multipoles, it is an array. + Excitation voltage of the deflector. For dipoles it is a single number. For + higher orders, it is an array. @@ -61,34 +54,4 @@ higher orders, it is an array. - - - Spatial offset of the deflector in x direction (perpendicular to - ```offset_y```). - - - - - Spatial offset of the deflector in y direction (perpendicular to - ```offset_x```). - - - - - Specifies the position of the deflector by pointing to the last transformation - in the transformation chain in the NXtransformations group. - - - - - Collection of axis-based translations and rotations to describe the location and - geometry of the deflector as a component in the instrument. Conventions from the - :ref:`NXtransformations` base class are used. In principle, the McStas coordinate - system is used. The first transformation has to point either to another - component of the system or . (for pointing to the reference frame) to relate it - relative to the experimental setup. Typically, the components of a system should - all be related relative to each other and only one component should relate to - the reference coordinate system. - - - + \ No newline at end of file diff --git a/base_classes/NXebeam_column.nxdl.xml b/base_classes/NXebeam_column.nxdl.xml index d4fc0f1538..d9a43c076d 100644 --- a/base_classes/NXebeam_column.nxdl.xml +++ b/base_classes/NXebeam_column.nxdl.xml @@ -3,7 +3,7 @@ - - + - Base class for a set of components providing a controllable electron beam. + Base class for a set of components providing a controllable electron beam. + + The idea behind defining NXebeam_column as an own base class vs. adding these + concepts in NXinstrument_em is that the electron beam generating component + might be worthwhile to use in other experiments also. - Typically tech-partner, microscope-, and control software-specific - name of the specific operation mode how the ebeam_column and its - components are controlled to achieve a specific illumination condition. - - In most cases users do not know, have to care, or are able to disentangle the - details of the spatiotemporal dynamics of the components of the microscope. - Instead, they rely on the assumption that the microscope and control software - work as expected. Selecting then a specific operation_mode assures some level - of reproducibility in the illumination conditions. + Tech-partner, microscope-, and control-software-specific name of the + specific operation mode how the ebeam_column and its components are controlled + to achieve specific illumination conditions. + + In many cases the users of an instrument do not or can not be expected to know + all intricate spatiotemporal dynamics of their hardware. Instead, they rely of + assumptions that the instrument, its control software, and components work as + expected to focus on their research questions. + + For these cases, having a place for documenting the operation_mode is useful + in as much as at least some constraints on how the illumination conditions were + get documented. - - - The source which creates the electron beam. + A physical part of an electron or ion microscope from which + the particles that form the beam are emitted. + + The hardware for an electron source in an electron microscope + may contain several components which affect the beam path. + + This concept is related to term `Source`_ of the EMglossary standard. + + .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 - + - Given name/alias. + The potential difference between anode and cathode. + + This concept is related to term `Acceleration Voltage`_ of the EMglossary standard. + + .. _Acceleration Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 - - + + + Voltage which is utilised to create an electric field that draws particles from + the source. + + This concept is related to term `Extraction Voltage`_ of the EMglossary standard. + + .. _Extraction Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 + + + - Voltage relevant to compute the energy of the electrons - immediately after they left the gun. + Electrical current which is released from the source. + + This concept is related to term `Emission Current`_ of the EMglossary standard. + + .. _Emission Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 + + + + + Electrical current which flows through the source. + + This concept is related to term `Filament Current`_ of the EMglossary standard. + + .. _Filament Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 - Type of radiation. + Type of radiation. @@ -69,49 +104,129 @@ part "an electron gun" reusable in other context--> - Emitter type used to create the beam. - - If the emitter type is other, give further details - in the description field. + Emitter type used to create the beam. + + If the emitter type is other, give further details + in the description field. - Material of which the emitter is build, e.g. the filament material. + Material of which the emitter is build, e.g. the filament material. - - + + - Ideally, a (globally) unique persistent identifier, link, - or text to a resource which gives further details. + How long has the source been in operation. - - - - Collection of axis-based translations and rotations to describe the - location and geometry of the component in the instrument. - - - - - + + + + Device to improve energy resolution or chromatic aberration. + + Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector + like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ + + + + + Qualitative type of the component. + + + + + + + + + + + + + + Was the corrector used? + + + + + + Energy dispersion in e.g. µm/eV. + + + + + Corresponding voltage for that energy dispersion. + + + + + + + Component that reshapes an ellipse-shaped electron beam into a circular one. + + * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ + * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ + + Stigmator is an exact synonym. + + + + Descriptor for the correction strength along the first direction when exact technical details + are unknown or not directly controllable as the control software of the microscope does not + enable or was not configured to display these values for users. + + + + + Descriptor for the correction strength along the second direction when exact technical details + are unknown or not directly controllable as the control software of the microscope does not + enable or was not configured to display these values for users. + + + + + + Electron biprism as it is used e.g. for electron holography. + + + + + + Device that causes a change in the phase of an electron wave. + + * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ + * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ + + + + Qualitative type + + + + + + + + - Individual characterization results for the position, shape, - and characteristics of the electron beam. - - :ref:`NXtransformations` should be used to specify the location - of the position at which the beam was probed. + Individual characterization results for the position, shape, + and characteristics of the electron beam at a given location. + + :ref:`NXtransformations` should be used to specify the location + or the position at which details about the beam were probed. + + This concept is related to term `Electron Beam`_ of the EMglossary standard. + + .. _Electron Beam: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 - diff --git a/base_classes/NXem_ebsd.nxdl.xml b/base_classes/NXem_ebsd.nxdl.xml index 9fd2495181..86fe5e4343 100644 --- a/base_classes/NXem_ebsd.nxdl.xml +++ b/base_classes/NXem_ebsd.nxdl.xml @@ -3,7 +3,7 @@ - + - Number of arguments per orientation for given parameterization. + Number of arguments per orientation for given parameterization. - Number of scan points. + Number of scan points. - Number of pixel along the slowest changing dimension for a rediscretized, - i.e. standardized default plot orientation mapping. + Number of pixel along the slowest changing dimension for a rediscretized, + i.e. standardized default plot orientation mapping. - Number of pixel along slow changing dimension for a rediscretized i.e. - standardized default plot orientation mapping. + Number of pixel along slow changing dimension for a rediscretized i.e. + standardized default plot orientation mapping. - Number of pixel along fast changing dimension for a rediscretized i.e. - standardized default plot orientation mapping. + Number of pixel along fast changing dimension for a rediscretized i.e. + standardized default plot orientation mapping. - Number of phase solutions + Number of phase solutions + + + + + Number of reflectors (Miller crystallographic plane triplets). - Base class method-specific for Electron Backscatter Diffraction (EBSD). - - The general procedure of an EBSD experiment is as follows. - Users load the specimen, collect first a coarse image of the surface. - Next, they set an approximate value for the calibrated working distance and - tilt the stage to set the desired diffraction conditions. - - Users then typically configure the microscope for collecting higher quality data - and push in the EBSD detector. Subsequently, they fine tune the illumination - and aberration corrector settings and select one or multiple ROIs for - the microscope to machine off automatically. They configure on-the-fly - indexing parameter and start the measurement queue. - - Nowadays, this is in most cases an automated process. The pattern - collection runs during the allocated microscope session until the - queue finishes or gets interrupted by errors or the next user terminates - sessions which run over time. - - Kikuchi pattern surplus eventually multi-modal detector signals are - collected and usually indexed on-the-fly. Patterns may be stored or not - so one should not assume that raw data are always stored. - - Results are stored in files, which afterwards are typically copied - automatically or manual for archival purposes to certain storage - locations or further consumption. The result of such an EBSD - measurement/experiment is a set of usually proprietary or open files - from technology partners. - - This :ref:`NXem_ebsd` base class is a proposal how to represent method-specific - data, metadata, and connections between these for the research field of - electron microscopy. - - More specifically, exemplified here for electron backscatter diffraction (EBSD) - we show how NeXus can be used to solve two key documentation issues so far - missing in the field of EBSD. - - Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file which is formatted - according to NXem_ebsd) stores the connection between the microscope session and - the key datasets which are considered typically results of the various processing - steps involved when working with EBSD data. - - Different groups in NXem_ebsd make connections to data artifacts which were collected - when working with electron microscopes via the NXem application definition. - Using a file which stores information according to the NXem application definition - has the benefit that it connects the sample, references to the sample processing, - the user operating the microscope, details about the microscope session, - and details about the acquisition and eventual indexing of Kikuchi pattern, - associated overview images, like secondary electron or backscattered electron - images of the region-of-interest probed and many more pieces of information. - - Secondly, NXem_ebsd connects and stores the conventions and reference frames - which were used and which are the key to a correct mathematical interpretation - of every EBSD result. Otherwise, results would be ripped out of their context, - as it is the current situation with many traditional studies where EBSD data - were indexed on-the-fly and shared with the community only via sharing - the strongly processed results file in some technology-partner-specific file - format but without communicating all conventions or relying on the assumptions - that colleagues likely know these conventions even though multiple definitions - are possible. - - NXem_ebsd covers experiments with one-, two-dimensional, and so-called three- - dimensional EBSD datasets. The third dimension is either time (in the case of - quasi in-situ experiments) or space (in the case of serial-sectioning) methods - where a combination of mechanical or ion milling is used repetitively to measure - the same region-of-interest at different depth increments. Material removal - can be achieved with electron or ion polishing, using manual - steps or using automated equipment like a robot system. - - Three-dimensional experiments require to follow a sequence of specimen, surface - preparation, and data collection steps. By nature these methods are destructive - in that they either require the removal of the previously measured material region - or that the sample surface can degrade due to e.g. contamination or other - electron-matter interaction. - - For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings are - combined into one reconstructed stack. That is serial-sectioning is mainly a - computational workflow. Users collect data for each serial sectioning step - via an experiment. This assures that data for associated microscope sessions - and steps of data processing stay connected and contextualized. - - Eventual tomography methods also use such a workflow because first diffraction - images are collected (e.g. with X-ray) and then these imagres are indexed and - computed into a 3D orientation mapping. The here proposed NXem_ebsd application - definition contains conceptual ideas how this splitting between measurement and - post-processing can be granularized also for such X-ray-based techniques, whether - it be 3DXRD or HEDM. - - This concept is related to term `Electron Backscatter Diffraction`_ of the EMglossary standard. - - .. _Electron Backscatter Diffraction: https://purls.helmholtz-metadaten.de/emg/EMG_00000019 + Base class method-specific for Electron Backscatter Diffraction (EBSD). + + The general procedure of an EBSD experiment is as follows: + Users load the specimen, collect first a coarse image of the surface. + Next, they set an approximate value for the calibrated working distance + and tilt the stage into diffraction conditions. + + Users then typically configure the microscope for collecting quality data. + The EBSD detector is pushed in (if retractable). Subsequently, they fine tune + the illumination and aberration corrector settings and select one or multiple ROIs + for the microscope to machine off automatically. They configure on-the-fly + indexing parameter and then typically start the measurement queue. + From this point onwards typically the microscope runs automatically. + + Diffraction pattern get collected until the queue finishes or gets interrupted by + either errors or arrival at the end of the users' allocated timeslot at the instrument. + + Kikuchi pattern (EBSP) are usually indexed on-the-fly. These patterns are the raw data. + Once indexed, these patterns are often not stored. + + Results are stored in files, which afterwards are typically copied + automatically or manually for archival purposes to certain storage + locations for further consumption. The result of such an EBSD + measurement/experiment is a set of usually proprietary or open files + from technology partners. + + This :ref:`NXem_ebsd` base class is a proposal how to represent method-specific + data, metadata, and connections between these for the research field of + electron microscopy exemplified here for electron backscatter diffraction (EBSD). + The base class solves two key documentation issues within the EBSD community: + + Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file that is formatted + according to NXem_ebsd) stores the connection between the microscope session and + the key datasets which are considered typically results of the afore-mentioned + steps involved in an EBSD experiment. + + Different groups in NXem_ebsd make connections to data artifacts which were collected + when working with electron microscopes via the NXem application definition. + Using a file which stores information according to the NXem application definition + has the benefit that it connects the sample, references to the sample processing, + the user operating the microscope, details about the microscope session, + and details about the acquisition and eventual indexing of Kikuchi patterns, + associated overview images, like secondary electron or backscattered electron + images of the region-of-interest probed, and many more (meta)data. + + Secondly, NXem_ebsd connects and stores the conventions and reference frames + which were used and which are the key to a correct mathematical interpretation + of every experiment or simulation using EBSD. + + Otherwise, results would be ripped out of their context like it is the current situation + with many traditional studies where EBSD data were indexed on-the-fly and shared + with the community only via sharing the strongly processed files with results in some + formatting but without communicating all conventions used or just relying on the assumptions + that colleagues likely know these conventions even though + multiple definitions are possible. + + NXem_ebsd covers experiments with one-, two-dimensional, and so-called three- + dimensional EBSD datasets. The third dimension is either time (in the case of + quasi in-situ experiments) or space (in the case of serial-sectioning) experiments + where a combination of repetitive removal of material from the surface layer to measure + otherwise the same region-of-interest at different depth increments. Material removal + can be achieved with mechanical, electron, or ion polishing, using manual steps or + automated equipment like a robot system `S. Tsai et al. <https://doi.org/10.1063/5.0087945>`_. + + Three-dimensional experiments require to follow a sequence of specimen, surface + preparation, and data collection steps. By virtue of design, these methods are destructive + either because of the necessary material removal or surface degradation due to e.g. + contamination or other electron-matter interaction. + + For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings + are combined into one reconstructed stack via a computational workflow. Users collect + data for each serial sectioning step via an experiment. This assures that data for associated + microscope sessions and steps of data processing stay contextualized and connected. + + Eventual tomography methods also use such a workflow because first diffraction + images are collected (e.g. with X-ray) and then these images are indexed to process + a 3D orientation mapping. Therefore, the here proposed base class can be a blueprint + also for future classes to embrace our colleagues from X-ray-based techniques be it 3DXRD or HEDM. + + This concept is related to term `Electron Backscatter Diffraction`_ of the EMglossary standard. + + .. _Electron Backscatter Diffraction: https://purls.helmholtz-metadaten.de/emg/EMG_00000019 - - Details about the gnomonic (projection) reference frame. - - It is assumed that the configuration is inspected by looking towards the sample surface. - If a detector is involved, it is assumed that the configuration is inspected from a position - that is located behind this detector. - - If any of these assumptions is not met, the user is required to explicitly state this. - - Reference DOI: 10.1016/j.matchar.2016.04.008 suggests to label the - base vectors of this coordinate system as Xg, Yg, Zg. + Details about the gnomonic (projection) reference frame. + + It is assumed that the configuration is inspected by looking towards the sample surface. + If a detector is involved, it is assumed that the configuration is inspected from a position + that is located behind this detector. + + If any of these assumptions are not met, the user is required to explicitly state this. + + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the + base vectors of this coordinate system as :math:`X_g, Y_g, Z_g`. - Origin of the gnomonic_projection_reference_frame. - - Reference DOI: 10.1016/j.matchar.2016.04.008 suggests to - assume that this is coordinate Xg = 0, Yg = 0, Zg = 0. + Origin of the gnomonic_reference_frame. + + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to + assume that this is coordinate :math:`Xg = 0, Yg = 0, Zg = 0`. - - Direction of the positively pointing x-axis base vector of the - gnomonic_reference_frame. + Direction of the positively pointing x-axis base vector of the + gnomonic_reference_frame. - @@ -192,11 +186,10 @@ - Direction of the positively pointing y-axis base vector of the - gnomonic_reference_frame. + Direction of the positively pointing y-axis base vector of the + gnomonic_reference_frame. - @@ -207,11 +200,10 @@ - Direction of the positively pointing z-axis base vector of the - gnomonic_reference_frame. + Direction of the positively pointing z-axis base vector of the + gnomonic_reference_frame. - @@ -223,31 +215,31 @@ - Details about the definition of the pattern centre as a special point in the gnomonic_reference_frame. - - Keep in mind that the gnomonic space is in virtually all cases embedded in the detector space. - Specifically, the XgYg plane is defined such that it is laying inside the XdYd plane - (of the detector reference frame). - - When the normalization direction is the same as e.g. the detector x-axis direction one - effectively normalizes in fractions of the width of the detector. - - The issue with terms like width and height is that these degenerate if the detector - region-of-interest is square-shaped. This is why instead of referring to width and height - one should report as if one were to measure practically with a ruler and one is specific - about in which direction positive distances are measured. - - For the concepts used to specify the boundary_convention it is assumed that the - region-of-interest is defined by a rectangle, referring to the direction of outer-unit - normals to the respective edges of this rectangle. + Details about the definition of the pattern centre as a special point in the + gnomonic_reference_frame. + + Typically the gnomonic space is embedded in the detector space. + Specifically, the XgYg plane is defined such that it is laying inside the + XdYd plane (of the detector reference frame). + + When the normalization direction is the same as e.g. the detector x-axis direction + one effectively normalizes in fractions of the width of the detector. + + The issue with terms like width and height, though, is that these become degenerated + if the detector region-of-interest is square-shaped. This is why instead of referring to + width and height it is better to state explicitly which direction is considered positive + when measuring distances. + + For the concepts used to specify the boundary_convention it is assumed that the + region-of-interest is defined by a rectangle, referring to the direction of outer-unit + normals to the respective edges of this rectangle. - From which border of the EBSP (in the detector reference frame) is the pattern - centre's x-position (PCx) measured. + From which border of the EBSP (in the detector reference frame) is the pattern + centre's x-position (PCx) measured. - @@ -256,11 +248,10 @@ - In which direction are positive values for the x-axis coordinate value measured - from the specified boundary. + In which direction are positive values for the x-axis coordinate value measured + from the specified boundary. - @@ -269,11 +260,10 @@ - From which border of the EBSP (in the detector reference frame) is the pattern - centre's y-position (PCy) measured. + From which border of the EBSP (in the detector reference frame) is the pattern + centre's y-position (PCy) measured. - @@ -282,11 +272,10 @@ - In which direction are positive values for the y-axis coordinate value measured - from the specified boundary. + In which direction are positive values for the y-axis coordinate value measured + from the specified boundary. - @@ -294,326 +283,316 @@ - - This group documents relevant details about the conditions and the tools - used for measuring a stack of Kikuchi diffraction pattern with an - electron microscope. - - The most frequently collected EBSD data are captured for rectangular - regions-of-interested which are sampled with regular square or - hexagon-shaped pixels. + This group documents relevant details about the conditions and the + tools for measuring diffraction patterns with an electron microscope. + + The most frequently collected EBSD data are captured for rectangular + regions-of-interest using a discretization into square or hexagon tiles. - Physical time since the beginning of a timestamp that is required to be - same for all experiments in the set. The purpose of this marker is - to identify how all experiments in the set need to be arranged - sequentially based on the time elapsed. - The time is relevant to sort e.g. experiments of consecutive quasi - in-situ experiments where a measurement was e.g. taken after 0 minutes, - 30 minutes, 6 hours, or 24 hours of annealing. + Physical time since the beginning of a timestamp that is required to be + the same for all experiments in the set. The purpose of this marker is + to identify how all experiments in the set need to be arranged + sequentially based on the time elapsed. + The time is relevant to sort e.g. experiments of consecutive quasi + in-situ experiments where a measurement was e.g. taken after 0 minutes, + 30 minutes, 6 hours, or 24 hours of annealing. - Timestamp relative to which time was counted to aid - converting between time and timestamp. + Timestamp relative to which time was counted to aid + converting between time and timestamp. - - If available and it is stored in an instance of an application definition this field - specifies the path to an instance of :ref:`NXdata` where the measured patterns - are stored. + Path to an instance of :ref:`NXdata` where the measured patterns are stored. - + - Reference (e.g. path and filename) to an existent data artifact which - stores either the measured pattern or input (already processed EBSD data). + Reference (e.g. path and filename) to an existent data artifact which + stores either the measured patterns or input (already processed EBSD data). - This group documents relevant details about the conditions and the tools - used for simulating a stack of Kikuchi diffraction pattern with some - physical model. - - This group should not be confused with a group named simulation that - is however an instance of NXem_sim. Instead, the simulation group here - should be used if (e.g. instead of a measurement) a stack of pattern - were simulated that one wishes to use for indexing patterns. + This group documents relevant details about the conditions and the tools + used for simulating diffraction patterns with some physical model. + + This group should be used if (e.g. instead of a measurement) the patterns + were simulated (possibly awaiting indexing). - In many practical cases where pattern are analyzed on-the-fly and dictionary - indexing strategies are used, so-called master pattern(s) are used to compare - measured or simulated pattern with the master pattern. In this case, - master pattern are the result of a computer simulation and thus should - be stored using an own properly documented entry within a simulation - group as an instance of :ref:`NXem_sim`. + In many practical cases where patterns are analyzed on-the-fly and dictionary + indexing strategies used, so-called master pattern(s) are used to compare + measured or simulated patterns with the master patterns. - If available and it is stored in an instance of an application definition this field specifies - the path to an instance of :ref:`NXimage_set` where the simulated patterns are stored. + Path to an instance of :ref:`NXimage` where the simulated patterns are stored. - + - Reference (e.g. path and filename) to an existent digital resource which - stores either the pattern or input (already processed EBSD data) - which is now processed further as described by this NXem_ebsd instance. + Reference (e.g. path and filename) to an existent digital resource which + stores either the patterns or input (already processed EBSD data) that are + about to become processed further as described by this NXem_ebsd instance. - The EBSD system, including components like the electron gun, pole-piece, - stage tilting, EBSD detector, and the gnomonic projection have to be - calibrated to achieve reliable indexing results. - - Specifically, the gnomonic projection has to be calibrated. - Typically, silicon or quartz crystals are used for this purpose. - - Considering a system is well-calibrated, it is much more frequently the - case in practice that users assume the system is calibrated (and thus usable) - vs. they perform the calibration of the EBSD system. - - In the first case, the user assumes that the principle geometry of the - hardware components and the settings in the control and EBSD pattern - acquisition software has been calibrated. Consequently, users pick from - an existent library of phase candidates, i.e. - :ref:`NXcrystal_structure` instances. Examples are - reflector models as stored in CRY files (HKL/Channel 5/Flamenco). - - In the second case, users calibrate the system during the session - using standards (silicon, quartz, or other common specimens). - There is usually one person in each lab responsible for doing such - calibrations. Often this person or technician is also in charge of - configuring the graphical user interface and software with which most - users control and perform their analyses. - - For EBSD this has key implications: Taking TSL OIM/EDAX as an example, - the conventions how orientations are stored is affected by how the - reference frames are configured and this setup is made at the level - of the GUI software. - - Unfortunately, these pieces of information are not necessarily stored - in the results files. In effect, key conventions become disconnected - from the data so it remains the users' obligation to remember these - settings or write these down in a lab notebook. Otherwise, these metadata - get lost. All these issues are a motivation and problem which - :ref:`NXem_ebsd` solves in that all conventions can be specified explicitly. + The EBSD system, including components like the electron gun, pole-piece, + stage tilt, EBSD detector, and the gnomonic projection have to be + calibrated to achieve reliable, precise, and accurate scientific results. + + Specifically, the gnomonic projection has to be calibrated. + Typically, standard specimens made from silicon or quartz crystals + in specific orientations are used for this purpose. + + Considering that a system used is already calibrated well-enough is much + more frequently the case in practice than that users perform the calibration + themselves (with above-mentioned standard specimens). + + In the first case, the user assumes that the principle geometry of the + hardware components and the settings in the control and EBSD pattern + acquisition software has been calibrated already. Consequently, users pick from + an existent library of phase candidates, i.e. :ref:`NXunit_cell` instances. + Examples are reflector models as stored in CRY files (HKL/Channel 5/Flamenco). + + In the second case, users calibrate the system during the session + using standards (silicon, quartz, or other common specimens). + There is usually one person in each lab responsible for doing such + calibrations. Often this person or technician is also in charge of + configuring the graphical user interface and software with which most + users control and perform their analyses. + + For EBSD this has key implications: Taking TSL OIM/EDAX as an example, + the conventions how orientations are stored is affected by how the + reference frames are configured and how this setup in the GUI. + + Unfortunately, these pieces of information are not necessarily stored + in the results files. In effect, key conventions become disconnected + from the data so it remains the users' obligation to remember these + settings or write these down in a lab notebook. Otherwise, these metadata + get lost. All these issues are a motivation and problem which :ref:`NXem_ebsd` + solves in that all conventions can be specified explicitly. - If available and it is stored in an instance of an application definition this field specifies - the path to an instance of :ref:`NXem_msr` where calibration is stored. + Path to an instance of :ref:`NXem` where calibration data are stored. - + - Reference to a digital resource where the calibration is stored. + Reference to a digital resource where the calibration is stored. - Indexing is a data processing step performed either after or while - (on-the-fly) the beam scans the specimen. The resulting method is also - known as orientation imaging microscopy (OIM). - - Different algorithms can be used to index EBSD pattern. Common to them - is the computational step where simulated reference pattern are compared - with measured or simulated patterns. These latter patterns are referred - to via the measurement or simulation groups of this base class. - - Quality descriptors are defined based on which an indexing algorithm - yields a quantitative measure of how similar measured and reference - pattern are, and thus if no, one, or multiple so-called solutions - were found. - - Assumed or simulated pattern are simulated using kinematic or dynamical - theory of electron diffraction delivering master pattern. - - The Hough transform is essentially a discretized Radon transform (for details see `M. van Ginkel et al. <https://www.semanticscholar.org/paper/A-short-introduction-to-the-Radon-and-Hough-and-how-Ginkel/fb6226f606cad489a15e38ed961c419037ccc858>`_). - Recently, dictionary-based indexing methods are increasingly becoming used - partly driven by the interest to use artificial intelligence algorithms. + Indexing is a data processing step performed either after or while (aka on-the-fly) + the beam scans the specimen. The resulting method is also + known as orientation imaging microscopy (OIM). + + Different algorithms can be used to index EBSP. Common to them is the + computational step where simulated or theoretically assumed patterns + are compared with the measured ones. These latter patterns are referred + to via the measurement or simulation groups of this base class respectively. + + Quality descriptors are defined based on which an indexing algorithm + yields a quantitative measure of how similar measured and reference + patterns are, and thus if no, one, or multiple so-called solutions were found. + + Assumed or simulated patterns are simulated using kinematical or dynamical + theory of electron diffraction delivering master patterns. + + The Hough transform, one of the most frequently used traditional method for indexing + EBSP is essentially a discretized Radon transform (for details see `M. van Ginkel et al. <https://www.semanticscholar.org/paper/A-short-introduction-to-the-Radon-and-Hough-and-how-Ginkel/fb6226f606cad489a15e38ed961c419037ccc858>`_). Recently, dictionary-based and artificial intelligence-based methods + find more widespread usage for indexing. - + - This group enables to establish a logical connection between previous - processing steps or on-the-fly-performed indexing of the EBSD map. - Typically these processing steps are performed with commercial software. - Therefore, in many cases a results file from this indexing is often - all that is communicated and saved. These are typically files in a format - specific to the instrument and its configuration. - - Typical file formats are CPR/CRC, ANG, OSC, HDF5, H5EBSD, EDAXH5. + This group enables to establish a logical connection between previous + processing steps or on-the-fly-performed indexing of the EBSD map. + Typically these processing steps are performed with commercial software. + Therefore, in many cases a results file from this indexing is often + all that is communicated and saved. These are typically files in a format + specific to the instrument and its configuration. + + Typical file formats are CPR/CRC, ANG, OSC, HDF5, H5EBSD, EDAXH5. - Principal algorithm used for indexing. + Principal algorithm used for indexing. - - + - - Details about the background correction applied to each Kikuchi pattern. + Details about the background correction applied to each Kikuchi pattern. - Binning i.e. downsampling of the pattern. + Binning i.e. downsampling to each pattern. - + - Specific parameter relevant only for certain algorithms used. + Specific parameter relevant only for certain algorithms used. - + - Details for each phase used as a model with which the patterns were - indexed. Instances of :ref:`NXcrystal_structure` in this group must - have the group name prefix phase. The identifier in the name is an - integer. We start counting from 1 because the value 0 is reserved for - the special phase that is the null-model, i.e. the null phase, notIndexed. + Details for each phase used as a model with which the patterns were + indexed. Instances of :ref:`NXunit_cell` in this group must + have the group name prefixed with phase. The identifier in the name is an + integer. Start counting from 1 because the value 0 is reserved for + the special phase that is the null-model, the null phase also known + as notIndexed. + + + Spacing between the crystallographic planes that are defined via ``miller``. + + + + + + + + Relative intensity for the computed diffraction intensity (signal) for the + plane. + + + + + + + + In case the :ref:`NXunit_cell` base class is used with analyzed orientation maps + this field stores how many scan points of the map were identified as matching best + with this phase. + + + + + How many reflectors for crystallographic planes are distinguished. + + + + + Miller indices :math:`(hkl)[uvw]` of the planes. + + The first triplet specifies :math:`(hkl)`. The second triplet specifies :math:`[uvw]`. + Miller indices refer to the Cartesian right-handed coordinate system of the unit cell. + + + + + + - Which return value did the indexing algorithm yield for each scan point. - Practically useful is to use an uint8 mask. - - * 0 - Not analyzed - * 1 - Too high angular deviation - * 2 - No solution - * 100 - Success - * 255 - Unexpected errors + Which return value did the indexing algorithm yield for each scan point. + + * 0 - Not analyzed + * 1 - Too high angular deviation + * 2 - No solution + * 100 - Success + * 255 - Unexpected errors - - - How many phases i.e. crystal structure models were used to index each - scan point if any? Let's assume an example to explain how this field - should be used: In the simplest case users collected one pattern for - each scan point and have indexed using one phase, i.e. one instance - of an NXem_ebsd_crystal_structure_model. - - In another example users may have skipped some scan points (not indexed) - them at all) and/or used differing numbers of phases for different scan - points. - - The cumulated of this array decodes how phase_identifier and phase_matching - arrays have to be interpreted. In the simplest case (one pattern per scan - point, and all scan points indexed using that same single phase model), - phase_identifier has as many entries as scan points - and phase_matching has also as many entries as scan points. + + + How many phases i.e. crystal structure models were used to index each + scan point if any? Let's assume an example to explain how this field + should be used: In the simplest case users collected one pattern for + each scan point and have indexed using one phase, i.e. one instance + of an :ref:`NXunit_cell`. + + In another example users may have skipped some scan points (not indexed + them at all) or used differing numbers of phases for indexing different scan points. + + The cumulated of this array decodes how identifier_phase and matching_phase + arrays have to be interpreted. In the simplest case (one pattern per scan + point, and all scan points indexed using that same single phase model), + identifier_phase has as many entries as scan points + and matching_phase has also as many entries as scan points. - - - The array n_phases_per_scan_point details how the phase_identifier - and the phase_matching arrays have to be interpreted. - - For the example with a single phase phase_identifier has trivial - values either 0 (no solution) or 1 (solution matching - sufficiently significant with the model for phase 1). - - When there are multiple phases, it is possible (although not frequently - needed) that a pattern matches eventually (not equally well) sufficiently - significant with multiple pattern. This can especially happen in cases of - pseudosymmetry and more frequently with an improperly calibrated system - or false or inaccurate phase models e.g. (ferrite, austenite). - Having such field is especially relevant for recent machine learning - or dictionary based indexing schemes because in combination with - phase_matching these fields communicate the results in a model-agnostic - way. - - Depending on the n_phases_per_scan_point value phase_identifier and - phase_matching arrays represent a collection of concatenated tuples, - which are organized in sequence: The solutions for the 0-th scan point, - the 1-th scan point, the n_sc - 1 th scan point and omitting tuples - for those scan points with no phases according to n_phases_per_scan_point + + + The array phases_per_scan_point details how the identifier_phase + and the matching_phase arrays have to be interpreted. + + For the example with a single phase identifier_phase has trivial + values either 0 (no solution) or 1 (solution matching + sufficiently significant with the model for phase 1). + + When there are multiple phases, it is possible (although not frequently + required) that a pattern matches eventually (not equally well) sufficiently + significant with multiple patterns. This can especially happen in cases of + pseudosymmetry and more frequently with an improperly calibrated system + or false or inaccurate phase models. Having such field is especially relevant + for recent dictionary- or artificial intelligence-based indexing methods to communicate + the results in a model-agnostic way in combination with matching_phase. + + Depending on the phases_per_scan_point value, identifier_phase and + matching_phase arrays represent a collection of concatenated tuples. + These are organized in sequence: The solutions for the 0-th scan point, + the 1-th scan point, the n_sc - 1 th scan point and omitting tuples + for those scan points with no phases according to phases_per_scan_point. - + - One-dimensional array, pattern by pattern labelling the solutions found. - The array n_phases_per_scan_point has to be specified because it details - how the phase_identifier and the phase_matching arrays have to be interpreted. - See documentation of phase_identifier for further details. + One-dimensional array, pattern by pattern labelling the solutions found. + The array phases_per_scan_point has to be specified because it details + how the identifier_phase and the matching_phase arrays are interpreted. + See documentation of identifier_phase for further details. - + - Phase_matching is a descriptor for how well the solution matches or not. - Examples can be confidence_index, mean_angular_deviation, some AI-based - matching probability (other), i.e. the details are implementation-specific. + Phase_matching is a descriptor for how well the solution matches or not. + Examples can be confidence_index, mean_angular_deviation, or other. - - - + - em_lab/ebeam_deflector to retrieve the actual scan positions -although this would be cleaner, also scan_point_positions could be -an instance of NXcg_point with a depends_on pointing -to sample_reference_frame ---> - Calibrated center positions of each scan point - in the sample surface reference system. + Calibrated centre positions of each scan point + in the sample surface reference system. @@ -622,88 +601,77 @@ to sample_reference_frame - Fraction of successfully indexed pattern with a phase - not the null-phase vs the number_of_scan_points. + Fraction of successfully indexed patterns with a phase + not the null-phase vs the number_of_scan_points. - Number of scan points in the original mapping. + Number of scan points in the original mapping. - - An overview of the entire ROI. + An overview of the entire ROI. - Descriptor representing the image contrast. + Descriptor representing the image contrast. - - - Title of the default plot. + Title of the default plot. - Descriptor values displaying the ROI. + Descriptor values displaying the ROI. - - Descriptor values. + Descriptor values - Calibrated coordinate along the y-axis. + Calibrated coordinate along the y-axis. - Label for the y axis + Label for the y axis - Calibrated coordinate along the x-axis. + Calibrated coordinate along the x-axis. - Label for the x axis + Label for the x axis diff --git a/base_classes/NXem_eds.nxdl.xml b/base_classes/NXem_eds.nxdl.xml index 6e3d797332..524a3efe09 100644 --- a/base_classes/NXem_eds.nxdl.xml +++ b/base_classes/NXem_eds.nxdl.xml @@ -3,7 +3,7 @@ - + - Number of X-ray photon energy (bins) + Number of X-ray photon energy (bins) - Number of identified elements + Number of identified elements - Number of peaks detected + Number of peaks detected - Number of IUPAC line names + Number of IUPAC line names - Base class method-specific for energy-dispersive X-ray spectroscopy (EDS/EDXS). - - `IUPAC instead of Siegbahn notation <https://doi.org/10.1002/xrs.1300200308>`_ should be used. - - X-ray spectroscopy is a surface-sensitive technique. Therefore, three-dimensional elemental - characterzation requires typically a sequence of characterization and preparation of the - surface to expose a new surface layer that can be characterized in the next acquisition. - In effect, the resulting three-dimensional elemental information mappings are truely the - result of a correlation and post-processing of several measurements which is the field - of correlative tomographic usage of electron microscopy. + Base class method-specific for energy-dispersive X-ray spectroscopy (EDS/EDXS). + + `IUPAC instead of Siegbahn notation <https://doi.org/10.1002/xrs.1300200308>`_ should be used. + + X-ray spectroscopy is a surface-sensitive technique. Therefore, three-dimensional elemental + characterzation requires typically a sequence of characterization and preparation of the + surface to expose new surface layer that can be characterized in the next acquisition. + In effect, the resulting three-dimensional elemental information mappings are truely the + result of a correlation and post-processing of several measurements which is the field + of correlative tomographic usage of electron microscopy. - - Details about computational steps how peaks were indexed as elements. + Details about computational steps how peaks were indexed as elements. - The program with which the indexing was performed. + The program with which the indexing was performed. - Accumulated intensity over all pixels of the region-of-interest. + Accumulated intensity over all pixels of the region-of-interest. - Accumulated counts + Accumulated counts - Counts + Counts - Energy axis + Energy axis - Energy + Energy + + + Comma-separated list of symbols for elements from the periodic table that have + been confirmed present by the here reported EDS analysis. + + This field can be used when creating instances of :ref:`NXpeak` is not desired. + However, a collection of instances of NXpeak with individual NXatom + can be used to add isotopic information and other relevant context. + + + + + - Name and location of each X-ray line which was indexed as a known ion. - For each ion, an NXion instance should be created which specifies - the origin of the signal. For each ion also the relevant IUPAC notation - X-ray lines should be specified. + Details about individual indexed peaks. - + - Associated lower :math:`[e_{min}, e_{max}]` bounds of the - energy which is assumed associated with this peak. + Associated lower :math:`[e_{min}, e_{max}]` bounds of the + energy which is assumed associated with this peak. @@ -124,15 +128,15 @@ and Adrien Teutrie, Cecile Hebert (EPFL)--> - Theoretical energy of the line according to IUPAC. + Theoretical energy of the line according to IUPAC. - + - IUPAC notation identifier of the line which the peak represents. - - This can be a list of IUPAC notations for (the seldom) case that - multiple lines are grouped with the same peak. + IUPAC notation identifier of the line which the peak represents. + + This can be a list of IUPAC notations for (the seldom) case that + multiple lines are grouped with the same peak. @@ -140,83 +144,60 @@ and Adrien Teutrie, Cecile Hebert (EPFL)--> - - - Comma-separated list of names of elements confirmed in the sample via EDS analysis. - - All members of the list have to be valid chemical_symbols from the periodic table. - - This field can be used when creating instances of NXpeak is not desired. - However, a collection of instances of NXpeak with individual NXion specified - enables also to distinguish isotopic information. - - - - - - - + - Individual element-specific EDS/EDX/EDXS/SXES mapping - - A composition map is an image whose intensities for each pixel are the - accumulated X-ray quanta *under the curve(s)* of a set of peaks. - - These element-specific EDS maps are :ref:`NXimage_set` instances - and need to be named with the name of the element from the - atom_types field. - - We often observe that signal contributions from several peaks - are summarized and shown together, e.g. the combined signal - under the curve of carbon and oxygen. - - In this case specify the processing details using peaks and weights. + Individual element-specific EDS/EDX/EDXS/SXES mapping + + A composition map is an image whose intensities for each pixel are the + accumulated X-ray quanta *under the curve(s)* of a set of peaks. + + These element-specific EDS maps are instances of :ref:`NXimage` + that should be named by the element from the atom_types field. + + When signal contributions from several peaks were decomposed + users should ideally use a respective number of NXpeak instances + to give further context about the individual signal contributions + are summarized and shown together, e.g. the combined signal + under the curve of carbon and oxygen. + + In this case specify the processing details use peak and weight. - Discouraged free-text field to add additional information. + Discouraged free-text field to add additional information. - + - Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that - documents which elements and their specific lines are theoretically located within - the energy_range of the spectrum from which the EDS (element) map has been computed. + Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that + documents which elements and their specific lines are theoretically located within + the energy_range of the spectrum from which the EDS (element) map was computed. - Associated :math:`[e_{min}, e_{max}]` bounds of the energy - range for which spectrum counts have been accumulated. + Associated :math:`[e_{min}, e_{max}]` bounds of the energy + range for which spectrum counts were accumulated. - + - A list of NXpeak instance names whose X-ray quanta - where accumulated for each pixel which yields an element-specific - EDS map. + A list of :ref:`NXpeak` instance names whose X-ray quanta were + accumulated for each pixel to obtain an element-specific + EDS map. - + - A list of weights by how much the intensity of each peak - under peaks was factorized to display the joint intensity - of the image. + A list of weights by how much the intensity of each peak + contributes to the intensity of the EDS map. diff --git a/base_classes/NXem_eels.nxdl.xml b/base_classes/NXem_eels.nxdl.xml index 4ddef01176..881f78b886 100644 --- a/base_classes/NXem_eels.nxdl.xml +++ b/base_classes/NXem_eels.nxdl.xml @@ -3,7 +3,7 @@ - - + Base class method-specific for Electron Energy Loss Spectroscopy (EELS). - Details about computational stesp how the zero-loss peak was threaded. @@ -54,9 +49,9 @@ specialized to include EELS-specific post-processing--> Name and location of each peak in the spectrum considered to be of relevance. - + - NXspectrum_set_em specialized for EELS. + NXspectrum specialized for EELS. diff --git a/base_classes/NXem_img.nxdl.xml b/base_classes/NXem_img.nxdl.xml index 5574965371..d016e1c6d7 100644 --- a/base_classes/NXem_img.nxdl.xml +++ b/base_classes/NXem_img.nxdl.xml @@ -3,7 +3,7 @@ - + - Base class for method-specific generic imaging. - - In the majority of cases simple d-dimensional regular scan patterns are used - to probe a region-of-interest (ROI). Examples can be single point aka spot - measurements, line profiles, or (rectangular) surface mappings. - The latter pattern is the most frequently used. - - For now the base class provides for scans for which the settings, - binning, and energy resolution is the same for each scan point. + Base class for method-specific generic imaging with electron microscopes. + + In the majority of cases simple d-dimensional regular scan patterns are used + to probe regions-of-interest (ROIs). Examples can be single point aka spot + measurements, line profiles, or (rectangular) surface mappings. + The latter pattern is the most frequently used. + + For now the base class provides for scans for which the settings, + binning, and energy resolution is the same for each scan point. - - - Which imaging mode was used? - - - - - - - - - + + + + Which imaging mode was used? + + + + + + + + - Annulus inner (first value) and outer (second value) half angle. + Annulus inner (first value) and outer (second value) half angle. - diff --git a/base_classes/NXevent_data_em.nxdl.xml b/base_classes/NXevent_data_em.nxdl.xml index 85f847e3da..8153b3ae9e 100644 --- a/base_classes/NXevent_data_em.nxdl.xml +++ b/base_classes/NXevent_data_em.nxdl.xml @@ -3,7 +3,7 @@ - Base class to store state and (meta)data of events with an electron microscopy. - - Electron microscopes are dynamic. Scientists often report that microscopes - *perform differently* across sessions, that they perform differently from - one day or another. In some cases, root causes for performance differences - are unclear. Users of the instrument may consider such conditions impractical, - or *too poor*, and thus abort their session. Alternatively, users may try to - bring the microscope into a state where conditions are considered better - or of whatever high enough quality for continuing the measurement. - - In all these use cases in practice it would be useful to have a mechanism - whereby time-dependent data of the instrument state can be stored and - documented with an interoperable representation. Indeed, how a session on an - electron microscope is spent depends strongly on the research question, - the user, and the imaging modalities used. - - :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly - whatever is considered a time interval during which the instrument is - considered as stable enough for performing a task with the microscope. - Examples of such tasks are the collecting of data (images and spectra) or - the calibrating of some component of the instrument. Users may wish to take - only a single scan or image and complete their microscope session thereafter. - Alternatively, users are working for much longer time at the microscope, - perform recalibrations in between and take several scans (of different - regions-of-interest of the specimen), or they explore the state of the - microscope for service or maintenance tasks. - - :ref:`NXevent_data_em` serves the harmonization and documentation of this situation - with providing three key sections: Firstly, there is a header section whose - purpose is to contextualize and identify the event instance in time. - Secondly, there is a data and metadata section where individual data collections - can be stored using a standardized representation. - - The idea of the first, the event-based em_lab section, is to document the - state of the microscope as it was during the event. The idea of the other, - the NXem application based em_lab(NXinstrument) section is to keep all those - pieces of information which are static in the sense that they are the same - across multiple :ref:`NXevent_data_em` instance. This reduces the amount of pieces of - information that have to be stored repetitively. - - We are aware of the fact that given the variety how an electron microscope - is used, there is a need for a flexible and adaptive documentation system. - At the same time we are also convinced though that just because one has - different requirements for some specific aspect under the umbrella of settings - to an electron microscope, this does not necessarily warrant that one has to - cook up an own schema. - - Instead, the electron microscopy community should work towards reusing schema - components as frequently as possible. This will enable that there is at all - not only a value of harmonizing electron microscopy research content but also - the technical possibility to build services around such harmonized - pieces of information. - - Arguably it is oftentimes tricky to specify a clear time interval when the - microscope is *stable enough*. Take for instance the acquisition of an image - or a stack of spectra. Having to deal with instabilities is a common theme in - electron microscopy practice. Numerical protocols can be used during data - post-processing to correct for some of the instabilities. - A few exemplar references to provide an overview on the subject is - available in the literature: - - * `C. Ophus et al. <https://dx.doi.org/10.1016/j.ultramic.2015.12.002>`_ - * `B. Berkels et al. <https://doi.org/10.1016/j.ultramic.2018.12.016>`_ - * `L. Jones et al. <https://link.springer.com/article/10.1186/s40679-015-0008-4>`_ - - For specific simulation purposes, mainly in an effort to digitally repeat - or simulate the experiment, it is tempting to consider dynamics of the instrument, - implemented as time-dependent functional descriptions of e.g. lens excitations, - beam shape functions, trajectories of groups of electrons and ions, - or detector noise models. This warrants to document the time-dependent - details of individual components of the microscope - as is implemented in :ref:`NXevent_data_em`. + Base class to store state and (meta)data of events for electron microscopy. + + Electron microscopes are dynamic. Scientists often report that microscopes + *perform differently* across sessions. That *they* perform differently from + one day or another. In some cases, root causes for performance differences + are unclear. Users of the instrument may consider such conditions impractical, + or *too poor*, and thus abort their session. Alternatively, users may try to + bring the microscope into a state where conditions are considered better + or of whatever high enough quality for starting or continuing the measurement. + + Which temporal granularity is adequate to log events depends on the situation and + research question. Using a model which enables a collection of events offers + the most flexible way to cater for both experiments with controlled electron + beams in a real microscope or the simulation of such experiments or + individual aspects of such experiments. + + In all these use cases it is useful to have a mechanism whereby time-dependent + data of the instrument state can be stored and documented in an representation + that facilitates interoperability. + + :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly + whatever is considered a time interval during which the instrument is + considered stable enough for allowing any working on tasks with the microscope. + Examples of such tasks are the collecting of data (images and spectra) or + the calibrating the instrument or individual of its components. Users may wish to take + only a single scan or image and complete their microscope session thereafter. + Alternatively, users are working for much longer time at the microscope, + perform recalibrations in between and take several scans (of different + ROIs on the specimen), or they explore the state of the microscope for + service or maintenance tasks. + + :ref:`NXevent_data_em` serves the harmonization and documentation of these cases: + + * Firstly, via a header section whose purpose is to contextualize + and identify the event instance in time. + * Secondly, via a data and metadata section where individual data + collections can be stored in a standardized representation. + + The idea of the first section, the event-based em_lab, is to document the + state of the microscope as it was found during the event. The idea of the other, + the :ref:`NXem` application-definition-based em_lab(NXinstrument) section is to + keep all those data that are static in the sense that they remain the same + across multiple :ref:`NXevent_data_em` instances. + This reduces the need for having many copies of the same metadata. + + We are aware of the fact that given the variety how an electron microscope + is used, there is a need for a flexible and adaptive documentation system. + At the same time we are also convinced though that just because one has + different requirements for some specific aspect under the umbrella of settings + to an electron microscope, this does not necessarily warrant that one has to + cook up an own data schema. + + Instead, the electron microscopy community should work towards reusing schema + components as frequently as possible. This will enable that there is at all + not only a value of harmonizing electron microscopy research content but also + there is a technical possibility to build services around such harmonized data. + + Arguably it is oftentimes tricky to specify a clear time interval when the + microscope is *stable enough*. Take for instance the acquisition of an image + or a stack of spectra. Having to deal with instabilities is a common theme in + electron microscopy practice. Numerical protocols can be used during data + post-processing to correct for some of the instabilities. + A few exemplar references to provide an overview on the subject is + available in the literature: + + * `C. Ophus et al. <https://dx.doi.org/10.1016/j.ultramic.2015.12.002>`_ + * `B. Berkels et al. <https://doi.org/10.1016/j.ultramic.2018.12.016>`_ + * `L. Jones et al. <https://link.springer.com/article/10.1186/s40679-015-0008-4>`_ + + For specific simulation purposes, mainly in an effort to digitally repeat or simulate + the experiment, it is tempting to consider dynamics of the instrument, + implemented as time-dependent functional descriptions of e.g. lens excitations, + beam shape functions, trajectories of groups of electrons and ions, + or detector noise models. This warrants to document the time-dependent + details of individual components of the microscope + as is implemented in :ref:`NXevent_data_em`. - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while - the end_time specifies the end (right bound) of the time interval. + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval started. If the user wishes to specify an + interval of time that the snapshot should represent during which the instrument + was stable and configured using specific settings and calibrations, + the start_time is the start (left bound of the time interval) while + the end_time specifies the end (right bound) of the time interval. - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval ended. + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval ended. - + - Identifier of a specific state and setting of the microscope. + Identifier of a specific state and setting of the microscope. - + - Which specific event/measurement type. Examples are: - - * In-lens/backscattered electron, usually has quadrants - * Secondary_electron, image, topography, fractography, overview images - * Backscattered_electron, image, Z or channeling contrast (ECCI) - * Bright_field, image, TEM - * Dark_field, image, crystal defects - * Annular dark field, image (medium- or high-angle), TEM - * Diffraction, image, TEM, or a comparable technique in the SEM - * Kikuchi, image, SEM EBSD and TEM diffraction - * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) - * Electron energy loss spectra for points, lines, surfaces, TEM - * Auger, spectrum, (low Z contrast element composition) - * Cathodoluminescence (optical spectra) - * Ronchigram, image, alignment utility specifically in TEM - * Chamber, e.g. TV camera inside the chamber, education purposes. - - This field may also be used for storing additional information - about the event. For which there is at the moment no other place. - - In the long run such free-text field description should be avoided as - they are difficult to machine-interpret. Instead, reference should be given - to refactoring these descriptions into structured metadata. - The reason why in this base class the field event_type is nonetheless kept - is to offer a place whereby practically users may enter data for - follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. + Which specific event/measurement type. Examples are: + + * In-lens/backscattered electron, usually has quadrants + * Secondary_electron, image, topography, fractography, overview images + * Backscattered_electron, image, Z or channeling contrast (ECCI) + * Bright_field, image, TEM + * Dark_field, image, crystal defects + * Annular dark field, image (medium- or high-angle), TEM + * Diffraction, image, TEM, or a comparable technique in the SEM + * Kikuchi, image, SEM EBSD and TEM diffraction + * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) + * Electron energy loss spectra for points, lines, surfaces, TEM + * Auger, spectrum, (low Z contrast element composition) + * Cathodoluminescence (optical spectra) + * Ronchigram, image, alignment utility specifically in TEM + * Chamber, e.g. TV camera inside the chamber, education purposes. + + This field may also be used for storing additional information + about the event for which there is at the moment no other place. + + In the long run such free-text field description should be avoided as + they are difficult to machine-interpret. Instead, reference should be given + to refactoring these descriptions into structured metadata. + The reason why in this base class the field event_type is nonetheless kept + is to offer a place whereby practically users may enter data for + follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. - - - - - (Meta)data of the dynamics and changes of the microscope during the event. - - - - - - - - - - - - + + + From d60e1d13ab88a6fdb164a8a048f3dbe34be5d497 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 17:23:56 +0100 Subject: [PATCH 54/75] Syncing up with NIAC changes on PR #1423 em, cherry-picking base classes from #1423 ee40f515 after comparison to current state as used in eventually apm, cg, ms 3 --- base_classes/NXinstrument_em.nxdl.xml | 203 ++++++++++++++++++++++ base_classes/NXlens_em.nxdl.xml | 89 ++++++---- base_classes/NXoptical_system_em.nxdl.xml | 168 +++++++++--------- base_classes/NXpeak.nxdl.xml | 93 +++++----- base_classes/NXphase.nxdl.xml | 60 +++++++ base_classes/NXpid_controller.nxdl.xml | 142 +++++++++++++++ base_classes/NXpump.nxdl.xml | 7 +- base_classes/NXrotations.nxdl.xml | 73 ++++---- base_classes/NXscanbox_em.nxdl.xml | 107 ++++-------- base_classes/NXspectrum.nxdl.xml | 77 ++++---- base_classes/NXunit_cell.nxdl.xml | 193 ++++++-------------- 11 files changed, 745 insertions(+), 467 deletions(-) create mode 100644 base_classes/NXinstrument_em.nxdl.xml create mode 100644 base_classes/NXphase.nxdl.xml create mode 100644 base_classes/NXpid_controller.nxdl.xml diff --git a/base_classes/NXinstrument_em.nxdl.xml b/base_classes/NXinstrument_em.nxdl.xml new file mode 100644 index 0000000000..f197b981d4 --- /dev/null +++ b/base_classes/NXinstrument_em.nxdl.xml @@ -0,0 +1,203 @@ + + + + + + Base class for instrument-related details of a real or simulated electron microscope. + + For collecting data and experiments which are simulations of an electron + microscope (or such session) use the :ref:`NXem` application definition and + the :ref:`NXevent_data_em` groups it provides. + + This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished + whether these typically change during a session (dynamic) or not (static metadata). + This design allows to store e.g. hardware related concepts only once instead of demanding + that each image or spectrum from the session needs to be stored also with the static metadata. + + + + Given name of the microscope at the hosting institution. + This is an alias. Examples could be NionHermes, Titan, JEOL, + Gemini, etc. + + + + + Location of the lab or place where the instrument is installed. + Using GEOREF is preferred. + + + + + + + + + + Description of the type of the detector. + + Electron microscopes have typically multiple detectors. + Different technologies are in use like CCD, scintillator, + direct electron, CMOS, or image plate to name but a few. + + + + + + Stages in an electron microscope are multi-functional devices. + + Stages enable experimentalists the application of controlled external stimuli + on the specimen. Modern stages realize a hierarchy of components. + A multi-axial tilt rotation holder is a good example where the control of + each degree of freedom is technically implemented via providing instances + of either :ref:`NXpositioner`, :ref:`NXactuator`, or specialized :ref:`NXobject` + that achieve the rotating and positioning of the specimen. + + The physical process of mounting a specimen on a stage in practice often + comes with an own hierarchy of fixtures to bridge e.g. length scales technically. + An example from atom probe microscopy is that researchers may work + with wire samples which are clipped into a larger fixing unit to enable + careful specimen handling. Alternatively, a microtip is a silicon post + upon which e.g. an atom probe specimen is mounted. Multiple of such microtips + are then grouped into a microtip array to conveniently enable loading of multiple + specimens into the instrument with fewer operations. There are further scenarios + typically encountered related to mounting and locating specimens inside an + electron microscope, a few examples follow: + + * A nanoparticle on a copper grid. The copper grid is the holder. + This grid itself is fixed to a stage. + * An atom probe specimen fixed in a stub. In this case the stub can be + considered the holder, while the cryostat temperature control unit is + a component of the stage. + * For in-situ experiments with e.g. chips with read-out electronics + as actuators, the chips are again placed in a larger unit. A typical + example are in-situ experiments using e.g. the tools of `Protochips <https://www.protochips.com>`_. + * Other examples are (quasi) in-situ experiments where experimentalists + anneal or deform the specimen via e.g. in-situ tensile testing machines + which are mounted on the specimen holder. + + For specific details and inspiration about stages in electron microscopes: + + * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ + * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ + * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ + * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) + * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) + * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) + * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ + + + + + + Principal design of the stage. + + Exemplar terms could be side_entry, top_entry, + single_tilt, quick_change, multiple_specimen, + bulk_specimen, double_tilt, tilt_rotate, + heating_chip, atmosphere_chip, + electrical_biasing_chip, liquid_cell_chip + + + + + Free-text field to give a term how that a stage_lab at this level of the + stage_lab hierarchy is commonly referred to. Examples could be stub, + puck, carousel, microtip, clip, holder, etc. + + + + + + The interpretation of this tilt1 value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + tilt is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + + + + Discouraged free-text field to provide details about how to interpret tilt1. + + + + + + The interpretation of this tilt2 value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + tilt is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + + + + Discouraged free-text field to provide details about how to interpret tilt2. + + + + + + The interpretation of this rotation value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + rotation is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + + + + Discouraged free-text field to provide details about how to interpret rotation. + + + + + + The interpretation of these position values can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + position values are defined explicitly using instances of :ref:`NXtransformations` + and respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + + + + + + + + + In contrast to the stage, the nanoprobe is an additional manipulator that is specifically + frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and + relocated portions of the specimen that have been cut free to realize specialized + geometries locally and enable site-specific measurements. + + + + + + + + diff --git a/base_classes/NXlens_em.nxdl.xml b/base_classes/NXlens_em.nxdl.xml index 97450992a9..9617896e05 100644 --- a/base_classes/NXlens_em.nxdl.xml +++ b/base_classes/NXlens_em.nxdl.xml @@ -2,9 +2,9 @@ - Base class for an electro-magnetic lens or a compound lens. - - For :ref:`NXtransformations` the origin of the coordinate system is placed - in the center of the lens (its polepiece, pinhole, or another - point of reference). The origin should be specified in the :ref:`NXtransformations`. - - For details of electro-magnetic lenses in the literature - see e.g. `L. Reimer <https://doi.org/10.1007/978-3-540-38967-5>`_ + Base class for an electro-magnetic lens or a compound lens. + + For :ref:`NXtransformations` the origin of the coordinate system is placed + in the center of the lens (its polepiece, pinhole, or another + point of reference). The origin should be specified in the :ref:`NXtransformations`. + + For details of electro-magnetic lenses in the literature see e.g. + + * `L. Reimer: Scanning Electron Microscopy <https://doi.org/10.1007/978-3-540-38967-5>`_ + * `P. Hawkes: Magnetic Electron Lenses <https://link.springer.com/book/10.1007/978-3-642-81516-4>`_ + * `Y. Liao: Practical Electron Microscopy and Database <https://www.globalsino.com/EM/>`_ - + + + Name of the lens. + + + + + Ideally, use instances of ``identifierNAME`` to point to a resource + that provides further details. + + If such a resource does not exist or should not be used, use this free text, + although it is not recommended. + + + - Descriptor for the lens excitation when the exact technical details - are unknown or not directly controllable as the control software of - the microscope does not enable or was not configured to display these - values (for end users). - - Although this value does not document the exact physical voltage or - excitation, it can still give useful context to reproduce the lens - setting, provided a properly working instrument and software sets the lens - into a similar state to the technical level possible when no more - information is available physically or accessible legally. + Descriptor for the lens excitation when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. + + Although this value does not document the exact physical voltage or + excitation, it can still give useful context to reproduce the lens + setting, provided a properly working instrument and software sets the lens + into a similar state to the technical level possible when no more + information is available physically or accessible legally. - Descriptor for the operation mode of the lens when other details are not - directly controllable as the control software of the microscope - does not enable or is not configured to display these values. - - Like value, the mode can only be interpreted for a specific microscope - but can still be useful to guide users as to how to repeat the measurement. + Descriptor for the operation mode of the lens when other details are not + directly controllable as the control software of the microscope + does not enable or is not configured to display these values. + + Like value, the mode can only be interpreted for a specific microscope + but can still be useful to guide users as to how to repeat the measurement. - Excitation voltage of the lens. - - For dipoles it is a single number. - For higher order multipoles, it is an array. + Excitation voltage of the lens. + + For dipoles it is a single number. + For higher order multipoles, it is an array. - Excitation current of the lens. - - For dipoles it is a single number. - For higher-order multipoles, it is an array. + Excitation current of the lens. + + For dipoles it is a single number. + For higher-order multipoles, it is an array. - Qualitative type of lens with respect to the number of pole pieces. + Qualitative type of lens with respect to the number of pole pieces. diff --git a/base_classes/NXoptical_system_em.nxdl.xml b/base_classes/NXoptical_system_em.nxdl.xml index f38e6cff5a..05f9ce318f 100644 --- a/base_classes/NXoptical_system_em.nxdl.xml +++ b/base_classes/NXoptical_system_em.nxdl.xml @@ -3,7 +3,7 @@ - A container for qualifying an electron optical system. + Base class for qualifying an electron optical system. - - Distance which is present between the specimen surface and the detector plane. - - This concept is related to term `Camera Length`_ of the EMglossary standard. - - .. _Camera Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 + Distance which is present between the specimen surface and the detector plane. + + This concept is related to term `Camera Length`_ of the EMglossary standard. + + .. _Camera Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 - The factor of enlargement of the apparent size, - not the physical size, of an object. + The factor of enlargement of the apparent size, + not the physical size, of an object. - The defocus aberration constant (oftentimes referred to as C_1_0). - See respective details in :ref:`NXaberration` class instances. + The defocus aberration constant (oftentimes referred to as c_1_0). + See respective details in :ref:`NXaberration` class instances. - The angle which is given by the semi-opening angle of the cone in a convergent - beam. - - This concept is related to term `Convergence Angle`_ of the EMglossary standard. - - .. _Convergence Angle: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 + The angle which is given by the semi-opening angle of the cone in a convergent + beam. + + This concept is related to term `Convergence Angle`_ of the EMglossary standard. + + .. _Convergence Angle: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 - The extent of the observable parts of the specimen given the current - magnification and other settings of the instrument. + The extent of the observable parts of the specimen given the current + magnification and other settings of the instrument. - Distance which is determined along the optical axis within the column from (1) the - lower end of the final optical element between the source and the specimen stage; - to (2) the point where the beam is focused. - - This concept is related to term `Working Distance`_ of the EMglossary standard. - - .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 + Distance which is determined along the optical axis within the column from (1) the + lower end of the final optical element between the source and the specimen stage; + to (2) the point where the beam is focused. + + This concept is related to term `Working Distance`_ of the EMglossary standard. + + .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 - - + - Geometry of the cross-section formed when the primary beam shines onto the - specimen surface. + Geometry of the cross-section formed when the primary beam shines onto the + specimen surface. + - Electrical current which arrives at the specimen. - - This concept is related to term `Probe Current`_ of the EMglossary standard. - - .. _Probe Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 + Electrical current which arrives at the specimen. + + This concept is related to term `Probe Current`_ of the EMglossary standard. + + .. _Probe Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 - - - Specify further details how incipient electron or ion dose was quantified (using - beam_current, probe_current). + Specify further details how incipient electron or ion dose was quantified + (using beam_current, probe_current). + + `Reference <https://doi.org/10.1017/S1551929522000840>`_ discusses + an approach for (electron) dose monitoring in an electron microscope. + + The unit of the nominal dose rate is e-/(angstrom^2*s). - - + - Details about an imaging setting used during acquisition to correct perspective - distortion when imaging a tilted surface or cross section. - - This concept is related to term `Tilt Correction`_ of the EMglossary standard. - - .. _Tilt Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 + Nominal dose rate. - + - Details about a dynamic focus correction used. - - This concept is related to term `Dynamic Focus Correction`_ of the EMglossary standard. - - .. _Dynamic Focus Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 + In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated + on a helical path about the optical axis. This causes an image rotation whose strength + is affected by the magnification. + + Microscopes may be equipped with compensation methods (implemented in hardware + or software) that reduce but not necessarily eliminate this rotation. + + See `L. Reimer <https://doi.org/10.1007/978-3-540-38967-5>`_ for details. - + - Details about a workflow used to keep the specimen in focus by automatic means. - - This concept is related to term `Dynamic Refocusing`_ of the EMglossary standard. - - .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 + Distance which lies between the principal plane of the lens and the focal point + along the optical axis. + + This concept is related to term `Focal Length`_ of the EMglossary standard. + + .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 - + + + Details about an imaging setting used during acquisition to correct perspective + distortion when imaging a tilted surface or cross section. + + This concept is related to term `Tilt Correction`_ of the EMglossary standard. + + .. _Tilt Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 + + + + + Details about a dynamic focus correction used. + + This concept is related to term `Dynamic Focus Correction`_ of the EMglossary standard. + + .. _Dynamic Focus Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 + + + - Distance which lies between the principal plane of the lens and the focal point - along the optical axis. - - This concept is related to term `Focal Length`_ of the EMglossary standard. - - .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 + Details about a workflow used to keep the specimen in focus by automatic means. + + This concept is related to term `Dynamic Refocusing`_ of the EMglossary standard. + + .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 diff --git a/base_classes/NXpeak.nxdl.xml b/base_classes/NXpeak.nxdl.xml index 4a030c6844..eb1115f99a 100644 --- a/base_classes/NXpeak.nxdl.xml +++ b/base_classes/NXpeak.nxdl.xml @@ -1,10 +1,10 @@ - + - + The symbols used in the schema to specify e.g. dimensions of arrays. - + - Number of support points + Rank of the dependent and independent data arrays (for + multidimensional/multivariate fit.) - Description of peaks, their functional form or measured support. + Base class for describing a peak, its functional form, and support values + (i.e., the discretization (points) at which the function has been evaluated). - + - Human-readable identifier to specify which concept/entity + Human-readable label which specifies which concept/entity the peak represents/identifies. - - - Is the peak described analytically via a functional form - or is it empirically defined via measured/reported - intensity/counts as a function of an independent variable. - - If the functional form is not empirical or gaussian, users - should enter other for the peak_model and add relevant details - in the NXcollection. - - - - - - - - - + + + + Position values along one or more data dimensions (to hold the + values for the independent variable). + + + + The ``position`` field must have the same rank (``dimRank``) + as the ``intensity`` field. Each individual dimension of ``position`` + must have the same number of points as the corresponding dimension in + the ``intensity`` field. + + + + + + This array holds the intensity/count values of the fitted peak at each position. + + + + The ``intensity`` field must have the same rank (``dimRank``) + as the ``intensity`` field. Each individual dimension of ``position`` + must have the same number of points as the corresponding dimension in + the ``position`` field. + + + + + + - In the case of an empirical description of the peak and its shoulders, - this array holds the intensity/count values at each position. + Total area under the curve. - - - - - - In the case of an analytical description (or if peak_model is other) this - collection holds parameter of (and eventually) the functional form. - For example in the case of Gaussians mu, sigma, cut-off values, - and background intensity are relevant parameter. - - diff --git a/base_classes/NXphase.nxdl.xml b/base_classes/NXphase.nxdl.xml new file mode 100644 index 0000000000..b1e16305a9 --- /dev/null +++ b/base_classes/NXphase.nxdl.xml @@ -0,0 +1,60 @@ + + + + + + Base class to describe a (thermodynamic) phase as a component of a material. + + Instances of phases can be crystalline. + + + + Identifier for each phase. + + The value 0 is reserved for the unknown phase that represents the + null-model (no sufficiently significant information available). + In other words, the phase_name is n/a aka notIndexed. + + The identifier_phase value should match with the integer suffix of the + group name which represents that instance in a NeXus/HDF5 file, i.e. + if three phases were used e.g. 0, 1, and 2, three instances of :ref:`NXphase` + named phase0, phase1, and phase2 should be stored in that HDF5 file. + + + + + Given name as an alias for identifying this phase. + + If the identifier_phase is 0 and one would like to use + the field name, the value should be n/a or notIndexed. + + + + + + + diff --git a/base_classes/NXpid_controller.nxdl.xml b/base_classes/NXpid_controller.nxdl.xml new file mode 100644 index 0000000000..4f22762bc7 --- /dev/null +++ b/base_classes/NXpid_controller.nxdl.xml @@ -0,0 +1,142 @@ + + + + + + A description of a feedback system in terms of the settings of a proportional-integral-derivative (PID) controller. + + Automated control of a physical quantity is often achieved by connecting the output of a sensor to an actuator + (e.g. using a thermocouple to monitor the effect of a heater and influence the power provided to it). The physical + quantity being operated on is typically referred to as the "Process Variable", with the desired value being the + "Setpoint" (which may vary as a function of time) and the "Error Value" is the time-varying function of the difference + between the Setpoint value and the concurrent measurement of the Process Variable (Error Value = Setpoint - Process Variable). + + A PID controller calculates an output value for use as an input signal to an actuator via the weighted sum of four terms: + * Proportional: the current Error Value + * Integral: the integral of the Error Value function + * Derivative: the first derivative of the Error Value function + * Feed Forward: A model of the physical system (optional) + + The weightings of these terms are given by the corresponding constants: + * K_p + * K_i + * K_d + * K_ff + + A classic PID controller only implements the P, I and D terms and the values of the K_p, K_i and K_d constants are sufficient to fully + describe the behaviour of the feedback system implemented by such a PID controller. The inclusion of a Feed Forward term in a feedback system + is a modern adaptation that aids optimisation of the automated control. It is not present in all PID controllers, but it is also not uncommon. + + Note that the ``NXpid_controller`` is designed to be a child object of the actuator that its output is connected to. The parent object + representing the actuator is likely to be represented by an ``NXactuator`` or ``NXpositioner`` base class, but there is a wide variety + of possible applications for PID controllers. + + + + Description of how the Process Value for the PID controller is produced by sensor(s) in the setup. + + For example, a set of sensors could be averaged over before feeding it back into the loop. + + + + + The sensor representing the Process Value used in the feedback loop for the PID. + + In case multiple sensors were used, this NXsensor should contain the proper calculated/aggregated value. + + + + + The actual timeseries data fed back into the PID controller. + + + + + + + The Setpoint(s) used as an input for the PID controller. + + It can also be a link to an ``NXsensor.value`` field. + + + + + Proportional gain constant. This constant determines how strongly the output value + directly follows the current Error Value. When this constant dominates, the output + value is linearly proportional to the Error Value. + + + + + Integral gain constant. This constant determines how strongly the output value + should react to an accumulated offset in the Error Value that should have + been corrected previously. since the integral term is proportional to both + the magnitude and persistence of the Error Value over time. + + + + + Derivative gain constant. This constant determines how much the feedback system + should anticipate the future value of the Error Value function through adjustment of the + output value that is proportional to the rate of change (i.e. derivative) of the Error Value. + This term is important for damping oscillations in the feedback system. + + + + + Feed Forward gain constant. This constant determines how much the feedback system + should rely on a calculated output value to achieve the desired Process Variable value. + A Feed Forward system uses a model of the physical system to calculate an appropriate + output value to achieve a desired Setpoint value. A description of this model should be provided + in the ``feed_forward_model`` field. + + + + + A description of the model used for the Feed Forward part of the feedback system. Note that such models typically + involve the Setpoint value, but not the Error Value. The simplest model is simply proportional to the Setpoint value. + For example, the position (Process Variable) of a sample is measured by a a linear optical encoder (sensor) and + manipulated by a piezoelectric scanning stage (actuator). The corresponding Feed Forward model could be that the + output value (voltage applied to the piezo) is proportional to the Setpoint value (measured position of the sample). + + A complex model could involve any number of input variables, mathematical functions, and coefficients in order to + describe the physical system relevant to the PID controller. + + + + + The Error Value of PID feedback system is normally constructed in terms of the correction needed to bring + the Process Variable towards a match with the Setpoint. This "direct" control action means that a measurement of + the Process Variable that is lower than the Setpoint results in a positive Error Value and a generally positive + control output that tells the actuator to push the value of the Process Variable upwards. In some implementations, + the actuator will respond to a more positive control output by pushing the Process Variable towards lower values (e.g. + a Peltier cooler) and so the output of the feedback system must be reversed to match the behaviour of the physical system. + A feedback system may also be implemented with reverse action in order to ensure that failures (e.g. disconnected sensor + output or actuator input) result in a safe state (e.g. a valve should be left open to release pressure). + + + + + + + diff --git a/base_classes/NXpump.nxdl.xml b/base_classes/NXpump.nxdl.xml index f5b3cd8986..ffe91102d2 100644 --- a/base_classes/NXpump.nxdl.xml +++ b/base_classes/NXpump.nxdl.xml @@ -21,14 +21,13 @@ # # For further information, see http://www.nexusformat.org --> - + - Device to reduce an atmosphere (real or simulated) to a controlled pressure. + Device to reduce an atmosphere (real or simulated) to a controlled pressure. - - Principle type of the pump. + Principle type of the pump. diff --git a/base_classes/NXrotations.nxdl.xml b/base_classes/NXrotations.nxdl.xml index a304e3f47b..4b47437dee 100644 --- a/base_classes/NXrotations.nxdl.xml +++ b/base_classes/NXrotations.nxdl.xml @@ -2,9 +2,9 @@ - - + The symbols used in the schema to specify e.g. dimensions of arrays. @@ -46,6 +37,7 @@ different conventions--> + Base class to detail a set of rotations, orientations, and disorientations. @@ -64,25 +56,23 @@ different conventions--> * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ - + - Reference to an instance of :ref:`NXcoordinate_system_set` which contextualizes + Reference to an instance of :ref:`NXcoordinate_system` which contextualizes how the here reported parameterized quantities can be interpreted. - Point group which defines the symmetry of the crystal. This has to be at least a single string. If crystal_symmetry is not - provided point group 1 is assumed. + provided, point group 1 is assumed. In the case that misorientation or disorientation fields are used and the two crystal sets resolve for phases with a different - crystal symmetry, this field has to encode two string. - In this case the first string is for phase A the second one for phase B. + crystal symmetry, this field needs to encode two strings: + The first string is for phase A. The second string is for phase B. An example of this most complex case is the description of the disorientation between crystals adjoining a hetero-phase boundary. @@ -98,15 +88,14 @@ just how to rotate the object into the reference frame defined by depends_on--> and disorientations via numerical procedures that are known as symmetrization. - If sample_symmetry is not provided point group 1 is assumed. + If sample_symmetry is not provided, point group 1 is assumed. The traditionally used symmetrization operations within the texture - community in Materials Science, though, are thanks to methodology and - software improvements no longer strictly needed. Therefore, users are - encouraged to set the sample_symmetry to 1 (triclinic) and thus assume - there is no justification to assume the imprinting of additional - symmetry because of the processing. - + community in Materials Science, though, have become obsolete thanks + to improvements in methods, software, and available computing power. + + Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). + In practice one often faces situations where indeed these assumed symmetries are anyway not fully observed, and thus an accepting of eventual inaccuracies just for the sake of reporting a simplified @@ -131,9 +120,9 @@ just how to rotate the object into the reference frame defined by depends_on--> The set of rotations expressed in Euler angle parameterization considering the same applied symmetries as detailed for the field rotation_quaternion. - To interpret Euler angles correctly, it is necessary to inspect the - conventions behind depends_on to resolve which of the many Euler-angle - conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. + To interpret Euler angles correctly, it is necessary to inspect the rotation + conventions behind reference_frame to resolve which of the many possible + Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. @@ -169,8 +158,8 @@ rotation_axis_angle(NX_NUMBER):--> The set of orientations expressed in Euler angle parameterization following the same assumptions like for orientation_quaternion. - To interpret Euler angles correctly, it is necessary to inspect the - conventions behind depends_on to resolve which of the many Euler-angle + To interpret Euler angles correctly, it is necessary to inspect the rotation + conventions behind reference_frame to resolve which of the many Euler-angle conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. @@ -181,15 +170,15 @@ rotation_axis_angle(NX_NUMBER):--> - The set of misorientations expressed in quaternion parameterization obeying symmetry operations for equivalent misorientations as defined by crystal_symmetry and sample_symmetry. + + The misorientation should not be confused with the disorientation, + as for the latter the angular argument is expected to be the minimal + obeying symmetries. @@ -219,8 +208,8 @@ misorientation is not necessarily in the fundamental zone--> fundamental zone of SO3 for given crystal and sample symmetry--> - The set of disorientation expressed in quaternion parameterization - obeying symmetry operations for equivalent misorientations + The set of disorientations expressed in quaternion parameterization + obeying symmetry operations for equivalent disorientations as defined by crystal_symmetry and sample_symmetry. @@ -230,7 +219,7 @@ fundamental zone of SO3 for given crystal and sample symmetry--> - Disorientation angular argument (should not be signed, see + Disorientations angular argument (should not be signed, see `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) following the same symmetry assumptions as expressed for the field disorientation_quaternion. @@ -241,7 +230,7 @@ fundamental zone of SO3 for given crystal and sample symmetry--> - Disorientation axis (normalized) following the same symmetry assumptions + Disorientations axis (normalized) following the same symmetry assumptions as expressed for the field disorientation_angle. @@ -249,8 +238,4 @@ fundamental zone of SO3 for given crystal and sample symmetry--> - diff --git a/base_classes/NXscanbox_em.nxdl.xml b/base_classes/NXscanbox_em.nxdl.xml index a2ac1f2495..2f2cc440e2 100644 --- a/base_classes/NXscanbox_em.nxdl.xml +++ b/base_classes/NXscanbox_em.nxdl.xml @@ -3,7 +3,7 @@ - Scan box and coils which deflect a beam of charged particles in a controlled manner. - - The scan box is instructed by an instance of :ref:`NXprogram`, some control software, - which is not necessarily the same program as for all components of a microscope. - - The scanbox directs the probe of charged particles (electrons, ions) - to controlled locations according to a scan scheme and plan. + Scan box and coils which deflect a beam of charged particles in a controlled manner. + + The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, + which is not necessarily the same program as for all components of an instrument. + + The scanbox directs the probe of charged particles (electrons, ions) + to controlled locations according to a scan scheme and plan. - Name of the typically tech-partner-specific term that specifies - an automated protocol which controls the details how the components - of the microscope work together to achieve a controlled scanning of the - beam over the sample surface. - - In most cases users do not know, have to care, or are able to disentangle the - details of the spatiotemporal dynamics of the components of the microscope. - Instead, they rely on the assumption that the microscope and control software - work as expected. Selecting then a specific scan_schema assures some level - of reproducibility in the way how the beam is scanned over the surface. + Name of the typically tech-partner-specific term that specifies an + automated protocol which controls the details how the components + of the scan_box and instrument work together to achieve a controlled + scanning of the beam over the sample surface. + + In most cases users do not know, have to care, or are able to disentangle the + details of the spatiotemporal dynamics of the components of the instrument. + Instead, they often rely on the assumption that the microscope and control software + work as expected. The field scan_schema can be used to add some constraints + on how the beam was scanned over the surface. - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - + - Time period during which the beam remains at one position. - - This concept is related to term `Dwell Time`_ of the EMglossary standard. - - .. _Dwell Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 + Time period during which the beam remains at one position. + + This concept is related to term `Dwell Time`_ of the EMglossary standard. + + .. _Dwell Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 - Time period during which the beam moves from the final position of one scan - line to the starting position of the subsequent scan line. - - This concept is related to term `Flyback Time`_ of the EMglossary standard. - - .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 + Time period during which the beam moves from the final position of one scan + line to the starting position of the subsequent scan line. + + This concept is related to term `Flyback Time`_ of the EMglossary standard. + + .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 - + + - TODO discuss with the electron microscopists. + Details about components which realize the deflection technically. + + This concept should be used for all those components that implement + the scanning of the beam, while components like beam blankers etc. should + use rather the NXdeflector concept of the NXebeam_column base class. - - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - - - TODO discuss with the electron microscopists. - - - - + - diff --git a/base_classes/NXspectrum.nxdl.xml b/base_classes/NXspectrum.nxdl.xml index 3a34762545..7f8c285d95 100644 --- a/base_classes/NXspectrum.nxdl.xml +++ b/base_classes/NXspectrum.nxdl.xml @@ -3,7 +3,7 @@ - - + + @@ -58,17 +58,14 @@ Use stack for all other tilings. - Details how spectra were processed from the detector readings. - + Resolvable data artifact (e.g. filename) from which all values in the :ref:`NXdata` - instances in this :ref:`NXspectrum_set` were loaded during parsing. + instances in this :ref:`NXspectrum` were loaded during parsing. Possibility to document from which specific other serialized resource as the source pieces of information were processed when using NeXus as a semantic file format @@ -87,10 +84,10 @@ NXspectrum_set to reduce redundant fields and specialized NXspectrum_r/c_set--> Imaging (data collection) mode of the instrument during acquisition - of the data in this :ref:`NXspectrum_set` instance. + of the data in this :ref:`NXspectrum` instance. - + Link or name of an :ref:`NXdetector` instance with which the data were collected. @@ -98,8 +95,6 @@ NXspectrum_set to reduce redundant fields and specialized NXspectrum_r/c_set--> - One spectrum for a point of a 0d ROI. Also known as spot measurement. @@ -151,7 +146,7 @@ like omega/q mapping more complicated scan pattern than rectangular ones.--> - Point coordinate along the fast dimension. + Point coordinate along the fast dimension @@ -197,27 +192,27 @@ like omega/q mapping more complicated scan pattern than rectangular ones.--> - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension @@ -257,40 +252,40 @@ like omega/q mapping more complicated scan pattern than rectangular ones.--> - Point coordinate along the slower dimension. + Point coordinate along the slower dimension - Point coordinate along the slower dimension. + Point coordinate along the slower dimension - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension @@ -308,10 +303,6 @@ like omega/q mapping more complicated scan pattern than rectangular ones.--> - Multiple instances of spectrum_0d. @@ -330,7 +321,7 @@ base classes--> - + Group identifier @@ -343,7 +334,7 @@ base classes--> - + Spectrum identifier @@ -390,7 +381,7 @@ base classes--> - + Group identifier @@ -403,7 +394,7 @@ base classes--> - + Spectrum identifier @@ -418,27 +409,27 @@ base classes--> - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension @@ -477,7 +468,7 @@ base classes--> - + Group identifier @@ -490,7 +481,7 @@ base classes--> - + Spectrum identifier @@ -505,40 +496,40 @@ base classes--> - Point coordinate along the slower dimension. + Point coordinate along the slower dimension - Point coordinate along the slower dimension. + Point coordinate along the slower dimension - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the slow dimension. + Point coordinate along the slow dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension - Point coordinate along the fast dimension. + Point coordinate along the fast dimension diff --git a/base_classes/NXunit_cell.nxdl.xml b/base_classes/NXunit_cell.nxdl.xml index 4dcc5af26d..30d32c90a0 100644 --- a/base_classes/NXunit_cell.nxdl.xml +++ b/base_classes/NXunit_cell.nxdl.xml @@ -3,7 +3,7 @@ - + - Number of atom positions. + Dimensionality of the lattice. - Description of a unit cell, i.e., the crystal structure of a single - thermodynamic phase. + Base class to describe structural aspects of an arrangement of + atoms or ions including a crystallographic unit cell. + + Following recommendations of `CIF <https://www.iucr.org/resources/cif/spec/version1.1>`_ and `International Tables of Crystallography <https://it.iucr.org/>`_. - + - Identifier of an entry resolvable via crystallographic_database - which was used for creating this structure model. + Path to a reference frame in which the unit cell is defined + to resolve ambiguity in cases when e.g. a different reference frame + than the NeXus default reference frame (McStas) was chosen. - + - Name of the crystallographic database to resolve - crystallographic_database_identifier e.g. COD, ICSD, or others. - - - - - A lattice system is a group of lattices with the same set of lattice point groups. - For further information, see https://en.wikipedia.org/wiki/Crystal_system. + Dimensionality of the structure. - - - - - - - + + + - - - Crystallographic space group. - A space group is the symmetry group of a repeating pattern in space. - For further information, see International Table for Crystallography (https://it.iucr.org/). - - - + - Crystallographic point group. - A crystallographic point group is a set of symmetry operations, corresponding to one of the point groups in three dimensions, - such that each operation (perhaps followed by a translation) would leave the structure of a crystal unchanged. - This field should use Schoenflies notation (see Schoenflies, A., Krystallsysteme und Krystallstructur, 1891). - For further information, see https://dictionary.iucr.org/Point_group. - - - - - Laue group (also called Laue class). - The Laue classes are eleven geometric crystal classes containing centrosymmetric crystallographic types of point groups and their subgroups. - When absorption is negligible and Friedel's law applies, it is impossible to distinguish by diffraction between a centrosymmetric point group - and one of its non-centrosymmetric subgroups; only point groups belonging to different Laue classes can then be distinguished. - For further information, see https://dictionary.iucr.org/Laue_class. - - - - - - Crystallography unit cell parameters a, b, and c + Geometry of the unit cell quantified via parameters a, b, and c. - + - + + - Crystallography unit cell vector a + Geometry of the unit cell quantified via parameters alpha, beta, and gamma. - + - - - For definining which coordinate system the unit cell vector a is defined in. - - - + - Crystallography unit cell vector b + Crystal system. + + For a crystal system in 2D space monoclinic is an exact synonym for oblique. + For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. + For a crystal system in 2D space tetragonal is an exact synonym for square. - - - - - - For definining which coordinate system the unit cell vector b is defined in. - - + + + + + + + + + - + - Crystallography unit cell vector c + Laue group using International Table of Crystallography notation. - - - - - - For definining which coordinate system the unit cell vector c is defined in. - - - + + - Crystallography unit cell angles alpha, beta, and gamma + Point group using International Table of Crystallography notation. - - - - + - Volume of the unit cell + Space group from the International Table of Crystallography notation. - True if space group is considered a centrosymmetric one. False if space group is considered a non-centrosymmetric one. + Centrosymmetric has all types and combinations of symmetry elements (translation, rotational axis, mirror planes, center of inversion) Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). @@ -163,63 +120,15 @@ False if space group is consider a non-chiral one. - + - Identifier for the phase. - The value 0 is reserved for the unknown phase which represents the null-model - that no phase model was sufficiently significantly confirmed. + Area of the unit cell if dimensionality is 2. - - - Trivial name of the phase/alias. - - - - - Labels for each atom position - - - - - - - - The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - the number of protons and :math:`N` the number of neutrons - of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - For the rationale behind this `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - Atom positions x, y, z. - - - - - - - - Reference to an instance of NXcoordinate_system whereby the positions can be - resolved. - - - - - - Relative occupancy of the atom position. - - - - - - + - For definining which coordinate system the unit cell parameters are defined in. + Volume of the unit cell if dimensionality is 3. + From 7cbb89255cff08a66c1bb8a092e0d810504a84e3 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Mon, 10 Mar 2025 17:33:52 +0100 Subject: [PATCH 55/75] Syncing up with NIAC changes on PR #1423 em, removal of old baseclasses that were considered as not meaty enough --- .../NXcrystal_structure.nxdl.xml | 274 ------------------ .../NXmicrostructure_ipf.nxdl.xml | 4 +- contributed_definitions/NXroi.nxdl.xml | 34 --- 3 files changed, 2 insertions(+), 310 deletions(-) delete mode 100644 contributed_definitions/NXcrystal_structure.nxdl.xml delete mode 100644 contributed_definitions/NXroi.nxdl.xml diff --git a/contributed_definitions/NXcrystal_structure.nxdl.xml b/contributed_definitions/NXcrystal_structure.nxdl.xml deleted file mode 100644 index 90cbb13f31..0000000000 --- a/contributed_definitions/NXcrystal_structure.nxdl.xml +++ /dev/null @@ -1,274 +0,0 @@ - - - - - - - - - Number of reflectors (Miller crystallographic plane triplets). - - - - - Number of atom positions. - - - - - Dimensionality of the lattice. - - - - - Base class to describe the atomic crystal structure of a phase. - - This base class contains key metadata that are relevant parameter to every - physics-based model to simulate radiation matter interaction. - - Examples where such base class is useful are kinematic or dynamic - diffraction simulations of e.g. (Kikuchi or other type of) patterns. - - - - Details in which reference frame the unit cell is defined. - - - - - Dimensionality of the lattice. - - - - - - - - - - Reference to another resource that was used for - instantiating this structure model. - - - - - Crystallography unit cell parameters a, b, and c. - - - - - - - - - Crystallography unit cell parameters alpha, beta, and gamma. - - - - - - - - Area of the unit cell considering that d = 2. - - - - - Volume of the unit cell considering that d = 3. - - - - - Crystal system - - - - - - - - - - - - - - - Laue group using International Table of Crystallography Notation. - - - - - - Point group using International Table of Crystallography Notation. - - - - - - Space group from the International Table of Crystallography Notation. - - - - - - True if space group is considered a centrosymmetric one. - False if space group is considered a non-centrosymmetric one. - Centrosymmetric has all types and combinations of symmetry elements - (translation, rotational axis, mirror planes, center of inversion) - Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). - Chiral compared to non-centrosymmetric is constrained (no mirror planes). - - - - - True if space group is considered a chiral one. - False if space group is consider a non-chiral one. - - - - - Identifier for each phase. - - The value 0 is reserved for the unknown phase that represents the - null-model no sufficiently significant confirmation. In other words, - the phase_name is n/a, notIndexed. - - The phase identifier value has to match with the integer postfix of the - group name which represents that instance in a NeXus/HDF5 file, i.e. - if two phases were used e.g. 0 and 1, two instances of an - :ref:`NXcrystal_structure` named phase0 and phase1 - should be stored in the HDF5 file. - - - - - Name of the phase/alias. - - If the phase_identifier is 0 and one would like to use the field - phase_name the value should be n/a. - - - - - Label for each atom position. - - - - - - - - The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - the number of protons and :math:`N` the number of neutrons - of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - For the rationale behind this `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ - - - - - - - - - Atom positions. - - - - - - - - Details the reference frame in which the positions are defined. - - - - - - - Relative occupancy of the atom position. - - - - - - - - How many reflectors are distinguished. - - Value has to match value for symbol n_hkl. - - - - - - Miller indices :math:`(hkl)[uvw]` of the planes. - - The first triplet specify :math:`(hkl)` the second triplet :math:`[uvw]`. - Miller indices refer to the Cartesian right-handed coordinate system - of the unit cell. - - - - - - - - - Spacing between crystallographic planes as defined by field miller. - - - - - - - - Relative intensity of the signal for the plane. - - - - - - - - In case the :ref:`NXcrystal_structure` base class is used - with analyzed orientation maps this field stores how many scan points - of the map were identified as that phase. - - - - diff --git a/contributed_definitions/NXmicrostructure_ipf.nxdl.xml b/contributed_definitions/NXmicrostructure_ipf.nxdl.xml index 38256637b9..ea2b79c135 100644 --- a/contributed_definitions/NXmicrostructure_ipf.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_ipf.nxdl.xml @@ -98,8 +98,8 @@ phase. No ipf_mapID instances for non-indexed scan points as these are by definition assigned the null phase with phase_identifier 0. - Inspect the definition of :ref:`NXcrystal_structure` and its field - phase_identifier for further details. + Inspect the definition of :ref:`NXphase` and its field identifier_phase + for further details. Details about possible regridding and associated interpolation during the computation of the IPF map visualization can be stored diff --git a/contributed_definitions/NXroi.nxdl.xml b/contributed_definitions/NXroi.nxdl.xml deleted file mode 100644 index 94857e74cb..0000000000 --- a/contributed_definitions/NXroi.nxdl.xml +++ /dev/null @@ -1,34 +0,0 @@ - - - - - - Base class to describe a region-of-interest analyzed. - - - - Details about processing steps. - - - - From 3b81a5a6a28064ac7cf4a5b5e5b3886e09eafbe6 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Tue, 11 Mar 2025 13:27:00 +0100 Subject: [PATCH 56/75] Fixing of references in the manual to classes that were removed during the discussions with NIAC --- .../contributed_definitions/apm-structure.rst | 6 +- .../cgms-structure.rst | 7 +- .../contributed_definitions/em-structure.rst | 90 +++++++++---------- 3 files changed, 49 insertions(+), 54 deletions(-) diff --git a/manual/source/classes/contributed_definitions/apm-structure.rst b/manual/source/classes/contributed_definitions/apm-structure.rst index b88af07a6c..94bdc84c8e 100644 --- a/manual/source/classes/contributed_definitions/apm-structure.rst +++ b/manual/source/classes/contributed_definitions/apm-structure.rst @@ -61,7 +61,7 @@ The following base classes are proposed to support modularizing the storage of p :ref:`NXpump`: A base class to describe details about pump(s) used as components of an instrument. - :ref:`NXstage_lab`: + :ref:`NXmanipulator`: A base class to describe the specimen fixture including the cryo-head. Nowadays, stages of microscopes represent small-scale laboratory platforms. Therefore, there is a need to define the characteristics of such stages in more detail, @@ -86,8 +86,8 @@ data revealed that it is better to define atom-probe-agnostic reusable concepts :ref:`NXspatial_filter`: A base class proposing how a point cloud can be spatially filtered in a specific yet general manner. - This base class takes advantage of :ref:`NXcg_ellipsoid_set`, :ref:`NXcg_cylinder_set`, - and :ref:`NXcg_hexahedron_set` to cater for commonly used geometric primitives in atom probe. + This base class takes advantage of :ref:`NXcg_ellipsoid`, :ref:`NXcg_cylinder`, and :ref:`NXcg_hexahedron` + to cater for commonly used geometric primitives in atom probe. The primitives are used for defining the shape and extent of a region of interest (ROI). :ref:`NXsubsampling_filter`: diff --git a/manual/source/classes/contributed_definitions/cgms-structure.rst b/manual/source/classes/contributed_definitions/cgms-structure.rst index af55e2ae59..1922d7a13b 100644 --- a/manual/source/classes/contributed_definitions/cgms-structure.rst +++ b/manual/source/classes/contributed_definitions/cgms-structure.rst @@ -1,8 +1,8 @@ .. _CgmsFeatures-Structure: -========================= +==================== Geometry & Microstructure -========================= +==================== .. index:: CgmsBC @@ -85,9 +85,6 @@ of material (area or volume) which can be useful not only for stencil-based meth is smoothed in a controlled manner. :ref:`NXsimilarity_grouping`: - An alternative for NXclustering. - - :ref:`NXclustering`: A description for clustering of objects (such as atoms or features). TODO CHECK THAT MICROSTRUCTURE PART IS COVERED IN ICME WHEN MICROSTRUCTURE PROPOSAL SYNCED UP diff --git a/manual/source/classes/contributed_definitions/em-structure.rst b/manual/source/classes/contributed_definitions/em-structure.rst index bd37436503..c3ce7e6670 100644 --- a/manual/source/classes/contributed_definitions/em-structure.rst +++ b/manual/source/classes/contributed_definitions/em-structure.rst @@ -1,19 +1,20 @@ .. _Em-Structure: -=================== +=============== Electron microscopy -=================== +=============== .. index:: IntroductionEm EmAppDef EmBC EmAnalysisClasses + EmExamples .. _IntroductionEm: Introduction -############ +########## A set of data schemas is proposed to describe components of an electron microscope and its eventually available focused-ion beam functionalities. The data schemas were designed from the perspective of how electron microscopes are used by colleagues in the materials-science-branch of electron microscopy. @@ -27,8 +28,8 @@ Electron microscopes are functionally very customizable tools: Examples include .. _EmAppDef: -Application Definitions -####################### +Application Definition NXem +###################### We acknowledge that it can be difficult to agree on a single application definition which is generally enough applicable yet not unnecessarily complex and useful for applications across a variety of instruments, technology partners, and instrument use cases. In what follows, the proposal conceptualizes first the basic components of an electron microscope and the usual workflow of how an electron microscope is used for collecting data with detectors via probing radiation-specimen-matter interaction mechanisms. @@ -37,25 +38,24 @@ In summary, scientists place a specimen/sample into the microscope, calibrate th A microscope session ends with the scientist removing the specimen from the instrument or parking it so that the next user can start a session. Occasionally, service technicians perform calibrations and maintenance which also can be described as a session on the microscope. We have provided base classes to describe these steps and events and an application definition for electron microscopy: :ref:`NXem`: - An application definition which explores the possibilities of electron microscopes. + An application definition which explores the possibilities of research on electron-beam matter interaction with (real or simulated) electron microscopes. .. _EmBC: Base Classes -############ +########### The following base classes are proposed to support modularizing the storage of pieces of information related to electron microscopy research: - :ref:`NXem_msr`, :ref:`NXem_sim`: - Base classes to distinguish descriptions relevant for an experiment that is performed with a real microscope or a computer simulation of - electron matter interaction. Through these base classes NeXus supports to serialize details of a measurement and a related computer simulation - into one data artifact. + :ref:`NXcomponent`: + A base class to describe components aka devices to building an instrument like a microscope irrespective whether that is a real one or a simulated one. - :ref:`NXidentifier`, :ref:`NXserialized`: - Base classes to support storage of metadata whereby the source of information stored in a NeXus data artifact or class instances can be - documented especially when one does not store all relevant information using NeXus but one would like to refer to a specific other resource - where these pieces of information are stored. + :ref:`NXfabrication`: + A base class to bundle manufacturer/technology-partner-specific details about a component or device of an instrument. + + :ref:`NXcircuit`: + A base class to describe a logical unit of at least one integrated circuit. :ref:`NXebeam_column`: A base class serving the possibility to group the components relevant for generating @@ -65,29 +65,15 @@ The following base classes are proposed to support modularizing the storage of p A base class serving the possibility to group the components relevant for generating and shaping an ion beam of an instrument to offer focused-ion beam (milling) capabilities. - :ref:`NXcomponent`: - A base class to describe components aka devices to building an instrument like a microscope irrespective whether that is a real one or a simulated one. - :ref:`NXlens_em`: A base class to detail an electro-magnetic lens. In practice, an electron microscope has many such lenses. It is possible to specify as many lenses as necessary to represent eventually each single lens of the microscope and thus describe how the lenses are affecting the electron beam. This can offer opportunities for developers of software tools which strive to model the instrument e.g. to create digital twins of the instrument. We understand there is still a way to go with this to arrive there though. Consequently, we suggest to focus first on which details should be collected for a lens as a component so that developers of application definitions can take immediate advantage of this work. :ref:`NXdeflector`: A base class to describe a component to deflect a beam of charged particles. - :ref:`NXchamber`: - A base class to describe the chamber as a part of the microscope or storage unit - for transferring specimens in between or within an instrument. - :ref:`NXpump`: A base class to describe details about pump(s) as components of an electron microscope. - :ref:`NXfabrication`: - A base class to bundle manufacturer/technology-partner-specific details about a component or device of an instrument. - - :ref:`NXcoordinate_system_set`, :ref:`NXcoordinate_system`, :ref:`NXtransformations`: - Base classes to describe different coordinate systems used and/or to be harmonized - or transformed into one another and respective transformations. - :ref:`NXcorrector_cs`, :ref:`NXaberration`: Base classes to describe procedures and values for the calibration of aberrations based on conventions of different companies active in the field of aberration correction including a base class @@ -101,27 +87,30 @@ The following base classes are proposed to support modularizing the storage of p is a component in a microscope which controls eventually multiple other components such as beam deflectors to achieve deflection and thus a controlled scanning of the beam over the sample/specimen surface. - :ref:`NXstage_lab`: + :ref:`NXmanipulator`: A base class to describe the stage/specimen holder which offers place for the documentation of the small-scale laboratory functionalities which modern stages of electron microscopes typically offer. + :ref:`NXinstrument_em`: + A base class to group the components that make up an electron microscope. + +Contextualizing and defining definitions of reference frames and transformations of these and rotations and orientations defined within such reference frames: + + :ref:`NXcoordinate_system_set`, :ref:`NXcoordinate_system`, :ref:`NXtransformations`: + Base classes to describe different coordinate systems used and/or to be harmonized + or transformed into one another and respective transformations. + :ref:`NXevent_data_em`: A base class representing a container to hold time-stamped and microscope-state-annotated data during a session at an electron microscope. - :ref:`NXevent_data_em_set`: - A base class to group all :ref:`NXevent_data_em` instances. - - :ref:`NXimage_set`: + :ref:`NXimage`: Base classes for storing acquisition details for individual images or stacks of images. - :ref:`NXspectrum_set`: + :ref:`NXspectrum`: A base class and specializations comparable to :ref:`NXimage_set` but for storing spectra. - :ref:`NXinteraction_vol_em`: - A base class to describe details about e.g. the assumed or simulated volume of interaction of the electrons with the specimen. - - :ref:`NXion`: + :ref:`NXion` (about to become replaced by :ref:`NXatom`): A base class to describe molecular ions with an adjustable number of atoms/isotopes building each ion. Right now the maximum number of atoms supported building a molecular ion is 32. Suggestions made in reference `DOI: 10.1017/S1431927621012241 `_ are used to map isotope to hash values with which all possible isotopes can be described. :ref:`NXoptical_system_em`: @@ -132,12 +121,12 @@ The following base classes are proposed to support modularizing the storage of p :ref:`NXpeak`: A base class to describe peaks mathematically. - :ref:`NXcircuit`: - A base class to describe a logical unit of at least one integrated circuit. - .. _EmAnalysisClasses: +Storage of event-base data and results of post-processing +############################################### + We provide specific base classes which granularize frequently collected or analyzed quantities in specific application fields of electron microscopy to deal with the situation that there are cases were logical connections between generated data artifacts mainly exist for the fact that the data artifacts were collected during a workflow of electron microscopy research (e.g. taking measurements and then performing method-specific analyses generating new data and conclusions). @@ -154,11 +143,20 @@ storage (i.e. serialization) using NeXus. More consolidation through the use of NXsubentry classes should be considered in the future. For now we use an approach whereby base classes are combined to reuse vocabulary and a hierarchical organization of pieces of information with specific constraints which are relevant only for specific usage of such data by specific tools used by an eventually smaller circle of users. - :ref:`NXem_method`, :ref:`NXem_ebsd`, :ref:`NXem_eds`, :ref:`NXem_eels`, :ref:`NXem_img`, :ref:`NXem_correlation`: + :ref:`NXem_ebsd`, :ref:`NXem_eds`, :ref:`NXem_eels`, :ref:`NXem_img`: Base classes with method-specific details especially when it comes to reporting post-processed data within electron microscopy. - :ref:`NXcrystal_structure`: - A base class to store crystalline phase/structure used for a simulation of diffraction pattern and comparison of these pattern against patterns to support indexing. + :ref:`NXphase`, :ref:`NXunit_cell`, :ref:`NXatom`: + Base classes to store crystal structure specific details e.g. to support simulation of and post-processing of diffraction patterns. - :ref:`NXroi`: + :ref:`NXcg_roi`: A base class to granularize information collected and relevant for the characterization of a region-of-interest. + + +.. _EMExamples: + +Domain-specific data analysis +######################## + + :ref:`NXem_calorimetry`: + Example together with the IKZ in Berlin and FAIRmat, in-situ (transmission) electron microscopy with a heating stage. From a070a03f7b895d759f74c50b116e6b582b38ec63 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Tue, 11 Mar 2025 15:21:03 +0100 Subject: [PATCH 57/75] Firstly, ran make clean, secondly, ran make nyaml to regenerate nyaml files that are consistent with the XML files and also thereby remove nyaml files for dangling NXDLs for which the discussions with NIAC suggested their removal like NXsingle_crystal, NXphysical_process --- applications/nyaml/NXapm.yaml | 2556 +++++++++++++++++ .../nyaml/NXem.yaml | 1515 +++++----- .../nyaml/NXaberration.yaml | 32 +- .../nyaml/NXapm_charge_state_analysis.yaml | 0 base_classes/nyaml/NXapm_ranging.yaml | 188 ++ .../nyaml/NXapm_reconstruction.yaml | 147 +- base_classes/nyaml/NXatom.yaml | 230 ++ base_classes/nyaml/NXcg_alpha_complex.yaml | 167 ++ .../nyaml/NXcg_cylinder.yaml | 90 +- .../nyaml/NXcg_ellipsoid.yaml | 55 +- .../nyaml/NXcg_face_list_data_structure.yaml | 93 +- .../nyaml/NXcg_grid.yaml | 74 +- .../nyaml/NXcg_half_edge_data_structure.yaml | 77 +- .../nyaml/NXcg_hexahedron.yaml | 163 +- .../nyaml/NXcg_parallelogram.yaml | 104 +- .../nyaml/NXcg_point.yaml | 16 +- .../nyaml/NXcg_polygon.yaml | 111 +- .../nyaml/NXcg_polyhedron.yaml | 54 +- .../nyaml/NXcg_polyline.yaml | 59 +- base_classes/nyaml/NXcg_primitive.yaml | 428 +++ .../nyaml/NXcg_roi.yaml | 38 +- .../nyaml/NXcg_tetrahedron.yaml | 51 +- .../nyaml/NXcg_triangle.yaml | 61 +- .../nyaml/NXcg_unit_normal.yaml | 16 +- .../nyaml/NXchemical_composition.yaml | 6 +- base_classes/nyaml/NXcircuit.yaml | 227 ++ .../nyaml/NXcoordinate_system.yaml | 38 +- .../nyaml/NXcoordinate_system_set.yaml | 19 +- .../nyaml/NXcorrector_cs.yaml | 97 +- .../nyaml/NXcs_computer.yaml | 9 +- .../nyaml/NXcs_filter_boolean_mask.yaml | 6 +- .../nyaml/NXcs_prng.yaml | 2 +- .../nyaml/NXcs_profiling.yaml | 0 .../nyaml/NXcs_profiling_event.yaml | 0 .../nyaml/NXcsg.yaml | 62 +- .../nyaml/NXdeflector.yaml | 64 +- base_classes/nyaml/NXebeam_column.yaml | 415 +++ .../nyaml/NXem_ebsd.yaml | 842 +++--- .../nyaml/NXem_eds.yaml | 172 +- .../nyaml/NXem_eels.yaml | 39 +- .../nyaml/NXem_img.yaml | 56 +- base_classes/nyaml/NXevent_data_apm.yaml | 284 ++ base_classes/nyaml/NXevent_data_em.yaml | 289 ++ .../nyaml/NXibeam_column.yaml | 0 .../nyaml/NXimage.yaml | 410 ++- base_classes/nyaml/NXinstrument_apm.yaml | 677 +++++ base_classes/nyaml/NXinstrument_em.yaml | 366 +++ .../nyaml/NXion.yaml | 6 +- .../nyaml/NXmanipulator.yaml | 124 +- base_classes/nyaml/NXoptical_system_em.yaml | 295 ++ .../nyaml/NXpeak.yaml | 17 +- base_classes/nyaml/NXphase.yaml | 99 + .../nyaml/NXprogram.yaml | 0 .../nyaml/NXpump.yaml | 18 +- .../nyaml/NXquadric.yaml | 6 +- base_classes/nyaml/NXrotations.yaml | 433 +++ base_classes/nyaml/NXscanbox_em.yaml | 141 + .../nyaml/NXsolid_geometry.yaml | 27 +- .../nyaml/NXspectrum.yaml | 153 +- base_classes/nyaml/NXunit_cell.yaml | 214 ++ contributed_definitions/nyaml/NXapm.yaml | 1130 -------- .../nyaml/NXapm_compositionspace_config.yaml | 21 +- .../nyaml/NXapm_compositionspace_results.yaml | 562 +++- .../NXapm_paraprobe_clusterer_config.yaml | 18 +- .../NXapm_paraprobe_distancer_config.yaml | 18 +- .../NXapm_paraprobe_intersector_config.yaml | 210 +- .../NXapm_paraprobe_nanochem_config.yaml | 200 +- .../NXapm_paraprobe_nanochem_results.yaml | 754 +++-- .../nyaml/NXapm_paraprobe_ranger_config.yaml | 18 +- .../NXapm_paraprobe_selector_config.yaml | 18 +- .../NXapm_paraprobe_spatstat_config.yaml | 18 +- .../NXapm_paraprobe_surfacer_config.yaml | 18 +- .../NXapm_paraprobe_surfacer_results.yaml | 10 +- .../NXapm_paraprobe_tessellator_config.yaml | 18 +- .../NXapm_paraprobe_tessellator_results.yaml | 10 +- .../nyaml/NXapm_ranging.yaml | 74 - contributed_definitions/nyaml/NXatom_set.yaml | 272 -- .../nyaml/NXcg_alpha_complex.yaml | 213 -- .../nyaml/NXcg_geodesic_mesh.yaml | 89 - .../nyaml/NXcg_marching_cubes.yaml | 92 - .../nyaml/NXcg_primitive_set.yaml | 375 --- .../nyaml/NXcg_sphere_set.yaml | 92 - .../nyaml/NXcg_triangulated_surface_mesh.yaml | 60 - contributed_definitions/nyaml/NXchamber.yaml | 56 - .../nyaml/NXchemical_process.yaml | 90 - contributed_definitions/nyaml/NXcircuit.yaml | 270 -- .../nyaml/NXcrystal_structure.yaml | 477 --- .../nyaml/NXebeam_column.yaml | 195 -- .../nyaml/NXem_calorimetry.yaml | 412 ++- .../nyaml/NXem_correlation.yaml | 450 --- .../nyaml/NXem_method.yaml | 69 - contributed_definitions/nyaml/NXem_msr.yaml | 169 -- contributed_definitions/nyaml/NXem_sim.yaml | 97 - .../nyaml/NXevent_data_apm.yaml | 119 - .../nyaml/NXevent_data_em.yaml | 309 -- .../nyaml/NXevent_data_em_set.yaml | 80 - .../nyaml/NXgraph_edge_set.yaml | 6 +- .../nyaml/NXgraph_node_set.yaml | 6 +- .../nyaml/NXinstrument_apm.yaml | 267 -- .../nyaml/NXinteraction_vol_em.yaml | 94 - .../nyaml/NXlab_sample_mounting.yaml | 6 +- .../nyaml/NXmicrostructure.yaml | 1105 ++++++- .../nyaml/NXmicrostructure_ipf.yaml | 178 +- .../nyaml/NXmicrostructure_odf.yaml | 1 - .../nyaml/NXmicrostructure_score_config.yaml | 935 +++++- .../nyaml/NXmicrostructure_score_results.yaml | 794 ++++- .../nyaml/NXoptical_system_em.yaml | 291 -- .../nyaml/NXphysical_process.yaml | 92 - contributed_definitions/nyaml/NXroi.yaml | 46 - .../nyaml/NXrotation_set.yaml | 466 --- .../nyaml/NXscanbox_em.yaml | 197 -- .../nyaml/NXsingle_crystal.yaml | 113 - .../nyaml/NXspatial_filter.yaml | 18 +- .../nyaml/NXstage_lab.yaml | 319 -- .../nyaml/NXunit_cell.yaml | 379 --- 115 files changed, 13506 insertions(+), 10828 deletions(-) create mode 100644 applications/nyaml/NXapm.yaml rename {contributed_definitions => applications}/nyaml/NXem.yaml (71%) rename {contributed_definitions => base_classes}/nyaml/NXaberration.yaml (79%) rename {contributed_definitions => base_classes}/nyaml/NXapm_charge_state_analysis.yaml (100%) create mode 100644 base_classes/nyaml/NXapm_ranging.yaml rename {contributed_definitions => base_classes}/nyaml/NXapm_reconstruction.yaml (74%) create mode 100644 base_classes/nyaml/NXatom.yaml create mode 100644 base_classes/nyaml/NXcg_alpha_complex.yaml rename contributed_definitions/nyaml/NXcg_cylinder_set.yaml => base_classes/nyaml/NXcg_cylinder.yaml (65%) rename contributed_definitions/nyaml/NXcg_ellipsoid_set.yaml => base_classes/nyaml/NXcg_ellipsoid.yaml (61%) rename {contributed_definitions => base_classes}/nyaml/NXcg_face_list_data_structure.yaml (80%) rename {contributed_definitions => base_classes}/nyaml/NXcg_grid.yaml (73%) rename {contributed_definitions => base_classes}/nyaml/NXcg_half_edge_data_structure.yaml (83%) rename contributed_definitions/nyaml/NXcg_hexahedron_set.yaml => base_classes/nyaml/NXcg_hexahedron.yaml (63%) rename contributed_definitions/nyaml/NXcg_parallelogram_set.yaml => base_classes/nyaml/NXcg_parallelogram.yaml (57%) rename contributed_definitions/nyaml/NXcg_point_set.yaml => base_classes/nyaml/NXcg_point.yaml (90%) rename contributed_definitions/nyaml/NXcg_polygon_set.yaml => base_classes/nyaml/NXcg_polygon.yaml (60%) rename contributed_definitions/nyaml/NXcg_polyhedron_set.yaml => base_classes/nyaml/NXcg_polyhedron.yaml (76%) rename contributed_definitions/nyaml/NXcg_polyline_set.yaml => base_classes/nyaml/NXcg_polyline.yaml (82%) create mode 100644 base_classes/nyaml/NXcg_primitive.yaml rename contributed_definitions/nyaml/NXcg_roi_set.yaml => base_classes/nyaml/NXcg_roi.yaml (80%) rename contributed_definitions/nyaml/NXcg_tetrahedron_set.yaml => base_classes/nyaml/NXcg_tetrahedron.yaml (63%) rename contributed_definitions/nyaml/NXcg_triangle_set.yaml => base_classes/nyaml/NXcg_triangle.yaml (67%) rename contributed_definitions/nyaml/NXcg_unit_normal_set.yaml => base_classes/nyaml/NXcg_unit_normal.yaml (90%) rename {contributed_definitions => base_classes}/nyaml/NXchemical_composition.yaml (96%) create mode 100644 base_classes/nyaml/NXcircuit.yaml rename {contributed_definitions => base_classes}/nyaml/NXcoordinate_system.yaml (92%) rename {contributed_definitions => base_classes}/nyaml/NXcoordinate_system_set.yaml (97%) rename {contributed_definitions => base_classes}/nyaml/NXcorrector_cs.yaml (85%) rename {contributed_definitions => base_classes}/nyaml/NXcs_computer.yaml (97%) rename {contributed_definitions => base_classes}/nyaml/NXcs_filter_boolean_mask.yaml (99%) rename {contributed_definitions => base_classes}/nyaml/NXcs_prng.yaml (99%) rename {contributed_definitions => base_classes}/nyaml/NXcs_profiling.yaml (100%) rename {contributed_definitions => base_classes}/nyaml/NXcs_profiling_event.yaml (100%) rename {contributed_definitions => base_classes}/nyaml/NXcsg.yaml (58%) rename {contributed_definitions => base_classes}/nyaml/NXdeflector.yaml (57%) create mode 100644 base_classes/nyaml/NXebeam_column.yaml rename {contributed_definitions => base_classes}/nyaml/NXem_ebsd.yaml (55%) rename {contributed_definitions => base_classes}/nyaml/NXem_eds.yaml (66%) rename {contributed_definitions => base_classes}/nyaml/NXem_eels.yaml (64%) rename {contributed_definitions => base_classes}/nyaml/NXem_img.yaml (65%) create mode 100644 base_classes/nyaml/NXevent_data_apm.yaml create mode 100644 base_classes/nyaml/NXevent_data_em.yaml rename {contributed_definitions => base_classes}/nyaml/NXibeam_column.yaml (100%) rename contributed_definitions/nyaml/NXimage_set.yaml => base_classes/nyaml/NXimage.yaml (65%) create mode 100644 base_classes/nyaml/NXinstrument_apm.yaml create mode 100644 base_classes/nyaml/NXinstrument_em.yaml rename {contributed_definitions => base_classes}/nyaml/NXion.yaml (99%) rename {contributed_definitions => base_classes}/nyaml/NXmanipulator.yaml (70%) create mode 100644 base_classes/nyaml/NXoptical_system_em.yaml rename {contributed_definitions => base_classes}/nyaml/NXpeak.yaml (94%) create mode 100644 base_classes/nyaml/NXphase.yaml rename {contributed_definitions => base_classes}/nyaml/NXprogram.yaml (100%) rename {contributed_definitions => base_classes}/nyaml/NXpump.yaml (85%) rename {contributed_definitions => base_classes}/nyaml/NXquadric.yaml (96%) create mode 100644 base_classes/nyaml/NXrotations.yaml create mode 100644 base_classes/nyaml/NXscanbox_em.yaml rename {contributed_definitions => base_classes}/nyaml/NXsolid_geometry.yaml (66%) rename contributed_definitions/nyaml/NXspectrum_set.yaml => base_classes/nyaml/NXspectrum.yaml (85%) create mode 100644 base_classes/nyaml/NXunit_cell.yaml delete mode 100644 contributed_definitions/nyaml/NXapm.yaml delete mode 100644 contributed_definitions/nyaml/NXapm_ranging.yaml delete mode 100644 contributed_definitions/nyaml/NXatom_set.yaml delete mode 100644 contributed_definitions/nyaml/NXcg_alpha_complex.yaml delete mode 100644 contributed_definitions/nyaml/NXcg_geodesic_mesh.yaml delete mode 100644 contributed_definitions/nyaml/NXcg_marching_cubes.yaml delete mode 100644 contributed_definitions/nyaml/NXcg_primitive_set.yaml delete mode 100644 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symbols used in the schema to specify e.g. dimensions of arrays. + n_ht: | + Number of hit qualities (hit types) distinguished. + n_dld: | + Number of delay-line wires of the detector. + n_bins: | + Number of bins used in the mass-to-charge-state-ratio spectrum. + p: | + Number of pulses collected in between start_time and end_time resolved by an + instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of + ions included in the reconstructed volume if the application definition is used + to store results of an already reconstructed datasets. + p_out: | + Number of pulses returned by the hit finding algorithm. + Neither necessarily equal to p nor to n. + n: | + Number of ions spatially filtered from results of the hit_finding algorithm + from which an instance of a reconstructed volume has been generated. + These ions get new identifier assigned in the process (the so-called + evaporation_identifier). This identifier must not be confused with + the pulse_identifier. Typically smaller than both p_out and p_out. +type: group +NXapm(NXobject): + (NXentry): + exists: ['min', '1', 'max', 'unbounded'] + definition(NX_CHAR): + \@version(NX_CHAR): + exists: optional + enumeration: [NXapm] + profiling(NXcs_profiling): + exists: optional + doc: | + The configuration of the I/O writer software (e.g. `pynxtools `_ or its plugins) + which was used to generate this NeXus file instance. + + # command_line_call(NX_CHAR): + programID(NXprogram): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doc: | + A collection of all programs and libraries which are considered relevant + to understand with which software tools this NeXus file instance was + generated. Ideally, to enable a binary recreation from the input data. + + Examples include the name and version of the libraries used to write the + instance. Ideally, the software which writes these NXprogram instances + also includes the version of the set of NeXus classes i.e. the specific + set of base classes, application definitions, and contributed definitions + with which the here described concepts can be resolved. + + For the `pynxtools library `_ + which is used by the `NOMAD `_ + research data management system, it makes sense to store e.g. the GitHub + repository commit and respective submodule references used. + program(NX_CHAR): + \@version(NX_CHAR): + + # \@url: + experiment_identifier(NX_CHAR): + exists: recommended + run_number(NX_UINT): + exists: recommended + unit: NX_UNITLESS + + # cannot be made required as for simulations you do not have a run number! + doc: | + The identifier whereby the experiment is referred to in the control software. + This is neither the specimen_name nor the experiment_identifier. For + Local Electrode Atom Probe (LEAP) instruments, it is recommended to use the + run_number from the proprietary software IVAS/APSuite of AMETEK/Cameca. + For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, + or the instruments at GPM in Rouen, use the identifier which matches + best conceptually to the LEAP run number. + The field does not have to be required if the information is recoverable + in the dataset which for LEAP instruments is the case (provided these + RHIT or HITS files respectively are stored alongside a data artifact). + With NXapm the RHIT or HITS can be stored via NXnote in the + hit_finding algorithm section. + + As a destructive microscopy technique, a run can be performed only once. + It is possible, however, to interrupt a run and restart data acquisition + while still using the same specimen. In this case, each evaporation run + needs to be distinguished with different run numbers. + We follow this habit of most atom probe groups. Such interrupted runs + should be stored as individual :ref:`NXentry` instances in one NeXus file. + experiment_alias(NX_CHAR): + exists: recommended + doc: | + Either an identifier or an alias that is human-friendly so that scientists find that experiment again. + For experiments usually this is the run_number but for simulation typically no run_numbers are issued. + experiment_description(NX_CHAR): + exists: optional + doc: | + Free-text description about the experiment. + + Users are strongly advised to parameterize the description of their experiment + by using respective groups and fields and base classes instead of writing prose + into this field. + + The reason is that such free-text field is difficult to machine-interpret. + The motivation behind keeping this field for now is to learn in how far the + current base classes need extension based on user feedback. + + # optional quantities do not need to be mentioned in an appdef because they can always be added + # if NXapm inherits from NXapm_base having this optional field does not need to be + # mentioned because optional nodes can always be added to a NeXus file instance without + # making it thereby non-compliant to the application definition + # the only difference is that if the consuming application wishes to demand to find that field + # it has to be specified in the appdef for the appdef to be a useful document of the contract + # which pieces of information a software expects to find and which not + # if you think about you being the consuming human (agent) also you would like to know + # if there is a run_number for the atom probe measurement from your colleague i.e. you + # effectively ask your colleague for that information while working off your imagined list of requirements + # the appdef definition here is nothing else then the documentation of this for a software + start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information + included when the atom probe session started. If the exact duration of + the measurement is not relevant start_time only should be used. + + Often though it is useful to specify both start_time and end_time to + capture more detailed bookkeeping of the experiment. The user should + be aware that even with having both dates specified, it may not be + possible to infer how long the experiment took or for how long data + were collected. + + More detailed timing data over the course of the experiment have to be + collected to compute this event chain during the experiment. For this + purpose the :ref:`NXevent_data_apm` instance should be used. + end_time(NX_DATE_TIME): + exists: recommended + doc: | + ISO 8601 time code with local time zone offset to UTC included + when the atom probe session ended. + elapsed_time(NX_FLOAT): + exists: recommended + unit: NX_TIME + doc: | + How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime + citeID(NXcite): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + doi(NX_CHAR): + noteID(NXnote): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + operation_mode(NX_CHAR): + doc: | + What type of atom probe experiment is performed? This field is meant to + inform research data management systems to allow filtering: + + * apt are experiments where the analysis_chamber has no imaging gas. + experiment with LEAP instruments are typically performed such. + * fim are experiments where the analysis_chamber has an imaging gas, + which should be specified with the atmosphere in the analysis_chamber group. + * apt_fim should be used for combinations of the two imaging modes. + few experiments of this type have been performed as this can be detrimental + to LEAP systems (see `S. Katnagallu et al. `_). + * other should be used in combination with the user specifying details + in the experiment_documentation field. + + If NXapm is used for storing details about a simulation use other for now. + enumeration: + open_enum: true + items: [apt, fim, apt_fim] + userID(NXuser): + exists: recommended + nameType: partial + name(NX_CHAR): + exists: optional + identifierNAME(NX_CHAR): + exists: recommended + nameType: partial + sample(NXsample): + exists: recommended + doc: | + Description of the sample from which the specimen was prepared or + site-specifically cut out using e.g. a focused-ion beam instrument. + + The sample group is currently a place for storing suggestions from + atom probers about knowledge they have gained about the sample. + There are cases where the specimen is machined further or exposed to + external stimuli during the experiment. In this case, these details should + not be stored under sample but suggestions should be made + how this application definition can be improved. + + In the future also details like how the grain_diameter was characterized, + how the sample was prepared, how the material was heat-treated etc., + should be stored. For this specific application definitions/schemas can be + used which are then arranged and documented with a description of the + workflow so that actionable graphs become instantiatable. + type(NX_CHAR): + doc: | + A qualifier whether the sample is a real one + or a virtual one (in a computer simulation). + enumeration: [experiment, simulation] + alias(NX_CHAR): + doc: | + Given name/alias for the sample. + identifierNAME(NX_CHAR): + exists: recommended + nameType: partial + grain_diameter(NX_FLOAT): + exists: optional + unit: NX_LENGTH + doc: | + Qualitative information about the grain size, here specifically + described as the equivalent spherical diameter of an assumed + average grain size for the crystal ensemble. + Users of this information should be aware that although the grain + diameter or radius is often referred to as grain size. + + In atom probe it is possible that the specimen may contain a few + crystals only. In this case the grain_diameter is not a reliable + descriptor. Reporting a grain size may be useful though as it allows + judging if specific features are expected to be found in the + detector hit map. + grain_diameter_error(NX_FLOAT): + exists: optional + unit: NX_LENGTH + doc: | + Magnitude of the standard deviation of the grain_diameter. + + # schema for heat treatment + heat_treatment_temperature(NX_FLOAT): + exists: optional + unit: NX_TEMPERATURE + doc: | + The temperature of the last heat treatment step before quenching. + Knowledge about this value can give an idea how the sample + was heat treated. However, if a documentation of the annealing + treatment as a function of time is available one should better + rely on this information and have it stored alongside the NeXus file. + heat_treatment_temperature_error(NX_FLOAT): + exists: optional + unit: NX_TEMPERATURE + doc: | + Magnitude of the standard deviation of the heat_treatment_temperature. + heat_treatment_quenching_rate(NX_FLOAT): + exists: optional + unit: NX_ANY + doc: | + Rate of the last quenching step. Knowledge about this value can give + an idea how the sample was heat treated. However, there are many + situations where one can imagine that the scalar value for just the + quenching rate is insufficient. + + An example is when the sample was left in the furnace after the + furnace was switched off. In this case the sample cools down with + a specific rate of how this furnace cools down in the lab. + Processes which in practice are often not documented. + + This can be problematic though because when the furnace door was left open + or the ambient temperature in the lab changed, i.e. for a series of + experiments where one is conducted on a hot summer day and the next + during winter this can have an effect on the evolution of the microstructure. + There are many cases where this has been reported to be an QA issue in industry, + e.g. think about aging aluminium samples left on the factory + parking lot on a hot summer day. + heat_treatment_quenching_rate_error(NX_FLOAT): + exists: optional + unit: NX_ANY + doc: | + Magnitude of the standard deviation of the heat_treatment_quenching_rate. + description(NX_CHAR): + exists: optional + chemical_composition(NXchemical_composition): + exists: recommended + doc: | + The chemical composition of the sample. Typically, it is assumed that + this more macroscopic composition is representative for the material + so that the composition of the typically substantially less voluminous + specimen probes from the more voluminous sample. + normalization(NX_CHAR): + doc: | + Reporting compositions as atom and weight percent yields both + dimensionless quantities but their conceptual interpretation differs. + A normalization based on atom_percent counts relative to the + total number of atoms which are of a particular type. + By contrast, weight_percent normalization factorizes in the + respective mass of the elements. Python libraries like pint are + challenged by these differences as at.-% and wt.-% are both + fractional quantities. + enumeration: [atom_percent, weight_percent] + ionID(NXion): + exists: ['min', '1', 'max', '118'] + nameType: partial + chemical_symbol(NX_CHAR): + doc: | + Human-readable name of the element (e.g. Fe). + Name has to be a symbol of an element from the periodic table. + All symbols in the set of NXion instances inside the group + chemical_composition need to be disjoint. + composition(NX_FLOAT): + unit: NX_DIMENSIONLESS + doc: | + Composition value for the element/ion referred to under name. + The value is normalized based on normalization, i.e. composition + is either an atom or weight percent quantity. + composition_error(NX_FLOAT): + exists: optional + unit: NX_DIMENSIONLESS + doc: | + Magnitude of the standard deviation of the composition (value). + specimen(NXsample): + type(NX_CHAR): + doc: | + A qualifier whether the specimen is a real one or a virtual one. + enumeration: [experiment, simulation] + alias(NX_CHAR): + exists: recommended + doc: | + Given name an alias. Better use identifierNAME and identifier_parent instead. + A single NXentry should be used only for the characterization of a single specimen. + identifierNAME(NX_CHAR): + exists: recommended + nameType: partial + identifier_parent(NX_CHAR): + exists: recommended + doc: | + Identifier of the sample from which the specimen was cut or the string + n/a. The purpose of this field is to support functionalities for + tracking sample provenance via a research data management system. + preparation_date(NX_DATE_TIME): + exists: recommended + doc: | + ISO 8601 time code with local time zone offset to UTC information + when the specimen was prepared. + + Ideally, report the end of the preparation, i.e. the last known time + the measured specimen surface was actively prepared. Ideally, this + matches the last timestamp that is mentioned in the digital resource + pointed to by identifier_parent. + + Knowing when the specimen was exposed to e.g. specific atmosphere is + especially required for environmentally sensitive material such as + hydrogen charged specimens or experiments including tracers with a + short half time. Additional time stamps prior to preparation_date + should better be placed in resources which describe but which do not + pollute the description here with prose. Resolving these connected + pieces of information is considered within the responsibility of the + research data management system. + atom_types(NX_CHAR): + doc: | + List of comma-separated elements from the periodic table that are + contained in the specimen. If the specimen substance has multiple + components, all elements from each component must be included in + `atom_types`. + + The purpose of the field is to offer research data management systems an + opportunity to parse the relevant elements without having to interpret + these from the resources pointed to by identifier_parent or walk through + eventually deeply nested groups in data instances. + description(NX_CHAR): + exists: optional + doc: | + Discouraged free-text field. + is_polycrystalline(NX_BOOLEAN): + exists: recommended + doc: | + Report if the specimen is polycrystalline, in which case it + contains a grain or phase boundary, or if the specimen is a + single crystal. + is_amorphous(NX_BOOLEAN): + exists: recommended + doc: | + Report if the specimen is amorphous. + initial_radius(NX_FLOAT): + exists: recommended + unit: NX_LENGTH + doc: | + Ideally measured otherwise best elaborated guess of the initial radius of the + specimen. + shank_angle(NX_FLOAT): + exists: recommended + unit: NX_ANGLE + doc: | + Ideally measured otherwise best elaborated guess of the (initial) shank angle. + This is a measure of the specimen taper. Define it in such a way that the base of the specimen + is modelled as a conical frustrum so that the shank angle is the (shortest) angle between + the specimen space z-axis and a vector on the lateral surface of the cone. + + # describing the geometry of the specimen + coordinate_system_set(NXcoordinate_system_set): + exists: recommended + doc: | + Set to hold different coordinate systems conventions. + Inspect the description of the :ref:`NXcoordinate_system_set` + and :ref:`NXcoordinate_system` base classes how to define + coordinate systems in NeXus. Specific details for application + in atom probe microscopy follow. + + In this research field scientists usually distinguish several + Euclidean coordinate systems (CS): + + * World space; + a CS specifying a local coordinate system of the planet earth which + identifies into which direction gravity is pointing such that + the laboratory space CS can be rotated into this world CS. + * The laboratory space; + a CS specifying the room where the instrument is located in or + a physical landmark on the instrument, e.g. the direction of the + transfer rod where positive is the direction how the rod + has to be pushed during loading a specimen into the instrument. + In summary, this CS is defined by the chassis of the instrument. + * The specimen space; + a CS affixed to either the base or the initial apex of the specimen, + whose z axis points towards the detector. + * The detector space; + a CS affixed to the detector plane whose xy plane is usually in the + detector and whose z axis points towards the specimen. + This is a distorted space with respect to the reconstructed ion + positions. + * The reconstruction space; + a CS in which the reconstructed ion positions are defined. + The orientation depends on the analysis software used. + * Eventually further coordinate systems attached to the + flight path of individual ions might be defined. + + In atom probe microscopy a frequently used choice for the detector + space (CS) is discussed with the so-called detector space image + (stack). This is a stack of two-dimensional histograms of detected ions + within a predefined evaporation identifier interval. Typically, the set of + ion evaporation sequence IDs is grouped into chunks. + + For each chunk a histogram of the ion hit positions on the detector + is computed. This leaves the possibility for inconsistency between + the so-called detector space and the e.g. specimen space. + + To avoid these ambiguities, instances of :ref:`NXtransformations` should + be used. + (NXcoordinate_system): + exists: ['min', '1', 'max', 'unbounded'] + origin(NX_CHAR): + alias(NX_CHAR): + type(NX_CHAR): + handedness(NX_CHAR): + x_direction(NX_CHAR): + y_direction(NX_CHAR): + z_direction(NX_CHAR): + measurement(NXobject): + exists: optional + doc: | + Base class for collecting a session with a real atom probe or field-ion microscope. + + Workflows used during experiments or simulations of atom probe and related field-evaporation + research should be documented in more detail and be better contextualized not only because of + ongoing developments and the tighter becoming connection between atom probe and other + methods for material characterization foremost electron microscopy see e.g.: + + * `T. Kelly et al. `_ + * `C. Fleischmann et al. `_ + * `W. Windl et al. `_ + * `C. Freysoldt et al. `_ + * `G. da Costa et al. `_ + + to mention but a few. + + To arrive at a design of base classes and an application definition that can be used + for both real and simulated atom probe experiments it is worthwhile to recall concepts that are + related to events and (molecular) ions: + + * Pulsing events which are used to trigger ion extraction events. + * Physical events and corresponding signal triggered by an ion hitting the detector. + Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. + * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input + and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are + wortwhile to be considered further and eventually included in the reconstructed volume. + * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually + selected (molecular) ions based on which an instance of a reconstruction is created. + * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values + and charge states of the (molecular) ions to substantiate that some of these ions can be considered + as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms + and subsequent peak labeling. In the field of atom probe this these peak identification methods + are known as ranging definitions. + + Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts + are well distinguished. However, the algorithms used to transform correlations between pulses and physical events + into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. + + Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme + where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier + i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. + That is evaporation_identifier values take the role of an implicit time and course of the experiment given that + ion extraction physically is a sequential process. + + There is a number of research groups who build own instruments and share different aspects of their technical + specifications and approaches how they apply data processing e.g.: + + * `M. Monajem et al. `_ + * `P. Stender et al. `_ + * `I. Dimkou et al. `_ + + to name but a few. + + Despite some of these activities embrace practices of open-source development, they use essentially the same + workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface + software is used to explore and thus analyze reconstructed atom probe datasets. + + Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. + Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which + scientific conclusions about the characterized material volume are made. Also here a reconstruction is + point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. + + By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all + the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. + Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. + We argue that this divide can be bridged with realizing the above-mentioned context and the realization that + similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. + + A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed + datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment + and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting + a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as + (spatial) filtering and reconstruction algorithms. + + Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation + simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. + Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. + Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. + Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require + simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps + in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. + Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) + than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path + such as local electrodes or physical obstacles and electric fields (controlled or stray fields). + instrument(NXinstrument_apm): + type(NX_CHAR): + exists: recommended + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + reflectron(NXcomponent): + exists: optional + applied(NX_BOOLEAN): + local_electrode(NXlens_em): + exists: recommended + name(NX_CHAR): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + ion_detector(NXdetector): + exists: recommended + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + pulser(NXcomponent): + exists: recommended + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + sourceID(NXsource): + exists: ['min', '0', 'max', '2'] + nameType: partial + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + + # wavelength and pulse_energy as dynamic/volatile quantities stored in event data part + comment(NX_CHAR): + doc: | + Free text field for additional comments. + status(NX_CHAR): + exists: recommended + doc: | + A statement whether the measurement was successful or failed prematurely. + quality(NX_CHAR): + exists: recommended + doc: | + CAnalysis.CResults.fQuality + events(NXobject): + exists: optional + + # the case of allowing to not have event_data but only the above-mentioned instrument + # details can be useful to convey details about an atom probe instrument in general + doc: | + Group to hold instances of :ref:`NXevent_data_apm`. + + Which temporal granularity is adequate depends on the situation and research + question. Using a model which enables a collection of events offers the most + flexible way to cater for both atom probe experiments or simulation. + + To monitor the course of an ion extraction experiment (or simulation) + it makes sense to track time explicitly via time stamps or implicitly + via e.g. a clock inside the instrument, such as the clock of the pulser + and respective pulsing event identifier. + + As set and measured quantities typically change over time and we do not + yet know during the measurement which of the events have associated + (molecular) ions that will end up in the reconstructed volume, we must not + document quantities as a function of the evaporated_identifier but as a + function of the (pulsing) event_identifier. + eventID(NXevent_data_apm): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + + # all these cannot be made required because for LEAP only stored in RHIT/HITS + # but for M-TAP and Oxcart these pieces of information are available. + start_time(NX_DATE_TIME): + exists: recommended + end_time(NX_DATE_TIME): + exists: recommended + + # delta_time(NX_NUMBER): + # pulse_identifier_offset(NX_INT): + # pulse_identifier(NX_INT): + instrument(NXinstrument_apm): + exists: recommended + reflectron(NXcomponent): + exists: recommended + voltage(NX_FLOAT): + + # decelerate_electrode(NXlens_em): + local_electrode(NXlens_em): + exists: recommended + voltage(NX_FLOAT): + + # ion_detector(NXdetector): + pulser(NXcomponent): + exists: recommended + pulse_mode(NX_CHAR): + pulse_frequency(NX_FLOAT): + + # \@logged_against(NX_CHAR): + pulse_fraction(NX_FLOAT): + + # \@logged_against(NX_CHAR): + pulse_voltage(NX_FLOAT): + exists: optional + dimensions: + rank: 1 + dim: (n,) + + # \@logged_against(NX_CHAR): + pulse_number(NX_UINT): + exists: optional + dimensions: + rank: 1 + dim: (n,) + + # \@logged_against(NX_CHAR): + standing_voltage(NX_FLOAT): + exists: optional + dimensions: + rank: 1 + dim: (n,) + + # \@logged_against(NX_CHAR): + sourceID(NXsource): + exists: ['min', '0', 'max', '2'] + nameType: partial + pulse_energy(NX_FLOAT): + dimensions: + rank: 1 + dim: (n,) + + # \@logged_against(NX_CHAR): + # laser geometry at the moment has neither a worked out example + # nor any feedback from the community despite the work from B. Gault + # on laser atom probe was granted a Leibnitz award + stage(NXmanipulator): + temperature_sensor(NXsensor): + measurement(NX_CHAR): + value(NX_FLOAT): + analysis_chamber(NXcomponent): + pressure_sensor(NXsensor): + measurement(NX_CHAR): + value(NX_FLOAT): + control(NXcollection): + exists: recommended + evaporation_control(NX_CHAR): + target_detection_rate(NX_NUMBER): + simulation(NXobject): + exists: optional + doc: | + Simulation of ion extraction from matter via laser and/or voltage pulsing. + + # future possibility to reuse concepts from NXinstrument_apm again without + # the need for defining them again + atom_probe(NXobject): + exists: recommended + doc: | + A region-of-interest analyzed either during or after the session for which + specific processed data of the measured or simulated data are available. + + # earlier comments here https://github.com/FAIRmat-NFDI/nexus_definitions/commit/a8602870f13f04b8befc902efb345afe650d8dd3 + initial_specimen(NXimage): + exists: recommended + doc: | + SEM or TEM image of the initial specimen (ideally taken prior data acquisition). + image_2d(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_CHAR): + nameType: partial + real(NX_NUMBER): + axis_j(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_j,) + \@long_name(NX_CHAR): + axis_i(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_i,) + \@long_name(NX_CHAR): + + # could use a stack_3d(NXdata) to record time series of specimen shape evolution + raw_data(NXprocess): + exists: recommended + doc: | + For almost atom probe instruments (meta)data about raw data follow proprietary semantics. + Therefore, this group can currently be used only to point to these digital artifacts + in an effort to document all step of an analysis workflow. + + The physical quantities measured in an atom probe experiment are time-of-flight and + tuples of arrival_time_pairs as a function of the event chain on the pulser. + From these tuples hits are computed in a process called hit_finding. + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + + # point at least to the proprietary artifact + source(NXnote): + exists: recommended + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + + # technical details of data the ion_detector collects + number_of_dld_wires(NX_UINT): + exists: recommended + unit: NX_UNITLESS + doc: | + The number of wires in the detector. + enumeration: [1, 2, 3] + dld_wire_names(NX_CHAR): + exists: optional + doc: | + Alias tuple (begin, end) of each DLD wire of the detector. + Order follows arrival_time_pairs. + dimensions: + rank: 2 + dim: (n_dld, 2) + arrival_time_pairs(NX_NUMBER): + exists: optional + unit: NX_TIME + doc: | + Raw readings from the analog-to-digital-converter + timing circuits of the detector wires. + dimensions: + rank: 3 + dim: (p, n_dld, 2) + hit_finding(NXprocess): + exists: recommended + doc: | + Configuration of and results obtained from a hit finding algorithm. + + # we careful how we go about doing this here, we recommended to make some details of the hit_finding + # algorithm open namely the input and the output what the black box then does by AMETEK/Cameca + # does not have to be exposed (although this clearly is against FAIR principles but the scientific community + # is does not have the authority to decide which portions of proprietary code have to be public + # we can only make recommendations + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + + # config of the hit_finding algorithm + config(NXnote): + exists: recommended + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + + # results of the hit_finding algorithm + hit_positions(NX_NUMBER): + exists: recommended + unit: NX_LENGTH + doc: | + Evaluated ion impact coordinates on the detector. + Use the depends_on field to specify which reference + frame the positions are defined. + dimensions: + rank: 2 + dim: (p_out, 2) + \@depends_on(NX_CHAR): + doc: | + Defines in which reference frame the positions are defined. + total_event_golden(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + CRunHeader.fTotalEventGolden + total_event_incomplete(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + CRunHeader.fTotalEventIncomplete + total_event_multiple(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + CRunHeader.fTotalEventMultiple + total_event_partial(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + CRunHeader.fTotalEventPartials + total_event_record(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + CRunHeader.fTotalEventRecords + hit_quality_identifier(NX_UINT): + exists: optional + doc: | + Identifier used for each hit_quality type. + Following the order of hit_quality_types. + dimensions: + rank: 1 + dim: (n_ht,) + hit_quality(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + Hit quality identifier for each pulse. + Identifier have to be within hit_quality_identifier. + dimensions: + rank: 1 + dim: (p_out,) + hit_multiplicity(NX_UINT): + exists: optional + unit: NX_UNITLESS + doc: | + This processing yields for each ion with how many others it evaporated + if these were collected on the same pulse. Extraction of multiple ions + on one pulse on different or even the same pixel of the detector are possible. + + Multiplicity must not be confused with how many atoms of the same element + a molecular ion contains. + dimensions: + rank: 1 + dim: (p_out,) + + # the following two quantities are relicts from ePOS files used to give some + # insight into the results of the hit_finding algorithm of IVAS/APSuite but typically + # used only in the context to learn about the multiplicity of an ion. + # pulses_since_last_ion(NX_UINT): + # dim: (n,) + # pulse_identifier(NX_INT): + # dim: (n,) + # at this point the original set of events p has been filtered down to p_out + hit_spatial_filtering(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: optional + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + evaporation_identifier_offset(NX_INT): + unit: NX_UNITLESS + doc: | + Integer used to name the first pulse to know if there is an + offset of the evaporation_identifier to zero. + + Identifiers can be defined either implicitly or explicitly. + For implicit indexing identifiers are defined on the interval + :math:`[identifier\_offset, identifier\_offset + c - 1]`. + + Therefore, implicit identifier are completely defined by the value of + identifier_offset and cardinality. For example if identifier run from + -2 to 3 the value for identifier_offset is -2. + + For explicit indexing the field identifier has to be used. + Fortran-/Matlab- and C-/Python-style indexing have specific implicit + identifier conventions where identifier_offset is 1 and 0 respectively. + evaporation_identifier(NX_INT): + unit: NX_UNITLESS + doc: | + (Molecular) ion identifier which resolves the sequence in which + the ions were evaporated but taking into account that a hit_finding + and spatial_filtering was applied. + dimensions: + rank: 1 + dim: (n,) + hit_filter(NXcs_filter_boolean_mask): + exists: recommended + + # use NXcs_filter needs conditionally an instance of concept ../../hit_finding + number_of_objects(NX_UINT): + bitdepth(NX_UINT): + mask(NX_UINT): + identifier(NX_INT): + + # at this point the set of events p_out has been filtered down to n + voltage_and_bowl(NXprocess): + exists: recommended + doc: | + Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. + + The voltage-and-bowl correction is a data post-processing step to correct ion impact + positions for flight path differences, detector biases, and nonlinearities. + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXserialized): + exists: optional + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + + # currently cannot be made required because of being a quantity measured + # by proprietary hardware with proprietary semantics + raw_tof(NX_FLOAT): + exists: recommended + doc: | + Raw time-of-flight data without corrections. + dimensions: + rank: 1 + dim: (n,) + + # result + tof_zero_estimate(NX_FLOAT): + exists: optional + unit: NX_TIME + doc: | + The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate + calibrated_tof(NX_FLOAT): + exists: recommended + doc: | + Calibrated time-of-flight. + dimensions: + rank: 1 + dim: (n,) + mass_to_charge_conversion(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + source(NXnote): + exists: recommended + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + + # config/input + # results + mass_to_charge(NX_FLOAT): + dimensions: + rank: 1 + dim: (n,) + reconstruction(NXapm_reconstruction): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + config(NXnote): + exists: recommended + doc: | + For LEAP and IVAS/APSuite-based analyses root file which stores + the settings whereby an RHIT/HITS file can be used to regenerate the + reconstruction that is here referred to. + + The respective RHIT/HITS file should ideally be specified in the serialized + group of the hit_finding section of this application definition. + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + results(NXnote): + exists: recommended + doc: | + For LEAP and IVAS/APSuite-based analyses the resulting typically + file with the reconstructed positions and (calibrated) mass-to-charge + state ratio values. + + For other data collection/analysis software the data artifact which comes + closest conceptually to AMETEK/Cameca's typical file formats. + + These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, + which should be stored alongside this record in the research data + management system. + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + + # config/input + parameter(NX_CHAR): + exists: recommended + protocol_name(NX_CHAR): + exists: recommended + crystallographic_calibration(NX_CHAR): + exists: recommended + field_of_view(NX_FLOAT): + exists: recommended + reconstructed_positions(NX_FLOAT): + dimensions: + rank: 2 + dim: (n, 3) + naive_discretization(NXprocess): + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + + # config/input + # results + (NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_CHAR): + nameType: partial + + # dim: (3,) + # \@long_name: + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + dimensions: + rank: 3 + dim: (n_z, n_y, n_x) + axis_z(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_z,) + \@long_name(NX_CHAR): + axis_y(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_y,) + \@long_name(NX_CHAR): + axis_x(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_x,) + \@long_name(NX_CHAR): + ranging(NXapm_ranging): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + definitions(NXnote): + exists: recommended + doc: | + The respective ranging definitions file RNG/RRNG/ENV/HDF5. + type(NX_CHAR): + file_name(NX_CHAR): + checksum(NX_CHAR): + algorithm(NX_CHAR): + mass_to_charge_distribution(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + min_incr_max(NX_FLOAT): + mass_spectrum(NXdata): + \@signal(NX_CHAR): + \@axes(NX_CHAR): + \@AXISNAME_indices(NX_CHAR): + nameType: partial + + # \@long_name(NX_CHAR): + title(NX_CHAR): + exists: recommended + intensity(NX_NUMBER): + dimensions: + rank: 1 + dim: (n_bins,) + \@long_name(NX_CHAR): + axis_mass_to_charge(NX_FLOAT): + dimensions: + rank: 1 + dim: (n_bins,) + \@long_name(NX_CHAR): + background_quantification(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + background(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + (Out-of-sync) background levels in ppm/ns + reported by e.g. IVAS/APSuite for LEAP systems. + mrp_value(NX_FLOAT): + exists: recommended + unit: NX_DIMENSIONLESS + doc: | + MRP, mass-resolving power, `D. Larson et al. + `_ (p282, Eqs. D.7 and D.8). + mrp_mass_to_charge(NX_FLOAT): + exists: recommended + unit: NX_ANY + doc: | + MRP, at which mrp_value was specified. + + # config/input + # results + # NEW ISSUE: add parameters of the background model + # in an e.g. work of A. London et al. + peak_search(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + peakID(NXpeak): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + label(NX_CHAR): + exists: recommended + description(NX_CHAR): + category(NX_CHAR): + exists: recommended + doc: | + Category for the peak offering a qualitative statement of the location of the peak + in light of limited mass-resolving power that is relevant for + composition quantification. See `D. Larson et al. (p172) `_ + for examples of each category: + + * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` + * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` + * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states + * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` + * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` + * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` + enumeration: [0, 1, 2, 3, 4, 5] + position(NX_NUMBER): + + # peak deconvolution(NXprocess): + peak_identification(NXprocess): + exists: recommended + sequence_index(NX_POSINT): + exists: recommended + programID(NXprogram): + exists: ['min', '1', 'max', 'unbounded'] + nameType: partial + program(NX_CHAR): + \@version(NX_CHAR): + number_of_ion_types(NX_UINT): + maximum_number_of_atoms_per_molecular_ion(NX_UINT): + ionID(NXion): + exists: ['min', '1', 'max', '256'] + nameType: partial + nuclide_hash(NX_UINT): + charge_state(NX_INT): + charge_state_analysis(NXapm_charge_state_analysis): + exists: optional + + # config + nuclides(NX_UINT): + mass_to_charge_range(NX_FLOAT): + min_half_life(NX_FLOAT): + min_abundance(NX_FLOAT): + min_abundance_product(NX_FLOAT): + sacrifice_isotopic_uniqueness(NX_BOOLEAN): + + # results + charge_state(NX_INT): + nuclide_hash(NX_UINT): + mass(NX_FLOAT): + natural_abundance_product(NX_FLOAT): + shortest_half_life(NX_FLOAT): + mass_to_charge_range(NX_FLOAT): + nuclide_list(NX_UINT): + exists: recommended + name(NX_CHAR): + exists: recommended + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 4608ef7f304b5992a148c7a7b247888b099fa2c869ef71809a4be6c2a19c83d2 +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of hit qualities (hit types) distinguished. +# +# +# +# +# Number of delay-line wires of the detector. +# +# +# +# +# Number of bins used in the mass-to-charge-state-ratio spectrum. +# +# +# +# +# Number of pulses collected in between start_time and end_time resolved by an +# instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of +# ions included in the reconstructed volume if the application definition is used +# to store results of an already reconstructed datasets. +# +# +# +# +# Number of pulses returned by the hit finding algorithm. +# Neither necessarily equal to p nor to n. +# +# +# +# +# Number of ions spatially filtered from results of the hit_finding algorithm +# from which an instance of a reconstructed volume has been generated. +# These ions get new identifier assigned in the process (the so-called +# evaporation_identifier). This identifier must not be confused with +# the pulse_identifier. Typically smaller than both p_out and p_out. +# +# +# +# +# Application definition for atom probe and field ion microscopy experiments. +# +# +# +# +# +# +# +# +# +# +# The configuration of the I/O writer software (e.g. `pynxtools <https://github.com/FAIRmat-NFDI/pynxtools>`_ or its plugins) +# which was used to generate this NeXus file instance. +# +# +# +# +# A collection of all programs and libraries which are considered relevant +# to understand with which software tools this NeXus file instance was +# generated. Ideally, to enable a binary recreation from the input data. +# +# Examples include the name and version of the libraries used to write the +# instance. Ideally, the software which writes these NXprogram instances +# also includes the version of the set of NeXus classes i.e. the specific +# set of base classes, application definitions, and contributed definitions +# with which the here described concepts can be resolved. +# +# For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ +# which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ +# research data management system, it makes sense to store e.g. the GitHub +# repository commit and respective submodule references used. +# +# +# +# +# +# +# +# +# +# +# +# The identifier whereby the experiment is referred to in the control software. +# This is neither the specimen_name nor the experiment_identifier. For +# Local Electrode Atom Probe (LEAP) instruments, it is recommended to use the +# run_number from the proprietary software IVAS/APSuite of AMETEK/Cameca. +# For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, +# or the instruments at GPM in Rouen, use the identifier which matches +# best conceptually to the LEAP run number. +# The field does not have to be required if the information is recoverable +# in the dataset which for LEAP instruments is the case (provided these +# RHIT or HITS files respectively are stored alongside a data artifact). +# With NXapm the RHIT or HITS can be stored via NXnote in the +# hit_finding algorithm section. +# +# As a destructive microscopy technique, a run can be performed only once. +# It is possible, however, to interrupt a run and restart data acquisition +# while still using the same specimen. In this case, each evaporation run +# needs to be distinguished with different run numbers. +# We follow this habit of most atom probe groups. Such interrupted runs +# should be stored as individual :ref:`NXentry` instances in one NeXus file. +# +# +# +# +# Either an identifier or an alias that is human-friendly so that scientists find that experiment again. +# For experiments usually this is the run_number but for simulation typically no run_numbers are issued. +# +# +# +# +# Free-text description about the experiment. +# +# Users are strongly advised to parameterize the description of their experiment +# by using respective groups and fields and base classes instead of writing prose +# into this field. +# +# The reason is that such free-text field is difficult to machine-interpret. +# The motivation behind keeping this field for now is to learn in how far the +# current base classes need extension based on user feedback. +# +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the atom probe session started. If the exact duration of +# the measurement is not relevant start_time only should be used. +# +# Often though it is useful to specify both start_time and end_time to +# capture more detailed bookkeeping of the experiment. The user should +# be aware that even with having both dates specified, it may not be +# possible to infer how long the experiment took or for how long data +# were collected. +# +# More detailed timing data over the course of the experiment have to be +# collected to compute this event chain during the experiment. For this +# purpose the :ref:`NXevent_data_apm` instance should be used. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC included +# when the atom probe session ended. +# +# +# +# +# How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime +# +# +# +# +# +# +# +# +# +# +# +# +# +# What type of atom probe experiment is performed? This field is meant to +# inform research data management systems to allow filtering: +# +# * apt are experiments where the analysis_chamber has no imaging gas. +# experiment with LEAP instruments are typically performed such. +# * fim are experiments where the analysis_chamber has an imaging gas, +# which should be specified with the atmosphere in the analysis_chamber group. +# * apt_fim should be used for combinations of the two imaging modes. +# few experiments of this type have been performed as this can be detrimental +# to LEAP systems (see `S. Katnagallu et al. <https://doi.org/10.1017/S1431927621012381>`_). +# * other should be used in combination with the user specifying details +# in the experiment_documentation field. +# +# If NXapm is used for storing details about a simulation use other for now. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Description of the sample from which the specimen was prepared or +# site-specifically cut out using e.g. a focused-ion beam instrument. +# +# The sample group is currently a place for storing suggestions from +# atom probers about knowledge they have gained about the sample. +# There are cases where the specimen is machined further or exposed to +# external stimuli during the experiment. In this case, these details should +# not be stored under sample but suggestions should be made +# how this application definition can be improved. +# +# In the future also details like how the grain_diameter was characterized, +# how the sample was prepared, how the material was heat-treated etc., +# should be stored. For this specific application definitions/schemas can be +# used which are then arranged and documented with a description of the +# workflow so that actionable graphs become instantiatable. +# +# +# +# A qualifier whether the sample is a real one +# or a virtual one (in a computer simulation). +# +# +# +# +# +# +# +# +# Given name/alias for the sample. +# +# +# +# +# +# Qualitative information about the grain size, here specifically +# described as the equivalent spherical diameter of an assumed +# average grain size for the crystal ensemble. +# Users of this information should be aware that although the grain +# diameter or radius is often referred to as grain size. +# +# In atom probe it is possible that the specimen may contain a few +# crystals only. In this case the grain_diameter is not a reliable +# descriptor. Reporting a grain size may be useful though as it allows +# judging if specific features are expected to be found in the +# detector hit map. +# +# +# +# +# Magnitude of the standard deviation of the grain_diameter. +# +# +# +# +# +# The temperature of the last heat treatment step before quenching. +# Knowledge about this value can give an idea how the sample +# was heat treated. However, if a documentation of the annealing +# treatment as a function of time is available one should better +# rely on this information and have it stored alongside the NeXus file. +# +# +# +# +# Magnitude of the standard deviation of the heat_treatment_temperature. +# +# +# +# +# Rate of the last quenching step. Knowledge about this value can give +# an idea how the sample was heat treated. However, there are many +# situations where one can imagine that the scalar value for just the +# quenching rate is insufficient. +# +# An example is when the sample was left in the furnace after the +# furnace was switched off. In this case the sample cools down with +# a specific rate of how this furnace cools down in the lab. +# Processes which in practice are often not documented. +# +# This can be problematic though because when the furnace door was left open +# or the ambient temperature in the lab changed, i.e. for a series of +# experiments where one is conducted on a hot summer day and the next +# during winter this can have an effect on the evolution of the microstructure. +# There are many cases where this has been reported to be an QA issue in industry, +# e.g. think about aging aluminium samples left on the factory +# parking lot on a hot summer day. +# +# +# +# +# Magnitude of the standard deviation of the heat_treatment_quenching_rate. +# +# +# +# +# +# The chemical composition of the sample. Typically, it is assumed that +# this more macroscopic composition is representative for the material +# so that the composition of the typically substantially less voluminous +# specimen probes from the more voluminous sample. +# +# +# +# Reporting compositions as atom and weight percent yields both +# dimensionless quantities but their conceptual interpretation differs. +# A normalization based on atom_percent counts relative to the +# total number of atoms which are of a particular type. +# By contrast, weight_percent normalization factorizes in the +# respective mass of the elements. Python libraries like pint are +# challenged by these differences as at.-% and wt.-% are both +# fractional quantities. +# +# +# +# +# +# +# +# +# +# Human-readable name of the element (e.g. Fe). +# Name has to be a symbol of an element from the periodic table. +# All symbols in the set of NXion instances inside the group +# chemical_composition need to be disjoint. +# +# +# +# +# Composition value for the element/ion referred to under name. +# The value is normalized based on normalization, i.e. composition +# is either an atom or weight percent quantity. +# +# +# +# +# Magnitude of the standard deviation of the composition (value). +# +# +# +# +# +# +# +# +# A qualifier whether the specimen is a real one or a virtual one. +# +# +# +# +# +# +# +# +# Given name an alias. Better use identifierNAME and identifier_parent instead. +# A single NXentry should be used only for the characterization of a single specimen. +# +# +# +# +# +# Identifier of the sample from which the specimen was cut or the string +# n/a. The purpose of this field is to support functionalities for +# tracking sample provenance via a research data management system. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# when the specimen was prepared. +# +# Ideally, report the end of the preparation, i.e. the last known time +# the measured specimen surface was actively prepared. Ideally, this +# matches the last timestamp that is mentioned in the digital resource +# pointed to by identifier_parent. +# +# Knowing when the specimen was exposed to e.g. specific atmosphere is +# especially required for environmentally sensitive material such as +# hydrogen charged specimens or experiments including tracers with a +# short half time. Additional time stamps prior to preparation_date +# should better be placed in resources which describe but which do not +# pollute the description here with prose. Resolving these connected +# pieces of information is considered within the responsibility of the +# research data management system. +# +# +# +# +# List of comma-separated elements from the periodic table that are +# contained in the specimen. If the specimen substance has multiple +# components, all elements from each component must be included in +# `atom_types`. +# +# The purpose of the field is to offer research data management systems an +# opportunity to parse the relevant elements without having to interpret +# these from the resources pointed to by identifier_parent or walk through +# eventually deeply nested groups in data instances. +# +# +# +# +# Discouraged free-text field. +# +# +# +# +# Report if the specimen is polycrystalline, in which case it +# contains a grain or phase boundary, or if the specimen is a +# single crystal. +# +# +# +# +# Report if the specimen is amorphous. +# +# +# +# +# Ideally measured otherwise best elaborated guess of the initial radius of the +# specimen. +# +# +# +# +# Ideally measured otherwise best elaborated guess of the (initial) shank angle. +# This is a measure of the specimen taper. Define it in such a way that the base of the specimen +# is modelled as a conical frustrum so that the shank angle is the (shortest) angle between +# the specimen space z-axis and a vector on the lateral surface of the cone. +# +# +# +# +# +# +# Set to hold different coordinate systems conventions. +# Inspect the description of the :ref:`NXcoordinate_system_set` +# and :ref:`NXcoordinate_system` base classes how to define +# coordinate systems in NeXus. Specific details for application +# in atom probe microscopy follow. +# +# In this research field scientists usually distinguish several +# Euclidean coordinate systems (CS): +# +# * World space; +# a CS specifying a local coordinate system of the planet earth which +# identifies into which direction gravity is pointing such that +# the laboratory space CS can be rotated into this world CS. +# * The laboratory space; +# a CS specifying the room where the instrument is located in or +# a physical landmark on the instrument, e.g. the direction of the +# transfer rod where positive is the direction how the rod +# has to be pushed during loading a specimen into the instrument. +# In summary, this CS is defined by the chassis of the instrument. +# * The specimen space; +# a CS affixed to either the base or the initial apex of the specimen, +# whose z axis points towards the detector. +# * The detector space; +# a CS affixed to the detector plane whose xy plane is usually in the +# detector and whose z axis points towards the specimen. +# This is a distorted space with respect to the reconstructed ion +# positions. +# * The reconstruction space; +# a CS in which the reconstructed ion positions are defined. +# The orientation depends on the analysis software used. +# * Eventually further coordinate systems attached to the +# flight path of individual ions might be defined. +# +# In atom probe microscopy a frequently used choice for the detector +# space (CS) is discussed with the so-called detector space image +# (stack). This is a stack of two-dimensional histograms of detected ions +# within a predefined evaporation identifier interval. Typically, the set of +# ion evaporation sequence IDs is grouped into chunks. +# +# For each chunk a histogram of the ion hit positions on the detector +# is computed. This leaves the possibility for inconsistency between +# the so-called detector space and the e.g. specimen space. +# +# To avoid these ambiguities, instances of :ref:`NXtransformations` should +# be used. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Base class for collecting a session with a real atom probe or field-ion microscope. +# +# Workflows used during experiments or simulations of atom probe and related field-evaporation +# research should be documented in more detail and be better contextualized not only because of +# ongoing developments and the tighter becoming connection between atom probe and other +# methods for material characterization foremost electron microscopy see e.g.: +# +# * `T. Kelly et al. <https://doi.org/10.1017/S1431927620022205>`_ +# * `C. Fleischmann et al. <https://doi.org/10.1016/j.ultramic.2018.08.010>`_ +# * `W. Windl et al. <https://doi.org/10.1093/micmic/ozad067.294>`_ +# * `C. Freysoldt et al. <https://doi.org/10.1103/PhysRevLett.124.176801>`_ +# * `G. da Costa et al. <https://doi.org/10.1038/s41467-024-54169-2>`_ +# +# to mention but a few. +# +# To arrive at a design of base classes and an application definition that can be used +# for both real and simulated atom probe experiments it is worthwhile to recall concepts that are +# related to events and (molecular) ions: +# +# * Pulsing events which are used to trigger ion extraction events. +# * Physical events and corresponding signal triggered by an ion hitting the detector. +# Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. +# * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input +# and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are +# wortwhile to be considered further and eventually included in the reconstructed volume. +# * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually +# selected (molecular) ions based on which an instance of a reconstruction is created. +# * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values +# and charge states of the (molecular) ions to substantiate that some of these ions can be considered +# as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms +# and subsequent peak labeling. In the field of atom probe this these peak identification methods +# are known as ranging definitions. +# +# Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts +# are well distinguished. However, the algorithms used to transform correlations between pulses and physical events +# into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. +# +# Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme +# where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier +# i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. +# That is evaporation_identifier values take the role of an implicit time and course of the experiment given that +# ion extraction physically is a sequential process. +# +# There is a number of research groups who build own instruments and share different aspects of their technical +# specifications and approaches how they apply data processing e.g.: +# +# * `M. Monajem et al. <https://doi.org/10.1017/S1431927622003397>`_ +# * `P. Stender et al. <https://doi.org/10.1017/S1431927621013982>`_ +# * `I. Dimkou et al. <https://doi.org/10.1093/micmic/ozac051>`_ +# +# to name but a few. +# +# Despite some of these activities embrace practices of open-source development, they use essentially the same +# workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface +# software is used to explore and thus analyze reconstructed atom probe datasets. +# +# Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. +# Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which +# scientific conclusions about the characterized material volume are made. Also here a reconstruction is +# point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. +# +# By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all +# the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. +# Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. +# We argue that this divide can be bridged with realizing the above-mentioned context and the realization that +# similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. +# +# A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed +# datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment +# and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting +# a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as +# (spatial) filtering and reconstruction algorithms. +# +# Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation +# simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. +# Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. +# Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. +# Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require +# simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps +# in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. +# Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) +# than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path +# such as local electrodes or physical obstacles and electric fields (controlled or stray fields). +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Free text field for additional comments. +# +# +# +# +# +# A statement whether the measurement was successful or failed prematurely. +# +# +# +# +# CAnalysis.CResults.fQuality +# +# +# +# +# +# Group to hold instances of :ref:`NXevent_data_apm`. +# +# Which temporal granularity is adequate depends on the situation and research +# question. Using a model which enables a collection of events offers the most +# flexible way to cater for both atom probe experiments or simulation. +# +# To monitor the course of an ion extraction experiment (or simulation) +# it makes sense to track time explicitly via time stamps or implicitly +# via e.g. a clock inside the instrument, such as the clock of the pulser +# and respective pulsing event identifier. +# +# As set and measured quantities typically change over time and we do not +# yet know during the measurement which of the events have associated +# (molecular) ions that will end up in the reconstructed volume, we must not +# document quantities as a function of the evaporated_identifier but as a +# function of the (pulsing) event_identifier. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Simulation of ion extraction from matter via laser and/or voltage pulsing. +# +# +# +# +# +# A region-of-interest analyzed either during or after the session for which +# specific processed data of the measured or simulated data are available. +# +# +# +# +# SEM or TEM image of the initial specimen (ideally taken prior data acquisition). +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# For almost atom probe instruments (meta)data about raw data follow proprietary semantics. +# Therefore, this group can currently be used only to point to these digital artifacts +# in an effort to document all step of an analysis workflow. +# +# The physical quantities measured in an atom probe experiment are time-of-flight and +# tuples of arrival_time_pairs as a function of the event chain on the pulser. +# From these tuples hits are computed in a process called hit_finding. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# The number of wires in the detector. +# +# +# +# +# +# +# +# +# +# Alias tuple (begin, end) of each DLD wire of the detector. +# Order follows arrival_time_pairs. +# +# +# +# +# +# +# +# +# Raw readings from the analog-to-digital-converter +# timing circuits of the detector wires. +# +# +# +# +# +# +# +# +# +# +# Configuration of and results obtained from a hit finding algorithm. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Evaluated ion impact coordinates on the detector. +# Use the depends_on field to specify which reference +# frame the positions are defined. +# +# +# +# +# +# +# +# Defines in which reference frame the positions are defined. +# +# +# +# +# +# CRunHeader.fTotalEventGolden +# +# +# +# +# CRunHeader.fTotalEventIncomplete +# +# +# +# +# CRunHeader.fTotalEventMultiple +# +# +# +# +# CRunHeader.fTotalEventPartials +# +# +# +# +# CRunHeader.fTotalEventRecords +# +# +# +# +# Identifier used for each hit_quality type. +# Following the order of hit_quality_types. +# +# +# +# +# +# +# +# Hit quality identifier for each pulse. +# Identifier have to be within hit_quality_identifier. +# +# +# +# +# +# +# +# This processing yields for each ion with how many others it evaporated +# if these were collected on the same pulse. Extraction of multiple ions +# on one pulse on different or even the same pixel of the detector are possible. +# +# Multiplicity must not be confused with how many atoms of the same element +# a molecular ion contains. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Integer used to name the first pulse to know if there is an +# offset of the evaporation_identifier to zero. +# +# Identifiers can be defined either implicitly or explicitly. +# For implicit indexing identifiers are defined on the interval +# :math:`[identifier\_offset, identifier\_offset + c - 1]`. +# +# Therefore, implicit identifier are completely defined by the value of +# identifier_offset and cardinality. For example if identifier run from +# -2 to 3 the value for identifier_offset is -2. +# +# For explicit indexing the field identifier has to be used. +# Fortran-/Matlab- and C-/Python-style indexing have specific implicit +# identifier conventions where identifier_offset is 1 and 0 respectively. +# +# +# +# +# (Molecular) ion identifier which resolves the sequence in which +# the ions were evaporated but taking into account that a hit_finding +# and spatial_filtering was applied. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. +# +# The voltage-and-bowl correction is a data post-processing step to correct ion impact +# positions for flight path differences, detector biases, and nonlinearities. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Raw time-of-flight data without corrections. +# +# +# +# +# +# +# +# +# The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate +# +# +# +# +# Calibrated time-of-flight. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# For LEAP and IVAS/APSuite-based analyses root file which stores +# the settings whereby an RHIT/HITS file can be used to regenerate the +# reconstruction that is here referred to. +# +# The respective RHIT/HITS file should ideally be specified in the serialized +# group of the hit_finding section of this application definition. +# +# +# +# +# +# +# +# +# For LEAP and IVAS/APSuite-based analyses the resulting typically +# file with the reconstructed positions and (calibrated) mass-to-charge +# state ratio values. +# +# For other data collection/analysis software the data artifact which comes +# closest conceptually to AMETEK/Cameca's typical file formats. +# +# These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, +# which should be stored alongside this record in the research data +# management system. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# The respective ranging definitions file RNG/RRNG/ENV/HDF5. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# (Out-of-sync) background levels in ppm/ns +# reported by e.g. IVAS/APSuite for LEAP systems. +# +# +# +# +# MRP, mass-resolving power, `D. Larson et al. +# <https://doi.org/10.1007/978-1-4614-8721-0>`_ (p282, Eqs. D.7 and D.8). +# +# +# +# +# MRP, at which mrp_value was specified. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Category for the peak offering a qualitative statement of the location of the peak +# in light of limited mass-resolving power that is relevant for +# composition quantification. See `D. Larson et al. (p172) <https://doi.org/10.1007/978-1-4614-8721-0>`_ +# for examples of each category: +# +# * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` +# * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` +# * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states +# * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` +# * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` +# * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXem.yaml b/applications/nyaml/NXem.yaml similarity index 71% rename from contributed_definitions/nyaml/NXem.yaml rename to applications/nyaml/NXem.yaml index 3a76a7eb99..f9519d97c3 100644 --- a/contributed_definitions/nyaml/NXem.yaml +++ b/applications/nyaml/NXem.yaml @@ -3,42 +3,31 @@ doc: | Application definition for normalized representation of electron microscopy research. This application definition is a comprehensive example for a general description - with which to normalize specific pieces of information and data collected within - electron microscopy research. + with which to normalize specific (meta)data collected from the research field + of electron microscopy NXem is designed to be used for documenting experiments or computer simulations in which controlled electron beams are used for studying electron-beam matter interaction to explore - physical mechanisms and phenomena, or to characterize materials with an electron microscope. + physical mechanisms and phenomena or to characterize materials with an electron microscope. type: group NXem(NXobject): - # \@NX_class: - # \@file_time(NX_DATE_TIME): - # \@file_name(NX_CHAR): - # \@file_update_time(NX_DATE_TIME): - # \@NeXus_version(NX_CHAR): - # \@HDF5_Version(NX_CHAR): - # \@h5py_version(NX_CHAR): - # \@default(NX_CHAR): - # starting to reorganize the docstrings, as a list of blocks: + # docstrings should be organize as such a list of blocks: # -| req: first part, concept definition, human-readable but such that one could take as is to define an concept in OWL # -| opt: second part, comment, i.e. information that in an ideal world would be ideal if represented strongly semantic # but for practical purposes currently is interpretable only by human to provide them further contextualization - # -| recommended: xref part (ideally also as a list of triple (spec, term, url to uri) + # -| recommended: xref part ideally also as a list of triple (spec, term, url to uri) (NXentry): exists: ['min', '1', 'max', 'unbounded'] definition(NX_CHAR): - \@version(NX_CHAR): - exists: optional enumeration: [NXem] profiling(NXcs_profiling): exists: optional doc: | - The configuration of the I/O writer software (e.g. `pynxtools `_ or its plugins) - which was used to generate this NeXus file instance. + The configuration of the software that was used to generate this NeXus file. programID(NXprogram): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial doc: | A collection of all programs and libraries that are considered as relevant to understand with which software tools this NeXus file instance was @@ -46,17 +35,21 @@ NXem(NXobject): Examples include the name and version of the libraries used to write the instance. Ideally, the software which writes these NXprogram instances - also includes the version of the set of NeXus classes i.e. the specific - set of base classes, application definitions, and contributed definitions + also includes the version of the set of NeXus classes i.e. the specific set + of base classes, application definitions, and contributed definitions with which the here described concepts can be resolved. For the `pynxtools library `_ which is used by the `NOMAD `_ research data management system, it makes sense to store e.g. the GitHub repository commit and respective submodule references used. + + Instances of programID can also be used to document the modules and + libraries that are offered by the computational environment such as those + parsed from conda or python virtualenv environments. program(NX_CHAR): \@version(NX_CHAR): - identifier_experiment: + experiment_identifier(NX_CHAR): exists: recommended doc: | Ideally, a (globally) unique persistent identifier for referring to this experiment. @@ -69,8 +62,9 @@ NXem(NXobject): The identifier is usually issued by the facility, laboratory, or the principle investigator. The identifier enables to link experiments/simulations to e.g. proposals. experiment_alias(NX_CHAR): + exists: optional doc: | - Alias which scientists can easier identify this experiment by. + Alias (short name) which scientists can use to refer to this experiment. experiment_description(NX_CHAR): exists: optional doc: | @@ -87,20 +81,17 @@ NXem(NXobject): when the microscope session started. If the application demands that time codes in this section of the application definition should only be used for specifying when the experiment was performed - and the exact - duration is not relevant use this start_time field. + duration is not relevant - use this start_time field. Often though it is useful to specify a time interval via setting both a start_time and an end_time because this enables software tools and users to collect a more detailed bookkeeping of the experiment. - Users should be aware though that even with having both time instances - specified, it may not be possible to infer how long the experiment took or - for how long data were acquired. - - More detailed timing data over the course of the experiment have - to be collected to compute this. These computations can take - advantage of individual time stamps start_time and end_time - in :ref:`NXevent_data_em` instances. + Users should be aware though that even using only start_time and end_time + may not be sufficient to infer how long the experiment took or for how long + data were acquired. To bookkeep more fine-grained timestamps over the + course of the experiment is possible with start_time and end_time fields + of respective :ref:`NXevent_data_em` instances. end_time(NX_DATE_TIME): exists: recommended doc: | @@ -110,34 +101,37 @@ NXem(NXobject): See docstring of the start_time field to see how to use the start_time and end_time together. citeID(NXcite): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - serializedID(NXnote): nameType: partial + noteID(NXnote): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial doc: | - Possibility to store a collection of serialized resources associated with the - experiment. + Collection of serialized resources associated with the experiment. - An example how to use this set could be to document from which files, which have been - e.g. generated by software of technology partners, the information in an instance of - NXem was filled with during parsing or transcoding between different formats. + An example how to use this set is to document from which files in formatting + of technology partners, the (meta)data in an instance of NXem were filled with + during parsing to NeXus. type(NX_CHAR): - identifier(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - - # this is one of the few examples where groups may end up without fields because - # for reasons of not breaking GDPR compliance userID(NXuser): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial doc: | Information about persons who performed or were involved in the microscope session or simulation run. - This can be the principle investigator who performed this experiment or the student who performed simulations. + Examples could be to put here the principle investigator who performed this + experiment or students who performed simulations to name but a few. Adding multiple users if relevant is recommended. + + The protection of personal data by laws is in different stages of development + and strictness. For this reason no field of a userID instance is required. + identifierNAME(NX_CHAR): + exists: recommended + \@type(NX_CHAR): name(NX_CHAR): exists: optional doc: | @@ -167,12 +161,6 @@ NXem(NXobject): Examples are technician operating the microscope, student, postdoc, principle investigator, or guest. - identifier: - exists: optional - doc: | - Identifier offered by a service to report the user other than by using its name. - - Examples could be an ORCID or social media account of the user. sample(NXsample): doc: - | @@ -187,27 +175,30 @@ NXem(NXobject): doc: | Qualifier whether the sample is a real or a virtual one. enumeration: [experiment, simulation] - identifier: + identifier_sample(NX_CHAR): exists: recommended doc: | - Ideally, (globally) unique persistent identifier which distinguishes the sample from all others + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others and especially the predecessor/origin from where that sample was cut. The terms sample and specimen are here considered as exact synonyms. - This field must not be used for an alias! Instead, use name. + This field must not be used for an alias for the sample! Instead, use name. In cases where multiple specimens were loaded into the microscope, the identifier has to resolve the specific sample, whose results are stored by this :ref:`NXentry` instance because a single NXentry should be used for the characterization of a single specimen. - Details about the specimen preparation should be stored in resources referring to parent_identifier. - identifier_parent: + Details about the specimen preparation should be stored in resources referring to identifier_parent. + \@type(NX_CHAR): + identifier_parent(NX_CHAR): exists: recommended doc: | - Identifier of the sample from which the sample was cut or the string *None*. + Identifier of the sample from which the sample was cut or the string *None*, + i.e. the parent to this sample. The purpose of this field is to support functionalities for tracking sample provenance in a research data management system. + \@type(NX_CHAR): preparation_date(NX_DATE_TIME): doc: | ISO 8601 time code with local time zone offset to UTC information @@ -219,12 +210,13 @@ NXem(NXobject): identifier_parent. Knowing when the specimen was exposed to e.g. specific atmosphere is especially - required for environmentally sensitive material such as specimen charged with hydrogen - or experiments including tracers that have a short halflife. Additional time stamps - prior to preparation_date should better be placed in resources which describe but - which do not pollute the description here with prose. Resolving these connected - pieces of information is considered the responsibility of the - research data management system not of a NeXus file. + required for material that is sensitive to the environment such as specimens that were + charged with fast diffusing elements or short-lived radioactive tracers. + + Additional time stamps prior to preparation_date should better be placed in resources + which describe but do not pollute the description here with prose. Resolving these + connected metadata is considered as within the responsibility of the + research data management system and not the a NeXus file. name(NX_CHAR): exists: recommended doc: | @@ -250,22 +242,9 @@ NXem(NXobject): in many cases the specimen is typically thicker than what is illuminatable by the electron beam. - In this case the value should be set to the actual thickness of - the specimen viewed for an illumination situation where the nominal - surface normal of the specimen is parallel to the optical axis. - - # \@units: nm - # NEW ISSUE: error estimates of the thickness and origin, i.e. how the value was obtained would be useful - # NEW ISSUE: error model - # NEW ISSUE: the KIT/SCC SEM, TEM schemata further qualify samples whether they are conductive e/ibeam sensitive - # etc. The problem with this is that beam sensitivity is too vague but spatiotemporal electron dose integral dependent - # KIT/SCC distinguish further conductivity and magnetic properties. While the motivation is clear, making - # it thus simple is likely problematic when the data entered in such fields remaining qualitative. - # what are good or bad properties, it would make sense though to quantify these values - # this includes the description of eventual plasma cleaning steps, - # just knowing that a sample was plasma cleaned is insufficient, maybe it was not cleaned long enough - # if plasma cleaning is done outside the EM than its certainly history, if it happens inside the EM - # are the ibeam description capabilities not sufficient enough? + In this case the value should be set to the actual thickness of the specimen + viewed for an illumination situation where the nominal surface normal of the + specimen is parallel to the optical axis. density(NX_NUMBER): exists: optional unit: NX_ANY @@ -274,16 +253,13 @@ NXem(NXobject): For multi-layered specimens this field should only be used to describe the density of the excited volume. For scanning electron microscopy - the usage of this field is discouraged and instead an instance of an - :ref:`NXinteraction_vol_em` within individual :ref:`NXevent_data_em` + the usage of this field is discouraged and instead an instance of a region-of-interest within connection to individual :ref:`NXevent_data_em` instances can provide a cleaner description of the relevant details why one may wish to store the density of the specimen. description(NX_CHAR): exists: optional doc: | - Discouraged free-text field to provide further detail although adding - identifier_parent and having a working research data management system - should provide this contextualization. + Discouraged free-text field to provide further detail. coordinate_system_set(NXcoordinate_system_set): exists: ['min', '1', 'max', '1'] doc: | @@ -315,25 +291,25 @@ NXem(NXobject): of the reference frame. If any of these assumptions is not met, the user is required to explicitly state this. - enumeration: [undefined, front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] + enumeration: [front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] x_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing x-axis base vector of the processing_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] y_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing y-axis base vector of the processing_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] z_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing z-axis base vector of the processing_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] sample_reference_frame(NXcoordinate_system): exists: recommended depends_on(NX_CHAR): @@ -356,28 +332,28 @@ NXem(NXobject): of the reference frame. If any of these assumptions is not met, the user is required to explicitly state this. - enumeration: [undefined, front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] + enumeration: [front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] x_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing x-axis base vector of the sample_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] y_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing y-axis base vector of the sample_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] z_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing z-axis base vector of the sample_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] detector_reference_frameID(NXcoordinate_system): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial depends_on(NX_CHAR): exists: optional doc: | @@ -397,63 +373,60 @@ NXem(NXobject): along respective base vector direction of the reference frame. If any of these assumptions is not met, the user is required to explicitly state this. - enumeration: [undefined, front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] + enumeration: [front_top_left, front_top_right, front_bottom_right, front_bottom_left, back_top_left, back_top_right, back_bottom_right, back_bottom_left] x_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing x-axis base vector of the detector_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] y_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing y-axis base vector of the detector_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] z_direction(NX_CHAR): exists: recommended doc: | Direction of the positively pointing z-axis base vector of the detector_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] - - # the description can be so lean because we do not need to overwrite here s.th. as everything is defined already - # we just say we compose using the base class NXcoordinate_system - measurement(NXem_msr): + enumeration: [north, east, south, west, in, out] + measurement(NXobject): exists: optional - em_lab(NXinstrument): - instrument_name(NX_CHAR): + + # the choice if a concept filling content in NXfabrication is recommended or optional + # was made such that all for all those components which are typically add-ons in a + # microscope it is more likely that individuals will have bought different third-party tools + # and therefore, for these typically more optional add-ons NXfabrication is recommended + # for others commercial microscopes often come with model-specific predefined parts + # hence using optional is sufficient + instrument(NXinstrument_em): + name(NX_CHAR): exists: recommended location(NX_CHAR): exists: recommended fabrication(NXfabrication): - exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended control_programID(NXprogram): + exists: recommended nameType: partial - exists: ['min', '1', 'max', 'unbounded'] doc: | Details about the control program used for operating the microscope. program(NX_CHAR): \@version(NX_CHAR): ebeam_column(NXebeam_column): - chamber(NXchamber): - exists: optional fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended electron_source(NXsource): - doc: | - xref: - spec: EMglossary - term: Source - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 + exists: recommended emitter_type(NX_CHAR): probe(NX_CHAR): @@ -462,230 +435,227 @@ NXem(NXobject): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended - - # fabrication is an example which shows when one needs to specify in the appdef if some of the - # inherited objects from NXebeam_column have to be specified that is when one wishes to document - # e.g. a combination of cardinality constraints or concept symbol constraints - # i.e. use NXfabrication from NXsource but demand it to be labelled with the symbol fabrication - # likewise if you provide fabrication details you need to provide vendor and model but not necessarily identifier lensID(NXlens_em): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended apertureID(NXaperture): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended monochromatorID(NXmonochromator): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - doc: | - Device for improving energy resolution or reducing chromatic aberration. - - Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector - like `_ - - # user perspective + nameType: partial type(NX_CHAR): - doc: | - Qualitative type of the component. - enumeration: [wien, alfa, omega, castaing_henry, gatan_imaging, sector_analyzer] - - # control level perspective - # technical design perspective fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended corrector_cs(NXcorrector_cs): exists: ['min', '0', 'max', '1'] fabrication(NXfabrication): - exists: optional + exists: recommended vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended corrector_ax(NXcomponent): exists: ['min', '0', 'max', '1'] - doc: | - Device reshaping an ellipse-shaped electron beam to a circular one. - - * `L. Reimer 1998, Springer, 1998 `_ - * `M. Tanaka et al., Electron Microscopy Glossary, 2024 `_ - - Stigmator is an exact synonym. fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended biprism(NXcomponent): - exists: optional - doc: | - Electron biprism as it is used e.g. for electron holography. + exists: ['min', '0', 'max', '1'] fabrication(NXfabrication): - exists: optional + exists: recommended vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended - - # contributed definition NXwaveplate is a closely related concept but may fit even better but waveplate - # has been defined from the perspective of classical optics - # same challenge like with NXlens and NXlens_em, an electrostatic lens is not the same concept - # like it is an glass lens (i.e. optical) NXlens - # but both concepts have in common that they can be assumed to be specialization of a super class - # lenses i.e. devices which can affect the pathes of beams phaseplateID(NXcomponent): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - doc: | - Device that causes a change in the phase of an electron wave. - - * `M. Malac et al. `_ - * `R. R. Schröder et al. `_ + nameType: partial type(NX_CHAR): - doc: | - Qualitative type - enumeration: [thin_film, electrostatic] fabrication(NXfabrication): - exists: optional + exists: recommended vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended sensorID(NXsensor): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial actuatorID(NXactuator): + exists: ['min', '0', 'max', 'unbounded'] nameType: partial + beamID(NXbeam): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + deflectorID(NXdeflector): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial ibeam_column(NXibeam_column): exists: ['min', '0', 'max', '1'] - # there are tri-beam SEMs but they typically use a laser for which we should have an own base class - chamber(NXchamber): - exists: optional + # there are tri-beam SEMs, but with a laser for which one should add NXsource + # fabrication groups often were not made recommended or required because in practice + # often scientific groups buy a commercial microscope for which the type and serial number + # of the microscope (as in the top-level fabrication of instrument) suffices to recover + # which components that microscope was built from fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended ion_source(NXsource): - probe(NXion): + emitter_type(NX_CHAR): + probe(NXatom): + fabrication(NXfabrication): + exists: optional + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended lensID(NXlens_em): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended apertureID(NXaperture): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended monochromatorID(NXmonochromator): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - doc: | - Device for improving energy resolution or reducing chromatic aberration. - - Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector - like `_ - type(NX_CHAR): - doc: | - Qualitative type of the component. - enumeration: [wien, alfa, omega, castaing_henry, gatan_imaging, sector_analyzer] + nameType: partial fabrication(NXfabrication): exists: optional vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended # device for correcting axial astigmatism of ion beam? sensorID(NXsensor): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial actuatorID(NXactuator): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + beamID(NXbeam): + exists: ['min', '0', 'max', 'unbounded'] nameType: partial + deflectorID(NXdeflector): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial detectorID(NXdetector): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): fabrication(NXfabrication): + exists: recommended vendor(NX_CHAR): model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended scan_controller(NXscanbox_em): exists: optional fabrication(NXfabrication): - exists: optional + exists: recommended vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended - (NXsensor): - exists: ['min', '0', 'max', 'unbounded'] - (NXactuator): - exists: ['min', '0', 'max', 'unbounded'] - (NXstage_lab): + stage(NXmanipulator): exists: ['min', '0', 'max', 'unbounded'] + design(NX_CHAR): + exists: recommended + + # add enumeration values from old NXstage_lab fabrication(NXfabrication): - exists: optional + exists: recommended vendor(NX_CHAR): model(NX_CHAR): - identifier: + serial_number(NX_CHAR): exists: recommended - (NXchamber): + nanoprobe(NXmanipulator): + exists: optional + fabrication(NXfabrication): + exists: recommended + vendor(NX_CHAR): + model(NX_CHAR): + serial_number(NX_CHAR): + exists: recommended + pumpID(NXpump): + exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + design(NX_CHAR): + sensorID(NXsensor): exists: ['min', '0', 'max', 'unbounded'] - (NXpump): + nameType: partial + actuatorID(NXactuator): exists: ['min', '0', 'max', 'unbounded'] - event_data_em_set(NXevent_data_em_set): + nameType: partial + events(NXobject): exists: ['min', '0', 'max', '1'] # an instance must not have an NXevent_data_em_set but if it has one it must not be more than 1 ! - (NXevent_data_em): + doc: | + This group should be used to store all event-related (meta)data, + which are typically measured datasets like images and spectra. + To avoid that static instrument-related metadata need to be stored + repetitively the NXem application definitions splits the storage of the + dynamic (meta)data that typically change for each image and spectrum + from the static one. + eventID(NXevent_data_em): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial start_time(NX_DATE_TIME): exists: recommended end_time(NX_DATE_TIME): exists: recommended - (NXimage_set): + imageID(NXimage): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial (NXprocess): source(NXnote): exists: recommended type(NX_CHAR): - identifier(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - absolute_path(NX_CHAR): - exists: recommended - identifier_detector: - exists: recommended + identifier_detector(NX_CHAR): image_1d(NXdata): exists: optional \@signal(NX_CHAR): @@ -693,6 +663,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended real(NX_NUMBER): \@long_name(NX_CHAR): imag(NX_NUMBER): @@ -713,6 +684,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended real(NX_NUMBER): \@long_name(NX_CHAR): imag(NX_NUMBER): @@ -735,6 +707,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended real(NX_NUMBER): \@long_name(NX_CHAR): imag(NX_NUMBER): @@ -759,6 +732,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended real(NX_NUMBER): \@long_name(NX_CHAR): imag(NX_NUMBER): @@ -784,6 +758,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended real(NX_NUMBER): \@long_name(NX_CHAR): imag(NX_NUMBER): @@ -811,6 +786,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended real(NX_NUMBER): \@long_name(NX_CHAR): imag(NX_NUMBER): @@ -833,17 +809,16 @@ NXem(NXobject): \@long_name(NX_CHAR): axis_i(NX_NUMBER): \@long_name(NX_CHAR): - (NXspectrum_set): + spectrumID(NXspectrum): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial (NXprocess): source(NXnote): exists: recommended type(NX_CHAR): - identifier(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - absolute_path(NX_CHAR): - exists: recommended identifier_detector(NX_CHAR): spectrum_0d(NXdata): exists: optional @@ -852,6 +827,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): axis_energy(NX_NUMBER): @@ -863,6 +839,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): axis_i(NX_NUMBER): @@ -876,6 +853,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): axis_j(NX_NUMBER): @@ -891,6 +869,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): axis_k(NX_NUMBER): @@ -908,6 +887,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): identifier_spectrum(NX_INT): @@ -921,6 +901,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): identifier_spectrum(NX_INT): @@ -936,6 +917,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): identifier_spectrum(NX_INT): @@ -953,6 +935,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_INT): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): \@long_name(NX_CHAR): identifier_spectrum(NX_INT): @@ -965,118 +948,50 @@ NXem(NXobject): \@long_name(NX_CHAR): axis_energy(NX_NUMBER): \@long_name(NX_CHAR): - em_lab(NXinstrument): + instrument(NXinstrument_em): exists: recommended ebeam_column(NXebeam_column): operation_mode(NX_CHAR): electron_source(NXsource): - doc: | - xref: - spec: EMglossary - term: Source - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 + exists: optional voltage(NX_NUMBER): - doc: - - | - The potential difference between anode and cathode. - - | - xref: - spec: EMglossary - term: Acceleration Voltage - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 extraction_voltage(NX_NUMBER): exists: optional - unit: NX_VOLTAGE - doc: - - | - Voltage which is utilised to create an electric field that draws particles from - the source. - - | - xref: - spec: EMglossary - term: Extraction Voltage - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 emission_current(NX_NUMBER): exists: optional - unit: NX_CURRENT - doc: - - | - Electrical current which is released from the source. - - | - xref: - spec: EMglossary - term: Emission Current - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 filament_current(NX_NUMBER): exists: optional - unit: NX_CURRENT - doc: - - | - Electrical current which flows through the source. - - | - xref: - spec: EMglossary - term: Filament Current - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 lensID(NXlens_em): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - value(NX_NUMBER): - apertureID(NXaperture): nameType: partial + power_setting(NX_CHAR_OR_NUMBER): + apertureID(NXaperture): exists: ['min', '0', 'max', 'unbounded'] - value(NX_NUMBER): - unit: NX_ANY + nameType: partial + setting(NX_CHAR_OR_NUMBER): doc: | - Relevant value from the control software. - - This is not always just the diameter of the aperture (not even in the case) - of a circular aperture. Usually, it is a value that is set in the control - software whereby a specific configuration of an aperture is selected by the - software. - - The control software of commercial microscope typically offers the user - access at a high abstraction level because of which many details about - the actual settings of the electrical components are typically unknown. - - However, if more details are known or should be documented one should - use the description field for this. + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. monochromatorID(NXmonochromator): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - doc: | - Device to improve energy resolution or chromatic aberration. - - Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector - like `_ - - # user perspective + nameType: partial applied(NX_BOOLEAN): - doc: | - Was the corrector used? - - # control level perspective - # technical components of the corrector dispersion(NX_NUMBER): exists: recommended - unit: NX_ANY - doc: | - Energy dispersion in e.g. µm/eV. voltage(NX_NUMBER): exists: recommended - unit: NX_VOLTAGE - doc: | - Corresponding voltage for that energy dispersion. corrector_cs(NXcorrector_cs): exists: ['min', '0', 'max', '1'] applied(NX_BOOLEAN): exists: recommended tableauID(NXprocess): - nameType: partial exists: ['min', '1', 'max', 'unbounded'] + nameType: partial # model(NX_CHAR): - # exists: optional + # ceos c_1(NXaberration): exists: optional @@ -1202,131 +1117,144 @@ NXem(NXobject): # basically optional use of NXaberration therein at least some value required corrector_ax(NXcomponent): exists: ['min', '0', 'max', '1'] - doc: | - Device reshaping an ellipse-shaped electron beam to a circular one. - - * `L. Reimer 1998, Springer, 1998 `_ - * `M. Tanaka et al., Electron Microscopy Glossary, 2024 `_ - - Stigmator is an exact synonym. applied(NX_BOOLEAN): - doc: | - Was the corrector used? value_x(NX_NUMBER): - unit: NX_ANY - doc: | - Descriptor for the correction strength along the first direction when exact technical details - are unknown or not directly controllable as the control software of the microscope does not - enable or was not configured to display these values (for end users). value_y(NX_NUMBER): - unit: NX_ANY - doc: | - Descriptor for the correction strength along the second direction when exact technical details - are unknown or not directly controllable as the control software of the microscope does not - enable or was not configured to display these values (for end users). - biprism(NXcomponent): - exists: ['min', '0', 'max', '1'] - phaseplateID(NXcomponent): - nameType: partial - exists: ['min', '0', 'max', 'unbounded'] + + # biprism(NXcomponent): + # phaseplateID(NXcomponent): sensorID(NXsensor): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial actuatorID(NXactuator): + exists: ['min', '0', 'max', 'unbounded'] nameType: partial + beamID(NXbeam): exists: ['min', '0', 'max', 'unbounded'] - (NXbeam): + nameType: partial + deflectorID(NXdeflector): exists: ['min', '0', 'max', 'unbounded'] - doc: | - xref: - spec: EMglossary - term: Electron Beam - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 + nameType: partial ibeam_column(NXibeam_column): exists: ['min', '0', 'max', '1'] ion_source(NXsource): - probe(NXion): + probe(NXatom): voltage(NX_NUMBER): + flux(NX_NUMBER): lensID(NXlens_em): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] - value(NX_NUMBER): - apertureID(NXaperture): nameType: partial + power_setting(NX_CHAR_OR_NUMBER): + apertureID(NXaperture): exists: ['min', '0', 'max', 'unbounded'] - value(NX_NUMBER): - unit: NX_ANY + nameType: partial + setting(NX_CHAR_OR_NUMBER): doc: | - Relevant value from the control software. - - This is not always just the diameter of the aperture (not even in the case) - of a circular aperture. Usually, it is a value that is set in the control - software whereby a specific configuration of an aperture is selected by the - software. - - The control software of commercial microscope typically offers the user - access at a high abstraction level because of which many details about - the actual settings of the electrical components are typically unknown. - - However, if more details are known or should be documented one should - use the description field for this. + Descriptor for the aperture setting when the exact technical details + are unknown or not directly controllable as the control software of + the microscope does not enable or was not configured to display these + values for users. monochromatorID(NXmonochromator): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial applied(NX_BOOLEAN): sensorID(NXsensor): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial actuatorID(NXactuator): + exists: ['min', '0', 'max', 'unbounded'] nameType: partial + beamID(NXbeam): exists: ['min', '0', 'max', 'unbounded'] - (NXbeam): + nameType: partial + deflectorID(NXdeflector): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial detectorID(NXdetector): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] + nameType: partial mode(NX_CHAR): + doc: | + Operation mode of the detector as displayed by the control software. scan_controller(NXscanbox_em): exists: optional scan_schema(NX_CHAR): dwell_time(NX_NUMBER): - (NXsensor): + sensorID(NXsensor): exists: ['min', '0', 'max', 'unbounded'] - (NXactuator): + nameType: partial + actuatorID(NXactuator): exists: ['min', '0', 'max', 'unbounded'] - heater(NXactuator): - exists: optional - current(NX_NUMBER): - unit: NX_CURRENT - doc: | - Nominal current of the heater. - voltage(NX_NUMBER): - unit: NX_VOLTAGE - doc: | - Nominal voltage of the heater. - power(NX_NUMBER): - unit: NX_POWER - doc: | - Nominal power of the heater. - (NXstage_lab): + nameType: partial + stage(NXobject): exists: ['min', '0', 'max', 'unbounded'] design(NX_CHAR): exists: recommended - (NXchamber): - exists: ['min', '0', 'max', 'unbounded'] - (NXpump): - exists: ['min', '0', 'max', 'unbounded'] - simulation(NXem_sim): - exists: optional + tilt1(NX_NUMBER): + tilt2(NX_NUMBER): + rotation(NX_NUMBER): + position(NX_NUMBER): + sample_heater(NXactuator): + exists: optional + physical_quantity(NX_CHAR): + heater_current(NX_NUMBER): + exists: optional + unit: NX_CURRENT + doc: | + Nominal current of the heater. + heater_voltage(NX_NUMBER): + exists: optional + unit: NX_VOLTAGE + doc: | + Nominal voltage of the heater. + heater_power(NX_NUMBER): + unit: NX_POWER # remains to be discussed based on examples + simulation(NXobject): + exists: optional + interaction_volumeID(NXobject): + exists: optional + nameType: partial + doc: | + Description of the volume of interaction between of particle-matter interaction. + + Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam + interaction simulations can be used to qualify and (or) quantify the shape of + the interaction volume. Results of such simulations can be summary statistics + or single-particle-resolved sets of trajectories. + + Explicit or implicit descriptions of the geometry of this + interaction volume are possible: + + * An implicit description is via a set of electron/specimen interactions + represented ideally as trajectory data from the computer simulation. + * An explicit description is via iso-contour surface using either + a simulation grid or a triangulated surface mesh of the approximated + iso-contour surface evaluated at specific threshold values. + Iso-contours could be computed from electron or particle flux through + an imaginary control surface (the iso-surface) or energy-levels + (e.g. the case of X-rays). Details depend on the model. + * Another explicit description is via theoretical models which may + be relevant e.g. for X-ray spectroscopy + + Further details on how the interaction volume can be quantified + is available in the literature for example: + + * `S. Richter et al. `_ + * `J. Bünger et al. `_ + * `J. F. Ziegler et al. `_ + (NXdata): + exists: recommended + (NXprocess): + exists: recommended # relevant research result post-processed for specific community methods - # but normalized in its representation ready to be consumed for a - # research data management system - roiID(NXroi): - nameType: partial + # but normalized in its representation ready to be consumed for + # research data management systems + roiID(NXobject): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial doc: - | A region-of-interest analyzed either during or after the session @@ -1341,21 +1269,17 @@ NXem(NXobject): # an RDM can be sure to find specific pieces of information in a # specific way but then every user of this application definition # is required to provide such information in this way! - imaging(NXem_img): + img(NXem_img): exists: optional - imaging_mode(NX_CHAR): - (NXimage_set): - exists: ['min', '0', 'max', 'unbounded'] - half_angle_interval(NX_NUMBER): - exists: optional + imageID(NXimage): + exists: ['min', '1', 'max', 'unbounded'] + imaging_mode(NX_CHAR): + # connection point to store serialized representations of microstructures # microstructureID(NXmicrostructure): - # nameType: partial # exists: optional ebsd(NXem_ebsd): exists: optional - - # remains to be discussed based on examples gnomonic_reference_frame(NXcoordinate_system): exists: optional alias(NX_CHAR): @@ -1377,7 +1301,7 @@ NXem(NXobject): depends_on(NX_CHAR): source(NXnote): type(NX_CHAR): - identifier(NX_CHAR): + path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): simulation(NXprocess): @@ -1385,9 +1309,11 @@ NXem(NXobject): depends_on(NX_CHAR): source(NXnote): type(NX_CHAR): - identifier(NX_CHAR): + path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): + calibration(NXprocess): + exists: recommended indexing(NXprocess): exists: optional number_of_scan_points(NX_UINT): @@ -1396,28 +1322,29 @@ NXem(NXobject): source(NXnote): exists: optional type(NX_CHAR): - identifier(NX_CHAR): + path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - phaseID(NXcrystal_structure): - nameType: partial + identifier_phase(NX_INT): + phaseID(NXphase): exists: ['min', '0', 'max', 'unbounded'] + nameType: partial + name(NX_CHAR): + exists: recommended number_of_scan_points(NX_UINT): - a_b_c(NX_NUMBER): - alpha_beta_gamma(NX_NUMBER): - space_group(NX_CHAR): - identifier_phase(NX_INT): - phase_name(NX_CHAR): + unit_cell(NXunit_cell): + a_b_c(NX_NUMBER): + alpha_beta_gamma(NX_NUMBER): + space_group(NX_CHAR): + # foreseen place for phase-specific texture and microstructure representations and statistics # ipfID(NXmicrostructure_ipf): - # nameType: partial # exists: recommended # projection_direction(NX_NUMBER): # map(NXdata): # \@signal(NX_CHAR): # \@axes(NX_CHAR): # \@AXISNAME_indices(NX_INT): - # nameType: partial # title(NX_CHAR): # data(NX_NUMBER): # \@long_name(NX_CHAR): @@ -1433,7 +1360,6 @@ NXem(NXobject): # \@signal(NX_CHAR): # \@axes(NX_CHAR): # \@AXISNAME_indices(NX_INT): - # nameType: partial # title(NX_CHAR): # data(NX_NUMBER): # \@long_name(NX_CHAR): @@ -1448,8 +1374,12 @@ NXem(NXobject): \@AXISNAME_indices(NX_CHAR): nameType: partial title(NX_CHAR): + exists: recommended descriptor(NX_CHAR): data(NX_NUMBER): + axis_z(NX_NUMBER): + exists: optional + \@long_name(NX_CHAR): axis_y(NX_NUMBER): \@long_name(NX_CHAR): axis_x(NX_NUMBER): @@ -1466,11 +1396,12 @@ NXem(NXobject): \@AXISNAME_indices(NX_CHAR): nameType: partial title(NX_CHAR): + exists: recommended intensity(NX_NUMBER): axis_energy(NX_CHAR): \@long_name(NX_CHAR): atom_types(NX_CHAR): - (NXimage_set): + (NXimage): exists: ['min', '0', 'max', '118'] iupac_line_candidates(NX_CHAR): exists: recommended @@ -1481,7 +1412,7 @@ NXem(NXobject): \@AXISNAME_indices(NX_CHAR): nameType: partial title(NX_CHAR): - exists: optional + exists: recommended intensity(NX_NUMBER): \@units(NX_CHAR): exists: recommended @@ -1493,22 +1424,18 @@ NXem(NXobject): \@units(NX_CHAR): eels(NXem_eels): exists: optional - correlation(NXem_correlation): - exists: optional - - # remains to be discussed based on examples # see an example how to map e.g. the following flat schema https://www.zenodo.org/record/6513745 to NXem # in https://github.com/FAIRmat-NFDI/nexus_definitions/commit/0b928c4352bc5636f673b5fb25ce990f1af8a099 # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 935d30bbf847d5225eb415457d6393a37e753d89b5a1410521f2924e3a9aeab2 +# e22fe23e54131af18ebd877bd258a0d46ba4f50a350b9ea07322cf8ed2531cd0 # # # +# -| recommended: xref part ideally also as a list of triple (spec, term, url to uri)--> # # -# # # # # # # -# The configuration of the I/O writer software (e.g. `pynxtools <https://github.com/FAIRmat-NFDI/pynxtools>`_ or its plugins) -# which was used to generate this NeXus file instance. +# The configuration of the software that was used to generate this NeXus file. # -# +# # # A collection of all programs and libraries that are considered as relevant # to understand with which software tools this NeXus file instance was @@ -1571,21 +1488,25 @@ NXem(NXobject): # # Examples include the name and version of the libraries used to write the # instance. Ideally, the software which writes these NXprogram instances -# also includes the version of the set of NeXus classes i.e. the specific -# set of base classes, application definitions, and contributed definitions +# also includes the version of the set of NeXus classes i.e. the specific set +# of base classes, application definitions, and contributed definitions # with which the here described concepts can be resolved. # # For the `pynxtools library <https://github.com/FAIRmat-NFDI/pynxtools>`_ # which is used by the `NOMAD <https://nomad-lab.eu/nomad-lab>`_ # research data management system, it makes sense to store e.g. the GitHub # repository commit and respective submodule references used. +# +# Instances of programID can also be used to document the modules and +# libraries that are offered by the computational environment such as those +# parsed from conda or python virtualenv environments. # # # # # # -# +# # # Ideally, a (globally) unique persistent identifier for referring to this experiment. # @@ -1598,9 +1519,9 @@ NXem(NXobject): # The identifier enables to link experiments/simulations to e.g. proposals. # # -# +# # -# Alias which scientists can easier identify this experiment by. +# Alias (short name) which scientists can use to refer to this experiment. # # # @@ -1620,20 +1541,17 @@ NXem(NXobject): # when the microscope session started. If the application demands that time # codes in this section of the application definition should only be used # for specifying when the experiment was performed - and the exact -# duration is not relevant use this start_time field. +# duration is not relevant - use this start_time field. # # Often though it is useful to specify a time interval via setting both a start_time # and an end_time because this enables software tools and users to collect a # more detailed bookkeeping of the experiment. # -# Users should be aware though that even with having both time instances -# specified, it may not be possible to infer how long the experiment took or -# for how long data were acquired. -# -# More detailed timing data over the course of the experiment have -# to be collected to compute this. These computations can take -# advantage of individual time stamps start_time and end_time -# in :ref:`NXevent_data_em` instances. +# Users should be aware though that even using only start_time and end_time +# may not be sufficient to infer how long the experiment took or for how long +# data were acquired. To bookkeep more fine-grained timestamps over the +# course of the experiment is possible with start_time and end_time fields +# of respective :ref:`NXevent_data_em` instances. # # # @@ -1645,31 +1563,35 @@ NXem(NXobject): # start_time and end_time together. # # -# -# +# +# # -# Possibility to store a collection of serialized resources associated with the -# experiment. +# Collection of serialized resources associated with the experiment. # -# An example how to use this set could be to document from which files, which have been -# e.g. generated by software of technology partners, the information in an instance of -# NXem was filled with during parsing or transcoding between different formats. +# An example how to use this set is to document from which files in formatting +# of technology partners, the (meta)data in an instance of NXem were filled with +# during parsing to NeXus. # # -# +# # # # -# -# +# # # Information about persons who performed or were involved in the microscope # session or simulation run. # -# This can be the principle investigator who performed this experiment or the student who performed simulations. +# Examples could be to put here the principle investigator who performed this +# experiment or students who performed simulations to name but a few. # Adding multiple users if relevant is recommended. +# +# The protection of personal data by laws is in different stages of development +# and strictness. For this reason no field of a userID instance is required. # +# +# +# # # # Given (first) name and surname. @@ -1705,13 +1627,6 @@ NXem(NXobject): # principle investigator, or guest. # # -# -# -# Identifier offered by a service to report the user other than by using its name. -# -# Examples could be an ORCID or social media account of the user. -# -# # # # @@ -1731,28 +1646,31 @@ NXem(NXobject): # # # -# +# # -# Ideally, (globally) unique persistent identifier which distinguishes the sample from all others +# Ideally, (globally) unique persistent identifier which distinguishes this sample from all others # and especially the predecessor/origin from where that sample was cut. The terms sample # and specimen are here considered as exact synonyms. # -# This field must not be used for an alias! Instead, use name. +# This field must not be used for an alias for the sample! Instead, use name. # # In cases where multiple specimens were loaded into the microscope, the identifier has to resolve # the specific sample, whose results are stored by this :ref:`NXentry` instance because a single # NXentry should be used for the characterization of a single specimen. # -# Details about the specimen preparation should be stored in resources referring to parent_identifier. +# Details about the specimen preparation should be stored in resources referring to identifier_parent. # +# # -# +# # -# Identifier of the sample from which the sample was cut or the string *None*. +# Identifier of the sample from which the sample was cut or the string *None*, +# i.e. the parent to this sample. # # The purpose of this field is to support functionalities for tracking # sample provenance in a research data management system. # +# # # # @@ -1765,12 +1683,13 @@ NXem(NXobject): # identifier_parent. # # Knowing when the specimen was exposed to e.g. specific atmosphere is especially -# required for environmentally sensitive material such as specimen charged with hydrogen -# or experiments including tracers that have a short halflife. Additional time stamps -# prior to preparation_date should better be placed in resources which describe but -# which do not pollute the description here with prose. Resolving these connected -# pieces of information is considered the responsibility of the -# research data management system not of a NeXus file. +# required for material that is sensitive to the environment such as specimens that were +# charged with fast diffusing elements or short-lived radioactive tracers. +# +# Additional time stamps prior to preparation_date should better be placed in resources +# which describe but do not pollute the description here with prose. Resolving these +# connected metadata is considered as within the responsibility of the +# research data management system and not the a NeXus file. # # # @@ -1799,40 +1718,25 @@ NXem(NXobject): # in many cases the specimen is typically thicker than what is # illuminatable by the electron beam. # -# In this case the value should be set to the actual thickness of -# the specimen viewed for an illumination situation where the nominal -# surface normal of the specimen is parallel to the optical axis. +# In this case the value should be set to the actual thickness of the specimen +# viewed for an illumination situation where the nominal surface normal of the +# specimen is parallel to the optical axis. # # -# # # # (Measured) density of the specimen. # # For multi-layered specimens this field should only be used to describe # the density of the excited volume. For scanning electron microscopy -# the usage of this field is discouraged and instead an instance of an -# :ref:`NXinteraction_vol_em` within individual :ref:`NXevent_data_em` +# the usage of this field is discouraged and instead an instance of a region-of-interest within connection to individual :ref:`NXevent_data_em` # instances can provide a cleaner description of the relevant details # why one may wish to store the density of the specimen. # # # # -# Discouraged free-text field to provide further detail although adding -# identifier_parent and having a working research data management system -# should provide this contextualization. +# Discouraged free-text field to provide further detail. # # # @@ -1865,7 +1769,6 @@ NXem(NXobject): # If any of these assumptions is not met, the user is required to explicitly state this. # # -# # # # @@ -1882,7 +1785,6 @@ NXem(NXobject): # processing_reference_frame. # # -# # # # @@ -1897,7 +1799,6 @@ NXem(NXobject): # processing_reference_frame. # # -# # # # @@ -1912,7 +1813,6 @@ NXem(NXobject): # processing_reference_frame. # # -# # # # @@ -1944,7 +1844,6 @@ NXem(NXobject): # If any of these assumptions is not met, the user is required to explicitly state this. # # -# # # # @@ -1961,7 +1860,6 @@ NXem(NXobject): # sample_reference_frame. # # -# # # # @@ -1976,7 +1874,6 @@ NXem(NXobject): # sample_reference_frame. # # -# # # # @@ -1991,7 +1888,6 @@ NXem(NXobject): # sample_reference_frame. # # -# # # # @@ -2001,7 +1897,7 @@ NXem(NXobject): # # # -# +# # # # Reference to the specifically named :ref:`NXdetector` instance for @@ -2022,7 +1918,6 @@ NXem(NXobject): # If any of these assumptions is not met, the user is required to explicitly state this. # # -# # # # @@ -2039,7 +1934,6 @@ NXem(NXobject): # detector_reference_frame. # # -# # # # @@ -2054,7 +1948,6 @@ NXem(NXobject): # detector_reference_frame. # # -# # # # @@ -2069,7 +1962,6 @@ NXem(NXobject): # detector_reference_frame. # # -# # # # @@ -2080,18 +1972,22 @@ NXem(NXobject): # # # -# -# -# -# +# +# +# +# # -# +# # # -# +# # -# +# # # Details about the control program used for operating the microscope. # @@ -2100,239 +1996,193 @@ NXem(NXobject): # # # -# # # # -# +# # -# -# -# This concept is related to term `Source`_ of the EMglossary standard. -# -# .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 -# +# # # # # # # -# +# # # -# -# +# +# # # # -# +# # # -# +# +# # # # -# +# # # -# -# -# Device for improving energy resolution or reducing chromatic aberration. -# -# Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector -# like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ -# -# -# -# -# Qualitative type of the component. -# -# -# -# -# -# -# -# -# -# -# +# +# # # # -# +# # # # -# +# # # -# +# # # # -# -# Device reshaping an ellipse-shaped electron beam to a circular one. -# -# * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ -# * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ -# -# Stigmator is an exact synonym. -# # # # -# +# # # -# -# -# Electron biprism as it is used e.g. for electron holography. -# -# +# +# # # -# +# # # -# -# -# -# Device that causes a change in the phase of an electron wave. -# -# * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ -# * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ -# -# -# -# Qualitative type -# -# -# -# -# -# -# +# +# +# # # -# +# # # -# -# +# +# +# +# # # -# -# +# # # # -# +# # # -# +# +# +# +# +# +# +# # -# +# +# # # # -# +# # # -# +# +# # # # -# +# # # -# -# -# Device for improving energy resolution or reducing chromatic aberration. -# -# Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector -# like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ -# -# -# -# Qualitative type of the component. -# -# -# -# -# -# -# -# -# -# +# # # # -# +# # # # -# -# +# +# +# +# # -# -# +# +# +# # # +# # # # -# +# # # -# +# # # -# -# -# -# +# +# +# +# # # -# +# # # -# -# +# +# +# +# +# +# +# +# +# +# +# +# # -# +# # -# +# +# This group should be used to store all event-related (meta)data, +# which are typically measured datasets like images and spectra. +# To avoid that static instrument-related metadata need to be stored +# repetitively the NXem application definitions splits the storage of the +# dynamic (meta)data that typically change for each image and spectrum +# from the static one. +# +# # # -# +# # # # -# +# # # -# # -# +# # # # # # -# +# # # # @@ -2353,7 +2203,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2377,7 +2227,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2404,7 +2254,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2431,7 +2281,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2461,7 +2311,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2491,14 +2341,13 @@ NXem(NXobject): # # # -# +# # # # -# +# # # -# # # # @@ -2506,7 +2355,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2518,7 +2367,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2533,7 +2382,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2551,7 +2400,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2572,7 +2421,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2587,7 +2436,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2605,7 +2454,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2626,7 +2475,7 @@ NXem(NXobject): # # # -# +# # # # @@ -2647,107 +2496,38 @@ NXem(NXobject): # # # -# +# # # -# -# -# This concept is related to term `Source`_ of the EMglossary standard. -# -# .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 -# -# -# -# The potential difference between anode and cathode. -# -# This concept is related to term `Acceleration Voltage`_ of the EMglossary standard. -# -# .. _Acceleration Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 -# -# -# -# -# Voltage which is utilised to create an electric field that draws particles from -# the source. -# -# This concept is related to term `Extraction Voltage`_ of the EMglossary standard. -# -# .. _Extraction Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 -# -# -# -# -# Electrical current which is released from the source. -# -# This concept is related to term `Emission Current`_ of the EMglossary standard. -# -# .. _Emission Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 -# -# -# -# -# Electrical current which flows through the source. -# -# This concept is related to term `Filament Current`_ of the EMglossary standard. -# -# .. _Filament Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 -# -# +# +# +# +# +# # -# -# +# +# # -# -# +# +# # -# Relevant value from the control software. -# -# This is not always just the diameter of the aperture (not even in the case) -# of a circular aperture. Usually, it is a value that is set in the control -# software whereby a specific configuration of an aperture is selected by the -# software. -# -# The control software of commercial microscope typically offers the user -# access at a high abstraction level because of which many details about -# the actual settings of the electrical components are typically unknown. -# -# However, if more details are known or should be documented one should -# use the description field for this. +# Descriptor for the aperture setting when the exact technical details +# are unknown or not directly controllable as the control software of +# the microscope does not enable or was not configured to display these +# values for users. # # # -# -# -# Device to improve energy resolution or chromatic aberration. -# -# Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector -# like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ -# -# -# -# -# Was the corrector used? -# -# -# -# -# -# Energy dispersion in e.g. µm/eV. -# -# -# -# -# Corresponding voltage for that energy dispersion. -# -# +# +# +# +# # # # -# -# +# +# +# # # # @@ -2871,121 +2651,122 @@ NXem(NXobject): # # -# -# Device reshaping an ellipse-shaped electron beam to a circular one. -# -# * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ -# * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ -# -# Stigmator is an exact synonym. -# -# -# -# Was the corrector used? -# -# -# -# -# Descriptor for the correction strength along the first direction when exact technical details -# are unknown or not directly controllable as the control software of the microscope does not -# enable or was not configured to display these values (for end users). -# -# -# -# -# Descriptor for the correction strength along the second direction when exact technical details -# are unknown or not directly controllable as the control software of the microscope does not -# enable or was not configured to display these values (for end users). -# -# -# -# -# -# -# -# -# -# This concept is related to term `Electron Beam`_ of the EMglossary standard. -# -# .. _Electron Beam: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 -# +# +# +# # +# +# +# +# +# # # # -# +# # +# # -# -# +# +# # -# -# +# +# # -# Relevant value from the control software. -# -# This is not always just the diameter of the aperture (not even in the case) -# of a circular aperture. Usually, it is a value that is set in the control -# software whereby a specific configuration of an aperture is selected by the -# software. -# -# The control software of commercial microscope typically offers the user -# access at a high abstraction level because of which many details about -# the actual settings of the electrical components are typically unknown. -# -# However, if more details are known or should be documented one should -# use the description field for this. +# Descriptor for the aperture setting when the exact technical details +# are unknown or not directly controllable as the control software of +# the microscope does not enable or was not configured to display these +# values for users. # # # -# +# # # -# -# -# +# +# +# +# # -# -# +# +# +# +# Operation mode of the detector as displayed by the control software. +# +# # # # # # -# -# -# -# -# -# Nominal current of the heater. -# -# -# -# -# Nominal voltage of the heater. -# -# -# -# -# Nominal power of the heater. -# -# -# -# +# +# +# # +# +# +# +# +# +# +# +# +# Nominal current of the heater. +# +# +# +# +# Nominal voltage of the heater. +# +# +# +# # -# -# # # # # -# # +# +# +# +# Description of the volume of interaction between of particle-matter interaction. +# +# Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam +# interaction simulations can be used to qualify and (or) quantify the shape of +# the interaction volume. Results of such simulations can be summary statistics +# or single-particle-resolved sets of trajectories. +# +# Explicit or implicit descriptions of the geometry of this +# interaction volume are possible: +# +# * An implicit description is via a set of electron/specimen interactions +# represented ideally as trajectory data from the computer simulation. +# * An explicit description is via iso-contour surface using either +# a simulation grid or a triangulated surface mesh of the approximated +# iso-contour surface evaluated at specific threshold values. +# Iso-contours could be computed from electron or particle flux through +# an imaginary control surface (the iso-surface) or energy-levels +# (e.g. the case of X-rays). Details depend on the model. +# * Another explicit description is via theoretical models which may +# be relevant e.g. for X-ray spectroscopy +# +# Further details on how the interaction volume can be quantified +# is available in the literature for example: +# +# * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ +# * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ +# * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ +# +# +# +# +# # -# +# but normalized in its representation ready to be consumed for +# research data management systems--> +# # # A region-of-interest analyzed either during or after the session # for which specific processed data are available. @@ -2998,17 +2779,15 @@ NXem(NXobject): # an RDM can be sure to find specific pieces of information in a # specific way but then every user of this application definition # is required to provide such information in this way!--> -# -# -# -# +# +# +# # # -# # -# # # # @@ -3028,7 +2807,7 @@ NXem(NXobject): # # # -# +# # # # @@ -3037,37 +2816,39 @@ NXem(NXobject): # # # -# +# # # # # +# # # # # # -# +# # # # -# +# +# +# # -# -# -# -# -# +# +# +# +# +# # -# # # diff --git a/contributed_definitions/nyaml/NXaberration.yaml b/base_classes/nyaml/NXaberration.yaml similarity index 79% rename from contributed_definitions/nyaml/NXaberration.yaml rename to base_classes/nyaml/NXaberration.yaml index 7b769dac82..d109235779 100644 --- a/contributed_definitions/nyaml/NXaberration.yaml +++ b/base_classes/nyaml/NXaberration.yaml @@ -6,16 +6,16 @@ NXaberration(NXobject): magnitude(NX_NUMBER): unit: NX_ANY doc: | - Value of the aberration coefficient. - uncertainty(NX_NUMBER): + Magnitude of the aberration + magnitude_errors(NX_NUMBER): unit: NX_ANY doc: | - Uncertainty of the value of the aberration coefficient - according to uncertainty_model. - uncertainty_model(NX_CHAR): + Uncertainty of the magnitude of the aberration + magnitude_errors_model(NX_CHAR): doc: | - How was the uncertainty quantified e.g. via the 95% confidence interval - and using which algorithm or statistical model. + Free-text description how magnitude_errors was quantified + e.g. via the 95% confidence interval, variance, standard deviation, + using which algorithm or statistical model. delta_time(NX_NUMBER): unit: NX_TIME doc: | @@ -36,13 +36,13 @@ NXaberration(NXobject): Alias also used to name and refer to this specific type of aberration. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# e7d666328004bd15b31e3bf00651fc93114bcdc659cff327522ed4916dbe6865 +# 0886da2916670a78790d1d643a4dcd05706da7f69d5605ad5456265640041c73 # # # +# +# +# Base class for the configuration and results of ranging definitions. +# +# Ranging is a data post-processing step used in the research field of +# atom probe during which elemental, isotopic, and/or molecular identities +# are assigned to mass-to-charge-state-ratios within a certain interval. +# The documentation of these steps is based on ideas that +# have been described in the literature: +# +# * `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ +# * `D. Haley et al. <https://doi.org/10.1017/S1431927620024290>`_ +# * `M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_ +# +# +# +# +# +# Specifies the mass-to-charge-state-ratio histogram. +# +# +# +# +# Smallest, increment, and largest mass-to-charge-state ratio value. +# +# +# +# +# +# +# +# A default histogram aka mass spectrum of +# the mass-to-charge-state ratio values. +# +# +# +# +# +# Details of the background model that was used to +# correct the total counts per bin into counts. +# +# +# +# +# To begin with we use a free-text field to learn how +# atom probers define a background model. Future versions +# of NXapm_ranging can then use this information to parameterize +# these models. +# +# +# +# +# +# +# How where peaks in the background-corrected in the histogram +# of mass-to-charge-state ratio values identified? +# +# +# +# +# +# +# Details about how peaks, with taking into account +# error models, were interpreted as ion types or not. +# +# +# +# +# How many ion types are distinguished. If no ranging was performed, each +# ion is of the special unknown type. The iontype ID of this unknown type +# is 0 representing a reserve value. Consequently, +# iontypes start counting from 1. +# +# +# +# +# Assumed maximum value that suffices to store all relevant +# molecular ions, even the most complicated ones. +# Currently, a value of 32 is used (see M. Kühbach et al. <https://doi.org/10.1017/S1431927621012241>`_). +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXapm_reconstruction.yaml b/base_classes/nyaml/NXapm_reconstruction.yaml similarity index 74% rename from contributed_definitions/nyaml/NXapm_reconstruction.yaml rename to base_classes/nyaml/NXapm_reconstruction.yaml index 481d760195..b6d3a80740 100644 --- a/contributed_definitions/nyaml/NXapm_reconstruction.yaml +++ b/base_classes/nyaml/NXapm_reconstruction.yaml @@ -35,84 +35,86 @@ NXapm_reconstruction(NXprocess): doc: | CAnalysis.CSpatial.fPrimaryElement efficiency(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | CAnalysis.CSpatial.fEfficiency - unit: NX_DIMENSIONLESS flight_path(NX_FLOAT): + unit: NX_LENGTH doc: | CAnalysis.CSpatial.fFlightPath - unit: NX_LENGTH evaporation_field(NX_FLOAT): + unit: NX_ANY doc: | CAnalysis.CSpatial.fEvaporationField - unit: NX_ANY image_compression(NX_FLOAT): + unit: NX_UNITLESS doc: | CAnalysis.CSpatial.fImageCompression Image compression factor (ICF) - unit: NX_UNITLESS kfactor(NX_FLOAT): + unit: NX_UNITLESS doc: | CAnalysis.CSpatial.fKfactor k factor - unit: NX_UNITLESS volume(NX_FLOAT): + unit: NX_VOLUME doc: | CAnalysis.CSpatial.fRecoVolume Sum of ion volumes - unit: NX_VOLUME shank_angle(NX_FLOAT): + unit: NX_ANGLE doc: | CAnalysis.CSpatial.fShankAngle Shank angle - unit: NX_ANGLE tip_radius(NX_FLOAT): + unit: NX_LENGTH doc: | CAnalysis.CSpatial.fTipRadius - unit: NX_LENGTH tip_radius_zero(NX_FLOAT): + unit: NX_LENGTH doc: | CAnalysis.CSpatial.fTipRadius0 - unit: NX_LENGTH voltage_zero(NX_FLOAT): + unit: NX_VOLTAGE doc: | CAnalysis.CSpatial.fVoltage0 - unit: NX_VOLTAGE - obb(NXobject): # NXcg_polyhedron + obb(NXobject): doc: | Tight, axis-aligned bounding box about the point cloud of the reconstruction. xmin(NX_FLOAT): + unit: NX_LENGTH doc: | TODO - unit: NX_LENGTH xmax(NX_FLOAT): + unit: NX_LENGTH doc: | TODO - unit: NX_LENGTH ymin(NX_FLOAT): + unit: NX_LENGTH doc: | TODO - unit: NX_LENGTH ymax(NX_FLOAT): + unit: NX_LENGTH doc: | TODO - unit: NX_LENGTH zmin(NX_FLOAT): + unit: NX_LENGTH doc: | TODO - unit: NX_LENGTH zmax(NX_FLOAT): + unit: NX_LENGTH doc: | TODO - unit: NX_LENGTH protocol_name(NX_CHAR): doc: | Qualitative statement about which reconstruction protocol was used. - enumeration: [bas, geiser, gault, cameca, other] + enumeration: + open_enum: true + items: [bas, geiser, gault, cameca, other] crystallographic_calibration(NX_CHAR): doc: | Different strategies for crystallographic calibration of the @@ -155,7 +157,7 @@ NXapm_reconstruction(NXprocess): algorithms during the histogram computation. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8e4a2244387473484405fd142c0b0f4431cad4e816923c9c905f5740158ed7ec +# a3a8cbc9d4a1ef760dcd3e206b211d41a3c7ecc8a3f708efdd0e8147a24670a9 # # # +# +# +# Base class for documenting a set of atoms. +# +# Atoms in the set may be bonded. +# The set may have a net charge to represent +# an ion. Ions can be molecular ions. +# +# +# +# Given name for the set. +# +# This field could for example be used in the research field +# of atom probe tomography for storing a standardized +# human-readable name of the element or (molecular) ion +# like such as Al +++ or 12C +. +# +# +# +# +# Identifier used to refer to if the set of atoms represents a substance. +# +# +# +# +# +# +# +# Signed net (partial) charge of the (molecular) ion. +# +# Different methods for computing charge are in use. +# Care needs to be exercised with respect to the integration. +# `T. A. Manz <10.1039/c6ra04656h>`_ and `N. G. Limas <10.1039/C6RA05507A>`_ discuss computational details. +# +# +# +# +# Charge reported in multiples of the charge of an electron. +# +# For research using atom probe tomography the value should be set to +# zero if the charge_state is unknown and irrecoverable. This can happen +# when classical ranging definition files in formats like RNG, RRNG are used. +# These file formats do not document the charge state explicitly but only +# the number of atoms of each element per molecular ion surplus the +# respective mass-to-charge-state-ratio interval. +# +# Details on ranging definition files in the literature are `M. K. Miller <https://doi.org/10.1002/sia.1719>`_. +# +# +# +# +# Assumed volume affected by the set of atoms. +# +# Neither individual atoms nor a set of cluster of these have a volume +# that is unique as a some cut-off criterion is required. +# +# +# +# +# +# Identifier for each atom at locations as detailed by position. +# +# +# +# +# +# +# +# Nuclide information for each atom at locations as detailed by position. +# +# One `approach <https://doi.org/10.1017/S1431927621012241>`_ for storing nuclide information efficiently +# is via hashing with the following formula +# +# :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` +# +# the number of protons and :math:`N` the number of neutrons +# of each nuclide given as 8-bit unsigned integer values. +# +# +# +# +# +# +# +# Position of each atom. +# +# +# +# +# +# +# +# Path to a reference frame in which positions are defined +# to resolve ambiguity when the reference frame is different +# to the NeXus default reference frame (McStas). +# +# +# +# +# +# Relative occupancy of the atom position. +# +# This field is useful for specifying the atomic motif in +# instances of :ref:`NXunit_cell`. +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXcg_alpha_complex.yaml b/base_classes/nyaml/NXcg_alpha_complex.yaml new file mode 100644 index 0000000000..6b2a5fa8f3 --- /dev/null +++ b/base_classes/nyaml/NXcg_alpha_complex.yaml @@ -0,0 +1,167 @@ +category: base +doc: | + Computational geometry of alpha complexes (alpha shapes or alpha wrappings) about primitives. + + For details see: + + * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, + * https://dx.doi.org/10.1145/174462.156635 for 3D, + * https://dl.acm.org/doi/10.5555/871114 for weighted, and + * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation of alpha shapes, and + * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D alpha wrappings + + in CGAL, the Computational Geometry Algorithms Library respectively. + As a starting point, we follow the conventions of the CGAL library. + + In general, an alpha complex is a not necessarily connected or not necessarily pure complex, + i.e. singular faces may exist. The number of cells, faces, and edges depends on how a specific + alpha complex is filtered for lower-dimensional simplices. The fields is_regularized and + regularization can be used to provide details about regularization procedures. + +# The so-called spectrum or sets of (weighted) alpha shapes includes the convex hull of a point set. +type: group +NXcg_alpha_complex(NXcg_primitive): + type: + doc: | + Type of alpha complex following the terminology used by CGAL for now. + + Alpha_shape means meshes created using one of the alpha_shape algorithm. + Alpha_wrapping means meshes created using the alpha_wrapping algorithm. + enumeration: [convex_hull, alpha_shape, alpha_wrapping] + regularization: + doc: | + Human-readable description about regularization procedures. + is_regularized(NX_BOOLEAN): + doc: | + Was the alpha complex regularized, i.e. have singular faces been removed, or not. + alpha(NX_NUMBER): + unit: NX_ANY + doc: | + The alpha parameter, i.e. the squared radius of the alpha-sphere + that is used when computing the alpha complex. + offset(NX_NUMBER): + unit: NX_LENGTH + doc: | + The offset distance parameter used when computing alpha_wrappings. + + # check again carefully the CGAL documentation talks about, for 3D, the square of the radius! + point_cloudID(NXcg_point): + nameType: partial + doc: | + Point cloud serving as input for the computation of the alpha complex. + triangle_soupID(NXcg_triangle): + nameType: partial + doc: | + Triangle soup serving as input for the computation of the alpha complex. + alpha_complexID(NXcg_triangle): + nameType: partial + doc: | + Triangle mesh representing the output of the computation, i.e. the alpha complex. + tetrahedralizationID(NXcg_tetrahedron): + nameType: partial + doc: | + Tetrahedra representing an interior volume of the alpha complex (if such exists). + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 1c85190cd1bdf41496a2001fc39ecae4c248aef369b155d9ed67fea177fd286a +# +# +# +# +# +# +# Computational geometry of alpha complexes (alpha shapes or alpha wrappings) about primitives. +# +# For details see: +# +# * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, +# * https://dx.doi.org/10.1145/174462.156635 for 3D, +# * https://dl.acm.org/doi/10.5555/871114 for weighted, and +# * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation of alpha shapes, and +# * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D alpha wrappings +# +# in CGAL, the Computational Geometry Algorithms Library respectively. +# As a starting point, we follow the conventions of the CGAL library. +# +# In general, an alpha complex is a not necessarily connected or not necessarily pure complex, +# i.e. singular faces may exist. The number of cells, faces, and edges depends on how a specific +# alpha complex is filtered for lower-dimensional simplices. The fields is_regularized and +# regularization can be used to provide details about regularization procedures. +# +# +# +# Type of alpha complex following the terminology used by CGAL for now. +# +# Alpha_shape means meshes created using one of the alpha_shape algorithm. +# Alpha_wrapping means meshes created using the alpha_wrapping algorithm. +# +# +# +# +# +# +# +# +# +# Human-readable description about regularization procedures. +# +# +# +# +# Was the alpha complex regularized, i.e. have singular faces been removed, or not. +# +# +# +# +# The alpha parameter, i.e. the squared radius of the alpha-sphere +# that is used when computing the alpha complex. +# +# +# +# +# The offset distance parameter used when computing alpha_wrappings. +# +# +# +# +# +# Point cloud serving as input for the computation of the alpha complex. +# +# +# +# +# Triangle soup serving as input for the computation of the alpha complex. +# +# +# +# +# Triangle mesh representing the output of the computation, i.e. the alpha complex. +# +# +# +# +# Tetrahedra representing an interior volume of the alpha complex (if such exists). +# +# +# diff --git a/contributed_definitions/nyaml/NXcg_cylinder_set.yaml b/base_classes/nyaml/NXcg_cylinder.yaml similarity index 65% rename from contributed_definitions/nyaml/NXcg_cylinder_set.yaml rename to base_classes/nyaml/NXcg_cylinder.yaml index ed3c8ddc94..2a9155f042 100644 --- a/contributed_definitions/nyaml/NXcg_cylinder_set.yaml +++ b/base_classes/nyaml/NXcg_cylinder.yaml @@ -1,10 +1,13 @@ category: base doc: | - Computational geometry description of a set of cylinders. + Computational geometry description of a set of cylinders or (truncated) cones. - The radius can either be defined in the radii field or by filling both - the upper_cap_radii or lower_cap_radii field. The latter field case can - thus be used to represent truncated cones. + The radius can either be defined in the radii field or by filling the upper_cap_radii + and lower_cap_radii fields respectively. The latter field case can + thus be used to represent (truncated) cones. + + It is possible to define only one of the cap_radii fields + to represent half-open cylinder. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -12,31 +15,21 @@ symbols: The dimensionality of the space in which the members are assumed embedded. c: | The cardinality of the set, i.e. the number of members. - -# redundant as there is NXcsg, NXquadric, NXsolid_geometry with which -# cylinder could be constructed, but NXcylinder is easier to understand type: group -NXcg_cylinder_set(NXcg_primitive_set): +NXcg_cylinder(NXcg_primitive): height(NX_NUMBER): unit: NX_LENGTH doc: | A direction vector which is parallel to the cylinder/cone axis and whose magnitude is the height of the cylinder/cone. + + The upper_cap is assumed to represent the end while the + lower_cap is assumed to represent the start of the + respective cylinder instances when inspecting along the + direction vector. dimensions: rank: 2 dim: (c, d) - - # observe that although we claim that d is the dimensionality we have - # currently no strategy to tell it must not be d but the actual value - # equally so the symbol c, currently all we say that in the specialization - # defined here the fields radii, upper_cap_radius, and others are all having - # value arguments of the same shape, i.e. these are arrays of rank one with some length c! - # behind the dimensionality field defined either in the here defined specialization - # of NXcg_primitive_set or otherwise that variable is undefined - # alternatively one could store the center of the lower and upper cap but - # these are then no longer necessarily on the same axis - # maybe a future feature for representing skewed cylinder, but then - # one should really better use NXquadric... radius(NX_NUMBER): unit: NX_LENGTH doc: | @@ -73,7 +66,7 @@ NXcg_cylinder_set(NXcg_primitive_set): lateral_surface_area(NX_NUMBER): unit: NX_AREA doc: | - Lateral surface area + Lateral surface area of each cylinder. dimensions: rank: 1 dim: (c,) @@ -94,26 +87,19 @@ NXcg_cylinder_set(NXcg_primitive_set): total_surface_area(NX_NUMBER): unit: NX_AREA doc: | - Sum of upper and lower cap areas and lateral surface area - of each cylinder. + Sum of upper and lower cap area and lateral surface area of each cylinder. dimensions: rank: 1 dim: (c,) - - # again cap, lateral surface area and volume are so trivial to compute - # do we need really storage for this or recompute on-the-fly? - # similarly to hollow sphere discussion, hollow cylinder, cylinder stack - # do wish to define intersections?, if this is the case, one - # should use the NXcsg and NXquadric descriptions? # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 2fe46e954c7c41952646ac69579cba7ddb90a0895ec9e18aa90504eea9a6cf3d +# 76c5b4bd257f27b6a670bec467a805643b68451a1ce96c9ecabd18c1499ee413 # # # -# -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. @@ -151,33 +134,30 @@ NXcg_cylinder_set(NXcg_primitive_set): # # # -# Computational geometry description of a set of cylinders. +# Computational geometry description of a set of cylinders or (truncated) cones. # -# The radius can either be defined in the radii field or by filling both -# the upper_cap_radii or lower_cap_radii field. The latter field case can -# thus be used to represent truncated cones. +# The radius can either be defined in the radii field or by filling the upper_cap_radii +# and lower_cap_radii fields respectively. The latter field case can +# thus be used to represent (truncated) cones. +# +# It is possible to define only one of the cap_radii fields +# to represent half-open cylinder. # # # # A direction vector which is parallel to the cylinder/cone axis # and whose magnitude is the height of the cylinder/cone. +# +# The upper_cap is assumed to represent the end while the +# lower_cap is assumed to represent the start of the +# respective cylinder instances when inspecting along the +# direction vector. # # # # # # -# # # # Radius of the cylinder if all have the same radius. @@ -216,7 +196,7 @@ NXcg_cylinder_set(NXcg_primitive_set): # # # -# Lateral surface area +# Lateral surface area of each cylinder. # # # @@ -240,16 +220,10 @@ NXcg_cylinder_set(NXcg_primitive_set): # # # -# Sum of upper and lower cap areas and lateral surface area -# of each cylinder. +# Sum of upper and lower cap area and lateral surface area of each cylinder. # # # # # -# # diff --git a/contributed_definitions/nyaml/NXcg_ellipsoid_set.yaml b/base_classes/nyaml/NXcg_ellipsoid.yaml similarity index 61% rename from contributed_definitions/nyaml/NXcg_ellipsoid_set.yaml rename to base_classes/nyaml/NXcg_ellipsoid.yaml index f7e3479bf4..444294105a 100644 --- a/contributed_definitions/nyaml/NXcg_ellipsoid_set.yaml +++ b/base_classes/nyaml/NXcg_ellipsoid.yaml @@ -11,34 +11,49 @@ symbols: # redundant as there is NXcsg, and NXquadric but easier to understand type: group -NXcg_ellipsoid_set(NXcg_primitive_set): - half_axes_radius(NX_NUMBER): +NXcg_ellipsoid(NXcg_primitive): + semi_axes_value(NX_NUMBER): unit: NX_LENGTH doc: | - Radius of the half axes. + Length of the semi-axes (e.g. semi-major and semi-minor + respectively for an ellipse). Use if all ellipsoids in the set have the same half-axes. dimensions: rank: 1 dim: (d,) - half_axes_radii(NX_NUMBER): + semi_axes_values(NX_NUMBER): unit: NX_LENGTH doc: | - Half-axes radii of each ellipsoid. + Length of the semi-axes if ellipsoids have individually different lengths. dimensions: rank: 2 dim: (c, d) + # convenience dictionary entries when all ellipsoids in the set are spheres. + radius(NX_NUMBER): + unit: NX_LENGTH + doc: | + In the case that all ellipsoids are spheres. + radii(NX_NUMBER): + unit: NX_LENGTH + doc: | + In the case that all ellipsoids are spheres whose radii differ. + For a mixture of spheres use semi_axes_values. + dimensions: + rank: 1 + dim: (c,) + # properties of ellipsoids # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# eceb310583e02dd5119f7e63423aba121a760055290833677d4aeaf6dc974ba3 +# eff8af12e9566880c60a744fdb0bd00203c6f04da4bdaffedc16def5d6a3bb29 # # # # -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. @@ -77,9 +92,10 @@ NXcg_ellipsoid_set(NXcg_primitive_set): # # Computational geometry description of a set of ellipsoids. # -# +# # -# Radius of the half axes. +# Length of the semi-axes (e.g. semi-major and semi-minor +# respectively for an ellipse). # # Use if all ellipsoids in the set have the same half-axes. # @@ -87,14 +103,29 @@ NXcg_ellipsoid_set(NXcg_primitive_set): # # # -# +# # -# Half-axes radii of each ellipsoid. +# Length of the semi-axes if ellipsoids have individually different lengths. # # # # # # +# +# +# +# In the case that all ellipsoids are spheres. +# +# +# +# +# In the case that all ellipsoids are spheres whose radii differ. +# For a mixture of spheres use semi_axes_values. +# +# +# +# +# # # diff --git a/contributed_definitions/nyaml/NXcg_face_list_data_structure.yaml b/base_classes/nyaml/NXcg_face_list_data_structure.yaml similarity index 80% rename from contributed_definitions/nyaml/NXcg_face_list_data_structure.yaml rename to base_classes/nyaml/NXcg_face_list_data_structure.yaml index 201a45e1ca..ae62a8ee63 100644 --- a/contributed_definitions/nyaml/NXcg_face_list_data_structure.yaml +++ b/base_classes/nyaml/NXcg_face_list_data_structure.yaml @@ -2,18 +2,17 @@ category: base doc: | Computational geometry of primitives via a face-and-edge-list data structure. - Primitives must neither be degenerated nor self-intersect but can differ in - their properties. A face-and-edge-list-based description of primitives is + Primitives must neither be degenerated nor self-intersect but can have different + properties. A face-and-edge-list-based description of primitives is frequently used for triangles and polyhedra to store them on disk for visualization purposes (see OFF, PLY, VTK, or STL file formats). - Although this description is storage efficient it is not well suited for - topological analyses though. In this case, scientists may need a different - view on the primitives which is better represented with e.g. a - half_edge_data_structure. + Although this description is storage efficient, it is not well-suited for + topological analyses. In this case using a half-edge data structure is + an alternative. Having an own base class for the data structure how primitives are stored is - useful to embrace both users with small or very detailed specification demands. + useful to embrace both users with small or detailed specification demands. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -27,12 +26,10 @@ symbols: The number of faces. n_total: | The total number of vertices of all faces. Faces are polygons. - n_weinberg: | - The total number of Weinberg vector values of all faces. # duplicate of an NXoff_geometry ? type: group -NXcg_face_list_data_structure(NXcg_primitive_set): +NXcg_face_list_data_structure(NXcg_primitive): # resulting in a design similar to that of NXoff_geometry and the XDMF mixed primitive topology number_of_vertices(NX_INT): @@ -59,45 +56,45 @@ NXcg_face_list_data_structure(NXcg_primitive_set): unit: NX_UNITLESS doc: | Number of faces of the primitives. - vertex_identifier_offset(NX_INT): + identifier_vertex_offset(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member of the vertices differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of NXcg_primitive_set for further details. - edge_identifier_offset(NX_INT): + Inspect the definition of NXcg_primitive for further details. + identifier_edge_offset(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member of the edges differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of NXcg_primitive_set for further details. - face_identifier_offset(NX_INT): + Inspect the definition of NXcg_primitive for further details. + identifier_face_offset(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member of the faces differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of NXcg_primitive_set for further details. - vertex_identifier(NX_INT): + Inspect the definition of NXcg_primitive for further details. + identifier_vertex(NX_INT): unit: NX_UNITLESS doc: | Integer identifier to distinguish all vertices explicitly. dimensions: rank: 1 dim: (n_v,) - edge_identifier(NX_INT): + identifier_edge(NX_INT): unit: NX_UNITLESS doc: | Integer used to distinguish all edges explicitly. dimensions: rank: 1 dim: (n_e,) - face_identifier(NX_INT): + identifier_face(NX_INT): unit: NX_UNITLESS doc: | Integer used to distinguish all faces explicitly. @@ -110,10 +107,10 @@ NXcg_face_list_data_structure(NXcg_primitive_set): Positions of the vertices. Users are encouraged to reduce the vertices to a unique set as this may - result in a more efficient storage of the geometry data. - It is also possible though to store the vertex positions naively in which - case vertices_are_unique is likely False. Naively here means that each - vertex is stored even though many share the same positions. + result in more efficient storage. Alternatively, storing vertex positions naively + should be indicated with setting vertices_are_unique to False. + Naively means that each vertex is stored even though many vertices may + share the same positions. dimensions: rank: 2 dim: (n_v, d) @@ -168,13 +165,13 @@ NXcg_face_list_data_structure(NXcg_primitive_set): dim: (n_f,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 868aab78567b429975fe68fcaf69c02ec683668247ae94d5bc695cd2d3710af2 +# 5995e7b7684abe457db2bc9ed0f30a7993a6d8e39238eb2e19f454fa18ec19db # # # # -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. @@ -224,27 +221,21 @@ NXcg_face_list_data_structure(NXcg_primitive_set): # The total number of vertices of all faces. Faces are polygons. # # -# -# -# The total number of Weinberg vector values of all faces. -# -# # # # Computational geometry of primitives via a face-and-edge-list data structure. # -# Primitives must neither be degenerated nor self-intersect but can differ in -# their properties. A face-and-edge-list-based description of primitives is +# Primitives must neither be degenerated nor self-intersect but can have different +# properties. A face-and-edge-list-based description of primitives is # frequently used for triangles and polyhedra to store them on disk for # visualization purposes (see OFF, PLY, VTK, or STL file formats). # -# Although this description is storage efficient it is not well suited for -# topological analyses though. In this case, scientists may need a different -# view on the primitives which is better represented with e.g. a -# half_edge_data_structure. +# Although this description is storage efficient, it is not well-suited for +# topological analyses. In this case using a half-edge data structure is +# an alternative. # # Having an own base class for the data structure how primitives are stored is -# useful to embrace both users with small or very detailed specification demands. +# useful to embrace both users with small or detailed specification demands. # # # @@ -274,34 +265,34 @@ NXcg_face_list_data_structure(NXcg_primitive_set): # Number of faces of the primitives. # # -# +# # # Integer offset whereby the identifier of the first member # of the vertices differs from zero. # # Identifier can be defined explicitly or implicitly. -# Inspect the definition of NXcg_primitive_set for further details. +# Inspect the definition of NXcg_primitive for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the edges differs from zero. # # Identifier can be defined explicitly or implicitly. -# Inspect the definition of NXcg_primitive_set for further details. +# Inspect the definition of NXcg_primitive for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the faces differs from zero. # # Identifier can be defined explicitly or implicitly. -# Inspect the definition of NXcg_primitive_set for further details. +# Inspect the definition of NXcg_primitive for further details. # # -# +# # # Integer identifier to distinguish all vertices explicitly. # @@ -309,7 +300,7 @@ NXcg_face_list_data_structure(NXcg_primitive_set): # # # -# +# # # Integer used to distinguish all edges explicitly. # @@ -317,7 +308,7 @@ NXcg_face_list_data_structure(NXcg_primitive_set): # # # -# +# # # Integer used to distinguish all faces explicitly. # @@ -330,10 +321,10 @@ NXcg_face_list_data_structure(NXcg_primitive_set): # Positions of the vertices. # # Users are encouraged to reduce the vertices to a unique set as this may -# result in a more efficient storage of the geometry data. -# It is also possible though to store the vertex positions naively in which -# case vertices_are_unique is likely False. Naively here means that each -# vertex is stored even though many share the same positions. +# result in more efficient storage. Alternatively, storing vertex positions naively +# should be indicated with setting vertices_are_unique to False. +# Naively means that each vertex is stored even though many vertices may +# share the same positions. # # # diff --git a/contributed_definitions/nyaml/NXcg_grid.yaml b/base_classes/nyaml/NXcg_grid.yaml similarity index 73% rename from contributed_definitions/nyaml/NXcg_grid.yaml rename to base_classes/nyaml/NXcg_grid.yaml index 1742f31576..e5ed7956c2 100644 --- a/contributed_definitions/nyaml/NXcg_grid.yaml +++ b/base_classes/nyaml/NXcg_grid.yaml @@ -3,9 +3,10 @@ doc: | Computational geometry description of a grid of Wigner-Seitz cells in Euclidean space. Three-dimensional grids with cubic cells are if not the most frequently used - example of such grids. Examples of numerical methods where grids are used - are spectral-solver based crystal plasticity or other stencil methods like - phase-field or cellular automata. + example of such grids. Numerical methods and models that use grids are used + in many cases in the natural sciences and engineering disciplines. Examples are + discretizations in space and time used for phase-field, cellular automata, or Monte Carlo + modeling. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -16,13 +17,13 @@ symbols: n_b: | Number of boundaries of the bounding box or primitive housing the grid. type: group -NXcg_grid(NXcg_primitive_set): +NXcg_grid(NXcg_primitive): origin(NX_NUMBER): unit: NX_ANY doc: | Location of the origin of the grid. - Use the depends_on field that is inherited from the :ref:`NXcg_primitive_set` + Use the depends_on field that is inherited from the :ref:`NXcg_primitive` class to specify the coordinate system in which the origin location is defined. dimensions: rank: 1 @@ -38,7 +39,7 @@ NXcg_grid(NXcg_primitive_set): dimensions: rank: 1 dim: (d,) - extent(NX_UINT): + extent(NX_INT): unit: NX_UNITLESS doc: | Number of unit cells along each of the d unit vectors. @@ -70,7 +71,7 @@ NXcg_grid(NXcg_primitive_set): dim: (c, d) # this should be a ROI - bounding_box(NXcg_polyhedron_set): + bounding_box(NXcg_polyhedron): doc: | A tight bounding box about the grid. @@ -105,15 +106,34 @@ NXcg_grid(NXcg_primitive_set): dimensions: rank: 1 dim: (n_b,) + surface_reconstruction(NX_CHAR): + doc: | + Details about the computational geometry method and implementation + used for discretizing internal surfaces as e.g. obtained with marching methods, + like marching squares or marching cubes. + + Documenting which specific version was used helps with understanding how + robust the results are with respect to the topology of the triangulation. + Reference to the specific implementation of marching cubes used. + + See for example the following papers for details about how to identify a + DOI which specifies the implementation used: + + * `W. E. Lorensen `_ + * `T. S. Newman and H. Yi `_ + + The value placed here should ideally be an identifier of a program. + If not possible, an identifier for a paper, technical report, or free-text + description can be used instead. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 38e2bcd19bea6226e79f858da6a2c6f088479718a181c40f012cd337e308b531 +# 9ae5f6a385db0e8c9c49989e03d512f279fbf61becb69b11c8fa012dbdb01893 # # # -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. @@ -156,15 +176,16 @@ NXcg_grid(NXcg_primitive_set): # Computational geometry description of a grid of Wigner-Seitz cells in Euclidean space. # # Three-dimensional grids with cubic cells are if not the most frequently used -# example of such grids. Examples of numerical methods where grids are used -# are spectral-solver based crystal plasticity or other stencil methods like -# phase-field or cellular automata. +# example of such grids. Numerical methods and models that use grids are used +# in many cases in the natural sciences and engineering disciplines. Examples are +# discretizations in space and time used for phase-field, cellular automata, or Monte Carlo +# modeling. # # # # Location of the origin of the grid. # -# Use the depends_on field that is inherited from the :ref:`NXcg_primitive_set` +# Use the depends_on field that is inherited from the :ref:`NXcg_primitive` # class to specify the coordinate system in which the origin location is defined. # # @@ -187,7 +208,7 @@ NXcg_grid(NXcg_primitive_set): # # # -# +# # # Number of unit cells along each of the d unit vectors. # @@ -222,7 +243,7 @@ NXcg_grid(NXcg_primitive_set): # # # -# +# # # A tight bounding box about the grid. # @@ -262,4 +283,25 @@ NXcg_grid(NXcg_primitive_set): # # # +# +# +# Details about the computational geometry method and implementation +# used for discretizing internal surfaces as e.g. obtained with marching methods, +# like marching squares or marching cubes. +# +# Documenting which specific version was used helps with understanding how +# robust the results are with respect to the topology of the triangulation. +# Reference to the specific implementation of marching cubes used. +# +# See for example the following papers for details about how to identify a +# DOI which specifies the implementation used: +# +# * `W. E. Lorensen <https://doi.org/10.1109/MCG.2020.2971284>`_ +# * `T. S. Newman and H. Yi <https://doi.org/10.1016/j.cag.2006.07.021>`_ +# +# The value placed here should ideally be an identifier of a program. +# If not possible, an identifier for a paper, technical report, or free-text +# description can be used instead. +# +# # diff --git a/contributed_definitions/nyaml/NXcg_half_edge_data_structure.yaml b/base_classes/nyaml/NXcg_half_edge_data_structure.yaml similarity index 83% rename from contributed_definitions/nyaml/NXcg_half_edge_data_structure.yaml rename to base_classes/nyaml/NXcg_half_edge_data_structure.yaml index 8cc0669332..dc864911c2 100644 --- a/contributed_definitions/nyaml/NXcg_half_edge_data_structure.yaml +++ b/base_classes/nyaml/NXcg_half_edge_data_structure.yaml @@ -3,7 +3,8 @@ doc: | Computational geeometry description of a half-edge data structure. Such a data structure can be used to efficiently circulate around faces - and iterate over vertices of a planar graph. + and iterate over vertices of a planar graph. The data structure is also + known as a doubly connected edge list. # holes in the polygon mesh can be handled symbols: @@ -18,7 +19,11 @@ symbols: n_he: | The number of half-edges. type: group -NXcg_half_edge_data_structure(NXcg_primitive_set): +NXcg_half_edge_data_structure(NXcg_primitive): + dimensionality(NX_POSINT): + unit: NX_UNITLESS + doc: | + Dimensionality of the primitives described. # resulting in a design similar to that of NXoff_geometry and the XDMF mixed primitive topology number_of_vertices(NX_INT): @@ -40,36 +45,32 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): irrespectively whether edges are shared across faces or not. dimensions: rank: 1 - dim: (n_e,) - number_of_faces(NX_INT): - unit: NX_UNITLESS - doc: | - Number of faces of the primitives. - vertex_identifier_offset(NX_INT): + dim: (n_he,) + identifier_vertex_offset(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member of the vertices differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of :ref:`NXcg_primitive_set` for further details. - edge_identifier_offset(NX_INT): + Inspect the definition of :ref:`NXcg_primitive` for further details. + identifier_edge_offset(NX_INT): unit: NX_UNITLESS doc: | Integer offset whereby the identifier of the first member of the edges differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of :ref:`NXcg_primitive_set` for further details. - face_identifier_offset(NX_INT): + Inspect the definition of :ref:`NXcg_primitive` for further details. + identifier_face_offset(NX_INT): doc: | Integer offset whereby the identifier of the first member of the faces differs from zero. Identifier can be defined explicitly or implicitly. - Inspect the definition of :ref:`NXcg_primitive_set` for further details. + Inspect the definition of :ref:`NXcg_primitive` for further details. - # therefore, vertex_-, face_-, half_edge_-identifier are implicit + # therefore, identifier_ -vertex, -face, -half_edge are implicit position(NX_NUMBER): unit: NX_ANY doc: | @@ -127,7 +128,7 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): dimensions: rank: 1 dim: (n_he,) - weinberg_vector(NX_CHAR): + weinberg_vector: doc: | Users are referred to the literature for the background of L. Weinberg's work about topological characterization of planar graphs: @@ -138,20 +139,15 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): and how this work can e.g. be applied in space-filling tessellations of microstructural objects like crystals/grains. - - # eventually store the Weinberg vector as an integer array - # which could be more efficient - # see https://jerryyin.info/geometry-processing-algorithms/half-edge/ - # for an illustrative example of half-edge data structures # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 2f61ea1efe2812ef2f05c6cd1d04f3eecd72ced613d36923f32037ecb342f6aa +# a1a129e0fc0006c11237cf35ce7db70d503acc0ec953bafc563e577553801c79 # # # -# +# # # # @@ -200,8 +196,14 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): # Computational geeometry description of a half-edge data structure. # # Such a data structure can be used to efficiently circulate around faces -# and iterate over vertices of a planar graph. +# and iterate over vertices of a planar graph. The data structure is also +# known as a doubly connected edge list. # +# +# +# Dimensionality of the primitives described. +# +# # # # @@ -222,42 +224,37 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): # irrespectively whether edges are shared across faces or not. # # -# +# # # -# -# -# Number of faces of the primitives. -# -# -# +# # # Integer offset whereby the identifier of the first member # of the vertices differs from zero. # # Identifier can be defined explicitly or implicitly. -# Inspect the definition of :ref:`NXcg_primitive_set` for further details. +# Inspect the definition of :ref:`NXcg_primitive` for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the edges differs from zero. # # Identifier can be defined explicitly or implicitly. -# Inspect the definition of :ref:`NXcg_primitive_set` for further details. +# Inspect the definition of :ref:`NXcg_primitive` for further details. # # -# +# # # Integer offset whereby the identifier of the first member # of the faces differs from zero. # # Identifier can be defined explicitly or implicitly. -# Inspect the definition of :ref:`NXcg_primitive_set` for further details. +# Inspect the definition of :ref:`NXcg_primitive` for further details. # # -# +# # # # The position of the vertices. @@ -324,7 +321,7 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): # # # -# +# # # Users are referred to the literature for the background of L. Weinberg's # work about topological characterization of planar graphs: @@ -337,8 +334,4 @@ NXcg_half_edge_data_structure(NXcg_primitive_set): # of microstructural objects like crystals/grains. # # -# # diff --git a/contributed_definitions/nyaml/NXcg_hexahedron_set.yaml b/base_classes/nyaml/NXcg_hexahedron.yaml similarity index 63% rename from contributed_definitions/nyaml/NXcg_hexahedron_set.yaml rename to base_classes/nyaml/NXcg_hexahedron.yaml index e9aa1a381a..0a3fbc13db 100644 --- a/contributed_definitions/nyaml/NXcg_hexahedron_set.yaml +++ b/base_classes/nyaml/NXcg_hexahedron.yaml @@ -26,7 +26,7 @@ doc: | Hexahedra are important geometrical primitives, which are among the most frequently used elements in finite element meshing/modeling. - As a specialization of the :ref:`NXcg_primitive_set` base class hexahedra + As a specialization of the :ref:`NXcg_primitive` base class hexahedra are assumed non-degenerated, closed, and built of polygons that are not self-intersecting. @@ -56,7 +56,7 @@ symbols: # as they are used in numerics etc. maybe reach out here to our friends # from MarDI, for now let's assume we do not need polytopes for d > 3 type: group -NXcg_hexahedron_set(NXcg_primitive_set): +NXcg_hexahedron(NXcg_primitive): # qualifiers and properties of hexahedra shape(NX_NUMBER): @@ -130,12 +130,9 @@ NXcg_hexahedron_set(NXcg_primitive_set): dimensions: rank: 1 dim: (c,) - - # substantially more detailed descriptors of the shape, the mesh - # orientation(NXorientation_set): - vertex_normal(NXcg_unit_normal_set): - edge_normal(NXcg_unit_normal_set): - face_normal(NXcg_unit_normal_set): + vertex_normal(NXcg_unit_normal): + edge_normal(NXcg_unit_normal): + face_normal(NXcg_unit_normal): # detailed mesh-based representation hexahedra(NXcg_face_list_data_structure): @@ -151,13 +148,13 @@ NXcg_hexahedron_set(NXcg_primitive_set): Individual storage of each hexahedron as a graph. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 049c073b7eb887853e65f048ffc2c2d689b5464c6a43c379dd9df0bcf02b687c +# f67f7ce071e318711ece618dd5305357a9bdea87336fa43b55b4788cbc1205a2 # # # -# +# # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The cardinality of the set, i.e. the number of hexahedra. +# The cardinality of the set, i.e. the number of hexahedra. # # # # -# Computational geometry description of a set of hexahedra in Euclidean space. -# -# This class can also be used to describe cuboids or cubes, axis-aligned or not. -# The class represents different access and description levels to offer both -# applied scientists and computational geometry experts an approach whereby -# different specific views can be implemented using the same base class: -# -# * In the simplest case experimentalists may use this base class to describe -# the dimensions or size of a specimen. In this case the alignment with axes -# is not relevant as eventually only the volume of the specimen is of interest. -# * In many cases, take for example an experiment where a specimen was cut out -# from a specifically deformed piece of material, the orientation of the -# specimen's edges with the experiment coordinate system is of high relevance. -# Examples include knowledge about the specimen edge, whether it is -# parallel to the rolling, the transverse, or the normal direction. -# * While the above-mentioned use cases are sufficient to pinpoint the sample -# within a known laboratory/experiment coordinate system, these descriptions -# are not detailed enough to specify e.g. a CAD model of the specimen. -# * Therefore, groups and fields for an additional, computational-geometry- -# based view of hexahedra is offered to serve additional computational -# tasks: storage-oriented simple views or detailed topological/graph-based -# descriptions. -# -# Hexahedra are important geometrical primitives, which are among the most -# frequently used elements in finite element meshing/modeling. -# -# As a specialization of the :ref:`NXcg_primitive_set` base class hexahedra -# are assumed non-degenerated, closed, and built of polygons that are -# not self-intersecting. -# -# The term hexahedra will be used throughout this base class but includes -# the special cases cuboid, cube, box, axis-aligned bounding box (AABB), -# and optimal bounding box (OBB). -# -# An axis-aligned bounding box is a common data object in computational science -# and simulation codes to represent a cuboid whose edges are aligned with the -# base vectors of a coordinate system. As a part of binary trees, these data -# objects are important for making time- as well as space-efficient queries -# of geometric primitives in techniques like kd-trees. -# -# An optimal bounding box is a common data object which provides the best -# tightly fitting box about an arbitrary object. In general, such boxes are -# rotated. Exact and substantially faster in practice approximate algorithms -# exist to compute optimal or near optimal bounding boxes for sets of points. +# Computational geometry description of a set of hexahedra in Euclidean space. +# +# This class can also be used to describe cuboids or cubes, axis-aligned or not. +# The class represents different access and description levels to offer both +# applied scientists and computational geometry experts an approach whereby +# different specific views can be implemented using the same base class: +# +# * In the simplest case experimentalists may use this base class to describe +# the dimensions or size of a specimen. In this case the alignment with axes +# is not relevant as eventually only the volume of the specimen is of interest. +# * In many cases, take for example an experiment where a specimen was cut out +# from a specifically deformed piece of material, the orientation of the +# specimen's edges with the experiment coordinate system is of high relevance. +# Examples include knowledge about the specimen edge, whether it is +# parallel to the rolling, the transverse, or the normal direction. +# * While the above-mentioned use cases are sufficient to pinpoint the sample +# within a known laboratory/experiment coordinate system, these descriptions +# are not detailed enough to specify e.g. a CAD model of the specimen. +# * Therefore, groups and fields for an additional, computational-geometry- +# based view of hexahedra is offered to serve additional computational +# tasks: storage-oriented simple views or detailed topological/graph-based +# descriptions. +# +# Hexahedra are important geometrical primitives, which are among the most +# frequently used elements in finite element meshing/modeling. +# +# As a specialization of the :ref:`NXcg_primitive` base class hexahedra +# are assumed non-degenerated, closed, and built of polygons that are +# not self-intersecting. +# +# The term hexahedra will be used throughout this base class but includes +# the special cases cuboid, cube, box, axis-aligned bounding box (AABB), +# and optimal bounding box (OBB). +# +# An axis-aligned bounding box is a common data object in computational science +# and simulation codes to represent a cuboid whose edges are aligned with the +# base vectors of a coordinate system. As a part of binary trees, these data +# objects are important for making time- as well as space-efficient queries +# of geometric primitives in techniques like kd-trees. +# +# An optimal bounding box is a common data object which provides the best +# tightly fitting box about an arbitrary object. In general, such boxes are +# rotated. Exact and substantially faster in practice approximate algorithms +# exist to compute optimal or near optimal bounding boxes for sets of points. # # # # -# Qualifier for the shape of each hexahedron. +# Qualifier for the shape of each hexahedron. # # # @@ -250,9 +247,9 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Qualifier that is useful in cases when one edge is longer than all other -# edges of the hexahedra. Often the term length is associated with the -# assumption that one edge is parallel to an axis of the coordinate system. +# Qualifier that is useful in cases when one edge is longer than all other +# edges of the hexahedra. Often the term length is associated with the +# assumption that one edge is parallel to an axis of the coordinate system. # # # @@ -260,11 +257,11 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Qualifier often used to describe the extent of an object in the horizontal -# direction assuming a specific coordinate system. -# -# For the sake of explicitness quantities like length, width, and height -# should not be reported without specifying also the assumed reference frame. +# Qualifier often used to describe the extent of an object in the horizontal +# direction assuming a specific coordinate system. +# +# For the sake of explicitness quantities like length, width, and height +# should not be reported without specifying also the assumed reference frame. # # # @@ -272,8 +269,8 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Qualifier often used to describe the extent of an object in the vertical -# direction assuming a specific coordinate system. +# Qualifier often used to describe the extent of an object in the vertical +# direction assuming a specific coordinate system. # # # @@ -281,7 +278,7 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Volume of each hexahedron. +# Volume of each hexahedron. # # # @@ -289,7 +286,7 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Total (surface) area (of all six faces) of each hexahedron. +# Total (surface) area (of all six faces) of each hexahedron. # # # @@ -297,7 +294,7 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Area of each of the six faces of each hexahedron. +# Area of each of the six faces of each hexahedron. # # # @@ -306,8 +303,8 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Specifies if the hexahedra represent cuboids or cubes eventually rotated -# ones but at least not too exotic six-faced polyhedra. +# Specifies if the hexahedra represent cuboids or cubes eventually rotated +# ones but at least not too exotic six-faced polyhedra. # # # @@ -315,33 +312,31 @@ NXcg_hexahedron_set(NXcg_primitive_set): # # # -# Only to be used if is_box is present. In this case, this field describes -# whether hexahedra are boxes whose primary edges are parallel to the -# axes of the coordinate system. +# Only to be used if is_box is present. In this case, this field describes +# whether hexahedra are boxes whose primary edges are parallel to the +# axes of the coordinate system. # # # # # -# -# -# -# +# +# +# # # # -# Combined storage of all primitives of all hexahedra. +# Combined storage of all primitives of all hexahedra. # # # # -# Individual storage of each hexahedron. +# Individual storage of each hexahedron. # # # # -# Individual storage of each hexahedron as a graph. +# Individual storage of each hexahedron as a graph. # # # diff --git a/contributed_definitions/nyaml/NXcg_parallelogram_set.yaml b/base_classes/nyaml/NXcg_parallelogram.yaml similarity index 57% rename from contributed_definitions/nyaml/NXcg_parallelogram_set.yaml rename to base_classes/nyaml/NXcg_parallelogram.yaml index 1c0b570598..f8ab3d5baa 100644 --- a/contributed_definitions/nyaml/NXcg_parallelogram_set.yaml +++ b/base_classes/nyaml/NXcg_parallelogram.yaml @@ -22,7 +22,7 @@ doc: | The term parallelogram will be used throughout this base class thus including the important special cases rectangle, square, 2D box, axis-aligned bounding box (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D - counterparts. See :ref:`NXcg_hexahedron_set` for the generalization in 3D. + counterparts. See :ref:`NXcg_hexahedron` for the generalization in 3D. An axis-aligned bounding box is a common data object in computational science and simulation codes to represent a rectangle whose edges are aligned with the @@ -40,7 +40,7 @@ symbols: c: | The cardinality of the set, i.e. the number of parallelograms. type: group -NXcg_parallelogram_set(NXcg_primitive_set): +NXcg_parallelogram(NXcg_primitive): # qualifiers and properties of parallelograms is_rectangle(NX_BOOLEAN): @@ -60,26 +60,21 @@ NXcg_parallelogram_set(NXcg_primitive_set): # detailed mesh-based representation parallelograms(NXcg_face_list_data_structure): - - # exists: [min, 0, max, 1] doc: | - Combined storage of all primitives of all parallelograms. + Combined storage of all parallelograms. parallelogramID(NXcg_face_list_data_structure): nameType: partial doc: | Individual storage of each parallelogram. - - # MK::parallelogram_half_edgeID(NXcg_half_edge_data_structure) - # a half-edge structure would be overkill as this is a simple primitive # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 187fcae08726cb89911d53b6a47fe2caa37da4859687fda856927f8391a986e6 +# 925993111384a8a2e209475675f51f560114d21c32b9ed50c5f4f8db413a87af # # # -# +# # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The cardinality of the set, i.e. the number of parallelograms. +# The cardinality of the set, i.e. the number of parallelograms. # # # # -# Computational geometry description of a set of parallelograms. -# -# This class can also be used to describe rectangles or squares, irrespective -# whether these are axis-aligned or not. The class represents different -# access and description levels to embrace applied scientists and computational -# geometry experts with their different views: -# -# * The simplest case is the communication of dimensions aka the size of a -# region of interest in the 2D plane. In this case, communicating the -# alignment with axes is maybe not as relevant as it is to report the area -# of the ROI. -# * In other cases the extent of the parallelogram is relevant though. -# * Finally, in CAD models it should be possible to specify the polygons -# which the parallelograms represent with exact numerical details. -# -# Parallelograms are important geometrical primitives as their usage for -# describing many scanning experiments shows where typically parallelogram-shaped -# ROIs are scanned across the surface of a sample. -# -# The term parallelogram will be used throughout this base class thus including -# the important special cases rectangle, square, 2D box, axis-aligned bounding box -# (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D -# counterparts. See :ref:`NXcg_hexahedron_set` for the generalization in 3D. -# -# An axis-aligned bounding box is a common data object in computational science -# and simulation codes to represent a rectangle whose edges are aligned with the -# axes of a coordinate system. As a part of binary trees AABBs are important data -# objects for executing time- as well as space-efficient queries -# of geometric primitives in techniques like kd-trees. -# -# An optimal bounding box is a common data object which provides the best, i.e. -# most tightly fitting box about an arbitrary object. In general such boxes are -# rotated. Other than in 3D dimensions, the rotation calipher method offers -# a rigorous approach to compute an optimal bounding box to a point set in 2D. +# Computational geometry description of a set of parallelograms. +# +# This class can also be used to describe rectangles or squares, irrespective +# whether these are axis-aligned or not. The class represents different +# access and description levels to embrace applied scientists and computational +# geometry experts with their different views: +# +# * The simplest case is the communication of dimensions aka the size of a +# region of interest in the 2D plane. In this case, communicating the +# alignment with axes is maybe not as relevant as it is to report the area +# of the ROI. +# * In other cases the extent of the parallelogram is relevant though. +# * Finally, in CAD models it should be possible to specify the polygons +# which the parallelograms represent with exact numerical details. +# +# Parallelograms are important geometrical primitives as their usage for +# describing many scanning experiments shows where typically parallelogram-shaped +# ROIs are scanned across the surface of a sample. +# +# The term parallelogram will be used throughout this base class thus including +# the important special cases rectangle, square, 2D box, axis-aligned bounding box +# (AABB), or optimal bounding box (OBB) as analogous 2D variants to their 3D +# counterparts. See :ref:`NXcg_hexahedron` for the generalization in 3D. +# +# An axis-aligned bounding box is a common data object in computational science +# and simulation codes to represent a rectangle whose edges are aligned with the +# axes of a coordinate system. As a part of binary trees AABBs are important data +# objects for executing time- as well as space-efficient queries +# of geometric primitives in techniques like kd-trees. +# +# An optimal bounding box is a common data object which provides the best, i.e. +# most tightly fitting box about an arbitrary object. In general such boxes are +# rotated. Other than in 3D dimensions, the rotation calipher method offers +# a rigorous approach to compute an optimal bounding box to a point set in 2D. # # # # -# To specify which parallelogram is a rectangle. +# To specify which parallelogram is a rectangle. # # # @@ -155,9 +150,9 @@ NXcg_parallelogram_set(NXcg_primitive_set): # # # -# Only to be used if is_rectangle is present. In this case, this field -# describes whether parallelograms are rectangles whose primary edges -# are parallel to the axes of the coordinate system. +# Only to be used if is_rectangle is present. In this case, this field +# describes whether parallelograms are rectangles whose primary edges +# are parallel to the axes of the coordinate system. # # # @@ -165,16 +160,13 @@ NXcg_parallelogram_set(NXcg_primitive_set): # # # -# # -# Combined storage of all primitives of all parallelograms. +# Combined storage of all parallelograms. # # # # -# Individual storage of each parallelogram. +# Individual storage of each parallelogram. # # -# # diff --git a/contributed_definitions/nyaml/NXcg_point_set.yaml b/base_classes/nyaml/NXcg_point.yaml similarity index 90% rename from contributed_definitions/nyaml/NXcg_point_set.yaml rename to base_classes/nyaml/NXcg_point.yaml index 47a51dd5d1..a16bfd654d 100644 --- a/contributed_definitions/nyaml/NXcg_point_set.yaml +++ b/base_classes/nyaml/NXcg_point.yaml @@ -4,12 +4,12 @@ doc: | Points may have an associated time value. Users are advised though to store time data of point sets rather as instances of time events, where for each - point in time there is an :ref:`NXcg_point_set` instance which specifies the + point in time there is an :ref:`NXcg_point` instance which specifies the points' locations. This is a frequent situation in experiments and computer simulations, where positions of points are taken at the same point in time (real time or - simulated physical time). Thereby, the storage of redundant time stamp + simulated physical time). Thereby, the storage of redundant timestamp information per point is considered as obsolete. symbols: doc: | @@ -19,7 +19,7 @@ symbols: c: | The cardinality of the set, i.e. the number of points. type: group -NXcg_point_set(NXcg_primitive_set): +NXcg_point(NXcg_primitive): position(NX_NUMBER): unit: NX_ANY doc: | @@ -49,13 +49,13 @@ NXcg_point_set(NXcg_primitive_set): for values in the field time. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# bbb028db0c5e3b365ba2e6ae32111ab4f2ec2302072cd5b81a53af058e9f8827 +# 14c313890564590cf516821eca33c4e26bed72d15a8078e0dc52a5bff904ad30 # # # -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. @@ -94,12 +94,12 @@ NXcg_point_set(NXcg_primitive_set): # # Points may have an associated time value. Users are advised though to store # time data of point sets rather as instances of time events, where for each -# point in time there is an :ref:`NXcg_point_set` instance which specifies the +# point in time there is an :ref:`NXcg_point` instance which specifies the # points' locations. # # This is a frequent situation in experiments and computer simulations, where # positions of points are taken at the same point in time (real time or -# simulated physical time). Thereby, the storage of redundant time stamp +# simulated physical time). Thereby, the storage of redundant timestamp # information per point is considered as obsolete. # # diff --git a/contributed_definitions/nyaml/NXcg_polygon_set.yaml b/base_classes/nyaml/NXcg_polygon.yaml similarity index 60% rename from contributed_definitions/nyaml/NXcg_polygon_set.yaml rename to base_classes/nyaml/NXcg_polygon.yaml index 390c54cffa..a3eba06277 100644 --- a/contributed_definitions/nyaml/NXcg_polygon_set.yaml +++ b/base_classes/nyaml/NXcg_polygon.yaml @@ -1,6 +1,6 @@ category: base -# somewhat redundant as there is NXoff_geometry but easier to understand +# similar design like NXoff_geometry but easier to understand doc: | Computational geometry description of a set of polygons in Euclidean space. @@ -17,18 +17,14 @@ doc: | As three-dimensional objects, a set of polygons can be used to define the hull of what is effectively a polyhedron; however users are advised to use - the specific :ref:`NXcg_polyhedron_set` base class if they wish to describe closed + the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed polyhedra. Even more general complexes can be thought of. An example are the so-called piecewise-linear complexes used in the TetGen library. As these complexes can have holes though, polyhedra without holes are one - subclass of such complexes, users should rather design an own - base class e.g. NXcg_polytope_set to describe such even more - complex primitives instead of abusing this base class for such purposes. - -# Users can take advantage of NXcg_polygon_set to describe such complexes -# when using the defines_plc and related topological and boundary constraint -# descriptors. + subclass of such complexes, users should rather design an own base class + e.g. NXcg_polytope to describe such even more complex primitives instead + of abusing this base class for such purposes. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -41,7 +37,7 @@ symbols: n_total: | The total number of vertices when visiting every polygon. type: group -NXcg_polygon_set(NXcg_primitive_set): +NXcg_polygon(NXcg_primitive): number_of_total_vertices(NX_INT): unit: NX_UNITLESS doc: | @@ -92,13 +88,13 @@ NXcg_polygon_set(NXcg_primitive_set): dim: (c,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8bf58f13110dc373800ee8818212b4ded2ac57a0f651795dc2c16e123e2c54cb +# 18764efbb4d4ded89f6a0db6e22c1e5b337f6611c02ca763dee7414fbfa307c6 # # # -# -# +# # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The dimensionality, which has to be either 2 or 3. +# The dimensionality, which has to be either 2 or 3. # # # # -# The cardinality of the set, i.e. the number of polygons. +# The cardinality of the set, i.e. the number of polygons. # # # # # -# The total number of vertices when visiting every polygon. +# The total number of vertices when visiting every polygon. # # # -# +# # -# Computational geometry description of a set of polygons in Euclidean space. -# -# Polygons are specialized polylines: -# -# * A polygon is a geometric primitive that is bounded by a closed polyline -# * All vertices of this polyline lay in the d-1 dimensional plane. -# whereas vertices of a polyline do not necessarily lay on a plane. -# * A polygon has at least three vertices. -# -# Each polygon is built from a sequence of vertices (points with identifiers). -# The members of a set of polygons may have a different number of vertices. -# Sometimes a collection/set of polygons is referred to as a soup of polygons. -# -# As three-dimensional objects, a set of polygons can be used to define the -# hull of what is effectively a polyhedron; however users are advised to use -# the specific :ref:`NXcg_polyhedron_set` base class if they wish to describe closed -# polyhedra. Even more general complexes can be thought of. An example are the -# so-called piecewise-linear complexes used in the TetGen library. -# -# As these complexes can have holes though, polyhedra without holes are one -# subclass of such complexes, users should rather design an own -# base class e.g. NXcg_polytope_set to describe such even more -# complex primitives instead of abusing this base class for such purposes. +# Computational geometry description of a set of polygons in Euclidean space. +# +# Polygons are specialized polylines: +# +# * A polygon is a geometric primitive that is bounded by a closed polyline +# * All vertices of this polyline lay in the d-1 dimensional plane. +# whereas vertices of a polyline do not necessarily lay on a plane. +# * A polygon has at least three vertices. +# +# Each polygon is built from a sequence of vertices (points with identifiers). +# The members of a set of polygons may have a different number of vertices. +# Sometimes a collection/set of polygons is referred to as a soup of polygons. +# +# As three-dimensional objects, a set of polygons can be used to define the +# hull of what is effectively a polyhedron; however users are advised to use +# the specific :ref:`NXcg_polyhedron` base class if they wish to describe closed +# polyhedra. Even more general complexes can be thought of. An example are the +# so-called piecewise-linear complexes used in the TetGen library. +# +# As these complexes can have holes though, polyhedra without holes are one +# subclass of such complexes, users should rather design an own base class +# e.g. NXcg_polytope to describe such even more complex primitives instead +# of abusing this base class for such purposes. # # # -# The total number of vertices in the set. +# The total number of vertices in the set. # # # # # -# Combined storage of all primitives of all polygons. +# Combined storage of all primitives of all polygons. # # # # -# Individual storage of the mesh of each polygon. +# Individual storage of the mesh of each polygon. # # # # -# Individual storage of each polygon as a graph. +# Individual storage of each polygon as a graph. # # # # # -# For each polygon its accumulated length along its edges. +# For each polygon its accumulated length along its edges. # # # @@ -199,11 +192,11 @@ NXcg_polygon_set(NXcg_primitive_set): # # # -# Interior angles for each polygon. There are as many values per polygon -# as the are number_of_vertices. -# The angle is the angle at the specific vertex, i.e. between the adjoining -# edges of the vertex according to the sequence in the polygons array. -# Usually, the winding_order field is required to interpret the value. +# Interior angles for each polygon. There are as many values per polygon +# as the are number_of_vertices. +# The angle is the angle at the specific vertex, i.e. between the adjoining +# edges of the vertex according to the sequence in the polygons array. +# Usually, the winding_order field is required to interpret the value. # # # @@ -211,11 +204,11 @@ NXcg_polygon_set(NXcg_primitive_set): # # # -# Curvature type: -# -# * 0 - unspecified, -# * 1 - convex, -# * 2 - concave +# Curvature type: +# +# * 0 - unspecified, +# * 1 - convex, +# * 2 - concave # # # diff --git a/contributed_definitions/nyaml/NXcg_polyhedron_set.yaml b/base_classes/nyaml/NXcg_polyhedron.yaml similarity index 76% rename from contributed_definitions/nyaml/NXcg_polyhedron_set.yaml rename to base_classes/nyaml/NXcg_polyhedron.yaml index 5ed60132b1..681699ad6c 100644 --- a/contributed_definitions/nyaml/NXcg_polyhedron_set.yaml +++ b/base_classes/nyaml/NXcg_polyhedron.yaml @@ -8,7 +8,7 @@ doc: | For the description of more complicated manifolds and especially for polyhedra with holes, users are advised to check if their particular needs are described - by creating customized instances of an :ref:`NXcg_polygon_set`. + by creating customized instances of an :ref:`NXcg_polygon`. symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. @@ -29,7 +29,7 @@ symbols: # polyhedra and also half_edge_data_structures that can be useful # for clean graph-based descriptions of polyhedra. type: group -NXcg_polyhedron_set(NXcg_primitive_set): +NXcg_polyhedron(NXcg_primitive): # qualifiers and properties of polyhedra number_of_faces(NX_INT): @@ -73,13 +73,13 @@ NXcg_polyhedron_set(NXcg_primitive_set): Individual storage of each polygon as a graph. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# e291b7a90f8a679ff8dffbf38903db0540afad9e9d4d62945756e9fc7f45320b +# 9d922551ffc0d7096f4706fd65df4bcfe410ffee1972a510f47e68f65261dccc # # # -# +# # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The cardinality of the set, i.e. the number of polyhedra. +# The cardinality of the set, i.e. the number of polyhedra. # # # # -# The total number of edges for all polyhedra. +# The total number of edges for all polyhedra. # # # # -# The total number of faces for all polyhedra. +# The total number of faces for all polyhedra. # # # # -# Computational geometry description of a set of polyhedra in Euclidean space. -# -# Polyhedra or so-called cells (especially in the convex of tessellations) are -# constructed from polygon meshes. Polyhedra may make contact to allow a usage -# of this base class for a description of tessellations. -# -# For the description of more complicated manifolds and especially for polyhedra -# with holes, users are advised to check if their particular needs are described -# by creating customized instances of an :ref:`NXcg_polygon_set`. +# Computational geometry description of a set of polyhedra in Euclidean space. +# +# Polyhedra or so-called cells (especially in the convex of tessellations) are +# constructed from polygon meshes. Polyhedra may make contact to allow a usage +# of this base class for a description of tessellations. +# +# For the description of more complicated manifolds and especially for polyhedra +# with holes, users are advised to check if their particular needs are described +# by creating customized instances of an :ref:`NXcg_polygon`. # # # # -# The number of faces for each polyhedron. Faces of adjoining polyhedra -# are counted for each polyhedron. +# The number of faces for each polyhedron. Faces of adjoining polyhedra +# are counted for each polyhedron. # # # @@ -151,7 +151,7 @@ NXcg_polyhedron_set(NXcg_primitive_set): # # # -# Area of each of faces. +# Area of each of faces. # # # @@ -159,13 +159,13 @@ NXcg_polyhedron_set(NXcg_primitive_set): # # # -# The number of edges for each polyhedron. Edges of adjoining polyhedra -# are counterd for each polyhedron. +# The number of edges for each polyhedron. Edges of adjoining polyhedra +# are counterd for each polyhedron. # # # # -# Length of each edge. +# Length of each edge. # # # @@ -174,17 +174,17 @@ NXcg_polyhedron_set(NXcg_primitive_set): # # # -# Combined storage of all primitives of all polyhedra. +# Combined storage of all primitives of all polyhedra. # # # # -# Individual storage of each polyhedron. +# Individual storage of each polyhedron. # # # # -# Individual storage of each polygon as a graph. +# Individual storage of each polygon as a graph. # # # diff --git a/contributed_definitions/nyaml/NXcg_polyline_set.yaml b/base_classes/nyaml/NXcg_polyline.yaml similarity index 82% rename from contributed_definitions/nyaml/NXcg_polyline_set.yaml rename to base_classes/nyaml/NXcg_polyline.yaml index c73e971c1c..22841804d5 100644 --- a/contributed_definitions/nyaml/NXcg_polyline_set.yaml +++ b/base_classes/nyaml/NXcg_polyline.yaml @@ -4,7 +4,7 @@ doc: | Each polyline is built from a sequence of vertices (points with identifiers). Each polyline must have a start and an end point. - The sequence describes the positive traversal along the polyline when + The sequence describes the traversal along the polyline when walking from the first to the last vertex. symbols: doc: | @@ -21,7 +21,12 @@ symbols: n_total: | The total number of vertices traversed when visiting every polyline. type: group -NXcg_polyline_set(NXcg_primitive_set): +NXcg_polyline(NXcg_primitive): + depends_on(NX_CHAR): + doc: | + Reference to an instance of :ref:`NXcg_point` which defines the + location of the vertices that are referred to in this + NXcg_polyline instance. number_of_unique_vertices(NX_POSINT): unit: NX_UNITLESS doc: | @@ -35,8 +40,6 @@ NXcg_polyline_set(NXcg_primitive_set): doc: | The total number of vertices of each polyline, irrespectively whether vertices are shared by vertices or not. - See the docstring for polylines for further details about how - a set with different polyline members should be stored. dimensions: rank: 1 dim: (c,) @@ -60,10 +63,6 @@ NXcg_polyline_set(NXcg_primitive_set): dimensions: rank: 2 dim: (n_v, d) - - # alternatively we may store the actual vertices in an instance of - # NXcg_point_set and (e.g. to promote compact storage of information and primitives) - # and then use vertices_are_unique(NX_BOOLEAN): doc: | If true indicates that the vertices are all placed at different @@ -75,9 +74,9 @@ NXcg_polyline_set(NXcg_primitive_set): Sequence of identifier for vertices how they build each polyline. A trivial example is a set with two polylines with three vertices each. - If the polylines meet in a junction, say the second vertex is shared - and marking the junction between the two polylines, it is possible that - there are only five unique positions. This suggests to store five + If the polylines meet at a vertex (assume for example that the second vertex + is shared and marking the junction between the two polylines), it is possible + that there are only five unique positions. This suggests to store five unique vertices. A non-trivial example is a set with several polylines. Assume that each @@ -88,21 +87,21 @@ NXcg_polyline_set(NXcg_primitive_set): followed by the second vertex of the first polyline, until the last vertex of the first polyline. Thereafter, the first vertex of the second polyline, and so on and so forth. - Using the (cumulated) counts in number_of_vertices, the vertices of the - n-th polyline can be accessed on the following array index interval: - :math:`[\sum_{i=0}^{i=N-1}, \sum_{i=0}^{i=N}]`. + Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`), + the vertices of the N-th polyline can be accessed on the array + index interval :math:`[\sum_{i=0}^{i=N-1} n^v_i, \sum_{i=0}^{i=N} n^v_i]`. dimensions: rank: 1 dim: (n_total,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 3a283b6af746b1f28cca7d7a8eee8b36002ffe4595eb5066af8365b68aba746e +# f838ec9411d9e75d720c6e986fbaa571e08927458a68c6e48d9272421b5742b9 # # # -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. @@ -153,9 +152,16 @@ NXcg_polyline_set(NXcg_primitive_set): # # Each polyline is built from a sequence of vertices (points with identifiers). # Each polyline must have a start and an end point. -# The sequence describes the positive traversal along the polyline when +# The sequence describes the traversal along the polyline when # walking from the first to the last vertex. # +# +# +# Reference to an instance of :ref:`NXcg_point` which defines the +# location of the vertices that are referred to in this +# NXcg_polyline instance. +# +# # # # The total number of vertices that have different positions. @@ -170,8 +176,6 @@ NXcg_polyline_set(NXcg_primitive_set): # # The total number of vertices of each polyline, irrespectively # whether vertices are shared by vertices or not. -# See the docstring for polylines for further details about how -# a set with different polyline members should be stored. # # # @@ -198,9 +202,6 @@ NXcg_polyline_set(NXcg_primitive_set): # # # -# # # # If true indicates that the vertices are all placed at different @@ -213,9 +214,9 @@ NXcg_polyline_set(NXcg_primitive_set): # Sequence of identifier for vertices how they build each polyline. # # A trivial example is a set with two polylines with three vertices each. -# If the polylines meet in a junction, say the second vertex is shared -# and marking the junction between the two polylines, it is possible that -# there are only five unique positions. This suggests to store five +# If the polylines meet at a vertex (assume for example that the second vertex +# is shared and marking the junction between the two polylines), it is possible +# that there are only five unique positions. This suggests to store five # unique vertices. # # A non-trivial example is a set with several polylines. Assume that each @@ -226,9 +227,9 @@ NXcg_polyline_set(NXcg_primitive_set): # followed by the second vertex of the first polyline, until the last vertex # of the first polyline. # Thereafter, the first vertex of the second polyline, and so on and so forth. -# Using the (cumulated) counts in number_of_vertices, the vertices of the -# n-th polyline can be accessed on the following array index interval: -# :math:`[\sum_{i=0}^{i=N-1}, \sum_{i=0}^{i=N}]`. +# Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`), +# the vertices of the N-th polyline can be accessed on the array +# index interval :math:`[\sum_{i=0}^{i=N-1} n^v_i, \sum_{i=0}^{i=N} n^v_i]`. # # # diff --git a/base_classes/nyaml/NXcg_primitive.yaml b/base_classes/nyaml/NXcg_primitive.yaml new file mode 100644 index 0000000000..56c1520693 --- /dev/null +++ b/base_classes/nyaml/NXcg_primitive.yaml @@ -0,0 +1,428 @@ +category: base +doc: | + Computational geometry description of a set of primitives in Euclidean space. + + Primitives must neither be degenerated nor self-intersect. + Individual primitives can differ in their properties (e.g. size, shape, rotation). +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + d: | + The dimensionality of the embedding space. + c: | + The cardinality of the set, i.e. the number of members. +type: group +NXcg_primitive(NXobject): + depends_on(NX_CHAR): + doc: | + Reference to an instance of :ref:`NXcoordinate_system` in which these primitives + are defined. + dimensionality(NX_POSINT): + unit: NX_UNITLESS + doc: | + The dimensionality of the primitive set with value up to d. + enumeration: + + # add when 1521 has been merged open="true" + items: [1, 2, 3] + cardinality(NX_POSINT): + unit: NX_UNITLESS + doc: | + The cardinality of the primitive set. Value should be equal to c. + identifier_offset(NX_INT): + unit: NX_UNITLESS + doc: | + Integer offset whereby the identifier of the first member + of the set differs from zero. + + Identifiers can be defined either implicitly or explicitly. + For implicit indexing identifiers are defined on the interval + :math:`[identifier\_offset, identifier\_offset + c - 1]`. + + Therefore, implicit identifier are completely defined by the value of + identifier_offset and cardinality. For example if identifier run from + -2 to 3 the value for identifier_offset is -2. + + For explicit indexing the field identifier has to be used. + Fortran-/Matlab- and C-/Python-style indexing have specific implicit + identifier conventions where identifier_offset is 1 and 0 respectively. + identifier(NX_INT): + doc: | + Identifier of each member for explicit indexing. + dimensions: + rank: 1 + dim: (c,) + center(NX_NUMBER): + unit: NX_ANY + doc: | + The center of each primitive + dimensions: + rank: 2 + dim: (c, d) + is_center_of_mass(NX_BOOLEAN): + doc: | + True if the center is a center of mass. + dimensions: + rank: 1 + dim: (c,) + shape(NX_NUMBER): + unit: NX_LENGTH + doc: | + Shape of each primitive + dimensions: + rank: 2 + dim: (c, d) + length(NX_NUMBER): + unit: NX_LENGTH + doc: | + Length of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + dimensions: + rank: 1 + dim: (c,) + width(NX_NUMBER): + unit: NX_LENGTH + doc: | + Width of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + dimensions: + rank: 1 + dim: (c,) + height(NX_NUMBER): + unit: NX_LENGTH + doc: | + Height of each primitive + + Often the term is associated with the assumption that one + edge is parallel to an axis of the coordinate system. + dimensions: + rank: 1 + dim: (c,) + is_closed(NX_BOOLEAN): + doc: | + True if primitive is closed such that it has properties like area or volume. + dimensions: + rank: 1 + dim: (c,) + volume(NX_NUMBER): + unit: NX_ANY + doc: | + Volume of each primitive. + + Set to NaN if does not apply for primitives for which is_closed is False. + Volume is an N-D concept for values of dimensionality larger than 1, + Area is an alias for the two-dimensional case. + dimensions: + rank: 1 + dim: (c,) + area(NX_NUMBER): + unit: NX_AREA + doc: | + Alias for surface_area of each primitive. + + Set to NaN if does not apply for primitives for which is_closed is False. + dimensions: + rank: 1 + dim: (c,) + orientation(NX_NUMBER): + unit: NX_DIMENSIONLESS + doc: | + Direction unit vector which points along the + longest principal axis of each primitive. + + Use the depends_on attribute to specify in which coordinate system + these direction unit vectors are defined. + dimensions: + rank: 2 + dim: (c, d) + is_mesh(NX_BOOLEAN): + doc: | + Do the primitives define a mesh. + is_triangle_mesh(NX_BOOLEAN): + doc: | + Do the primitives define a triangle mesh or not. + is_surface_mesh(NX_BOOLEAN): + doc: | + Do the primitives discretize the surface of an object or not. + is_geodesic_mesh(NX_BOOLEAN): + doc: | + Do the primitives define a geodesic mesh or not. + + A geodesic surface mesh is a triangulated surface mesh with metadata which + can be used as an approximation to describe the surface of a sphere. + Triangulation of spheres are commonly used in Materials Science + for quantifying texture of materials, i.e. the relative rotation of + crystals to sample directions. + + For additional details or an introduction into the topic of geodesic meshes + see (from which specifically the section on subdivision schemes is relevant). + + * `E. S. Popko and C. J. Kitrick `_ + + Earth scientists have specific demands and different views about what should + be included in such a base class, given that nested geodesic meshes are a key + component of climate modelling software. For now we propose to use this + base class as a container for organizing data related to geodesic meshes. + + Specifically an instance of this base class should detail the rule set how + e.g. a geodesic (surface) mesh was instantiated as there are many + possibilities to do so. + description: + doc: | + Possibility to store details such as when primitives form a (specific) type + of mesh such as geodesic meshes. + vertex_normal(NXcg_unit_normal): + edge_normal(NXcg_unit_normal): + face_normal(NXcg_unit_normal): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# aa99ded7f5d1a78a62579d68cb46df21baef3a813e34ec58443605280aa4f10a +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# The dimensionality of the embedding space. +# +# +# +# +# The cardinality of the set, i.e. the number of members. +# +# +# +# +# Computational geometry description of a set of primitives in Euclidean space. +# +# Primitives must neither be degenerated nor self-intersect. +# Individual primitives can differ in their properties (e.g. size, shape, rotation). +# +# +# +# Reference to an instance of :ref:`NXcoordinate_system` in which these primitives +# are defined. +# +# +# +# +# The dimensionality of the primitive set with value up to d. +# +# +# +# +# +# +# +# +# +# +# The cardinality of the primitive set. Value should be equal to c. +# +# +# +# +# Integer offset whereby the identifier of the first member +# of the set differs from zero. +# +# Identifiers can be defined either implicitly or explicitly. +# For implicit indexing identifiers are defined on the interval +# :math:`[identifier\_offset, identifier\_offset + c - 1]`. +# +# Therefore, implicit identifier are completely defined by the value of +# identifier_offset and cardinality. For example if identifier run from +# -2 to 3 the value for identifier_offset is -2. +# +# For explicit indexing the field identifier has to be used. +# Fortran-/Matlab- and C-/Python-style indexing have specific implicit +# identifier conventions where identifier_offset is 1 and 0 respectively. +# +# +# +# +# Identifier of each member for explicit indexing. +# +# +# +# +# +# +# +# The center of each primitive +# +# +# +# +# +# +# +# +# True if the center is a center of mass. +# +# +# +# +# +# +# +# Shape of each primitive +# +# +# +# +# +# +# +# +# Length of each primitive +# +# Often the term is associated with the assumption that one +# edge is parallel to an axis of the coordinate system. +# +# +# +# +# +# +# +# Width of each primitive +# +# Often the term is associated with the assumption that one +# edge is parallel to an axis of the coordinate system. +# +# +# +# +# +# +# +# Height of each primitive +# +# Often the term is associated with the assumption that one +# edge is parallel to an axis of the coordinate system. +# +# +# +# +# +# +# +# True if primitive is closed such that it has properties like area or volume. +# +# +# +# +# +# +# +# Volume of each primitive. +# +# Set to NaN if does not apply for primitives for which is_closed is False. +# Volume is an N-D concept for values of dimensionality larger than 1, +# Area is an alias for the two-dimensional case. +# +# +# +# +# +# +# +# Alias for surface_area of each primitive. +# +# Set to NaN if does not apply for primitives for which is_closed is False. +# +# +# +# +# +# +# +# Direction unit vector which points along the +# longest principal axis of each primitive. +# +# Use the depends_on attribute to specify in which coordinate system +# these direction unit vectors are defined. +# +# +# +# +# +# +# +# +# Do the primitives define a mesh. +# +# +# +# +# Do the primitives define a triangle mesh or not. +# +# +# +# +# Do the primitives discretize the surface of an object or not. +# +# +# +# +# Do the primitives define a geodesic mesh or not. +# +# A geodesic surface mesh is a triangulated surface mesh with metadata which +# can be used as an approximation to describe the surface of a sphere. +# Triangulation of spheres are commonly used in Materials Science +# for quantifying texture of materials, i.e. the relative rotation of +# crystals to sample directions. +# +# For additional details or an introduction into the topic of geodesic meshes +# see (from which specifically the section on subdivision schemes is relevant). +# +# * `E. S. Popko and C. J. Kitrick <https://doi.org/10.1201/9781003134114>`_ +# +# Earth scientists have specific demands and different views about what should +# be included in such a base class, given that nested geodesic meshes are a key +# component of climate modelling software. For now we propose to use this +# base class as a container for organizing data related to geodesic meshes. +# +# Specifically an instance of this base class should detail the rule set how +# e.g. a geodesic (surface) mesh was instantiated as there are many +# possibilities to do so. +# +# +# +# +# Possibility to store details such as when primitives form a (specific) type +# of mesh such as geodesic meshes. +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXcg_roi_set.yaml b/base_classes/nyaml/NXcg_roi.yaml similarity index 80% rename from contributed_definitions/nyaml/NXcg_roi_set.yaml rename to base_classes/nyaml/NXcg_roi.yaml index 99cfb2b487..a4775fcd38 100644 --- a/contributed_definitions/nyaml/NXcg_roi_set.yaml +++ b/base_classes/nyaml/NXcg_roi.yaml @@ -9,7 +9,7 @@ symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. Use the depends_on fields of the respective specialized - :ref:`NXcg_primitive_set` base class surplus + :ref:`NXcg_primitive` base class surplus :ref:`NXcoordinate_system_set` with at least one instance of :ref:`NXcoordinate_system` to define explicitly the reference frame in which the primitives are defined. Alternatively, although @@ -21,25 +21,24 @@ symbols: # eventually redundant NXsolid_geometry? type: group -NXcg_roi_set(NXobject): - (NXcg_sphere_set): - (NXcg_ellipsoid_set): - (NXcg_cylinder_set): - (NXcg_parallelogram_set): - (NXcg_hexahedron_set): - (NXcg_polyhedron_set): +NXcg_roi(NXobject): + (NXcg_ellipsoid): + (NXcg_cylinder): + (NXcg_parallelogram): + (NXcg_hexahedron): + (NXcg_polyhedron): # how to handle cases where multiple primitives should be included? - # see comment to NXcg_triangle_set roi + # see comment to NXcg_triangle roi # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 04608b03b57e48185fc46ae2b7d1bdadbae59955a821f33b8f8447d80aad83e3 +# 5e4de587b962e26cedc27cb007a65f2528ad4d3473f83e6ad1d2dad6e18b651c # # # # -# +# # # # The symbols used in the schema to specify e.g. dimensions of arrays. # Use the depends_on fields of the respective specialized -# :ref:`NXcg_primitive_set` base class surplus +# :ref:`NXcg_primitive` base class surplus # :ref:`NXcoordinate_system_set` with at least one instance of # :ref:`NXcoordinate_system` to define explicitly the reference frame in # which the primitives are defined. Alternatively, although @@ -82,12 +81,11 @@ NXcg_roi_set(NXobject): # region in space (and time) where an observation is made or for which # a computer simulation is performed with given boundary conditions. # -# -# -# -# -# -# +# +# +# +# +# # +# see comment to NXcg_triangle roi--> # diff --git a/contributed_definitions/nyaml/NXcg_tetrahedron_set.yaml b/base_classes/nyaml/NXcg_tetrahedron.yaml similarity index 63% rename from contributed_definitions/nyaml/NXcg_tetrahedron_set.yaml rename to base_classes/nyaml/NXcg_tetrahedron.yaml index 9243bc30f1..2d65426ebd 100644 --- a/contributed_definitions/nyaml/NXcg_tetrahedron_set.yaml +++ b/base_classes/nyaml/NXcg_tetrahedron.yaml @@ -11,7 +11,7 @@ symbols: c: | The cardinality of the set, i.e. the number of tetrahedra. type: group -NXcg_tetrahedron_set(NXcg_primitive_set): +NXcg_tetrahedron(NXcg_primitive): # qualifiers and properties of tetrahedra face_area(NX_NUMBER): @@ -28,16 +28,6 @@ NXcg_tetrahedron_set(NXcg_primitive_set): dimensions: rank: 2 dim: (c, 6) - - # substantially more detailed descriptors of the shape, the mesh - # currently not used should be discussed as sequence might not be clear to everybody - # interior_angle(NX_NUMBER): - # doc: | - # Interior angle values for each tetrahedron. - # The quadruplet of angles is a sequence following the order of the vertices. - # The angle is the angle at the specific vertex. - # The sequence of the vertices follows their definition in tetrahedra. - # detailed mesh-based representation tetrahedra(NXcg_face_list_data_structure): doc: | Combined storage of all primitives of all tetrahedra. @@ -51,13 +41,13 @@ NXcg_tetrahedron_set(NXcg_primitive_set): Individual storage of each tetrahedron as a graph. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# d8ccc211c8894acc7eac6b81ef354cd5af5a92dd0b9bd3a2dca403bbe6004f92 +# f772d6a0bf5b431dc18eb9da83598d71137a3c858351d4290df0a101c89759e5 # # # -# +# # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The cardinality of the set, i.e. the number of tetrahedra. +# The cardinality of the set, i.e. the number of tetrahedra. # # # # -# Computational geometry description of a set of tetrahedra. -# -# Among hexahedral elements, tetrahedral elements are one of the most -# frequently used geometric primitive for meshing and describing volumetric -# objects in continuum-field simulations. +# Computational geometry description of a set of tetrahedra. +# +# Among hexahedral elements, tetrahedral elements are one of the most +# frequently used geometric primitive for meshing and describing volumetric +# objects in continuum-field simulations. # # # # -# Area of each of the four triangular faces of each tetrahedron. +# Area of each of the four triangular faces of each tetrahedron. # # # @@ -105,35 +95,26 @@ NXcg_tetrahedron_set(NXcg_primitive_set): # # # -# Length of each edge of each tetrahedron. +# Length of each edge of each tetrahedron. # # # # # # -# # # -# Combined storage of all primitives of all tetrahedra. +# Combined storage of all primitives of all tetrahedra. # # # # -# Individual storage of each tetrahedron. +# Individual storage of each tetrahedron. # # # # -# Individual storage of each tetrahedron as a graph. +# Individual storage of each tetrahedron as a graph. # # # diff --git a/contributed_definitions/nyaml/NXcg_triangle_set.yaml b/base_classes/nyaml/NXcg_triangle.yaml similarity index 67% rename from contributed_definitions/nyaml/NXcg_triangle_set.yaml rename to base_classes/nyaml/NXcg_triangle.yaml index ded2cf6e70..eee7642d9a 100644 --- a/contributed_definitions/nyaml/NXcg_triangle_set.yaml +++ b/base_classes/nyaml/NXcg_triangle.yaml @@ -11,7 +11,7 @@ symbols: n_unique: | The number of unique vertices supporting the triangles. type: group -NXcg_triangle_set(NXcg_primitive_set): +NXcg_triangle(NXcg_primitive): number_of_unique_vertices(NX_INT): unit: NX_UNITLESS doc: | @@ -28,12 +28,6 @@ NXcg_triangle_set(NXcg_primitive_set): Individual storage of each triangle. Users are advised that using such individual storage of primitives may be less storage efficient than creating a combined storage. - - #MK::considered too trivial: - # triangle_half_edgeID(NXcg_half_edge_data_structure): - # doc: | - # Individual storage of each triangle as a graph. - # properties of triangles edge_length(NX_NUMBER): unit: NX_LENGTH doc: | @@ -56,13 +50,13 @@ NXcg_triangle_set(NXcg_primitive_set): dim: (c, 3) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1d848f77305e03ff65e6574b889212b49e0c38694054821abd000e5583980e2a +# fe99956b8b305e0e920fc7b726b5f8ed243fefa82c6ebb87f13e1ce8cdebef9d # # # -# +# # # -# The symbols used in the schema to specify e.g. dimensions of arrays. +# The symbols used in the schema to specify e.g. dimensions of arrays. # # # -# The dimensionality, which has to be at least 2. +# The dimensionality, which has to be at least 2. # # # # -# The cardinality of the set, i.e. the number of triangles. +# The cardinality of the set, i.e. the number of triangles. # # # # -# The number of unique vertices supporting the triangles. +# The number of unique vertices supporting the triangles. # # # # -# Computational geometry description of a set of triangles. +# Computational geometry description of a set of triangles. # # # -# Number of unique vertices in the triangle set. +# Number of unique vertices in the triangle set. # # # # -# Combined storage of all primitives of all triangles. -# -# This description resembles the typical representation of primitives -# in file formats such as OFF, PLY, VTK, or STL. +# Combined storage of all primitives of all triangles. +# +# This description resembles the typical representation of primitives +# in file formats such as OFF, PLY, VTK, or STL. # # # # -# Individual storage of each triangle. -# Users are advised that using such individual storage of primitives -# may be less storage efficient than creating a combined storage. +# Individual storage of each triangle. +# Users are advised that using such individual storage of primitives +# may be less storage efficient than creating a combined storage. # # -# # # -# Length of the edges of each triangle. -# -# For each triangle values are reported via traversing -# the vertices in the sequence as these are defined. +# Length of the edges of each triangle. +# +# For each triangle values are reported via traversing +# the vertices in the sequence as these are defined. # # # @@ -143,10 +132,10 @@ NXcg_triangle_set(NXcg_primitive_set): # # # -# Interior angles of each triangle. -# -# For each triangle values are reported for the angle opposite -# to the respective edges in the sequence how vertices are defined. +# Interior angles of each triangle. +# +# For each triangle values are reported for the angle opposite +# to the respective edges in the sequence how vertices are defined. # # # diff --git a/contributed_definitions/nyaml/NXcg_unit_normal_set.yaml b/base_classes/nyaml/NXcg_unit_normal.yaml similarity index 90% rename from contributed_definitions/nyaml/NXcg_unit_normal_set.yaml rename to base_classes/nyaml/NXcg_unit_normal.yaml index 9acaa01aa9..657048e250 100644 --- a/contributed_definitions/nyaml/NXcg_unit_normal_set.yaml +++ b/base_classes/nyaml/NXcg_unit_normal.yaml @@ -3,7 +3,7 @@ doc: | Computational geometry description of a set of (oriented) unit normal vectors. Store normal vector information as properties of primitives. - Use only only as a child of an instance of :ref:`NXcg_primitive_set` + Use only only as a child of an instance of :ref:`NXcg_primitive` so that this instance acts as the parent to define a context. # eventually remove this base class and make normal vector a property of the primitive @@ -19,7 +19,7 @@ symbols: # how to resolve the association between the unit normal and its associated primitive? # rather make this a set of vectors, irrespective whether these are unit or not type: group -NXcg_unit_normal_set(NXobject): +NXcg_unit_normal(NXobject): normals(NX_NUMBER): unit: NX_LENGTH doc: | @@ -30,7 +30,7 @@ NXcg_unit_normal_set(NXobject): orientation(NX_INT): unit: NX_UNITLESS doc: | - Qualifier which details the orientation of each normal vector + An indicator which details the orientation of each normal vector in relation to its primitive, assuming the object is viewed from a position outside the object. @@ -42,13 +42,13 @@ NXcg_unit_normal_set(NXobject): dim: (c,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# b1c14f59c3e36c2e69443da6e9157c75336944d5da147c85e77f6ba3103afaa8 +# f987a47e06d87c7a3835affeda661ac97e7939eb67c9775e11698bc408a0b88e # # # -# +# # # # @@ -91,7 +91,7 @@ NXcg_unit_normal_set(NXobject): # Computational geometry description of a set of (oriented) unit normal vectors. # # Store normal vector information as properties of primitives. -# Use only only as a child of an instance of :ref:`NXcg_primitive_set` +# Use only only as a child of an instance of :ref:`NXcg_primitive` # so that this instance acts as the parent to define a context. # # @@ -105,7 +105,7 @@ NXcg_unit_normal_set(NXobject): # # # -# Qualifier which details the orientation of each normal vector +# An indicator which details the orientation of each normal vector # in relation to its primitive, assuming the object is viewed # from a position outside the object. # diff --git a/contributed_definitions/nyaml/NXchemical_composition.yaml b/base_classes/nyaml/NXchemical_composition.yaml similarity index 96% rename from contributed_definitions/nyaml/NXchemical_composition.yaml rename to base_classes/nyaml/NXchemical_composition.yaml index 7346a98cca..28d9b9078e 100644 --- a/contributed_definitions/nyaml/NXchemical_composition.yaml +++ b/base_classes/nyaml/NXchemical_composition.yaml @@ -20,7 +20,7 @@ NXchemical_composition(NXobject): dimensions: rank: 1 dim: (n,) - ION(NXion): + (NXion): count(NX_NUMBER): unit: NX_UNITLESS doc: | @@ -38,7 +38,7 @@ NXchemical_composition(NXobject): dim: (n,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fbca5dfb6c37256e42ed91f943ee132998118294efc98cdd60e237a8a42d6b30 +# 6e15c54d538e7c8579228cf237a7f19402e134b6b8aee0d9db1a88abb3fdaad4 # # # +# +# +# Base class for circuit devices. +# +# +# +# Hardware type used in circuit, includes hardware manufacturers and type +# +# +# +# +# The tunneling current between tip and sample after application of bias voltage. +# +# +# +# +# Calibration of the current measurement (A/V). +# +# +# +# +# Offset of the current measurement. +# +# +# +# +# Proportional relationship between the probe output voltage and the actual +# tunneling current when measuring the tunneling current. +# +# +# +# +# The scan channels are selected by users (in scan contronaller). +# +# +# +# +# The bandwitdh of the Hardware and/or Software +# +# +# +# +# (Signals Periods) The Signals Period is the rate at which the signals are +# transferred to the host computer running the control software. This is usually +# lower by a factor of 10 than the sampling rate, because an internal oversampling +# of the signal is done on the real time engine. You can reduce the oversampling +# down to 1 in order to resolve higher frequencies in the Spectrum Analyzer. +# +# +# +# +# Update rate for several processes like History Graph, Auto-Approach, and for +# many Programming Interface functions. This is usually set to 20 ms. All +# additional timings (7-9) can only be integer multiples of this value. They can +# be set to different values, but the actual timing value will be coerced to a +# multiple of the Acquisition Period. +# +# +# +# +# Update rate of animated graphical indicators. These are e.g. some graphs & +# sliders. A reasonable value is 40 ms (25 updates per second). Increase this +# period to reduce the processor load for the graphical user interface, especially +# on slow computers. This value is purely a user interface update rate and does +# not affect measurements in any way. +# +# +# +# +# Update rate of digital indicators, e.g. the numbers displayed besides each +# slider. Here, 3 updates per second, or 300 ms is enough. This value is purely a +# user interface update rate and does not affect measurements in any way. +# +# +# +# +# The Measurements period is the integration time for precise measurements +# (averaging over specified period), mostly used in sweep modules. Examples are +# recording of a force-distance curve or a resonance of a cantilever. For fast +# measurements with small steps, a value of 40 ms may be reasonable. For normal +# use, 300-500 ms is a good value, but for recording a resonance of a high-Q +# cantilever, values of several seconds might be necessary. Usually this parameter +# doesn’t need to be set from this module; the sweep modules will set this value +# according to the sweep timings. +# +# +# +# +# Number of output channels +# +# +# +# +# The user output in each monitor mode. +# +# +# +# +# The values for each output channel. +# +# +# +# +# User outputs whose name can be modified in the corresponding module. +# +# +# +# +# The rate at which the one of the signal changes when ramping to the starting +# point. (V/s) +# +# +# diff --git a/contributed_definitions/nyaml/NXcoordinate_system.yaml b/base_classes/nyaml/NXcoordinate_system.yaml similarity index 92% rename from contributed_definitions/nyaml/NXcoordinate_system.yaml rename to base_classes/nyaml/NXcoordinate_system.yaml index 808664665b..93a6b8f0c8 100644 --- a/contributed_definitions/nyaml/NXcoordinate_system.yaml +++ b/base_classes/nyaml/NXcoordinate_system.yaml @@ -30,23 +30,23 @@ NXcoordinate_system(NXobject): type(NX_CHAR): doc: | Coordinate system type. - enumeration: [undefined, cartesian] + enumeration: [cartesian] handedness(NX_CHAR): doc: | Handedness of the coordinate system if it is a Cartesian. - enumeration: [undefined, right_handed, left_handed] + enumeration: [right_handed, left_handed] x_alias(NX_CHAR): doc: | Possibility to define an alias for the name of the x-axis. x_direction(NX_CHAR): doc: | Human-readable field telling in which direction the x-axis points if that - instance of :ref:`NXcoordinate_system` has no reference to any parent and as such - is the mighty world reference frame. + instance of :ref:`NXcoordinate_system` has no reference to any parent + and as such is the world reference frame. Exemplar values could be direction of gravity. - # enumeration: [undefined, north, east, south, west, in, out] + # enumeration: [north, east, south, west, in, out] x(NX_NUMBER): unit: NX_LENGTH doc: | @@ -62,8 +62,8 @@ NXcoordinate_system(NXobject): y_direction(NX_CHAR): doc: | Human-readable field telling in which direction the y-axis points if that - instance of :ref:`NXcoordinate_system` has no reference to any parent and as such - is the mighty world reference frame. + instance of :ref:`NXcoordinate_system` has no reference to any parent + and as such is the world reference frame. See docstring of x_alias for further details. y(NX_NUMBER): @@ -81,8 +81,8 @@ NXcoordinate_system(NXobject): z_direction(NX_CHAR): doc: | Human-readable field telling in which direction the z-axis points if that - instance of :ref:`NXcoordinate_system` has no reference to any parent and as such - is the mighty world reference frame. + instance of :ref:`NXcoordinate_system` has no reference to any parent + and as such is the world reference frame. See docstring of x_alias for further details. z(NX_NUMBER): @@ -104,13 +104,13 @@ NXcoordinate_system(NXobject): with respect to another coordinate system. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# cdafd39940ce435a04df7033700314c640435fe409182e7d4c10bb159f423f1d +# 28d94e75a287b51c7eef7633c029c110ffb68f06280dd8847b78784fbc3f1072 # # # +# # # # Base unit vector along the first axis which spans the coordinate system. @@ -211,8 +209,8 @@ NXcoordinate_system(NXobject): # # # Human-readable field telling in which direction the y-axis points if that -# instance of :ref:`NXcoordinate_system` has no reference to any parent and as such -# is the mighty world reference frame. +# instance of :ref:`NXcoordinate_system` has no reference to any parent +# and as such is the world reference frame. # # See docstring of x_alias for further details. # @@ -235,8 +233,8 @@ NXcoordinate_system(NXobject): # # # Human-readable field telling in which direction the z-axis points if that -# instance of :ref:`NXcoordinate_system` has no reference to any parent and as such -# is the mighty world reference frame. +# instance of :ref:`NXcoordinate_system` has no reference to any parent +# and as such is the world reference frame. # # See docstring of x_alias for further details. # diff --git a/contributed_definitions/nyaml/NXcoordinate_system_set.yaml b/base_classes/nyaml/NXcoordinate_system_set.yaml similarity index 97% rename from contributed_definitions/nyaml/NXcoordinate_system_set.yaml rename to base_classes/nyaml/NXcoordinate_system_set.yaml index 09f7679601..5436256a0a 100644 --- a/contributed_definitions/nyaml/NXcoordinate_system_set.yaml +++ b/base_classes/nyaml/NXcoordinate_system_set.yaml @@ -100,13 +100,13 @@ NXcoordinate_system_set(NXobject): DOI: 10.1088/0965-0393/23/8/083501. Counter_clockwise is equivalent to a right-handed choice. Clockwise is equivalent to a left-handed choice. - enumeration: [undefined, counter_clockwise, clockwise] + enumeration: [counter_clockwise, clockwise] rotation_convention(NX_CHAR): doc: | How are rotations interpreted into an orientation according to convention 3 of DOI: 10.1088/0965-0393/23/8/083501. - enumeration: [undefined, passive, active] + enumeration: [passive, active] euler_angle_convention(NX_CHAR): doc: | How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) @@ -115,19 +115,19 @@ NXcoordinate_system_set(NXobject): The most frequently used convention is zxz, which is based on the work of H.-J. Bunge but other conventions are possible. Apart from undefined, proper Euler angles are distinguished from (improper) Tait-Bryan angles. - enumeration: [undefined, zxz, xyx, yzy, zyz, xzx, yxy, xyz, yzx, zxy, xzy, zyx, yxz] + enumeration: [zxz, xyx, yzy, zyz, xzx, yxy, xyz, yzx, zxy, xzy, zyx, yxz] axis_angle_convention(NX_CHAR): doc: | To which angular range is the rotation angle argument of an axis-angle pair parameterization constrained according to convention 5 of DOI: 10.1088/0965-0393/23/8/083501. - enumeration: [undefined, rotation_angle_on_interval_zero_to_pi] + enumeration: [rotation_angle_on_interval_zero_to_pi] sign_convention(NX_CHAR): doc: | Which sign convention is followed when converting orientations between different parameterizations/representations according to convention 6 of DOI: 10.1088/0965-0393/23/8/083501. - enumeration: [undefined, p_plus_one, p_minus_one] + enumeration: [p_plus_one, p_minus_one] # possibility to add further coordinate systems (NXcoordinate_system): @@ -175,13 +175,13 @@ NXcoordinate_system_set(NXobject): If any of these assumptions is not met, the user is required to explicitly state this. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 48bceaace0f0a0d1cf74dcce9bf1b1159743ca4ff30afa8f2909b4901535aff2 +# be80f169a337c2ba3b5495688f18a429e2a7a26c5a8e38d6e62102eafb387b1d # # # # @@ -252,15 +230,13 @@ NXcorrector_cs(NXcomponent): # Was the corrector used? # # -# # # # Specific information about the alignment procedure that is a process during which # the corrector is configured to enable calibrated usage of the instrument. # # This :ref:`NXprocess` group should also be used when one describes in a computer -# simulation the specific details about the modelled or assumed aberration -# corrections. +# simulation the specific details about the modelled or assumed aberrations. # # # @@ -296,14 +272,15 @@ NXcorrector_cs(NXcomponent): # # # -# +# # -# The images taken during the alignment procedure. +# Image(s) taken during the alignment procedure # # # # -# Place for storing measured or estimated aberrations (for each image or final). +# Convention used for storing measured or estimated aberrations (for each image or final) +# via fields c_1, a_1, c_1_0, c_1_2_a, and so on and so forth. # # See `S. J. Pennycock and P. D. Nellist <https://doi.org/10.1007/978-1-4419-7200-2>`_ (page 44ff, and page 118ff) # for different definitions available and further details. Table 7-2 of Ibid. publication (page 305ff) documents how @@ -316,14 +293,10 @@ NXcorrector_cs(NXcomponent): # # # -# # # # # -# # # # # # # # # -# # # # @@ -348,8 +317,6 @@ NXcorrector_cs(NXcomponent): # # # -# # # # @@ -361,8 +328,6 @@ NXcorrector_cs(NXcomponent): # # # -# # # # @@ -411,5 +376,5 @@ NXcorrector_cs(NXcomponent): # technical design perspective--> # # -# +# # diff --git a/contributed_definitions/nyaml/NXcs_computer.yaml b/base_classes/nyaml/NXcs_computer.yaml similarity index 97% rename from contributed_definitions/nyaml/NXcs_computer.yaml rename to base_classes/nyaml/NXcs_computer.yaml index a55b1c3c1e..d5dba84770 100644 --- a/contributed_definitions/nyaml/NXcs_computer.yaml +++ b/base_classes/nyaml/NXcs_computer.yaml @@ -38,7 +38,9 @@ NXcs_computer(NXobject): type(NX_CHAR): doc: | General type of the processing unit - enumeration: [cpu, gpu, fpga, other] + enumeration: + open_enum: true + items: [cpu, gpu, fpga] name(NX_CHAR): doc: | Given name @@ -80,7 +82,7 @@ NXcs_computer(NXobject): # NXcircuit inherits fabrication from NXcomponent # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0a23c5f869599abf23d78cffd35f5d515ba0e068b21449b74cb878b744eb5fb3 +# def5b601cc7944d9508ed1a048390db9b67fbacb57891fb83b83252ffda54459 # # # -# +# # -# Deflectors as they are used e.g. in an electron analyzer. +# Deflectors as they are used e.g. in an electron analyser. # -# +# # -# Qualitative type of deflector with respect to the number of pole pieces. +# Qualitative type of deflector with respect to the number of pole pieces # # # @@ -74,32 +64,20 @@ NXdeflector(NXcomponent): # # # -# Colloquial or short name for the deflector. For manufacturer names and -# identifiers use ``NXfabrication`` and ``identifierNAME``. +# Colloquial or short name for the deflector. For manufacturer names and +# identifiers use ``NXfabrication`` and ``identifierNAME``. # # # # -# Excitation voltage of the deflector. For dipoles it is a single number. -# For higher order multipoles, it is an array. +# Excitation voltage of the deflector. For dipoles it is a single number. For +# higher orders, it is an array. # # # # -# Excitation current of the deflector. For dipoles it is a single number. For -# higher orders, it is an array. -# -# -# -# -# Spatial offset of the deflector in x direction (perpendicular to -# ```offset_y```). -# -# -# -# -# Spatial offset of the deflector in y direction (perpendicular to -# ```offset_x```). +# Excitation current of the deflector. For dipoles it is a single number. For +# higher orders, it is an array. # # -# +# \ No newline at end of file diff --git a/base_classes/nyaml/NXebeam_column.yaml b/base_classes/nyaml/NXebeam_column.yaml new file mode 100644 index 0000000000..c6e732c969 --- /dev/null +++ b/base_classes/nyaml/NXebeam_column.yaml @@ -0,0 +1,415 @@ +category: base +doc: | + Base class for a set of components providing a controllable electron beam. + + The idea behind defining NXebeam_column as an own base class vs. adding these + concepts in NXinstrument_em is that the electron beam generating component + might be worthwhile to use in other experiments also. +type: group +NXebeam_column(NXcomponent): + operation_mode(NX_CHAR): + doc: | + Tech-partner, microscope-, and control-software-specific name of the + specific operation mode how the ebeam_column and its components are controlled + to achieve specific illumination conditions. + + In many cases the users of an instrument do not or can not be expected to know + all intricate spatiotemporal dynamics of their hardware. Instead, they rely of + assumptions that the instrument, its control software, and components work as + expected to focus on their research questions. + + For these cases, having a place for documenting the operation_mode is useful + in as much as at least some constraints on how the illumination conditions were + get documented. + electron_source(NXsource): + doc: + - | + A physical part of an electron or ion microscope from which + the particles that form the beam are emitted. + - | + The hardware for an electron source in an electron microscope + may contain several components which affect the beam path. + - | + xref: + spec: EMglossary + term: Source + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 + voltage(NX_NUMBER): + unit: NX_VOLTAGE + doc: + - | + The potential difference between anode and cathode. + - | + xref: + spec: EMglossary + term: Acceleration Voltage + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 + extraction_voltage(NX_NUMBER): + unit: NX_VOLTAGE + doc: + - | + Voltage which is utilised to create an electric field that draws particles from + the source. + - | + xref: + spec: EMglossary + term: Extraction Voltage + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 + emission_current(NX_NUMBER): + unit: NX_CURRENT + doc: + - | + Electrical current which is released from the source. + - | + xref: + spec: EMglossary + term: Emission Current + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 + filament_current(NX_NUMBER): + unit: NX_CURRENT + doc: + - | + Electrical current which flows through the source. + - | + xref: + spec: EMglossary + term: Filament Current + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 + probe(NX_CHAR): + doc: | + Type of radiation. + enumeration: [electron] + emitter_type(NX_CHAR): + doc: | + Emitter type used to create the beam. + + If the emitter type is other, give further details + in the description field. + + # enumeration: [filament, schottky, cold_cathode_field_emitter, other] + emitter_material(NX_CHAR): + doc: | + Material of which the emitter is build, e.g. the filament material. + + # emitter material could inherit from NXsample + lifetime(NX_TIME): + doc: | + How long has the source been in operation. + (NXlens_em): + (NXaperture): + (NXdeflector): + (NXmonochromator): + doc: | + Device to improve energy resolution or chromatic aberration. + + Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector + like `_ + + # control level perspective + type(NX_CHAR): + doc: | + Qualitative type of the component. + enumeration: [wien, alfa, omega, castaing_henry, gatan_imaging, sector_analyzer] + (NXfabrication): + applied(NX_BOOLEAN): + doc: | + Was the corrector used? + + # technical level + dispersion(NX_NUMBER): + unit: NX_ANY + doc: | + Energy dispersion in e.g. µm/eV. + voltage(NX_NUMBER): + unit: NX_VOLTAGE + doc: | + Corresponding voltage for that energy dispersion. + corrector_cs(NXcorrector_cs): + corrector_ax(NXcomponent): + doc: | + Component that reshapes an ellipse-shaped electron beam into a circular one. + + * `L. Reimer 1998, Springer, 1998 `_ + * `M. Tanaka et al., Electron Microscopy Glossary, 2024 `_ + + Stigmator is an exact synonym. + value_x(NX_NUMBER): + unit: NX_ANY + doc: | + Descriptor for the correction strength along the first direction when exact technical details + are unknown or not directly controllable as the control software of the microscope does not + enable or was not configured to display these values for users. + value_y(NX_NUMBER): + unit: NX_ANY + doc: | + Descriptor for the correction strength along the second direction when exact technical details + are unknown or not directly controllable as the control software of the microscope does not + enable or was not configured to display these values for users. + biprism(NXcomponent): + doc: | + Electron biprism as it is used e.g. for electron holography. + (NXfabrication): + phaseplateID(NXcomponent): + nameType: partial + doc: | + Device that causes a change in the phase of an electron wave. + + * `M. Malac et al. `_ + * `R. R. Schröder et al. `_ + type(NX_CHAR): + doc: | + Qualitative type + enumeration: + open_enum: true + items: [thin_film, electrostatic] + (NXfabrication): + (NXsensor): + (NXactuator): + (NXbeam): + doc: + - | + Individual characterization results for the position, shape, + and characteristics of the electron beam at a given location. + - | + :ref:`NXtransformations` should be used to specify the location + or the position at which details about the beam were probed. + - | + xref: + spec: EMglossary + term: Electron Beam + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 95ecf99c7534745dabd2fab654f478d6f7d31bab753f17bca4c175a528c3d0d0 +# +# +# +# +# +# Base class for a set of components providing a controllable electron beam. +# +# The idea behind defining NXebeam_column as an own base class vs. adding these +# concepts in NXinstrument_em is that the electron beam generating component +# might be worthwhile to use in other experiments also. +# +# +# +# Tech-partner, microscope-, and control-software-specific name of the +# specific operation mode how the ebeam_column and its components are controlled +# to achieve specific illumination conditions. +# +# In many cases the users of an instrument do not or can not be expected to know +# all intricate spatiotemporal dynamics of their hardware. Instead, they rely of +# assumptions that the instrument, its control software, and components work as +# expected to focus on their research questions. +# +# For these cases, having a place for documenting the operation_mode is useful +# in as much as at least some constraints on how the illumination conditions were +# get documented. +# +# +# +# +# A physical part of an electron or ion microscope from which +# the particles that form the beam are emitted. +# +# The hardware for an electron source in an electron microscope +# may contain several components which affect the beam path. +# +# This concept is related to term `Source`_ of the EMglossary standard. +# +# .. _Source: https://purls.helmholtz-metadaten.de/emg/EMG_00000045 +# +# +# +# The potential difference between anode and cathode. +# +# This concept is related to term `Acceleration Voltage`_ of the EMglossary standard. +# +# .. _Acceleration Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000004 +# +# +# +# +# Voltage which is utilised to create an electric field that draws particles from +# the source. +# +# This concept is related to term `Extraction Voltage`_ of the EMglossary standard. +# +# .. _Extraction Voltage: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 +# +# +# +# +# Electrical current which is released from the source. +# +# This concept is related to term `Emission Current`_ of the EMglossary standard. +# +# .. _Emission Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000025 +# +# +# +# +# Electrical current which flows through the source. +# +# This concept is related to term `Filament Current`_ of the EMglossary standard. +# +# .. _Filament Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000027 +# +# +# +# +# Type of radiation. +# +# +# +# +# +# +# +# Emitter type used to create the beam. +# +# If the emitter type is other, give further details +# in the description field. +# +# +# +# +# +# Material of which the emitter is build, e.g. the filament material. +# +# +# +# +# +# How long has the source been in operation. +# +# +# +# +# +# +# +# +# Device to improve energy resolution or chromatic aberration. +# +# Examples are Wien, $\textalpha$-, or $\Omega$- energy filter or `cc corrector +# like <https://www.ceos-gmbh.de/en/basics/cc-corrector>`_ +# +# +# +# +# Qualitative type of the component. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Was the corrector used? +# +# +# +# +# +# Energy dispersion in e.g. µm/eV. +# +# +# +# +# Corresponding voltage for that energy dispersion. +# +# +# +# +# +# +# Component that reshapes an ellipse-shaped electron beam into a circular one. +# +# * `L. Reimer 1998, Springer, 1998 <https://dx.doi.org/10.1007/978-3-540-3896>`_ +# * `M. Tanaka et al., Electron Microscopy Glossary, 2024 <https://www.jeol.com/words/semterms/20201020.111014.php#gsc.tab=0>`_ +# +# Stigmator is an exact synonym. +# +# +# +# Descriptor for the correction strength along the first direction when exact technical details +# are unknown or not directly controllable as the control software of the microscope does not +# enable or was not configured to display these values for users. +# +# +# +# +# Descriptor for the correction strength along the second direction when exact technical details +# are unknown or not directly controllable as the control software of the microscope does not +# enable or was not configured to display these values for users. +# +# +# +# +# +# Electron biprism as it is used e.g. for electron holography. +# +# +# +# +# +# Device that causes a change in the phase of an electron wave. +# +# * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ +# * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ +# +# +# +# Qualitative type +# +# +# +# +# +# +# +# +# +# +# +# +# Individual characterization results for the position, shape, +# and characteristics of the electron beam at a given location. +# +# :ref:`NXtransformations` should be used to specify the location +# or the position at which details about the beam were probed. +# +# This concept is related to term `Electron Beam`_ of the EMglossary standard. +# +# .. _Electron Beam: https://purls.helmholtz-metadaten.de/emg/EMG_00000021 +# +# +# diff --git a/contributed_definitions/nyaml/NXem_ebsd.yaml b/base_classes/nyaml/NXem_ebsd.yaml similarity index 55% rename from contributed_definitions/nyaml/NXem_ebsd.yaml rename to base_classes/nyaml/NXem_ebsd.yaml index 760effb97d..7d413df5ae 100644 --- a/contributed_definitions/nyaml/NXem_ebsd.yaml +++ b/base_classes/nyaml/NXem_ebsd.yaml @@ -3,90 +3,82 @@ doc: - | Base class method-specific for Electron Backscatter Diffraction (EBSD). - | - The general procedure of an EBSD experiment is as follows. + The general procedure of an EBSD experiment is as follows: Users load the specimen, collect first a coarse image of the surface. - Next, they set an approximate value for the calibrated working distance and - tilt the stage to set the desired diffraction conditions. + Next, they set an approximate value for the calibrated working distance + and tilt the stage into diffraction conditions. - | - Users then typically configure the microscope for collecting higher quality data - and push in the EBSD detector. Subsequently, they fine tune the illumination - and aberration corrector settings and select one or multiple ROIs for - the microscope to machine off automatically. They configure on-the-fly - indexing parameter and start the measurement queue. + Users then typically configure the microscope for collecting quality data. + The EBSD detector is pushed in (if retractable). Subsequently, they fine tune + the illumination and aberration corrector settings and select one or multiple ROIs + for the microscope to machine off automatically. They configure on-the-fly + indexing parameter and then typically start the measurement queue. + From this point onwards typically the microscope runs automatically. - | - Nowadays, this is in most cases an automated process. The pattern - collection runs during the allocated microscope session until the - queue finishes or gets interrupted by errors or the next user terminates - sessions which run over time. + Diffraction pattern get collected until the queue finishes or gets interrupted by + either errors or arrival at the end of the users' allocated timeslot at the instrument. - | - Kikuchi pattern surplus eventually multi-modal detector signals are - collected and usually indexed on-the-fly. Patterns may be stored or not - so one should not assume that raw data are always stored. + Kikuchi pattern (EBSP) are usually indexed on-the-fly. These patterns are the raw data. + Once indexed, these patterns are often not stored. - | Results are stored in files, which afterwards are typically copied - automatically or manual for archival purposes to certain storage - locations or further consumption. The result of such an EBSD + automatically or manually for archival purposes to certain storage + locations for further consumption. The result of such an EBSD measurement/experiment is a set of usually proprietary or open files from technology partners. - | This :ref:`NXem_ebsd` base class is a proposal how to represent method-specific data, metadata, and connections between these for the research field of - electron microscopy. + electron microscopy exemplified here for electron backscatter diffraction (EBSD). + The base class solves two key documentation issues within the EBSD community: - | - More specifically, exemplified here for electron backscatter diffraction (EBSD) - we show how NeXus can be used to solve two key documentation issues so far - missing in the field of EBSD. -- | - Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file which is formatted + Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file that is formatted according to NXem_ebsd) stores the connection between the microscope session and - the key datasets which are considered typically results of the various processing - steps involved when working with EBSD data. + the key datasets which are considered typically results of the afore-mentioned + steps involved in an EBSD experiment. - | Different groups in NXem_ebsd make connections to data artifacts which were collected when working with electron microscopes via the NXem application definition. Using a file which stores information according to the NXem application definition has the benefit that it connects the sample, references to the sample processing, the user operating the microscope, details about the microscope session, - and details about the acquisition and eventual indexing of Kikuchi pattern, + and details about the acquisition and eventual indexing of Kikuchi patterns, associated overview images, like secondary electron or backscattered electron - images of the region-of-interest probed and many more pieces of information. + images of the region-of-interest probed, and many more (meta)data. - | Secondly, NXem_ebsd connects and stores the conventions and reference frames which were used and which are the key to a correct mathematical interpretation - of every EBSD result. Otherwise, results would be ripped out of their context, - as it is the current situation with many traditional studies where EBSD data - were indexed on-the-fly and shared with the community only via sharing - the strongly processed results file in some technology-partner-specific file - format but without communicating all conventions or relying on the assumptions - that colleagues likely know these conventions even though multiple definitions - are possible. + of every experiment or simulation using EBSD. +- | + Otherwise, results would be ripped out of their context like it is the current situation + with many traditional studies where EBSD data were indexed on-the-fly and shared + with the community only via sharing the strongly processed files with results in some + formatting but without communicating all conventions used or just relying on the assumptions + that colleagues likely know these conventions even though + multiple definitions are possible. - | NXem_ebsd covers experiments with one-, two-dimensional, and so-called three- dimensional EBSD datasets. The third dimension is either time (in the case of - quasi in-situ experiments) or space (in the case of serial-sectioning) methods - where a combination of mechanical or ion milling is used repetitively to measure - the same region-of-interest at different depth increments. Material removal - can be achieved with electron or ion polishing, using manual - steps or using automated equipment like a robot system. + quasi in-situ experiments) or space (in the case of serial-sectioning) experiments + where a combination of repetitive removal of material from the surface layer to measure + otherwise the same region-of-interest at different depth increments. Material removal + can be achieved with mechanical, electron, or ion polishing, using manual steps or + automated equipment like a robot system `S. Tsai et al. `_. - | Three-dimensional experiments require to follow a sequence of specimen, surface - preparation, and data collection steps. By nature these methods are destructive - in that they either require the removal of the previously measured material region - or that the sample surface can degrade due to e.g. contamination or other - electron-matter interaction. + preparation, and data collection steps. By virtue of design, these methods are destructive + either because of the necessary material removal or surface degradation due to e.g. + contamination or other electron-matter interaction. - | - For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings are - combined into one reconstructed stack. That is serial-sectioning is mainly a - computational workflow. Users collect data for each serial sectioning step - via an experiment. This assures that data for associated microscope sessions - and steps of data processing stay connected and contextualized. + For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings + are combined into one reconstructed stack via a computational workflow. Users collect + data for each serial sectioning step via an experiment. This assures that data for associated + microscope sessions and steps of data processing stay contextualized and connected. - | Eventual tomography methods also use such a workflow because first diffraction - images are collected (e.g. with X-ray) and then these imagres are indexed and - computed into a 3D orientation mapping. The here proposed NXem_ebsd application - definition contains conceptual ideas how this splitting between measurement and - post-processing can be granularized also for such X-ray-based techniques, whether - it be 3DXRD or HEDM. + images are collected (e.g. with X-ray) and then these images are indexed to process + a 3D orientation mapping. Therefore, the here proposed base class can be a blueprint + also for future classes to embrace our colleagues from X-ray-based techniques be it 3DXRD or HEDM. - | xref: spec: EMglossary @@ -108,10 +100,10 @@ symbols: standardized default plot orientation mapping. n_solutions: | Number of phase solutions + n_hkl: | + Number of reflectors (Miller crystallographic plane triplets). type: group -NXem_ebsd(NXem_method): - - # (NXcoordinate_system): +NXem_ebsd(NXprocess): gnomonic_reference_frame(NXcoordinate_system): doc: | Details about the gnomonic (projection) reference frame. @@ -120,47 +112,48 @@ NXem_ebsd(NXem_method): If a detector is involved, it is assumed that the configuration is inspected from a position that is located behind this detector. - If any of these assumptions is not met, the user is required to explicitly state this. + If any of these assumptions are not met, the user is required to explicitly state this. - Reference DOI: 10.1016/j.matchar.2016.04.008 suggests to label the - base vectors of this coordinate system as Xg, Yg, Zg. + Reference ``_ suggests to label the + base vectors of this coordinate system as :math:`X_g, Y_g, Z_g`. origin(NX_CHAR): doc: | - Origin of the gnomonic_projection_reference_frame. + Origin of the gnomonic_reference_frame. - Reference DOI: 10.1016/j.matchar.2016.04.008 suggests to - assume that this is coordinate Xg = 0, Yg = 0, Zg = 0. - enumeration: [undefined, in_the_pattern_centre] + Reference ``_ suggests to + assume that this is coordinate :math:`Xg = 0, Yg = 0, Zg = 0`. + enumeration: [in_the_pattern_centre] x_direction(NX_CHAR): doc: | Direction of the positively pointing x-axis base vector of the gnomonic_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] y_direction(NX_CHAR): doc: | Direction of the positively pointing y-axis base vector of the gnomonic_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] z_direction(NX_CHAR): doc: | Direction of the positively pointing z-axis base vector of the gnomonic_reference_frame. - enumeration: [undefined, north, east, south, west, in, out] + enumeration: [north, east, south, west, in, out] pattern_centre(NXprocess): doc: | - Details about the definition of the pattern centre as a special point in the gnomonic_reference_frame. + Details about the definition of the pattern centre as a special point in the + gnomonic_reference_frame. - Keep in mind that the gnomonic space is in virtually all cases embedded in the detector space. - Specifically, the XgYg plane is defined such that it is laying inside the XdYd plane - (of the detector reference frame). + Typically the gnomonic space is embedded in the detector space. + Specifically, the XgYg plane is defined such that it is laying inside the + XdYd plane (of the detector reference frame). - When the normalization direction is the same as e.g. the detector x-axis direction one - effectively normalizes in fractions of the width of the detector. + When the normalization direction is the same as e.g. the detector x-axis direction + one effectively normalizes in fractions of the width of the detector. - The issue with terms like width and height is that these degenerate if the detector - region-of-interest is square-shaped. This is why instead of referring to width and height - one should report as if one were to measure practically with a ruler and one is specific - about in which direction positive distances are measured. + The issue with terms like width and height, though, is that these become degenerated + if the detector region-of-interest is square-shaped. This is why instead of referring to + width and height it is better to state explicitly which direction is considered positive + when measuring distances. For the concepts used to specify the boundary_convention it is assumed that the region-of-interest is defined by a rectangle, referring to the direction of outer-unit @@ -169,47 +162,34 @@ NXem_ebsd(NXem_method): doc: | From which border of the EBSP (in the detector reference frame) is the pattern centre's x-position (PCx) measured. - enumeration: [undefined, top, right, bottom, left] + enumeration: [top, right, bottom, left] x_normalization_direction(NX_CHAR): doc: | In which direction are positive values for the x-axis coordinate value measured from the specified boundary. - enumeration: [undefined, north, east, south, west] + enumeration: [north, east, south, west] y_boundary_convention(NX_CHAR): doc: | From which border of the EBSP (in the detector reference frame) is the pattern centre's y-position (PCy) measured. - enumeration: [undefined, top, right, bottom, left] + enumeration: [top, right, bottom, left] y_normalization_direction(NX_CHAR): doc: | In which direction are positive values for the y-axis coordinate value measured from the specified boundary. - enumeration: [undefined, north, east, south, west] - - # distance_convention: - # doc: | - # How is the third of the three pattern centre parameter values, - # the (distance) parameter DD, normalized. Which convention - # is followed. We are aware that specifying one of the options here - # also implicitly comes with conventions for some of the parameter - # requested in this ELN. For now we would rather like to ask - # the users though to be specific also to learn how such an ELN - # will be used in practice. - # enumeration: [undefined, Bruker, JEOL, FEI, Oxford] + enumeration: [north, east, south, west] measurement(NXprocess): doc: | - This group documents relevant details about the conditions and the tools - used for measuring a stack of Kikuchi diffraction pattern with an - electron microscope. + This group documents relevant details about the conditions and the + tools for measuring diffraction patterns with an electron microscope. The most frequently collected EBSD data are captured for rectangular - regions-of-interested which are sampled with regular square or - hexagon-shaped pixels. + regions-of-interest using a discretization into square or hexagon tiles. time(NX_NUMBER): unit: NX_TIME doc: | Physical time since the beginning of a timestamp that is required to be - same for all experiments in the set. The purpose of this marker is + the same for all experiments in the set. The purpose of this marker is to identify how all experiments in the set need to be arranged sequentially based on the time elapsed. The time is relevant to sort e.g. experiments of consecutive quasi @@ -219,69 +199,51 @@ NXem_ebsd(NXem_method): doc: | Timestamp relative to which time was counted to aid converting between time and timestamp. - - # (NXtransformations): - # doc: | - # Transformation which details where the region-of-interest described under - # indexing is located in absolute coordinates and rotation with respect - # to which coordinate system. - # pattern_available(NX_BOOLEAN): - # doc: | - # True if pattern were stored and are retrieveable via depends_on or source. depends_on(NX_CHAR): doc: | - If available and it is stored in an instance of an application definition this field - specifies the path to an instance of :ref:`NXdata` where the measured patterns - are stored. + Path to an instance of :ref:`NXdata` where the measured patterns are stored. source(NXnote): doc: | Reference (e.g. path and filename) to an existent data artifact which - stores either the measured pattern or input (already processed EBSD data). + stores either the measured patterns or input (already processed EBSD data). simulation(NXprocess): doc: | This group documents relevant details about the conditions and the tools - used for simulating a stack of Kikuchi diffraction pattern with some - physical model. + used for simulating diffraction patterns with some physical model. - This group should not be confused with a group named simulation that - is however an instance of NXem_sim. Instead, the simulation group here - should be used if (e.g. instead of a measurement) a stack of pattern - were simulated that one wishes to use for indexing patterns. - - In many practical cases where pattern are analyzed on-the-fly and dictionary - indexing strategies are used, so-called master pattern(s) are used to compare - measured or simulated pattern with the master pattern. In this case, - master pattern are the result of a computer simulation and thus should - be stored using an own properly documented entry within a simulation - group as an instance of :ref:`NXem_sim`. + This group should be used if (e.g. instead of a measurement) the patterns + were simulated (possibly awaiting indexing). + + In many practical cases where patterns are analyzed on-the-fly and dictionary + indexing strategies used, so-called master pattern(s) are used to compare + measured or simulated patterns with the master patterns. depends_on(NX_CHAR): doc: | - If available and it is stored in an instance of an application definition this field specifies - the path to an instance of :ref:`NXimage_set` where the simulated patterns are stored. + Path to an instance of :ref:`NXimage` where the simulated patterns are stored. source(NXnote): doc: | Reference (e.g. path and filename) to an existent digital resource which - stores either the pattern or input (already processed EBSD data) - which is now processed further as described by this NXem_ebsd instance. + stores either the patterns or input (already processed EBSD data) that are + about to become processed further as described by this NXem_ebsd instance. calibration(NXprocess): doc: | The EBSD system, including components like the electron gun, pole-piece, - stage tilting, EBSD detector, and the gnomonic projection have to be - calibrated to achieve reliable indexing results. + stage tilt, EBSD detector, and the gnomonic projection have to be + calibrated to achieve reliable, precise, and accurate scientific results. Specifically, the gnomonic projection has to be calibrated. - Typically, silicon or quartz crystals are used for this purpose. + Typically, standard specimens made from silicon or quartz crystals + in specific orientations are used for this purpose. - Considering a system is well-calibrated, it is much more frequently the - case in practice that users assume the system is calibrated (and thus usable) - vs. they perform the calibration of the EBSD system. + Considering that a system used is already calibrated well-enough is much + more frequently the case in practice than that users perform the calibration + themselves (with above-mentioned standard specimens). In the first case, the user assumes that the principle geometry of the hardware components and the settings in the control and EBSD pattern - acquisition software has been calibrated. Consequently, users pick from - an existent library of phase candidates, i.e. - :ref:`NXcrystal_structure` instances. Examples are - reflector models as stored in CRY files (HKL/Channel 5/Flamenco). + acquisition software has been calibrated already. Consequently, users pick from + an existent library of phase candidates, i.e. :ref:`NXunit_cell` instances. + Examples are reflector models as stored in CRY files (HKL/Channel 5/Flamenco). In the second case, users calibrate the system during the session using standards (silicon, quartz, or other common specimens). @@ -292,44 +254,41 @@ NXem_ebsd(NXem_method): For EBSD this has key implications: Taking TSL OIM/EDAX as an example, the conventions how orientations are stored is affected by how the - reference frames are configured and this setup is made at the level - of the GUI software. + reference frames are configured and how this setup in the GUI. Unfortunately, these pieces of information are not necessarily stored in the results files. In effect, key conventions become disconnected from the data so it remains the users' obligation to remember these settings or write these down in a lab notebook. Otherwise, these metadata - get lost. All these issues are a motivation and problem which - :ref:`NXem_ebsd` solves in that all conventions can be specified explicitly. + get lost. All these issues are a motivation and problem which :ref:`NXem_ebsd` + solves in that all conventions can be specified explicitly. depends_on(NX_CHAR): doc: | - If available and it is stored in an instance of an application definition this field specifies - the path to an instance of :ref:`NXem_msr` where calibration is stored. + Path to an instance of :ref:`NXem` where calibration data are stored. source(NXnote): doc: | Reference to a digital resource where the calibration is stored. indexing(NXprocess): doc: | - Indexing is a data processing step performed either after or while - (on-the-fly) the beam scans the specimen. The resulting method is also + Indexing is a data processing step performed either after or while (aka on-the-fly) + the beam scans the specimen. The resulting method is also known as orientation imaging microscopy (OIM). - Different algorithms can be used to index EBSD pattern. Common to them - is the computational step where simulated reference pattern are compared - with measured or simulated patterns. These latter patterns are referred - to via the measurement or simulation groups of this base class. + Different algorithms can be used to index EBSP. Common to them is the + computational step where simulated or theoretically assumed patterns + are compared with the measured ones. These latter patterns are referred + to via the measurement or simulation groups of this base class respectively. Quality descriptors are defined based on which an indexing algorithm yields a quantitative measure of how similar measured and reference - pattern are, and thus if no, one, or multiple so-called solutions - were found. + patterns are, and thus if no, one, or multiple so-called solutions were found. - Assumed or simulated pattern are simulated using kinematic or dynamical - theory of electron diffraction delivering master pattern. + Assumed or simulated patterns are simulated using kinematical or dynamical + theory of electron diffraction delivering master patterns. - The Hough transform is essentially a discretized Radon transform (for details see `M. van Ginkel et al. `_). - Recently, dictionary-based indexing methods are increasingly becoming used - partly driven by the interest to use artificial intelligence algorithms. + The Hough transform, one of the most frequently used traditional method for indexing + EBSP is essentially a discretized Radon transform (for details see `M. van Ginkel et al. `_). Recently, dictionary-based and artificial intelligence-based methods + find more widespread usage for indexing. source(NXnote): doc: | This group enables to establish a logical connection between previous @@ -343,29 +302,66 @@ NXem_ebsd(NXem_method): method(NX_CHAR): doc: | Principal algorithm used for indexing. - enumeration: [undefined, hough_transform, dictionary, radon_transform, other] + enumeration: + open_enum: true + items: [hough_transform, dictionary, radon_transform] background_correction(NXprocess): doc: | Details about the background correction applied to each Kikuchi pattern. binning(NXprocess): doc: | - Binning i.e. downsampling of the pattern. - parameter(NXprocess): + Binning i.e. downsampling to each pattern. + parameter(NXcollection): doc: | Specific parameter relevant only for certain algorithms used. - phaseID(NXcrystal_structure): + phaseID(NXphase): nameType: partial doc: | Details for each phase used as a model with which the patterns were - indexed. Instances of :ref:`NXcrystal_structure` in this group must - have the group name prefix phase. The identifier in the name is an - integer. We start counting from 1 because the value 0 is reserved for - the special phase that is the null-model, i.e. the null phase, notIndexed. + indexed. Instances of :ref:`NXunit_cell` in this group must + have the group name prefixed with phase. The identifier in the name is an + integer. Start counting from 1 because the value 0 is reserved for + the special phase that is the null-model, the null phase also known + as notIndexed. + dspacing(NX_NUMBER): + unit: NX_LENGTH + doc: | + Spacing between the crystallographic planes that are defined via ``miller``. + dimensions: + rank: 1 + dim: (n_hkl,) + relative_intensity(NX_NUMBER): + unit: NX_DIMENSIONLESS + doc: | + Relative intensity for the computed diffraction intensity (signal) for the + plane. + dimensions: + rank: 1 + dim: (n_hkl,) + number_of_scan_points(NX_UINT): + unit: NX_UNITLESS + doc: | + In case the :ref:`NXunit_cell` base class is used with analyzed orientation maps + this field stores how many scan points of the map were identified as matching best + with this phase. + number_of_planes(NX_UINT): + unit: NX_UNITLESS + doc: | + How many reflectors for crystallographic planes are distinguished. + miller(NX_NUMBER): + unit: NX_UNITLESS + doc: | + Miller indices :math:`(hkl)[uvw]` of the planes. + + The first triplet specifies :math:`(hkl)`. The second triplet specifies :math:`[uvw]`. + Miller indices refer to the Cartesian right-handed coordinate system of the unit cell. + dimensions: + rank: 2 + dim: (n_hkl, 6) status(NX_UINT): unit: NX_UNITLESS doc: | Which return value did the indexing algorithm yield for each scan point. - Practically useful is to use an uint8 mask. * 0 - Not analyzed * 1 - Too high angular deviation @@ -375,86 +371,72 @@ NXem_ebsd(NXem_method): dimensions: rank: 1 dim: (n_sc,) - n_phases_per_scan_point(NX_INT): + phases_per_scan_point(NX_INT): unit: NX_UNITLESS doc: | How many phases i.e. crystal structure models were used to index each scan point if any? Let's assume an example to explain how this field should be used: In the simplest case users collected one pattern for each scan point and have indexed using one phase, i.e. one instance - of an NXem_ebsd_crystal_structure_model. + of an :ref:`NXunit_cell`. - In another example users may have skipped some scan points (not indexed) - them at all) and/or used differing numbers of phases for different scan - points. + In another example users may have skipped some scan points (not indexed + them at all) or used differing numbers of phases for indexing different scan points. - The cumulated of this array decodes how phase_identifier and phase_matching + The cumulated of this array decodes how identifier_phase and matching_phase arrays have to be interpreted. In the simplest case (one pattern per scan point, and all scan points indexed using that same single phase model), - phase_identifier has as many entries as scan points - and phase_matching has also as many entries as scan points. + identifier_phase has as many entries as scan points + and matching_phase has also as many entries as scan points. dimensions: rank: 1 dim: (n_sc,) - phase_identifier(NX_INT): + identifier_phase(NX_INT): unit: NX_UNITLESS doc: | - The array n_phases_per_scan_point details how the phase_identifier - and the phase_matching arrays have to be interpreted. + The array phases_per_scan_point details how the identifier_phase + and the matching_phase arrays have to be interpreted. - For the example with a single phase phase_identifier has trivial + For the example with a single phase identifier_phase has trivial values either 0 (no solution) or 1 (solution matching sufficiently significant with the model for phase 1). When there are multiple phases, it is possible (although not frequently - needed) that a pattern matches eventually (not equally well) sufficiently - significant with multiple pattern. This can especially happen in cases of + required) that a pattern matches eventually (not equally well) sufficiently + significant with multiple patterns. This can especially happen in cases of pseudosymmetry and more frequently with an improperly calibrated system - or false or inaccurate phase models e.g. (ferrite, austenite). - Having such field is especially relevant for recent machine learning - or dictionary based indexing schemes because in combination with - phase_matching these fields communicate the results in a model-agnostic - way. + or false or inaccurate phase models. Having such field is especially relevant + for recent dictionary- or artificial intelligence-based indexing methods to communicate + the results in a model-agnostic way in combination with matching_phase. - Depending on the n_phases_per_scan_point value phase_identifier and - phase_matching arrays represent a collection of concatenated tuples, - which are organized in sequence: The solutions for the 0-th scan point, + Depending on the phases_per_scan_point value, identifier_phase and + matching_phase arrays represent a collection of concatenated tuples. + These are organized in sequence: The solutions for the 0-th scan point, the 1-th scan point, the n_sc - 1 th scan point and omitting tuples - for those scan points with no phases according to n_phases_per_scan_point + for those scan points with no phases according to phases_per_scan_point. dimensions: rank: 1 dim: (n_solutions,) - phase_matching(NX_INT): + matching_phase(NX_INT): unit: NX_UNITLESS doc: | One-dimensional array, pattern by pattern labelling the solutions found. - The array n_phases_per_scan_point has to be specified because it details - how the phase_identifier and the phase_matching arrays have to be interpreted. - See documentation of phase_identifier for further details. + The array phases_per_scan_point has to be specified because it details + how the identifier_phase and the matching_phase arrays are interpreted. + See documentation of identifier_phase for further details. dimensions: rank: 1 dim: (n_solutions,) - phase_matching_descriptor(NX_CHAR): + matching_phase_descriptor(NX_CHAR): doc: | Phase_matching is a descriptor for how well the solution matches or not. - Examples can be confidence_index, mean_angular_deviation, some AI-based - matching probability (other), i.e. the details are implementation-specific. - enumeration: [undefined, confidence_index, mean_angular_deviation, other] - rotation_set(NXrotation_set): - - # px is no one of the following two calibrated i) is not px*stepsize or ii) is not - # px*stepsize + offset + Examples can be confidence_index, mean_angular_deviation, or other. + enumeration: [confidence_index, mean_angular_deviation, other] + rotation(NXrotation): scan_point_positions(NX_NUMBER): unit: NX_LENGTH - - # we make this only required as people may not yet be so happy with - # having to walk a graph from measurement -> path -> NXevent_data_em - # -> em_lab/ebeam_deflector to retrieve the actual scan positions - # although this would be cleaner, also scan_point_positions could be - # an instance of NXcg_point_set with a depends_on pointing - # to sample_reference_frame doc: | - Calibrated center positions of each scan point + Calibrated centre positions of each scan point in the sample surface reference system. dimensions: rank: 2 @@ -462,21 +444,18 @@ NXem_ebsd(NXem_method): indexing_rate(NX_NUMBER): unit: NX_DIMENSIONLESS doc: | - Fraction of successfully indexed pattern with a phase + Fraction of successfully indexed patterns with a phase not the null-phase vs the number_of_scan_points. number_of_scan_points(NX_UINT): unit: NX_UNITLESS doc: | Number of scan points in the original mapping. + # already implemented connections to representations of microstructures but in this PR not proposed # odfID(NXmicrostructure_odf): - # nameType: partial # pfID(NXmicrostructure_pf): - # nameType: partial # ipfID(NXmicrostructure_ipf): - # nameType: partial # microstructureID(NXmicrostructure): - # nameType: partial # overview over the entire map, rediscretized on a tight aabb roi(NXdata): doc: | @@ -484,18 +463,7 @@ NXem_ebsd(NXem_method): descriptor(NX_CHAR): doc: | Descriptor representing the image contrast. - - # taking two examples (CTF and H5OINA choked completely of possibility to find s.th. conceptually common to plot enumeration: [band_contrast, confidence_index, mean_angular_deviation] - - # \@signal: # data - # \@axes: # [axis_y, axis_x] - # \@axis_x_indices: 0 - # \@axis_y_indices: 1 - # \@signal: - # \@axes: - # \@AXISNAME_indices: - # \@long_name: title(NX_CHAR): doc: | Title of the default plot. @@ -506,13 +474,9 @@ NXem_ebsd(NXem_method): dimensions: rank: 2 dim: (n_y, n_x) - - # n_0 slow 2, n_1 fast 1, rgb triplet is fastest 0 - # in axes fast to fastest - # while for _indices fastest to fast \@long_name(NX_CHAR): doc: | - Descriptor values. + Descriptor values axis_y(NX_NUMBER): unit: NX_LENGTH doc: | @@ -535,13 +499,13 @@ NXem_ebsd(NXem_method): Label for the x axis # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0307e3cc196b1878d14dda47138f202aabeec278f976c43fa3d4f8229b7c05a2 +# d4cc9c2b63a41626f037d7d04501e81d5c389c6b7ab57b4c112ed2f336d8f064 # # # -# +# # # # @@ -594,100 +558,96 @@ NXem_ebsd(NXem_method): # Number of phase solutions # # +# +# +# Number of reflectors (Miller crystallographic plane triplets). +# +# # # # Base class method-specific for Electron Backscatter Diffraction (EBSD). # -# The general procedure of an EBSD experiment is as follows. +# The general procedure of an EBSD experiment is as follows: # Users load the specimen, collect first a coarse image of the surface. -# Next, they set an approximate value for the calibrated working distance and -# tilt the stage to set the desired diffraction conditions. +# Next, they set an approximate value for the calibrated working distance +# and tilt the stage into diffraction conditions. # -# Users then typically configure the microscope for collecting higher quality data -# and push in the EBSD detector. Subsequently, they fine tune the illumination -# and aberration corrector settings and select one or multiple ROIs for -# the microscope to machine off automatically. They configure on-the-fly -# indexing parameter and start the measurement queue. +# Users then typically configure the microscope for collecting quality data. +# The EBSD detector is pushed in (if retractable). Subsequently, they fine tune +# the illumination and aberration corrector settings and select one or multiple ROIs +# for the microscope to machine off automatically. They configure on-the-fly +# indexing parameter and then typically start the measurement queue. +# From this point onwards typically the microscope runs automatically. # -# Nowadays, this is in most cases an automated process. The pattern -# collection runs during the allocated microscope session until the -# queue finishes or gets interrupted by errors or the next user terminates -# sessions which run over time. +# Diffraction pattern get collected until the queue finishes or gets interrupted by +# either errors or arrival at the end of the users' allocated timeslot at the instrument. # -# Kikuchi pattern surplus eventually multi-modal detector signals are -# collected and usually indexed on-the-fly. Patterns may be stored or not -# so one should not assume that raw data are always stored. +# Kikuchi pattern (EBSP) are usually indexed on-the-fly. These patterns are the raw data. +# Once indexed, these patterns are often not stored. # # Results are stored in files, which afterwards are typically copied -# automatically or manual for archival purposes to certain storage -# locations or further consumption. The result of such an EBSD +# automatically or manually for archival purposes to certain storage +# locations for further consumption. The result of such an EBSD # measurement/experiment is a set of usually proprietary or open files # from technology partners. # # This :ref:`NXem_ebsd` base class is a proposal how to represent method-specific # data, metadata, and connections between these for the research field of -# electron microscopy. +# electron microscopy exemplified here for electron backscatter diffraction (EBSD). +# The base class solves two key documentation issues within the EBSD community: # -# More specifically, exemplified here for electron backscatter diffraction (EBSD) -# we show how NeXus can be used to solve two key documentation issues so far -# missing in the field of EBSD. -# -# Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file which is formatted +# Firstly, an instance of NXem_ebsd (such as a NeXus/HDF5 file that is formatted # according to NXem_ebsd) stores the connection between the microscope session and -# the key datasets which are considered typically results of the various processing -# steps involved when working with EBSD data. +# the key datasets which are considered typically results of the afore-mentioned +# steps involved in an EBSD experiment. # # Different groups in NXem_ebsd make connections to data artifacts which were collected # when working with electron microscopes via the NXem application definition. # Using a file which stores information according to the NXem application definition # has the benefit that it connects the sample, references to the sample processing, # the user operating the microscope, details about the microscope session, -# and details about the acquisition and eventual indexing of Kikuchi pattern, +# and details about the acquisition and eventual indexing of Kikuchi patterns, # associated overview images, like secondary electron or backscattered electron -# images of the region-of-interest probed and many more pieces of information. +# images of the region-of-interest probed, and many more (meta)data. # # Secondly, NXem_ebsd connects and stores the conventions and reference frames # which were used and which are the key to a correct mathematical interpretation -# of every EBSD result. Otherwise, results would be ripped out of their context, -# as it is the current situation with many traditional studies where EBSD data -# were indexed on-the-fly and shared with the community only via sharing -# the strongly processed results file in some technology-partner-specific file -# format but without communicating all conventions or relying on the assumptions -# that colleagues likely know these conventions even though multiple definitions -# are possible. +# of every experiment or simulation using EBSD. +# +# Otherwise, results would be ripped out of their context like it is the current situation +# with many traditional studies where EBSD data were indexed on-the-fly and shared +# with the community only via sharing the strongly processed files with results in some +# formatting but without communicating all conventions used or just relying on the assumptions +# that colleagues likely know these conventions even though +# multiple definitions are possible. # # NXem_ebsd covers experiments with one-, two-dimensional, and so-called three- # dimensional EBSD datasets. The third dimension is either time (in the case of -# quasi in-situ experiments) or space (in the case of serial-sectioning) methods -# where a combination of mechanical or ion milling is used repetitively to measure -# the same region-of-interest at different depth increments. Material removal -# can be achieved with electron or ion polishing, using manual -# steps or using automated equipment like a robot system. +# quasi in-situ experiments) or space (in the case of serial-sectioning) experiments +# where a combination of repetitive removal of material from the surface layer to measure +# otherwise the same region-of-interest at different depth increments. Material removal +# can be achieved with mechanical, electron, or ion polishing, using manual steps or +# automated equipment like a robot system `S. Tsai et al. <https://doi.org/10.1063/5.0087945>`_. # # Three-dimensional experiments require to follow a sequence of specimen, surface -# preparation, and data collection steps. By nature these methods are destructive -# in that they either require the removal of the previously measured material region -# or that the sample surface can degrade due to e.g. contamination or other -# electron-matter interaction. +# preparation, and data collection steps. By virtue of design, these methods are destructive +# either because of the necessary material removal or surface degradation due to e.g. +# contamination or other electron-matter interaction. # -# For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings are -# combined into one reconstructed stack. That is serial-sectioning is mainly a -# computational workflow. Users collect data for each serial sectioning step -# via an experiment. This assures that data for associated microscope sessions -# and steps of data processing stay connected and contextualized. +# For three-dimensional EBSD, multiple two-dimensional EBSD orientation mappings +# are combined into one reconstructed stack via a computational workflow. Users collect +# data for each serial sectioning step via an experiment. This assures that data for associated +# microscope sessions and steps of data processing stay contextualized and connected. # # Eventual tomography methods also use such a workflow because first diffraction -# images are collected (e.g. with X-ray) and then these imagres are indexed and -# computed into a 3D orientation mapping. The here proposed NXem_ebsd application -# definition contains conceptual ideas how this splitting between measurement and -# post-processing can be granularized also for such X-ray-based techniques, whether -# it be 3DXRD or HEDM. +# images are collected (e.g. with X-ray) and then these images are indexed to process +# a 3D orientation mapping. Therefore, the here proposed base class can be a blueprint +# also for future classes to embrace our colleagues from X-ray-based techniques be it 3DXRD or HEDM. # # This concept is related to term `Electron Backscatter Diffraction`_ of the EMglossary standard. # # .. _Electron Backscatter Diffraction: https://purls.helmholtz-metadaten.de/emg/EMG_00000019 # -# # # # Details about the gnomonic (projection) reference frame. @@ -696,20 +656,19 @@ NXem_ebsd(NXem_method): # If a detector is involved, it is assumed that the configuration is inspected from a position # that is located behind this detector. # -# If any of these assumptions is not met, the user is required to explicitly state this. +# If any of these assumptions are not met, the user is required to explicitly state this. # -# Reference DOI: 10.1016/j.matchar.2016.04.008 suggests to label the -# base vectors of this coordinate system as Xg, Yg, Zg. +# Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the +# base vectors of this coordinate system as :math:`X_g, Y_g, Z_g`. # # # -# Origin of the gnomonic_projection_reference_frame. +# Origin of the gnomonic_reference_frame. # -# Reference DOI: 10.1016/j.matchar.2016.04.008 suggests to -# assume that this is coordinate Xg = 0, Yg = 0, Zg = 0. +# Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to +# assume that this is coordinate :math:`Xg = 0, Yg = 0, Zg = 0`. # # -# # # # @@ -719,7 +678,6 @@ NXem_ebsd(NXem_method): # gnomonic_reference_frame. # # -# # # # @@ -734,7 +692,6 @@ NXem_ebsd(NXem_method): # gnomonic_reference_frame. # # -# # # # @@ -749,7 +706,6 @@ NXem_ebsd(NXem_method): # gnomonic_reference_frame. # # -# # # # @@ -761,19 +717,20 @@ NXem_ebsd(NXem_method): # # # -# Details about the definition of the pattern centre as a special point in the gnomonic_reference_frame. +# Details about the definition of the pattern centre as a special point in the +# gnomonic_reference_frame. # -# Keep in mind that the gnomonic space is in virtually all cases embedded in the detector space. -# Specifically, the XgYg plane is defined such that it is laying inside the XdYd plane -# (of the detector reference frame). +# Typically the gnomonic space is embedded in the detector space. +# Specifically, the XgYg plane is defined such that it is laying inside the +# XdYd plane (of the detector reference frame). # -# When the normalization direction is the same as e.g. the detector x-axis direction one -# effectively normalizes in fractions of the width of the detector. +# When the normalization direction is the same as e.g. the detector x-axis direction +# one effectively normalizes in fractions of the width of the detector. # -# The issue with terms like width and height is that these degenerate if the detector -# region-of-interest is square-shaped. This is why instead of referring to width and height -# one should report as if one were to measure practically with a ruler and one is specific -# about in which direction positive distances are measured. +# The issue with terms like width and height, though, is that these become degenerated +# if the detector region-of-interest is square-shaped. This is why instead of referring to +# width and height it is better to state explicitly which direction is considered positive +# when measuring distances. # # For the concepts used to specify the boundary_convention it is assumed that the # region-of-interest is defined by a rectangle, referring to the direction of outer-unit @@ -785,7 +742,6 @@ NXem_ebsd(NXem_method): # centre's x-position (PCx) measured. # # -# # # # @@ -798,7 +754,6 @@ NXem_ebsd(NXem_method): # from the specified boundary. # # -# # # # @@ -811,7 +766,6 @@ NXem_ebsd(NXem_method): # centre's y-position (PCy) measured. # # -# # # # @@ -824,7 +778,6 @@ NXem_ebsd(NXem_method): # from the specified boundary. # # -# # # # @@ -832,30 +785,18 @@ NXem_ebsd(NXem_method): # # # -# # # -# This group documents relevant details about the conditions and the tools -# used for measuring a stack of Kikuchi diffraction pattern with an -# electron microscope. +# This group documents relevant details about the conditions and the +# tools for measuring diffraction patterns with an electron microscope. # # The most frequently collected EBSD data are captured for rectangular -# regions-of-interested which are sampled with regular square or -# hexagon-shaped pixels. +# regions-of-interest using a discretization into square or hexagon tiles. # # # # Physical time since the beginning of a timestamp that is required to be -# same for all experiments in the set. The purpose of this marker is +# the same for all experiments in the set. The purpose of this marker is # to identify how all experiments in the set need to be arranged # sequentially based on the time elapsed. # The time is relevant to sort e.g. experiments of consecutive quasi @@ -869,79 +810,62 @@ NXem_ebsd(NXem_method): # # # -# # # -# If available and it is stored in an instance of an application definition this field -# specifies the path to an instance of :ref:`NXdata` where the measured patterns -# are stored. +# Path to an instance of :ref:`NXdata` where the measured patterns are stored. # # # # # Reference (e.g. path and filename) to an existent data artifact which -# stores either the measured pattern or input (already processed EBSD data). +# stores either the measured patterns or input (already processed EBSD data). # # # # # # This group documents relevant details about the conditions and the tools -# used for simulating a stack of Kikuchi diffraction pattern with some -# physical model. -# -# This group should not be confused with a group named simulation that -# is however an instance of NXem_sim. Instead, the simulation group here -# should be used if (e.g. instead of a measurement) a stack of pattern -# were simulated that one wishes to use for indexing patterns. +# used for simulating diffraction patterns with some physical model. # -# In many practical cases where pattern are analyzed on-the-fly and dictionary -# indexing strategies are used, so-called master pattern(s) are used to compare -# measured or simulated pattern with the master pattern. In this case, -# master pattern are the result of a computer simulation and thus should -# be stored using an own properly documented entry within a simulation -# group as an instance of :ref:`NXem_sim`. +# This group should be used if (e.g. instead of a measurement) the patterns +# were simulated (possibly awaiting indexing). +# +# In many practical cases where patterns are analyzed on-the-fly and dictionary +# indexing strategies used, so-called master pattern(s) are used to compare +# measured or simulated patterns with the master patterns. # # # -# If available and it is stored in an instance of an application definition this field specifies -# the path to an instance of :ref:`NXimage_set` where the simulated patterns are stored. +# Path to an instance of :ref:`NXimage` where the simulated patterns are stored. # # # # # Reference (e.g. path and filename) to an existent digital resource which -# stores either the pattern or input (already processed EBSD data) -# which is now processed further as described by this NXem_ebsd instance. +# stores either the patterns or input (already processed EBSD data) that are +# about to become processed further as described by this NXem_ebsd instance. # # # # # # The EBSD system, including components like the electron gun, pole-piece, -# stage tilting, EBSD detector, and the gnomonic projection have to be -# calibrated to achieve reliable indexing results. +# stage tilt, EBSD detector, and the gnomonic projection have to be +# calibrated to achieve reliable, precise, and accurate scientific results. # # Specifically, the gnomonic projection has to be calibrated. -# Typically, silicon or quartz crystals are used for this purpose. +# Typically, standard specimens made from silicon or quartz crystals +# in specific orientations are used for this purpose. # -# Considering a system is well-calibrated, it is much more frequently the -# case in practice that users assume the system is calibrated (and thus usable) -# vs. they perform the calibration of the EBSD system. +# Considering that a system used is already calibrated well-enough is much +# more frequently the case in practice than that users perform the calibration +# themselves (with above-mentioned standard specimens). # # In the first case, the user assumes that the principle geometry of the # hardware components and the settings in the control and EBSD pattern -# acquisition software has been calibrated. Consequently, users pick from -# an existent library of phase candidates, i.e. -# :ref:`NXcrystal_structure` instances. Examples are -# reflector models as stored in CRY files (HKL/Channel 5/Flamenco). +# acquisition software has been calibrated already. Consequently, users pick from +# an existent library of phase candidates, i.e. :ref:`NXunit_cell` instances. +# Examples are reflector models as stored in CRY files (HKL/Channel 5/Flamenco). # # In the second case, users calibrate the system during the session # using standards (silicon, quartz, or other common specimens). @@ -952,20 +876,18 @@ NXem_ebsd(NXem_method): # # For EBSD this has key implications: Taking TSL OIM/EDAX as an example, # the conventions how orientations are stored is affected by how the -# reference frames are configured and this setup is made at the level -# of the GUI software. +# reference frames are configured and how this setup in the GUI. # # Unfortunately, these pieces of information are not necessarily stored # in the results files. In effect, key conventions become disconnected # from the data so it remains the users' obligation to remember these # settings or write these down in a lab notebook. Otherwise, these metadata -# get lost. All these issues are a motivation and problem which -# :ref:`NXem_ebsd` solves in that all conventions can be specified explicitly. +# get lost. All these issues are a motivation and problem which :ref:`NXem_ebsd` +# solves in that all conventions can be specified explicitly. # # # -# If available and it is stored in an instance of an application definition this field specifies -# the path to an instance of :ref:`NXem_msr` where calibration is stored. +# Path to an instance of :ref:`NXem` where calibration data are stored. # # # @@ -976,26 +898,25 @@ NXem_ebsd(NXem_method): # # # -# Indexing is a data processing step performed either after or while -# (on-the-fly) the beam scans the specimen. The resulting method is also +# Indexing is a data processing step performed either after or while (aka on-the-fly) +# the beam scans the specimen. The resulting method is also # known as orientation imaging microscopy (OIM). # -# Different algorithms can be used to index EBSD pattern. Common to them -# is the computational step where simulated reference pattern are compared -# with measured or simulated patterns. These latter patterns are referred -# to via the measurement or simulation groups of this base class. +# Different algorithms can be used to index EBSP. Common to them is the +# computational step where simulated or theoretically assumed patterns +# are compared with the measured ones. These latter patterns are referred +# to via the measurement or simulation groups of this base class respectively. # # Quality descriptors are defined based on which an indexing algorithm # yields a quantitative measure of how similar measured and reference -# pattern are, and thus if no, one, or multiple so-called solutions -# were found. +# patterns are, and thus if no, one, or multiple so-called solutions were found. # -# Assumed or simulated pattern are simulated using kinematic or dynamical -# theory of electron diffraction delivering master pattern. +# Assumed or simulated patterns are simulated using kinematical or dynamical +# theory of electron diffraction delivering master patterns. # -# The Hough transform is essentially a discretized Radon transform (for details see `M. van Ginkel et al. <https://www.semanticscholar.org/paper/A-short-introduction-to-the-Radon-and-Hough-and-how-Ginkel/fb6226f606cad489a15e38ed961c419037ccc858>`_). -# Recently, dictionary-based indexing methods are increasingly becoming used -# partly driven by the interest to use artificial intelligence algorithms. +# The Hough transform, one of the most frequently used traditional method for indexing +# EBSP is essentially a discretized Radon transform (for details see `M. van Ginkel et al. <https://www.semanticscholar.org/paper/A-short-introduction-to-the-Radon-and-Hough-and-how-Ginkel/fb6226f606cad489a15e38ed961c419037ccc858>`_). Recently, dictionary-based and artificial intelligence-based methods +# find more widespread usage for indexing. # # # @@ -1013,12 +934,10 @@ NXem_ebsd(NXem_method): # # Principal algorithm used for indexing. # -# -# +# # # # -# # # # @@ -1028,27 +947,68 @@ NXem_ebsd(NXem_method): # # # -# Binning i.e. downsampling of the pattern. +# Binning i.e. downsampling to each pattern. # # -# +# # # Specific parameter relevant only for certain algorithms used. # # -# +# # # Details for each phase used as a model with which the patterns were -# indexed. Instances of :ref:`NXcrystal_structure` in this group must -# have the group name prefix phase. The identifier in the name is an -# integer. We start counting from 1 because the value 0 is reserved for -# the special phase that is the null-model, i.e. the null phase, notIndexed. +# indexed. Instances of :ref:`NXunit_cell` in this group must +# have the group name prefixed with phase. The identifier in the name is an +# integer. Start counting from 1 because the value 0 is reserved for +# the special phase that is the null-model, the null phase also known +# as notIndexed. # +# +# +# Spacing between the crystallographic planes that are defined via ``miller``. +# +# +# +# +# +# +# +# Relative intensity for the computed diffraction intensity (signal) for the +# plane. +# +# +# +# +# +# +# +# In case the :ref:`NXunit_cell` base class is used with analyzed orientation maps +# this field stores how many scan points of the map were identified as matching best +# with this phase. +# +# +# +# +# How many reflectors for crystallographic planes are distinguished. +# +# +# +# +# Miller indices :math:`(hkl)[uvw]` of the planes. +# +# The first triplet specifies :math:`(hkl)`. The second triplet specifies :math:`[uvw]`. +# Miller indices refer to the Cartesian right-handed coordinate system of the unit cell. +# +# +# +# +# +# # # # # Which return value did the indexing algorithm yield for each scan point. -# Practically useful is to use an uint8 mask. # # * 0 - Not analyzed # * 1 - Too high angular deviation @@ -1060,93 +1020,80 @@ NXem_ebsd(NXem_method): # # # -# +# # # How many phases i.e. crystal structure models were used to index each # scan point if any? Let's assume an example to explain how this field # should be used: In the simplest case users collected one pattern for # each scan point and have indexed using one phase, i.e. one instance -# of an NXem_ebsd_crystal_structure_model. +# of an :ref:`NXunit_cell`. # -# In another example users may have skipped some scan points (not indexed) -# them at all) and/or used differing numbers of phases for different scan -# points. +# In another example users may have skipped some scan points (not indexed +# them at all) or used differing numbers of phases for indexing different scan points. # -# The cumulated of this array decodes how phase_identifier and phase_matching +# The cumulated of this array decodes how identifier_phase and matching_phase # arrays have to be interpreted. In the simplest case (one pattern per scan # point, and all scan points indexed using that same single phase model), -# phase_identifier has as many entries as scan points -# and phase_matching has also as many entries as scan points. +# identifier_phase has as many entries as scan points +# and matching_phase has also as many entries as scan points. # # # # # -# +# # -# The array n_phases_per_scan_point details how the phase_identifier -# and the phase_matching arrays have to be interpreted. +# The array phases_per_scan_point details how the identifier_phase +# and the matching_phase arrays have to be interpreted. # -# For the example with a single phase phase_identifier has trivial +# For the example with a single phase identifier_phase has trivial # values either 0 (no solution) or 1 (solution matching # sufficiently significant with the model for phase 1). # # When there are multiple phases, it is possible (although not frequently -# needed) that a pattern matches eventually (not equally well) sufficiently -# significant with multiple pattern. This can especially happen in cases of +# required) that a pattern matches eventually (not equally well) sufficiently +# significant with multiple patterns. This can especially happen in cases of # pseudosymmetry and more frequently with an improperly calibrated system -# or false or inaccurate phase models e.g. (ferrite, austenite). -# Having such field is especially relevant for recent machine learning -# or dictionary based indexing schemes because in combination with -# phase_matching these fields communicate the results in a model-agnostic -# way. +# or false or inaccurate phase models. Having such field is especially relevant +# for recent dictionary- or artificial intelligence-based indexing methods to communicate +# the results in a model-agnostic way in combination with matching_phase. # -# Depending on the n_phases_per_scan_point value phase_identifier and -# phase_matching arrays represent a collection of concatenated tuples, -# which are organized in sequence: The solutions for the 0-th scan point, +# Depending on the phases_per_scan_point value, identifier_phase and +# matching_phase arrays represent a collection of concatenated tuples. +# These are organized in sequence: The solutions for the 0-th scan point, # the 1-th scan point, the n_sc - 1 th scan point and omitting tuples -# for those scan points with no phases according to n_phases_per_scan_point +# for those scan points with no phases according to phases_per_scan_point. # # # # # -# +# # # One-dimensional array, pattern by pattern labelling the solutions found. -# The array n_phases_per_scan_point has to be specified because it details -# how the phase_identifier and the phase_matching arrays have to be interpreted. -# See documentation of phase_identifier for further details. +# The array phases_per_scan_point has to be specified because it details +# how the identifier_phase and the matching_phase arrays are interpreted. +# See documentation of identifier_phase for further details. # # # # # -# +# # # Phase_matching is a descriptor for how well the solution matches or not. -# Examples can be confidence_index, mean_angular_deviation, some AI-based -# matching probability (other), i.e. the details are implementation-specific. +# Examples can be confidence_index, mean_angular_deviation, or other. # # -# # # # # # -# -# +# # -# # -# Calibrated center positions of each scan point +# Calibrated centre positions of each scan point # in the sample surface reference system. # # @@ -1156,7 +1103,7 @@ NXem_ebsd(NXem_method): # # # -# Fraction of successfully indexed pattern with a phase +# Fraction of successfully indexed patterns with a phase # not the null-phase vs the number_of_scan_points. # # @@ -1165,14 +1112,11 @@ NXem_ebsd(NXem_method): # Number of scan points in the original mapping. # # -# # # @@ -1182,21 +1126,12 @@ NXem_ebsd(NXem_method): # # Descriptor representing the image contrast. # -# # # # # # # -# # # # Title of the default plot. @@ -1210,12 +1145,9 @@ NXem_ebsd(NXem_method): # # # -# # # -# Descriptor values. +# Descriptor values # # # diff --git a/contributed_definitions/nyaml/NXem_eds.yaml b/base_classes/nyaml/NXem_eds.yaml similarity index 66% rename from contributed_definitions/nyaml/NXem_eds.yaml rename to base_classes/nyaml/NXem_eds.yaml index f027544bdb..f59273f71d 100644 --- a/contributed_definitions/nyaml/NXem_eds.yaml +++ b/base_classes/nyaml/NXem_eds.yaml @@ -6,7 +6,7 @@ doc: | X-ray spectroscopy is a surface-sensitive technique. Therefore, three-dimensional elemental characterzation requires typically a sequence of characterization and preparation of the - surface to expose a new surface layer that can be characterized in the next acquisition. + surface to expose new surface layer that can be characterized in the next acquisition. In effect, the resulting three-dimensional elemental information mappings are truely the result of a correlation and post-processing of several measurements which is the field of correlative tomographic usage of electron microscopy. @@ -24,14 +24,7 @@ symbols: n_iupac_line_names: | Number of IUPAC line names type: group -NXem_eds(NXem_method): - - # NXprocess is composed from NXem_method base class instances where the spectra - # are stored as instances of (NXspectrum_set) is composed from NXem_method base class - # for post-processing of/with the above-defined data entries - # including feedback from Christoph Pauly (from MX Uni Saarland, NFDI-MatWerk), - # Sabine Bergmann and Sebastian Brückner (both from FAIRmat, IKZ), - # and Adrien Teutrie, Cecile Hebert (EPFL) +NXem_eds(NXprocess): indexing(NXprocess): doc: | Details about computational steps how peaks were indexed as elements. @@ -61,13 +54,21 @@ NXem_eds(NXem_method): \@long_name(NX_CHAR): doc: | Energy + atom_types(NX_CHAR): + doc: | + Comma-separated list of symbols for elements from the periodic table that have + been confirmed present by the here reported EDS analysis. + + This field can be used when creating instances of :ref:`NXpeak` is not desired. + However, a collection of instances of NXpeak with individual NXatom + can be used to add isotopic information and other relevant context. + dimensions: + rank: 1 + dim: (n_elements,) (NXpeak): doc: | - Name and location of each X-ray line which was indexed as a known ion. - For each ion, an NXion instance should be created which specifies - the origin of the signal. For each ion also the relevant IUPAC notation - X-ray lines should be specified. - (NXion): + Details about individual indexed peaks. + (NXatom): energy_range(NX_NUMBER): unit: NX_ENERGY doc: | @@ -80,7 +81,7 @@ NXem_eds(NXem_method): unit: NX_ENERGY doc: | Theoretical energy of the line according to IUPAC. - iupac_line_names(NX_CHAR): + iupac_line_name(NX_CHAR): doc: | IUPAC notation identifier of the line which the peak represents. @@ -89,84 +90,62 @@ NXem_eds(NXem_method): dimensions: rank: 1 dim: (n_iupac_line_names,) - atom_types(NX_CHAR): - doc: | - Comma-separated list of names of elements confirmed in the sample via EDS analysis. - - All members of the list have to be valid chemical_symbols from the periodic table. - - This field can be used when creating instances of NXpeak is not desired. - However, a collection of instances of NXpeak with individual NXion specified - enables also to distinguish isotopic information. - dimensions: - rank: 1 - dim: (n_elements,) - - # often the details of implemented background models and ZAF corrections are - # implemented and processed using proprietary software, in that case it can be - # the proprietary file formats typically have this information not documented completely - # for the example of EDAX, APEX software e.g. one finds EDS maps with just human-editable - # labels such as InL or P K or In P Mn i.e. combinations of signals from multiple ROIs - # but even a label InL is not physically not meaning ful enough, only with the knowledge - # that in an SEM and using an EDS detector, i.e. not a monochromating unit the energy - # resolution is not sufficient to resolve specific signals like e.g. separate certain lines - # therefore we use for now the - (NXimage_set): + (NXimage): doc: | Individual element-specific EDS/EDX/EDXS/SXES mapping A composition map is an image whose intensities for each pixel are the accumulated X-ray quanta *under the curve(s)* of a set of peaks. - These element-specific EDS maps are :ref:`NXimage_set` instances - and need to be named with the name of the element from the - atom_types field. + These element-specific EDS maps are instances of :ref:`NXimage` + that should be named by the element from the atom_types field. - We often observe that signal contributions from several peaks + When signal contributions from several peaks were decomposed + users should ideally use a respective number of NXpeak instances + to give further context about the individual signal contributions are summarized and shown together, e.g. the combined signal under the curve of carbon and oxygen. - In this case specify the processing details using peaks and weights. + In this case specify the processing details use peak and weight. description(NX_CHAR): doc: | Discouraged free-text field to add additional information. - iupac_line_candidates(NX_CHAR): + iupac_line_candidate(NX_CHAR): doc: | Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that documents which elements and their specific lines are theoretically located within - the energy_range of the spectrum from which the EDS (element) map has been computed. + the energy_range of the spectrum from which the EDS (element) map was computed. energy_range(NX_NUMBER): unit: NX_ENERGY doc: | Associated :math:`[e_{min}, e_{max}]` bounds of the energy - range for which spectrum counts have been accumulated. + range for which spectrum counts were accumulated. dimensions: rank: 1 dim: (2,) (NXprocess): - peaks(NX_CHAR): + peak(NX_CHAR): doc: | - A list of NXpeak instance names whose X-ray quanta - where accumulated for each pixel which yields an element-specific + A list of :ref:`NXpeak` instance names whose X-ray quanta were + accumulated for each pixel to obtain an element-specific EDS map. dimensions: rank: 1 dim: (n_peaks,) - weights(NX_NUMBER): + weight(NX_NUMBER): unit: NX_UNITLESS doc: | A list of weights by how much the intensity of each peak - under peaks was factorized to display the joint intensity - of the image. + contributes to the intensity of the EDS map. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f0a21a21456db8b820a74ebbe5815f225a80a97f644baf54220b74aedcfd761a +# 488f9130ee79426637940dc4b0bbb269fb7401c328009506aef834d087ec52d7 # # # -# +# # @@ -217,17 +196,11 @@ NXem_eds(NXem_method): # # X-ray spectroscopy is a surface-sensitive technique. Therefore, three-dimensional elemental # characterzation requires typically a sequence of characterization and preparation of the -# surface to expose a new surface layer that can be characterized in the next acquisition. +# surface to expose new surface layer that can be characterized in the next acquisition. # In effect, the resulting three-dimensional elemental information mappings are truely the # result of a correlation and post-processing of several measurements which is the field # of correlative tomographic usage of electron microscopy. # -# # # # Details about computational steps how peaks were indexed as elements. @@ -268,14 +241,24 @@ NXem_eds(NXem_method): # # # +# +# +# Comma-separated list of symbols for elements from the periodic table that have +# been confirmed present by the here reported EDS analysis. +# +# This field can be used when creating instances of :ref:`NXpeak` is not desired. +# However, a collection of instances of NXpeak with individual NXatom +# can be used to add isotopic information and other relevant context. +# +# +# +# +# # # -# Name and location of each X-ray line which was indexed as a known ion. -# For each ion, an NXion instance should be created which specifies -# the origin of the signal. For each ion also the relevant IUPAC notation -# X-ray lines should be specified. +# Details about individual indexed peaks. # -# +# # # # Associated lower :math:`[e_{min}, e_{max}]` bounds of the @@ -290,7 +273,7 @@ NXem_eds(NXem_method): # Theoretical energy of the line according to IUPAC. # # -# +# # # IUPAC notation identifier of the line which the peak represents. # @@ -303,83 +286,60 @@ NXem_eds(NXem_method): # # # -# -# -# Comma-separated list of names of elements confirmed in the sample via EDS analysis. -# -# All members of the list have to be valid chemical_symbols from the periodic table. -# -# This field can be used when creating instances of NXpeak is not desired. -# However, a collection of instances of NXpeak with individual NXion specified -# enables also to distinguish isotopic information. -# -# -# -# -# -# -# +# # # Individual element-specific EDS/EDX/EDXS/SXES mapping # # A composition map is an image whose intensities for each pixel are the # accumulated X-ray quanta *under the curve(s)* of a set of peaks. # -# These element-specific EDS maps are :ref:`NXimage_set` instances -# and need to be named with the name of the element from the -# atom_types field. +# These element-specific EDS maps are instances of :ref:`NXimage` +# that should be named by the element from the atom_types field. # -# We often observe that signal contributions from several peaks +# When signal contributions from several peaks were decomposed +# users should ideally use a respective number of NXpeak instances +# to give further context about the individual signal contributions # are summarized and shown together, e.g. the combined signal # under the curve of carbon and oxygen. # -# In this case specify the processing details using peaks and weights. +# In this case specify the processing details use peak and weight. # # # # Discouraged free-text field to add additional information. # # -# +# # # Comma-separated list of chemical_symbol-IUPAC X-ray (emission) line name that # documents which elements and their specific lines are theoretically located within -# the energy_range of the spectrum from which the EDS (element) map has been computed. +# the energy_range of the spectrum from which the EDS (element) map was computed. # # # # # Associated :math:`[e_{min}, e_{max}]` bounds of the energy -# range for which spectrum counts have been accumulated. +# range for which spectrum counts were accumulated. # # # # # # -# +# # -# A list of NXpeak instance names whose X-ray quanta -# where accumulated for each pixel which yields an element-specific +# A list of :ref:`NXpeak` instance names whose X-ray quanta were +# accumulated for each pixel to obtain an element-specific # EDS map. # # # # # -# +# # # A list of weights by how much the intensity of each peak -# under peaks was factorized to display the joint intensity -# of the image. +# contributes to the intensity of the EDS map. # # # diff --git a/contributed_definitions/nyaml/NXem_eels.yaml b/base_classes/nyaml/NXem_eels.yaml similarity index 64% rename from contributed_definitions/nyaml/NXem_eels.yaml rename to base_classes/nyaml/NXem_eels.yaml index 317c990f25..6325614d15 100644 --- a/contributed_definitions/nyaml/NXem_eels.yaml +++ b/base_classes/nyaml/NXem_eels.yaml @@ -1,14 +1,8 @@ category: base doc: | Base class method-specific for Electron Energy Loss Spectroscopy (EELS). - -# symbols: -# n_energy_loss: Number of electron energy loss bins. type: group -NXem_eels(NXem_method): - - # NXem_method also has an NXprocess which in this base class can be - # specialized to include EELS-specific post-processing +NXem_eels(NXprocess): zlp_correction(NXprocess): doc: | Details about computational stesp how the zero-loss peak was threaded. @@ -24,18 +18,18 @@ NXem_eels(NXem_method): (NXpeak): doc: | Name and location of each peak in the spectrum considered to be of relevance. - (NXspectrum_set): + (NXspectrum): doc: | - NXspectrum_set_em specialized for EELS. + NXspectrum specialized for EELS. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 47a296ca2a928aa1eb6e0c0e8d866f01d2586e617a20e631b43b8595e85f3613 +# 8b438cc22910cf6ae9e117cc7013c8b1f0652ba643c8284b3421f733b6264b13 # # # -# -# +# # -# Base class method-specific for Electron Energy Loss Spectroscopy (EELS). +# Base class method-specific for Electron Energy Loss Spectroscopy (EELS). # -# # # -# Details about computational stesp how the zero-loss peak was threaded. +# Details about computational stesp how the zero-loss peak was threaded. # # # -# The program with which the zero-loss peak correction was performed. +# The program with which the zero-loss peak correction was performed. # # # # # -# Details about computational steps how peaks were indexed as elements. +# Details about computational steps how peaks were indexed as elements. # # # -# The program with which the indexing was performed. +# The program with which the indexing was performed. # # # # -# Name and location of each peak in the spectrum considered to be of relevance. +# Name and location of each peak in the spectrum considered to be of relevance. # # -# +# # -# NXspectrum_set_em specialized for EELS. +# NXspectrum specialized for EELS. # # # diff --git a/contributed_definitions/nyaml/NXem_img.yaml b/base_classes/nyaml/NXem_img.yaml similarity index 65% rename from contributed_definitions/nyaml/NXem_img.yaml rename to base_classes/nyaml/NXem_img.yaml index 85b3f7d801..8d81e4e7ac 100644 --- a/contributed_definitions/nyaml/NXem_img.yaml +++ b/base_classes/nyaml/NXem_img.yaml @@ -1,21 +1,23 @@ category: base doc: | - Base class for method-specific generic imaging. + Base class for method-specific generic imaging with electron microscopes. In the majority of cases simple d-dimensional regular scan patterns are used - to probe a region-of-interest (ROI). Examples can be single point aka spot + to probe regions-of-interest (ROIs). Examples can be single point aka spot measurements, line profiles, or (rectangular) surface mappings. The latter pattern is the most frequently used. For now the base class provides for scans for which the settings, binning, and energy resolution is the same for each scan point. type: group -NXem_img(NXem_method): - imaging_mode(NX_CHAR): - doc: | - Which imaging mode was used? - enumeration: [secondary_electron, backscattered_electron, annular_dark_field, cathodoluminescence] - (NXimage_set): +NXem_img(NXprocess): + (NXimage): + imaging_mode(NX_CHAR): + doc: | + Which imaging mode was used? + enumeration: + open_enum: true + items: [secondary_electron, backscattered_electron, annular_dark_field, cathodoluminescence] half_angle_interval(NX_NUMBER): unit: NX_ANGLE doc: | @@ -24,19 +26,20 @@ NXem_img(NXem_method): rank: 1 dim: (2,) + # already implemented connections to representations of microstructures but in this PR not proposed # (NXmicrostructure): # doc: | # A reconstruction of the microstructure or some of its features # based on image information in the parent class. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4db4021127a9125e25468c06f589ce9ab3b0d61f26818aaf1fa8e89bd19c2f27 +# 399e311c8610e60a5a7e0d69f1271d29d19e6f12bb1cfe372c34eb72118daf3a # # # -# +# # -# Base class for method-specific generic imaging. +# Base class for method-specific generic imaging with electron microscopes. # # In the majority of cases simple d-dimensional regular scan patterns are used -# to probe a region-of-interest (ROI). Examples can be single point aka spot +# to probe regions-of-interest (ROIs). Examples can be single point aka spot # measurements, line profiles, or (rectangular) surface mappings. # The latter pattern is the most frequently used. # # For now the base class provides for scans for which the settings, # binning, and energy resolution is the same for each scan point. # -# -# -# Which imaging mode was used? -# -# -# -# -# -# -# -# -# +# +# +# +# Which imaging mode was used? +# +# +# +# +# +# +# +# # # # Annulus inner (first value) and outer (second value) half angle. @@ -87,7 +90,8 @@ NXem_img(NXem_method): # # # -# diff --git a/base_classes/nyaml/NXevent_data_apm.yaml b/base_classes/nyaml/NXevent_data_apm.yaml new file mode 100644 index 0000000000..6069c9095b --- /dev/null +++ b/base_classes/nyaml/NXevent_data_apm.yaml @@ -0,0 +1,284 @@ +category: base +doc: | + Base class to store state and (meta)data of events over the course of an atom probe experiment. + + Having at least one instance for an instance of NXapm is recommended. + + This base class applies the concept of the NXevent_data_em base class to the specific needs + of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication + of information. Specifically, the time interval considered is the entire time + starting at start_time until end_time during which we assume the pulser triggered named pulses. + These pulses are identified via the pulse_identifier field. The point in time when each was issued + is specified via the combination of start_time and delta_time. + + Conceptually and technically NeXus currently stores tensorial information as arrays of values + (with each value of the same datatype). For instance, a field temperature(NX_FLOAT) stores + a set of temperature values but that field when used somewhere is a concept. However, that + concept has no information at which point in time these temperatures were taken. + An existent functional relationship between the two concepts is not defined. + + However, a correct interpretation of the temperature values demands knowledge about what is + the independent quantity on which temperature depends on or according to which frequency + temperature values were sampled. + In NeXus there are two approaches which cope with such correlations: + One is :ref:`NXdata` where the attribute signal specifies the correlation. + The other one is :ref:`NXlog` which, like NXdata, demands to granularize logged_against + (dependent signal) and independent quantities into an own group. + In many cases this additional grouping is not desired though. + + One naive solution typically employed is then to store the independent variable values via a second + vector e.g. time_stamp with the same number of entries (with dimensionality defined through symbols). + However, there is no independent logical connection between these two concepts, i.e. temperature + and time_stamp. + + In the case of atom probe though the time that one would use in NXlog is defined implicitly via pulse_identifier, + which is the independent variable vector against which eventually dozens of channels of data are logged. + Not only are these channels logged they should ideally also be self-descriptive in that these channels have + pulse_identifier as the independent variable but we do not wish to duplicate this information all the time but + reference it. + + Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the + symbol depends_on but this is easily to be confused with depends_on that is used for instances of + :ref:`NXtransformations`. Consequently, if depends_on were to be used extra logic is needed by consuming + applications to understand that the here build correlations are conceptually different ones. + + This issue should be discussed further by the NeXus community. +symbols: + doc: | + The symbols used in the schema to specify e.g. dimensions of arrays. + p: | + Number of pulses collected in between start_time and end_time. +type: group +NXevent_data_apm(NXobject): + start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval started. If the user wishes to specify an + interval of time that the snapshot should represent during which the instrument + was stable and configured using specific settings and calibrations, + the start_time is the start (left bound of the time interval) while + the end_time specifies the end (right bound) of the time interval. + end_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval ended. + delta_time(NX_NUMBER): + unit: NX_TIME + doc: | + Delta time array which resolves for each pulse_identifier the time difference + between when that pulse was issued and start_time. + + In summary, using start_time, end_time, delta_time, pulse_identifier_offset, + and pulse_identifier exactly specifies the connection between when a pulse was + issued relative to start and absolute in UTC. + dimensions: + rank: 1 + dim: (p,) + pulse_identifier_offset(NX_INT): + unit: NX_UNITLESS + doc: | + Integer used to name the first pulse to know if there is an + offset of the identifiers to zero. + + Identifiers can be defined either implicitly or explicitly. + For implicit indexing identifiers are defined on the interval + :math:`[identifier\_offset, identifier\_offset + c - 1]`. + + Therefore, implicit identifier are completely defined by the value of + identifier_offset and cardinality. For example if identifier run from + -2 to 3 the value for identifier_offset is -2. + + For explicit indexing the field identifier has to be used. + Fortran-/Matlab- and C-/Python-style indexing have specific implicit + identifier conventions where identifier_offset is 1 and 0 respectively. + pulse_identifier(NX_INT): + unit: NX_UNITLESS + doc: | + Identifier that contextualizes how the detector and pulser of an atom probe + instrument follows a sequence of pulses to trigger field evaporation. + + The pulse_identifier is used to associate thus an information about time + when quantities have been collected via sampling. + + In virtually all cases the pulser is a blackbox. Depending on how the + instrument is configured during a measurement the target + values and thus also the actual values may change. + + Maybe the first part of the experiment is run at a certain pulse fraction but thereafter + the pulse_fraction is changed. In this case the field pulse_fraction is a vector which + collects all measured values of the pulse_fraction, pulse_identifier is then an equally + long vector which stores the set of events (e.g. pulsing events) when that value was + measured. + + This may cause several situations: In the case that e.g. the pulse_fraction is never changed + and also exact details not interesting, one stores the set value for the pulse_fraction + and a single value for the pulse_identifier e.g. 0 to indicate that the pulse_fraction was set + at the beginning and it was maintained constant during the measurement. + If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a + vector with two values one for the first and another one for the value from the 100000-th + pulse onwards. The values of pulse_identifier are then [0, 99999] respectively. + dimensions: + rank: 1 + dim: (p,) + instrument(NXinstrument_apm): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 07658ee91d4228221572bfd3c1bd35594582b7f0eb2bc23551294b89cfe772e1 +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of pulses collected in between start_time and end_time. +# +# +# +# +# Base class to store state and (meta)data of events over the course of an atom probe experiment. +# +# Having at least one instance for an instance of NXapm is recommended. +# +# This base class applies the concept of the NXevent_data_em base class to the specific needs +# of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication +# of information. Specifically, the time interval considered is the entire time +# starting at start_time until end_time during which we assume the pulser triggered named pulses. +# These pulses are identified via the pulse_identifier field. The point in time when each was issued +# is specified via the combination of start_time and delta_time. +# +# Conceptually and technically NeXus currently stores tensorial information as arrays of values +# (with each value of the same datatype). For instance, a field temperature(NX_FLOAT) stores +# a set of temperature values but that field when used somewhere is a concept. However, that +# concept has no information at which point in time these temperatures were taken. +# An existent functional relationship between the two concepts is not defined. +# +# However, a correct interpretation of the temperature values demands knowledge about what is +# the independent quantity on which temperature depends on or according to which frequency +# temperature values were sampled. +# In NeXus there are two approaches which cope with such correlations: +# One is :ref:`NXdata` where the attribute signal specifies the correlation. +# The other one is :ref:`NXlog` which, like NXdata, demands to granularize logged_against +# (dependent signal) and independent quantities into an own group. +# In many cases this additional grouping is not desired though. +# +# One naive solution typically employed is then to store the independent variable values via a second +# vector e.g. time_stamp with the same number of entries (with dimensionality defined through symbols). +# However, there is no independent logical connection between these two concepts, i.e. temperature +# and time_stamp. +# +# In the case of atom probe though the time that one would use in NXlog is defined implicitly via pulse_identifier, +# which is the independent variable vector against which eventually dozens of channels of data are logged. +# Not only are these channels logged they should ideally also be self-descriptive in that these channels have +# pulse_identifier as the independent variable but we do not wish to duplicate this information all the time but +# reference it. +# +# Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the +# symbol depends_on but this is easily to be confused with depends_on that is used for instances of +# :ref:`NXtransformations`. Consequently, if depends_on were to be used extra logic is needed by consuming +# applications to understand that the here build correlations are conceptually different ones. +# +# This issue should be discussed further by the NeXus community. +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the snapshot time interval started. If the user wishes to specify an +# interval of time that the snapshot should represent during which the instrument +# was stable and configured using specific settings and calibrations, +# the start_time is the start (left bound of the time interval) while +# the end_time specifies the end (right bound) of the time interval. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the snapshot time interval ended. +# +# +# +# +# Delta time array which resolves for each pulse_identifier the time difference +# between when that pulse was issued and start_time. +# +# In summary, using start_time, end_time, delta_time, pulse_identifier_offset, +# and pulse_identifier exactly specifies the connection between when a pulse was +# issued relative to start and absolute in UTC. +# +# +# +# +# +# +# +# Integer used to name the first pulse to know if there is an +# offset of the identifiers to zero. +# +# Identifiers can be defined either implicitly or explicitly. +# For implicit indexing identifiers are defined on the interval +# :math:`[identifier\_offset, identifier\_offset + c - 1]`. +# +# Therefore, implicit identifier are completely defined by the value of +# identifier_offset and cardinality. For example if identifier run from +# -2 to 3 the value for identifier_offset is -2. +# +# For explicit indexing the field identifier has to be used. +# Fortran-/Matlab- and C-/Python-style indexing have specific implicit +# identifier conventions where identifier_offset is 1 and 0 respectively. +# +# +# +# +# Identifier that contextualizes how the detector and pulser of an atom probe +# instrument follows a sequence of pulses to trigger field evaporation. +# +# The pulse_identifier is used to associate thus an information about time +# when quantities have been collected via sampling. +# +# In virtually all cases the pulser is a blackbox. Depending on how the +# instrument is configured during a measurement the target +# values and thus also the actual values may change. +# +# Maybe the first part of the experiment is run at a certain pulse fraction but thereafter +# the pulse_fraction is changed. In this case the field pulse_fraction is a vector which +# collects all measured values of the pulse_fraction, pulse_identifier is then an equally +# long vector which stores the set of events (e.g. pulsing events) when that value was +# measured. +# +# This may cause several situations: In the case that e.g. the pulse_fraction is never changed +# and also exact details not interesting, one stores the set value for the pulse_fraction +# and a single value for the pulse_identifier e.g. 0 to indicate that the pulse_fraction was set +# at the beginning and it was maintained constant during the measurement. +# If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a +# vector with two values one for the first and another one for the value from the 100000-th +# pulse onwards. The values of pulse_identifier are then [0, 99999] respectively. +# +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXevent_data_em.yaml b/base_classes/nyaml/NXevent_data_em.yaml new file mode 100644 index 0000000000..3866ed243f --- /dev/null +++ b/base_classes/nyaml/NXevent_data_em.yaml @@ -0,0 +1,289 @@ +category: base +doc: | + Base class to store state and (meta)data of events for electron microscopy. + + Electron microscopes are dynamic. Scientists often report that microscopes + *perform differently* across sessions. That *they* perform differently from + one day or another. In some cases, root causes for performance differences + are unclear. Users of the instrument may consider such conditions impractical, + or *too poor*, and thus abort their session. Alternatively, users may try to + bring the microscope into a state where conditions are considered better + or of whatever high enough quality for starting or continuing the measurement. + + Which temporal granularity is adequate to log events depends on the situation and + research question. Using a model which enables a collection of events offers + the most flexible way to cater for both experiments with controlled electron + beams in a real microscope or the simulation of such experiments or + individual aspects of such experiments. + + In all these use cases it is useful to have a mechanism whereby time-dependent + data of the instrument state can be stored and documented in an representation + that facilitates interoperability. + + :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly + whatever is considered a time interval during which the instrument is + considered stable enough for allowing any working on tasks with the microscope. + Examples of such tasks are the collecting of data (images and spectra) or + the calibrating the instrument or individual of its components. Users may wish to take + only a single scan or image and complete their microscope session thereafter. + Alternatively, users are working for much longer time at the microscope, + perform recalibrations in between and take several scans (of different + ROIs on the specimen), or they explore the state of the microscope for + service or maintenance tasks. + + :ref:`NXevent_data_em` serves the harmonization and documentation of these cases: + + * Firstly, via a header section whose purpose is to contextualize + and identify the event instance in time. + * Secondly, via a data and metadata section where individual data + collections can be stored in a standardized representation. + + The idea of the first section, the event-based em_lab, is to document the + state of the microscope as it was found during the event. The idea of the other, + the :ref:`NXem` application-definition-based em_lab(NXinstrument) section is to + keep all those data that are static in the sense that they remain the same + across multiple :ref:`NXevent_data_em` instances. + This reduces the need for having many copies of the same metadata. + + We are aware of the fact that given the variety how an electron microscope + is used, there is a need for a flexible and adaptive documentation system. + At the same time we are also convinced though that just because one has + different requirements for some specific aspect under the umbrella of settings + to an electron microscope, this does not necessarily warrant that one has to + cook up an own data schema. + + Instead, the electron microscopy community should work towards reusing schema + components as frequently as possible. This will enable that there is at all + not only a value of harmonizing electron microscopy research content but also + there is a technical possibility to build services around such harmonized data. + + Arguably it is oftentimes tricky to specify a clear time interval when the + microscope is *stable enough*. Take for instance the acquisition of an image + or a stack of spectra. Having to deal with instabilities is a common theme in + electron microscopy practice. Numerical protocols can be used during data + post-processing to correct for some of the instabilities. + A few exemplar references to provide an overview on the subject is + available in the literature: + + * `C. Ophus et al. `_ + * `B. Berkels et al. `_ + * `L. Jones et al. `_ + + For specific simulation purposes, mainly in an effort to digitally repeat or simulate + the experiment, it is tempting to consider dynamics of the instrument, + implemented as time-dependent functional descriptions of e.g. lens excitations, + beam shape functions, trajectories of groups of electrons and ions, + or detector noise models. This warrants to document the time-dependent + details of individual components of the microscope + as is implemented in :ref:`NXevent_data_em`. +type: group +NXevent_data_em(NXobject): + start_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval started. If the user wishes to specify an + interval of time that the snapshot should represent during which the instrument + was stable and configured using specific settings and calibrations, + the start_time is the start (left bound of the time interval) while + the end_time specifies the end (right bound) of the time interval. + end_time(NX_DATE_TIME): + doc: | + ISO 8601 time code with local time zone offset to UTC information included + when the snapshot time interval ended. + identifier_event(NX_INT): + unit: NX_UNITLESS + doc: | + Identifier of a specific state and setting of the microscope. + type(NX_CHAR): + doc: | + Which specific event/measurement type. Examples are: + + * In-lens/backscattered electron, usually has quadrants + * Secondary_electron, image, topography, fractography, overview images + * Backscattered_electron, image, Z or channeling contrast (ECCI) + * Bright_field, image, TEM + * Dark_field, image, crystal defects + * Annular dark field, image (medium- or high-angle), TEM + * Diffraction, image, TEM, or a comparable technique in the SEM + * Kikuchi, image, SEM EBSD and TEM diffraction + * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) + * Electron energy loss spectra for points, lines, surfaces, TEM + * Auger, spectrum, (low Z contrast element composition) + * Cathodoluminescence (optical spectra) + * Ronchigram, image, alignment utility specifically in TEM + * Chamber, e.g. TV camera inside the chamber, education purposes. + + This field may also be used for storing additional information + about the event for which there is at the moment no other place. + + In the long run such free-text field description should be avoided as + they are difficult to machine-interpret. Instead, reference should be given + to refactoring these descriptions into structured metadata. + The reason why in this base class the field event_type is nonetheless kept + is to offer a place whereby practically users may enter data for + follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. + (NXuser): + (NXinstrument_em): + (NXimage): + (NXspectrum): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 7a369510bf4d0c4450c2d2a5f9f700e275bb60aa8acdec6d175158d8f1ca6dd4 +# +# +# +# +# +# Base class to store state and (meta)data of events for electron microscopy. +# +# Electron microscopes are dynamic. Scientists often report that microscopes +# *perform differently* across sessions. That *they* perform differently from +# one day or another. In some cases, root causes for performance differences +# are unclear. Users of the instrument may consider such conditions impractical, +# or *too poor*, and thus abort their session. Alternatively, users may try to +# bring the microscope into a state where conditions are considered better +# or of whatever high enough quality for starting or continuing the measurement. +# +# Which temporal granularity is adequate to log events depends on the situation and +# research question. Using a model which enables a collection of events offers +# the most flexible way to cater for both experiments with controlled electron +# beams in a real microscope or the simulation of such experiments or +# individual aspects of such experiments. +# +# In all these use cases it is useful to have a mechanism whereby time-dependent +# data of the instrument state can be stored and documented in an representation +# that facilitates interoperability. +# +# :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly +# whatever is considered a time interval during which the instrument is +# considered stable enough for allowing any working on tasks with the microscope. +# Examples of such tasks are the collecting of data (images and spectra) or +# the calibrating the instrument or individual of its components. Users may wish to take +# only a single scan or image and complete their microscope session thereafter. +# Alternatively, users are working for much longer time at the microscope, +# perform recalibrations in between and take several scans (of different +# ROIs on the specimen), or they explore the state of the microscope for +# service or maintenance tasks. +# +# :ref:`NXevent_data_em` serves the harmonization and documentation of these cases: +# +# * Firstly, via a header section whose purpose is to contextualize +# and identify the event instance in time. +# * Secondly, via a data and metadata section where individual data +# collections can be stored in a standardized representation. +# +# The idea of the first section, the event-based em_lab, is to document the +# state of the microscope as it was found during the event. The idea of the other, +# the :ref:`NXem` application-definition-based em_lab(NXinstrument) section is to +# keep all those data that are static in the sense that they remain the same +# across multiple :ref:`NXevent_data_em` instances. +# This reduces the need for having many copies of the same metadata. +# +# We are aware of the fact that given the variety how an electron microscope +# is used, there is a need for a flexible and adaptive documentation system. +# At the same time we are also convinced though that just because one has +# different requirements for some specific aspect under the umbrella of settings +# to an electron microscope, this does not necessarily warrant that one has to +# cook up an own data schema. +# +# Instead, the electron microscopy community should work towards reusing schema +# components as frequently as possible. This will enable that there is at all +# not only a value of harmonizing electron microscopy research content but also +# there is a technical possibility to build services around such harmonized data. +# +# Arguably it is oftentimes tricky to specify a clear time interval when the +# microscope is *stable enough*. Take for instance the acquisition of an image +# or a stack of spectra. Having to deal with instabilities is a common theme in +# electron microscopy practice. Numerical protocols can be used during data +# post-processing to correct for some of the instabilities. +# A few exemplar references to provide an overview on the subject is +# available in the literature: +# +# * `C. Ophus et al. <https://dx.doi.org/10.1016/j.ultramic.2015.12.002>`_ +# * `B. Berkels et al. <https://doi.org/10.1016/j.ultramic.2018.12.016>`_ +# * `L. Jones et al. <https://link.springer.com/article/10.1186/s40679-015-0008-4>`_ +# +# For specific simulation purposes, mainly in an effort to digitally repeat or simulate +# the experiment, it is tempting to consider dynamics of the instrument, +# implemented as time-dependent functional descriptions of e.g. lens excitations, +# beam shape functions, trajectories of groups of electrons and ions, +# or detector noise models. This warrants to document the time-dependent +# details of individual components of the microscope +# as is implemented in :ref:`NXevent_data_em`. +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the snapshot time interval started. If the user wishes to specify an +# interval of time that the snapshot should represent during which the instrument +# was stable and configured using specific settings and calibrations, +# the start_time is the start (left bound of the time interval) while +# the end_time specifies the end (right bound) of the time interval. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information included +# when the snapshot time interval ended. +# +# +# +# +# Identifier of a specific state and setting of the microscope. +# +# +# +# +# Which specific event/measurement type. Examples are: +# +# * In-lens/backscattered electron, usually has quadrants +# * Secondary_electron, image, topography, fractography, overview images +# * Backscattered_electron, image, Z or channeling contrast (ECCI) +# * Bright_field, image, TEM +# * Dark_field, image, crystal defects +# * Annular dark field, image (medium- or high-angle), TEM +# * Diffraction, image, TEM, or a comparable technique in the SEM +# * Kikuchi, image, SEM EBSD and TEM diffraction +# * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) +# * Electron energy loss spectra for points, lines, surfaces, TEM +# * Auger, spectrum, (low Z contrast element composition) +# * Cathodoluminescence (optical spectra) +# * Ronchigram, image, alignment utility specifically in TEM +# * Chamber, e.g. TV camera inside the chamber, education purposes. +# +# This field may also be used for storing additional information +# about the event for which there is at the moment no other place. +# +# In the long run such free-text field description should be avoided as +# they are difficult to machine-interpret. Instead, reference should be given +# to refactoring these descriptions into structured metadata. +# The reason why in this base class the field event_type is nonetheless kept +# is to offer a place whereby practically users may enter data for +# follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXibeam_column.yaml b/base_classes/nyaml/NXibeam_column.yaml similarity index 100% rename from contributed_definitions/nyaml/NXibeam_column.yaml rename to base_classes/nyaml/NXibeam_column.yaml diff --git a/contributed_definitions/nyaml/NXimage_set.yaml b/base_classes/nyaml/NXimage.yaml similarity index 65% rename from contributed_definitions/nyaml/NXimage_set.yaml rename to base_classes/nyaml/NXimage.yaml index 4e270c21aa..98666e46ac 100644 --- a/contributed_definitions/nyaml/NXimage_set.yaml +++ b/base_classes/nyaml/NXimage.yaml @@ -2,23 +2,24 @@ category: base doc: | Base class for reporting a set of images. - The mostly commonly used scanning methods are supported. That is one-, + The most commonly used scanning methods are supported. That is one-, two-, three-dimensional ROIs discretized using regular Euclidean tilings. Colloquially, an image is understood as a discretized representation of intensity distribution - that was detected or simulated for some ROI. When discretized with regular Euclidean tilings - the terms pixel and voxel identify the smallest discretization unit. Pixel and voxel are polygonal + detected or simulated for some ROI. When discretized with regular Euclidean tilings, the terms + pixel and voxel identify the smallest discretization unit. In this case, pixel and voxel are polygonal or polyhedral unit cells respectively of the underlying tiling of the ROI within the reference space. For all other tilings e.g. non-equispaced, the shape and size of pixel and voxel differs. Using the term - (image) point is eventually is more appropriate for such tilings. Therefore, all docstrings in this base class - refer to points (including pixel and voxel i.e. regular tilings). + (image) point is eventually more appropriate when working with such tilings. + + Therefore, all docstrings in this base class refer to points (including pixel and voxel i.e. regular tilings). Point coordinates identify the location of the barycentre. - For images in reciprocal space in practice, complex numbers are encoded via some - formatted pair of real values. Typically, fast algorithms for computing Fourier transformations - (FFT) are used to encode images in reciprocal (frequency) space. FFT libraries are used - for implementing the key functionalities of these mathematical operations. + For images in reciprocal space in practice, complex numbers are encoded via some formatted pair of real values. + Typically, fast algorithms for computing Fourier transformations (FFT) are used to encode + images in reciprocal (frequency) space. FFT libraries are used for implementing the key functionalities of + these mathematical operations. Different libraries use different representations and encoding of the images. Details can be found in the respective sections of the typical FFT libraries documentations @@ -26,23 +27,21 @@ doc: | * `FFTW by M. Frigo and S. G. Johnson `_ * `Intel MKL by the Intel Co. `_ * `cuFFT by the NVidia Co. `_ - * `NFFT by the Chemnitz group `_ for non-equispaced computations + * `NFFT by the TU Chemnitz group `_ for non-equispaced computations Users are strongly advised to inspect carefully which specific conventions their library uses to enable storing and modifying the implementation of their code such that the serialized representations as they are detailed here for NeXus match. It is often the case that several images are combined using processing. In this case, - the number of images which are combined in a collection is not necessarily the same - for each collection. The NXimage_set base class addresses this logical distinction - through the notation of image_identifier and group_identifier concepts. - That is image_identifier are always counting from offset in increments of one. + the number of images which are combined into collections is not necessarily the same + for each collection. The NXimage base class addresses this logical distinction + through the notation of identifier_image and identifier_group concepts. + That is identifier_image are always counting from offset in increments of one. as each image is its own entity. By contrast, a group may contain no, or several images. - Consequently, group_identifier are not required to be contiguous. + Consequently, identifier_group are not required to be contiguous. -# for earlier variants see here -# https://github.com/FAIRmat-NFDI/nexus_definitions/commit/0682943baaef54d4a6386b5433f9721af6d3d81b -# https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons +# set of frequently made specializations of NXdata instances for images symbols: n_img: | Number of images in the stack, for stacks the slowest dimension. @@ -52,29 +51,15 @@ symbols: Number of image points along the fast dimension (j equivalent to y). n_i: | Number of image points along the fastest dimension (i equivalent to x). - -# a key challenge is setting constraints, lets explain with contrasting two use cases: -# case 1 assuming an image is nothing but a collection of point-wise information without making explicit tiling and discretization information -# case 2 assuming that like most frequently assumed we understand an image probing Euclidean space -# assuming that we expect that the image is represented using a pixel grid because it was captured -# using sensors that are arranged on generator points of a regular tiling. -# in the first case, one should not constrain the dimensions for images beyond 1d -# because beyond 1d the question of offset and stride comes up i.e. the question which -# tiling is used to construct the sensor array -# in the second case, one should constrain the dimensions for all dimensions as otherwise -# there are no instructions how to arrange the sensors or the pixels for visualizing the image -# because the image is not just a bunch of point wise intensities -# but if the dimensions are not constrained again images in application definitions will be represented -# using different conventions. type: group -NXimage_set(NXobject): +NXimage(NXobject): (NXprocess): doc: | Details how NXdata instance were processed from detector readings/raw data. source(NXnote): doc: | Resolvable data artifact (e.g. file) from which all values in the :ref:`NXdata` - instances in this :ref:`NXimage_set` were loaded during parsing. + instances in this :ref:`NXimage` were loaded during parsing. Possibility to document from which specific other serialized resource as the source pieces of information were processed when using NeXus as a semantic file format @@ -86,23 +71,13 @@ NXimage_set(NXobject): Reference to a location inside the artifact that points to the specific group of values that were processed if the artifacts contains several groups of values and thus further resolving of ambiguities is required. - - # mode(NX_CHAR): - # doc: | - # Imaging (data collection) mode of the instrument during acquisition. - detector_identifier(NX_CHAR): + identifier_detector(NX_CHAR): doc: | Link or name of an :ref:`NXdetector` instance with which the data were collected. (NXprogram): doc: | Program used for processing. - - # space(NX_CHAR): - # doc: - # - | - # The reference space in which the image set is defined. - # enumeration: [real, reciprocal] image_1d(NXdata): doc: | One-dimensional image. @@ -132,7 +107,7 @@ NXimage_set(NXobject): unit: NX_UNITLESS doc: | Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. + imag fields if values are stored as interleaved complex numbers. dimensions: rank: 1 dim: (n_i,) @@ -175,7 +150,7 @@ NXimage_set(NXobject): unit: NX_UNITLESS doc: | Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. + imag fields if values are stored as interleaved complex numbers. dimensions: rank: 2 dim: (n_j, n_i) @@ -228,7 +203,7 @@ NXimage_set(NXobject): unit: NX_UNITLESS doc: | Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. + imag fields if values are stored as interleaved complex numbers. dimensions: rank: 3 dim: (n_k, n_j, n_i) @@ -264,7 +239,7 @@ NXimage_set(NXobject): Point coordinate along the fastest dimension. stack_1d(NXdata): doc: | - Collection of image_1d. + Collection of one-dimesional images. intensity(NX_NUMBER): unit: NX_UNITLESS doc: | @@ -291,11 +266,11 @@ NXimage_set(NXobject): unit: NX_UNITLESS doc: | Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. + imag fields if values are stored as interleaved complex numbers. dimensions: rank: 2 dim: (n_img, n_i) - group_identifier(NX_INT): + identifier_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -305,7 +280,7 @@ NXimage_set(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - image_identifier(NX_INT): + identifier_image(NX_INT): unit: NX_UNITLESS doc: | Image identifier @@ -354,11 +329,11 @@ NXimage_set(NXobject): unit: NX_UNITLESS doc: | Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. + imag fields if values are stored as interleaved complex numbers. dimensions: rank: 3 dim: (n_img, n_j, n_i) - group_identifier(NX_INT): + identifier_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -368,7 +343,7 @@ NXimage_set(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - image_identifier(NX_INT): + identifier_image(NX_INT): unit: NX_UNITLESS doc: | Image identifier @@ -427,11 +402,11 @@ NXimage_set(NXobject): unit: NX_UNITLESS doc: | Image intensity as a complex number as an alternative to real and - imaginary fields if values are stored as interleaved complex numbers. + imag fields if values are stored as interleaved complex numbers. dimensions: rank: 4 dim: (n_img, n_k, n_j, n_i) - group_identifier(NX_INT): + identifier_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -441,7 +416,7 @@ NXimage_set(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - image_identifier(NX_INT): + identifier_image(NX_INT): unit: NX_UNITLESS doc: | Image identifier @@ -483,13 +458,13 @@ NXimage_set(NXobject): Point coordinate along the fastest dimension. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 57504aef23c1b9f5eb3a257e702664fda6cbfd65141fb96587310b6988f4e893 +# 80a371b2fced61204773fd0d6a5b2f944206063758c40bbe0fef52155fb9130e # # # -# -# -# +# +# # # # -# Number of images in the stack, for stacks the slowest dimension. +# Number of images in the stack, for stacks the slowest dimension. # # # # -# Number of image points along the slow dimension (k equivalent to z). +# Number of image points along the slow dimension (k equivalent to z). # # # # -# Number of image points along the fast dimension (j equivalent to y). +# Number of image points along the fast dimension (j equivalent to y). # # # # -# Number of image points along the fastest dimension (i equivalent to x). +# Number of image points along the fastest dimension (i equivalent to x). # # # # -# Base class for reporting a set of images. -# -# The mostly commonly used scanning methods are supported. That is one-, -# two-, three-dimensional ROIs discretized using regular Euclidean tilings. -# -# Colloquially, an image is understood as a discretized representation of intensity distribution -# that was detected or simulated for some ROI. When discretized with regular Euclidean tilings -# the terms pixel and voxel identify the smallest discretization unit. Pixel and voxel are polygonal -# or polyhedral unit cells respectively of the underlying tiling of the ROI within the reference space. -# For all other tilings e.g. non-equispaced, the shape and size of pixel and voxel differs. Using the term -# (image) point is eventually is more appropriate for such tilings. Therefore, all docstrings in this base class -# refer to points (including pixel and voxel i.e. regular tilings). -# -# Point coordinates identify the location of the barycentre. -# -# For images in reciprocal space in practice, complex numbers are encoded via some -# formatted pair of real values. Typically, fast algorithms for computing Fourier transformations -# (FFT) are used to encode images in reciprocal (frequency) space. FFT libraries are used -# for implementing the key functionalities of these mathematical operations. -# -# Different libraries use different representations and encoding of the images. -# Details can be found in the respective sections of the typical FFT libraries documentations -# -# * `FFTW by M. Frigo and S. G. Johnson <https://www.fftw.org/fftw3_doc/Tutorial.html#Tutorial>`_ -# * `Intel MKL by the Intel Co. <https://www.intel.com/content/www/us/en/docs/onemkl/developer-reference-c/2024-2/fourier-transform-functions.html>`_ -# * `cuFFT by the NVidia Co. <https://docs.nvidia.com/cuda/cufft/index.html>`_ -# * `NFFT by the Chemnitz group <https://www-user.tu-chemnitz.de/~potts/nfft/>`_ for non-equispaced computations -# -# Users are strongly advised to inspect carefully which specific conventions their library uses -# to enable storing and modifying the implementation of their code such that the serialized -# representations as they are detailed here for NeXus match. -# -# It is often the case that several images are combined using processing. In this case, -# the number of images which are combined in a collection is not necessarily the same -# for each collection. The NXimage_set base class addresses this logical distinction -# through the notation of image_identifier and group_identifier concepts. -# That is image_identifier are always counting from offset in increments of one. -# as each image is its own entity. By contrast, a group may contain no, or several images. -# Consequently, group_identifier are not required to be contiguous. +# Base class for reporting a set of images. +# +# The most commonly used scanning methods are supported. That is one-, +# two-, three-dimensional ROIs discretized using regular Euclidean tilings. +# +# Colloquially, an image is understood as a discretized representation of intensity distribution +# detected or simulated for some ROI. When discretized with regular Euclidean tilings, the terms +# pixel and voxel identify the smallest discretization unit. In this case, pixel and voxel are polygonal +# or polyhedral unit cells respectively of the underlying tiling of the ROI within the reference space. +# For all other tilings e.g. non-equispaced, the shape and size of pixel and voxel differs. Using the term +# (image) point is eventually more appropriate when working with such tilings. +# +# Therefore, all docstrings in this base class refer to points (including pixel and voxel i.e. regular tilings). +# +# Point coordinates identify the location of the barycentre. +# +# For images in reciprocal space in practice, complex numbers are encoded via some formatted pair of real values. +# Typically, fast algorithms for computing Fourier transformations (FFT) are used to encode +# images in reciprocal (frequency) space. FFT libraries are used for implementing the key functionalities of +# these mathematical operations. +# +# Different libraries use different representations and encoding of the images. +# Details can be found in the respective sections of the typical FFT libraries documentations +# +# * `FFTW by M. Frigo and S. G. Johnson <https://www.fftw.org/fftw3_doc/Tutorial.html#Tutorial>`_ +# * `Intel MKL by the Intel Co. <https://www.intel.com/content/www/us/en/docs/onemkl/developer-reference-c/2024-2/fourier-transform-functions.html>`_ +# * `cuFFT by the NVidia Co. <https://docs.nvidia.com/cuda/cufft/index.html>`_ +# * `NFFT by the TU Chemnitz group <https://www-user.tu-chemnitz.de/~potts/nfft/>`_ for non-equispaced computations +# +# Users are strongly advised to inspect carefully which specific conventions their library uses +# to enable storing and modifying the implementation of their code such that the serialized +# representations as they are detailed here for NeXus match. +# +# It is often the case that several images are combined using processing. In this case, +# the number of images which are combined into collections is not necessarily the same +# for each collection. The NXimage base class addresses this logical distinction +# through the notation of identifier_image and identifier_group concepts. +# That is identifier_image are always counting from offset in increments of one. +# as each image is its own entity. By contrast, a group may contain no, or several images. +# Consequently, identifier_group are not required to be contiguous. # # # -# Details how NXdata instance were processed from detector readings/raw data. +# Details how NXdata instance were processed from detector readings/raw data. # # # -# Resolvable data artifact (e.g. file) from which all values in the :ref:`NXdata` -# instances in this :ref:`NXimage_set` were loaded during parsing. -# -# Possibility to document from which specific other serialized resource as the source -# pieces of information were processed when using NeXus as a semantic file format -# to serialize that information differently. -# -# The group in combination with an added field *absolute_path* therein adds context. +# Resolvable data artifact (e.g. file) from which all values in the :ref:`NXdata` +# instances in this :ref:`NXimage` were loaded during parsing. +# +# Possibility to document from which specific other serialized resource as the source +# pieces of information were processed when using NeXus as a semantic file format +# to serialize that information differently. +# +# The group in combination with an added field *absolute_path* therein adds context. # # # -# Reference to a location inside the artifact that points to the specific group of values -# that were processed if the artifacts contains several groups of values and thus -# further resolving of ambiguities is required. +# Reference to a location inside the artifact that points to the specific group of values +# that were processed if the artifacts contains several groups of values and thus +# further resolving of ambiguities is required. # # # -# -# +# # -# Link or name of an :ref:`NXdetector` instance with which the data were -# collected. +# Link or name of an :ref:`NXdetector` instance with which the data were +# collected. # # # # -# Program used for processing. +# Program used for processing. # # # -# # # -# One-dimensional image. +# One-dimensional image. # # # -# Intensity for real-valued images as an alternative for real. -# Magnitude of the image intensity for complex-valued data. +# Intensity for real-valued images as an alternative for real. +# Magnitude of the image intensity for complex-valued data. # # # @@ -646,7 +598,7 @@ NXimage_set(NXobject): # # # -# Real part of the image intensity per point. +# Real part of the image intensity per point. # # # @@ -654,7 +606,7 @@ NXimage_set(NXobject): # # # -# Imaginary part of the image intensity per point. +# Imaginary part of the image intensity per point. # # # @@ -662,8 +614,8 @@ NXimage_set(NXobject): # # # -# Image intensity as a complex number as an alternative to real and -# imaginary fields if values are stored as interleaved complex numbers. +# Image intensity as a complex number as an alternative to real and +# imag fields if values are stored as interleaved complex numbers. # # # @@ -671,26 +623,26 @@ NXimage_set(NXobject): # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Two-dimensional image. +# Two-dimensional image. # # # -# Intensity for real-valued images as an alternative for real. -# Magnitude of the image intensity for complex-valued data. +# Intensity for real-valued images as an alternative for real. +# Magnitude of the image intensity for complex-valued data. # # # @@ -699,7 +651,7 @@ NXimage_set(NXobject): # # # -# Real part of the image intensity per point. +# Real part of the image intensity per point. # # # @@ -708,7 +660,7 @@ NXimage_set(NXobject): # # # -# Imaginary part of the image intensity per point. +# Imaginary part of the image intensity per point. # # # @@ -717,8 +669,8 @@ NXimage_set(NXobject): # # # -# Image intensity as a complex number as an alternative to real and -# imaginary fields if values are stored as interleaved complex numbers. +# Image intensity as a complex number as an alternative to real and +# imag fields if values are stored as interleaved complex numbers. # # # @@ -727,39 +679,39 @@ NXimage_set(NXobject): # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Three-dimensional image. +# Three-dimensional image. # # # -# Intensity for real-valued images as an alternative for real. -# Magnitude of the image intensity for complex-valued data. +# Intensity for real-valued images as an alternative for real. +# Magnitude of the image intensity for complex-valued data. # # # @@ -769,7 +721,7 @@ NXimage_set(NXobject): # # # -# Real part of the image intensity per point. +# Real part of the image intensity per point. # # # @@ -779,7 +731,7 @@ NXimage_set(NXobject): # # # -# Imaginary part of the image intensity per point. +# Imaginary part of the image intensity per point. # # # @@ -789,8 +741,8 @@ NXimage_set(NXobject): # # # -# Image intensity as a complex number as an alternative to real and -# imaginary fields if values are stored as interleaved complex numbers. +# Image intensity as a complex number as an alternative to real and +# imag fields if values are stored as interleaved complex numbers. # # # @@ -800,52 +752,52 @@ NXimage_set(NXobject): # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension. # # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension. # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Collection of image_1d. +# Collection of one-dimesional images. # # # -# Intensity for real-valued images as an alternative for real. -# Magnitude of the image intensity for complex-valued data. +# Intensity for real-valued images as an alternative for real. +# Magnitude of the image intensity for complex-valued data. # # # @@ -854,7 +806,7 @@ NXimage_set(NXobject): # # # -# Real part of the image intensity per point. +# Real part of the image intensity per point. # # # @@ -863,7 +815,7 @@ NXimage_set(NXobject): # # # -# Imaginary part of the image intensity per point. +# Imaginary part of the image intensity per point. # # # @@ -872,62 +824,62 @@ NXimage_set(NXobject): # # # -# Image intensity as a complex number as an alternative to real and -# imaginary fields if values are stored as interleaved complex numbers. +# Image intensity as a complex number as an alternative to real and +# imag fields if values are stored as interleaved complex numbers. # # # # # # -# +# # -# Group identifier +# Group identifier # # # # # # -# Group identifier +# Group identifier # # # -# +# # -# Image identifier +# Image identifier # # # # # # -# Image identifier +# Image identifier # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Collection of two-dimensional images. +# Collection of two-dimensional images. # # # -# Intensity for real-valued images as an alternative for real. -# Magnitude of the image intensity for complex-valued data. +# Intensity for real-valued images as an alternative for real. +# Magnitude of the image intensity for complex-valued data. # # # @@ -937,7 +889,7 @@ NXimage_set(NXobject): # # # -# Real part of the image intensity per point. +# Real part of the image intensity per point. # # # @@ -947,7 +899,7 @@ NXimage_set(NXobject): # # # -# Imaginary part of the image intensity per point. +# Imaginary part of the image intensity per point. # # # @@ -957,8 +909,8 @@ NXimage_set(NXobject): # # # -# Image intensity as a complex number as an alternative to real and -# imaginary fields if values are stored as interleaved complex numbers. +# Image intensity as a complex number as an alternative to real and +# imag fields if values are stored as interleaved complex numbers. # # # @@ -966,67 +918,67 @@ NXimage_set(NXobject): # # # -# +# # -# Group identifier +# Group identifier # # # # # # -# Group identifier +# Group identifier # # # -# +# # -# Image identifier +# Image identifier # # # # # # -# Image identifier. +# Image identifier. # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Collection of three-dimensional images. +# Collection of three-dimensional images. # # # -# Intensity for real-valued images as an alternative for real. -# Magnitude of the image intensity for complex-valued data. +# Intensity for real-valued images as an alternative for real. +# Magnitude of the image intensity for complex-valued data. # # # @@ -1037,7 +989,7 @@ NXimage_set(NXobject): # # # -# Real part of the image intensity per point. +# Real part of the image intensity per point. # # # @@ -1048,7 +1000,7 @@ NXimage_set(NXobject): # # # -# Imaginary part of the image intensity per point. +# Imaginary part of the image intensity per point. # # # @@ -1059,8 +1011,8 @@ NXimage_set(NXobject): # # # -# Image intensity as a complex number as an alternative to real and -# imaginary fields if values are stored as interleaved complex numbers. +# Image intensity as a complex number as an alternative to real and +# imag fields if values are stored as interleaved complex numbers. # # # @@ -1069,68 +1021,68 @@ NXimage_set(NXobject): # # # -# +# # -# Group identifier +# Group identifier # # # # # # -# Group identifier +# Group identifier # # # -# +# # -# Image identifier +# Image identifier # # # # # # -# Image identifier +# Image identifier # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension. # # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension. # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension. # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # # # # -# Point coordinate along the fastest dimension. +# Point coordinate along the fastest dimension. # # # diff --git a/base_classes/nyaml/NXinstrument_apm.yaml b/base_classes/nyaml/NXinstrument_apm.yaml new file mode 100644 index 0000000000..40f849b14e --- /dev/null +++ b/base_classes/nyaml/NXinstrument_apm.yaml @@ -0,0 +1,677 @@ +category: base +doc: | + Base class to document an instrument used for atom probe microscopy. + + Inheriting from NXinstrument, this base class is designed to offer the same concepts about + instrument-centric metadata to be used in two places inside NXapm without demanding that + the application definition needs to define the concepts in two places as maintaining this is + prone to errors. This base class implements the key design idea behind the NXapm application + definition in that we would like to offer a design where all (meta)data which over the course + of a measurement remain static can be stored only once and without polluting the application + definition with another group with concepts that should be used for storing (meta)data about + the instrument during events that happen during the course of the measurement. + + This design was inspired by NXem and electron microscopy where typically the instrument is + used in sessions and dozens of logical sets of data are collected under not necessarily always + the same instrument conditions. We do not want to repeat therefore the static (meta)data, as + this is redundant storage by virtue of design. The typical example is an electron microscope + where hundreds of images are taken and all static instrument data stored with each image. + This makes sense in cases when the image is used as a digital artifact that is exchanged across + different software applications or research data management systems but as in NeXus there + is either all information bundled into one artifact or there is a coordinating master artifact + that references related artifacts there is no point to store hundreds of times that always the + same microscope with the same lens setup was used to collect these images. + +# One could use an NXnote or reference to another NeXus file where these static (meta)data +# are stored but then referencing this in an application definition would demand to make such +# file required, while NXinstrument_apm can be used directly for the static and the dynamic +# or volatile (meta)data. +type: group +NXinstrument_apm(NXinstrument): + type(NX_CHAR): + doc: | + Which type of instrument. + enumeration: + open_enum: true + items: [Inspico, 3DAP, LAWATAP, LEAP 3000 Si, LEAP 3000X Si, LEAP 3000 HR, LEAP 3000X HR, LEAP 4000 Si, LEAP 4000X Si, LEAP 4000 HR, LEAP 4000X HR, LEAP 5000 XS, LEAP 5000 XR, LEAP 5000 R, EIKOS, EIKOS-UV, LEAP 6000 XR, LEAP INVIZO, Photonic AP, TeraSAT, TAPHR, Modular AP, Titanium APT, Extreme UV APT] + fabrication(NXfabrication): + + # (NXcsg): + # doc: | + # Possibility to include a detailed computational geometry description of the instrument. + location(NX_CHAR): + doc: | + Location of the lab or place where the instrument is installed. Using GEOREF is + preferred. + reflectron(NXcomponent): + doc: | + Device which reduces ToF differences of ions in ToF experiments. + + For atom probe the reflectron can be considered an energy compensation device. + Such a device can be realized technically for example with a Poschenrieder lens. + + Consult the following U.S. patents for further details: + + * 3863068 and 6740872 for the reflectron + * 8134119 for the curved reflectron + applied(NX_BOOLEAN): + doc: | + Was the reflectron used? + voltage(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + The maximum voltage applied to the reflectron, relative to system ground. + decelerate_electrode(NXlens_em): + doc: | + A counter electrode of the LEAP 6000 series atom probes. + + # counter_electrodes being optional WO2016171675A1 + # see https://en.wikipedia.org/wiki/Einzel_lens for details double einzel lens in the invizo 6000 + # according to A. Breen (UNSW) + local_electrode(NXlens_em): + doc: | + A local electrode guiding the ion flight path. + Also called counter or extraction electrode. + voltage(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + Acceleration voltage + + # but the local_electrode does not really on purpose create a magnetic field, + # specific for an electro-magnetic lens is the symmetry of its field + # NEW ISSUE: for now keep that we have what is an NXlens_em + # NEW ISSUE: APEX MONITOR / LEAP distance monitoring + # NEW ISSUE: the definition of flat test data should be included and documented + # NEW ISSUE: local electrode, baking strategies, storage + ion_detector(NXdetector): + doc: | + Detector for taking raw time-of-flight and ion/hit impact positions data. + signal_amplitude(NX_FLOAT): + unit: NX_CURRENT + doc: | + Amplitude of the signal detected on the multi-channel plate (MCP). + + This field should be used for storing the signal amplitude quantity + within ATO files. The ATO file format is used primarily by the + atom probe groups of the GPM in Rouen, France. + dimensions: + rank: 1 + dim: (p,) + mcp_efficiency(NX_FLOAT): + unit: NX_DIMENSIONLESS + doc: | + CRunHeader.fMcpEfficiency + mesh_efficiency(NX_FLOAT): + unit: NX_DIMENSIONLESS + doc: | + CRunHeader.fMeshEfficiency + + # model, serial_number, manufacturer_name all inherited from NXdetector base class + pulser(NXcomponent): + doc: | + Laser- and/or voltage-pulsing device to trigger ion removal. + + # technical design + fabrication(NXfabrication): + pulse_mode(NX_CHAR): + doc: | + Detail whereby ion extraction is triggered methodologically. + enumeration: + open_enum: true + items: [laser, voltage, laser_and_voltage] + + # the example of how the IFES APT TC's HDF format deals with such data + # conceptually, concepts are mixed into superconcepts interleaved tuple with + # different units: "PulseFrequency : Real array, 2xn (Hz) This is the frequency of + # the high voltage or laser pulser. first entry : first pulse number where the + # spacing between this and all subsequent pulses are considered to be at the + # selected frequency. Each first entry must be strictly increasing in value. The + # second entry contains the frequency value" as data can be compressed in this + # case very efficiently we go for with an array of length 1xn_ions + pulse_frequency(NX_FLOAT): + unit: NX_FREQUENCY + doc: | + Frequency with which the pulser fire(s). + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pulse_fraction(NX_FLOAT): + unit: NX_DIMENSIONLESS + doc: | + Fraction of the pulse_voltage that is applied in addition + to the standing_voltage at peak voltage of a pulse. + + If a standing voltage is applied, this gives nominal pulse fraction + (as a function of standing voltage). Otherwise, this field should + not be present. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + + # example of a conditional requirement that can be dealt with igorously by OWL but not by NeXus! + # as either pulse_voltage is required in an appdef but then that + # existence constraint is independent of other values. + pulse_voltage(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + Pulsed voltage, in laser pulsing mode this field can be omitted. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pulse_number(NX_UINT): + unit: NX_UNITLESS + doc: | + Absolute number of pulses starting from the beginning of the experiment. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + + # eventually equivalent to pulse_identifier within NXevent_data_apm + standing_voltage(NX_FLOAT): + unit: NX_VOLTAGE + doc: | + Direct current voltage between the specimen and the (local electrode) in + the case of local electrode atom probe (LEAP) instrument. Otherwise, the + standing voltage applied to the sample, relative to system ground. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + sourceID(NXsource): + nameType: partial + doc: | + Atom probe microscopes use controlled laser, voltage, or a combination of + pulsing strategies to trigger ion extraction via exciting and eventual field evaporation + field emission of ion at the specimen surface. + wavelength(NX_FLOAT): + unit: NX_WAVELENGTH + doc: | + The wavelength of the radiation emitted by the source. + power(NX_FLOAT): + unit: NX_POWER + doc: | + Nominal power of the laser source while illuminating the specimen. + pulse_energy(NX_FLOAT): + unit: NX_ENERGY + doc: | + Average energy of the laser at peak of each pulse. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + (NXbeam): + doc: | + Details about specific positions along the laser beam + which illuminates the (atom probe) specimen. + incidence_vector(NX_NUMBER): + unit: NX_LENGTH + doc: | + Track time-dependent settings over the course of the measurement + how the laser beam shines on the specimen, i.e. the mean vector + is parallel to the laser propagation direction. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + pinhole_position(NX_NUMBER): + unit: NX_LENGTH + doc: | + Track time-dependent settings over the course of the measurement + where the laser beam exits the focusing optics. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier + spot_position(NX_NUMBER): + unit: NX_LENGTH + doc: | + Track time-dependent settings over the course of the + measurement where the laser hits the specimen. + \@logged_against(NX_CHAR): + doc: | + Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. + (NXtransformations): + doc: | + Affine transformations which describe the geometry how the + laser focusing optics/pinhole-attached coordinate system is + defined, how it has to be transformed so that it aligns with + the specimen coordinate system. + stage(NXmanipulator): + temperature_sensor(NXsensor): + value(NX_FLOAT): + doc: | + CRunHeader.CAnalysis.fSpecimenTemperature + + # NEW ISSUE: add NXapm_energy_analyzer, a voltage grid like done in Rouen/GPM + analysis_chamber(NXcomponent): + flight_path(NX_FLOAT): + unit: NX_LENGTH + doc: | + The space inside the atom probe along which ions pass nominally + when they leave the specimen and travel to the detector. + pressure_sensor(NXsensor): + measurement(NX_CHAR): + enumeration: [pressure] + value(NX_FLOAT): + unit: NX_PRESSURE + doc: | + CRunHeader.CLasHeader.fAnalysisPressure + buffer_chamber(NXcomponent): + load_lock_chamber(NXcomponent): + getter_pump(NXpump): + roughening_pump(NXpump): + turbomolecular_pump(NXpump): + comment(NX_CHAR): + doc: | + Free-text field for additional comments. + control(NXcollection): + doc: | + Relevant quantities during a measurement with a LEAP system as were + suggested by `T. Blum et al. `_. + evaporation_control(NX_CHAR): + doc: | + Parameter set typically in the GUI of the control software which + defines the rules and control loops whereby the pulser and other + components of the instrument are controlled during evaporation. + target_detection_rate(NX_NUMBER): + unit: NX_ANY + doc: | + Control parameter set typically in the GUI relevant to assure that + the instrument internally controls its settings such to assure a + significant yet not too high ion influx on the detector to avoid + detection losses. + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 883b8eb292f99e33fa9bf160c4329a3f081642a7d5f075a52818f5eecbc6529e +# +# +# +# +# +# +# Base class to document an instrument used for atom probe microscopy. +# +# Inheriting from NXinstrument, this base class is designed to offer the same concepts about +# instrument-centric metadata to be used in two places inside NXapm without demanding that +# the application definition needs to define the concepts in two places as maintaining this is +# prone to errors. This base class implements the key design idea behind the NXapm application +# definition in that we would like to offer a design where all (meta)data which over the course +# of a measurement remain static can be stored only once and without polluting the application +# definition with another group with concepts that should be used for storing (meta)data about +# the instrument during events that happen during the course of the measurement. +# +# This design was inspired by NXem and electron microscopy where typically the instrument is +# used in sessions and dozens of logical sets of data are collected under not necessarily always +# the same instrument conditions. We do not want to repeat therefore the static (meta)data, as +# this is redundant storage by virtue of design. The typical example is an electron microscope +# where hundreds of images are taken and all static instrument data stored with each image. +# This makes sense in cases when the image is used as a digital artifact that is exchanged across +# different software applications or research data management systems but as in NeXus there +# is either all information bundled into one artifact or there is a coordinating master artifact +# that references related artifacts there is no point to store hundreds of times that always the +# same microscope with the same lens setup was used to collect these images. +# +# +# +# Which type of instrument. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Location of the lab or place where the instrument is installed. Using GEOREF is +# preferred. +# +# +# +# +# Device which reduces ToF differences of ions in ToF experiments. +# +# For atom probe the reflectron can be considered an energy compensation device. +# Such a device can be realized technically for example with a Poschenrieder lens. +# +# Consult the following U.S. patents for further details: +# +# * 3863068 and 6740872 for the reflectron +# * 8134119 for the curved reflectron +# +# +# +# Was the reflectron used? +# +# +# +# +# The maximum voltage applied to the reflectron, relative to system ground. +# +# +# +# +# +# A counter electrode of the LEAP 6000 series atom probes. +# +# +# +# +# +# A local electrode guiding the ion flight path. +# Also called counter or extraction electrode. +# +# +# +# Acceleration voltage +# +# +# +# +# +# +# Detector for taking raw time-of-flight and ion/hit impact positions data. +# +# +# +# Amplitude of the signal detected on the multi-channel plate (MCP). +# +# This field should be used for storing the signal amplitude quantity +# within ATO files. The ATO file format is used primarily by the +# atom probe groups of the GPM in Rouen, France. +# +# +# +# +# +# +# +# CRunHeader.fMcpEfficiency +# +# +# +# +# CRunHeader.fMeshEfficiency +# +# +# +# +# +# +# Laser- and/or voltage-pulsing device to trigger ion removal. +# +# +# +# +# +# Detail whereby ion extraction is triggered methodologically. +# +# +# +# +# +# +# +# +# +# +# Frequency with which the pulser fire(s). +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# Fraction of the pulse_voltage that is applied in addition +# to the standing_voltage at peak voltage of a pulse. +# +# If a standing voltage is applied, this gives nominal pulse fraction +# (as a function of standing voltage). Otherwise, this field should +# not be present. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# +# Pulsed voltage, in laser pulsing mode this field can be omitted. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# Absolute number of pulses starting from the beginning of the experiment. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# +# Direct current voltage between the specimen and the (local electrode) in +# the case of local electrode atom probe (LEAP) instrument. Otherwise, the +# standing voltage applied to the sample, relative to system ground. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# Atom probe microscopes use controlled laser, voltage, or a combination of +# pulsing strategies to trigger ion extraction via exciting and eventual field evaporation +# field emission of ion at the specimen surface. +# +# +# +# The wavelength of the radiation emitted by the source. +# +# +# +# +# Nominal power of the laser source while illuminating the specimen. +# +# +# +# +# Average energy of the laser at peak of each pulse. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# Details about specific positions along the laser beam +# which illuminates the (atom probe) specimen. +# +# +# +# Track time-dependent settings over the course of the measurement +# how the laser beam shines on the specimen, i.e. the mean vector +# is parallel to the laser propagation direction. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# Track time-dependent settings over the course of the measurement +# where the laser beam exits the focusing optics. +# +# +# +# Path to pulse_identifier +# +# +# +# +# +# Track time-dependent settings over the course of the +# measurement where the laser hits the specimen. +# +# +# +# Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. +# +# +# +# +# +# +# Affine transformations which describe the geometry how the +# laser focusing optics/pinhole-attached coordinate system is +# defined, how it has to be transformed so that it aligns with +# the specimen coordinate system. +# +# +# +# +# +# +# +# +# CRunHeader.CAnalysis.fSpecimenTemperature +# +# +# +# +# +# +# +# +# The space inside the atom probe along which ions pass nominally +# when they leave the specimen and travel to the detector. +# +# +# +# +# +# +# +# +# +# +# CRunHeader.CLasHeader.fAnalysisPressure +# +# +# +# +# +# +# +# +# +# +# +# Free-text field for additional comments. +# +# +# +# +# Relevant quantities during a measurement with a LEAP system as were +# suggested by `T. Blum et al. <https://doi.org/10.1002/9781119227250.ch18>`_. +# +# +# +# Parameter set typically in the GUI of the control software which +# defines the rules and control loops whereby the pulser and other +# components of the instrument are controlled during evaporation. +# +# +# +# +# Control parameter set typically in the GUI relevant to assure that +# the instrument internally controls its settings such to assure a +# significant yet not too high ion influx on the detector to avoid +# detection losses. +# +# +# +# diff --git a/base_classes/nyaml/NXinstrument_em.yaml b/base_classes/nyaml/NXinstrument_em.yaml new file mode 100644 index 0000000000..63659d5bcc --- /dev/null +++ b/base_classes/nyaml/NXinstrument_em.yaml @@ -0,0 +1,366 @@ +category: base +doc: | + Base class for instrument-related details of a real or simulated electron microscope. + + For collecting data and experiments which are simulations of an electron + microscope (or such session) use the :ref:`NXem` application definition and + the :ref:`NXevent_data_em` groups it provides. + + This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished + whether these typically change during a session (dynamic) or not (static metadata). + This design allows to store e.g. hardware related concepts only once instead of demanding + that each image or spectrum from the session needs to be stored also with the static metadata. +type: group +NXinstrument_em(NXinstrument): + name(NX_CHAR): + doc: | + Given name of the microscope at the hosting institution. + This is an alias. Examples could be NionHermes, Titan, JEOL, + Gemini, etc. + location(NX_CHAR): + doc: | + Location of the lab or place where the instrument is installed. + Using GEOREF is preferred. + (NXfabrication): + (NXebeam_column): + (NXibeam_column): + + # (NXpbeam_column) for adding laser pulsing capabilities (NXsource + x) + (NXoptical_system_em): + (NXdetector): + doc: | + Description of the type of the detector. + + Electron microscopes have typically multiple detectors. + Different technologies are in use like CCD, scintillator, + direct electron, CMOS, or image plate to name but a few. + (NXscanbox_em): + stage(NXmanipulator): + doc: | + Stages in an electron microscope are multi-functional devices. + + Stages enable experimentalists the application of controlled external stimuli + on the specimen. Modern stages realize a hierarchy of components. + A multi-axial tilt rotation holder is a good example where the control of + each degree of freedom is technically implemented via providing instances + of either :ref:`NXpositioner`, :ref:`NXactuator`, or specialized :ref:`NXobject` + that achieve the rotating and positioning of the specimen. + + The physical process of mounting a specimen on a stage in practice often + comes with an own hierarchy of fixtures to bridge e.g. length scales technically. + An example from atom probe microscopy is that researchers may work + with wire samples which are clipped into a larger fixing unit to enable + careful specimen handling. Alternatively, a microtip is a silicon post + upon which e.g. an atom probe specimen is mounted. Multiple of such microtips + are then grouped into a microtip array to conveniently enable loading of multiple + specimens into the instrument with fewer operations. There are further scenarios + typically encountered related to mounting and locating specimens inside an + electron microscope, a few examples follow: + + * A nanoparticle on a copper grid. The copper grid is the holder. + This grid itself is fixed to a stage. + * An atom probe specimen fixed in a stub. In this case the stub can be + considered the holder, while the cryostat temperature control unit is + a component of the stage. + * For in-situ experiments with e.g. chips with read-out electronics + as actuators, the chips are again placed in a larger unit. A typical + example are in-situ experiments using e.g. the tools of `Protochips `_. + * Other examples are (quasi) in-situ experiments where experimentalists + anneal or deform the specimen via e.g. in-situ tensile testing machines + which are mounted on the specimen holder. + + For specific details and inspiration about stages in electron microscopes: + + * `Holders with multiple axes `_ + * `Chip-based designs `_ + * `Further chip-based designs `_ + * `Stages in transmission electron microscopy `_ (page 103, table 4.2) + * `Further stages in transmission electron microscopy `_ (page 124ff) + * `Specimens in atom probe `_ (page 47ff) + * `Exemplar micro-manipulators `_ + + # see for complicated positioning tools like an eucentric five-axis table stage in an SEM + # https://www.nanotechnik.com/e5as.html + (NXfabrication): + design(NX_CHAR): + doc: | + Principal design of the stage. + + Exemplar terms could be side_entry, top_entry, + single_tilt, quick_change, multiple_specimen, + bulk_specimen, double_tilt, tilt_rotate, + heating_chip, atmosphere_chip, + electrical_biasing_chip, liquid_cell_chip + alias(NX_CHAR): + doc: | + Free-text field to give a term how that a stage_lab at this level of the + stage_lab hierarchy is commonly referred to. Examples could be stub, + puck, carousel, microtip, clip, holder, etc. + + # the pragmatic view for the majority of published datasets and EM images + # only tilt and position values are reported but the coordinate systems and conventions + # used in which these were defined are often not reported in the associated scientific publications + # this can be interpreted as that position values and tilts are only meaningful for those users + # in a particular narrow community which work with that particular microscope + tilt1(NX_NUMBER): + unit: NX_ANGLE + doc: | + The interpretation of this tilt1 value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + tilt is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + \@comment(NX_CHAR): + doc: | + Discouraged free-text field to provide details about how to interpret tilt1. + tilt2(NX_NUMBER): + unit: NX_ANGLE + doc: | + The interpretation of this tilt2 value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + tilt is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + \@comment(NX_CHAR): + doc: | + Discouraged free-text field to provide details about how to interpret tilt2. + rotation(NX_NUMBER): + unit: NX_ANGLE + doc: | + The interpretation of this rotation value can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + rotation is defined explicitly using instances of :ref:`NXtransformations` and + respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + \@comment(NX_CHAR): + doc: | + Discouraged free-text field to provide details about how to interpret rotation. + position(NX_NUMBER): + unit: NX_LENGTH + doc: | + The interpretation of these position values can be contextualized via the comment + attribute. However, it is better to describe the reference frame in which the + position values are defined explicitly using instances of :ref:`NXtransformations` + and respective instances of :ref:`NXcoordinate_system`. Especially when this + NXinstrument_em base class is used in an application definition like NXem. + dimensions: + rank: 1 + dim: (3,) + nanoprobe(NXmanipulator): + doc: | + In contrast to the stage, the nanoprobe is an additional manipulator that is specifically + frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and + relocated portions of the specimen that have been cut free to realize specialized + geometries locally and enable site-specific measurements. + + # https://nano.oxinst.com/nanomanipulators. + (NXfabrication): + (NXpump): + (NXsensor): + (NXactuator): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# f32aa554bd148df75c20d3e5e7793b2c28059b3dd50bf9d541a996e874e6f17a +# +# +# +# +# +# Base class for instrument-related details of a real or simulated electron microscope. +# +# For collecting data and experiments which are simulations of an electron +# microscope (or such session) use the :ref:`NXem` application definition and +# the :ref:`NXevent_data_em` groups it provides. +# +# This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished +# whether these typically change during a session (dynamic) or not (static metadata). +# This design allows to store e.g. hardware related concepts only once instead of demanding +# that each image or spectrum from the session needs to be stored also with the static metadata. +# +# +# +# Given name of the microscope at the hosting institution. +# This is an alias. Examples could be NionHermes, Titan, JEOL, +# Gemini, etc. +# +# +# +# +# Location of the lab or place where the instrument is installed. +# Using GEOREF is preferred. +# +# +# +# +# +# +# +# +# +# Description of the type of the detector. +# +# Electron microscopes have typically multiple detectors. +# Different technologies are in use like CCD, scintillator, +# direct electron, CMOS, or image plate to name but a few. +# +# +# +# +# +# Stages in an electron microscope are multi-functional devices. +# +# Stages enable experimentalists the application of controlled external stimuli +# on the specimen. Modern stages realize a hierarchy of components. +# A multi-axial tilt rotation holder is a good example where the control of +# each degree of freedom is technically implemented via providing instances +# of either :ref:`NXpositioner`, :ref:`NXactuator`, or specialized :ref:`NXobject` +# that achieve the rotating and positioning of the specimen. +# +# The physical process of mounting a specimen on a stage in practice often +# comes with an own hierarchy of fixtures to bridge e.g. length scales technically. +# An example from atom probe microscopy is that researchers may work +# with wire samples which are clipped into a larger fixing unit to enable +# careful specimen handling. Alternatively, a microtip is a silicon post +# upon which e.g. an atom probe specimen is mounted. Multiple of such microtips +# are then grouped into a microtip array to conveniently enable loading of multiple +# specimens into the instrument with fewer operations. There are further scenarios +# typically encountered related to mounting and locating specimens inside an +# electron microscope, a few examples follow: +# +# * A nanoparticle on a copper grid. The copper grid is the holder. +# This grid itself is fixed to a stage. +# * An atom probe specimen fixed in a stub. In this case the stub can be +# considered the holder, while the cryostat temperature control unit is +# a component of the stage. +# * For in-situ experiments with e.g. chips with read-out electronics +# as actuators, the chips are again placed in a larger unit. A typical +# example are in-situ experiments using e.g. the tools of `Protochips <https://www.protochips.com>`_. +# * Other examples are (quasi) in-situ experiments where experimentalists +# anneal or deform the specimen via e.g. in-situ tensile testing machines +# which are mounted on the specimen holder. +# +# For specific details and inspiration about stages in electron microscopes: +# +# * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ +# * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ +# * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ +# * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) +# * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) +# * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) +# * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ +# +# +# +# +# +# Principal design of the stage. +# +# Exemplar terms could be side_entry, top_entry, +# single_tilt, quick_change, multiple_specimen, +# bulk_specimen, double_tilt, tilt_rotate, +# heating_chip, atmosphere_chip, +# electrical_biasing_chip, liquid_cell_chip +# +# +# +# +# Free-text field to give a term how that a stage_lab at this level of the +# stage_lab hierarchy is commonly referred to. Examples could be stub, +# puck, carousel, microtip, clip, holder, etc. +# +# +# +# +# +# The interpretation of this tilt1 value can be contextualized via the comment +# attribute. However, it is better to describe the reference frame in which the +# tilt is defined explicitly using instances of :ref:`NXtransformations` and +# respective instances of :ref:`NXcoordinate_system`. Especially when this +# NXinstrument_em base class is used in an application definition like NXem. +# +# +# +# Discouraged free-text field to provide details about how to interpret tilt1. +# +# +# +# +# +# The interpretation of this tilt2 value can be contextualized via the comment +# attribute. However, it is better to describe the reference frame in which the +# tilt is defined explicitly using instances of :ref:`NXtransformations` and +# respective instances of :ref:`NXcoordinate_system`. Especially when this +# NXinstrument_em base class is used in an application definition like NXem. +# +# +# +# Discouraged free-text field to provide details about how to interpret tilt2. +# +# +# +# +# +# The interpretation of this rotation value can be contextualized via the comment +# attribute. However, it is better to describe the reference frame in which the +# rotation is defined explicitly using instances of :ref:`NXtransformations` and +# respective instances of :ref:`NXcoordinate_system`. Especially when this +# NXinstrument_em base class is used in an application definition like NXem. +# +# +# +# Discouraged free-text field to provide details about how to interpret rotation. +# +# +# +# +# +# The interpretation of these position values can be contextualized via the comment +# attribute. However, it is better to describe the reference frame in which the +# position values are defined explicitly using instances of :ref:`NXtransformations` +# and respective instances of :ref:`NXcoordinate_system`. Especially when this +# NXinstrument_em base class is used in an application definition like NXem. +# +# +# +# +# +# +# +# +# In contrast to the stage, the nanoprobe is an additional manipulator that is specifically +# frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and +# relocated portions of the specimen that have been cut free to realize specialized +# geometries locally and enable site-specific measurements. +# +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXion.yaml b/base_classes/nyaml/NXion.yaml similarity index 99% rename from contributed_definitions/nyaml/NXion.yaml rename to base_classes/nyaml/NXion.yaml index 7f621685b3..3ee92fcd57 100644 --- a/contributed_definitions/nyaml/NXion.yaml +++ b/base_classes/nyaml/NXion.yaml @@ -116,9 +116,9 @@ NXion(NXobject): # # # # -# Base class to describe the use of manipulators and sample stages. +# Extension of NXpositioner to include fields to describe the use of manipulators +# in photoemission experiments. # # # -# Name of the manipulator. +# Name of the manipulator. # # # # -# A description of the manipulator. +# A description of the manipulator. # # # # -# Type of manipulator, Hexapod, Rod, etc. +# Type of manipulator, Hexapod, Rod, etc. # # # # -# Cryostat for cooling the sample. +# Cryostat for cooling the sample. # -# +# # # # @@ -190,15 +191,15 @@ NXmanipulator(NXcomponent): # # # -# In case of a fixed or averaged cooling temperature, this is the scalar temperature setpoint. -# It can also be a 1D array of temperature setpoints (without time stamps). +# In case of a fixed or averaged cooling temperature, this is the scalar temperature setpoint. +# It can also be a 1D array of temperature setpoints (without time stamps). # # # # # -# In the case of an experiment in which the temperature is changed and the setpoints are -# recorded with time stamps, this is an array of length m of temperature setpoints. +# In the case of an experiment in which the temperature is changed and the setpoints are +# recorded with time stamps, this is an array of length m of temperature setpoints. # # # @@ -206,7 +207,7 @@ NXmanipulator(NXcomponent): # # # -# Temperature sensor measuring the sample temperature. +# Temperature sensor measuring the sample temperature. # # # @@ -215,55 +216,55 @@ NXmanipulator(NXcomponent): # # # -# In case of a single or averaged temperature measurement, this is the scalar temperature measured -# by the sample temperature sensor. It can also be a 1D array of measured temperatures -# (without time stamps). +# In case of a single or averaged temperature measurement, this is the scalar temperature measured +# by the sample temperature sensor. It can also be a 1D array of measured temperatures +# (without time stamps). # # # # # -# In the case of an experiment in which the temperature changes and is recorded with time stamps, -# this is an array of length m of temperatures. +# In the case of an experiment in which the temperature changes and is recorded with time stamps, +# this is an array of length m of temperatures. # # # # # # -# Device to heat the sample. +# Device to heat the sample. # -# +# # # # # -# +# # -# In case of a fixed or averaged heating power, this is the scalar heater power. -# It can also be a 1D array of heater powers (without time stamps). +# In case of a fixed or averaged heating power, this is the scalar heater power. +# It can also be a 1D array of heater powers (without time stamps). # # -# +# # # -# In the case of an experiment in which the heater power is changed and recorded with time stamps, -# this is an array of length m of temperature setpoints. +# In the case of an experiment in which the heater power is changed and recorded with time stamps, +# this is an array of length m of temperature setpoints. # # # # # # -# In case of a fixed or averaged temperature, this is the scalar temperature setpoint. -# It can also be a 1D array of temperature setpoints (without time stamps). +# In case of a fixed or averaged temperature, this is the scalar temperature setpoint. +# It can also be a 1D array of temperature setpoints (without time stamps). # # # # # -# In the case of an experiment in which the temperature is changed and the setpoints are -# recorded with time stamps, this is an array of length m of temperature setpoints. +# In the case of an experiment in which the temperature is changed and the setpoints are +# recorded with time stamps, this is an array of length m of temperature setpoints. # # # @@ -271,7 +272,7 @@ NXmanipulator(NXcomponent): # # # -# Amperemeter measuring the drain current of the sample and sample holder. +# Amperemeter measuring the drain current of the sample and sample holder. # # # @@ -280,24 +281,24 @@ NXmanipulator(NXcomponent): # # # -# In case of a single or averaged drain current measurement, this is the scalar drain current measured between -# the sample and sample holder. It can also be an 1D array of measured currents (without time stamps). +# In case of a single or averaged drain current measurement, this is the scalar drain current measured between +# the sample and sample holder. It can also be an 1D array of measured currents (without time stamps). # # # # # -# In the case of an experiment in which the current changes and is recorded with -# time stamps, this is an array of length m of currents. +# In the case of an experiment in which the current changes and is recorded with +# time stamps, this is an array of length m of currents. # # # # # # -# Actuator applying a voltage to sample and sample holder. +# Actuator applying a voltage to sample and sample holder. # -# +# # # # @@ -305,15 +306,15 @@ NXmanipulator(NXcomponent): # # # -# In case of a fixed or averaged applied bias, this is the scalar voltage applied between -# sample and sample holder. It can also be an 1D array of voltage setpoints (without time stamps). +# In case of a fixed or averaged applied bias, this is the scalar voltage applied between +# sample and sample holder. It can also be an 1D array of voltage setpoints (without time stamps). # # # # # -# In the case of an experiment in which the bias is changed and the setpoints are -# recorded with time stamps, this is an array of length m of voltage setpoints. +# In the case of an experiment in which the bias is changed and the setpoints are +# recorded with time stamps, this is an array of length m of voltage setpoints. # # # @@ -321,7 +322,7 @@ NXmanipulator(NXcomponent): # # # -# Sensor measuring the voltage applied to sample and sample holder. +# Sensor measuring the voltage applied to sample and sample holder. # # # @@ -330,33 +331,32 @@ NXmanipulator(NXcomponent): # # # -# In case of a single or averaged bias measurement, this is the scalar voltage measured between -# sample and sample holder. It can also be an 1D array of measured voltages (without time stamps). +# In case of a single or averaged bias measurement, this is the scalar voltage measured between +# sample and sample holder. It can also be an 1D array of measured voltages (without time stamps). # # # # # -# In the case of an experiment in which the bias changes and is recorded with -# time stamps, this is an array of length m of voltages. +# In the case of an experiment in which the bias changes and is recorded with +# time stamps, this is an array of length m of voltages. # # # # # # -# Any additional actuator on the manipulator used to control an external -# condition. +# Any additional actuators on the manipulator. # # # # -# Any additional sensors on the manipulator used to monitor an external condition. +# Any additional sensors on the manipulator. # # # # -# Class to describe the motors that are used in the manipulator. +# Class to describe the motors that are used in the manipulator # # # diff --git a/base_classes/nyaml/NXoptical_system_em.yaml b/base_classes/nyaml/NXoptical_system_em.yaml new file mode 100644 index 0000000000..262b161899 --- /dev/null +++ b/base_classes/nyaml/NXoptical_system_em.yaml @@ -0,0 +1,295 @@ +category: base +doc: | + Base class for qualifying an electron optical system. +type: group +NXoptical_system_em(NXobject): + camera_length(NX_NUMBER): + unit: NX_LENGTH + doc: + - | + Distance which is present between the specimen surface and the detector plane. + - | + xref: + spec: EMglossary + term: Camera Length + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 + magnification(NX_NUMBER): + unit: NX_DIMENSIONLESS + doc: | + The factor of enlargement of the apparent size, + not the physical size, of an object. + defocus(NX_NUMBER): + unit: NX_LENGTH + doc: | + The defocus aberration constant (oftentimes referred to as c_1_0). + See respective details in :ref:`NXaberration` class instances. + semi_convergence_angle(NX_NUMBER): + unit: NX_ANGLE + doc: + - | + The angle which is given by the semi-opening angle of the cone in a convergent + beam. + - | + xref: + spec: EMglossary + term: Convergence Angle + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 + field_of_view(NX_NUMBER): + unit: NX_LENGTH + doc: | + The extent of the observable parts of the specimen given the current + magnification and other settings of the instrument. + working_distance(NX_NUMBER): + unit: NX_LENGTH + doc: + - | + Distance which is determined along the optical axis within the column from (1) the + lower end of the final optical element between the source and the specimen stage; + to (2) the point where the beam is focused. + - | + xref: + spec: EMglossary + term: Working Distance + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 + probe(NXcg_ellipsoid_set): + doc: | + Geometry of the cross-section formed when the primary beam shines onto the + specimen surface. + + # dimensions: + # rank: 2 + probe_current(NX_NUMBER): + unit: NX_CURRENT + doc: + - | + Electrical current which arrives at the specimen. + - | + xref: + spec: EMglossary + term: Probe Current + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 + dose_management(NX_CHAR): + doc: | + Specify further details how incipient electron or ion dose was quantified + (using beam_current, probe_current). + + `Reference `_ discusses + an approach for (electron) dose monitoring in an electron microscope. + + The unit of the nominal dose rate is e-/(angstrom^2*s). + dose_rate(NX_NUMBER): + unit: e-/(angstrom^2*s) + doc: | + Nominal dose rate. + rotation(NX_NUMBER): + unit: NX_ANGLE + doc: | + In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated + on a helical path about the optical axis. This causes an image rotation whose strength + is affected by the magnification. + + Microscopes may be equipped with compensation methods (implemented in hardware + or software) that reduce but not necessarily eliminate this rotation. + + See `L. Reimer `_ for details. + focal_length(NX_NUMBER): + unit: NX_LENGTH + doc: + - | + Distance which lies between the principal plane of the lens and the focal point + along the optical axis. + - | + xref: + spec: EMglossary + term: Focal Length + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 + tilt_correction(NX_BOOLEAN): + doc: + - | + Details about an imaging setting used during acquisition to correct perspective + distortion when imaging a tilted surface or cross section. + - | + xref: + spec: EMglossary + term: Tilt Correction + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 + dynamic_focus_correction(NX_BOOLEAN): + doc: + - | + Details about a dynamic focus correction used. + - | + xref: + spec: EMglossary + term: Dynamic Focus Correction + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 + dynamic_refocusing(NX_CHAR): + doc: + - | + Details about a workflow used to keep the specimen in focus by automatic means. + - | + xref: + spec: EMglossary + term: Dynamic Refocusing + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# cdbe244153f897754b0655eafa8d1f866ec0c8cc643962ab8d67672400e32830 +# +# +# +# +# +# Base class for qualifying an electron optical system. +# +# +# +# Distance which is present between the specimen surface and the detector plane. +# +# This concept is related to term `Camera Length`_ of the EMglossary standard. +# +# .. _Camera Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 +# +# +# +# +# The factor of enlargement of the apparent size, +# not the physical size, of an object. +# +# +# +# +# The defocus aberration constant (oftentimes referred to as c_1_0). +# See respective details in :ref:`NXaberration` class instances. +# +# +# +# +# The angle which is given by the semi-opening angle of the cone in a convergent +# beam. +# +# This concept is related to term `Convergence Angle`_ of the EMglossary standard. +# +# .. _Convergence Angle: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 +# +# +# +# +# The extent of the observable parts of the specimen given the current +# magnification and other settings of the instrument. +# +# +# +# +# Distance which is determined along the optical axis within the column from (1) the +# lower end of the final optical element between the source and the specimen stage; +# to (2) the point where the beam is focused. +# +# This concept is related to term `Working Distance`_ of the EMglossary standard. +# +# .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 +# +# +# +# +# Geometry of the cross-section formed when the primary beam shines onto the +# specimen surface. +# +# +# +# +# +# Electrical current which arrives at the specimen. +# +# This concept is related to term `Probe Current`_ of the EMglossary standard. +# +# .. _Probe Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 +# +# +# +# +# Specify further details how incipient electron or ion dose was quantified +# (using beam_current, probe_current). +# +# `Reference <https://doi.org/10.1017/S1551929522000840>`_ discusses +# an approach for (electron) dose monitoring in an electron microscope. +# +# The unit of the nominal dose rate is e-/(angstrom^2*s). +# +# +# +# +# Nominal dose rate. +# +# +# +# +# In the process of passing through an :ref:`NXlens_em` electrons are typically accelerated +# on a helical path about the optical axis. This causes an image rotation whose strength +# is affected by the magnification. +# +# Microscopes may be equipped with compensation methods (implemented in hardware +# or software) that reduce but not necessarily eliminate this rotation. +# +# See `L. Reimer <https://doi.org/10.1007/978-3-540-38967-5>`_ for details. +# +# +# +# +# Distance which lies between the principal plane of the lens and the focal point +# along the optical axis. +# +# This concept is related to term `Focal Length`_ of the EMglossary standard. +# +# .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 +# +# +# +# +# Details about an imaging setting used during acquisition to correct perspective +# distortion when imaging a tilted surface or cross section. +# +# This concept is related to term `Tilt Correction`_ of the EMglossary standard. +# +# .. _Tilt Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 +# +# +# +# +# Details about a dynamic focus correction used. +# +# This concept is related to term `Dynamic Focus Correction`_ of the EMglossary standard. +# +# .. _Dynamic Focus Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 +# +# +# +# +# Details about a workflow used to keep the specimen in focus by automatic means. +# +# This concept is related to term `Dynamic Refocusing`_ of the EMglossary standard. +# +# .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 +# +# +# diff --git a/contributed_definitions/nyaml/NXpeak.yaml b/base_classes/nyaml/NXpeak.yaml similarity index 94% rename from contributed_definitions/nyaml/NXpeak.yaml rename to base_classes/nyaml/NXpeak.yaml index 4f2226f224..84790386b0 100644 --- a/contributed_definitions/nyaml/NXpeak.yaml +++ b/base_classes/nyaml/NXpeak.yaml @@ -38,17 +38,20 @@ NXpeak(NXobject): as the ``intensity`` field. Each individual dimension of ``position`` must have the same number of points as the corresponding dimension in the ``position`` field. - function(NXfit_function): - doc: | - The functional form of the peak. This could be a Gaussian, Lorentzian, - Voigt, etc. + + # + # + # The functional form of the peak. This could be a Gaussian, Lorentzian, + # Voigt, etc. + # + # total_area(NX_NUMBER): unit: NX_ANY doc: | Total area under the curve. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# e16c2c1fd9e27c4eb6cd8d88d83142c72659d292ec8be6d1c3e74aa66ee7ecf3 +# a357991af8e44c04e4c01b49fe2b0d63a5adf1ad5fbc2c9bba3f9d0d870bc8b2 # # # # # # Total area under the curve. diff --git a/base_classes/nyaml/NXphase.yaml b/base_classes/nyaml/NXphase.yaml new file mode 100644 index 0000000000..234d580f41 --- /dev/null +++ b/base_classes/nyaml/NXphase.yaml @@ -0,0 +1,99 @@ +category: base +doc: | + Base class to describe a (thermodynamic) phase as a component of a material. + + Instances of phases can be crystalline. +type: group +NXphase(NXobject): + identifier(NX_INT): + unit: NX_UNITLESS + doc: | + Identifier for each phase. + + The value 0 is reserved for the unknown phase that represents the + null-model (no sufficiently significant information available). + In other words, the phase_name is n/a aka notIndexed. + + The identifier_phase value should match with the integer suffix of the + group name which represents that instance in a NeXus/HDF5 file, i.e. + if three phases were used e.g. 0, 1, and 2, three instances of :ref:`NXphase` + named phase0, phase1, and phase2 should be stored in that HDF5 file. + name(NX_CHAR): + doc: | + Given name as an alias for identifying this phase. + + If the identifier_phase is 0 and one would like to use + the field name, the value should be n/a or notIndexed. + + # group reference replaced by concept identifierNAME inherited from NXobject + (NXunit_cell): + (NXatom): + + # support for microstructures that are not proposed to the NIAC in this PR + # + # + # + # + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# bd0bd662fe6f1dbbf69709a777bf20916ec8caf8345b2d5461e18901d3f4631a +# +# +# +# +# +# Base class to describe a (thermodynamic) phase as a component of a material. +# +# Instances of phases can be crystalline. +# +# +# +# Identifier for each phase. +# +# The value 0 is reserved for the unknown phase that represents the +# null-model (no sufficiently significant information available). +# In other words, the phase_name is n/a aka notIndexed. +# +# The identifier_phase value should match with the integer suffix of the +# group name which represents that instance in a NeXus/HDF5 file, i.e. +# if three phases were used e.g. 0, 1, and 2, three instances of :ref:`NXphase` +# named phase0, phase1, and phase2 should be stored in that HDF5 file. +# +# +# +# +# Given name as an alias for identifying this phase. +# +# If the identifier_phase is 0 and one would like to use +# the field name, the value should be n/a or notIndexed. +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXprogram.yaml b/base_classes/nyaml/NXprogram.yaml similarity index 100% rename from contributed_definitions/nyaml/NXprogram.yaml rename to base_classes/nyaml/NXprogram.yaml diff --git a/contributed_definitions/nyaml/NXpump.yaml b/base_classes/nyaml/NXpump.yaml similarity index 85% rename from contributed_definitions/nyaml/NXpump.yaml rename to base_classes/nyaml/NXpump.yaml index 526611f9ff..6aace2c9f8 100644 --- a/contributed_definitions/nyaml/NXpump.yaml +++ b/base_classes/nyaml/NXpump.yaml @@ -3,7 +3,7 @@ doc: | Device to reduce an atmosphere (real or simulated) to a controlled pressure. type: group NXpump(NXcomponent): - design: + design(NX_CHAR): doc: | Principle type of the pump. enumeration: [membrane, rotary_vane, roots, turbo_molecular] @@ -13,14 +13,14 @@ NXpump(NXcomponent): # NEW ISSUE: the role, pros and cons of pump used for atom probe microscopy # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ba7fe5441162bb60b96d2a81243a59a26268401317ece2eb428aff7e23d88945 +# 75fd6bed9329fe18baeb5dfb2d5c24e2ac9e3c48d6b874b0e1cb03df60c0c9b4 # # # -# +# # -# Device to reduce an atmosphere (real or simulated) to a controlled pressure. +# Device to reduce an atmosphere (real or simulated) to a controlled pressure. # -# +# # -# Principle type of the pump. +# Principle type of the pump. # # # diff --git a/contributed_definitions/nyaml/NXquadric.yaml b/base_classes/nyaml/NXquadric.yaml similarity index 96% rename from contributed_definitions/nyaml/NXquadric.yaml rename to base_classes/nyaml/NXquadric.yaml index bbeee1f717..fb559c6fa4 100644 --- a/contributed_definitions/nyaml/NXquadric.yaml +++ b/base_classes/nyaml/NXquadric.yaml @@ -1,6 +1,6 @@ category: base doc: | - definition of a quadric surface. + Definition of a quadric surface. type: group NXquadric(NXobject): parameters(NX_NUMBER): @@ -26,7 +26,7 @@ NXquadric(NXobject): which the orientation of the surface depends. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7f63258dc3d5987ba946690fbd17a77b617973eef3e84f3649e6d7b0aa46d3ed +# 79892801401cf76574939685e97cf00ec543b652389c1f6d5799a340ea3f89fa # # # +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# The cardinality of the set, i.e. the number of value tuples. +# +# +# +# +# How many phases with usually different crystal and symmetry are distinguished. +# +# +# +# +# +# Base class to detail a set of rotations, orientations, and disorientations. +# +# For getting a more detailed insight into the discussion of the +# parameterized description of orientations in materials science see: +# +# * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ +# * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ +# * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ +# * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ +# +# Once orientations are defined, one can continue to characterize the +# misorientation and specifically the disorientation. The misorientation describes +# the rotation that is required to register the lattices of two oriented objects +# (like crystal lattice) into a crystallographic equivalent orientation: +# +# * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ +# +# +# +# Reference to an instance of :ref:`NXcoordinate_system` which contextualizes +# how the here reported parameterized quantities can be interpreted. +# +# +# +# +# Point group which defines the symmetry of the crystal. +# +# This has to be at least a single string. If crystal_symmetry is not +# provided, point group 1 is assumed. +# +# In the case that misorientation or disorientation fields are used +# and the two crystal sets resolve for phases with a different +# crystal symmetry, this field needs to encode two strings: +# The first string is for phase A. The second string is for phase B. +# An example of this most complex case is the description of the +# disorientation between crystals adjoining a hetero-phase boundary. +# +# +# +# +# +# +# +# Point group which defines an assumed symmetry imprinted upon processing +# the material/sample which could give rise to or may justify to use a +# simplified description of rotations, orientations, misorientations, +# and disorientations via numerical procedures that are known as +# symmetrization. +# +# If sample_symmetry is not provided, point group 1 is assumed. +# +# The traditionally used symmetrization operations within the texture +# community in Materials Science, though, have become obsolete thanks +# to improvements in methods, software, and available computing power. +# +# Therefore, users are encouraged to set the sample_symmetry to 1 (triclinic). +# +# In practice one often faces situations where indeed these assumed +# symmetries are anyway not fully observed, and thus an accepting of +# eventual inaccuracies just for the sake of reporting a simplified +# symmetrized description should be avoided. +# +# +# +# +# +# +# +# The set of rotations expressed in quaternion parameterization considering +# crystal_symmetry and sample_symmetry. Rotations which should be +# interpreted as antipodal are not marked as such. +# +# +# +# +# +# +# +# +# The set of rotations expressed in Euler angle parameterization considering +# the same applied symmetries as detailed for the field rotation_quaternion. +# To interpret Euler angles correctly, it is necessary to inspect the rotation +# conventions behind reference_frame to resolve which of the many possible +# Euler-angle conventions (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. +# +# +# +# +# +# +# +# +# +# +# True for all those value tuples which have assumed antipodal symmetry. +# False for all others. +# +# +# +# +# +# +# +# The set of orientations expressed in quaternion parameterization and +# obeying symmetry for equivalent cases as detailed in crystal_symmetry +# and sample_symmetry. The supplementary field is_antipodal can be used +# to mark orientations with the antipodal property. +# +# +# +# +# +# +# +# +# The set of orientations expressed in Euler angle parameterization following +# the same assumptions like for orientation_quaternion. +# To interpret Euler angles correctly, it is necessary to inspect the rotation +# conventions behind reference_frame to resolve which of the many Euler-angle +# conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. +# +# +# +# +# +# +# +# +# +# The set of misorientations expressed in quaternion parameterization +# obeying symmetry operations for equivalent misorientations +# as defined by crystal_symmetry and sample_symmetry. +# +# The misorientation should not be confused with the disorientation, +# as for the latter the angular argument is expected to be the minimal +# obeying symmetries. +# +# +# +# +# +# +# +# +# Misorientation angular argument (eventually signed) following the same +# symmetry assumptions as expressed for the field misorientation_quaternion. +# +# +# +# +# +# +# +# Misorientation axis (normalized) and signed following the same +# symmetry assumptions as expressed for the field misorientation_angle. +# +# +# +# +# +# +# +# +# +# The set of disorientations expressed in quaternion parameterization +# obeying symmetry operations for equivalent disorientations +# as defined by crystal_symmetry and sample_symmetry. +# +# +# +# +# +# +# +# +# Disorientations angular argument (should not be signed, see +# `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) +# following the same symmetry assumptions as expressed for the field +# disorientation_quaternion. +# +# +# +# +# +# +# +# Disorientations axis (normalized) following the same symmetry assumptions +# as expressed for the field disorientation_angle. +# +# +# +# +# +# +# diff --git a/base_classes/nyaml/NXscanbox_em.yaml b/base_classes/nyaml/NXscanbox_em.yaml new file mode 100644 index 0000000000..1d894263ae --- /dev/null +++ b/base_classes/nyaml/NXscanbox_em.yaml @@ -0,0 +1,141 @@ +category: base +doc: | + Scan box and coils which deflect a beam of charged particles in a controlled manner. + + The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, + which is not necessarily the same program as for all components of an instrument. + + The scanbox directs the probe of charged particles (electrons, ions) + to controlled locations according to a scan scheme and plan. +type: group +NXscanbox_em(NXcomponent): + + # user perspective + scan_schema(NX_CHAR): + doc: | + Name of the typically tech-partner-specific term that specifies an + automated protocol which controls the details how the components + of the scan_box and instrument work together to achieve a controlled + scanning of the beam over the sample surface. + + In most cases users do not know, have to care, or are able to disentangle the + details of the spatiotemporal dynamics of the components of the instrument. + Instead, they often rely on the assumption that the microscope and control software + work as expected. The field scan_schema can be used to add some constraints + on how the beam was scanned over the surface. + + # descriptors relevant from economic usage (costs) of the instrument and dose management perspective (radiation damage) + dwell_time(NX_NUMBER): + unit: NX_TIME + doc: + - | + Time period during which the beam remains at one position. + - | + xref: + spec: EMglossary + term: Dwell Time + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 + flyback_time(NX_NUMBER): + unit: NX_TIME + doc: + - | + Time period during which the beam moves from the final position of one scan + line to the starting position of the subsequent scan line. + - | + xref: + spec: EMglossary + term: Flyback Time + url: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 + + # technical design perspective + (NXdeflector): + doc: | + Details about components which realize the deflection technically. + + This concept should be used for all those components that implement + the scanning of the beam, while components like beam blankers etc. should + use rather the NXdeflector concept of the NXebeam_column base class. + (NXcircuit): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 3f374a059a0aa9d3a7e9cbf324b64fb43c925313c54d9bf84e3bc7561100d1ba +# +# +# +# +# +# Scan box and coils which deflect a beam of charged particles in a controlled manner. +# +# The scan box is instructed by (an) instance(s) of :ref:`NXprogram`, some control software, +# which is not necessarily the same program as for all components of an instrument. +# +# The scanbox directs the probe of charged particles (electrons, ions) +# to controlled locations according to a scan scheme and plan. +# +# +# +# +# Name of the typically tech-partner-specific term that specifies an +# automated protocol which controls the details how the components +# of the scan_box and instrument work together to achieve a controlled +# scanning of the beam over the sample surface. +# +# In most cases users do not know, have to care, or are able to disentangle the +# details of the spatiotemporal dynamics of the components of the instrument. +# Instead, they often rely on the assumption that the microscope and control software +# work as expected. The field scan_schema can be used to add some constraints +# on how the beam was scanned over the surface. +# +# +# +# +# +# Time period during which the beam remains at one position. +# +# This concept is related to term `Dwell Time`_ of the EMglossary standard. +# +# .. _Dwell Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 +# +# +# +# +# Time period during which the beam moves from the final position of one scan +# line to the starting position of the subsequent scan line. +# +# This concept is related to term `Flyback Time`_ of the EMglossary standard. +# +# .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 +# +# +# +# +# +# Details about components which realize the deflection technically. +# +# This concept should be used for all those components that implement +# the scanning of the beam, while components like beam blankers etc. should +# use rather the NXdeflector concept of the NXebeam_column base class. +# +# +# +# diff --git a/contributed_definitions/nyaml/NXsolid_geometry.yaml b/base_classes/nyaml/NXsolid_geometry.yaml similarity index 66% rename from contributed_definitions/nyaml/NXsolid_geometry.yaml rename to base_classes/nyaml/NXsolid_geometry.yaml index ce8b697fae..113b8a81a8 100644 --- a/contributed_definitions/nyaml/NXsolid_geometry.yaml +++ b/base_classes/nyaml/NXsolid_geometry.yaml @@ -1,6 +1,12 @@ category: base doc: | - the head node for constructively defined geometry + The head node for constructively defined geometry. + + * `S. Ghebi `_ + * `L. H. Laidlaw `_ + + for an introduction into the topic of modeling shapes with constructive + solid geometry (CSG). type: group NXsolid_geometry(NXobject): (NXquadric): @@ -11,13 +17,16 @@ NXsolid_geometry(NXobject): exists: ['min', '0'] doc: | Instances of :ref:`NXoff_geometry` making up elements of the geometry. + + # in the future allow also groups of other NXcg instances to make up the geometry (NXcsg): exists: ['min', '0'] doc: | - The geometries defined, made up of instances of :ref:`NXquadric` and :ref:`NXoff_geometry`. + The geometries defined, made up of e.g. instances of :ref:`NXquadric`, :ref:`NXoff_geometry`, + or instances of other base classes that define geometries. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 71a1b3ca39b88fdae9499a10284ddc6fd89423b5d2e3e1d544bacfa3793bb5c0 +# 5e75e1cc6b9967e5902fe5c1488245ae3f9df6df90eef899e4a7aef270936edd # # # # # -# The geometries defined, made up of instances of :ref:`NXquadric` and :ref:`NXoff_geometry`. +# The geometries defined, made up of e.g. instances of :ref:`NXquadric`, :ref:`NXoff_geometry`, +# or instances of other base classes that define geometries. # # # diff --git a/contributed_definitions/nyaml/NXspectrum_set.yaml b/base_classes/nyaml/NXspectrum.yaml similarity index 85% rename from contributed_definitions/nyaml/NXspectrum_set.yaml rename to base_classes/nyaml/NXspectrum.yaml index 3881853e75..9a8f69ddf5 100644 --- a/contributed_definitions/nyaml/NXspectrum_set.yaml +++ b/base_classes/nyaml/NXspectrum.yaml @@ -7,7 +7,7 @@ doc: | Use stack for all other tilings. -# https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons +# set of frequently made specializations of NXdata instances for spectra symbols: n_spc: | Number of spectra in the stack, for stacks the slowest dimension. @@ -20,18 +20,14 @@ symbols: n_energy: | Number of energy bins (always the fastest dimension). type: group -NXspectrum_set(NXobject): - - # for EELS we likely need a complex-valued NXspectrum_c_set to this - # NXspectrum_set base class here which should then be splitted into an - # NXspectrum_set to reduce redundant fields and specialized NXspectrum_r/c_set +NXspectrum(NXobject): (NXprocess): doc: | Details how spectra were processed from the detector readings. source(NXnote): doc: | Resolvable data artifact (e.g. filename) from which all values in the :ref:`NXdata` - instances in this :ref:`NXspectrum_set` were loaded during parsing. + instances in this :ref:`NXspectrum` were loaded during parsing. Possibility to document from which specific other serialized resource as the source pieces of information were processed when using NeXus as a semantic file format @@ -46,15 +42,12 @@ NXspectrum_set(NXobject): mode(NX_CHAR): doc: | Imaging (data collection) mode of the instrument during acquisition - of the data in this :ref:`NXspectrum_set` instance. - detector_identifier(NX_CHAR): + of the data in this :ref:`NXspectrum` instance. + identifier_detector(NX_CHAR): doc: | Link or name of an :ref:`NXdetector` instance with which the data were collected. (NXprogram): - - #MK::feel free to contact us when you would like to include - # like omega/q mapping more complicated scan pattern than rectangular ones. spectrum_0d(NXdata): doc: | One spectrum for a point of a 0d ROI. Also known as spot measurement. @@ -94,7 +87,7 @@ NXspectrum_set(NXobject): axis_i(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension dimensions: rank: 1 dim: (n_i,) @@ -127,23 +120,23 @@ NXspectrum_set(NXobject): axis_j(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension dimensions: rank: 1 dim: (n_j,) \@long_name(NX_CHAR): doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension axis_i(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension dimensions: rank: 1 dim: (n_i,) \@long_name(NX_CHAR): doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension axis_energy(NX_NUMBER): unit: NX_ENERGY doc: | @@ -170,33 +163,33 @@ NXspectrum_set(NXobject): axis_k(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the slower dimension. + Point coordinate along the slower dimension dimensions: rank: 1 dim: (n_k,) \@long_name(NX_CHAR): doc: | - Point coordinate along the slower dimension. + Point coordinate along the slower dimension axis_j(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension dimensions: rank: 1 dim: (n_j,) \@long_name(NX_CHAR): doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension axis_i(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension dimensions: rank: 1 dim: (n_i,) \@long_name(NX_CHAR): doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension axis_energy(NX_NUMBER): unit: NX_ENERGY doc: | @@ -207,11 +200,6 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Energy - - # in the majority of cases rectangular or line scans are performed - # if there is interest to support arbitrary scan pattern one should use - # scan points and contact us to generalize this base class and related - # base classes stack_0d(NXdata): doc: | Multiple instances of spectrum_0d. @@ -225,7 +213,7 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Counts - group_identifier(NX_INT): + identifier_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -235,7 +223,7 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - spectrum_identifier(NX_INT): + identifier_spectrum(NX_INT): unit: NX_UNITLESS doc: | Spectrum identifier @@ -268,7 +256,7 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Counts - group_identifier(NX_INT): + identifier_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -278,7 +266,7 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - spectrum_identifier(NX_INT): + identifier_spectrum(NX_INT): unit: NX_UNITLESS doc: | Spectrum identifier @@ -291,23 +279,23 @@ NXspectrum_set(NXobject): axis_j(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension dimensions: rank: 1 dim: (n_j,) \@long_name(NX_CHAR): doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension axis_i(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension dimensions: rank: 1 dim: (n_i,) \@long_name(NX_CHAR): doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension axis_energy(NX_NUMBER): unit: NX_ENERGY doc: | @@ -331,7 +319,7 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Counts - group_identifier(NX_INT): + identifier_group(NX_INT): unit: NX_UNITLESS doc: | Group identifier @@ -341,7 +329,7 @@ NXspectrum_set(NXobject): \@long_name(NX_CHAR): doc: | Group identifier - spectrum_identifier(NX_INT): + identifier_spectrum(NX_INT): unit: NX_UNITLESS doc: | Spectrum identifier @@ -354,33 +342,33 @@ NXspectrum_set(NXobject): axis_k(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the slower dimension. + Point coordinate along the slower dimension dimensions: rank: 1 dim: (n_k,) \@long_name(NX_CHAR): doc: | - Point coordinate along the slower dimension. + Point coordinate along the slower dimension axis_j(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension dimensions: rank: 1 dim: (n_j,) \@long_name(NX_CHAR): doc: | - Point coordinate along the slow dimension. + Point coordinate along the slow dimension axis_i(NX_NUMBER): unit: NX_LENGTH doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension dimensions: rank: 1 dim: (n_i,) \@long_name(NX_CHAR): doc: | - Point coordinate along the fast dimension. + Point coordinate along the fast dimension axis_energy(NX_NUMBER): unit: NX_ENERGY doc: | @@ -393,13 +381,13 @@ NXspectrum_set(NXobject): Energy # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 994a4d431f9e4940fd140a449201cd5b4253930791782b19b85d23abc967b522 +# 2b02d0385acf9f858b8ab4d96fa590c36d0280de1dbf35bc0be032ea4fa47a85 # # # -# -# +# +# # # # @@ -454,9 +442,6 @@ NXspectrum_set(NXobject): # # Use stack for all other tilings. # -# # # # Details how spectra were processed from the detector readings. @@ -464,7 +449,7 @@ NXspectrum_set(NXobject): # # # Resolvable data artifact (e.g. filename) from which all values in the :ref:`NXdata` -# instances in this :ref:`NXspectrum_set` were loaded during parsing. +# instances in this :ref:`NXspectrum` were loaded during parsing. # # Possibility to document from which specific other serialized resource as the source # pieces of information were processed when using NeXus as a semantic file format @@ -483,10 +468,10 @@ NXspectrum_set(NXobject): # # # Imaging (data collection) mode of the instrument during acquisition -# of the data in this :ref:`NXspectrum_set` instance. +# of the data in this :ref:`NXspectrum` instance. # # -# +# # # Link or name of an :ref:`NXdetector` instance with which the data were # collected. @@ -494,8 +479,6 @@ NXspectrum_set(NXobject): # # # -# # # # One spectrum for a point of a 0d ROI. Also known as spot measurement. @@ -547,7 +530,7 @@ NXspectrum_set(NXobject): # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # @@ -593,27 +576,27 @@ NXspectrum_set(NXobject): # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # @@ -653,40 +636,40 @@ NXspectrum_set(NXobject): # # # -# Point coordinate along the slower dimension. +# Point coordinate along the slower dimension # # # # # # -# Point coordinate along the slower dimension. +# Point coordinate along the slower dimension # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # @@ -704,10 +687,6 @@ NXspectrum_set(NXobject): # # # -# # # # Multiple instances of spectrum_0d. @@ -726,7 +705,7 @@ NXspectrum_set(NXobject): # # # -# +# # # Group identifier # @@ -739,7 +718,7 @@ NXspectrum_set(NXobject): # # # -# +# # # Spectrum identifier # @@ -786,7 +765,7 @@ NXspectrum_set(NXobject): # # # -# +# # # Group identifier # @@ -799,7 +778,7 @@ NXspectrum_set(NXobject): # # # -# +# # # Spectrum identifier # @@ -814,27 +793,27 @@ NXspectrum_set(NXobject): # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # @@ -873,7 +852,7 @@ NXspectrum_set(NXobject): # # # -# +# # # Group identifier # @@ -886,7 +865,7 @@ NXspectrum_set(NXobject): # # # -# +# # # Spectrum identifier # @@ -901,40 +880,40 @@ NXspectrum_set(NXobject): # # # -# Point coordinate along the slower dimension. +# Point coordinate along the slower dimension # # # # # # -# Point coordinate along the slower dimension. +# Point coordinate along the slower dimension # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # # -# Point coordinate along the slow dimension. +# Point coordinate along the slow dimension # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # # # # -# Point coordinate along the fast dimension. +# Point coordinate along the fast dimension # # # diff --git a/base_classes/nyaml/NXunit_cell.yaml b/base_classes/nyaml/NXunit_cell.yaml new file mode 100644 index 0000000000..53e07a7c5d --- /dev/null +++ b/base_classes/nyaml/NXunit_cell.yaml @@ -0,0 +1,214 @@ +category: base +doc: | + Base class to describe structural aspects of an arrangement of + atoms or ions including a crystallographic unit cell. + + Following recommendations of `CIF `_ and `International Tables of Crystallography `_. +symbols: + d: | + Dimensionality of the lattice. +type: group +NXunit_cell(NXobject): + reference_frame(NX_CHAR): + doc: | + Path to a reference frame in which the unit cell is defined + to resolve ambiguity in cases when e.g. a different reference frame + than the NeXus default reference frame (McStas) was chosen. + dimensionality(NX_POSINT): + doc: | + Dimensionality of the structure. + enumeration: [1, 2, 3] + a_b_c(NX_NUMBER): + unit: NX_LENGTH + doc: | + Geometry of the unit cell quantified via parameters a, b, and c. + dimensions: + rank: 1 + dim: (d,) + + # defined using which convention? + alpha_beta_gamma(NX_NUMBER): + unit: NX_ANGLE + doc: | + Geometry of the unit cell quantified via parameters alpha, beta, and gamma. + dimensions: + rank: 1 + dim: (d,) + crystal_system(NX_CHAR): + doc: | + Crystal system. + + For a crystal system in 2D space monoclinic is an exact synonym for oblique. + For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. + For a crystal system in 2D space tetragonal is an exact synonym for square. + enumeration: [triclinic, monoclinic, orthorhombic, tetragonal, rhombohedral, hexagonal, cubic] + laue_group(NX_CHAR): + doc: | + Laue group using International Table of Crystallography notation. + + # add enumeration of all possible ones here to create a closed enum? + point_group(NX_CHAR): + doc: | + Point group using International Table of Crystallography notation. + space_group(NX_CHAR): + doc: | + Space group from the International Table of Crystallography notation. + is_centrosymmetric(NX_BOOLEAN): + doc: | + True if space group is considered a centrosymmetric one. + False if space group is considered a non-centrosymmetric one. + + Centrosymmetric has all types and combinations of symmetry elements + (translation, rotational axis, mirror planes, center of inversion) + Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). + Chiral compared to non-centrosymmetric is constrained (no mirror planes). + is_chiral(NX_BOOLEAN): + doc: | + True if space group is considered a chiral one. + False if space group is consider a non-chiral one. + area(NX_NUMBER): + unit: NX_AREA + doc: | + Area of the unit cell if dimensionality is 2. + volume(NX_NUMBER): + unit: NX_VOLUME + doc: | + Volume of the unit cell if dimensionality is 3. + (NXatom): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 4ba67e02f7c0510351f900e50337dc1662a9ceb9256ba3f0ea1d3c12c76e7e7d +# +# +# +# +# +# +# +# Dimensionality of the lattice. +# +# +# +# +# Base class to describe structural aspects of an arrangement of +# atoms or ions including a crystallographic unit cell. +# +# Following recommendations of `CIF <https://www.iucr.org/resources/cif/spec/version1.1>`_ and `International Tables of Crystallography <https://it.iucr.org/>`_. +# +# +# +# Path to a reference frame in which the unit cell is defined +# to resolve ambiguity in cases when e.g. a different reference frame +# than the NeXus default reference frame (McStas) was chosen. +# +# +# +# +# Dimensionality of the structure. +# +# +# +# +# +# +# +# +# +# Geometry of the unit cell quantified via parameters a, b, and c. +# +# +# +# +# +# +# +# +# Geometry of the unit cell quantified via parameters alpha, beta, and gamma. +# +# +# +# +# +# +# +# Crystal system. +# +# For a crystal system in 2D space monoclinic is an exact synonym for oblique. +# For a crystal system in 2D space orthorhombic is an exact synonym for rectangular. +# For a crystal system in 2D space tetragonal is an exact synonym for square. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Laue group using International Table of Crystallography notation. +# +# +# +# +# +# Point group using International Table of Crystallography notation. +# +# +# +# +# Space group from the International Table of Crystallography notation. +# +# +# +# +# True if space group is considered a centrosymmetric one. +# False if space group is considered a non-centrosymmetric one. +# +# Centrosymmetric has all types and combinations of symmetry elements +# (translation, rotational axis, mirror planes, center of inversion) +# Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). +# Chiral compared to non-centrosymmetric is constrained (no mirror planes). +# +# +# +# +# True if space group is considered a chiral one. +# False if space group is consider a non-chiral one. +# +# +# +# +# Area of the unit cell if dimensionality is 2. +# +# +# +# +# Volume of the unit cell if dimensionality is 3. +# +# +# +# diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml deleted file mode 100644 index c708d221ff..0000000000 --- a/contributed_definitions/nyaml/NXapm.yaml +++ /dev/null @@ -1,1130 +0,0 @@ -category: application -doc: | - Application definition for atom probe and field ion microscopy experiments. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_ht: | - Number of hit qualities (hit types) distinguished. - n_dld: | - Number of delay-line wires of the detector. - n_bins: | - Number of bins used in the mass-to-charge-state-ratio spectrum. - p: | - Number of pulses collected in between start_time and end_time resolved by an - instance of :ref:`NXevent_data_apm`. If this is not defined, p is the number of - ions included in the reconstructed volume if the application definition is used - to store results of an already reconstructed datasets. - p_out: | - Number of pulses returned by the hit finding algorithm. - Neither necessarily equal to p nor to n. - n: | - Number of ions spatially filtered from results of the hit_finding algorithm - from which an instance of a reconstructed volume has been generated. - These ions get new identifier assigned in the process (the so-called - evaporation_identifier). This identifier must not be confused with - the pulse_identifier. Typically smaller than both p_out and p_out. -type: group -NXapm(NXobject): - (NXentry): # entryID - exists: [min, 1, max, infty] - definition(NX_CHAR): - \@version(NX_CHAR): - exists: optional - enumeration: [NXapm] - profiling(NXcs_profiling): - exists: optional - doc: | - The configuration of the I/O writer software (e.g. `pynxtools `_ or its plugins) - which was used to generate this NeXus file instance. - # command_line_call(NX_CHAR): - programID(NXprogram): # program1, program2, ... - exists: [min, 0, max, infty] - doc: | - A collection of all programs and libraries which are considered relevant - to understand with which software tools this NeXus file instance was - generated. Ideally, to enable a binary recreation from the input data. - - Examples include the name and version of the libraries used to write the - instance. Ideally, the software which writes these NXprogram instances - also includes the version of the set of NeXus classes i.e. the specific - set of base classes, application definitions, and contributed definitions - with which the here described concepts can be resolved. - - For the `pynxtools library `_ - which is used by the `NOMAD `_ - research data management system, it makes sense to store e.g. the GitHub - repository commit and respective submodule references used. - program(NX_CHAR): - \@version(NX_CHAR): - # \@url: - experiment_identifier(NXidentifier): - exists: recommended - service(NX_CHAR): - identifier(NX_CHAR): - is_persistent(NX_BOOLEAN): - run_number(NX_UINT): - exists: recommended - # cannot be made required as for simulations you do not have a run number! - doc: | - The identifier whereby the experiment is referred to in the control software. - This is neither the specimen_name nor the experiment_identifier. For - Local Electrode Atom Probe (LEAP) instruments, it is recommended to use the - run_number from the proprietary software IVAS/APSuite of AMETEK/Cameca. - For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, - or the instruments at GPM in Rouen, use the identifier which matches - best conceptually to the LEAP run number. - The field does not have to be required if the information is recoverable - in the dataset which for LEAP instruments is the case (provided these - RHIT or HITS files respectively are stored alongside a data artifact). - With NXapm the RHIT or HITS can be stored as via the NXserialized group - in the hit_finding algorithm section. - - As a destructive microscopy technique, a run can be performed only once. - It is possible, however, to interrupt a run and restart data acquisition - while still using the same specimen. In this case, each evaporation run - needs to be distinguished with different run numbers. - We follow this habit of most atom probe groups. Such interrupted runs - should be stored as individual :ref:`NXentry` instances in one NeXus file. - unit: NX_UNITLESS - experiment_alias(NX_CHAR): - exists: recommended - doc: | - Either an identifier or an alias that is human-friendly so that scientists find that experiment again. - For experiments usually this is the run_number but for simulation typically no run_numbers are issued. - experiment_description(NX_CHAR): - exists: optional - doc: | - Free-text description about the experiment. - - Users are strongly advised to parameterize the description of their experiment - by using respective groups and fields and base classes instead of writing prose - into this field. - - The reason is that such free-text field is difficult to machine-interpret. - The motivation behind keeping this field for now is to learn in how far the - current base classes need extension based on user feedback. - # optional quantities do not need to be mentioned in an appdef because they can always be added - # if NXapm inherits from NXapm_base having this optional field does not need to be - # mentioned because optional nodes can always be added to a NeXus file instance without - # making it thereby non-compliant to the application definition - # the only difference is that if the consuming application wishes to demand to find that field - # it has to be specified in the appdef for the appdef to be a useful document of the contract - # which pieces of information a software expects to find and which not - # if you think about you being the consuming human (agent) also you would like to know - # if there is a run_number for the atom probe measurement from your colleague i.e. you - # effectively ask your colleague for that information while working off your imagined list of requirements - # the appdef definition here is nothing else then the documentation of this for a software - start_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information - included when the atom probe session started. If the exact duration of - the measurement is not relevant start_time only should be used. - - Often though it is useful to specify both start_time and end_time to - capture more detailed bookkeeping of the experiment. The user should - be aware that even with having both dates specified, it may not be - possible to infer how long the experiment took or for how long data - were collected. - - More detailed timing data over the course of the experiment have to be - collected to compute this event chain during the experiment. For this - purpose the :ref:`NXevent_data_apm` instance should be used. - end_time(NX_DATE_TIME): - exists: recommended - doc: | - ISO 8601 time code with local time zone offset to UTC included - when the atom probe session ended. - elapsed_time(NX_FLOAT): - exists: recommended - doc: | - How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime - unit: NX_TIME - (NXcite): - exists: [min, 0, max, infty] - doi(NX_CHAR): - serializedID(NXserialized): - exists: [min, 0, max, infty] - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - operation_mode(NX_CHAR): - doc: | - What type of atom probe experiment is performed? This field is meant to - inform research data management systems to allow filtering: - - * apt are experiments where the analysis_chamber has no imaging gas. - experiment with LEAP instruments are typically performed such. - * fim are experiments where the analysis_chamber has an imaging gas, - which should be specified with the atmosphere in the analysis_chamber group. - * apt_fim should be used for combinations of the two imaging modes. - few experiments of this type have been performed as this can be detrimental - to LEAP systems (see `S. Katnagallu et al. `_). - * other should be used in combination with the user specifying details - in the experiment_documentation field. - - If NXapm is used for storing details about a simulation use other for now. - enumeration: [apt, fim, apt_fim, other] - (NXuser): - exists: recommended - name(NX_CHAR): - exists: optional - identifier(NXidentifier): - exists: recommended - service(NX_CHAR): - identifier(NX_CHAR): - is_persistent(NX_BOOLEAN): - sample(NXsample): - exists: recommended - doc: | - Description of the sample from which the specimen was prepared or - site-specifically cut out using e.g. a focused-ion beam instrument. - - The sample group is currently a place for storing suggestions from - atom probers about knowledge they have gained about the sample. - There are cases where the specimen is machined further or exposed to - external stimuli during the experiment. In this case, these details should - not be stored under sample but suggestions should be made - how this application definition can be improved. - - In the future also details like how the grain_diameter was characterized, - how the sample was prepared, how the material was heat-treated etc., - should be stored. For this specific application definitions/schemas can be - used which are then arranged and documented with a description of the - workflow so that actionable graphs become instantiatable. - type(NX_CHAR): - doc: | - A qualifier whether the sample is a real one - or a virtual one (in a computer simulation). - enumeration: [experiment, simulation] - alias(NX_CHAR): - doc: | - Given name/alias for the sample. - identifier(NXidentifier): - exists: recommended - service(NX_CHAR): - identifier(NX_CHAR): - is_persistent(NX_BOOLEAN): - grain_diameter(NX_FLOAT): - exists: optional - doc: | - Qualitative information about the grain size, here specifically - described as the equivalent spherical diameter of an assumed - average grain size for the crystal ensemble. - Users of this information should be aware that although the grain - diameter or radius is often referred to as grain size. - - In atom probe it is possible that the specimen may contain a few - crystals only. In this case the grain_diameter is not a reliable - descriptor. Reporting a grain size may be useful though as it allows - judging if specific features are expected to be found in the - detector hit map. - unit: NX_LENGTH - grain_diameter_error(NX_FLOAT): - exists: optional - doc: | - Magnitude of the standard deviation of the grain_diameter. - unit: NX_LENGTH - heat_treatment_temperature(NX_FLOAT): - exists: optional - doc: | - The temperature of the last heat treatment step before quenching. - Knowledge about this value can give an idea how the sample - was heat treated. However, if a documentation of the annealing - treatment as a function of time is available one should better - rely on this information and have it stored alongside the NeXus file. - # schema for heat treatment - unit: NX_TEMPERATURE - heat_treatment_temperature_error(NX_FLOAT): - exists: optional - doc: | - Magnitude of the standard deviation of the heat_treatment_temperature. - unit: NX_TEMPERATURE - heat_treatment_quenching_rate(NX_FLOAT): - exists: optional - doc: | - Rate of the last quenching step. Knowledge about this value can give - an idea how the sample was heat treated. However, there are many - situations where one can imagine that the scalar value for just the - quenching rate is insufficient. - - An example is when the sample was left in the furnace after the - furnace was switched off. In this case the sample cools down with - a specific rate of how this furnace cools down in the lab. - Processes which in practice are often not documented. - - This can be problematic though because when the furnace door was left open - or the ambient temperature in the lab changed, i.e. for a series of - experiments where one is conducted on a hot summer day and the next - during winter this can have an effect on the evolution of the microstructure. - There are many cases where this has been reported to be an QA issue in industry, - e.g. think about aging aluminium samples left on the factory - parking lot on a hot summer day. - unit: NX_ANY # K/s - heat_treatment_quenching_rate_error(NX_FLOAT): - exists: optional - doc: | - Magnitude of the standard deviation of the heat_treatment_quenching_rate. - unit: NX_ANY - description(NX_CHAR): - exists: optional - chemical_composition(NXchemical_composition): - exists: recommended - doc: | - The chemical composition of the sample. Typically, it is assumed that - this more macroscopic composition is representative for the material - so that the composition of the typically substantially less voluminous - specimen probes from the more voluminous sample. - normalization(NX_CHAR): - doc: | - Reporting compositions as atom and weight percent yields both - dimensionless quantities but their conceptual interpretation differs. - A normalization based on atom_percent counts relative to the - total number of atoms which are of a particular type. - By contrast, weight_percent normalization factorizes in the - respective mass of the elements. Python libraries like pint are - challenged by these differences as at.-% and wt.-% are both - fractional quantities. - enumeration: [atom_percent, weight_percent] - ionID(NXion): - exists: [min, 1, max, 118] - chemical_symbol(NX_CHAR): - doc: | - Human-readable name of the element (e.g. Fe). - Name has to be a symbol of an element from the periodic table. - All symbols in the set of NXion instances inside the group - chemical_composition need to be disjoint. - composition(NX_FLOAT): - doc: | - Composition value for the element/ion referred to under name. - The value is normalized based on normalization, i.e. composition - is either an atom or weight percent quantity. - unit: NX_DIMENSIONLESS - composition_error(NX_FLOAT): - exists: optional - doc: | - Magnitude of the standard deviation of the composition (value). - unit: NX_DIMENSIONLESS - specimen(NXsample): - type(NX_CHAR): - doc: | - A qualifier whether the specimen is a real one or a virtual one. - enumeration: [experiment, simulation] - alias(NX_CHAR): - exists: recommended - doc: | - Given name an alias. Better use identifier and parent_identifier instead. - A single NXentry should be used only for the characterization of a single specimen. - identifier(NXidentifier): - exists: recommended - service(NX_CHAR): - identifier(NX_CHAR): - is_persistent(NX_BOOLEAN): - parent_identifier(NXidentifier): - exists: recommended - doc: | - Identifier of the sample from which the specimen was cut or the string - n/a. The purpose of this field is to support functionalities for - tracking sample provenance via a research data management system. - service(NX_CHAR): - identifier(NX_CHAR): - is_persistent(NX_BOOLEAN): - preparation_date(NX_DATE_TIME): - exists: recommended - doc: | - ISO 8601 time code with local time zone offset to UTC information - when the specimen was prepared. - - Ideally, report the end of the preparation, i.e. the last known time - the measured specimen surface was actively prepared. Ideally, this - matches the last timestamp that is mentioned in the digital resource - pointed to by parent_identifier. - - Knowing when the specimen was exposed to e.g. specific atmosphere is - especially required for environmentally sensitive material such as - hydrogen charged specimens or experiments including tracers with a - short half time. Additional time stamps prior to preparation_date - should better be placed in resources which describe but which do not - pollute the description here with prose. Resolving these connected - pieces of information is considered within the responsibility of the - research data management system. - atom_types(NX_CHAR): - doc: | - List of comma-separated elements from the periodic table that are - contained in the specimen. If the specimen substance has multiple - components, all elements from each component must be included in - `atom_types`. - - The purpose of the field is to offer research data management systems an - opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by parent_identifier or walk through - eventually deeply nested groups in data instances. - description(NX_CHAR): - exists: optional - doc: | - Discouraged free-text field. - is_polycrystalline(NX_BOOLEAN): - exists: recommended - doc: | - Report if the specimen is polycrystalline, in which case it - contains a grain or phase boundary, or if the specimen is a - single crystal. - is_amorphous(NX_BOOLEAN): - exists: recommended - doc: | - Report if the specimen is amorphous. - initial_radius(NX_FLOAT): - exists: recommended - doc: | - Ideally measured otherwise best elaborated guess of the initial radius of the specimen. - unit: NX_LENGTH - shank_angle(NX_FLOAT): - exists: recommended - doc: | - Ideally measured otherwise best elaborated guess of the (initial) shank angle. - This is a measure of the specimen taper. Define it in such a way that the base of the specimen - is modelled as a conical frustrum so that the shank angle is the (shortest) angle between - the specimen space z-axis and a vector on the lateral surface of the cone. - unit: NX_ANGLE - # describing the geometry of the specimen - coordinate_system_set(NXcoordinate_system_set): - exists: recommended # should be made required - doc: | - Set to hold different coordinate systems conventions. - Inspect the description of the :ref:`NXcoordinate_system_set` - and :ref:`NXcoordinate_system` base classes how to define - coordinate systems in NeXus. Specific details for application - in atom probe microscopy follow. - - In this research field scientists usually distinguish several - Euclidean coordinate systems (CS): - - * World space; - a CS specifying a local coordinate system of the planet earth which - identifies into which direction gravity is pointing such that - the laboratory space CS can be rotated into this world CS. - * The laboratory space; - a CS specifying the room where the instrument is located in or - a physical landmark on the instrument, e.g. the direction of the - transfer rod where positive is the direction how the rod - has to be pushed during loading a specimen into the instrument. - In summary, this CS is defined by the chassis of the instrument. - * The specimen space; - a CS affixed to either the base or the initial apex of the specimen, - whose z axis points towards the detector. - * The detector space; - a CS affixed to the detector plane whose xy plane is usually in the - detector and whose z axis points towards the specimen. - This is a distorted space with respect to the reconstructed ion - positions. - * The reconstruction space; - a CS in which the reconstructed ion positions are defined. - The orientation depends on the analysis software used. - * Eventually further coordinate systems attached to the - flight path of individual ions might be defined. - - In atom probe microscopy a frequently used choice for the detector - space (CS) is discussed with the so-called detector space image - (stack). This is a stack of two-dimensional histograms of detected ions - within a predefined evaporation identifier interval. Typically, the set of - ion evaporation sequence IDs is grouped into chunks. - - For each chunk a histogram of the ion hit positions on the detector - is computed. This leaves the possibility for inconsistency between - the so-called detector space and the e.g. specimen space. - - To avoid these ambiguities, instances of :ref:`NXtransformations` should - be used. - (NXcoordinate_system): - exists: [min, 1, max, infty] - origin(NX_CHAR): - alias(NX_CHAR): - type(NX_CHAR): - handedness(NX_CHAR): - x_direction(NX_CHAR): - y_direction(NX_CHAR): - z_direction(NX_CHAR): - - measurement(NXobject): - exists: optional - doc: | - Base class for collecting a session with a real atom probe or field-ion microscope. - - Workflows used during experiments or simulations of atom probe and related field-evaporation - research should be documented in more detail and be better contextualized not only because of - ongoing developments and the tighter becoming connection between atom probe and other - methods for material characterization foremost electron microscopy see e.g.: - - * `T. Kelly et al. `_ - * `C. Fleischmann et al. `_ - * `W. Windl et al. `_ - * `C. Freysoldt et al. `_ - * `G. da Costa et al. `_ - - to mention but a few. - - To arrive at a design of base classes and an application definition that can be used - for both real and simulated atom probe experiments it is worthwhile to recall concepts that are - related to events and (molecular) ions: - - * Pulsing events which are used to trigger ion extraction events. - * Physical events and corresponding signal triggered by an ion hitting the detector. - Some of these events are not necessarily caused by or directly correlated with an identifiable pulsing event. - * Processed ion hits which are the result of an algorithm that took the physical and pulsing events as input - and qualified some of these events as to be of sufficiently high quality to call them (molecular) ions that are - wortwhile to be considered further and eventually included in the reconstructed volume. - * Calibration and signal filtering steps applied to these processed ion hits as input which results in actually - selected (molecular) ions based on which an instance of a reconstruction is created. - * Correlation of these ions with a statistics and theoretical model of mass-to-charge-state ratio values - and charge states of the (molecular) ions to substantiate that some of these ions can be considered - as rangable ions and hence an iontype can be assigned to these via running peak finding algorithms - and subsequent peak labeling. In the field of atom probe this these peak identification methods - are known as ranging definitions. - - Not only in AMETEK/Cameca's IVAS/APSuite software, which the majority of atom probers use, these concepts - are well distinguished. However, the algorithms used to transform correlations between pulses and physical events - into actual events (detector hits) ions is a proprietary one - the so-called hit finding algorithm. - - Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme - where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier - i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. - That is evaporation_identifier values take the role of an implicit time and course of the experiment given that - ion extraction physically is a sequential process. - - There is a number of research groups who build own instruments and share different aspects of their technical - specifications and approaches how they apply data processing e.g.: - - * `M. Monajem et al. `_ - * `P. Stender et al. `_ - * `I. Dimkou et al. `_ - - to name but a few. - - Despite some of these activities embrace practices of open-source development, they use essentially the same - workflow that has been proposed by AMETEK/Cameca and its forerunner company Imago: A graphical user interface - software is used to explore and thus analyze reconstructed atom probe datasets. - - Specifically, software is used to correlate and interpret pulsing and physical events into processed ion hits. - Some of these ion hits are reported as (molecular) ions with ranged iontypes to yield a dataset based on which - scientific conclusions about the characterized material volume are made. Also here a reconstruction is - point cloud that serves as the proxy for the characterized material volume, i.e. the reconstruction is a model. - - By contrast, simulations of field-evaporation have the luxury to document the flight path and allow a following of all - the whereabouts of each ion evaporated if this is desired. This level of detail is currently not characterizable in experiment. - Thus, there is a divide between schemas describing simulations of atom probe vs measurements of atom probe. - We argue that this divide can be bridged with realizing the above-mentioned context and the realization that - similar concepts are used in both research realms with many concepts not only being similar but being exactly the same. - - A further argument to support this view is that computer simulations of atom probe usually are compared to reconstructed - datasets, either to the input configuration that served as the virtual specimen or to a real world atom probe experiment - and reconstructions computed from these. In both cases, the recorded simulated physical events of simulated ions hitting - a simulated detector is not the end of the research workflow but typically the input to apply additional algorithms such as - (spatial) filtering and reconstruction algorithms. - - Only the practical need for making ranging definitions is (at least as of now) not as much needed in field-evaporation - simulations than it is in real world measurements because each ion has a prescribed iontype in the simulation. - Be it a specifically charged nuclid or a molecular ion whose flight path the simulation resolves. - Although, in principle simpler though, we have to consider that this is caused by many assumptions made in the simulations. - Indeed, the multi-scale (time and space) aspects of the challenge that is the simulating of field-evaporation often require - simplifications because of otherwise too high becoming computing resource demands and existent knowledge gaps - in how to deal with all quantum physics complexities. Molecular ion dissociation upon flight is one such complexity. - Also the complexity of simulation setups is typically defined simpler in simulation (e.g. straight flight path assumption) - than in a measurement with a real instrument. In addition, simulation often also ignore objects and fields in the flight path - such as local electrodes or physical obstacles and electric fields (controlled or stray fields). - instrument(NXinstrument_apm): - type(NX_CHAR): - exists: recommended - fabrication(NXfabrication): - exists: recommended - vendor(NX_CHAR): - model(NX_CHAR): - serial_number(NX_CHAR): - reflectron(NXobject): - exists: optional - status(NX_CHAR): - local_electrode(NXlens_em): - exists: recommended - name(NX_CHAR): - fabrication(NXfabrication): - exists: optional - vendor(NX_CHAR): - model(NX_CHAR): - ion_detector(NXdetector): - exists: recommended - fabrication(NXfabrication): - exists: optional - vendor(NX_CHAR): - model(NX_CHAR): - pulser(NXobject): - exists: recommended - fabrication(NXfabrication): - exists: optional - vendor(NX_CHAR): - model(NX_CHAR): - sourceID(NXsource): - exists: [min, 0, max, 2] # conditionally required, sourceID only if pulse_mode is not voltage! - fabrication(NXfabrication): - exists: recommended - vendor(NX_CHAR): - model(NX_CHAR): - # wavelength and pulse_energy as dynamic/volatile quantities stored in event data part - comment(NX_CHAR): - doc: | - Free text field for additional comments. - status(NX_CHAR): - exists: recommended - doc: | - A statement whether the measurement was successful or failed prematurely. - quality(NX_CHAR): - exists: recommended - doc: | - CAnalysis.CResults.fQuality - events(NXobject): - exists: optional - # the case of allowing to not have event_data but only the above-mentioned instrument - # details can be useful to convey details about an atom probe instrument in general - doc: | - Group to hold instances of :ref:`NXevent_data_apm`. - - Which temporal granularity is adequate depends on the situation and research - question. Using a model which enables a collection of events offers the most - flexible way to cater for both atom probe experiments or simulation. - - To monitor the course of an ion extraction experiment (or simulation) - it makes sense to track time explicitly via time stamps or implicitly - via e.g. a clock inside the instrument, such as the clock of the pulser - and respective pulsing event identifier. - - As set and measured quantities typically change over time and we do not - yet know during the measurement which of the events have associated - (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the evaporated_identifier but as a - function of the (pulsing) event_identifier. - eventID(NXevent_data_apm): - exists: [min, 0, max, infty] - # all these cannot be made required because for LEAP only stored in RHIT/HITS - # but for M-TAP and Oxcart these pieces of information are available. - start_time(NX_DATE_TIME): - exists: recommended - end_time(NX_DATE_TIME): - exists: recommended - # delta_time(NX_NUMBER): - # pulse_identifier_offset(NX_INT): - # pulse_identifier(NX_INT): - instrument(NXinstrument_apm): - exists: recommended - reflectron(NXobject): - exists: recommended - voltage(NX_FLOAT): - # decelerate_electrode(NXlens_em): - local_electrode(NXlens_em): - exists: recommended - voltage(NX_FLOAT): - # ion_detector(NXdetector): - pulser(NXobject): - exists: recommended - pulse_mode(NX_CHAR): - pulse_frequency(NX_FLOAT): - # \@logged_against(NX_CHAR): - pulse_fraction(NX_FLOAT): - # \@logged_against(NX_CHAR): - pulse_voltage(NX_FLOAT): # ePOS, APT pulsed voltage - exists: optional # not required for voltage pulsing - dim: (n,) - # \@logged_against(NX_CHAR): - pulse_number(NX_UINT): - exists: optional - dim: (n,) - # \@logged_against(NX_CHAR): - standing_voltage(NX_FLOAT): # ePOS, APT standing voltage - exists: optional - dim: (n,) - # \@logged_against(NX_CHAR): - sourceID(NXsource): - exists: [min, 0, max, 2] # not required for voltage pulsing - pulse_energy(NX_FLOAT): - dim: (n,) - # \@logged_against(NX_CHAR): - # laser geometry at the moment has neither a worked out example - # nor any feedback from the community despite the work from B. Gault - # on laser atom probe was granted a Leibnitz award - stage(NXstage_lab): - specimen_temperature(NX_FLOAT): - analysis_chamber(NXchamber): - pressure(NX_FLOAT): - control(NXcollection): - exists: recommended - evaporation_control(NX_CHAR): - target_detection_rate(NX_NUMBER): - simulation(NXobject): - exists: optional - doc: | - Simulation of ion extraction from matter via laser and/or voltage pulsing. - # future possibility to reuse concepts from NXinstrument_apm again without - # the need for defining them again - atom_probe(NXroi): - exists: recommended # [min, 0, max, infty] - doc: | - A region-of-interest analyzed either during or after the session for which - specific processed data of the measured or simulated data are available. - # earlier comments here https://github.com/FAIRmat-NFDI/nexus_definitions/commit/a8602870f13f04b8befc902efb345afe650d8dd3 - initial_specimen(NXimage_set): - exists: recommended - doc: | - SEM or TEM image of the initial specimen (ideally taken prior data acquisition). - image_2d(NXdata): - \@signal(NX_CHAR): - \@axes(NX_CHAR): - \@AXISNAME_indices(NX_CHAR): - real(NX_NUMBER): - axis_j(NX_NUMBER): - dim: (n_j,) - \@long_name(NX_CHAR): - axis_i(NX_NUMBER): - dim: (n_i,) - \@long_name(NX_CHAR): - # could use a stack_3d(NXdata) to record time series of specimen shape evolution - raw_data(NXprocess): - exists: recommended - doc: | - For almost atom probe instruments (meta)data about raw data follow proprietary semantics. - Therefore, this group can currently be used only to point to these digital artifacts - in an effort to document all step of an analysis workflow. - - The physical quantities measured in an atom probe experiment are time-of-flight and - tuples of arrival_time_pairs as a function of the event chain on the pulser. - From these tuples hits are computed in a process called hit_finding. - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 0, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - # point at least to the proprietary artifact - serialized(NXserialized): - exists: recommended - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - exists: optional - algorithm(NX_CHAR): - exists: optional - # technical details of data the ion_detector collects - number_of_dld_wires(NX_UINT): - exists: recommended - doc: | - The number of wires in the detector. - unit: NX_UNITLESS - enumeration: [1, 2, 3] - dld_wire_names(NX_CHAR): - exists: optional - doc: | - Alias tuple (begin, end) of each DLD wire of the detector. - Order follows arrival_time_pairs. - dim: (n_dld, 2) - arrival_time_pairs(NX_NUMBER): - exists: optional - doc: | - Raw readings from the analog-to-digital-converter - timing circuits of the detector wires. - unit: NX_TIME - dim: (p, n_dld, 2) - hit_finding(NXprocess): - exists: recommended - doc: | - Configuration of and results obtained from a hit finding algorithm. - # we careful how we go about doing this here, we recommended to make some details of the hit_finding - # algorithm open namely the input and the output what the black box then does by AMETEK/Cameca - # does not have to be exposed (although this clearly is against FAIR principles but the scientific community - # is does not have the authority to decide which portions of proprietary code have to be public - # we can only make recommendations - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 0, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - # config of the hit_finding algorithm - serialized(NXserialized): - exists: recommended - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - # results of the hit_finding algorithm - hit_positions(NX_NUMBER): - exists: recommended - doc: | - Evaluated ion impact coordinates on the detector. - Use the depends_on field to specify which reference - frame the positions are defined. - unit: NX_LENGTH - dim: (p_out, 2) - \@depends_on(NX_CHAR): - doc: | - Defines in which reference frame the positions are defined. - total_event_golden(NX_UINT): - exists: optional - doc: | - CRunHeader.fTotalEventGolden - unit: NX_UNITLESS - total_event_incomplete(NX_UINT): - exists: optional - doc: | - CRunHeader.fTotalEventIncomplete - unit: NX_UNITLESS - total_event_multiple(NX_UINT): - exists: optional - doc: | - CRunHeader.fTotalEventMultiple - unit: NX_UNITLESS - total_event_partial(NX_UINT): - exists: optional - doc: | - CRunHeader.fTotalEventPartials - unit: NX_UNITLESS - total_event_record(NX_UINT): - exists: optional - doc: | - CRunHeader.fTotalEventRecords - unit: NX_UNITLESS - hit_quality_identifier(NX_UINT): - exists: optional - doc: | - Identifier used for each hit_quality type. - Following the order of hit_quality_types. - dim: (n_ht,) - hit_quality(NX_UINT): - exists: optional - doc: | - Hit quality identifier for each pulse. - Identifier have to be within hit_quality_identifier. - unit: NX_UNITLESS - dim: (p_out,) - hit_multiplicity(NX_UINT): - exists: optional - doc: | - This processing yields for each ion with how many others it evaporated - if these were collected on the same pulse. Extraction of multiple ions - on one pulse on different or even the same pixel of the detector are possible. - - Multiplicity must not be confused with how many atoms of the same element - a molecular ion contains. - unit: NX_UNITLESS - dim: (p_out,) - # the following two quantities are relicts from ePOS files used to give some - # insight into the results of the hit_finding algorithm of IVAS/APSuite but typically - # used only in the context to learn about the multiplicity of an ion. - # pulses_since_last_ion(NX_UINT): - # dim: (n,) - # pulse_identifier(NX_INT): - # dim: (n,) - # at this point the original set of events p has been filtered down to p_out - hit_spatial_filtering(NXprocess): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - serialized(NXserialized): - exists: optional - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - evaporation_identifier_offset(NX_INT): - doc: | - Integer used to name the first pulse to know if there is an - offset of the evaporation_identifier to zero. - - Identifiers can be defined either implicitly or explicitly. - For implicit indexing identifiers are defined on the interval - :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - Therefore, implicit identifier are completely defined by the value of - identifier_offset and cardinality. For example if identifier run from - -2 to 3 the value for identifier_offset is -2. - - For explicit indexing the field identifier has to be used. - Fortran-/Matlab- and C-/Python-style indexing have specific implicit - identifier conventions where identifier_offset is 1 and 0 respectively. - unit: NX_UNITLESS - evaporation_identifier(NX_INT): - doc: | - (Molecular) ion identifier which resolves the sequence in which - the ions were evaporated but taking into account that a hit_finding - and spatial_filtering was applied. - unit: NX_UNITLESS - dim: (n,) - hit_filter(NXcs_filter_boolean_mask): - exists: recommended - # use NXcs_filter needs conditionally an instance of concept ../../hit_finding - number_of_objects(NX_UINT): - bitdepth(NX_UINT): - mask(NX_UINT): - identifier(NX_INT): - # at this point the set of events p_out has been filtered down to n - voltage_and_bowl(NXprocess): - exists: recommended - doc: | - Configuration of and results obtained from a voltage-and-bowl time-of-flight correction algorithm. - - The voltage-and-bowl correction is a data post-processing step to correct ion impact - positions for flight path differences, detector biases, and nonlinearities. - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - serialized(NXserialized): - exists: optional - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - raw_tof(NX_FLOAT): - # currently cannot be made required because of being a quantity measured - # by proprietary hardware with proprietary semantics - exists: recommended - doc: | - Raw time-of-flight data without corrections. - dim: (n,) - # result - tof_zero_estimate(NX_FLOAT): - exists: optional - doc: | - The parameter :math:`t_0`, CAnalysis.CCalibMass.fT0Estimate - unit: NX_TIME - calibrated_tof(NX_FLOAT): - exists: recommended - doc: | - Calibrated time-of-flight. - dim: (n,) - mass_to_charge_conversion(NXprocess): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - serialized(NXserialized): - exists: recommended - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - # config/input - # results - mass_to_charge(NX_FLOAT): - dim: (n,) - reconstruction(NXapm_reconstruction): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - config(NXserialized): - exists: recommended - doc: | - For LEAP and IVAS/APSuite-based analyses root file which stores - the settings whereby an RHIT/HITS file can be used to regenerate the - reconstruction that is here referred to. - - The respective RHIT/HITS file should ideally be specified in the serialized - group of the hit_finding section of this application definition. - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - results(NXserialized): - exists: recommended - doc: | - For LEAP and IVAS/APSuite-based analyses the resulting typically - file with the reconstructed positions and (calibrated) mass-to-charge - state ratio values. - - For other data collection/analysis software the data artifact which comes - closest conceptually to AMETEK/Cameca's typical file formats. - - These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, - which should be stored alongside this record in the research data - management system. - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - # config/input - parameter(NX_CHAR): - exists: recommended - protocol_name(NX_CHAR): - exists: recommended - crystallographic_calibration(NX_CHAR): - exists: recommended - field_of_view(NX_FLOAT): - exists: recommended - reconstructed_positions(NX_FLOAT): - dim: (n, 3) - naive_discretization(NXprocess): - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - # config/input - # results - (NXdata): - \@signal(NX_CHAR): - \@axes(NX_CHAR): - \@AXISNAME_indices(NX_CHAR): - # dim: (3,) - # \@long_name: - title(NX_CHAR): - intensity(NX_NUMBER): - dim: (n_z, n_y, n_x) - axis_z(NX_FLOAT): - dim: (n_z,) - \@long_name(NX_CHAR): - axis_y(NX_FLOAT): - dim: (n_y,) - \@long_name(NX_CHAR): - axis_x(NX_FLOAT): - dim: (n_x,) - \@long_name(NX_CHAR): - ranging(NXapm_ranging): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - definitions(NXserialized): - exists: recommended - doc: | - The respective ranging definitions file RNG/RRNG/ENV/HDF5. - type(NX_CHAR): - path(NX_CHAR): - checksum(NX_CHAR): - algorithm(NX_CHAR): - mass_to_charge_distribution(NXprocess): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - min_incr_max(NX_FLOAT): - mass_spectrum(NXdata): - \@signal(NX_CHAR): - \@axes(NX_CHAR): - \@AXISNAME_indices(NX_CHAR): - # \@long_name(NX_CHAR): - title(NX_CHAR): - intensity(NX_NUMBER): - dim: (n_bins,) - \@long_name(NX_CHAR): - axis_mass_to_charge(NX_FLOAT): - dim: (n_bins,) - \@long_name(NX_CHAR): - background_quantification(NXprocess): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - background(NX_FLOAT): - exists: recommended - doc: | - (Out-of-sync) background levels in ppm/ns - reported by e.g. IVAS/APSuite for LEAP systems. - unit: NX_ANY # ppm/ns - mrp_value(NX_FLOAT): - exists: recommended - doc: | - MRP, mass-resolving power, `D. Larson et al. `_ (p282, Eqs. D.7 and D.8). - unit: NX_DIMENSIONLESS - mrp_mass_to_charge(NX_FLOAT): - exists: recommended - doc: | - MRP, at which mrp_value was specified. - unit: NX_ANY # u - # config/input - # results - # NEW ISSUE: add parameters of the background model - # in an e.g. work of A. London et al. - - peak_search(NXprocess): - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - peakID(NXpeak): - exists: [min, 0, max, infty] - label(NX_CHAR): - exists: recommended - description(NX_CHAR): - category(NX_CHAR): - exists: recommended - doc: | - Category for the peak offering a qualitative statement of the location of the peak - in light of limited mass-resolving power that is relevant for - composition quantification. See `D. Larson et al. (p172) `_ - for examples of each category: - - * 0, well-separated, :math:`^{10}B^{+}`, :math:`^{28}Si^{2+}` - * 1, close, but can be sufficiently separated for quantification in a LEAP system, :math:`^{94}Mo^{3+}`, :math:`^{63}Cu^{2+}` - * 2, closely overlapping, demands better than LEAP4000X MRP can provide :math:`^{14}N^{+}`, :math:`^{28}Si^{2+}` at different charge states - * 3, overlapped exactly due to multi-charge molecular species, :math:`^{16}{O_{2}}^{2+}`, :math:`^{16}O^{+}` - * 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, :math:`^{14}{N_{2}}^{+}`, :math:`^{28}Si^{+}` - * 5, overlapped, same charge state, any expectation of resolvability, :math:`^{54}Cr^{2+}`, :math:`^{54}Fe^{2+}` - - enumeration: [0, 1, 2, 3, 4, 5] - position(NX_NUMBER): - - # peak deconvolution(NXprocess): - peak_identification(NXprocess): # aka specify ranging definitions i.e. mqmin, mqmax intervals (ranges) and (molecular) ion candidates - exists: recommended - sequence_index(NX_POSINT): - exists: recommended - programID(NXprogram): - exists: [min, 1, max, infty] - program(NX_CHAR): - \@version(NX_CHAR): - number_of_ion_types(NX_UINT): - maximum_number_of_atoms_per_molecular_ion(NX_UINT): - ionID(NXion): - exists: [min, 1, max, 256] - nuclide_hash(NX_UINT): - charge_state(NX_INT): - charge_state_analysis(NXapm_charge_state_analysis): - exists: optional - # config - nuclides(NX_UINT): - mass_to_charge_range(NX_FLOAT): - min_half_life(NX_FLOAT): - min_abundance(NX_FLOAT): - min_abundance_product(NX_FLOAT): - sacrifice_isotopic_uniqueness(NX_BOOLEAN): - # results - charge_state(NX_INT): - nuclide_hash(NX_UINT): - mass(NX_FLOAT): - natural_abundance_product(NX_FLOAT): - shortest_half_life(NX_FLOAT): - mass_to_charge_range(NX_FLOAT): - nuclide_list(NX_UINT): - exists: recommended - name(NX_CHAR): - exists: recommended diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml index 8334236ad1..e632b76f11 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml @@ -18,9 +18,11 @@ NXapm_compositionspace_config(NXobject): exists: optional enumeration: [NXapm_compositionspace_config] config(NXobject): + (NXidentifier): + exists: optional analysis_identifier(NX_UINT): exists: recommended - reconstruction(NXnote): + reconstruction(NXserialized): doc: | Specification of the tomographic reconstruction used for this analysis. Typically, reconstructions in the field of atom probe tomography are communicated via @@ -44,7 +46,7 @@ NXapm_compositionspace_config(NXobject): doc: | Name of the node which resolves the mass-to-charge-state ratio values for each reconstructed ion to use for this analysis. - ranging(NXnote): + ranging(NXserialized): doc: | Specification of the ranging definitions used for this analysis. @@ -52,7 +54,7 @@ NXapm_compositionspace_config(NXobject): iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. type(NX_CHAR): exists: optional - identifier(NX_CHAR): + path(NX_CHAR): checksum(NX_CHAR): exists: recommended algorithm(NX_CHAR): @@ -140,13 +142,13 @@ NXapm_compositionspace_config(NXobject): point. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# b2999b7a1f4a3e8cedd9d811e64b9eda121c689ea42f8a688b6e676cb9a588c9 +# d9a35f2e23414520c75c5bcda07f70e886a1a0b18c19f7e7e78166fb789a2363 # # # # @@ -183,8 +185,9 @@ NXapm_compositionspace_config(NXobject): # # # +# # -# +# # # Specification of the tomographic reconstruction used for this analysis. # Typically, reconstructions in the field of atom probe tomography are communicated via @@ -210,7 +213,7 @@ NXapm_compositionspace_config(NXobject): # # # -# +# # # Specification of the ranging definitions used for this analysis. # @@ -218,7 +221,7 @@ NXapm_compositionspace_config(NXobject): # iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml index 9659ad99a7..4f1a6fcbcf 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml @@ -18,17 +18,19 @@ symbols: Total number of ions in the reconstructed dataset. type: group NXapm_compositionspace_results(NXobject): + # by default for appdefs the value of the exists keyword is required unless it is explicitly specified differently (NXentry): - exists: [min, 1, max, 1] + exists: ['min', '1', 'max', '1'] definition(NX_CHAR): \@version(NX_CHAR): exists: optional enumeration: [NXapm_compositionspace_results] + # can be used for the name of the tool and version but also # for if desired all the dependencies and libraries programID(NXprogram): - exists: [min, 1, max, infty] + exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): \@url(NX_CHAR): @@ -37,6 +39,7 @@ NXapm_compositionspace_results(NXobject): exists: optional analysis_identifier(NX_UINT): exists: recommended + # config config(NXserialized): doc: | @@ -48,6 +51,7 @@ NXapm_compositionspace_results(NXobject): exists: recommended checksum(NX_CHAR): exists: recommended + # results (NXuser): exists: optional @@ -72,7 +76,7 @@ NXapm_compositionspace_results(NXobject): these from the resources pointed to by parent_identifier or walk through eventually deeply nested groups in data instances. voxelization(NXprocess): - exists: [min, 0, max, 1] + exists: ['min', '0', 'max', '1'] doc: | Step during which the point cloud is discretized to compute element-specific composition fields. Iontypes are atomically decomposed to correctly account for the multiplicity of each element that @@ -88,52 +92,62 @@ NXapm_compositionspace_results(NXobject): enumeration: [3] cardinality(NX_POSINT): origin(NX_NUMBER): - dim: (grid_dim,) + dimensions: + dim: (grid_dim,) symmetry: enumeration: [cubic] cell_dimensions(NX_NUMBER): - dim: (grid_dim,) + dimensions: + dim: (grid_dim,) extent(NX_POSINT): - dim: (grid_dim,) + dimensions: + dim: (grid_dim,) identifier_offset(NX_INT): unit: NX_UNITLESS position(NX_NUMBER): + unit: NX_LENGTH doc: | Position of each cell in Euclidean space. - unit: NX_LENGTH - dim: (n_voxels, grid_dim) + dimensions: + dim: (n_voxels, grid_dim) coordinate(NX_INT): + unit: NX_DIMENSIONLESS doc: | Discrete coordinate of each voxel. - unit: NX_DIMENSIONLESS - dim: (n_voxels, grid_dim) + dimensions: + dim: (n_voxels, grid_dim) + # bounding box if needed voxel_identifier(NX_UINT): + unit: NX_UNITLESS doc: | For each ion, the identifier of the voxel into which the ion binned. - unit: NX_UNITLESS - dim: (n_ions) + dimensions: + dim: (n_ions,) weight(NX_NUMBER): + unit: NX_UNITLESS doc: | Total number of weight (counts for discretization with a rectangular transfer function) for the occupancy of each voxel with atoms. - unit: NX_UNITLESS - dim: (n_voxels,) + dimensions: + dim: (n_voxels,) elementID(NXion): - exists: [min, 1, max, infty] + exists: ['min', '1', 'max', 'unbounded'] name(NX_CHAR): doc: | Chemical symbol of the element from the periodic table. weight(NX_NUMBER): + unit: NX_UNITLESS doc: | Element-specific weight (counts for discretization with a rectangular transfer function) for the occupancy of each voxel with atoms of this element. - unit: NX_UNITLESS - dim: (n_voxels,) + dimensions: + dim: (n_voxels,) autophase(NXprocess): - exists: [min, 0, max, 1] + exists: ['min', '0', 'max', '1'] doc: | - Optional step during which the subsequent segmentation step is prepared to improve the segmentation. + Optional step during which the subsequent segmentation step is prepared to + improve the segmentation. sequence_index(NX_POSINT): enumeration: [2] result(NXdata): @@ -143,27 +157,31 @@ NXapm_compositionspace_results(NXobject): title(NX_CHAR): exists: recommended axis_feature_identifier(NX_UINT): + unit: NX_DIMENSIONLESS doc: | Element identifier stored sorted in descending order of feature importance. - unit: NX_DIMENSIONLESS - dim: (i,) + dimensions: + dim: (i,) \@long_name(NX_CHAR): doc: | Axis caption axis_feature_importance(NX_FLOAT): - doc: | - Element relative feature importance stored sorted in descending order of feature importance. unit: NX_DIMENSIONLESS - dim: (i,) + doc: | + Element relative feature importance stored sorted in descending order of feature + importance. + dimensions: + dim: (i,) \@long_name(NX_CHAR): doc: | Axis caption segmentation(NXprocess): - exists: [min, 0, max, 1] + exists: ['min', '0', 'max', '1'] doc: | - Step during which the voxel set is segmented into voxel sets with different chemical composition. + Step during which the voxel set is segmented into voxel sets with different + chemical composition. pca(NXprocess): - exists: [min, 1, max, 1] + exists: ['min', '1', 'max', '1'] doc: | PCA in the chemical space (essentially composition correlation analyses). sequence_index(NX_POSINT): @@ -175,15 +193,18 @@ NXapm_compositionspace_results(NXobject): title(NX_CHAR): exists: recommended axis_explained_variance(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | Explained variance values - unit: NX_DIMENSIONLESS - dim: (i,) + dimensions: + dim: (i,) axis_pca_dimension(NX_UINT): - doc: | - Elements identifier matching those from ENTRY/voxelization/elementID as the principal component analysis. unit: NX_UNITLESS - dim: (i,) + doc: | + Elements identifier matching those from ENTRY/voxelization/elementID as the + principal component analysis. + dimensions: + dim: (i,) ic_opt(NXprocess): doc: | Information criterion minimization. @@ -193,14 +214,15 @@ NXapm_compositionspace_results(NXobject): doc: | Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. n_ic_cluster(NX_UINT): + unit: NX_UNITLESS doc: | n_components argument of the Gaussian mixture model. - unit: NX_UNITLESS y_pred(NX_UINT): + unit: NX_UNITLESS doc: | y_pred return values of the computation. - unit: NX_UNITLESS - dim: (n_voxels,) + dimensions: + dim: (n_voxels,) result(NXdata): doc: | Information criterion as a function of number of n_ic_cluster aka dimensions. @@ -211,22 +233,25 @@ NXapm_compositionspace_results(NXobject): exists: recommended axis_aic(NX_FLOAT): exists: recommended + unit: NX_ANY doc: | Akaike information criterion values - unit: NX_ANY - dim: (i,) + dimensions: + dim: (i,) axis_bic(NX_FLOAT): + unit: NX_UNITLESS doc: | Bayes information criterion values - unit: NX_UNITLESS - dim: (i,) + dimensions: + dim: (i,) axis_dimension(NX_UINT): + unit: NX_UNITLESS doc: | Actual n_ic_cluster values used - unit: NX_UNITLESS - dim: (i,) + dimensions: + dim: (i,) clustering(NXprocess): - exists: [min, 0, max, 1] + exists: ['min', '0', 'max', '1'] doc: | Step during which the chemically segmented voxel sets are analyzed for their spatial organization into different spatial clusters of voxels in the same chemical set but representing individual object @@ -237,30 +262,34 @@ NXapm_compositionspace_results(NXobject): doc: | Respective DBScan clustering result for each segmentation/ic_opt case. cluster_analysisID(NXprocess): - exists: [min, 0, max, infty] + exists: ['min', '0', 'max', 'unbounded'] dbscanID(NXprocess): - exists: [min, 1, max, infty] # max as many as n_ic_cluster + exists: ['min', '1', 'max', 'unbounded'] epsilon(NX_FLOAT): - doc: | - The maximum distance between voxel pairs in a neighborhood to be considered connected. unit: NX_LENGTH - min_samples(NX_UINT): doc: | - The number of voxels in a neighborhood for a voxel to be considered as a core point. + The maximum distance between voxel pairs in a neighborhood to be considered + connected. + min_samples(NX_UINT): unit: NX_UNITLESS + doc: | + The number of voxels in a neighborhood for a voxel to be considered as a core + point. label(NX_INT): + unit: NX_UNITLESS doc: | Raw label return values - unit: NX_UNITLESS - dim: (k,) + dimensions: + dim: (k,) voxel(NX_UINT): + unit: NX_UNITLESS doc: | Voxel identifier Using these identifiers correlated element-wise with the values in the label array specifies for which voxel in the grid clusters from this process were found. - unit: NX_UNITLESS - dim: (n_voxels,) + dimensions: + dim: (n_voxels,) profiling(NXcs_profiling): exists: optional current_working_directory(NX_CHAR): @@ -270,6 +299,429 @@ NXapm_compositionspace_results(NXobject): end_time(NX_DATE_TIME): exists: recommended total_elapsed_time(NX_NUMBER): - # number_of_processes(NX_POSINT): - # number_of_threads(NX_POSINT): - # number_of_gpus(NX_POSINT): + + # number_of_processes(NX_POSINT): + # number_of_threads(NX_POSINT): + # number_of_gpus(NX_POSINT): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# 1601361961b96221780e9cbbda4652579aee0f5fd84bdab98c81e841ddea496e +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# The dimensionality of the grid. +# +# +# +# +# Total number of voxels. +# +# +# +# +# Total number of ions in the reconstructed dataset. +# +# +# +# +# Application definition for results of the CompositionSpace tool used in atom probe. +# +# * `A. Saxena et al. <https://www.github.com/eisenforschung/CompositionSpace.git>`_ +# +# This is an application definition for the common NFDI-MatWerk/FAIRmat infrastructure +# use case IUC09 that explores how to improve the organization and results storage of the +# CompositionSpace software using NeXus. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Configuration file that was used in this analysis. +# +# +# +# +# +# +# +# +# +# +# Contextualize back to the specimen from which the +# dataset was collected that was here analyzed with +# CompositionSpace tool. +# +# +# +# A qualifier whether the specimen is a real one or a virtual one. +# +# +# +# +# +# +# +# +# List of comma-separated elements from the periodic table that are +# contained in the specimen. If the specimen substance has multiple +# components, all elements from each component must be included in +# `atom_types`. +# +# The purpose of the field is to offer research data management systems an +# opportunity to parse the relevant elements without having to interpret +# these from the resources pointed to by parent_identifier or walk through +# eventually deeply nested groups in data instances. +# +# +# +# +# +# Step during which the point cloud is discretized to compute element-specific composition fields. +# Iontypes are atomically decomposed to correctly account for the multiplicity of each element that +# was ranged for each ion. +# +# Using a discretization grid that is larger than the average distance between reconstructed ion positions +# reduces computational costs. This is the key idea of the CompositionSpace tool compared to other methods +# used in atom probe for characterizing microstructural features that use the ion position data directly. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Position of each cell in Euclidean space. +# +# +# +# +# +# +# +# +# Discrete coordinate of each voxel. +# +# +# +# +# +# +# +# +# +# For each ion, the identifier of the voxel into which the ion binned. +# +# +# +# +# +# +# +# +# Total number of weight (counts for discretization with a rectangular transfer function) +# for the occupancy of each voxel with atoms. +# +# +# +# +# +# +# +# +# Chemical symbol of the element from the periodic table. +# +# +# +# +# Element-specific weight (counts for discretization with a rectangular transfer function) +# for the occupancy of each voxel with atoms of this element. +# +# +# +# +# +# +# +# +# +# Optional step during which the subsequent segmentation step is prepared to +# improve the segmentation. +# +# +# +# +# +# +# +# +# +# +# +# +# +# Element identifier stored sorted in descending order of feature importance. +# +# +# +# +# +# +# Axis caption +# +# +# +# +# +# Element relative feature importance stored sorted in descending order of feature +# importance. +# +# +# +# +# +# +# Axis caption +# +# +# +# +# +# +# +# Step during which the voxel set is segmented into voxel sets with different +# chemical composition. +# +# +# +# PCA in the chemical space (essentially composition correlation analyses). +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Explained variance values +# +# +# +# +# +# +# +# Elements identifier matching those from ENTRY/voxelization/elementID as the +# principal component analysis. +# +# +# +# +# +# +# +# +# +# Information criterion minimization. +# +# +# +# +# +# +# +# +# +# Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. +# +# +# +# n_components argument of the Gaussian mixture model. +# +# +# +# +# y_pred return values of the computation. +# +# +# +# +# +# +# +# +# Information criterion as a function of number of n_ic_cluster aka dimensions. +# +# +# +# +# +# +# +# Akaike information criterion values +# +# +# +# +# +# +# +# Bayes information criterion values +# +# +# +# +# +# +# +# Actual n_ic_cluster values used +# +# +# +# +# +# +# +# +# +# +# Step during which the chemically segmented voxel sets are analyzed for their spatial organization +# into different spatial clusters of voxels in the same chemical set but representing individual object +# not-necessarily watertight or topologically closed objects built from individual voxels. +# +# +# +# +# +# +# +# +# +# Respective DBScan clustering result for each segmentation/ic_opt case. +# +# +# +# +# +# The maximum distance between voxel pairs in a neighborhood to be considered +# connected. +# +# +# +# +# The number of voxels in a neighborhood for a voxel to be considered as a core +# point. +# +# +# +# +# Raw label return values +# +# +# +# +# +# +# +# Voxel identifier +# +# Using these identifiers correlated element-wise with the values in the label array +# specifies for which voxel in the grid clusters from this process were found. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml index 35837a3efa..4f37bea148 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml @@ -99,14 +99,14 @@ NXapm_paraprobe_clusterer_config(NXobject): distance(NX_CHAR): spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -114,7 +114,7 @@ NXapm_paraprobe_clusterer_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -122,7 +122,7 @@ NXapm_paraprobe_clusterer_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -317,7 +317,7 @@ NXapm_paraprobe_clusterer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7656aee2c9515f245a9b1031f90c7b2fbe6ccb25dda2c15c7cff115491ba1241 +# 0322fd640efdc4a02141e6b3a0d77a32039da1202bf6794892b00669475ba4b0 # # # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml index a69c2a6ebb..fe7ddf2316 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml @@ -34,14 +34,14 @@ NXapm_paraprobe_distancer_config(NXobject): # filter that are here tool-specific parameter spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -49,7 +49,7 @@ NXapm_paraprobe_distancer_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -57,7 +57,7 @@ NXapm_paraprobe_distancer_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -163,7 +163,7 @@ NXapm_paraprobe_distancer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# c1544b4249ed356b23729a485c3e97821d9ca9e23ba820e3087fa21808102968 +# 43ab448e71aec1b1b7b13f9fff2b7510faa87396399daf74f64476e17ac4cb80 # # # # # -# +# # # # @@ -233,7 +233,7 @@ NXapm_paraprobe_distancer_config(NXobject): # # # -# +# # # # @@ -241,7 +241,7 @@ NXapm_paraprobe_distancer_config(NXobject): # # # -# +# # # # @@ -249,7 +249,7 @@ NXapm_paraprobe_distancer_config(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml index 8e7ad4dfac..c8cbf8c28c 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml @@ -20,7 +20,6 @@ NXapm_paraprobe_intersector_config(NXobject): doc: | How many v_v_spatial_correlation tasks should the tool execute. v_v_spatial_correlationID(NXapm_paraprobe_tool_config): - nameType: partial exists: ['min', '1', 'max', 'unbounded'] doc: | Tracking volume_volume_spatial_correlations (v_v) is the process of building logical @@ -108,12 +107,11 @@ NXapm_paraprobe_intersector_config(NXobject): So while these four sub-sets contain different so-called types of features, key is that they were all generated for one set, here the current_set. - featureID(NXnote): - nameType: partial + featureID(NXserialized): exists: ['min', '1', 'max', '4'] doc: | Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the - members of the set as instances of NXcg_polyhedron_set. + members of the set as instances of NXcg_polyhedron. feature_type(NX_CHAR): doc: | Descriptive category explaining what these features are. @@ -165,8 +163,7 @@ NXapm_paraprobe_intersector_config(NXobject): So while these four sub-sets contain different so-called types of features key is that they were all generated for one set, here the next_set. - featureID(NXnote): - nameType: partial + featureID(NXserialized): exists: ['min', '1', 'max', '4'] feature_type(NX_CHAR): doc: | @@ -191,13 +188,12 @@ NXapm_paraprobe_intersector_config(NXobject): rank: 1 dim: (n_variable,) - # MK::tetrahedra volume intersection and tessellation and Nef polyhedra intersection are considered guru features + #MK::tetrahedra volume intersection and tessellation and Nef polyhedra intersection are considered guru features # and therefore currently supported only via modifying the C/C++ source code directly as one should know exactly # what one is doing here before using these functionalities common(NXapm_paraprobe_tool_common): status(NX_CHAR): programID(NXprogram): - nameType: partial exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -209,13 +205,13 @@ NXapm_paraprobe_intersector_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# be96bcc2e250fefbab6f1049369a6eeb9570d38a27c81c1309ec4190236e8cd4 +# fddda801044f2faa89da2349a7fbe9e8f5febac802740927208f2056b6f6e5d3 # # # # # -# Specifies the method whereby to decide if two objects intersect volumetrically. -# For reasons which are detailed in the supplementary material of `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, -# it is assumed by default that two objects intersect if they share at least one ion with the same evaporation ID (shared_ion). -# -# Alternatively, with specifying tetrahedra_intersections, the tool can perform an intersection analysis which attempts to -# tetrahedralize first each polyhedron. If successful, the tool then checks for at least one pair of intersecting tetrahedra -# to identify if two objects intersect or not. However, we found that these geometrical analyses can result in corner -# cases which the tetrahedralization library used in the tests (TetGen) was not unable to tetrahedralize successfully. -# These cases were virtually always associated with complicated non-convex polyhedra which had portions -# of the mesh that were connected by almost point like tubes of triangles. -# -# Finding more robust methods for computing intersections between not necessarily convex polyhedra might improve -# the situation in the future. For practical reasons we have thus deactivated the functionality of tetrahedra-tetrahedron -# intersections in paraprobe-intersector. +# Specifies the method whereby to decide if two objects intersect volumetrically. +# For reasons which are detailed in the supplementary material of `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_, +# it is assumed by default that two objects intersect if they share at least one ion with the same evaporation ID (shared_ion). +# +# Alternatively, with specifying tetrahedra_intersections, the tool can perform an intersection analysis which attempts to +# tetrahedralize first each polyhedron. If successful, the tool then checks for at least one pair of intersecting tetrahedra +# to identify if two objects intersect or not. However, we found that these geometrical analyses can result in corner +# cases which the tetrahedralization library used in the tests (TetGen) was not unable to tetrahedralize successfully. +# These cases were virtually always associated with complicated non-convex polyhedra which had portions +# of the mesh that were connected by almost point like tubes of triangles. +# +# Finding more robust methods for computing intersections between not necessarily convex polyhedra might improve +# the situation in the future. For practical reasons we have thus deactivated the functionality of tetrahedra-tetrahedron +# intersections in paraprobe-intersector. # # # @@ -297,81 +293,81 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# Specifies if the tool evaluates if objects intersect volumetrically. +# Specifies if the tool evaluates if objects intersect volumetrically. # # # # -# Specifies if the tool evaluates if objects lay closer to one another than -# threshold_proximity. +# Specifies if the tool evaluates if objects lay closer to one another than +# threshold_proximity. # # # # -# Specifies if the tool evaluates, provided that all (preprocessing tasks were successful), how intersecting -# or proximity related objects build sub-graphs. This is the feature that was used in `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_ -# for the high-throughput analyses of how many objects are coprecipitates in the sense that they are single, -# duplet, triplet, or high-order local groups. +# Specifies if the tool evaluates, provided that all (preprocessing tasks were successful), how intersecting +# or proximity related objects build sub-graphs. This is the feature that was used in `M. Kühbach et al. <https://arxiv.org/abs/2205.13510>`_ +# for the high-throughput analyses of how many objects are coprecipitates in the sense that they are single, +# duplet, triplet, or high-order local groups. # # # # # -# The maximum Euclidean distance between two objects below which they are -# considered within proximity. +# The maximum Euclidean distance between two objects below which they are +# considered within proximity. # # # # -# Specifies if the tool stores the so-called forward relations between nodes representing members of the -# current_set to nodes representing members of the next_set. +# Specifies if the tool stores the so-called forward relations between nodes representing members of the +# current_set to nodes representing members of the next_set. # # # # -# Specifies if the tool stores the so-called backward relations between nodes representing members of the -# next_set to nodes representing members of the current_set. +# Specifies if the tool stores the so-called backward relations between nodes representing members of the +# next_set to nodes representing members of the current_set. # # # # -# Current set stores a set of members, meshes of volumetric features, -# which will be checked for proximity and/or volumetric intersection, -# to members of the current_set. -# The meshes were generated as a result of some other meshing process. +# Current set stores a set of members, meshes of volumetric features, +# which will be checked for proximity and/or volumetric intersection, +# to members of the current_set. +# The meshes were generated as a result of some other meshing process. # # # -# This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k`) -# step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). +# This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k`) +# step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). # # # # # -# The total number of distinguished feature sets featureID. -# It is assumed that the members within all these featureID sets -# are representing a set together. As an example this set might represent -# all volumetric_features. However, users might have formed -# a subset of this set where individuals were regrouped. -# For paraprobe-nanochem this is the case for objects and proxies. -# Specifically, objects are distinguished further into those far -# from and those close to the edge of the dataset. -# Similarly, proxies are distinguished further into those far -# from and those close to the edge of the dataset. -# So while these four sub-sets contain different so-called types of -# features, key is that they were all generated for one set, here the -# current_set. +# The total number of distinguished feature sets featureID. +# It is assumed that the members within all these featureID sets +# are representing a set together. As an example this set might represent +# all volumetric_features. However, users might have formed +# a subset of this set where individuals were regrouped. +# For paraprobe-nanochem this is the case for objects and proxies. +# Specifically, objects are distinguished further into those far +# from and those close to the edge of the dataset. +# Similarly, proxies are distinguished further into those far +# from and those close to the edge of the dataset. +# So while these four sub-sets contain different so-called types of +# features, key is that they were all generated for one set, here the +# current_set. # # -# +# # -# Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the -# members of the set as instances of NXcg_polyhedron_set. +# Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the +# members of the set as instances of NXcg_polyhedron. # # # -# Descriptive category explaining what these features are. +# Descriptive category explaining what these features are. # # # @@ -387,15 +383,15 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# Absolute path to the group with geometry data in the HDF5 file referred to by -# path. +# Absolute path to the group with geometry data in the HDF5 file referred to by +# path. # # # # # -# Array of identifier whereby the path to the geometry data can be interferred -# automatically. +# Array of identifier whereby the path to the geometry data can be interferred +# automatically. # # # @@ -405,39 +401,39 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# Next set stores a set of members, meshes of volumetric features, -# which will be checked for proximity and/or volumetric intersection, -# to members of the next_set. -# The meshes were generated as a result of some other meshing process. +# Next set stores a set of members, meshes of volumetric features, +# which will be checked for proximity and/or volumetric intersection, +# to members of the next_set. +# The meshes were generated as a result of some other meshing process. # # # -# This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) -# step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). +# This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) +# step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). # # # # # -# The total number of distinguished feature sets featureID. -# It is assumed that the members within all these featureID sets -# are representing a set together. As an example this set might represent -# all volumetric_features. However, users might have formed -# a subset of this set where individuals were regrouped. -# For paraprobe-nanochem this is the case for objects and proxies. -# Specifically, objects are distinguished further into those far -# from and those close to the edge of the dataset. -# Similarly, proxies are distinguished further into those far -# from and those close to the edge of the dataset. -# So while these four sub-sets contain different so-called types of -# features key is that they were all generated for one set, here the -# next_set. +# The total number of distinguished feature sets featureID. +# It is assumed that the members within all these featureID sets +# are representing a set together. As an example this set might represent +# all volumetric_features. However, users might have formed +# a subset of this set where individuals were regrouped. +# For paraprobe-nanochem this is the case for objects and proxies. +# Specifically, objects are distinguished further into those far +# from and those close to the edge of the dataset. +# Similarly, proxies are distinguished further into those far +# from and those close to the edge of the dataset. +# So while these four sub-sets contain different so-called types of +# features key is that they were all generated for one set, here the +# next_set. # # -# +# # # -# Descriptive category explaining what these features are. +# Descriptive category explaining what these features are. # # # @@ -452,15 +448,15 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# Absolute path to the group with geometry data in the HDF5 file referred to by -# path. +# Absolute path to the group with geometry data in the HDF5 file referred to by +# path. # # # # # -# Array of identifier whereby the path to the geometry data can be interferred -# automatically. +# Array of identifier whereby the path to the geometry data can be interferred +# automatically. # # # @@ -469,12 +465,12 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml index 7e5cd19934..dfc5ec21cc 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml @@ -47,22 +47,24 @@ NXapm_paraprobe_nanochem_config(NXobject): # Although, this uses an efficient multithreaded algorithm the computation is costly. # Therefore, it can be advantageous for users to load an already computed delocalization. # This can be achieved with the load_existent option. + (NXidentifier): + exists: optional analysis_identifier(NX_UINT): exists: recommended - reconstruction(NXnote): + reconstruction(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): position(NX_CHAR): mass_to_charge(NX_CHAR): - ranging(NXnote): + ranging(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): ranging_definitions(NX_CHAR): - surface(NXnote): + surface(NXserialized): doc: | A precomputed triangulated surface mesh representing a model (of the surface) of the edge of the dataset. This model can be used to detect and control @@ -79,7 +81,7 @@ NXapm_paraprobe_nanochem_config(NXobject): doc: | Absolute path in the (HDF5) file that points to the array of vertex indices for the triangles in that triangle_set. - surface_distance(NXnote): + surface_distance(NXserialized): exists: recommended doc: | Distance between each ion and triangulated surface mesh. @@ -90,14 +92,14 @@ NXapm_paraprobe_nanochem_config(NXobject): distance(NX_CHAR): spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -105,7 +107,7 @@ NXapm_paraprobe_nanochem_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -113,7 +115,7 @@ NXapm_paraprobe_nanochem_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -138,15 +140,17 @@ NXapm_paraprobe_nanochem_config(NXobject): TODO enumeration: [resolve_unknown, resolve_point, resolve_atom, resolve_element, resolve_element_charge, resolve_isotope, resolve_isotope_charge] nuclide_whitelist(NX_UINT): + unit: NX_UNITLESS doc: | TODO - unit: NX_UNITLESS - # dim: ??? + + # dim: ??? charge_state_whitelist(NX_INT): + unit: NX_DIMENSIONLESS doc: | TODO - unit: NX_DIMENSIONLESS - # dim: ??? + + # dim: ??? iontype_filter(NXmatch_filter): exists: optional method(NX_CHAR): @@ -161,7 +165,7 @@ NXapm_paraprobe_nanochem_config(NXobject): doc: | Compute delocalization or load an existent one from input. enumeration: [compute, load_existent] - input(NXnote): + input(NXserialized): doc: | Serialized result of an already computed delocalization which is for performance reasons here just loaded and not computed again. @@ -205,7 +209,6 @@ NXapm_paraprobe_nanochem_config(NXobject): Unused values in each row of the matrix are nullified. Nuclides are identified as hashed nuclide (see :ref:`NXion`) for further details. dimensions: - rank: 2 dim: (n_ityp_deloc_cand, n_ivec_max) grid_resolution(NX_FLOAT): unit: NX_LENGTH @@ -214,7 +217,6 @@ NXapm_paraprobe_nanochem_config(NXobject): on a cuboidal 3D grid (:ref:`NXcg_grid`). The tool performs as many delocalization computations as values are specified in grid_resolution. dimensions: - rank: 1 dim: (n_grid,) kernel_size(NX_UINT): unit: NX_UNITLESS @@ -230,7 +232,6 @@ NXapm_paraprobe_nanochem_config(NXobject): The tool performs as many delocalization computations as values are specified in kernel_variance. dimensions: - rank: 1 dim: (n_var,) normalization(NX_CHAR): doc: | @@ -463,22 +464,24 @@ NXapm_paraprobe_nanochem_config(NXobject): Noteworthy to mention is that the method used is conceptually similar to the work of `Z. Peng et al. `_ and related work (DCOM algorithm) by `P. Felfer et al. `_. Compared to these implementations paraprobe-nanochem uses inspection functionalities which detect potential geometric inconsistencies or self-interactions of the evolved DCOM mesh. + (NXidentifier): + exists: optional analysis_identifier(NX_UINT): exists: recommended - reconstruction(NXnote): + reconstruction(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): position(NX_CHAR): mass_to_charge(NX_CHAR): - ranging(NXnote): + ranging(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): ranging_definitions(NX_CHAR): - surface(NXnote): + surface(NXserialized): exists: optional doc: | A precomputed triangulated surface mesh representing a model (of the surface) @@ -498,14 +501,14 @@ NXapm_paraprobe_nanochem_config(NXobject): of vertex indices for the triangles in that triangle_set. spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -513,7 +516,7 @@ NXapm_paraprobe_nanochem_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -521,7 +524,7 @@ NXapm_paraprobe_nanochem_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -560,7 +563,7 @@ NXapm_paraprobe_nanochem_config(NXobject): can be parsed by paraprobe-parmsetup-nanochem to match the here required formatting in control_points. enumeration: [default, control_point_file] - control_point(NXnote): + control_point(NXserialized): doc: | Details about the control point file used. type(NX_CHAR): @@ -589,7 +592,6 @@ NXapm_paraprobe_nanochem_config(NXobject): doc: | Array of nuclide iontypes to filter. dimensions: - rank: 2 dim: (n_fct_filter_cand, n_ivec_max) number_of_iterations(NX_UINT): unit: NX_UNITLESS @@ -602,7 +604,6 @@ NXapm_paraprobe_nanochem_config(NXobject): which specify how the initial triangles of the mesh should be iteratively refined by edge splitting and related mesh refinement operations. dimensions: - rank: 1 dim: (n_fct_iterations,) target_dcom_radius(NX_FLOAT): unit: NX_LENGTH @@ -616,7 +617,6 @@ NXapm_paraprobe_nanochem_config(NXobject): self-intersections may occur. The tool detects these and stops in a controlled manner so that the user can repeat the analyses with using a different parameterization. dimensions: - rank: 1 dim: (n_fct_iterations,) target_smoothing_step(NX_UINT): unit: NX_UNITLESS @@ -628,7 +628,6 @@ NXapm_paraprobe_nanochem_config(NXobject): parameter values to be used in the first DCOM iteration. The first entry of each array those for the second DCOM iteration and so on and so forth. dimensions: - rank: 1 dim: (n_fct_iterations,) oned_profile(NXapm_paraprobe_tool_config): exists: ['min', '0', 'max', '1'] @@ -662,22 +661,24 @@ NXapm_paraprobe_nanochem_config(NXobject): even watertight distance-based segmentation in combination with again intersection of triangles and convex polyhedra is a robust but currently not implemented method to quantify intersections. + (NXidentifier): + exists: optional analysis_identifier(NX_UINT): exists: recommended - reconstruction(NXnote): + reconstruction(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): position(NX_CHAR): mass_to_charge(NX_CHAR): - ranging(NXnote): + ranging(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): ranging_definitions(NX_CHAR): - surface(NXnote): + surface(NXserialized): exists: optional doc: | A precomputed triangulated surface mesh representing a model (of the surface) @@ -695,7 +696,7 @@ NXapm_paraprobe_nanochem_config(NXobject): doc: | Absolute path in the (HDF5) file that points to the array of vertex indices for the triangles in that triangle_set. - surface_distance(NXnote): + surface_distance(NXserialized): exists: recommended doc: | Distance between each ion and triangulated surface mesh. @@ -708,7 +709,7 @@ NXapm_paraprobe_nanochem_config(NXobject): Absolute path in the (HDF5) file that points to the distance values. The tool assumes that the values are stored in the same order as points (ions). - feature(NXnote): + feature(NXserialized): exists: optional doc: | A precomputed triangulated mesh of the feature representing a model of the @@ -745,7 +746,7 @@ NXapm_paraprobe_nanochem_config(NXobject): patches of an iso-surface. method(NX_CHAR): match(NX_NUMBER): - feature_distance(NXnote): + feature_distance(NXserialized): exists: optional doc: | To enable an additional filtration of specific parts of the feature @@ -762,14 +763,14 @@ NXapm_paraprobe_nanochem_config(NXobject): points (ions). spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -777,7 +778,7 @@ NXapm_paraprobe_nanochem_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -785,7 +786,7 @@ NXapm_paraprobe_nanochem_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -819,22 +820,19 @@ NXapm_paraprobe_nanochem_config(NXobject): equivalent to the classical approach in atom probe to place ROIs for composition analyses via positioning and rotating them via a graphical user interface (such as in IVAS / AP Suite). - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): # dimensionality(NX_POSINT): # cardinality(NX_POSINT): identifier_offset(NX_INT): center(NX_NUMBER): dimensions: - rank: 2 dim: (n_rois, 3) height(NX_NUMBER): dimensions: - rank: 2 dim: (n_rois, 3) radii(NX_NUMBER): dimensions: - rank: 1 dim: (n_rois,) # could add other shapes in the future if necessary @@ -862,7 +860,6 @@ NXapm_paraprobe_nanochem_config(NXobject): common(NXapm_paraprobe_tool_common): status(NX_CHAR): programID(NXprogram): - nameType: partial exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -874,13 +871,13 @@ NXapm_paraprobe_nanochem_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fdab5afc493335e16828cc3c0302ba652f4aa12cef076c43105eb9f4d41d6618 +# e844ff49e54d0093434bcfe7d622bd812628d3a692880b7bdb6ef5a4621fe98b # # # +# # -# +# # # # @@ -982,14 +980,14 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # # # # -# +# # # A precomputed triangulated surface mesh representing a model (of the surface) # of the edge of the dataset. This model can be used to detect and control @@ -1012,7 +1010,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Distance between each ion and triangulated surface mesh. # @@ -1024,7 +1022,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1032,7 +1030,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1040,7 +1038,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1048,7 +1046,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1062,6 +1060,38 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # +# +# +# Configuration for the algorithm that defines how the multiplicity of all +# those ions are computed that are considered in the delocalization. +# +# +# +# TODO +# +# +# +# +# +# +# +# +# +# +# +# +# +# TODO +# +# +# +# +# +# TODO +# +# +# +# # # # @@ -1080,7 +1110,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Serialized result of an already computed delocalization which is for performance # reasons here just loaded and not computed again. @@ -1126,7 +1156,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # Unused values in each row of the matrix are nullified. # Nuclides are identified as hashed nuclide (see :ref:`NXion`) for further details. # -# +# # # # @@ -1137,7 +1167,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # on a cuboidal 3D grid (:ref:`NXcg_grid`). The tool performs as many delocalization # computations as values are specified in grid_resolution. # -# +# # # # @@ -1155,7 +1185,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # The tool performs as many delocalization computations as values are specified # in kernel_variance. # -# +# # # # @@ -1436,8 +1466,9 @@ NXapm_paraprobe_nanochem_config(NXobject): # paraprobe-nanochem uses inspection functionalities which detect potential geometric # inconsistencies or self-interactions of the evolved DCOM mesh. # +# # -# +# # # # @@ -1445,14 +1476,14 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # # # # -# +# # # A precomputed triangulated surface mesh representing a model (of the surface) # of the edge of the dataset. This model can be used to detect and control @@ -1477,7 +1508,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1485,7 +1516,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1493,7 +1524,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1501,7 +1532,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1542,7 +1573,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Details about the control point file used. # @@ -1582,7 +1613,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # Array of nuclide iontypes to filter. # -# +# # # # @@ -1599,7 +1630,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # which specify how the initial triangles of the mesh should be iteratively # refined by edge splitting and related mesh refinement operations. # -# +# # # # @@ -1614,7 +1645,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # self-intersections may occur. The tool detects these and stops in a controlled # manner so that the user can repeat the analyses with using a different parameterization. # -# +# # # # @@ -1627,7 +1658,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # parameter values to be used in the first DCOM iteration. The first entry of each array # those for the second DCOM iteration and so on and so forth. # -# +# # # # @@ -1664,8 +1695,9 @@ NXapm_paraprobe_nanochem_config(NXobject): # intersection of triangles and convex polyhedra is a robust but currently # not implemented method to quantify intersections. # +# # -# +# # # # @@ -1673,14 +1705,14 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # # # # -# +# # # A precomputed triangulated surface mesh representing a model (of the surface) # of the edge of the dataset. This model can be used to detect and control @@ -1703,7 +1735,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Distance between each ion and triangulated surface mesh. # @@ -1719,7 +1751,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # A precomputed triangulated mesh of the feature representing a model of the # interface at which to place ROIs to profile. This can be the mesh of an @@ -1765,7 +1797,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # To enable an additional filtration of specific parts of the feature # mesh it is recommended to feed precomputed distances of each ion to @@ -1785,7 +1817,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1793,7 +1825,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1801,7 +1833,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1809,7 +1841,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # @@ -1840,24 +1872,24 @@ NXapm_paraprobe_nanochem_config(NXobject): # for composition analyses via positioning and rotating them via # a graphical user interface (such as in IVAS / AP Suite). # -# +# # # # -# +# # # # # # -# +# # # # # # -# +# # # # @@ -1898,7 +1930,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml index 71dd323863..e1069aa879 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml @@ -41,7 +41,6 @@ NXapm_paraprobe_nanochem_results(NXobject): # tasks delocalizationID(NXdelocalization): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] window(NXcs_filter_boolean_mask): number_of_ions(NX_UINT): @@ -136,7 +135,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (3,) - bounding_box(NXcg_hexahedron_set): + bounding_box(NXcg_hexahedron): doc: | A tight axis-aligned bounding box about the grid. is_axis_aligned(NX_BOOLEAN): @@ -238,9 +237,8 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 1 dim: (6,) - # MK::how to avoid storing it for once in NeXus for H5Web and for XDMF in ParaView ? + #MK::how to avoid storing it for once in NeXus for H5Web and for XDMF in ParaView ? scalar_field_magn_SUFFIX(NXdata): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] doc: | The result of the delocalization :math:`\Phi = f(x, y, z)` based on which subsequent iso-surfaces @@ -315,7 +313,6 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 1 dim: (i,) scalar_field_grad_SUFFIX(NXdata): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] doc: | The three-dimensional gradient :math:`\nabla \Phi`. @@ -382,9 +379,8 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 1 dim: (i,) - # MK:: + #MK:: iso_surfaceID(NXisocontour): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] doc: | An iso-surface is the boundary between two regions across which the magnitude of a @@ -411,7 +407,7 @@ NXapm_paraprobe_nanochem_results(NXobject): DOI or details write not_further_specified, or give at least a free-text description. The program and version used is the specific paraprobe-nanochem. - triangle_soup(NXcg_triangle_set): + triangle_soup(NXcg_triangle): exists: optional doc: | The resulting triangle soup computed via marching cubes. @@ -468,7 +464,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (n_f_tri_xdmf,) - vertex_normal(NXcg_unit_normal_set): + vertex_normal(NXcg_unit_normal): exists: optional normals(NX_FLOAT): unit: NX_DIMENSIONLESS @@ -491,9 +487,9 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 1 dim: (j,) - # edge_normal(NXcg_unit_normal_set): + # edge_normal(NXcg_unit_normal): # exists: optional - face_normal(NXcg_unit_normal_set): + face_normal(NXcg_unit_normal): exists: optional normals(NX_FLOAT): unit: NX_DIMENSIONLESS @@ -679,7 +675,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (i,) - obb(NXcg_hexahedron_set): + obb(NXcg_hexahedron): exists: optional doc: | An oriented bounding box (OBB) to each object. @@ -721,8 +717,8 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 2 dim: (k, 3) - # MK::again we have no effective way to pinpoint the n_rows - # MK::namely k != i each OBB has eight vertices + #MK::again we have no effective way to pinpoint the n_rows + #MK::namely k != i each OBB has eight vertices xdmf_topology(NX_UINT): unit: NX_UNITLESS dimensions: @@ -733,8 +729,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (k,) - objectID(NXcg_polyhedron_set): - nameType: partial + objectID(NXcg_polyhedron): exists: ['min', '0', 'max', 'unbounded'] polyhedron(NXcg_face_list_data_structure): @@ -789,7 +784,6 @@ NXapm_paraprobe_nanochem_results(NXobject): rank: 1 dim: (i,) ionID(NXion): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] charge_state(NX_INT): @@ -849,8 +843,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (4,) - mesh_stateID(NXcg_triangle_set): - nameType: partial + mesh_stateID(NXcg_triangle): exists: ['min', '0', 'max', 'unbounded'] doc: | The triangle surface mesh representing the interface model. @@ -968,7 +961,7 @@ NXapm_paraprobe_nanochem_results(NXobject): mask(NX_UINT): # results - xdmf_cylinder(NXcg_polyhedron_set): + xdmf_cylinder(NXcg_polyhedron): doc: | The ROIs are defined as cylinders for the computations. To visualize these we discretize them into regular n-gons. Using for instance 360-gons, i.e. a regular n-gon with 360 edges, @@ -1042,7 +1035,6 @@ NXapm_paraprobe_nanochem_results(NXobject): if all ions are built from a single atom only. roiID(NXobject): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial signed_distance(NX_FLOAT): unit: NX_LENGTH doc: | @@ -1061,13 +1053,12 @@ NXapm_paraprobe_nanochem_results(NXobject): common(NXapm_paraprobe_tool_common): status(NX_CHAR): analysis_identifier(NX_UINT): - config(NXnote): + config(NXserialized): type(NX_CHAR): path(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): programID(NXprogram): - nameType: partial exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -1081,7 +1072,6 @@ NXapm_paraprobe_nanochem_results(NXobject): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): userID(NXuser): - nameType: partial exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -1108,13 +1098,13 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# cc84efcb4713ea73b25baac2d30ecde427d5f18a73459cc2838797e159a6239a +# 4f0c86e1b684c38da662dae0e2ce450be35822c2e16e6d9c05eda16aba035c5f # # # # # -# The total number of faces of triangles. +# The total number of faces of triangles. # # # # -# The total number of XDMF values to represent all faces of triangles via XDMF. +# The total number of XDMF values to represent all faces of triangles via XDMF. # # # # -# The total number of entries in a feature dictionary. +# The total number of entries in a feature dictionary. # # # # -# The total number of volumetric features. +# The total number of volumetric features. # # # # -# The total number of member distinguished when reporting composition. +# The total number of member distinguished when reporting composition. # # # # -# The total number of ROIs placed in an oned_profile task. +# The total number of ROIs placed in an oned_profile task. # # # # -# Application definition for results files of the paraprobe-nanochem tool. -# -# This tool is part of the paraprobe-toolbox. Inspect the base class :ref:`NXapm_paraprobe_tool_results`. +# Application definition for results files of the paraprobe-nanochem tool. +# +# This tool is part of the paraprobe-toolbox. Inspect the base class :ref:`NXapm_paraprobe_tool_results`. # # # @@ -1208,7 +1198,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # @@ -1222,11 +1212,11 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# How were results of the kernel-density estimation normalized: -# * total, the total number (intensity) of ions or elements. -# * candidates, the total number (intensity) of ions matching weighting_model -# * composition, the value for candidates divided by the value for total, -# * concentration, the value for candidates divided by the volume of the cell. +# How were results of the kernel-density estimation normalized: +# * total, the total number (intensity) of ions or elements. +# * candidates, the total number (intensity) of ions matching weighting_model +# * composition, the value for candidates divided by the value for total, +# * concentration, the value for candidates divided by the volume of the cell. # # # @@ -1237,7 +1227,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The discretized domain/grid on which the delocalization is applied. +# The discretized domain/grid on which the delocalization is applied. # # # @@ -1248,7 +1238,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The total number of cells/voxels of the grid. +# The total number of cells/voxels of the grid. # # # @@ -1258,7 +1248,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The symmetry of the lattice defining the shape of the unit cell. +# The symmetry of the lattice defining the shape of the unit cell. # # # @@ -1266,8 +1256,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The unit cell dimensions according to the coordinate system defined under -# coordinate_system. +# The unit cell dimensions according to the coordinate system defined under +# coordinate_system. # # # @@ -1275,12 +1265,12 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Number of unit cells along each of the d-dimensional base vectors. -# The total number of cells, or grid points has to be the cardinality. -# If the grid has an irregular number of grid positions in each direction, -# as it could be for instance the case of a grid where all grid points -# outside some masking primitive are removed, this extent field should -# not be used. Instead use the coordinate field. +# Number of unit cells along each of the d-dimensional base vectors. +# The total number of cells, or grid points has to be the cardinality. +# If the grid has an irregular number of grid positions in each direction, +# as it could be for instance the case of a grid where all grid points +# outside some masking primitive are removed, this extent field should +# not be used. Instead use the coordinate field. # # # @@ -1289,17 +1279,17 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Integer which specifies the first index to be used for distinguishing identifiers for cells. -# Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are -# defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. -# For explicit indexing the identifier array has to be defined. +# Integer which specifies the first index to be used for distinguishing identifiers for cells. +# Identifiers are defined either implicitly or explicitly. For implicit indexing the identifiers are +# defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. +# For explicit indexing the identifier array has to be defined. # # # # -# Halfwidth of the kernel about the central voxel. -# The shape of the kernel is that of a cuboid -# of extent 2*kernel_extent[i] + 1 in each dimension i. +# Halfwidth of the kernel about the central voxel. +# The shape of the kernel is that of a cuboid +# of extent 2*kernel_extent[i] + 1 in each dimension i. # # # @@ -1307,7 +1297,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Functional form of the kernel (Ansatz function). +# Functional form of the kernel (Ansatz function). # # # @@ -1315,8 +1305,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Standard deviation :math:`\sigma_i` of the kernel in each dimension -# in the paraprobe coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. +# Standard deviation :math:`\sigma_i` of the kernel in each dimension +# in the paraprobe coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. # # # @@ -1324,60 +1314,60 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Expectation value :math:`\mu_i` of the kernel in each dimension -# in the paraprobe coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. +# Expectation value :math:`\mu_i` of the kernel in each dimension +# in the paraprobe coordinate_system with i = 0 is x, i = 1 is y, i = 2 is z. # # # # # -# +# # -# A tight axis-aligned bounding box about the grid. +# A tight axis-aligned bounding box about the grid. # # # -# For atom probe should be set to true. +# For atom probe should be set to true. # # # # -# Integer which specifies the first index to be used for distinguishing -# hexahedra. Identifiers are defined either implicitly or explicitly. -# For implicit indexing the identifiers are defined on the interval -# :math:`[identifier\_offset, identifier\_offset + c - 1]`. -# For explicit indexing the identifier array has to be defined. +# Integer which specifies the first index to be used for distinguishing +# hexahedra. Identifiers are defined either implicitly or explicitly. +# For implicit indexing the identifiers are defined on the interval +# :math:`[identifier\_offset, identifier\_offset + c - 1]`. +# For explicit indexing the identifier array has to be defined. # # # # # -# Integer which specifies the first index to be used for distinguishing -# identifiers for vertices. Identifiers are defined either implicitly or explicitly. -# For implicit indexing the identifiers are defined on the interval -# :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array -# has to be defined. +# Integer which specifies the first index to be used for distinguishing +# identifiers for vertices. Identifiers are defined either implicitly or explicitly. +# For implicit indexing the identifiers are defined on the interval +# :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array +# has to be defined. # # # # -# Integer which specifies the first index to be used for distinguishing -# identifiers for faces. Identifiers are defined either implicitly or explicitly. -# For implicit indexing the identifiers are defined on the interval -# :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array -# has to be defined. +# Integer which specifies the first index to be used for distinguishing +# identifiers for faces. Identifiers are defined either implicitly or explicitly. +# For implicit indexing the identifiers are defined on the interval +# :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing the identifier array +# has to be defined. # # # # -# Positions of the vertices. -# Users are encouraged to reduce the vertices to unique set of positions -# and vertices as this supports a more efficient storage of the geometry data. -# It is also possible though to store the vertex positions naively in which -# case vertices_are_unique is likely False. -# Naively here means that one for example stores each vertex of a triangle -# mesh even though many vertices are shared between triangles and thus -# the positions of these vertices do not have to be duplicated. +# Positions of the vertices. +# Users are encouraged to reduce the vertices to unique set of positions +# and vertices as this supports a more efficient storage of the geometry data. +# It is also possible though to store the vertex positions naively in which +# case vertices_are_unique is likely False. +# Naively here means that one for example stores each vertex of a triangle +# mesh even though many vertices are shared between triangles and thus +# the positions of these vertices do not have to be duplicated. # # # @@ -1386,16 +1376,16 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Array of identifiers from vertices which describe each face. -# -# The first entry is the identifier of the start vertex of the first face, -# followed by the second vertex of the first face, until the last vertex -# of the first face. Thereafter, the start vertex of the second face, the -# second vertex of the second face, and so on and so forth. -# -# Therefore, summating over the number_of_vertices, allows to extract -# the vertex identifiers for the i-th face on the following index interval -# of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. +# Array of identifiers from vertices which describe each face. +# +# The first entry is the identifier of the start vertex of the first face, +# followed by the second vertex of the first face, until the last vertex +# of the first face. Thereafter, the start vertex of the second face, the +# second vertex of the second face, and so on and so forth. +# +# Therefore, summating over the number_of_vertices, allows to extract +# the vertex identifiers for the i-th face on the following index interval +# of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. # # # @@ -1404,10 +1394,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Six equally formatted sextets chained together. For each sextett the first entry is an -# XDMF primitive topology key (here 5 for polygon), the second entry the XDMF -# primitive count value (here 4 because each face is a quad). -# The remaining four values are the vertex indices. +# Six equally formatted sextets chained together. For each sextett the first entry is an +# XDMF primitive topology key (here 5 for polygon), the second entry the XDMF +# primitive count value (here 4 because each face is a quad). +# The remaining four values are the vertex indices. # # # @@ -1415,15 +1405,15 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# How many distinct boundaries are distinguished? -# Most grids discretize a cubic or cuboidal region. In this case -# six sides can be distinguished, each making an own boundary. +# How many distinct boundaries are distinguished? +# Most grids discretize a cubic or cuboidal region. In this case +# six sides can be distinguished, each making an own boundary. # # # # -# Name of the boundaries. E.g. left, right, front, back, bottom, top, -# The field must have as many entries as there are number_of_boundaries. +# Name of the boundaries. E.g. left, right, front, back, bottom, top, +# The field must have as many entries as there are number_of_boundaries. # # # @@ -1431,14 +1421,14 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The boundary conditions for each boundary: -# -# 0 - undefined -# 1 - open -# 2 - periodic -# 3 - mirror -# 4 - von Neumann -# 5 - Dirichlet +# The boundary conditions for each boundary: +# +# 0 - undefined +# 1 - open +# 2 - periodic +# 3 - mirror +# 4 - von Neumann +# 5 - Dirichlet # # # @@ -1446,20 +1436,20 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# -# +# +# # -# The result of the delocalization :math:`\Phi = f(x, y, z)` based on which subsequent iso-surfaces -# will be computed. In commercial software so far there is no possibility to export this information. -# -# If the intensity for all matches of the weighting_model are summarized name this NXdata instance -# scalar_field_magn_total. -# -# If the intensity is reported for each iontype one can avoid many subsequent -# computations as individual intensities can be reinterpreted using a different weighting_model in -# down-stream usage of the here reported values (e.g. with Python scripting). -# In this case name the individual NXdata instances scalar_field_magn_ionID using the ID of the ion as -# per the configuration of the ranging definitions used. +# The result of the delocalization :math:`\Phi = f(x, y, z)` based on which subsequent iso-surfaces +# will be computed. In commercial software so far there is no possibility to export this information. +# +# If the intensity for all matches of the weighting_model are summarized name this NXdata instance +# scalar_field_magn_total. +# +# If the intensity is reported for each iontype one can avoid many subsequent +# computations as individual intensities can be reinterpreted using a different weighting_model in +# down-stream usage of the here reported values (e.g. with Python scripting). +# In this case name the individual NXdata instances scalar_field_magn_ionID using the ID of the ion as +# per the configuration of the ranging definitions used. # # # @@ -1469,7 +1459,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The actual delocalized intensity values. +# The actual delocalized intensity values. # # # @@ -1479,7 +1469,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Cell center of mass positions along x. +# Cell center of mass positions along x. # # # @@ -1487,7 +1477,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Cell center of mass positions along y. +# Cell center of mass positions along y. # # # @@ -1495,7 +1485,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Cell center of mass positions along z. +# Cell center of mass positions along z. # # # @@ -1503,7 +1493,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Intensity of the field at given point +# Intensity of the field at given point # # # @@ -1511,8 +1501,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Center of mass positions of each voxel for rendering the scalar field -# via XDMF in e.g. Paraview. +# Center of mass positions of each voxel for rendering the scalar field +# via XDMF in e.g. Paraview. # # # @@ -1521,18 +1511,18 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# XDMF topology for rendering in combination with xdmf_xyz the scalar field -# via XDMF in e.g. Paraview. +# XDMF topology for rendering in combination with xdmf_xyz the scalar field +# via XDMF in e.g. Paraview. # # # # # # -# +# # -# The three-dimensional gradient :math:`\nabla \Phi`. -# Follow the naming convention of scalar_field_magn_SUFFIX to report parallel structures. +# The three-dimensional gradient :math:`\nabla \Phi`. +# Follow the naming convention of scalar_field_magn_SUFFIX to report parallel structures. # # # @@ -1542,7 +1532,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The actual point-wise component values. +# The actual point-wise component values. # # # @@ -1553,7 +1543,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Cell center of mass positions along x. +# Cell center of mass positions along x. # # # @@ -1561,7 +1551,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Cell center of mass positions along y. +# Cell center of mass positions along y. # # # @@ -1569,7 +1559,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Cell center of mass positions along z. +# Cell center of mass positions along z. # # # @@ -1577,8 +1567,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The gradient vector formatted for direct visualization via XDMF in e.g. -# Paraview. +# The gradient vector formatted for direct visualization via XDMF in e.g. +# Paraview. # # # @@ -1587,8 +1577,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Center of mass positions of each voxel for rendering the scalar field gradient -# via XDMF in e.g. Paraview. +# Center of mass positions of each voxel for rendering the scalar field gradient +# via XDMF in e.g. Paraview. # # # @@ -1597,58 +1587,58 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# XDMF topology for rendering in combination with xdmf_xyz the scalar field -# via XDFM in e.g. Paraview. +# XDMF topology for rendering in combination with xdmf_xyz the scalar field +# via XDFM in e.g. Paraview. # # # # # # -# -# +# +# # -# An iso-surface is the boundary between two regions across which the magnitude of a -# scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. -# -# For applications in atom probe microscopy, the location and shape of such a boundary (set) -# is typically approximated by discretization - triangulation to be specific. -# -# This yields a complex of not necessarily connected geometric primitives. -# Paraprobe-nanochem approximates this complex with a soup of triangles. +# An iso-surface is the boundary between two regions across which the magnitude of a +# scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. +# +# For applications in atom probe microscopy, the location and shape of such a boundary (set) +# is typically approximated by discretization - triangulation to be specific. +# +# This yields a complex of not necessarily connected geometric primitives. +# Paraprobe-nanochem approximates this complex with a soup of triangles. # # # # -# The threshold or iso-contour value :math:`\varphi`. +# The threshold or iso-contour value :math:`\varphi`. # # # # -# Details about the specific marching cubes algorithm that was used for computing -# the iso-surface. +# Details about the specific marching cubes algorithm that was used for computing +# the iso-surface. # # # -# Reference to the specific implementation of marching cubes used. -# The value placed here should be a DOI. If there are no specific -# DOI or details write not_further_specified, or give at least a -# free-text description. The program and version used is the -# specific paraprobe-nanochem. +# Reference to the specific implementation of marching cubes used. +# The value placed here should be a DOI. If there are no specific +# DOI or details write not_further_specified, or give at least a +# free-text description. The program and version used is the +# specific paraprobe-nanochem. # # # -# +# # -# The resulting triangle soup computed via marching cubes. +# The resulting triangle soup computed via marching cubes. # # # # # -# Integer which specifies the first index to be used for distinguishing triangles. -# Identifiers are defined either implicitly or explicitly. For implicit indexing the -# identifiers are defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. +# Integer which specifies the first index to be used for distinguishing triangles. +# Identifiers are defined either implicitly or explicitly. For implicit indexing the +# identifiers are defined on the interval :math:`[identifier\_offset, identifier\_offset + c - 1]`. # # # @@ -1658,13 +1648,13 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Positions of the vertices. -# -# Users are encouraged to reduce the vertices to a unique set as this may -# result in a more efficient storage of the geometry data. -# It is also possible though to store the vertex positions naively in which -# case vertices_are_unique is likely False. Naively here means that each -# vertex is stored even though many share the same positions. +# Positions of the vertices. +# +# Users are encouraged to reduce the vertices to a unique set as this may +# result in a more efficient storage of the geometry data. +# It is also possible though to store the vertex positions naively in which +# case vertices_are_unique is likely False. Naively here means that each +# vertex is stored even though many share the same positions. # # # @@ -1673,16 +1663,16 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Array of identifiers from vertices which describe each face. -# -# The first entry is the identifier of the start vertex of the first face, -# followed by the second vertex of the first face, until the last vertex -# of the first face. Thereafter, the start vertex of the second face, the -# second vertex of the second face, and so on and so forth. -# -# Therefore, summating over the number_of_vertices, allows to extract -# the vertex identifiers for the i-th face on the following index interval -# of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. +# Array of identifiers from vertices which describe each face. +# +# The first entry is the identifier of the start vertex of the first face, +# followed by the second vertex of the first face, until the last vertex +# of the first face. Thereafter, the start vertex of the second face, the +# second vertex of the second face, and so on and so forth. +# +# Therefore, summating over the number_of_vertices, allows to extract +# the vertex identifiers for the i-th face on the following index interval +# of the faces array: :math:`[\sum_{i = 0}^{i = n-1}, \sum_{i=0}^{i = n}]`. # # # @@ -1690,18 +1680,18 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# A list of as many tuples of XDMF topology key, XDMF number -# of vertices and a triple of vertex indices specifying each -# triangle. The total number of entries is n_f_tri * (1+1+3). +# A list of as many tuples of XDMF topology key, XDMF number +# of vertices and a triple of vertex indices specifying each +# triangle. The total number of entries is n_f_tri * (1+1+3). # # # # # -# +# # # -# Direction of each normal. +# Direction of each normal. # # # @@ -1710,24 +1700,24 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Qualifier how which specifically oriented normal to its -# primitive each normal represents. -# -# * 0 - undefined -# * 1 - outer -# * 2 - inner +# Qualifier how which specifically oriented normal to its +# primitive each normal represents. +# +# * 0 - undefined +# * 1 - outer +# * 2 - inner # # # # # # -# -# +# +# # # -# Direction of each normal. +# Direction of each normal. # # # @@ -1736,12 +1726,12 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Qualifier how which specifically oriented normal to its -# primitive each normal represents. -# -# * 0 - undefined -# * 1 - outer -# * 2 - inner +# Qualifier how which specifically oriented normal to its +# primitive each normal represents. +# +# * 0 - undefined +# * 1 - outer +# * 2 - inner # # # @@ -1749,32 +1739,32 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Triangle normals are oriented in the direction of the -# gradient vector of the local delocalized scalar field. -# :math:`\sum_{x, y, z} {\nabla{c}_i}^2`. +# Triangle normals are oriented in the direction of the +# gradient vector of the local delocalized scalar field. +# :math:`\sum_{x, y, z} {\nabla{c}_i}^2`. # # # # # # +# doc: | +# Triangle normals are oriented in the direction of the +# gradient vector of the local delocalized scalar field. +# Sum of squared values of cross product of triangle normal +# construction. +# unit: NX_ANY +# dim: (k,)--> # # -# Triangle normals are oriented in the direction of the -# gradient vector of the local delocalized scalar field. -# The projection variable here describes the cosine of the -# angle between the gradient direction and the normal -# direction vector. -# This is a descriptor of how parallel the projection is -# that is especially useful to document those triangles -# for whose the projection is almost perpendicular. +# Triangle normals are oriented in the direction of the +# gradient vector of the local delocalized scalar field. +# The projection variable here describes the cosine of the +# angle between the gradient direction and the normal +# direction vector. +# This is a descriptor of how parallel the projection is +# that is especially useful to document those triangles +# for whose the projection is almost perpendicular. # # # @@ -1788,9 +1778,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Array of edge length values. For each triangle the edge length -# is reported for the edges traversed according to the sequence -# in which vertices are indexed in triangles. +# Array of edge length values. For each triangle the edge length +# is reported for the edges traversed according to the sequence +# in which vertices are indexed in triangles. # # # @@ -1799,10 +1789,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Array of interior angle values. For each triangle the angle -# is reported for the angle opposite to the edges which are -# traversed according to the sequence in which vertices -# are indexed in triangles. +# Array of interior angle values. For each triangle the angle +# is reported for the angle opposite to the edges which are +# traversed according to the sequence in which vertices +# are indexed in triangles. # # # @@ -1811,7 +1801,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The center of mass of each triangle. +# The center of mass of each triangle. # # # @@ -1820,36 +1810,36 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Iso-surfaces of arbitrary scalar three-dimensional fields can show a complicated topology. -# Paraprobe-nanochem can run a DBScan-like clustering algorithm which performs a -# connectivity analysis on the triangle soup representation of such iso-surface. -# This may yield a set of connected features whose individual surfaces are discretized -# by a triangulated mesh each. Such volumetric features can be processed further using -# paraprobe-nanochem using a workflow with at most two steps. -# -# In the first step, the tool distinguishes three types of (v) i.e. volumetric features: -# -# 1. So-called objects, i.e. necessarily watertight features represented by polyhedra. -# These objects were already watertight within the triangulated iso-surface. -# 2. So-called proxies, i.e. features that were not necessarily watertight within the triangulated -# iso-surface but were subsequently replaced by a watertight mesh using polyhedral mesh -# processing operations (hole filling, refinement, fairing operations). -# 3. Remaining triangle surface meshes or parts of these of arbitrary shape and cardinality -# that are not transformable into proxies or for which no transformation into proxies was -# instructed. -# -# These features can be interpreted as microstructural features. Some of them may be precipitates, -# some of them may be poles, some of them may be segments of dislocation lines or other -# crystal defects which are decorated (or not) with solutes. -# -# In the second step, the tool can be used to analyze the proximity of these objects to a -# model of the surface (edge) of the dataset. +# Iso-surfaces of arbitrary scalar three-dimensional fields can show a complicated topology. +# Paraprobe-nanochem can run a DBScan-like clustering algorithm which performs a +# connectivity analysis on the triangle soup representation of such iso-surface. +# This may yield a set of connected features whose individual surfaces are discretized +# by a triangulated mesh each. Such volumetric features can be processed further using +# paraprobe-nanochem using a workflow with at most two steps. +# +# In the first step, the tool distinguishes three types of (v) i.e. volumetric features: +# +# 1. So-called objects, i.e. necessarily watertight features represented by polyhedra. +# These objects were already watertight within the triangulated iso-surface. +# 2. So-called proxies, i.e. features that were not necessarily watertight within the triangulated +# iso-surface but were subsequently replaced by a watertight mesh using polyhedral mesh +# processing operations (hole filling, refinement, fairing operations). +# 3. Remaining triangle surface meshes or parts of these of arbitrary shape and cardinality +# that are not transformable into proxies or for which no transformation into proxies was +# instructed. +# +# These features can be interpreted as microstructural features. Some of them may be precipitates, +# some of them may be poles, some of them may be segments of dislocation lines or other +# crystal defects which are decorated (or not) with solutes. +# +# In the second step, the tool can be used to analyze the proximity of these objects to a +# model of the surface (edge) of the dataset. # # # -# The identifier which the triangle_soup connectivity analysis -# returned, which constitutes the first step of the -# volumetric_feature identification process. +# The identifier which the triangle_soup connectivity analysis +# returned, which constitutes the first step of the +# volumetric_feature identification process. # # # @@ -1857,7 +1847,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The array of keywords of feature_type dictionary. +# The array of keywords of feature_type dictionary. # # # @@ -1865,8 +1855,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The array of values for each keyword of the -# feature_type dictionary. +# The array of values for each keyword of the +# feature_type dictionary. # # # @@ -1874,10 +1864,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The array of controlled keywords, need to be from -# feature_type_dict_keyword, which specify which type -# each feature triangle cluster belongs to. -# Keep in mind that not each feature is an object or proxy. +# The array of controlled keywords, need to be from +# feature_type_dict_keyword, which specify which type +# each feature triangle cluster belongs to. +# Keep in mind that not each feature is an object or proxy. # # # @@ -1885,7 +1875,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The explicit identifier of features. +# The explicit identifier of features. # # # @@ -1893,21 +1883,21 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# In all situations instances of the parent NXprocess group are returned with a very similar -# information structuring and thus we here replace the template name FEATURE -# with one of the following types feature-specific group names: -# -# * objects, objects, irrespective their distance to the surface -# * objects_close_to_edge, sub-set of v_feature_object close surface -# * objects_far_from_edge, sub-set of v_feature_object not close to the surface -# * proxies, proxies, irrespective their distance to the surface -# * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface -# * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface +# In all situations instances of the parent NXprocess group are returned with a very similar +# information structuring and thus we here replace the template name FEATURE +# with one of the following types feature-specific group names: +# +# * objects, objects, irrespective their distance to the surface +# * objects_close_to_edge, sub-set of v_feature_object close surface +# * objects_far_from_edge, sub-set of v_feature_object not close to the surface +# * proxies, proxies, irrespective their distance to the surface +# * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface +# * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface # # # -# Explicit identifier of the feature a sub-set of the feature_identifier in the -# parent group. +# Explicit identifier of the feature a sub-set of the feature_identifier in the +# parent group. # # # @@ -1915,19 +1905,19 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Volume of the feature. NaN for non-watertight objects. +# Volume of the feature. NaN for non-watertight objects. # # # # # -# +# # -# An oriented bounding box (OBB) to each object. +# An oriented bounding box (OBB) to each object. # # # -# Edge length of the oriented bounding box from largest to smallest value. +# Edge length of the oriented bounding box from largest to smallest value. # # # @@ -1936,8 +1926,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Oriented bounding box aspect ratio. -# YX versus ZY or second-largest over largest and smallest over second largest. +# Oriented bounding box aspect ratio. +# YX versus ZY or second-largest over largest and smallest over second largest. # # # @@ -1946,9 +1936,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Position of the geometric center, which often is but -# not necessarily has to be the center_of_mass of the -# hexahedrally-shaped sample/sample part. +# Position of the geometric center, which often is but +# not necessarily has to be the center_of_mass of the +# hexahedrally-shaped sample/sample part. # # # @@ -1957,8 +1947,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# A simple approach to describe the entire set of hexahedra when the main intention -# is to store the shape of the hexahedra for visualization. +# A simple approach to describe the entire set of hexahedra when the main intention +# is to store the shape of the hexahedra for visualization. # # # @@ -1966,8 +1956,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # @@ -1980,7 +1970,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # # # # -# Count or weight which, when divided by total, yields the composition of this element, -# nuclide, or (molecular) ion within the volume of the feature/object. +# Count or weight which, when divided by total, yields the composition of this element, +# nuclide, or (molecular) ion within the volume of the feature/object. # # # @@ -2067,16 +2057,16 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The multiplicity whereby the ion position is accounted for -# irrespective whether the ion is considered as a decorator -# of the interface or not. -# As an example, with atom probe it is typically not possible -# to resolve the positions of the atoms which arrive at the detector -# as molecular ions. Therefore, an exemplar molecular ion of two carbon -# atoms can be considered to have a multiplicity of two to account that -# this molecular ion contributes two carbon atoms at the reconstructed -# location considering that the spatial resolution of atom probe -# experiments is limited. +# The multiplicity whereby the ion position is accounted for +# irrespective whether the ion is considered as a decorator +# of the interface or not. +# As an example, with atom probe it is typically not possible +# to resolve the positions of the atoms which arrive at the detector +# as molecular ions. Therefore, an exemplar molecular ion of two carbon +# atoms can be considered to have a multiplicity of two to account that +# this molecular ion contributes two carbon atoms at the reconstructed +# location considering that the spatial resolution of atom probe +# experiments is limited. # # # @@ -2084,8 +2074,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The multiplicity whereby the ion position is accounted for when -# the ion is considered one which is a decorator of the interface. +# The multiplicity whereby the ion position is accounted for when +# the ion is considered one which is a decorator of the interface. # # # @@ -2093,25 +2083,25 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The equation of the plane that is fitted initially. +# The equation of the plane that is fitted initially. # # # -# The four parameter :math:`ax + by + cz + d = 0` which define the plane. +# The four parameter :math:`ax + by + cz + d = 0` which define the plane. # # # # # # -# +# # -# The triangle surface mesh representing the interface model. -# Exported at state before or after the next DCOM step. +# The triangle surface mesh representing the interface model. +# Exported at state before or after the next DCOM step. # # # -# Was this state exported before or after the next DCOM step. +# Was this state exported before or after the next DCOM step. # # # @@ -2141,7 +2131,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Direction of each vertex normal. +# Direction of each vertex normal. # # # @@ -2150,12 +2140,12 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Qualifier which details how specifically oriented the -# face normal is with respect to its primitive (triangle): -# -# * 0 - undefined -# * 1 - outer -# * 2 - inner +# Qualifier which details how specifically oriented the +# face normal is with respect to its primitive (triangle): +# +# * 0 - undefined +# * 1 - outer +# * 2 - inner # # # @@ -2169,7 +2159,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Direction of each face normal. +# Direction of each face normal. # # # @@ -2178,12 +2168,12 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Qualifier which details how specifically oriented the -# face normal is with respect to its primitive (triangle): -# -# * 0 - undefined -# * 1 - outer -# * 2 - inner +# Qualifier which details how specifically oriented the +# face normal is with respect to its primitive (triangle): +# +# * 0 - undefined +# * 1 - outer +# * 2 - inner # # # @@ -2202,9 +2192,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Array of edge length values. For each triangle the edge length is -# reported for the edges traversed according to the sequence -# in which vertices are indexed in triangles. +# Array of edge length values. For each triangle the edge length is +# reported for the edges traversed according to the sequence +# in which vertices are indexed in triangles. # # # @@ -2213,9 +2203,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Array of interior angle values. For each triangle the angle is -# reported for the angle opposite to the edges which are traversed -# according to the sequence in which vertices are indexed in triangles. +# Array of interior angle values. For each triangle the angle is +# reported for the angle opposite to the edges which are traversed +# according to the sequence in which vertices are indexed in triangles. # # # @@ -2231,19 +2221,19 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # -# The ROIs are defined as cylinders for the computations. To visualize these we discretize -# them into regular n-gons. Using for instance 360-gons, i.e. a regular n-gon with 360 edges, -# resolves the lateral surface of each cylinder such that their renditions are smooth in -# visualization software like Paraview. +# The ROIs are defined as cylinders for the computations. To visualize these we discretize +# them into regular n-gons. Using for instance 360-gons, i.e. a regular n-gon with 360 edges, +# resolves the lateral surface of each cylinder such that their renditions are smooth in +# visualization software like Paraview. # # # # # -# Position of the geometric center, which often is but not -# necessarily has to be the center_of_mass of the polyhedra. +# Position of the geometric center, which often is but not +# necessarily has to be the center_of_mass of the polyhedra. # # # @@ -2252,8 +2242,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# The orientation of the ROI defined via a vector which points along -# the cylinder axis and whose length is the height of the cylinder. +# The orientation of the ROI defined via a vector which points along +# the cylinder axis and whose length is the height of the cylinder. # # # @@ -2263,7 +2253,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# XDMF support to enable colouring each ROI by its identifier. +# XDMF support to enable colouring each ROI by its identifier. # # # @@ -2271,7 +2261,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# XDMF support to enable colouring each ROI whether it has edge contact or not. +# XDMF support to enable colouring each ROI whether it has edge contact or not. # # # @@ -2279,7 +2269,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# XDMF support to enable colouring each ROI by its number of atoms. +# XDMF support to enable colouring each ROI by its number of atoms. # # # @@ -2287,7 +2277,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# XDMF support to enable colouring each ROI by its number of ions. +# XDMF support to enable colouring each ROI by its number of ions. # # # @@ -2295,22 +2285,22 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Distance and iontype-specific processed data for each ROI. -# Arrays signed_distance and nuclide_hash are sorted by increasing -# distance. -# Array nuclide_hash reports one hash for each atom of each isotope. -# Effectively, this can yield to groups of values on signed_distance -# with the same distance value as molecular ions are reported decomposed -# into their atoms. -# Therefore, the XDMF support fields number_of_atoms and number_of_ions -# are only expected to display pairwise the same values respectively, -# if all ions are built from a single atom only. +# Distance and iontype-specific processed data for each ROI. +# Arrays signed_distance and nuclide_hash are sorted by increasing +# distance. +# Array nuclide_hash reports one hash for each atom of each isotope. +# Effectively, this can yield to groups of values on signed_distance +# with the same distance value as molecular ions are reported decomposed +# into their atoms. +# Therefore, the XDMF support fields number_of_atoms and number_of_ions +# are only expected to display pairwise the same values respectively, +# if all ions are built from a single atom only. # -# +# # # -# Sorted in increasing order projected along the positive direction -# of the ROI as defined by orientation in the parent group. +# Sorted in increasing order projected along the positive direction +# of the ROI as defined by orientation in the parent group. # # # @@ -2318,7 +2308,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# Hashvalue as defined in :ref:`NXion`. +# Hashvalue as defined in :ref:`NXion`. # # # @@ -2331,13 +2321,13 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # # # -# +# # # # @@ -2351,9 +2341,9 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # -# If used, metadata of at least the person who performed this analysis. +# If used, metadata of at least the person who performed this analysis. # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml index c5c82e9296..59c5e379b9 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml @@ -41,14 +41,14 @@ NXapm_paraprobe_ranger_config(NXobject): # filter spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -56,7 +56,7 @@ NXapm_paraprobe_ranger_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -64,7 +64,7 @@ NXapm_paraprobe_ranger_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -220,7 +220,7 @@ NXapm_paraprobe_ranger_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6ff641838cd8f9e766fa687e8da14cd73057561d6f8c28e40fcf841e38c752b7 +# 06557aa7674bd79aaff50c0fd9fa1442490dde36f049e44b610e6ba19e364e15 # # # # # -# +# # # # @@ -302,7 +302,7 @@ NXapm_paraprobe_ranger_config(NXobject): # # # -# +# # # # @@ -310,7 +310,7 @@ NXapm_paraprobe_ranger_config(NXobject): # # # -# +# # # # @@ -318,7 +318,7 @@ NXapm_paraprobe_ranger_config(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml index c49a4a91ca..4924bf236a 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_selector_config.yaml @@ -34,14 +34,14 @@ NXapm_paraprobe_selector_config(NXobject): # filter that represent here also the tool-specific config spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -49,7 +49,7 @@ NXapm_paraprobe_selector_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -57,7 +57,7 @@ NXapm_paraprobe_selector_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -96,7 +96,7 @@ NXapm_paraprobe_selector_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 9f78e5c2c657c039426d3523f3181e17e859777c4910bdf814ffafce12cc6397 +# 6afb643069be7929aec360e4e35654217e7dda5f4eef011d07d22e26c8c6ac70 # # # # # -# +# # # # @@ -166,7 +166,7 @@ NXapm_paraprobe_selector_config(NXobject): # # # -# +# # # # @@ -174,7 +174,7 @@ NXapm_paraprobe_selector_config(NXobject): # # # -# +# # # # @@ -182,7 +182,7 @@ NXapm_paraprobe_selector_config(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_config.yaml index 16b3ea7f6c..27774846d9 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_config.yaml @@ -94,14 +94,14 @@ NXapm_paraprobe_spatstat_config(NXobject): with the edge_distance threshold when placing ROI about source ions. spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -109,7 +109,7 @@ NXapm_paraprobe_spatstat_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -117,7 +117,7 @@ NXapm_paraprobe_spatstat_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -270,7 +270,7 @@ NXapm_paraprobe_spatstat_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7970d7ef4e5fcd24825c673aa87df5ca586815b98ae7c13f9a874e7c1b48932c +# ebb2adcad98a496f132f8ff37bfc6041c54372a2a43b33070acecf0960dd8bec # # # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml index 0e381b0710..5f42a2fdab 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml @@ -38,14 +38,14 @@ NXapm_paraprobe_surfacer_config(NXobject): # filter that are here tool-specific parameter spatial_filter(NXspatial_filter): windowing_method(NX_CHAR): - hexahedron_set(NXcg_hexahedron_set): + hexahedron_set(NXcg_hexahedron): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): identifier_offset(NX_INT): hexahedra(NXcg_face_list_data_structure): vertices(NX_UINT): - cylinder_set(NXcg_cylinder_set): + cylinder_set(NXcg_cylinder): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -53,7 +53,7 @@ NXapm_paraprobe_surfacer_config(NXobject): center(NX_NUMBER): height(NX_NUMBER): radii(NX_NUMBER): - ellipsoid_set(NXcg_ellipsoid_set): + ellipsoid_set(NXcg_ellipsoid): exists: optional dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -61,7 +61,7 @@ NXapm_paraprobe_surfacer_config(NXobject): center(NX_NUMBER): half_axes_radii(NX_NUMBER): orientation(NX_NUMBER): - polyhedron_set(NXcg_polyhedron_set): + polyhedron_set(NXcg_polyhedron): exists: optional # TODO @@ -178,7 +178,7 @@ NXapm_paraprobe_surfacer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 22584d36a5b5f662bb3ad6c60b0b6d195c9e4d2857f5e07526b35ab84ddaf34e +# b501cfb46acc9fc32b65d9ec4954c39d9c56c0118849bcbab85cee2fcf3323b1 # # # # # -# +# # # # @@ -258,7 +258,7 @@ NXapm_paraprobe_surfacer_config(NXobject): # # # -# +# # # # @@ -266,7 +266,7 @@ NXapm_paraprobe_surfacer_config(NXobject): # # # -# +# # # # @@ -274,7 +274,7 @@ NXapm_paraprobe_surfacer_config(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml index 9df193f3c7..58ce841bd6 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml @@ -97,7 +97,7 @@ NXapm_paraprobe_surfacer_results(NXobject): offset(NX_NUMBER): exists: optional unit: NX_LENGTH - triangle_set(NXcg_triangle_set): + triangle_set(NXcg_triangle): exists: optional doc: | The set of triangles in the coordinate system paraprobe @@ -138,7 +138,7 @@ NXapm_paraprobe_surfacer_results(NXobject): doc: | The volume which the triangulated surface mesh encloses if that mesh is watertight. - interior_tetrahedra(NXcg_tetrahedron_set): + interior_tetrahedra(NXcg_tetrahedron): exists: optional doc: | The set of tetrahedra which represent the interior volume @@ -223,7 +223,7 @@ NXapm_paraprobe_surfacer_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ca34a5157db8e6c9f46b686bf6d57930d008bdf896f2f83a02ee353d7584bd01 +# 89312d5651b0800b1ef9d1707d964f32433f01d8374a08a1098006b27ed7d578 # # # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml index d546999b61..30f9bbb58b 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml @@ -40,7 +40,7 @@ NXapm_paraprobe_tessellator_results(NXobject): mask(NX_UINT): # results - wall(NXcg_hexahedron_set): + wall(NXcg_hexahedron): exists: recommended doc: | The (tight) axis-aligned bounding box about the point cloud. @@ -60,7 +60,7 @@ NXapm_paraprobe_tessellator_results(NXobject): dimensions: rank: 1 dim: (3,) - voronoi_cells(NXcg_polyhedron_set): + voronoi_cells(NXcg_polyhedron): exists: optional dimensionality(NX_POSINT): unit: NX_UNITLESS @@ -274,7 +274,7 @@ NXapm_paraprobe_tessellator_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# b081bda676f53f985af253e4b79d3be52d410d5f4ef83f497fffbf4486e7440d +# 42a204540cc1fd534ff40313303b3a4fbceda59cf3ad3df48d422ebed32b32c0 # # # -# +# # # The (tight) axis-aligned bounding box about the point cloud. # @@ -373,7 +373,7 @@ NXapm_paraprobe_tessellator_results(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_ranging.yaml b/contributed_definitions/nyaml/NXapm_ranging.yaml deleted file mode 100644 index 1246600c98..0000000000 --- a/contributed_definitions/nyaml/NXapm_ranging.yaml +++ /dev/null @@ -1,74 +0,0 @@ -category: base -doc: | - Base class for the configuration and results of ranging definitions. - - Ranging is a data post-processing step used in the research field of - atom probe during which elemental, isotopic, and/or molecular identities - are assigned to mass-to-charge-state-ratios within a certain interval. - The documentation of these steps is based on ideas that - have been described in the literature: - - * `M. K. Miller `_ - * `D. Haley et al. `_ - * `M. Kühbach et al. `_ - -type: group -NXapm_ranging(NXprocess): # when evolving these ideas further inherit from NXapm_method instead - (NXprogram): - (NXserialized): - mass_to_charge_distribution(NXprocess): - doc: | - Specifies the mass-to-charge-state-ratio histogram. - (NXprogram): - min_incr_max(NX_FLOAT): - doc: | - Smallest, increment, and largest mass-to-charge-state ratio value. - unit: NX_ANY # Da - dim: (3,) - mass_spectrum(NXdata): - doc: | - A default histogram aka mass spectrum of - the mass-to-charge-state ratio values. - - background_quantification(NXprocess): - doc: | - Details of the background model that was used to - correct the total counts per bin into counts. - (NXprogram): - description(NX_CHAR): - doc: | - To begin with we use a free-text field to learn how - atom probers define a background model. Future versions - of NXapm_ranging can then use this information to parameterize - these models. - # NEW ISSUE: add parameters of the background model in an e.g. - # NXcollection as these are specific to every background model - # NEW ISSUE: touching upon i.e. research activities by Andrew London et al. - # substantiating the need for a clearer description how peak/signals were - # eventually processed via deconvolution methods - - peak_search_and_deconvolution(NXprocess): - doc: | - How where peaks in the background-corrected in the histogram - of mass-to-charge-state ratio values identified? - (NXprogram): - (NXpeak): - peak_identification(NXprocess): - doc: | - Details about how peaks, with taking into account - error models, were interpreted as ion types or not. - (NXprogram): - number_of_ion_types(NX_UINT): - doc: | - How many ion types are distinguished. If no ranging was performed, each - ion is of the special unknown type. The iontype ID of this unknown type - is 0 representing a reserve value. Consequently, - iontypes start counting from 1. - unit: NX_UNITLESS - maximum_number_of_atoms_per_molecular_ion(NX_UINT): - doc: | - Assumed maximum value that suffices to store all relevant - molecular ions, even the most complicated ones. - Currently, a value of 32 is used (see `M. Kühbach et al. `_). - unit: NX_UNITLESS - (NXion): diff --git a/contributed_definitions/nyaml/NXatom_set.yaml b/contributed_definitions/nyaml/NXatom_set.yaml deleted file mode 100644 index 91021e353a..0000000000 --- a/contributed_definitions/nyaml/NXatom_set.yaml +++ /dev/null @@ -1,272 +0,0 @@ -category: base -doc: | - Base class for documenting a set of atoms. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - n_ivec_max: | - Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). - n_ranges: | - Number of mass-to-charge-state-ratio range intervals for ion type. -type: group -NXatom_set(NXobject): - identifier(NX_CHAR): - doc: | - A unique identifier whereby such an ion can be referred to - via the service offered as described in identifier_type. - identifier_type(NX_CHAR): - doc: | - How can the identifier be resolved? - enumeration: [inchi] - ion_type(NX_UINT): - unit: NX_UNITLESS - doc: | - Ion type (ion species) identifier. - - The identifier zero is reserved for the special unknown ion type. - nuclide_hash(NX_UINT): - unit: NX_UNITLESS - doc: | - Vector of nuclide hash values. - - Individual hash values :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - encode the number of protons :math:`Z` and the number of neutrons :math:`N` - of each nuclide respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - - The array is sorted in decreasing order. For the rationale behind this see `M. Kühbach et al. (2021) `_ - dimensions: - rank: 1 - dim: (n_ivec_max,) - nuclide_list(NX_UINT): - unit: NX_UNITLESS - doc: | - Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. - The first column specifies the nuclide mass number, i.e. using the hashvalues - from the isotope_vector this is :math:`Z + N` or 0. The value 0 documents that no - isotope-specific information about the element encoded is relevant. - The second row specifies the number of protons :math:`Z` or 0. - The value 0 in this case documents a placeholder or that no element-specific - information is relevant. - Taking a carbon-14 nuclide as an example the mass number is 14. - That is encoded as a value pair (14, 6) as one row of the table. - - Therefore, this notation is the typical superscribed nuclide mass number - and subscripted number of protons element notation e.g. :math:`^{14}C`. - The array is stored matching the order of nuclide_hash. - dimensions: - rank: 2 - dim: (n_ivecmax, 2) - - # color(NX_CHAR): - # doc: | - # Color code used for visualizing such ions. - volume(NX_NUMBER): - unit: NX_VOLUME - doc: | - Assumed volume of the ion. - - In atom probe microscopy this field can be used to store the reconstructed - volume per ion (average) which is typically stored alongside ranging - definitions. - charge(NX_NUMBER): - unit: NX_CHARGE - doc: | - Charge of the ion. - charge_state(NX_NUMBER): - unit: NX_UNITLESS - doc: | - Signed charge state if the atoms form an ion reported in multiples of electron charge. - - In the example of atom probe microscopy, only positive values will be measured - as the ions are accelerated by a negatively signed bias electric field. - In the case that the charge state is not explicitly recoverable, the value should - be set to zero. - - In atom probe microscopy this is for example the case when using - classical ranging definition files in formats like RNG, RRNG. - These file formats do not document the charge state explicitly - but the number of atoms of each element per molecular ion - surplus the mass-to-charge-state-ratio interval. - Details on ranging definition files can be found in the literature: - `M. K. Miller `_ - name(NX_CHAR): - doc: | - Human-readable name (e.g. Al +++) of the atom set, the atom group, or ion type. - The string should consists of UTF-8 characters, ideally using LaTeX - notation to specify the isotopes, ions, and charge state. - Examples are 12C + or Al +++. - - To ease automated parsing, isotope_vector should be the - preferred machine-readable information used. - mass_to_charge_range(NX_NUMBER): - unit: NX_ANY - doc: | - Associated lower (mqmin) and upper (mqmax) bounds of the - mass-to-charge-state ratio interval(s) [mqmin, mqmax] - (boundaries inclusive). This field is primarily of interest - for documenting :ref:`NXprocess` steps of indexing a - ToF/mass-to-charge state histogram. - dimensions: - rank: 2 - dim: (n_ranges, 2) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# e01b7928821295f155c19b6f8aada52214b290bf71cbc1dc02d76e3fbefd92a6 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Maximum number of atoms/isotopes allowed per (molecular) ion (fragment). -# -# -# -# -# Number of mass-to-charge-state-ratio range intervals for ion type. -# -# -# -# -# Base class for documenting a set of atoms. -# -# -# -# A unique identifier whereby such an ion can be referred to -# via the service offered as described in identifier_type. -# -# -# -# -# How can the identifier be resolved? -# -# -# -# -# -# -# -# Ion type (ion species) identifier. -# -# The identifier zero is reserved for the special unknown ion type. -# -# -# -# -# Vector of nuclide hash values. -# -# Individual hash values :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` -# encode the number of protons :math:`Z` and the number of neutrons :math:`N` -# of each nuclide respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. -# -# The array is sorted in decreasing order. For the rationale behind this see `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ -# -# -# -# -# -# -# -# Table which decodes the entries in nuclide_hash into a human-readable matrix of instances. -# The first column specifies the nuclide mass number, i.e. using the hashvalues -# from the isotope_vector this is :math:`Z + N` or 0. The value 0 documents that no -# isotope-specific information about the element encoded is relevant. -# The second row specifies the number of protons :math:`Z` or 0. -# The value 0 in this case documents a placeholder or that no element-specific -# information is relevant. -# Taking a carbon-14 nuclide as an example the mass number is 14. -# That is encoded as a value pair (14, 6) as one row of the table. -# -# Therefore, this notation is the typical superscribed nuclide mass number -# and subscripted number of protons element notation e.g. :math:`^{14}C`. -# The array is stored matching the order of nuclide_hash. -# -# -# -# -# -# -# -# -# -# Assumed volume of the ion. -# -# In atom probe microscopy this field can be used to store the reconstructed -# volume per ion (average) which is typically stored alongside ranging -# definitions. -# -# -# -# -# Charge of the ion. -# -# -# -# -# Signed charge state if the atoms form an ion reported in multiples of electron charge. -# -# In the example of atom probe microscopy, only positive values will be measured -# as the ions are accelerated by a negatively signed bias electric field. -# In the case that the charge state is not explicitly recoverable, the value should -# be set to zero. -# -# In atom probe microscopy this is for example the case when using -# classical ranging definition files in formats like RNG, RRNG. -# These file formats do not document the charge state explicitly -# but the number of atoms of each element per molecular ion -# surplus the mass-to-charge-state-ratio interval. -# Details on ranging definition files can be found in the literature: -# `M. K. Miller <https://doi.org/10.1002/sia.1719>`_ -# -# -# -# -# Human-readable name (e.g. Al +++) of the atom set, the atom group, or ion type. -# The string should consists of UTF-8 characters, ideally using LaTeX -# notation to specify the isotopes, ions, and charge state. -# Examples are 12C + or Al +++. -# -# To ease automated parsing, isotope_vector should be the -# preferred machine-readable information used. -# -# -# -# -# Associated lower (mqmin) and upper (mqmax) bounds of the -# mass-to-charge-state ratio interval(s) [mqmin, mqmax] -# (boundaries inclusive). This field is primarily of interest -# for documenting :ref:`NXprocess` steps of indexing a -# ToF/mass-to-charge state histogram. -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcg_alpha_complex.yaml b/contributed_definitions/nyaml/NXcg_alpha_complex.yaml deleted file mode 100644 index a64fe44def..0000000000 --- a/contributed_definitions/nyaml/NXcg_alpha_complex.yaml +++ /dev/null @@ -1,213 +0,0 @@ -category: base -doc: | - Computational geometry of alpha shapes or alpha wrappings about primitives. - - For details see: - - * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, - * https://dx.doi.org/10.1145/174462.156635 for 3D, - * https://dl.acm.org/doi/10.5555/871114 for weighted, and - * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation - * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D wrappings - - in CGAL, the Computational Geometry Algorithms Library. - As a starting point, we follow the conventions of the CGAL library. - -# The so-called spectrum or sets of (weighted) alpha shapes includes the convex hull of a point set. -type: group -NXcg_alpha_complex(NXcg_primitive_set): - type: - doc: | - Type of alpha complex following the terminology used by CGAL for now. - - Basic means (unweighted) alpha shapes. Alpha_wrapping means meshes - created using the alpha_wrapping algorithm. - enumeration: [convex_hull, alpha_shape, alpha_wrapping] - regularize_alpha_complex(NX_BOOLEAN): - doc: | - Are singular faces removed, i.e. has the alpha complex - been regularized or not. - - # R+0 means positive real number including zero which is a super set of NX_FLOAT and a sub-set of NX_NUMBER - alpha(NX_NUMBER): - unit: NX_LENGTH - doc: | - The alpha parameter, i.e. the radius of the alpha-sphere that - is used when computing the alpha complex. - - # the dim: argument can be omitted to indicate that a scalar is expected - # means a length quantity, i.e. m, km, or nm is possible i.e. has to be length but no further constraints - # stating meter is a stronger constraint while m is the strongest constraint, meaning literally the value is m. - offset(NX_NUMBER): - unit: NX_LENGTH - doc: | - The offset distance parameter used when computing alpha_wrappings. - - # check again carefully the CGAL documentation talks about, for 3D, the square of the radius! - point_setID(NXcg_point_set): - nameType: partial - - # basically just constraints that if you use one or more instances of NXcg_point_set - # inside an instance of NXcg_alpha_complex, name that group with the prefix "point_set" - doc: | - Point cloud for which the alpha shape or wrapping has been computed. - - # this could also just be implemented as a link but how would this be possible - # unfold the NXcg_point_set and add a - # weight(NX_NUMBER): - # doc: Weights for each point - # In general, an alpha complex is a disconnected and non-pure complex, - # meaning in particular that the alpha complex may have singular faces. - # so the number of cells, faces and edges depends on how a specific alpha complex, - # i.e. an alpha-shape of S for alpha, is filtrated with respect to k < d-dimensional - # simplices. Here we assume that number_of_cells, number_of_faces, number_of_edges - # are reported assuming one filtrates these simplices according to type. - # also using the assumption the base class reports the unique vertices - # of the specifically filtrated alpha complex. - triangle_setID(NXcg_triangle_set): - nameType: partial - doc: | - Triangle soup for which the alpha wrapping has been computed. - triangle_meshID(NXcg_triangle_set): - nameType: partial - doc: | - Triangle mesh representing the alpha complex. - - # add for each triangle if desirable a notation of whether the simplex is - # exterior, regular, singular, or interior with respect to the alpha complex - # a triangulation is more than a triangle (soup)/set because there it has connectivity - # customize the NXcg_triangle_set base class members such that connectivity can be contained naturally - # we need to find also a better name for this, what people intutive understand - # as the interior, may not even exist for a given alpha value - # more specifically it is the set of filtrated cells acknowledging mode - # e.g. the interior cells of the regularized alpha complex - interior_cellsID(NXcg_tetrahedron_set): - nameType: partial - doc: | - Set of tetrahedra representing the volume inside the alpha complex. - - # document the alpha status - # https://doc.cgal.org/latest/Alpha_shapes_3/classCGAL_1_1Alpha__status.html - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ac8bae322b29a5639cc19e742441020340a4e8646ab23e58aabbaf6800b02bfe -# -# -# -# -# -# -# Computational geometry of alpha shapes or alpha wrappings about primitives. -# -# For details see: -# -# * https://dx.doi.org/10.1109/TIT.1983.1056714 for 2D, -# * https://dx.doi.org/10.1145/174462.156635 for 3D, -# * https://dl.acm.org/doi/10.5555/871114 for weighted, and -# * https://doc.cgal.org/latest/Alpha_shapes_3 for 3D implementation -# * https://doc.cgal.org/latest/Manual/packages.html#PkgAlphaWrap3 for 3D wrappings -# -# in CGAL, the Computational Geometry Algorithms Library. -# As a starting point, we follow the conventions of the CGAL library. -# -# -# -# Type of alpha complex following the terminology used by CGAL for now. -# -# Basic means (unweighted) alpha shapes. Alpha_wrapping means meshes -# created using the alpha_wrapping algorithm. -# -# -# -# -# -# -# -# -# -# Are singular faces removed, i.e. has the alpha complex -# been regularized or not. -# -# -# -# -# -# The alpha parameter, i.e. the radius of the alpha-sphere that -# is used when computing the alpha complex. -# -# -# -# -# -# The offset distance parameter used when computing alpha_wrappings. -# -# -# -# -# -# -# Point cloud for which the alpha shape or wrapping has been computed. -# -# -# -# -# -# Triangle soup for which the alpha wrapping has been computed. -# -# -# -# -# Triangle mesh representing the alpha complex. -# -# -# -# -# -# Set of tetrahedra representing the volume inside the alpha complex. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcg_geodesic_mesh.yaml b/contributed_definitions/nyaml/NXcg_geodesic_mesh.yaml deleted file mode 100644 index e18d17a688..0000000000 --- a/contributed_definitions/nyaml/NXcg_geodesic_mesh.yaml +++ /dev/null @@ -1,89 +0,0 @@ -category: base -doc: | - Computational geometry description of a geodesic mesh. - - A geodesic surface mesh is a triangulated surface mesh with metadata which - can be used as an approximation to describe the surface of a sphere. - Triangulation of spheres are commonly used in Materials Science - for quantifying texture of materials, i.e. the relative rotation of - crystals to sample directions. - - For additional details or an introduction into the topic of geodesic meshes - see (from which specifically the section on subdivision schemes is relevant). - - * `E. S. Popko and C. J. Kitrick `_ - - Earth scientists have specific demands and different views about what should - be included in such a base class, given that nested geodesic meshes are a key - component of climate modelling software. For now we propose to use this - base class as a container for organizing data related to geodesic meshes. - - Specifically an instance of this base class should detail the rule set how - e.g. a geodesic (surface) mesh was instantiated as there are many - possibilities to do so. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. -type: group -NXcg_geodesic_mesh(NXcg_primitive_set): - (NXcg_triangulated_surface_mesh): - - # Discussions with NFDI-Earth could make this base class more meaty and detailed. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4b22eae681c375adaabee22b22047f389318cd6956aa2722c7d13ada42160e16 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Computational geometry description of a geodesic mesh. -# -# A geodesic surface mesh is a triangulated surface mesh with metadata which -# can be used as an approximation to describe the surface of a sphere. -# Triangulation of spheres are commonly used in Materials Science -# for quantifying texture of materials, i.e. the relative rotation of -# crystals to sample directions. -# -# For additional details or an introduction into the topic of geodesic meshes -# see (from which specifically the section on subdivision schemes is relevant). -# -# * `E. S. Popko and C. J. Kitrick <https://doi.org/10.1201/9781003134114>`_ -# -# Earth scientists have specific demands and different views about what should -# be included in such a base class, given that nested geodesic meshes are a key -# component of climate modelling software. For now we propose to use this -# base class as a container for organizing data related to geodesic meshes. -# -# Specifically an instance of this base class should detail the rule set how -# e.g. a geodesic (surface) mesh was instantiated as there are many -# possibilities to do so. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcg_marching_cubes.yaml b/contributed_definitions/nyaml/NXcg_marching_cubes.yaml deleted file mode 100644 index e6ce43c650..0000000000 --- a/contributed_definitions/nyaml/NXcg_marching_cubes.yaml +++ /dev/null @@ -1,92 +0,0 @@ -category: base -doc: | - Base class to detail the marching cubes (MC) algorithm. - - Documenting which specific version of MC was used helps with understanding - how robust the results are with respect to the topology of the triangulation. - -# symbols: -type: group -NXcg_marching_cubes(NXobject): - grid(NXcg_grid): - doc: | - Metadata of the grid on which the here specified MC is operating. - identifierNAME: - nameType: partial - doc: | - Reference to the specific implementation of marching cubes used. - - See for example the following papers for details about specific - MC implementations: - - * `W. E. Lorensen `_ - * `T. S. Newman and H. Yi `_ - description(NX_CHAR): - doc: | - Free text field in case a proper identifier is not available. - (NXprogram): - - # we could also think about storing the rule sets in here explicitly including the - # coordinate system conventions; however, the problem is that many commercial - # tools like Matlab do not expose the rule set. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7ee43a95a3b4510e6ec3b55be5cfd8b0bfbc850b56f0fdf8796fc25c3ad013a8 -# -# -# -# -# -# -# Base class to detail the marching cubes (MC) algorithm. -# -# Documenting which specific version of MC was used helps with understanding -# how robust the results are with respect to the topology of the triangulation. -# -# -# -# Metadata of the grid on which the here specified MC is operating. -# -# -# -# -# Reference to the specific implementation of marching cubes used. -# -# See for example the following papers for details about specific -# MC implementations: -# -# * `W. E. Lorensen <https://doi.org/10.1109/MCG.2020.2971284>`_ -# * `T. S. Newman and H. Yi <https://doi.org/10.1016/j.cag.2006.07.021>`_ -# -# -# -# -# Free text field in case a proper identifier is not available. -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcg_primitive_set.yaml b/contributed_definitions/nyaml/NXcg_primitive_set.yaml deleted file mode 100644 index f0b851f33a..0000000000 --- a/contributed_definitions/nyaml/NXcg_primitive_set.yaml +++ /dev/null @@ -1,375 +0,0 @@ -category: base -doc: | - Computational geometry description of a set of primitives in Euclidean space. - - Primitives must neither be degenerated nor self-intersect. - Individual primitives can differ in their properties (e.g. size, shape, rotation). - -# this base class defines common fields and properties of geometric primitives -# more complex primitive sets like NXcg_cylinder_set are considered specializations -# of NXcg_primitive_set. They contain all fields and groups which NXcg_primitive_set -# defines. This is an action of compositing an information set; an act of inheriting -# TODO:: many properties of non-degenerate primitives are in the number set -# R+ instead of in R+0 but currently NeXus does not allow for such value range -# constraints unless the coarsely discretized NX_INT, NX_POSINT, NX_FLOAT -# but there is no say NX_FLOAT+0 -# MK::but in computational geometry numerical precision matters as it defines -# whether objects numerically intersect or not and thus it can make a real difference -# if one stores triangles with 16, 32, or 64 bit precision, however: -# are two triangle_set instance A and B no longer conceptually triangle sets -# because A stores the positions of vertices using int8 while B stores such using float64 ? -# we here assume that we still conceptually talk that A and B are triangle sets -# but this brings at the level of the application definition the problem that if the -# precision is not properly constrainted a consuming application will not obtain -# the instances of the concept triangle_set with relevant high enough precision -# and thus neither the base class nor the application definition is specific enough -# for what it was designed in the first place - be specific about the requirements -# on your data... -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - d: | - The dimensionality of the space. - c: | - The cardinality of the set, i.e. the number of members. -type: group -NXcg_primitive_set(NXobject): - - # individual specializations like NXcg_polyline_set typically overwrite - # the meaning of the depends_on concept to build consistent inference chains - # to enable an instantiation of the actual geometric primitives - depends_on(NX_CHAR): - doc: | - Reference to an instance of :ref:`NXcoordinate_system` in which these primitives - are defined. - dimensionality(NX_POSINT): - unit: NX_UNITLESS - doc: | - The dimensionality of the primitive set. - enumeration: [1, 2, 3] - cardinality(NX_POSINT): - unit: NX_UNITLESS - doc: | - The cardinality of the primitive set. - identifier_offset(NX_INT): - unit: NX_UNITLESS - doc: | - Integer offset whereby the identifier of the first member - of the set differs from zero. - - Identifiers can be defined either implicitly or explicitly. - For implicit indexing identifiers are defined on the interval - :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - Therefore, implicit identifier are completely defined by the value of - identifier_offset and cardinality. For example if identifier run from - -2 to 3 the value for identifier_offset is -2. - - For explicit indexing the field identifier has to be used. - Fortran-/Matlab- and C-/Python-style indexing have specific implicit - identifier conventions where identifier_offset is 1 and 0 respectively. - identifier(NX_INT): - doc: | - Identifier of each member for explicit indexing. - dimensions: - rank: 1 - dim: (c,) - center(NX_NUMBER): - unit: NX_ANY - doc: | - The center of mass position of each primitive. - dimensions: - rank: 2 - dim: (c, d) - - # a depends_on to define in which coordinate system - is_center_of_mass(NX_BOOLEAN): - doc: | - True if the center is a center of mass. - dimensions: - rank: 1 - dim: (c,) - shape(NX_NUMBER): - unit: NX_LENGTH - doc: | - A qualitative description of the shape of each primitive. - dimensions: - rank: 2 - dim: (c, d) - length(NX_NUMBER): - unit: NX_LENGTH - doc: | - Qualifier for the length of characteristic features of the primitive. - - Often the term length is associated with the assumption that one - edge is parallel to an axis of the coordinate system. - dimensions: - rank: 1 - dim: (c,) - width(NX_NUMBER): - unit: NX_LENGTH - doc: | - Qualifier often used to describe the length of one characteristic edge - within the coordinate system. - dimensions: - rank: 1 - dim: (c,) - is_closed(NX_BOOLEAN): - doc: | - True if primitive is closed such that it has properties like area or volume. - dimensions: - rank: 1 - dim: (c,) - volume(NX_NUMBER): - unit: NX_VOLUME - doc: | - Volume of each primitive. - - Set to NaN if does not apply for primitives for which is_closed is False. - dimensions: - rank: 1 - dim: (c,) - area(NX_NUMBER): - unit: NX_AREA - doc: | - Alias for surface_area of each primitive. - - Set to NaN if does not apply for primitives for which is_closed is False. - dimensions: - rank: 1 - dim: (c,) - orientation(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - Direction unit vector which points along the - longest principal axis of each primitive. - - Use the depends_on attribute to specify in which coordinate system - these direction unit vectors are defined. - dimensions: - rank: 2 - dim: (c, d) - vertex_normal(NXcg_unit_normal_set): - edge_normal(NXcg_unit_normal_set): - face_normal(NXcg_unit_normal_set): - - # roi(NXcg_parallelogram_set or NXcg_hexahedron_set) - # aabb(NXcg_parallelogram_set or NXcg_hexahedron_set) - # obb(NXcg_parallelogram_set or NXcg_hexahedron_set) - # MK::one could add (NXcg_parallelogram_set) and/or (NXcg_hexahedron_set) - # but then one would not give any hint at the base class level how to name - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 292b5b3bc58425a2222b015c9853800659a824178e5928b90985ba17a560c635 -# -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# The dimensionality of the space. -# -# -# -# -# The cardinality of the set, i.e. the number of members. -# -# -# -# -# Computational geometry description of a set of primitives in Euclidean space. -# -# Primitives must neither be degenerated nor self-intersect. -# Individual primitives can differ in their properties (e.g. size, shape, rotation). -# -# -# -# -# Reference to an instance of :ref:`NXcoordinate_system` in which these primitives -# are defined. -# -# -# -# -# The dimensionality of the primitive set. -# -# -# -# -# -# -# -# -# -# The cardinality of the primitive set. -# -# -# -# -# Integer offset whereby the identifier of the first member -# of the set differs from zero. -# -# Identifiers can be defined either implicitly or explicitly. -# For implicit indexing identifiers are defined on the interval -# :math:`[identifier\_offset, identifier\_offset + c - 1]`. -# -# Therefore, implicit identifier are completely defined by the value of -# identifier_offset and cardinality. For example if identifier run from -# -2 to 3 the value for identifier_offset is -2. -# -# For explicit indexing the field identifier has to be used. -# Fortran-/Matlab- and C-/Python-style indexing have specific implicit -# identifier conventions where identifier_offset is 1 and 0 respectively. -# -# -# -# -# Identifier of each member for explicit indexing. -# -# -# -# -# -# -# -# The center of mass position of each primitive. -# -# -# -# -# -# -# -# -# -# True if the center is a center of mass. -# -# -# -# -# -# -# -# A qualitative description of the shape of each primitive. -# -# -# -# -# -# -# -# -# Qualifier for the length of characteristic features of the primitive. -# -# Often the term length is associated with the assumption that one -# edge is parallel to an axis of the coordinate system. -# -# -# -# -# -# -# -# Qualifier often used to describe the length of one characteristic edge -# within the coordinate system. -# -# -# -# -# -# -# -# True if primitive is closed such that it has properties like area or volume. -# -# -# -# -# -# -# -# Volume of each primitive. -# -# Set to NaN if does not apply for primitives for which is_closed is False. -# -# -# -# -# -# -# -# Alias for surface_area of each primitive. -# -# Set to NaN if does not apply for primitives for which is_closed is False. -# -# -# -# -# -# -# -# Direction unit vector which points along the -# longest principal axis of each primitive. -# -# Use the depends_on attribute to specify in which coordinate system -# these direction unit vectors are defined. -# -# -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcg_sphere_set.yaml b/contributed_definitions/nyaml/NXcg_sphere_set.yaml deleted file mode 100644 index d789bae3bc..0000000000 --- a/contributed_definitions/nyaml/NXcg_sphere_set.yaml +++ /dev/null @@ -1,92 +0,0 @@ -category: base -doc: | - Computational geometry description of a set of spheres. - - Each sphere can have a different radius but all need to have finite volume. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - d: | - The dimensionality, which has to be at least 2. - c: | - The cardinality of the set, i.e. the number of circles or spheres. - -# redundant as there is NXcsg, and NXquadric but easier to understand -type: group -NXcg_sphere_set(NXcg_ellipsoid_set): - radius(NX_NUMBER): - unit: NX_LENGTH - doc: | - In the case that all spheres have the same radius. - radii(NX_NUMBER): - unit: NX_LENGTH - doc: | - In the case that spheres have different radius use this - instead of the radius field. - dimensions: - rank: 1 - dim: (c,) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6a842f258fcf5cc8257d11725daf87d57e15c9d201b28db6a1f452609baeebe8 -# -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# The dimensionality, which has to be at least 2. -# -# -# -# -# The cardinality of the set, i.e. the number of circles or spheres. -# -# -# -# -# Computational geometry description of a set of spheres. -# -# Each sphere can have a different radius but all need to have finite volume. -# -# -# -# In the case that all spheres have the same radius. -# -# -# -# -# In the case that spheres have different radius use this -# instead of the radius field. -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXcg_triangulated_surface_mesh.yaml b/contributed_definitions/nyaml/NXcg_triangulated_surface_mesh.yaml deleted file mode 100644 index e205674feb..0000000000 --- a/contributed_definitions/nyaml/NXcg_triangulated_surface_mesh.yaml +++ /dev/null @@ -1,60 +0,0 @@ -category: base -doc: | - Computational geometry description of a mesh of triangles. - - The mesh may be self-intersecting and have holes but the - triangles used must not be degenerated. -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. -type: group -NXcg_triangulated_surface_mesh(NXcg_triangle_set): - (NXcg_half_edge_data_structure): - doc: | - A graph-based approach to describe the mesh when it is also desired - to perform topological processing or analyses on the mesh. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6283d6a8902ad3480cd578c68048083d473e42819b044c5477edeb0e6dd01824 -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# Computational geometry description of a mesh of triangles. -# -# The mesh may be self-intersecting and have holes but the -# triangles used must not be degenerated. -# -# -# -# A graph-based approach to describe the mesh when it is also desired -# to perform topological processing or analyses on the mesh. -# -# -# diff --git a/contributed_definitions/nyaml/NXchamber.yaml b/contributed_definitions/nyaml/NXchamber.yaml deleted file mode 100644 index bf132ad1e2..0000000000 --- a/contributed_definitions/nyaml/NXchamber.yaml +++ /dev/null @@ -1,56 +0,0 @@ -category: base -doc: | - Base class for a chamber in an instrument that stores real or simulated objects. -type: group -NXchamber(NXcomponent): - name(NX_CHAR): - doc: | - Given name for the chamber of this component e.g. analysis chamber - or buffer chamber, load-lock chamber, microscope column, glove box. - description(NX_CHAR): - doc: | - Free-text field for describing details about the chamber. - For example out of which material was the chamber built. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 57f86db83a26a7a0f384c5ab4d3219af0bbb0abb50a78ff7efb71c35cf6d0bc9 -# -# -# -# -# -# Base class for a chamber in an instrument that stores real or simulated objects. -# -# -# -# Given name for the chamber of this component e.g. analysis chamber -# or buffer chamber, load-lock chamber, microscope column, glove box. -# -# -# -# -# Free-text field for describing details about the chamber. -# For example out of which material was the chamber built. -# -# -# diff --git a/contributed_definitions/nyaml/NXchemical_process.yaml b/contributed_definitions/nyaml/NXchemical_process.yaml deleted file mode 100644 index 6ccf1e3022..0000000000 --- a/contributed_definitions/nyaml/NXchemical_process.yaml +++ /dev/null @@ -1,90 +0,0 @@ -category: base -doc: | - A planned or unplanned process which results in chemical changes (i.e., changes in the chemical bonds) in a specified material. - - Examples include any chemical reactions (addition, subtraction, replacement, ...). -type: group -NXchemical_process(NXobject): - start_time(NX_DATE_TIME): - doc: | - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process started. - end_time(NX_DATE_TIME): - doc: | - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process ended. - description: - doc: | - Short description of the chemical process. - method: - doc: | - Method by which this process was performed. - notes(NXnote): - doc: | - This can be any data or other descriptor acquired during the chemical process - (NXnote allows to add pictures, audio, movies). Alternatively, a - reference to the location or a unique identifier or other metadata file. In the - case these are not available, free-text description. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 9ab9d17820c3d4b4853123d5dc1181d8a2a008936a1a67bf83913552bfeaf033 -# -# -# -# -# -# A planned or unplanned process which results in chemical changes (i.e., changes in the chemical bonds) in a specified material. -# -# Examples include any chemical reactions (addition, subtraction, replacement, ...). -# -# -# -# ISO 8601 formatted time code (with local time zone offset to UTC information -# included) when this process started. -# -# -# -# -# ISO 8601 formatted time code (with local time zone offset to UTC information -# included) when this process ended. -# -# -# -# -# Short description of the chemical process. -# -# -# -# -# Method by which this process was performed. -# -# -# -# -# This can be any data or other descriptor acquired during the chemical process -# (NXnote allows to add pictures, audio, movies). Alternatively, a -# reference to the location or a unique identifier or other metadata file. In the -# case these are not available, free-text description. -# -# -# diff --git a/contributed_definitions/nyaml/NXcircuit.yaml b/contributed_definitions/nyaml/NXcircuit.yaml deleted file mode 100644 index 6b02f48200..0000000000 --- a/contributed_definitions/nyaml/NXcircuit.yaml +++ /dev/null @@ -1,270 +0,0 @@ -category: base -doc: | - Application definition for circuit devices. - - Electronic circuits are hardware components connecting several electronic components to achieve - specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. -symbols: - doc: | - Constant to be used in the definition: the number of channels of the - circuit board. - N_channel: | - number of channels of the circuit board. -type: group -NXcircuit(NXobject): - hardware(NXfabrication): - doc: | - Hardware where the circuit is implanted; includes information about the hardware manufacturers and - type (e.g. part number) - All the elements below may be single numbers of an array of values with length N_channel - describing multiple input and output channels. - components: - doc: | - List of components used in the circuit, e.g., resistors, capacitors, transistors or any - other complex components. - connections: - doc: | - Description of how components are interconnected, including connection points - and wiring. - power_source: - doc: | - Details of the power source for the circuit, including voltage and current - ratings. - signal_type: - doc: | - Type of signal (input signal) the circuit is designed to handle, e.g., analog, - digital, mixed-signal. - - # should this be a min / max range? - operating_frequency(NX_NUMBER): - unit: NX_FREQUENCY - doc: | - The operating frequency of the circuit, see also bandwidth below, which is possibly - centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth - amplifier at low, audio frequencies 1 - 20,000 Hz) - - # we may need an NX_RESISTANCE defined - input_impedance(NX_NUMBER): - unit: NX_ANY - doc: | - Input impedance of the circuit. - output_impedance(NX_NUMBER): - unit: NX_ANY - doc: | - Output impedance of the circuit. - gain(NX_NUMBER): - unit: NX_UNITLESS - doc: | - Gain of the circuit, if applicable, usually all instruments have a gain which might be - important or not. - noise_level(NX_NUMBER): - unit: NX_ANY - doc: | - RMS noise level (in current or voltage) in the circuit in voltage or current. - bandwidth(NX_NUMBER): - unit: NX_FREQUENCY - doc: | - The bandwidth of the frequency response of the circuit. - temperature_range(NX_NUMBER): - unit: NX_ANY - doc: | - Operating temperature range of the circuit. - calibration(NXcalibration): - doc: | - Calibration data for the circuit. - offset(NX_NUMBER): - unit: NX_ANY - doc: | - Offset value for current or voltage. - output_channels(NX_NUMBER): - doc: | - Number of output channels collected to this circuit. Most probably N_channel. - output_signal(NX_NUMBER): - unit: NX_ANY - doc: | - Type of output signal, e.g., voltage, current, digital. - power_consumption(NX_NUMBER): - unit: NX_ANY - doc: | - Power consumption of the circuit per unit time. - status_indicators: - doc: | - Status indicators for the circuit, e.g., LEDs, display readouts. - protection_features(NX_CHAR): - doc: | - Protection features built into the circuit, e.g., overvoltage protection, - thermal shutdown. - acquisition_time(NX_NUMBER): - unit: NX_TIME - doc: | - Updated rate for several processes using the input signal, e.g., History Graph, the circuit - uses for any such process. - output_slew_rate(NX_CHAR): - doc: | - The rate at which the signal changes when ramping from the starting - value. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# a9455117da8b441d29ef1660d4c789c8d044ced52dacd958c0a82ca13594cee0 -# -# -# -# -# -# -# Constant to be used in the definition: the number of channels of the -# circuit board. -# -# -# -# number of channels of the circuit board. -# -# -# -# -# Application definition for circuit devices. -# -# Electronic circuits are hardware components connecting several electronic components to achieve -# specific functionality, e.g. amplifying a voltage or convert a voltage to binary numbers, etc. -# -# -# -# Hardware where the circuit is implanted; includes information about the hardware manufacturers and -# type (e.g. part number) -# All the elements below may be single numbers of an array of values with length N_channel -# describing multiple input and output channels. -# -# -# -# -# List of components used in the circuit, e.g., resistors, capacitors, transistors or any -# other complex components. -# -# -# -# -# Description of how components are interconnected, including connection points -# and wiring. -# -# -# -# -# Details of the power source for the circuit, including voltage and current -# ratings. -# -# -# -# -# Type of signal (input signal) the circuit is designed to handle, e.g., analog, -# digital, mixed-signal. -# -# -# -# -# -# The operating frequency of the circuit, see also bandwidth below, which is possibly -# centered around this frequency. However, not necessarily (e.g. running a 100 kHz bandwidth -# amplifier at low, audio frequencies 1 - 20,000 Hz) -# -# -# -# -# -# Input impedance of the circuit. -# -# -# -# -# Output impedance of the circuit. -# -# -# -# -# Gain of the circuit, if applicable, usually all instruments have a gain which might be -# important or not. -# -# -# -# -# RMS noise level (in current or voltage) in the circuit in voltage or current. -# -# -# -# -# The bandwidth of the frequency response of the circuit. -# -# -# -# -# Operating temperature range of the circuit. -# -# -# -# -# Calibration data for the circuit. -# -# -# -# -# Offset value for current or voltage. -# -# -# -# -# Number of output channels collected to this circuit. Most probably N_channel. -# -# -# -# -# Type of output signal, e.g., voltage, current, digital. -# -# -# -# -# Power consumption of the circuit per unit time. -# -# -# -# -# Status indicators for the circuit, e.g., LEDs, display readouts. -# -# -# -# -# Protection features built into the circuit, e.g., overvoltage protection, -# thermal shutdown. -# -# -# -# -# Updated rate for several processes using the input signal, e.g., History Graph, the circuit -# uses for any such process. -# -# -# -# -# The rate at which the signal changes when ramping from the starting -# value. -# -# -# diff --git a/contributed_definitions/nyaml/NXcrystal_structure.yaml b/contributed_definitions/nyaml/NXcrystal_structure.yaml deleted file mode 100644 index 119b1b4510..0000000000 --- a/contributed_definitions/nyaml/NXcrystal_structure.yaml +++ /dev/null @@ -1,477 +0,0 @@ -category: base -doc: | - Base class to describe the atomic crystal structure of a phase. - - This base class contains key metadata that are relevant parameter to every - physics-based model to simulate radiation matter interaction. - - Examples where such base class is useful are kinematic or dynamic - diffraction simulations of e.g. (Kikuchi or other type of) patterns. - -# The actual indexing of Kikuchi patterns may use different algorithms. -# Such are used within different workflows where simulated and measured -# Kikuchi pattern are compared to rate which phase and orientation is the most -# likely candidate describing the pattern measured at that each scan point -# respectively. If this evaluation yields scan points without any solutions, -# these are represented using the null-phase model phase0, aka n/a aka notIndexed. -# Traditionally, Hough transformation-based indexing has been the most frequently -# used algorithm. Dictionary-based alternatives are emerging. -symbols: - n_hkl: | - Number of reflectors (Miller crystallographic plane triplets). - n_pos: | - Number of atom positions. - d: | - Dimensionality of the lattice. -type: group -NXcrystal_structure(NXobject): - depends_on(NX_CHAR): - doc: | - Details in which reference frame the unit cell is defined. - dimensionality(NX_POSINT): - doc: | - Dimensionality of the lattice. - enumeration: [1, 2, 3] - identifier_reference: - doc: | - Reference to another resource that was used for - instantiating this structure model. - a_b_c(NX_NUMBER): - unit: NX_LENGTH - doc: | - Crystallography unit cell parameters a, b, and c. - dimensions: - rank: 1 - dim: (d,) - - # defined using which convention? - alpha_beta_gamma(NX_NUMBER): - unit: NX_ANGLE - doc: | - Crystallography unit cell parameters alpha, beta, and gamma. - dimensions: - rank: 1 - dim: (d,) - area(NX_NUMBER): - unit: NX_AREA - doc: | - Area of the unit cell considering that d = 2. - volume(NX_NUMBER): - unit: NX_VOLUME - doc: | - Volume of the unit cell considering that d = 3. - crystal_system(NX_CHAR): - doc: | - Crystal system - enumeration: [triclinic, monoclinic, orthorhombic, tetragonal, rhombohedral, hexagonal, cubic] - - # 2d - laue_group(NX_CHAR): - doc: | - Laue group using International Table of Crystallography Notation. - - # add enumeration of all possible - point_group(NX_CHAR): - doc: | - Point group using International Table of Crystallography Notation. - - # add enumeration all possible - # 3d - space_group(NX_CHAR): - doc: | - Space group from the International Table of Crystallography Notation. - - # add enumeration of all possible - is_centrosymmetric(NX_BOOLEAN): - doc: | - True if space group is considered a centrosymmetric one. - False if space group is considered a non-centrosymmetric one. - Centrosymmetric has all types and combinations of symmetry elements - (translation, rotational axis, mirror planes, center of inversion) - Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). - Chiral compared to non-centrosymmetric is constrained (no mirror planes). - is_chiral(NX_BOOLEAN): - doc: | - True if space group is considered a chiral one. - False if space group is consider a non-chiral one. - identifier_phase(NX_INT): - unit: NX_UNITLESS - doc: | - Identifier for each phase. - - The value 0 is reserved for the unknown phase that represents the - null-model no sufficiently significant confirmation. In other words, - the phase_name is n/a, notIndexed. - - The phase identifier value has to match with the integer postfix of the - group name which represents that instance in a NeXus/HDF5 file, i.e. - if two phases were used e.g. 0 and 1, two instances of an - :ref:`NXcrystal_structure` named phase0 and phase1 - should be stored in the HDF5 file. - phase_name(NX_CHAR): - doc: | - Name of the phase/alias. - - If the ``identifier_phase`` is 0 and one would like to use the field - ``phase_name``, the value should be n/a. - identifier_atom(NX_CHAR): - doc: | - Label for each atom position. - dimensions: - rank: 1 - dim: (n_pos,) - atom_type(NX_UINT): - unit: NX_UNITLESS - doc: | - The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - the number of protons and :math:`N` the number of neutrons - of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - For the rationale behind this `M. Kühbach et al. (2021) `_ - dimensions: - rank: 1 - dim: (n_pos,) - - # atom_position(NXcg_point_set): - atom_position(NX_NUMBER): - unit: NX_ANY - doc: | - Atom positions. - dimensions: - rank: 2 - dim: (n_pos, d) - \@depends_on(NX_CHAR): - doc: | - Details the reference frame in which the positions are defined. - - # in addition we need to have a physical model e.g. kinematic or dynamical e-diffraction theory - # to describe the simulated Kikuchi pattern generated from such a model - atom_occupancy(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - Relative occupancy of the atom position. - dimensions: - rank: 1 - dim: (n_pos,) - number_of_planes(NX_UINT): - unit: NX_UNITLESS - doc: | - How many reflectors are distinguished. - - Value has to match value for symbol n_hkl. - - # Miller indices :math:`(hkl)[uvw]`. - miller(NX_NUMBER): - unit: NX_UNITLESS - doc: | - Miller indices :math:`(hkl)[uvw]` of the planes. - - The first triplet specify :math:`(hkl)` the second triplet :math:`[uvw]`. - Miller indices refer to the Cartesian right-handed coordinate system - of the unit cell. - dimensions: - rank: 2 - dim: (n_hkl, 6) - dspacing(NX_NUMBER): - unit: NX_LENGTH - doc: | - Spacing between crystallographic planes as defined by field miller. - dimensions: - rank: 1 - dim: (n_hkl,) - relative_intensity(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - Relative intensity of the signal for the plane. - dimensions: - rank: 1 - dim: (n_hkl,) - number_of_scan_points(NX_UINT): - unit: NX_UNITLESS - doc: | - In case the :ref:`NXcrystal_structure` base class is used - with analyzed orientation maps this field stores how many scan points - of the map were identified as that phase. - - # ipfID(NXmicrostructure_ipf): - # pfID(NXmicrostructure_pf): - # odfID(NXmicrostructure_odf): - # here the theoreticians expert (Marc deGraeff, Aimo Winkelmann, Peter Rez) - # can give some good suggestions on how to improve and ideally make even - # more general this section - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 526f6e3673763658915517d57560a4c16a2d2b8b1c09d9c2d3d13c4e361fb3e8 -# -# -# -# -# -# -# -# -# Number of reflectors (Miller crystallographic plane triplets). -# -# -# -# -# Number of atom positions. -# -# -# -# -# Dimensionality of the lattice. -# -# -# -# -# Base class to describe the atomic crystal structure of a phase. -# -# This base class contains key metadata that are relevant parameter to every -# physics-based model to simulate radiation matter interaction. -# -# Examples where such base class is useful are kinematic or dynamic -# diffraction simulations of e.g. (Kikuchi or other type of) patterns. -# -# -# -# Details in which reference frame the unit cell is defined. -# -# -# -# -# Dimensionality of the lattice. -# -# -# -# -# -# -# -# -# -# Reference to another resource that was used for -# instantiating this structure model. -# -# -# -# -# Crystallography unit cell parameters a, b, and c. -# -# -# -# -# -# -# -# -# Crystallography unit cell parameters alpha, beta, and gamma. -# -# -# -# -# -# -# -# Area of the unit cell considering that d = 2. -# -# -# -# -# Volume of the unit cell considering that d = 3. -# -# -# -# -# Crystal system -# -# -# -# -# -# -# -# -# -# -# -# -# -# -# Laue group using International Table of Crystallography Notation. -# -# -# -# -# -# Point group using International Table of Crystallography Notation. -# -# -# -# -# -# Space group from the International Table of Crystallography Notation. -# -# -# -# -# -# True if space group is considered a centrosymmetric one. -# False if space group is considered a non-centrosymmetric one. -# Centrosymmetric has all types and combinations of symmetry elements -# (translation, rotational axis, mirror planes, center of inversion) -# Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). -# Chiral compared to non-centrosymmetric is constrained (no mirror planes). -# -# -# -# -# True if space group is considered a chiral one. -# False if space group is consider a non-chiral one. -# -# -# -# -# Identifier for each phase. -# -# The value 0 is reserved for the unknown phase that represents the -# null-model no sufficiently significant confirmation. In other words, -# the phase_name is n/a, notIndexed. -# -# The phase identifier value has to match with the integer postfix of the -# group name which represents that instance in a NeXus/HDF5 file, i.e. -# if two phases were used e.g. 0 and 1, two instances of an -# :ref:`NXcrystal_structure` named phase0 and phase1 -# should be stored in the HDF5 file. -# -# -# -# -# Name of the phase/alias. -# -# If the ``identifier_phase`` is 0 and one would like to use the field -# ``phase_name``, the value should be n/a. -# -# -# -# -# Label for each atom position. -# -# -# -# -# -# -# -# The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` -# the number of protons and :math:`N` the number of neutrons -# of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. -# For the rationale behind this `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ -# -# -# -# -# -# -# -# -# Atom positions. -# -# -# -# -# -# -# -# Details the reference frame in which the positions are defined. -# -# -# -# -# -# -# Relative occupancy of the atom position. -# -# -# -# -# -# -# -# How many reflectors are distinguished. -# -# Value has to match value for symbol n_hkl. -# -# -# -# -# -# Miller indices :math:`(hkl)[uvw]` of the planes. -# -# The first triplet specify :math:`(hkl)` the second triplet :math:`[uvw]`. -# Miller indices refer to the Cartesian right-handed coordinate system -# of the unit cell. -# -# -# -# -# -# -# -# -# Spacing between crystallographic planes as defined by field miller. -# -# -# -# -# -# -# -# Relative intensity of the signal for the plane. -# -# -# -# -# -# -# -# In case the :ref:`NXcrystal_structure` base class is used -# with analyzed orientation maps this field stores how many scan points -# of the map were identified as that phase. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXebeam_column.yaml b/contributed_definitions/nyaml/NXebeam_column.yaml deleted file mode 100644 index d86b7d7656..0000000000 --- a/contributed_definitions/nyaml/NXebeam_column.yaml +++ /dev/null @@ -1,195 +0,0 @@ -category: base -doc: | - Base class for a set of components providing a controllable electron beam. - -# symbols: -# doc: The symbols used in the schema to specify e.g. variables. -type: group -NXebeam_column(NXcomponent): - operation_mode(NX_CHAR): - doc: | - Typically tech-partner, microscope-, and control software-specific - name of the specific operation mode how the ebeam_column and its - components are controlled to achieve a specific illumination condition. - - In most cases users do not know, have to care, or are able to disentangle the - details of the spatiotemporal dynamics of the components of the microscope. - Instead, they rely on the assumption that the microscope and control software - work as expected. Selecting then a specific operation_mode assures some level - of reproducibility in the illumination conditions. - (NXfabrication): - (NXchamber): - electron_source(NXsource): - doc: | - The source which creates the electron beam. - name(NX_CHAR): - doc: | - Given name/alias. - (NXfabrication): - voltage(NX_NUMBER): - unit: NX_VOLTAGE - doc: | - Voltage relevant to compute the energy of the electrons - immediately after they left the gun. - probe(NX_CHAR): - doc: | - Type of radiation. - enumeration: [electron] - emitter_type(NX_CHAR): - doc: | - Emitter type used to create the beam. - - If the emitter type is other, give further details - in the description field. - - # enumeration: [filament, schottky, cold_cathode_field_emitter, other] - emitter_material(NX_CHAR): - doc: | - Material of which the emitter is build, e.g. the filament material. - - # MK could be made an instance of NXsample - description(NX_CHAR): - doc: | - Ideally, a (globally) unique persistent identifier, link, - or text to a resource which gives further details. - - # NEW ISSUE: details about the life/up-time of the source - # relevant from maintenance point of view - (NXtransformations): - doc: | - Collection of axis-based translations and rotations to describe the - location and geometry of the component in the instrument. - (NXlens_em): - (NXaperture): - (NXmonochromator): - (NXcorrector_cs): - (NXcomponent): - (NXsensor): - (NXactuator): - (NXbeam): - doc: | - Individual characterization results for the position, shape, - and characteristics of the electron beam. - - :ref:`NXtransformations` should be used to specify the location - of the position at which the beam was probed. - (NXdeflector): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ea5b38d017e38c479f28b8c793115e2860c2c2facfb3ab3316d5e237c54382b4 -# -# -# -# -# -# -# Base class for a set of components providing a controllable electron beam. -# -# -# -# Typically tech-partner, microscope-, and control software-specific -# name of the specific operation mode how the ebeam_column and its -# components are controlled to achieve a specific illumination condition. -# -# In most cases users do not know, have to care, or are able to disentangle the -# details of the spatiotemporal dynamics of the components of the microscope. -# Instead, they rely on the assumption that the microscope and control software -# work as expected. Selecting then a specific operation_mode assures some level -# of reproducibility in the illumination conditions. -# -# -# -# -# -# -# The source which creates the electron beam. -# -# -# -# Given name/alias. -# -# -# -# -# -# Voltage relevant to compute the energy of the electrons -# immediately after they left the gun. -# -# -# -# -# Type of radiation. -# -# -# -# -# -# -# -# Emitter type used to create the beam. -# -# If the emitter type is other, give further details -# in the description field. -# -# -# -# -# -# Material of which the emitter is build, e.g. the filament material. -# -# -# -# -# -# Ideally, a (globally) unique persistent identifier, link, -# or text to a resource which gives further details. -# -# -# -# -# -# Collection of axis-based translations and rotations to describe the -# location and geometry of the component in the instrument. -# -# -# -# -# -# -# -# -# -# -# -# -# Individual characterization results for the position, shape, -# and characteristics of the electron beam. -# -# :ref:`NXtransformations` should be used to specify the location -# of the position at which the beam was probed. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXem_calorimetry.yaml b/contributed_definitions/nyaml/NXem_calorimetry.yaml index 752626534f..62c3234827 100644 --- a/contributed_definitions/nyaml/NXem_calorimetry.yaml +++ b/contributed_definitions/nyaml/NXem_calorimetry.yaml @@ -7,7 +7,7 @@ doc: | * What is the technique about. * General context. * Literature references. - + # intentionally axes are not named x, y, z to # i) assure indices can be used for real and complex, # ii) that people think hard about how their base vectors @@ -26,7 +26,7 @@ symbols: type: group NXem_calorimetry(NXobject): (NXentry): - exists: [min, 1, max, 1] + exists: ['min', '1', 'max', '1'] definition(NX_CHAR): enumeration: [NXem_calorimetry] profiling(NXcs_profiling): @@ -49,12 +49,12 @@ NXem_calorimetry(NXobject): doc: | Programs and libraries representing the computational environment programID(NXprogram): - exists: [min, 1, max, infty] + exists: ['min', '1', 'max', 'unbounded'] nameType: partial program(NX_CHAR): \@version(NX_CHAR): userID(NXuser): - exists: [min, 0, max, infty] + exists: ['min', '0', 'max', 'unbounded'] nameType: partial sample(NXsample): exists: recommended @@ -74,9 +74,10 @@ NXem_calorimetry(NXobject): these from the resources pointed to by parent_identifier or walk through eventually deeply nested groups in data instances. citeID(NXcite): - exists: [min, 0, max, infty] + exists: ['min', '0', 'max', 'unbounded'] nameType: partial - # a place where to add citations for your work ... + + # a place where to add citations for your work ... diffraction_space(NXcoordinate_system): exists: optional diffraction(NXnote): @@ -118,97 +119,426 @@ NXem_calorimetry(NXobject): (e.g. obtained temperature via the actuator) are reported through delta_time. identifier_pattern(NX_UINT): - dim: (n_p,) unit: NX_UNITLESS + dimensions: + rank: 1 + dim: (n_p,) delta_time(NX_FLOAT): + unit: NX_TIME doc: | Time difference to start_time. Collecting diffraction pattern also takes some time. It is assumed that the acquisition time for each pattern is substantial shorter than the time it takes the actuator to - cause a change in stimulus (e.g. temperature). - unit: NX_TIME - dim: (n_p,) - # timestamp(NX_DATE_TIME): - # exists: optional - # doc: | - # Timestamp that is used for each diffraction pattern to correlate the results - # obtained from that pattern with associated actuator data. - # ISO8601 with local time zone information if possible and as precise as practically - # possible. The indices follow the same order as - # used for identifier_pattern. - # dim: (n_p,) + cause a change in stimulus (e.g. temperature). + dimensions: + rank: 1 + dim: (n_p,) + + # timestamp(NX_DATE_TIME): + # exists: optional + # doc: | + # Timestamp that is used for each diffraction pattern to correlate the results + # obtained from that pattern with associated actuator data. + # ISO8601 with local time zone information if possible and as precise as practically + # possible. The indices follow the same order as + # used for identifier_pattern. + # dim: (n_p,) pattern_center(NXprocess): doc: | - Computation of the centre for each pattern using e.g. a Circular Hough Transformation. + Computation of the centre for each pattern using e.g. a Circular Hough + Transformation. sequence_index(NX_POSINT): + # NXcg_point position(NX_FLOAT): + unit: NX_LENGTH doc: | Computed centre for each pattern. - unit: NX_LENGTH - dim: (n_p, 2) - #\@units: 1/nm + dimensions: + rank: 2 + dim: (n_p, 2) + + # \@units: 1/nm distortion_correction(NXprocess): exists: optional doc: | - Elliptical distortion correction as a step when computing the centre for patterns. + Elliptical distortion correction as a step when computing the centre for + patterns. sequence_index(NX_POSINT): + # TODO config(NXcollection): # NXcg_ellipsoid center(NX_NUMBER): + unit: NX_LENGTH doc: | Computed centre for each pattern. - unit: NX_LENGTH - dim: (n_p, 2) - #\@units: 1/nm + dimensions: + rank: 2 + dim: (n_p, 2) + + # \@units: 1/nm integration(NXprocess): doc: | Integrated diffraction pattern intensity as a function of radial distance from the centre azimuthally integrated as a function of time. sequence_index(NX_POSINT): + # TODO config(NXcollection): resultBACKGROUND(NXdata): - exists: [min, 0, max, 2] + exists: ['min', '0', 'max', '2'] doc: | The integrated intensities: * result_with_background * result_without_background - \@signal(NX_CHAR): - \@axes(NX_CHAR): # [s] + \@axes(NX_CHAR): \@AXISNAME_indices(NX_CHAR): title(NX_CHAR): intensity(NX_FLOAT): - doc: | - Integrated intensity as a function of time and the radial distance from the pattern centre. - dim: (n_p, n_f) unit: NX_UNITLESS + doc: | + Integrated intensity as a function of time and the radial distance from the + pattern centre. + dimensions: + rank: 2 + dim: (n_p, n_f) \@long_name(NX_CHAR): identifier_pattern(NX_UINT): exists: optional + unit: NX_UNITLESS doc: | Identifier for each pattern. - dim: (n_p,) - unit: NX_UNITLESS + dimensions: + rank: 1 + dim: (n_p,) \@long_name(NX_CHAR): s(NX_FLOAT): + unit: NX_ANY doc: | Positions in reciprocal space. - dim: (n_f,) - unit: NX_ANY - #\@units: 1/nm + dimensions: + rank: 1 + dim: (n_f,) + + # \@units: 1/nm \@long_name(NX_CHAR): time(NX_FLOAT): + unit: NX_TIME doc: | Time since start of the in-situ experiment - dim: (n_p,) - unit: NX_TIME - # \@units: s + dimensions: + rank: 1 + dim: (n_p,) + + # \@units: s # TODO e.g. could add parameter of functional forms for the background of each pattern # more NXprocess groups could follow only sky is the limit and your imagination and time devotion background_subtraction(NXprocess): exists: optional sequence_index(NX_POSINT): + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# f08363f38c031a857a82e75ea03d563b97be6e29bfeeedeb2bab0298125c46ed +# +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# Number of diffraction pattern. +# +# +# +# +# Number of radial integration bins. +# +# +# +# +# Number of coordinates along i axis. +# +# +# +# +# Number of coordinates along j axis. +# +# +# +# +# Application definition for minimal example in-situ calorimetry. +# +# TODO: +# +# * What is the technique about. +# * General context. +# * Literature references. +# +# +# +# +# +# +# +# +# +# Details about performance, profiling, etc. +# +# +# +# +# +# +# +# Name of the program whereby this config file was created. +# +# +# +# +# +# +# +# Programs and libraries representing the computational environment +# +# +# +# +# +# +# +# +# +# +# +# A qualifier whether the sample is a real one or a virtual one. +# +# +# +# +# +# +# +# +# List of comma-separated elements from the periodic table that are +# contained in the specimen. If the specimen substance has multiple +# components, all elements from each component must be included in +# `atom_types`. +# +# The purpose of the field is to offer research data management systems an +# opportunity to parse the relevant elements without having to interpret +# these from the resources pointed to by parent_identifier or walk through +# eventually deeply nested groups in data instances. +# +# +# +# +# +# +# +# +# Reference to the resource which stores acquired pattern from the +# experiment or simulation that are analyzed in this workflow. +# +# Can refer to the original EMD or MRC files or the parsed NXem +# in RDM e.g. NOMAD OASIS. +# +# +# +# +# +# +# +# Reference to the resource which stores actuator log file from the experiment. +# +# +# +# +# +# +# +# Configuration file that was used for parameterizing this analysis workflow. +# +# +# +# +# +# +# +# Assumptions and computations whereby timestamping data from +# the detector and actuator (e.g. heating chip) were synchronized. +# +# +# +# +# ISO8601 with local time zone reference timestamp that tells +# with which delta_time can be converted in timestamp. +# The reference timestamp is defined as the time when the +# actuator started acting on the sample. +# +# Time differences to this timestamp when correlated signals such +# as diffraction pattern matching with a specific state of the sample +# (e.g. obtained temperature via the actuator) are reported through +# delta_time. +# +# +# +# +# +# +# +# +# +# Time difference to start_time. +# +# Collecting diffraction pattern also takes some time. +# It is assumed that the acquisition time for each pattern is +# substantial shorter than the time it takes the actuator to +# cause a change in stimulus (e.g. temperature). +# +# +# +# +# +# +# +# +# +# Computation of the centre for each pattern using e.g. a Circular Hough +# Transformation. +# +# +# +# +# +# Computed centre for each pattern. +# +# +# +# +# +# +# +# +# +# +# Elliptical distortion correction as a step when computing the centre for +# patterns. +# +# +# +# +# +# Computed centre for each pattern. +# +# +# +# +# +# +# +# +# +# +# Integrated diffraction pattern intensity as a function of radial distance from the centre +# azimuthally integrated as a function of time. +# +# +# +# +# +# The integrated intensities: +# +# * result_with_background +# * result_without_background +# +# +# +# +# +# +# +# Integrated intensity as a function of time and the radial distance from the +# pattern centre. +# +# +# +# +# +# +# +# +# +# Identifier for each pattern. +# +# +# +# +# +# +# +# +# Positions in reciprocal space. +# +# +# +# +# +# +# +# +# +# Time since start of the in-situ experiment +# +# +# +# +# +# +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXem_correlation.yaml b/contributed_definitions/nyaml/NXem_correlation.yaml deleted file mode 100644 index f9682deedb..0000000000 --- a/contributed_definitions/nyaml/NXem_correlation.yaml +++ /dev/null @@ -1,450 +0,0 @@ -category: base -doc: | - Base class to combine different method-specific data in electron microscopy. - - This base class represent a template for documenting correlations - (spatial, temporal) between different method-specific results. -type: group -NXem_correlation(NXem_method): - (NXprocess): - doc: | - Details about processing steps. - sequence_index(NX_INT): - indexing(NXprocess): - doc: | - Details about correlated or logically connected EBSD datasets. - - One important class of such correlated experiments are the so-called - (quasi) in-situ experiments. In this case the same or nearly the same ROI - gets analyzed via a repetitive sequence of thermomechanical treatment, - sample preparation, measurement, on-the-fly-indexing. Phenomena - investigated are recrystallization, strain accumulation, material damage. - Post-processing is required to correlate and reidentify eventual - microstructural features or local ROIs across several orientation maps. - - Another important class of correlated experiments are the so-called - serial-sectioning experiments. Here the same sample is measured - repetitively after polishing each time, to create a stack of - orientation data which can be reconstructed to a - three-dimensional volume ROI. - - Data can be correlated in time, position (spatial), or both (spatiotemporal). - - Spatial correlations between repetitively characterized regions-of-interests - are typically correlated using image registration and alignment algorithms. - For this typically so-called landmarks are used. These can be grains with - a very large size or specific shape, i.e. grains which are qualitatively - different enough to be used as a guide how images are shifted relative to - one another. Other commonly used landmarks are fiducial marks which are - milled into the specimen surface using focus-ion beam milling and/or various - types of indentation methods. - - As far as the same physical region-of-interest is just measured several times, - the additional issue of the depth increment is not a concern. However, correct - assumptions for the depth increment, amount of material removed along the milling - direction is relevant for accurate and precise three-dimensional (serial-sectioning) - correlations. For these studies it can be tricky though to assume or estimate - useful depth increments. Different strategies have been proposed like - calibrations, wedged-shaped landmarks and computer simulation assisted - assumption making. - - Despite the use of landmarks, there are many practical issues which make the - processing of correlations imprecise and inaccurate. Among these are drift - and shift of the specimen, instabilities of the holder, the beam, irrespective - of the source of the drift, charging effects, here specifically causing local - image distortions and rotations which may require special processing algorithms - to reduce such imprecisions. - - Time correlations face all of the above-mentioned issues surplus the challenge - that specific experimental protocols have to be used to ensure the material state - is observed at specific physical time. The example of quasi in-situ characterization - of crystal growth phenomena, a common topic in engineering or modern catalysis research - makes it necessary to consider that e.g. the target value for the desired annealing - temperature is not just gauged based on macroscopic arguments but considers - that transient effects take place. Heating or quenching a sample might thus might - not have been executed under conditions in the interaction volume as they are - documented and/or assumed. - - These issue cause that correlations have an error margin as to how accurately - respective datasets were not only just synced based on the geometry of the - region-of-interests and the time markers but also to asssure which physical - conditions the specimen experienced over the course of the measurements. - - The fourth example of the em_om reference implementation explores the use of the - correlation group with a serial-sectioning datasets that was collected by the - classical Inconel 100 dataset collected by M. D. Uchic and colleagues - (M. Groeber M, Haley BK, Uchic MD, Dimiduk DM, Ghosh S 3d reconstruction and - characterization of polycrystalline microstructures using a fib-sem system data set. - Mater Charac 2006, 57 259–273. 10.1016/j.matchar.2006.01.019M). - - This dataset was specifically relevant in driving forward the implementation - of the DREAM.3D software. DREAM.3D is an open-source software project for - post-processing and reconstructing, i.e. correlating sets of orientation - microscopy data foremost spatially. One focus of the software is the - (post-)processing of EBSD datasets. Another cutting edge tool with similar - scope but a commercial solution by Bruker is QUBE which was developed by - P. Konijnenberg and coworkers. - - Conceptually, software like DREAM.3D supports users with creating linear - workflows of post-processing tasks. Workflows can be instructed via the - graphical user interface or via so-called pipeline processing via command line - calls. DREAM.3D is especially useful because its internal system documents all - input, output, and parameter of the processing steps. This makes DREAM.3D a - good candidate to interface with tools like em_om parser. Specifically, DREAM.3D - documents numerical results via a customized HDF5 file format called DREAM3D. - Workflow steps and settings are stored as nested dictionaries in JSON syntax - inside a supplementary JSON file or alongside the data in the DREAM3D file. - DREAM.3D has a few hundred algorithms implemented. These are called filters - in DREAM.3D terminology. - - Users configure a workflow which instructs DREAM.3D to send the data through - a chain of predefined and configured filters. Given that for each analysis - the filter is documented via its version tags surplus its parameter and setting - via a controlled vocabulary, interpreting the content of a DREAM3D HDF5 file - is possible in an automated manner using a parser. This makes DREAM.3D analyses - repeatable and self-descriptive. A key limitation though is that most frequently - the initial set of input data come from commercial files like ANG. - This missing link between the provenance of these input files, their associated - creation as electron microscope session, is also what NXem_ebsd solves. - - Nevertheless, as this can be solved with e.g. NXem_ebsd we are convinced that - the DREAM.3D and the em_om parser can work productively together to realize - RDMS-agnostic parsing of serial-section analyses. - - The internal documentation of the DREAM.3D workflow also simplifies the - provenance tracking represented by an instance of NXem_ebsd as not every - intermediate results has to be stored. Therefore, the fourth example - focuses on the key result obtained from DREAM.3D - the reconstructed - and aligned three-dimensional orientation map. - - Usually, this result is the starting point for further post-processing - and characterization of structural features. As here orientation microscopy - is insofar scale invariant using DREAM.3D, NXem_ebsd, and em_om should - be useful for different characterization methods, such as EBSD, Transmission - Kikuchi Diffraction (TKD), Automated Crystal Orientation Mapping (ACOM), - Nanobeam Electron Diffraction (using commercial systems like NanoMegas ASTAR) - or open-source implementations of these techniques (such as via pyxem/orix). - - The result of orientation microscopy methods are maps of local orientation - and thermodynamic phase (crystal structure) pieces of information. Virtually - all post-processing of such results for structural features includes again - a workflow of steps which are covered though by the NXmicrostructure partner application - definition. The respective source of the data in an instance of NXmicrostructure can - again be a link or reference to an instance of NXem_ebsd to complete the - chain of provenance. - (NXcrystal_structure): - roi(NXdata): - descriptor: - doc: | - Descriptor representing the image contrast. - - # \@signal: # data - # \@axes: # [axis_y, axis_x] - # \@axis_x_indices: 0 - # \@axis_y_indices: 1 - # \@signal: - # \@axes: - # \@AXISNAME_indices: - # \@long_name: - title: - doc: | - Title of the default plot. - data(NX_NUMBER): - unit: NX_UNITLESS - doc: | - Descriptor values displaying the ROI. - dimensions: - rank: 3 - dim: (n_z, n_y, n_x) - - # n_0 slowest 3, n_1 slow 2, n_2 fast 1, rgb triplet is fastest 0 - # in axes fast to fastest - # while for _indices fastest to fast - \@long_name: - doc: | - Descriptor values. - axis_z(NX_NUMBER): - unit: NX_LENGTH - doc: | - Calibrated coordinate along the z-axis. - dimensions: - rank: 1 - dim: (n_z,) - \@long_name: - doc: | - Label for the z axis - axis_y(NX_NUMBER): - unit: NX_LENGTH - doc: | - Calibrated coordinate along the y-axis. - dimensions: - rank: 1 - dim: (n_y,) - \@long_name: - doc: | - Label for the y axis - axis_x(NX_NUMBER): - unit: NX_LENGTH - doc: | - Calibrated coordinate along the x-axis. - dimensions: - rank: 1 - dim: (n_x,) - \@long_name: - doc: | - Label for the x axis - - # NEW ISSUE: implement support for filters eventually many of them - # NEW ISSUE: for now only show that data from DREAM3D can be loaded. - # NEW ISSUE: how to handle landmarks - # NEW ISSUE: again an entire set of workflows such as rigid or non-rigid - # image registration etc. - # sequence_index(N0): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 05d2b94d79da830808963d282d7d1db6eb6d7d56ed54896015a30641fcd46cd1 -# -# -# -# -# -# Base class to combine different method-specific data in electron microscopy. -# -# This base class represent a template for documenting correlations -# (spatial, temporal) between different method-specific results. -# -# -# -# Details about processing steps. -# -# -# -# -# -# Details about correlated or logically connected EBSD datasets. -# -# One important class of such correlated experiments are the so-called -# (quasi) in-situ experiments. In this case the same or nearly the same ROI -# gets analyzed via a repetitive sequence of thermomechanical treatment, -# sample preparation, measurement, on-the-fly-indexing. Phenomena -# investigated are recrystallization, strain accumulation, material damage. -# Post-processing is required to correlate and reidentify eventual -# microstructural features or local ROIs across several orientation maps. -# -# Another important class of correlated experiments are the so-called -# serial-sectioning experiments. Here the same sample is measured -# repetitively after polishing each time, to create a stack of -# orientation data which can be reconstructed to a -# three-dimensional volume ROI. -# -# Data can be correlated in time, position (spatial), or both (spatiotemporal). -# -# Spatial correlations between repetitively characterized regions-of-interests -# are typically correlated using image registration and alignment algorithms. -# For this typically so-called landmarks are used. These can be grains with -# a very large size or specific shape, i.e. grains which are qualitatively -# different enough to be used as a guide how images are shifted relative to -# one another. Other commonly used landmarks are fiducial marks which are -# milled into the specimen surface using focus-ion beam milling and/or various -# types of indentation methods. -# -# As far as the same physical region-of-interest is just measured several times, -# the additional issue of the depth increment is not a concern. However, correct -# assumptions for the depth increment, amount of material removed along the milling -# direction is relevant for accurate and precise three-dimensional (serial-sectioning) -# correlations. For these studies it can be tricky though to assume or estimate -# useful depth increments. Different strategies have been proposed like -# calibrations, wedged-shaped landmarks and computer simulation assisted -# assumption making. -# -# Despite the use of landmarks, there are many practical issues which make the -# processing of correlations imprecise and inaccurate. Among these are drift -# and shift of the specimen, instabilities of the holder, the beam, irrespective -# of the source of the drift, charging effects, here specifically causing local -# image distortions and rotations which may require special processing algorithms -# to reduce such imprecisions. -# -# Time correlations face all of the above-mentioned issues surplus the challenge -# that specific experimental protocols have to be used to ensure the material state -# is observed at specific physical time. The example of quasi in-situ characterization -# of crystal growth phenomena, a common topic in engineering or modern catalysis research -# makes it necessary to consider that e.g. the target value for the desired annealing -# temperature is not just gauged based on macroscopic arguments but considers -# that transient effects take place. Heating or quenching a sample might thus might -# not have been executed under conditions in the interaction volume as they are -# documented and/or assumed. -# -# These issue cause that correlations have an error margin as to how accurately -# respective datasets were not only just synced based on the geometry of the -# region-of-interests and the time markers but also to asssure which physical -# conditions the specimen experienced over the course of the measurements. -# -# The fourth example of the em_om reference implementation explores the use of the -# correlation group with a serial-sectioning datasets that was collected by the -# classical Inconel 100 dataset collected by M. D. Uchic and colleagues -# (M. Groeber M, Haley BK, Uchic MD, Dimiduk DM, Ghosh S 3d reconstruction and -# characterization of polycrystalline microstructures using a fib-sem system data set. -# Mater Charac 2006, 57 259–273. 10.1016/j.matchar.2006.01.019M). -# -# This dataset was specifically relevant in driving forward the implementation -# of the DREAM.3D software. DREAM.3D is an open-source software project for -# post-processing and reconstructing, i.e. correlating sets of orientation -# microscopy data foremost spatially. One focus of the software is the -# (post-)processing of EBSD datasets. Another cutting edge tool with similar -# scope but a commercial solution by Bruker is QUBE which was developed by -# P. Konijnenberg and coworkers. -# -# Conceptually, software like DREAM.3D supports users with creating linear -# workflows of post-processing tasks. Workflows can be instructed via the -# graphical user interface or via so-called pipeline processing via command line -# calls. DREAM.3D is especially useful because its internal system documents all -# input, output, and parameter of the processing steps. This makes DREAM.3D a -# good candidate to interface with tools like em_om parser. Specifically, DREAM.3D -# documents numerical results via a customized HDF5 file format called DREAM3D. -# Workflow steps and settings are stored as nested dictionaries in JSON syntax -# inside a supplementary JSON file or alongside the data in the DREAM3D file. -# DREAM.3D has a few hundred algorithms implemented. These are called filters -# in DREAM.3D terminology. -# -# Users configure a workflow which instructs DREAM.3D to send the data through -# a chain of predefined and configured filters. Given that for each analysis -# the filter is documented via its version tags surplus its parameter and setting -# via a controlled vocabulary, interpreting the content of a DREAM3D HDF5 file -# is possible in an automated manner using a parser. This makes DREAM.3D analyses -# repeatable and self-descriptive. A key limitation though is that most frequently -# the initial set of input data come from commercial files like ANG. -# This missing link between the provenance of these input files, their associated -# creation as electron microscope session, is also what NXem_ebsd solves. -# -# Nevertheless, as this can be solved with e.g. NXem_ebsd we are convinced that -# the DREAM.3D and the em_om parser can work productively together to realize -# RDMS-agnostic parsing of serial-section analyses. -# -# The internal documentation of the DREAM.3D workflow also simplifies the -# provenance tracking represented by an instance of NXem_ebsd as not every -# intermediate results has to be stored. Therefore, the fourth example -# focuses on the key result obtained from DREAM.3D - the reconstructed -# and aligned three-dimensional orientation map. -# -# Usually, this result is the starting point for further post-processing -# and characterization of structural features. As here orientation microscopy -# is insofar scale invariant using DREAM.3D, NXem_ebsd, and em_om should -# be useful for different characterization methods, such as EBSD, Transmission -# Kikuchi Diffraction (TKD), Automated Crystal Orientation Mapping (ACOM), -# Nanobeam Electron Diffraction (using commercial systems like NanoMegas ASTAR) -# or open-source implementations of these techniques (such as via pyxem/orix). -# -# The result of orientation microscopy methods are maps of local orientation -# and thermodynamic phase (crystal structure) pieces of information. Virtually -# all post-processing of such results for structural features includes again -# a workflow of steps which are covered though by the NXmicrostructure partner application -# definition. The respective source of the data in an instance of NXmicrostructure can -# again be a link or reference to an instance of NXem_ebsd to complete the -# chain of provenance. -# -# -# -# -# -# Descriptor representing the image contrast. -# -# -# -# -# -# Title of the default plot. -# -# -# -# -# Descriptor values displaying the ROI. -# -# -# -# -# -# -# -# -# -# Descriptor values. -# -# -# -# -# -# Calibrated coordinate along the z-axis. -# -# -# -# -# -# -# Label for the z axis -# -# -# -# -# -# Calibrated coordinate along the y-axis. -# -# -# -# -# -# -# Label for the y axis -# -# -# -# -# -# Calibrated coordinate along the x-axis. -# -# -# -# -# -# -# Label for the x axis -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXem_method.yaml b/contributed_definitions/nyaml/NXem_method.yaml deleted file mode 100644 index 29394e92d2..0000000000 --- a/contributed_definitions/nyaml/NXem_method.yaml +++ /dev/null @@ -1,69 +0,0 @@ -category: base -doc: | - Base class to describe specific analysis methods in electron microscopy. - - This base class represent a template how specialized, deep, and method-specific - base classes can be defined with which an (NXem) application - definition gets equipped with specific groups to document method-specific - processing steps and report analyzed quantities. - - The template base class name :ref:`NXem_method` needs to be changed for - each method e.g. :ref:`NXem_ebsd`, :ref:`NXem_eels`, :ref:`NXem_eds`. -type: group -NXem_method(NXobject): - (NXprocess): - doc: | - Details about processing steps. - sequence_index(NX_INT): - (NXimage_set): - (NXspectrum_set): - - # add links to relevant data - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 354ca4da36a8b1e488077a2a253137749aa101bfc4fe742b56a4f9aeac3b531e -# -# -# -# -# -# Base class to describe specific analysis methods in electron microscopy. -# -# This base class represent a template how specialized, deep, and method-specific -# base classes can be defined with which an (NXem) application -# definition gets equipped with specific groups to document method-specific -# processing steps and report analyzed quantities. -# -# The template base class name :ref:`NXem_method` needs to be changed for -# each method e.g. :ref:`NXem_ebsd`, :ref:`NXem_eels`, :ref:`NXem_eds`. -# -# -# -# Details about processing steps. -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXem_msr.yaml b/contributed_definitions/nyaml/NXem_msr.yaml deleted file mode 100644 index 1b484354a5..0000000000 --- a/contributed_definitions/nyaml/NXem_msr.yaml +++ /dev/null @@ -1,169 +0,0 @@ -category: base -doc: | - Base class for collecting a session with a real electron microscope. - - For collecting data and experiments which are simulations of an - electron microscope use the :ref:`NXem_sim` base class. -type: group -NXem_msr(NXem_method): - em_lab(NXinstrument): - doc: | - (Meta)data of the microscope and the lab in which it stands. - - This em_lab group differs from potential em_lab groups inside - :ref:`NXevent_data_em` instances in that here the more static descriptions - are kept while changing, i.e. time-dependent pieces of information are - logged, via the em_lab group inside the desired number of instances - of NXevent_data_em. - - While using an :ref:`NXevent_data_em` instance, users should store only those - settings about a component which are relevant to understand the current - state of the component. Here, current means for the time interval which - the event covers (as it is detailed via start_time and end_time) timestamps. - - For example it is not relevant to store in each :ref:`NXevent_data_em` - electron_source group again the details of the gun type and the manufacturer - but only the high-voltage value and that only if it is different from the value - that is specified in the em_lab section for the static settings. - - In effect, this defines an information inference hierarchy which starts - in an individual :ref:`NXevent_data_em` instance followed by a probing of the - static section. - instrument_name(NX_CHAR): - doc: | - Given name of the microscope at the hosting institution. - This is an alias. Examples could be NionHermes, Titan, JEOL, - Gemini, etc. - location(NX_CHAR): - doc: | - Location of the lab or place where the instrument is installed. - Using GEOREF is preferred. - (NXfabrication): - (NXchamber): - (NXebeam_column): - (NXibeam_column): - (NXoptical_system_em): - - # storing these data should happen in event_data, i.e. dynamic quantities - (NXscanbox_em): - (NXdetector): - doc: | - Description of the type of the detector. - - Electron microscopes have typically multiple detectors. - Different technologies are in use like CCD, scintillator, - direct electron, CMOS, or image plate to name but a few. - local_name(NX_CHAR): - doc: | - Instrument-specific alias/name - - # it is unfortunate that for NXdetector there are already many places - # how one can specify details which could equally end up in fabrications - # we should give better guidance which option to use, pr to niac - # (NXfabrication): - (NXpump): - (NXstage_lab): - (NXevent_data_em_set): - - # (NXevent_data_em): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0e01f3854fcca304e9e2fd278b8916b35d4da68dd4c0cb7993393ba8f0abee05 -# -# -# -# -# -# Base class for collecting a session with a real electron microscope. -# -# For collecting data and experiments which are simulations of an -# electron microscope use the :ref:`NXem_sim` base class. -# -# -# -# (Meta)data of the microscope and the lab in which it stands. -# -# This em_lab group differs from potential em_lab groups inside -# :ref:`NXevent_data_em` instances in that here the more static descriptions -# are kept while changing, i.e. time-dependent pieces of information are -# logged, via the em_lab group inside the desired number of instances -# of NXevent_data_em. -# -# While using an :ref:`NXevent_data_em` instance, users should store only those -# settings about a component which are relevant to understand the current -# state of the component. Here, current means for the time interval which -# the event covers (as it is detailed via start_time and end_time) timestamps. -# -# For example it is not relevant to store in each :ref:`NXevent_data_em` -# electron_source group again the details of the gun type and the manufacturer -# but only the high-voltage value and that only if it is different from the value -# that is specified in the em_lab section for the static settings. -# -# In effect, this defines an information inference hierarchy which starts -# in an individual :ref:`NXevent_data_em` instance followed by a probing of the -# static section. -# -# -# -# Given name of the microscope at the hosting institution. -# This is an alias. Examples could be NionHermes, Titan, JEOL, -# Gemini, etc. -# -# -# -# -# Location of the lab or place where the instrument is installed. -# Using GEOREF is preferred. -# -# -# -# -# -# -# -# -# -# -# -# Description of the type of the detector. -# -# Electron microscopes have typically multiple detectors. -# Different technologies are in use like CCD, scintillator, -# direct electron, CMOS, or image plate to name but a few. -# -# -# -# Instrument-specific alias/name -# -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXem_sim.yaml b/contributed_definitions/nyaml/NXem_sim.yaml deleted file mode 100644 index e7e255261f..0000000000 --- a/contributed_definitions/nyaml/NXem_sim.yaml +++ /dev/null @@ -1,97 +0,0 @@ -category: base -doc: | - Base class for simulating electron microscopy relevant beam-matter interaction. - - The concept behind this base class is to keep it as generic as possible - that simulations of electron/ion beam interaction with matter can be - represented. This base class is envisioned as the twin of the :ref:`NXem_msr` - base class. - - It is an attempt to test the idea if at some point one might even use the - same base class template to describe measurements and computer simulations - of electron microscopy. This idea is attractive because the only practical - difference between a description of a measurement with a microscope and a - computer simulation is that the latter is typically a substantially simplified - representation of the real microscope surplus the focus of the research - in such cases on specific questions. - - Such simplification can be with respect to the optical setup, typically the - ignoring of the fact that the electron beam is produced by a complex setup - of lenses while in simulations often single Einzel lenses are considered. - Dynamics of the environment like temperature fluctuation in a lab, vibrations, - users, and multiple detectors are typically either ignored or reduced in - complexity and number and coming with idealizations to keep the simulations - focused on the specific reason questions and efficiently numerically executable. - -# abTEM and other simulation packages, TEMgym, etc. -type: group -NXem_sim(NXem_method): - simulation(NXprocess): - doc: | - Details about the simulation. - - # sequence_index(N): - (NXprogram): - (NXcg_geodesic_mesh): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# a505636470b8d3ff0f80d1f120b806466d289fa97c3c5c2ba48f7ab788fa9fc2 -# -# -# -# -# -# -# Base class for simulating electron microscopy relevant beam-matter interaction. -# -# The concept behind this base class is to keep it as generic as possible -# that simulations of electron/ion beam interaction with matter can be -# represented. This base class is envisioned as the twin of the :ref:`NXem_msr` -# base class. -# -# It is an attempt to test the idea if at some point one might even use the -# same base class template to describe measurements and computer simulations -# of electron microscopy. This idea is attractive because the only practical -# difference between a description of a measurement with a microscope and a -# computer simulation is that the latter is typically a substantially simplified -# representation of the real microscope surplus the focus of the research -# in such cases on specific questions. -# -# Such simplification can be with respect to the optical setup, typically the -# ignoring of the fact that the electron beam is produced by a complex setup -# of lenses while in simulations often single Einzel lenses are considered. -# Dynamics of the environment like temperature fluctuation in a lab, vibrations, -# users, and multiple detectors are typically either ignored or reduced in -# complexity and number and coming with idealizations to keep the simulations -# focused on the specific reason questions and efficiently numerically executable. -# -# -# -# Details about the simulation. -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXevent_data_apm.yaml b/contributed_definitions/nyaml/NXevent_data_apm.yaml deleted file mode 100644 index 54ea678c16..0000000000 --- a/contributed_definitions/nyaml/NXevent_data_apm.yaml +++ /dev/null @@ -1,119 +0,0 @@ -category: base -doc: | - Base class to store state and (meta)data of events over the course of an atom probe experiment. - - Having at least one instance for an instance of NXapm is recommended. - - This base class applies the concept of the NXevent_data_em base class to the specific needs - of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication - of information. Specifically, the time interval considered is the entire time - starting at start_time until end_time during which we assume the pulser triggered named pulses. - These pulses are identified via the pulse_identifier field. The point in time when each was issued - is specified via the combination of start_time and delta_time. - - Conceptually and technically NeXus currently stores tensorial information as arrays of values - (with each value of the same datatype). For instance, a field temperature(NX_FLOAT) stores - a set of temperature values but that field when used somewhere is a concept. However, that - concept has no information at which point in time these temperatures were taken. - An existent functional relationship between the two concepts is not defined. - - However, a correct interpretation of the temperature values demands knowledge about what is - the independent quantity on which temperature depends on or according to which frequency - temperature values were sampled. - In NeXus there are two approaches which cope with such correlations: - One is :ref:`NXdata` where the attribute signal specifies the correlation. - The other one is :ref:`NXlog` which, like NXdata, demands to granularize logged_against - (dependent signal) and independent quantities into an own group. - In many cases this additional grouping is not desired though. - - One naive solution typically employed is then to store the independent variable values via a second - vector e.g. time_stamp with the same number of entries (with dimensionality defined through symbols). - However, there is no independent logical connection between these two concepts, i.e. temperature - and time_stamp. - - In the case of atom probe though the time that one would use in NXlog is defined implicitly via pulse_identifier, - which is the independent variable vector against which eventually dozens of channels of data are logged. - Not only are these channels logged they should ideally also be self-descriptive in that these channels have - pulse_identifier as the independent variable but we do not wish to duplicate this information all the time but - reference it. - - Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the - symbol depends_on but this is easily to be confused with depends_on that is used for instances of - :ref:`NXtransformations`. Consequently, if depends_on were to be used extra logic is needed by consuming - applications to understand that the here build correlations are conceptually different ones. - - This issue should be discussed further by the NeXus community. -type: group -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - p: | - Number of pulses collected in between start_time and end_time. -NXevent_data_apm(NXobject): - start_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while - the end_time specifies the end (right bound) of the time interval. - end_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval ended. - delta_time(NX_NUMBER): - doc: | - Delta time array which resolves for each pulse_identifier the time difference - between when that pulse was issued and start_time. - - In summary, using start_time, end_time, delta_time, pulse_identifier_offset, - and pulse_identifier exactly specifies the connection between when a pulse was - issued relative to start and absolute in UTC. - unit: NX_TIME - dim: (p,) - pulse_identifier_offset(NX_INT): - doc: | - Integer used to name the first pulse to know if there is an - offset of the identifiers to zero. - - Identifiers can be defined either implicitly or explicitly. - For implicit indexing identifiers are defined on the interval - :math:`[identifier\_offset, identifier\_offset + c - 1]`. - - Therefore, implicit identifier are completely defined by the value of - identifier_offset and cardinality. For example if identifier run from - -2 to 3 the value for identifier_offset is -2. - - For explicit indexing the field identifier has to be used. - Fortran-/Matlab- and C-/Python-style indexing have specific implicit - identifier conventions where identifier_offset is 1 and 0 respectively. - unit: NX_UNITLESS - pulse_identifier(NX_INT): - doc: | - Identifier that contextualizes how the detector and pulser of an atom probe - instrument follows a sequence of pulses to trigger field evaporation. - - The pulse_identifier is used to associate thus an information about time - when quantities have been collected via sampling. - - In virtually all cases the pulser is a blackbox. Depending on how the - instrument is configured during a measurement the target - values and thus also the actual values may change. - - Maybe the first part of the experiment is run at a certain pulse fraction but thereafter - the pulse_fraction is changed. In this case the field pulse_fraction is a vector which - collects all measured values of the pulse_fraction, pulse_identifier is then an equally - long vector which stores the set of events (e.g. pulsing events) when that value was - measured. - - This may cause several situations: In the case that e.g. the pulse_fraction is never changed - and also exact details not interesting, one stores the set value for the pulse_fraction - and a single value for the pulse_identifier e.g. 0 to indicate that the pulse_fraction was set - at the beginning and it was maintained constant during the measurement. - If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a - vector with two values one for the first and another one for the value from the 100000-th - pulse onwards. The values of pulse_identifier are then [0, 99999] respectively. - unit: NX_UNITLESS - dim: (p,) - instrument(NXinstrument_apm): diff --git a/contributed_definitions/nyaml/NXevent_data_em.yaml b/contributed_definitions/nyaml/NXevent_data_em.yaml deleted file mode 100644 index 2157dac560..0000000000 --- a/contributed_definitions/nyaml/NXevent_data_em.yaml +++ /dev/null @@ -1,309 +0,0 @@ -category: base -doc: | - Base class to store state and (meta)data of events with an electron microscopy. - - Electron microscopes are dynamic. Scientists often report that microscopes - *perform differently* across sessions, that they perform differently from - one day or another. In some cases, root causes for performance differences - are unclear. Users of the instrument may consider such conditions impractical, - or *too poor*, and thus abort their session. Alternatively, users may try to - bring the microscope into a state where conditions are considered better - or of whatever high enough quality for continuing the measurement. - - In all these use cases in practice it would be useful to have a mechanism - whereby time-dependent data of the instrument state can be stored and - documented with an interoperable representation. Indeed, how a session on an - electron microscope is spent depends strongly on the research question, - the user, and the imaging modalities used. - - :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly - whatever is considered a time interval during which the instrument is - considered as stable enough for performing a task with the microscope. - Examples of such tasks are the collecting of data (images and spectra) or - the calibrating of some component of the instrument. Users may wish to take - only a single scan or image and complete their microscope session thereafter. - Alternatively, users are working for much longer time at the microscope, - perform recalibrations in between and take several scans (of different - regions-of-interest of the specimen), or they explore the state of the - microscope for service or maintenance tasks. - - :ref:`NXevent_data_em` serves the harmonization and documentation of this situation - with providing three key sections: Firstly, there is a header section whose - purpose is to contextualize and identify the event instance in time. - Secondly, there is a data and metadata section where individual data collections - can be stored using a standardized representation. - - The idea of the first, the event-based em_lab section, is to document the - state of the microscope as it was during the event. The idea of the other, - the NXem application based em_lab(NXinstrument) section is to keep all those - pieces of information which are static in the sense that they are the same - across multiple :ref:`NXevent_data_em` instance. This reduces the amount of pieces of - information that have to be stored repetitively. - - We are aware of the fact that given the variety how an electron microscope - is used, there is a need for a flexible and adaptive documentation system. - At the same time we are also convinced though that just because one has - different requirements for some specific aspect under the umbrella of settings - to an electron microscope, this does not necessarily warrant that one has to - cook up an own schema. - - Instead, the electron microscopy community should work towards reusing schema - components as frequently as possible. This will enable that there is at all - not only a value of harmonizing electron microscopy research content but also - the technical possibility to build services around such harmonized - pieces of information. - - Arguably it is oftentimes tricky to specify a clear time interval when the - microscope is *stable enough*. Take for instance the acquisition of an image - or a stack of spectra. Having to deal with instabilities is a common theme in - electron microscopy practice. Numerical protocols can be used during data - post-processing to correct for some of the instabilities. - A few exemplar references to provide an overview on the subject is - available in the literature: - - * `C. Ophus et al. `_ - * `B. Berkels et al. `_ - * `L. Jones et al. `_ - - For specific simulation purposes, mainly in an effort to digitally repeat - or simulate the experiment, it is tempting to consider dynamics of the instrument, - implemented as time-dependent functional descriptions of e.g. lens excitations, - beam shape functions, trajectories of groups of electrons and ions, - or detector noise models. This warrants to document the time-dependent - details of individual components of the microscope - as is implemented in :ref:`NXevent_data_em`. -type: group -NXevent_data_em(NXobject): - start_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval started. If the user wishes to specify an - interval of time that the snapshot should represent during which the instrument - was stable and configured using specific settings and calibrations, - the start_time is the start (left bound of the time interval) while - the end_time specifies the end (right bound) of the time interval. - end_time(NX_DATE_TIME): - doc: | - ISO 8601 time code with local time zone offset to UTC information included - when the snapshot time interval ended. - event_identifier(NX_INT): - unit: NX_UNITLESS - doc: | - Identifier of a specific state and setting of the microscope. - event_type(NX_CHAR): - doc: | - Which specific event/measurement type. Examples are: - - * In-lens/backscattered electron, usually has quadrants - * Secondary_electron, image, topography, fractography, overview images - * Backscattered_electron, image, Z or channeling contrast (ECCI) - * Bright_field, image, TEM - * Dark_field, image, crystal defects - * Annular dark field, image (medium- or high-angle), TEM - * Diffraction, image, TEM, or a comparable technique in the SEM - * Kikuchi, image, SEM EBSD and TEM diffraction - * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) - * Electron energy loss spectra for points, lines, surfaces, TEM - * Auger, spectrum, (low Z contrast element composition) - * Cathodoluminescence (optical spectra) - * Ronchigram, image, alignment utility specifically in TEM - * Chamber, e.g. TV camera inside the chamber, education purposes. - - This field may also be used for storing additional information - about the event. For which there is at the moment no other place. - - In the long run such free-text field description should be avoided as - they are difficult to machine-interpret. Instead, reference should be given - to refactoring these descriptions into structured metadata. - The reason why in this base class the field event_type is nonetheless kept - is to offer a place whereby practically users may enter data for - follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. - (NXimage_set): - (NXspectrum_set): - em_lab(NXinstrument): - doc: | - (Meta)data of the dynamics and changes of the microscope during the event. - - # no need to duplicate the fabrication because that should remain the - (NXchamber): - (NXebeam_column): - (NXibeam_column): - (NXoptical_system_em): - (NXdetector): - (NXpump): - (NXstage_lab): - - # (NXactuator): - (NXuser): - (NXinteraction_vol_em): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 2848ccb16de0a30c69c5f3d3bd96c62001fc0f27643cbb31fdd81cc65114800f -# -# -# -# -# -# Base class to store state and (meta)data of events with an electron microscopy. -# -# Electron microscopes are dynamic. Scientists often report that microscopes -# *perform differently* across sessions, that they perform differently from -# one day or another. In some cases, root causes for performance differences -# are unclear. Users of the instrument may consider such conditions impractical, -# or *too poor*, and thus abort their session. Alternatively, users may try to -# bring the microscope into a state where conditions are considered better -# or of whatever high enough quality for continuing the measurement. -# -# In all these use cases in practice it would be useful to have a mechanism -# whereby time-dependent data of the instrument state can be stored and -# documented with an interoperable representation. Indeed, how a session on an -# electron microscope is spent depends strongly on the research question, -# the user, and the imaging modalities used. -# -# :ref:`NXevent_data_em` represents an instance to describe and serialize flexibly -# whatever is considered a time interval during which the instrument is -# considered as stable enough for performing a task with the microscope. -# Examples of such tasks are the collecting of data (images and spectra) or -# the calibrating of some component of the instrument. Users may wish to take -# only a single scan or image and complete their microscope session thereafter. -# Alternatively, users are working for much longer time at the microscope, -# perform recalibrations in between and take several scans (of different -# regions-of-interest of the specimen), or they explore the state of the -# microscope for service or maintenance tasks. -# -# :ref:`NXevent_data_em` serves the harmonization and documentation of this situation -# with providing three key sections: Firstly, there is a header section whose -# purpose is to contextualize and identify the event instance in time. -# Secondly, there is a data and metadata section where individual data collections -# can be stored using a standardized representation. -# -# The idea of the first, the event-based em_lab section, is to document the -# state of the microscope as it was during the event. The idea of the other, -# the NXem application based em_lab(NXinstrument) section is to keep all those -# pieces of information which are static in the sense that they are the same -# across multiple :ref:`NXevent_data_em` instance. This reduces the amount of pieces of -# information that have to be stored repetitively. -# -# We are aware of the fact that given the variety how an electron microscope -# is used, there is a need for a flexible and adaptive documentation system. -# At the same time we are also convinced though that just because one has -# different requirements for some specific aspect under the umbrella of settings -# to an electron microscope, this does not necessarily warrant that one has to -# cook up an own schema. -# -# Instead, the electron microscopy community should work towards reusing schema -# components as frequently as possible. This will enable that there is at all -# not only a value of harmonizing electron microscopy research content but also -# the technical possibility to build services around such harmonized -# pieces of information. -# -# Arguably it is oftentimes tricky to specify a clear time interval when the -# microscope is *stable enough*. Take for instance the acquisition of an image -# or a stack of spectra. Having to deal with instabilities is a common theme in -# electron microscopy practice. Numerical protocols can be used during data -# post-processing to correct for some of the instabilities. -# A few exemplar references to provide an overview on the subject is -# available in the literature: -# -# * `C. Ophus et al. <https://dx.doi.org/10.1016/j.ultramic.2015.12.002>`_ -# * `B. Berkels et al. <https://doi.org/10.1016/j.ultramic.2018.12.016>`_ -# * `L. Jones et al. <https://link.springer.com/article/10.1186/s40679-015-0008-4>`_ -# -# For specific simulation purposes, mainly in an effort to digitally repeat -# or simulate the experiment, it is tempting to consider dynamics of the instrument, -# implemented as time-dependent functional descriptions of e.g. lens excitations, -# beam shape functions, trajectories of groups of electrons and ions, -# or detector noise models. This warrants to document the time-dependent -# details of individual components of the microscope -# as is implemented in :ref:`NXevent_data_em`. -# -# -# -# ISO 8601 time code with local time zone offset to UTC information included -# when the snapshot time interval started. If the user wishes to specify an -# interval of time that the snapshot should represent during which the instrument -# was stable and configured using specific settings and calibrations, -# the start_time is the start (left bound of the time interval) while -# the end_time specifies the end (right bound) of the time interval. -# -# -# -# -# ISO 8601 time code with local time zone offset to UTC information included -# when the snapshot time interval ended. -# -# -# -# -# Identifier of a specific state and setting of the microscope. -# -# -# -# -# Which specific event/measurement type. Examples are: -# -# * In-lens/backscattered electron, usually has quadrants -# * Secondary_electron, image, topography, fractography, overview images -# * Backscattered_electron, image, Z or channeling contrast (ECCI) -# * Bright_field, image, TEM -# * Dark_field, image, crystal defects -# * Annular dark field, image (medium- or high-angle), TEM -# * Diffraction, image, TEM, or a comparable technique in the SEM -# * Kikuchi, image, SEM EBSD and TEM diffraction -# * X-ray spectra (point, line, surface, volume), composition EDS/EDX(S) -# * Electron energy loss spectra for points, lines, surfaces, TEM -# * Auger, spectrum, (low Z contrast element composition) -# * Cathodoluminescence (optical spectra) -# * Ronchigram, image, alignment utility specifically in TEM -# * Chamber, e.g. TV camera inside the chamber, education purposes. -# -# This field may also be used for storing additional information -# about the event. For which there is at the moment no other place. -# -# In the long run such free-text field description should be avoided as -# they are difficult to machine-interpret. Instead, reference should be given -# to refactoring these descriptions into structured metadata. -# The reason why in this base class the field event_type is nonetheless kept -# is to offer a place whereby practically users may enter data for -# follow-up modifications to support arriving at an improved :ref:`NXevent_data_em` base class. -# -# -# -# -# -# -# (Meta)data of the dynamics and changes of the microscope during the event. -# -# -# -# -# -# -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXevent_data_em_set.yaml b/contributed_definitions/nyaml/NXevent_data_em_set.yaml deleted file mode 100644 index 0c61ec663f..0000000000 --- a/contributed_definitions/nyaml/NXevent_data_em_set.yaml +++ /dev/null @@ -1,80 +0,0 @@ -category: base -doc: | - Base class for a set of :ref:`NXevent_data_em` instances. - - Members of the set are instances of :ref:`NXevent_data_em`. These have an associated - time interval during which the conditions were considered stable and - fit enough for purpose. - - Which temporal granularity is adequate depends on the situation and - research question. Using a model which enables a collection of events offers - the most flexible way to cater for both experiments with controlled electron - beams in a real microscope or the simulation of such experiments or - individual aspects of such experiments. -type: group -NXevent_data_em_set(NXobject): - - # because it should be possible to use the application definition - # to store e.g. just some descriptions about the instrument - # to which eventually no measurements are attached - # this would enable to use nxs files also for instrument - # inventory system like offered through ELNs/or LIMS - (NXevent_data_em): - - # because it should be possible to use the application definition - # to store e.g. just some descriptions about the instrument - # to which eventually no measurements are attached - # this would enable to use nxs files also for instrument - # inventory system like offered through ELNs/or LIMS - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 77495718dd84ccb1477c1a511d3d43b5b4412acc37a6c089a27a4d973a95b44f -# -# -# -# -# -# Base class for a set of :ref:`NXevent_data_em` instances. -# -# Members of the set are instances of :ref:`NXevent_data_em`. These have an associated -# time interval during which the conditions were considered stable and -# fit enough for purpose. -# -# Which temporal granularity is adequate depends on the situation and -# research question. Using a model which enables a collection of events offers -# the most flexible way to cater for both experiments with controlled electron -# beams in a real microscope or the simulation of such experiments or -# individual aspects of such experiments. -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXgraph_edge_set.yaml b/contributed_definitions/nyaml/NXgraph_edge_set.yaml index fbed1464c9..30e5f508ea 100644 --- a/contributed_definitions/nyaml/NXgraph_edge_set.yaml +++ b/contributed_definitions/nyaml/NXgraph_edge_set.yaml @@ -30,7 +30,7 @@ NXgraph_edge_set(NXobject): :math:`[identifier\_offset, identifier\_offset + c - 1]`. For explicit indexing use the field identifier. For implicit indexing, - consult :ref:`NXcg_primitive_set` to get guidance how to set identifier_offset. + consult :ref:`NXcg_primitive` to get guidance how to set identifier_offset. identifier(NX_INT): unit: NX_UNITLESS doc: | @@ -81,7 +81,7 @@ NXgraph_edge_set(NXobject): dim: (n_edges,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4acbec7565e4927095f08de332b2232b04525c16b425969050e1957fdb4f1d0d +# e93992b1b15211fcd64c99214a9a912a672fdb087d13c86e35cf974cff1163c3 # # # -# -# -# Base class for describing the interaction volume of particle-matter interaction. -# -# Computer models like Monte Carlo or molecular dynamics / electron- or ion-beam -# interaction simulations can be used to qualify and (or) quantify the shape of -# the interaction volume. Results of such simulations can be summary statistics -# or single-particle resolved sets of trajectories. -# -# Explicit or implicit descriptions are possible. -# -# * An implicit description is via a set of electron/specimen interactions -# represented ideally as trajectory data from the computer simulation. -# * An explicit description is via an iso-contour surface using either -# a simulation grid or a triangulated surface mesh of the approximated -# iso-contour surface evaluated at specific threshold values. -# Iso-contours could be computed from electron or particle fluxes through -# an imaginary control surface (the iso-surface). -# Threshold values can be defined by particles passing through a unit control -# volume (electrons) or energy-levels (e.g. the case of X-rays). -# Details depend on the model. -# * Another explicit description is via theoretical models which may -# be relevant e.g. for X-ray spectroscopy -# -# Further details on how the interaction volume can be quantified -# is available in the literature for example: -# -# * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ -# * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ -# * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ -# -# -# -# diff --git a/contributed_definitions/nyaml/NXlab_sample_mounting.yaml b/contributed_definitions/nyaml/NXlab_sample_mounting.yaml index 82b213ba48..7d23c1d621 100644 --- a/contributed_definitions/nyaml/NXlab_sample_mounting.yaml +++ b/contributed_definitions/nyaml/NXlab_sample_mounting.yaml @@ -49,13 +49,13 @@ NXlab_sample_mounting(NXobject): # stimuli (eventually) applied during mounting # temperature, mechanical, magnetic, electro-magnetic, are externally # applied stimuli on the sample, can we use one master schema? - # e.g. one can even store NXcg_polyhedron_set and NXcg_face_list_data_structure + # e.g. one can even store NXcg_polyhedron and NXcg_face_list_data_structure # instances to keep track of the geometry of specific instrument and how # the samples were arranged in these # key question is which steps has the sample experienced? # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ad85874b621c3063ca66ea36a945f5853110d63beaaa41f436ca58c6831888af +# 8a95efd90386a9da1b4a51b3a34d50f6f472881f2022c92e965312352e3dffd1 # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure.yaml b/contributed_definitions/nyaml/NXmicrostructure.yaml index 0bb671c863..f4bb35cecf 100644 --- a/contributed_definitions/nyaml/NXmicrostructure.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure.yaml @@ -18,7 +18,7 @@ doc: | specific states or via sampling coarsely in time relative to the timescale at which the physical phenomena take place. This is typically a compromise between the research questions at hand and technical surplus practical limitations. - The term microstructural feature covers here crystals and all sorts of crystal defects within the material. + The term microstructural feature covers here crystals and all sorts of crystal defects within the material. A key challenge with the description of representations and properties of microstructural features is that features with different dimensionality exist and combinations of features of different dimensionality are frequently expected to be documented with intuitive naming conventions using flat property lists. @@ -50,15 +50,18 @@ doc: | Identifiers can be defined either implicitly or explicitly. Identifiers for implicit indexing are defined on the interval :math:`[identifier\_offset, identifier\_offset + cardinality - 1]`. + # , and Volterra line defects (dislocation, disconnection, disclination). symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays. + # one-dimensional sections of either projections (see below) or true one-dimensional cuts across a volume of material n_c_one: | The number of one-dimensional crystal projections n_i_one: | The number of one-dimensional interface projections + # n__one, n__one are hypothetical scenarios such as line defect hitting right into a point # two-dimensional projections of three-dimensional objects using E. E. Underwood notation # crystals/grains are projections that are delineated by projections of interface, i.e. interface lines which meet at projections of triple lines aka triple points @@ -70,23 +73,29 @@ symbols: The number of two-dimensional triple line projections n_ld_two: | The number of two-dimensional line defect projections + # n__two is the hypothetical scenario when a point defect lies right in the projection plane # three-dimensional real objects, volumetrically characterized # crystals are delineated by interfaces that are delineated by triple lines that meet at quad junctions n_c_three: | The number of crystals (grain and sub-grain are exact synonyms for crystal). n_i_three: | - The number of interfaces (grain boundary and phase boundary are subclasses of interfaces). + The number of interfaces (grain boundary and phase boundary are subclasses of + interfaces). n_tj_three: | - The number of triple junctions (triple line is a exact synonym for triple junction, triple point is projection of a triple junction). + The number of triple junctions (triple line is a exact synonym for triple + junction, triple point is projection of a triple junction). n_qj_three: | The number of quadruple junctions. -# n_ld_three: -# The number of line defects. + + # n_ld_three: + # The number of line defects. d: | - The dimensionality of the representation that needs to match the value for configuration/dimensionality + The dimensionality of the representation that needs to match the value for + configuration/dimensionality type: group NXmicrostructure(NXobject): + # as e.g. a result of one grain reconstruction with an algorithm with MTex or the grain/phase i.e. interface network reconstruction software in commercial tools # the idea is we may wish to run as many grain reconstructions as we want and add details about the processing used for each of them if needed comment(NX_CHAR): @@ -96,25 +105,25 @@ NXmicrostructure(NXobject): doc: | ISO8601 with offset to local time zone included when a timestamp is required. time(NX_NUMBER): + unit: NX_TIME doc: | Measured or simulated physical time stamp for this microstructure snapshot. Not to be confused with wall-clock timing or profiling data. - unit: NX_TIME iteration(NX_INT): + unit: NX_UNITLESS doc: | Iteration or increment counter. - unit: NX_UNITLESS configuration(NXprocess): doc: | Group where to store details about the configuration and parameterization of algorithms used whereby microstructural features were identified. dimensionality(NX_POSINT): + unit: NX_UNITLESS doc: | Dimensionality of Euclidean space in which the analysis is performed. This field can be used e.g. by a research data management system to identify if the description specifies one-, two-, or three-dimensional microstructural representations. - unit: NX_UNITLESS enumeration: [1, 2, 3] algorithm(NX_CHAR): doc: | @@ -123,24 +132,26 @@ NXmicrostructure(NXobject): * Disorientation clustering groups nearby material points based on their crystallographic disorientation * Fast multiscale clustering based on `D. Kushnir et al. `_ * Markov chain clustering `F. Niessen et al. `_ - + # could also be used to specify algorithms for precipitate detection enumeration: [unknown, disorientation_clustering, fast_multiscale_clustering, markov_chain_clustering] disorientation_threshold(NX_NUMBER): + unit: NX_ANGLE doc: | Threshold to define at which disorientation angle to assume two crystalline regions have a significant orientation difference that warrants to assume that there exists an interface between the two regions. - unit: NX_ANGLE (NXprogram): doc: | The program with which the microstructure was reconstructed. + # use controlled vocabulary terms grid, point, line, surface, volume, use singular term when instantiating (NXcg_grid): - (NXcg_point_set): - (NXcg_polyline_set): - (NXcg_triangle_set): - (NXcg_polygon_set): - (NXcg_polyhedron_set): + (NXcg_point): + (NXcg_polyline): + (NXcg_triangle): + (NXcg_polygon): + (NXcg_polyhedron): + # constructive solid geometry to describe curved features # (NXcsg): # (NXcontinuous_function): @@ -158,74 +169,84 @@ NXmicrostructure(NXobject): Crystals are represented by a set of pixel, voxel, or polygons and their polyline boundaries. In rare cases the volume bounded gets represented using constructive solid geometry approaches. + # maybe some enum what this is representation(NX_CHAR): doc: | Reference to an instance of: - * :ref:`NXcg_polyline_set` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) - * :ref:`NXcg_polygon_set` for a two-dimensional representation as only a projection is available (like in most experiments) - * :ref:`NXcg_polyhedron_set` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions + * :ref:`NXcg_polyline` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) + * :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions (like in computer simulations or 3D experiments) which represent the geometrical entities of the discretization. number_of_crystals(NX_UINT): + unit: NX_UNITLESS doc: | How many crystals are distinguished. Crystals are listed irrespective of the phase to which these are assigned. - unit: NX_UNITLESS number_of_phases(NX_UINT): + unit: NX_UNITLESS doc: | How many phases are distinguished. Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. - unit: NX_UNITLESS identifier_offset_crystal(NX_INT): + unit: NX_UNITLESS doc: | First identifier whereby to identify crystals implicitly. - unit: NX_UNITLESS identifier_crystal(NX_INT): + unit: NX_UNITLESS doc: | Identifier whereby to identify each crystal explicitly. - unit: NX_UNITLESS - dim: (i,) # with i = n_c_one or n_c_two or n_c_three + dimensions: + dim: (i,) identifier_offset_phase(NX_INT): + unit: NX_UNITLESS doc: | First identifier whereby to identify phases implicitly. - unit: NX_UNITLESS identifier_phase(NX_INT): + unit: NX_UNITLESS doc: | Identifier whereby to identify phase for each crystal explicitly. - unit: NX_UNITLESS - dim: (i,) # with i = n_c_one or n_c_two or n_c_three for all use of i in of fields of group crystal + dimensions: + dim: (i,) + # EXAMPLES FOR DESCRIPTOR VALUES, SUMMARY STATISTICS boundary_contact(NX_BOOLEAN): doc: | - True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - dim: (i,) + True or false value, one for each crystal, to communicate whether that feature + makes contact with the edge of the ROI. + dimensions: + dim: (i,) orientation_spread(NX_NUMBER): + unit: NX_ANGLE doc: | Average disorientation angle for each crystal between individual orientations of that crystal evaluated as a summary statistic for all probed positions vs the average disorientation of that crystal. - unit: NX_ANGLE - dim: (i,) + dimensions: + dim: (i,) length(NX_NUMBER): + unit: NX_LENGTH doc: | Length of each crystal - unit: NX_LENGTH # m - dim: (i,) + dimensions: + dim: (i,) area(NX_NUMBER): + unit: NX_AREA doc: | Area of each crystal. - unit: NX_AREA # m^2 - dim: (i,) + dimensions: + dim: (i,) volume(NX_NUMBER): + unit: NX_VOLUME doc: | Volume of each crystal - unit: NX_VOLUME # m^3 - dim: (i,) + dimensions: + dim: (i,) interfaces(NXobject): doc: | One- or two-dimensional projections or three-dimensional representation of interfaces @@ -238,79 +259,92 @@ NXmicrostructure(NXobject): doc: | Reference to an instance of: - * :ref:`NXcg_point_set` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) - * :ref:`NXcg_polyline_set` or :ref:`NXcg_polygon_set` for a two-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) + * :ref:`NXcg_polyline` or :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks (like in computer simulations or 3D experiments) which represent the geometrical entities of the discretization. number_of_interfaces(NX_UINT): + unit: NX_UNITLESS doc: | How many interfaces are distinguished. - unit: NX_UNITLESS identifier_offset(NX_INT): + unit: NX_UNITLESS doc: | First identifier whereby to identify interfaces implicitly. - unit: NX_UNITLESS identifier(NX_INT): + unit: NX_UNITLESS doc: | Identifier whereby to identify each interface explicitly. - unit: NX_UNITLESS - dim: (i,) # with i == n_i_one or n_i_two or n_i_three for all fields of group interface + dimensions: + dim: (i,) + # topological view, interface specification through the the pair of crystals sharing an interface identifier_crystal(NX_INT): + unit: NX_UNITLESS doc: | Set of pairs of identifier_crystal for each interface. - unit: NX_UNITLESS - dim: (i, 2) + dimensions: + dim: (i, 2) \@use_these(NX_CHAR): doc: | The specific identifiers whereby to resolve ambiguities. identifier_phase(NX_INT): + unit: NX_UNITLESS doc: | Set of pairs of identifier_phase for each interface. - unit: NX_UNITLESS - dim: (i, 2) + dimensions: + dim: (i, 2) \@use_these(NX_CHAR): doc: | The specific identifiers whereby to resolve ambiguities. + # topological view, interface specification through the pair of triple line projections (i.e. triple points) adjoining the interface identifier_triple_junction(NX_INT): + unit: NX_UNITLESS doc: | Set of pairs of identifier_triple_junction for each interface. - unit: NX_UNITLESS - dim: (i, 2) # with i == n_i_two but junctions can be points or lines! + dimensions: + dim: (i, 2) \@use_these(NX_CHAR): doc: | The specific identifiers whereby to resolve ambiguities. + # EXAMPLES FOR DESCRIPTOR VALUES boundary_contact(NX_BOOLEAN): doc: | - True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - dim: (i,) + True or false value, one for each crystal, to communicate whether that feature + makes contact with the edge of the ROI. + dimensions: + dim: (i,) surface_energy(NX_NUMBER): + unit: NX_ANY doc: | Gibbs free surface energy for each interface. - unit: NX_ANY # J/m^2 - dim: (i,) + dimensions: + dim: (i,) mobility(NX_NUMBER): + unit: NX_ANY doc: | Non-intrinsic mobility of each interface. - unit: NX_ANY # m^4/Js - dim: (i,) + dimensions: + dim: (i,) length(NX_NUMBER): + unit: NX_LENGTH doc: | The length of each interface if only projections are available. This is not necessarily the same as the length of the individual polyline segments whereby the interface is discretized. - unit: NX_LENGTH - dim: (i,) + dimensions: + dim: (i,) area(NX_NUMBER): + unit: NX_AREA doc: | The surface area of all interfaces. - unit: NX_AREA - dim: (i,) + dimensions: + dim: (i,) triple_junctions(NXobject): doc: | Projections or representations of junctions at which three interfaces meet. @@ -322,94 +356,114 @@ NXmicrostructure(NXobject): doc: | Reference to an instance of: - * :ref:`NXcg_point_set` for a one-dimensional representation as only a projection is available (like in most experiments) - * :ref:`NXcg_polyline_set` for a two-dimensional representation as only a projection is available - * :ref:`NXcg_polygon_set` for a two-dimensional representation in the (seldom) case of sufficient spatial resolution + * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (like in most experiments) + * :ref:`NXcg_polyline` for a two-dimensional representation as only a projection is available + * :ref:`NXcg_polygon` for a two-dimensional representation in the (seldom) case of sufficient spatial resolution and the line in the projection plane or cases where triple junction locations are approximated e.g. using a set of triangles - * :ref:`NXcg_polyhedron_set` for a three-dimensional representation via e.g. a representation of Voronoi cells about atoms + * :ref:`NXcg_polyhedron` for a three-dimensional representation via e.g. a representation of Voronoi cells about atoms * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks which represent the geometrical entities of the discretization. number_of_junctions(NX_UINT): + unit: NX_UNITLESS doc: | Number of triple junctions. - unit: NX_UNITLESS identifier_offset(NX_INT): + unit: NX_UNITLESS doc: | First identifier to identify triple junctions implicitly. - unit: NX_UNITLESS identifier(NX_INT): + unit: NX_UNITLESS doc: | Identifier to identify each triple junction explicitly. - unit: NX_UNITLESS - dim: (i,) # with i == n_tj_one, n_tj_two, n_tj_three for all fields in group triple_junction + dimensions: + dim: (i,) + # various strategies are used to talk about aspects of triple junctions, some examples follow # example i) triple points as projections of triple lines have locations location(NX_INT): - doc: | - Set of identifier for positions whereby to identify the location of each junction. unit: NX_UNITLESS - dim: (i,) + doc: | + Set of identifier for positions whereby to identify the location of each + junction. + dimensions: + dim: (i,) \@use_these(NX_CHAR): doc: | The specific identifiers whereby to resolve ambiguities. position(NX_INT): + unit: NX_LENGTH doc: | Explicit positions. - unit: NX_LENGTH - dim: (i, d) + dimensions: + dim: (i, d) identifier_crystal(NX_INT): - doc: | - Set of tuples of identifier of crystals connected to the junction for each triple junction. unit: NX_UNITLESS - dim: (i, 3) + doc: | + Set of tuples of identifier of crystals connected to the junction for each + triple junction. + dimensions: + dim: (i, 3) + # example ii) three interfaces (maybe projections of them) meet at a triple junction identifier_interface(NX_INT): - doc: | - Set of tuples of identifier of interfaces connected to the junction for each triple junction. unit: NX_UNITLESS - dim: (i, 3) + doc: | + Set of tuples of identifier of interfaces connected to the junction for each + triple junction. + dimensions: + dim: (i, 3) \@use_these(NX_CHAR): doc: | The specific interface identifiers whereby to resolve ambiguities. + # example iii) three polyline segments meet at a triple junction, polyline segments of discretized interface segments identifier_polyline(NX_INT): - doc: | - Set of tuples of identifier for polyline segments connected to the junction for each triple junction. unit: NX_UNITLESS - dim: (i, 3) + doc: | + Set of tuples of identifier for polyline segments connected to the junction for + each triple junction. + dimensions: + dim: (i, 3) \@use_these(NX_CHAR): doc: | The specific identifier_polyline whereby to resolve ambiguities. + # example iv) e.g. crystals of three different phases meet at a triple junction # EXAMPLES FOR DESCRIPTOR VALUES boundary_contact(NX_BOOLEAN): doc: | - True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - dim: (i,) + True or false value, one for each crystal, to communicate whether that feature + makes contact with the edge of the ROI. + dimensions: + dim: (i,) line_energy(NX_NUMBER): + unit: NX_ANY doc: | Specific line energy of each triple junction - unit: NX_ANY - dim: (i,) + dimensions: + dim: (i,) mobility(NX_NUMBER): + unit: NX_ANY doc: | Non-intrinsic mobility of each triple junction. - unit: NX_ANY - dim: (i,) + dimensions: + dim: (i,) length(NX_NUMBER): + unit: NX_LENGTH doc: | The length of each triple junction. This is not necessarily the same as the length of the individual polyline segments whereby the junction is discretized. - unit: NX_LENGTH - dim: (i,) + dimensions: + dim: (i,) volume(NX_NUMBER): + unit: NX_VOLUME doc: | The volume of the each triple junction - unit: NX_VOLUME - dim: (i,) + dimensions: + dim: (i,) quadruple_junctions(NXobject): doc: | Quadruple junctions as a region where four crystals meet. @@ -419,84 +473,887 @@ NXmicrostructure(NXobject): doc: | Reference to an instance of: - * :ref:`NXcg_point_set` + * :ref:`NXcg_point` * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks - number_of_junctions(NX_UINT): + unit: NX_UNITLESS doc: | Number of quadruple junctions. - unit: NX_UNITLESS identifier_offset(NX_INT): + unit: NX_UNITLESS doc: | First identifier to identify quadruple junctions implicitly. - unit: NX_UNITLESS identifier(NX_INT): + unit: NX_UNITLESS doc: | Identifier to identify each quadruple junction explicitly. - unit: NX_UNITLESS - dim: (i,) # with i == n_qj_three or n_qj_two + dimensions: + dim: (i,) + # different scenarios can be envised how quadruple_junctions are discussed # example i) quadruple point locations explicitly location(NX_INT): - doc: | - Set of identifier for positions whereby to identify the location of each junction. unit: NX_UNITLESS - dim: (i,) + doc: | + Set of identifier for positions whereby to identify the location of each + junction. + dimensions: + dim: (i,) \@use_these(NX_CHAR): doc: | The specific point identifier whereby to resolve ambiguities. position(NX_INT): + unit: NX_LENGTH doc: | Explicit positions. - unit: NX_LENGTH - dim: (i, 3) + dimensions: + dim: (i, 3) + # example ii) four crystals meet at a quadruple junction identifier_crystal(NX_INT): - doc: | - Set of tuples of identifier of crystals connected to the junction for each junction. unit: NX_UNITLESS - dim: (i, 4) + doc: | + Set of tuples of identifier of crystals connected to the junction for each + junction. + dimensions: + dim: (i, 4) \@use_these(NX_CHAR): doc: | - The specific identifier to instances of crystal identifiers whereby to resolve ambiguities. + The specific identifier to instances of crystal identifiers whereby to resolve + ambiguities. identifier_interface(NX_INT): - doc: | - Set of tuples of identifier of interfaces connected to the junction for each junction. unit: NX_UNITLESS - dim: (i, 4) + doc: | + Set of tuples of identifier of interfaces connected to the junction for each + junction. + dimensions: + dim: (i, 4) \@use_these(NX_CHAR): doc: | - The specific identifier to instances of interface identifiers whereby to resolve ambiguities. + The specific identifier to instances of interface identifiers whereby to resolve + ambiguities. + # example iii) e.g. three triple lines meet at a quadruple junction identifier_triple_junction(NX_INT): - doc: | - Set of tuples of identifier for triple junctions connected to the junction for each quadruple junction. unit: NX_UNITLESS - dim: (i, 3) + doc: | + Set of tuples of identifier for triple junctions connected to the junction for + each quadruple junction. + dimensions: + dim: (i, 3) \@use_these(NX_CHAR): doc: | - The specific identifier to instances of triple junction identifiers whereby to resolve ambiguities. + The specific identifier to instances of triple junction identifiers whereby to + resolve ambiguities. + # example iv) crystals of eventually four different phases meet at a quadruple junction identifier_phase(NX_INT): - doc: | - Set of tuples of identifier for phases of crystals connected to the junction for each quadruple junction. unit: NX_UNITLESS - dim: (i, 4) + doc: | + Set of tuples of identifier for phases of crystals connected to the junction for + each quadruple junction. + dimensions: + dim: (i, 4) \@use_these(NX_CHAR): doc: | - The specific identifier to instances of phase identifier whereby to resolve ambiguities. + The specific identifier to instances of phase identifier whereby to resolve + ambiguities. + # EXAMPLES FOR DESCRIPTOR VALUES boundary_contact(NX_BOOLEAN): doc: | - True or false value, one for each crystal, to communicate whether that feature makes contact with the edge of the ROI. - dim: (i,) + True or false value, one for each crystal, to communicate whether that feature + makes contact with the edge of the ROI. + dimensions: + dim: (i,) energy(NX_NUMBER): + unit: NX_ANY doc: | Energy of the quadruple_junction as a defect. - unit: NX_ANY - dim: (i,) + dimensions: + dim: (i,) mobility(NX_NUMBER): + unit: NX_ANY doc: | Non-intrinsic mobility of each quadruple_junction. - unit: NX_ANY - dim: (i,) + dimensions: + dim: (i,) + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# e7669dc42df620a5373640459a790e5f58192cd911e0400727d4d2412e6a4400 +# +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays. +# +# +# +# +# The number of one-dimensional crystal projections +# +# +# +# +# The number of one-dimensional interface projections +# +# +# +# +# +# The number of two-dimensional crystal projections +# +# +# +# +# The number of two-dimensional interface projections +# +# +# +# +# The number of two-dimensional triple line projections +# +# +# +# +# The number of two-dimensional line defect projections +# +# +# +# +# +# The number of crystals (grain and sub-grain are exact synonyms for crystal). +# +# +# +# +# The number of interfaces (grain boundary and phase boundary are subclasses of +# interfaces). +# +# +# +# +# The number of triple junctions (triple line is a exact synonym for triple +# junction, triple point is projection of a triple junction). +# +# +# +# +# The number of quadruple junctions. +# +# +# +# +# +# The dimensionality of the representation that needs to match the value for +# configuration/dimensionality +# +# +# +# +# Base class to describe a microstructure, its structural aspects, associated descriptors, properties. +# +# Whether one uses a continuum or atomic scale description of materials, these are always a model only of +# the true internal structure of a material. Such models are useful as they enable a coarse-graining and +# categorizing of properties and representational aspects from which measured or simulated descriptions +# can be correlated with properties, i.e. descriptor values. +# +# Keep in mind that most specimens are thermo-chemo-mechanically processed prior characterization. +# Therefore, the characterized microstructure may not have probed the same structure as of the untreated +# sample from which the region-of-interests on the specimen were sampled. +# +# Fields such as time and increment enable a quantification of the spatiotemporal evolution of a materials' +# structure by using multiple instances of NXmicrostructure. Both measurements and simulation virtually +# always sample this evolution. Most microscopy techniques support to generate only a two-dimensional +# representation (projection) of the characterized material. Often materials are characterized only for +# specific states or via sampling coarsely in time relative to the timescale at which the +# physical phenomena take place. This is typically a compromise between the research questions at hand and technical surplus practical limitations. +# +# The term microstructural feature covers here crystals and all sorts of crystal defects within the material. +# A key challenge with the description of representations and properties of microstructural features is that +# features with different dimensionality exist and combinations of features of different dimensionality are +# frequently expected to be documented with intuitive naming conventions using flat property lists. +# For these key-value dictionaries often folksonomies are used. These can be based on ad hoc documentation +# of such dictionaries in the literature and the metadata section of public data repositories. +# +# NXmicrostructure is an attempt to standardize these descriptions stronger. +# +# The descriptive variety is large especially for junctions. Like crystals and interfaces, junctions are features in +# three-dimensional Euclidean space even if they are formed maybe only through a monolayer or pearl chain of atoms. +# Either way the local atomic and electronic environment is different compared to the situation of an ideal crystal, +# which gives typically rise to a plethora of configurations of which some yield useful properties. +# +# Like crystals and interfaces, junctions are assumed to represent groups of atoms that have specific descriptor values +# which are different to other features. Taking an example, a triple junction is practically a three-dimensional defect as its atoms +# are arranged in three-dimensional space but the characteristics of that defect can often be reduced to a lower-dimensional +# description such as a triple point or a triple line. Therefore, different representations can be used to describe the location, +# shape, and structure of the defect. As different types of crystal defects can interact, there is a substantial number of +# in principle characterizable and representable objects. Take again a triple line as an example. It is a tubular feature built from three +# adjoining interfaces. However, dislocations as line defects can interact with triple lines. Therefore, one can also argue that +# along a triple line there can be dislocation-line-triple-line junctions, likewise dislocations form own junctions. +# +# It is not the aim of this base class to cover all these cases, rather this base class currently provides examples how the +# typically most relevant types of features can be represented using a combination of base classes in NeXus. Currently, +# these are crystals, interfaces, triple lines, quadruple junctions. +# +# The description attempt here took inspiration from `E. E. Underwood <https://doi.org/10.1111/j.1365-2818.1972.tb03709.x>`_ +# and E. E. Underwood's book on Quantitative Stereology published 1970 to categorize features based on their dimensionality. +# +# Identifiers can be defined either implicitly or explicitly. Identifiers for implicit indexing are defined +# on the interval :math:`[identifier\_offset, identifier\_offset + cardinality - 1]`. +# +# +# +# +# Discouraged free-text field for leaving comments. +# +# +# +# +# ISO8601 with offset to local time zone included when a timestamp is required. +# +# +# +# +# Measured or simulated physical time stamp for this microstructure snapshot. +# Not to be confused with wall-clock timing or profiling data. +# +# +# +# +# Iteration or increment counter. +# +# +# +# +# Group where to store details about the configuration and parameterization of algorithms +# used whereby microstructural features were identified. +# +# +# +# Dimensionality of Euclidean space in which the analysis is performed. +# +# This field can be used e.g. by a research data management system to identify +# if the description specifies one-, two-, or three-dimensional microstructural representations. +# +# +# +# +# +# +# +# +# +# Algorithm whereby interfaces between crystals were reconstructed. +# +# * Disorientation clustering groups nearby material points based on their crystallographic disorientation +# * Fast multiscale clustering based on `D. Kushnir et al. <https://doi.org/10.1016/j.patcog.2006.04.007>`_ +# * Markov chain clustering `F. Niessen et al. <https://doi.org/10.1107/S1600576721011560>`_ +# +# +# +# +# +# +# +# +# +# +# +# Threshold to define at which disorientation angle to assume two crystalline regions have a significant +# orientation difference that warrants to assume that there exists an interface between the two regions. +# +# +# +# +# The program with which the microstructure was reconstructed. +# +# +# +# +# +# +# +# +# +# +# +# +# +# One- or two-dimensional projections, or three-dimensional representations of crystals. +# +# An example for a volume bounded by other crystal defects. Crystals can be grains of +# different phases, precipitates, dispersoids; there are many terms used specifically in +# the materials engineering community. +# +# Typically, crystals are measured on the surface of a sample via optical or electron microscopy. +# Using X-ray diffraction methods crystals can be observed in bulk specimens. +# +# Crystals are represented by a set of pixel, voxel, or polygons and their polyline boundaries. +# In rare cases the volume bounded gets represented using constructive solid geometry approaches. +# +# +# +# +# Reference to an instance of: +# +# * :ref:`NXcg_polyline` for a one-dimensional representation as only a projection is available (like in linear intercept analysis) +# * :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) +# * :ref:`NXcg_polyhedron` or :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions +# (like in computer simulations or 3D experiments) +# +# which represent the geometrical entities of the discretization. +# +# +# +# +# How many crystals are distinguished. +# +# Crystals are listed irrespective of the phase to which these are assigned. +# +# +# +# +# How many phases are distinguished. +# +# Phases are typically distinguished based on statistical thermodynamics argument and crystal structure. +# +# +# +# +# First identifier whereby to identify crystals implicitly. +# +# +# +# +# Identifier whereby to identify each crystal explicitly. +# +# +# +# +# +# +# +# First identifier whereby to identify phases implicitly. +# +# +# +# +# Identifier whereby to identify phase for each crystal explicitly. +# +# +# +# +# +# +# +# +# True or false value, one for each crystal, to communicate whether that feature +# makes contact with the edge of the ROI. +# +# +# +# +# +# +# +# Average disorientation angle for each crystal between individual orientations +# of that crystal evaluated as a summary statistic for all probed positions vs the +# average disorientation of that crystal. +# +# +# +# +# +# +# +# Length of each crystal +# +# +# +# +# +# +# +# Area of each crystal. +# +# +# +# +# +# +# +# Volume of each crystal +# +# +# +# +# +# +# +# +# One- or two-dimensional projections or three-dimensional representation of interfaces +# between crystals as topological entities equivalent to dual_junctions. +# +# An example for a surface defect. Most important are interfaces such as grain and phase boundaries +# but factually interfaces also exist between the environment and crystals exposed at the +# surface of the specimen or internal surfaces like between crystals, cracks, or pores. +# +# +# +# Reference to an instance of: +# +# * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (as in linear intercept analyses) +# * :ref:`NXcg_polyline` or :ref:`NXcg_polygon` for a two-dimensional representation as only a projection is available (like in most experiments) +# * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks +# (like in computer simulations or 3D experiments) +# +# which represent the geometrical entities of the discretization. +# +# +# +# +# How many interfaces are distinguished. +# +# +# +# +# First identifier whereby to identify interfaces implicitly. +# +# +# +# +# Identifier whereby to identify each interface explicitly. +# +# +# +# +# +# +# +# +# Set of pairs of identifier_crystal for each interface. +# +# +# +# +# +# +# +# The specific identifiers whereby to resolve ambiguities. +# +# +# +# +# +# Set of pairs of identifier_phase for each interface. +# +# +# +# +# +# +# +# The specific identifiers whereby to resolve ambiguities. +# +# +# +# +# +# +# Set of pairs of identifier_triple_junction for each interface. +# +# +# +# +# +# +# +# The specific identifiers whereby to resolve ambiguities. +# +# +# +# +# +# +# True or false value, one for each crystal, to communicate whether that feature +# makes contact with the edge of the ROI. +# +# +# +# +# +# +# +# Gibbs free surface energy for each interface. +# +# +# +# +# +# +# +# Non-intrinsic mobility of each interface. +# +# +# +# +# +# +# +# The length of each interface if only projections are available. +# +# This is not necessarily the same as the length of the individual +# polyline segments whereby the interface is discretized. +# +# +# +# +# +# +# +# The surface area of all interfaces. +# +# +# +# +# +# +# +# +# Projections or representations of junctions at which three interfaces meet. +# +# An example for a line defect. Triple junctions are characterized as triple lines or triple points as their projections, +# or junctions observed between crystals (at the specimen surface exposed to an environment) +# (including wetting phenomena) or inside the specimen (crack, pores). +# +# +# +# Reference to an instance of: +# +# * :ref:`NXcg_point` for a one-dimensional representation as only a projection is available (like in most experiments) +# * :ref:`NXcg_polyline` for a two-dimensional representation as only a projection is available +# * :ref:`NXcg_polygon` for a two-dimensional representation in the (seldom) case of sufficient spatial resolution +# and the line in the projection plane or cases where triple junction locations are approximated e.g. using a set of triangles +# * :ref:`NXcg_polyhedron` for a three-dimensional representation via e.g. a representation of Voronoi cells about atoms +# * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks +# +# which represent the geometrical entities of the discretization. +# +# +# +# +# Number of triple junctions. +# +# +# +# +# First identifier to identify triple junctions implicitly. +# +# +# +# +# Identifier to identify each triple junction explicitly. +# +# +# +# +# +# +# +# +# Set of identifier for positions whereby to identify the location of each +# junction. +# +# +# +# +# +# +# The specific identifiers whereby to resolve ambiguities. +# +# +# +# +# +# Explicit positions. +# +# +# +# +# +# +# +# +# Set of tuples of identifier of crystals connected to the junction for each +# triple junction. +# +# +# +# +# +# +# +# +# +# Set of tuples of identifier of interfaces connected to the junction for each +# triple junction. +# +# +# +# +# +# +# +# The specific interface identifiers whereby to resolve ambiguities. +# +# +# +# +# +# +# Set of tuples of identifier for polyline segments connected to the junction for +# each triple junction. +# +# +# +# +# +# +# +# The specific identifier_polyline whereby to resolve ambiguities. +# +# +# +# +# +# +# True or false value, one for each crystal, to communicate whether that feature +# makes contact with the edge of the ROI. +# +# +# +# +# +# +# +# Specific line energy of each triple junction +# +# +# +# +# +# +# +# Non-intrinsic mobility of each triple junction. +# +# +# +# +# +# +# +# The length of each triple junction. +# +# This is not necessarily the same as the length of the individual +# polyline segments whereby the junction is discretized. +# +# +# +# +# +# +# +# The volume of the each triple junction +# +# +# +# +# +# +# +# +# Quadruple junctions as a region where four crystals meet. +# +# An example for a point defect. +# +# +# +# Reference to an instance of: +# +# * :ref:`NXcg_point` +# * :ref:`NXcg_grid` for regularly pixelated or voxelated representation in one, two, or three dimensions using (boolean) masks +# +# +# +# +# Number of quadruple junctions. +# +# +# +# +# First identifier to identify quadruple junctions implicitly. +# +# +# +# +# Identifier to identify each quadruple junction explicitly. +# +# +# +# +# +# +# +# +# Set of identifier for positions whereby to identify the location of each +# junction. +# +# +# +# +# +# +# The specific point identifier whereby to resolve ambiguities. +# +# +# +# +# +# Explicit positions. +# +# +# +# +# +# +# +# +# +# Set of tuples of identifier of crystals connected to the junction for each +# junction. +# +# +# +# +# +# +# +# The specific identifier to instances of crystal identifiers whereby to resolve +# ambiguities. +# +# +# +# +# +# Set of tuples of identifier of interfaces connected to the junction for each +# junction. +# +# +# +# +# +# +# +# The specific identifier to instances of interface identifiers whereby to resolve +# ambiguities. +# +# +# +# +# +# +# Set of tuples of identifier for triple junctions connected to the junction for +# each quadruple junction. +# +# +# +# +# +# +# +# The specific identifier to instances of triple junction identifiers whereby to +# resolve ambiguities. +# +# +# +# +# +# +# Set of tuples of identifier for phases of crystals connected to the junction for +# each quadruple junction. +# +# +# +# +# +# +# +# The specific identifier to instances of phase identifier whereby to resolve +# ambiguities. +# +# +# +# +# +# +# True or false value, one for each crystal, to communicate whether that feature +# makes contact with the edge of the ROI. +# +# +# +# +# +# +# +# Energy of the quadruple_junction as a defect. +# +# +# +# +# +# +# +# Non-intrinsic mobility of each quadruple_junction. +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml b/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml index d19bc05a51..5d43f7d382 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_ipf.yaml @@ -52,8 +52,8 @@ NXmicrostructure_ipf(NXprocess): phase. No ipf_mapID instances for non-indexed scan points as these are by definition assigned the null phase with phase_identifier 0. - Inspect the definition of :ref:`NXcrystal_structure` and its field - phase_identifier for further details. + Inspect the definition of :ref:`NXphase` and its field identifier_phase + for further details. Details about possible regridding and associated interpolation during the computation of the IPF map visualization can be stored @@ -187,13 +187,13 @@ NXmicrostructure_ipf(NXprocess): # https://github.com/FAIRmat-NFDI/nexus_definitions/commit/26d4faa5c6950161e48f0672f3fdfd8c9bc907e2 # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1f7ab37daf33bffc8c676a0cfb6ec7d9846bc3199a10038181ded8d948754913 +# 3ca41aeeb04a201e6a1767c1be890b227be481301ec3b61b605df06ba046b28a # # # # -# +# tech partners oftentimes do not report to more than calibrated pixel position +# --> # -# Inverse pole figure color code for each map coordinate. +# Inverse pole figure color code for each map coordinate. # # # @@ -335,7 +337,7 @@ NXmicrostructure_ipf(NXprocess): # # # -# Pixel center coordinate calibrated for step size along the z axis of the map. +# Pixel center coordinate calibrated for step size along the z axis of the map. # # # @@ -344,7 +346,7 @@ NXmicrostructure_ipf(NXprocess): # # # -# Pixel center coordinate calibrated for step size along the y axis of the map. +# Pixel center coordinate calibrated for step size along the y axis of the map. # # # @@ -353,7 +355,7 @@ NXmicrostructure_ipf(NXprocess): # # # -# Pixel center coordinate calibrated for step size along the x axis of the map. +# Pixel center coordinate calibrated for step size along the x axis of the map. # # # @@ -364,39 +366,41 @@ NXmicrostructure_ipf(NXprocess): # title:--> # # -# The color code which maps colors to orientation in the fundamental zone. -# -# For each stereographic standard triangle (SST), i.e. a rendering of the -# fundamental zone of the crystal-symmetry-reduced orientation space -# SO3, it is possible to define a color model which assigns a color to each -# point in the fundamental zone. -# -# Different mapping models are used. These implement (slightly) different -# scaling relations. Differences exist across representations of tech partners. -# -# Differences are which base colors of the RGB color model are placed in -# which extremal position of the SST and where the white point is located. -# -# For further details see: -# -# * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) -# * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). -# -# Details are implementation-specific and not standardized yet. -# -# Given that the SST has a complicated geometry, it can not yet be -# visualized using tools like H5Web, which is why for now the matrix -# of a rasterized image which is rendered by the backend tool gets -# copied into an RGB matrix to offer a default plot. +# The color code which maps colors to orientation in the fundamental zone. +# +# For each stereographic standard triangle (SST), i.e. a rendering of the +# fundamental zone of the crystal-symmetry-reduced orientation space +# SO3, it is possible to define a color model which assigns a color to each +# point in the fundamental zone. +# +# Different mapping models are used. These implement (slightly) different +# scaling relations. Differences exist across representations of tech partners. +# +# Differences are which base colors of the RGB color model are placed in +# which extremal position of the SST and where the white point is located. +# +# For further details see: +# +# * [G. Nolze et al.](https://doi.org/10.1107/S1600576716012942) +# * [S. Patala et al.](https://doi.org/10.1016/j.pmatsci.2012.04.002). +# +# Details are implementation-specific and not standardized yet. +# +# Given that the SST has a complicated geometry, it can not yet be +# visualized using tools like H5Web, which is why for now the matrix +# of a rasterized image which is rendered by the backend tool gets +# copied into an RGB matrix to offer a default plot. # # # -# +# # -# Inverse pole figure color code for each map coordinate. +# Inverse pole figure color code for each map coordinate. # # # @@ -406,7 +410,7 @@ NXmicrostructure_ipf(NXprocess): # # # -# Pixel along the y-axis. +# Pixel along the y-axis. # # # @@ -415,7 +419,7 @@ NXmicrostructure_ipf(NXprocess): # # # -# Pixel along the x-axis. +# Pixel along the x-axis. # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_odf.yaml b/contributed_definitions/nyaml/NXmicrostructure_odf.yaml index 165cc1eb22..4af1faff5b 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_odf.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_odf.yaml @@ -47,7 +47,6 @@ NXmicrostructure_odf(NXprocess): kth_extrema(NXobject): doc: | Group to store descriptors and summary statistics for extrema of the ODF. - # name like in NXmicrostructure_score_config extrema(NX_CHAR): doc: | Minima or maxima, if extrema is set to minima values for location and volume_fraction diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index 387c5857a1..d58042d483 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -4,7 +4,6 @@ doc: | * `M. Kühbach et al. `_ * `M. Diehl et al. `_ - symbols: n_dg_ori: | Number of Bunge-Euler angle triplets for deformed grains. @@ -17,7 +16,8 @@ symbols: n_temp: | Number of suport points for the desired time-temperature profile. n_defrag: | - Number of entries when to defragment i.e. garbage collect the memory holding state information for recrystallized cells. + Number of entries when to defragment i.e. garbage collect the memory holding + state information for recrystallized cells. n_snapshot: | Number of entries when to collect snapshots of the evolving microstructure. n_su: | @@ -40,12 +40,13 @@ NXmicrostructure_score_config(NXobject): doc: | ISO 8601 time code with local time zone offset to UTC information included when the configuration file was created. + # end_time(NX_DATE_TIME): - # exists: optional + # exists: optional profiling(NXcs_profiling): exists: optional userID(NXuser): - exists: [min, 0, max, infty] + exists: ['min', '0', 'max', 'unbounded'] nameType: partial sample(NXsample): exists: recommended @@ -79,7 +80,7 @@ NXmicrostructure_score_config(NXobject): doc: | Programs and libraries representing the computational environment programID(NXprogram): - exists: [min, 1, max, infty] + exists: ['min', '1', 'max', 'unbounded'] nameType: partial program(NX_CHAR): \@version(NX_CHAR): @@ -89,21 +90,22 @@ NXmicrostructure_score_config(NXobject): amount of stored (elastic) energy in the system and thus mainly affect recrystallization kinetics. shear_modulus(NX_FLOAT): + unit: NX_PRESSURE doc: | Reference shear modulus at zero Kelvin. - unit: NX_PRESSURE burgers_vector(NX_FLOAT): + unit: NX_LENGTH doc: | Magnitude of the Burgers vector at zero Kelvin. - unit: NX_LENGTH + # firstOrderdG0dT # alloyConstantThermalExpCoeff # FirstOrderThermalExpCoeff # SecondOrderThermalExpCoeff melting_temperature(NX_FLOAT): + unit: NX_TEMPERATURE doc: | Melting temperature - unit: NX_TEMPERATURE deformation(NXobject): doc: | Details about the geometry and properties of the polycrystal that represents the @@ -116,36 +118,43 @@ NXmicrostructure_score_config(NXobject): * poisson_voronoi, a discretized poisson voronoi * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map * damask, the result of a simulation from `DAMASK `_. - enumeration: [cuboidal, poisson_voronoi, ebsd, damask] extent(NX_FLOAT): + unit: NX_LENGTH + # an example why a conditional exists statement is necessary to add in NeXus doc: | Extent of each deformed grain in voxel along the x, y, and z direction when model is cuboidal. - unit: NX_LENGTH - dim: (3,) + dimensions: + rank: 1 + dim: (3,) diameter(NX_FLOAT): + unit: NX_LENGTH doc: | Average spherical diameter when model is poisson_voronoi. - unit: NX_LENGTH ensemble(NXobject): exists: optional doc: | - Settings for instantiating properties of deformed grains when model is cuboidal or poisson. + Settings for instantiating properties of deformed grains when model is cuboidal + or poisson. bunge_euler(NX_FLOAT): + unit: NX_ANGLE doc: | Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) out of which the orientations of deformed grains are sampled. - unit: NX_ANGLE - dim: (n_dg_ori, 3) + dimensions: + rank: 2 + dim: (n_dg_ori, 3) stored_energy(NX_FLOAT): + unit: NX_ANY doc: | Set of stored elastic energy quantified as a dislocation density which is assigned to deformed grains with orientations from bunge_euler with index queries matching for the bunge_euler and stored_energy fields. - unit: NX_ANY - dim: (n_dg_ori,) + dimensions: + rank: 1 + dim: (n_dg_ori,) ebsd(NXnote): exists: optional doc: | @@ -156,15 +165,18 @@ NXmicrostructure_score_config(NXobject): enumeration: [sha256] checksum(NX_CHAR): stepsize(NX_FLOAT): + unit: NX_LENGTH doc: | Extent of the pixel of the EBSD orientation mapping assuming square-shaped pixels or cube-shaped voxels respectively. - unit: NX_LENGTH - dim: (d,) + dimensions: + rank: 1 + dim: (d,) damask(NXnote): exists: optional doc: | - Settings for instantiating properties of deformed grains and nuclei when model is damask. + Settings for instantiating properties of deformed grains and nuclei when model + is damask. file_name(NX_CHAR): doc: | Name of the DREAM.3D HDF5 file that was instantiated from the @@ -183,7 +195,6 @@ NXmicrostructure_score_config(NXobject): * csr, complete spatial randomness * custom, implementation-specific * gb, nuclei placed at grain boundaries - enumeration: [csr, damask] incubation_time(NX_CHAR): doc: | @@ -196,24 +207,28 @@ NXmicrostructure_score_config(NXobject): * ensemble, picking randomly one from ensemble/bunge_euler * random, picking randomly on the SO3 * damask, picking based on information provided in deformation/damask - enumeration: [ensemble, random, damask] ensemble(NXobject): + # required unless custom nucleation model doc: | Settings for instantiating properties of nuclei for recrystallizing grains. bunge_euler(NX_FLOAT): + unit: NX_ANGLE doc: | Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) out of which the orientations of nuclei/recrystallized grains are sampled. - unit: NX_ANGLE - dim: (n_rx_ori, 3) + dimensions: + rank: 2 + dim: (n_rx_ori, 3) incubation_time(NX_FLOAT): + unit: NX_TIME doc: | Incubation time which is assigned to deformed grains with orientations from bunge_euler with index queries matching for the bunge_euler and stored_energy fields. - unit: NX_TIME - dim: (n_rx_ori,) + dimensions: + rank: 1 + dim: (n_rx_ori,) grain_boundary_mobility(NXobject): doc: | Model for the assumed mobility of grain boundaries with different disorientation @@ -225,6 +240,7 @@ NXmicrostructure_score_config(NXobject): Grain boundaries with disorientation angle smaller than 15 degree are considered as low-angle grain boundaries. Other grain boundaries are high-angle boundaries. + # TODO: add equation for the Sebald-Gottstein model the following equation # TODO: add equation for the Rollett-Holm model the following equation enumeration: [sebald_gottstein, rollett_holm] @@ -232,66 +248,68 @@ NXmicrostructure_score_config(NXobject): exists: optional doc: | Parameter of the Sebald-Gottstein migration model. + # constant low value up to lagb_to_hagb_cut # constant plateau beyond # single peak function for particular disorientation # lagb_to_hagb_cut(NX_FLOAT): - # exists: optional - # doc: | - # At which disorientation angle are grain boundary considered as high-angle grain boundaries. - # unit: NX_ANGLE + # exists: optional + # doc: | + # At which disorientation angle are grain boundary considered as high-angle grain boundaries. + # unit: NX_ANGLE lagb_pre_factor(NX_FLOAT): + unit: NX_ANY doc: | Pre-exponential factor for low-angle grain boundaries. - unit: NX_ANY # m^4/Js lagb_enthalpy(NX_FLOAT): + unit: NX_ANY doc: | Migration activation enthalpy for low-angle grain boundaries. - unit: NX_ANY # eV hagb_pre_factor(NX_FLOAT): + unit: NX_ANY doc: | Pre-exponential factor for high-angle grain boundaries. - unit: NX_ANY # m^4/Js hagb_enthalpy(NX_FLOAT): + unit: NX_ANY doc: | Migration activation enthalpy for high-angle grain boundaries. - unit: NX_ANY # eV special_pre_factor(NX_FLOAT): + unit: NX_ANY doc: | Pre-exponential factor for high-angle grain boundaries which in bicrystal or other tailored experiments showed a particular high mobility. - unit: NX_ANY # m^4/Js special_enthalpy(NX_FLOAT): + unit: NX_ANY doc: | Migration activation enthalpy for high-angle grain boundaries which in bicrystal or other tailored experiments showed a particular high mobility. - unit: NX_ANY # eV rollett_holm(NXobject): doc: | Parameter of the Rollett-Holm migration model. + # For rollett_holm :math:`m(\Theta) = m_0 \cdot (1 - c_1 * exp(-c_2 \cdot \frac{\Theta}{15}^{c_3}))`. pre_factor(NX_FLOAT): + unit: NX_ANY doc: | Pre-exponential factor for the fastest grain boundary in the system. - unit: NX_ANY # m^4/Js enthalpy(NX_FLOAT): + unit: NX_ANY doc: | Migration activation enthalpy for the fastest grain boundary in the system. - unit: NX_ANY # eV c1(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. - unit: NX_DIMENSIONLESS c2(NX_FLOAT): + unit: NX_UNITLESS doc: | Mobility scaling factor :math:`c_2`. Typically 5. - unit: NX_UNITLESS c3(NX_FLOAT): + unit: NX_UNITLESS doc: | Mobility scaling factor :math:`c_3`. Typically 9. - unit: NX_UNITLESS stored_energy_recovery(NXobject): doc: | Time-dependent reduction of the stored energy to account for recovery effects. @@ -309,19 +327,21 @@ NXmicrostructure_score_config(NXobject): Which type of drag model. enumeration: [none, zener_smith] zener_smith(NXobject): + # required when model is zener_smith doc: | Parameter of the Zener-Smith drag model when model is zener_smith. pre_factor(NX_FLOAT): + unit: NX_UNITLESS doc: | Configuration-dependent constant which factorizes the drag pressure. - unit: NX_UNITLESS surface_energy(NX_FLOAT): + unit: NX_ANY doc: | Average surface energy of the grain-boundary-dispersoid-surface configuration which factorizes the drag pressure. - unit: NX_ANY # J/m^2 radius_evolution(NXdata): + # required when model is zener_smith # decorators to make the config file immediately useful # like showing a r(t) plot @@ -333,36 +353,46 @@ NXmicrostructure_score_config(NXobject): \@radius_indices(NX_UINT): title(NX_CHAR): time(NX_FLOAT): + unit: NX_TIME doc: | Support point of the linearized curve of simulated time matching a specific support point of the average dispersoid radius. - unit: NX_TIME - dim: (n_drag,) + dimensions: + rank: 1 + dim: (n_drag,) \@long_name(NX_CHAR): radius(NX_FLOAT): + unit: NX_LENGTH doc: | Support point of the linearized curve of the average dispersoid radius. - unit: NX_LENGTH - dim: (n_drag,) + dimensions: + rank: 1 + dim: (n_drag,) \@long_name(NX_CHAR): component_analysis(NXobject): name(NX_CHAR): doc: | Given name of a texture component. - dim: (n_ori,) + dimensions: + rank: 1 + dim: (n_ori,) bunge_euler(NX_FLOAT): + unit: NX_ANGLE doc: | Bunge-Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the of texture components in sequence of the name field. - unit: NX_ANGLE - dim: (n_ori, 3) + dimensions: + rank: 2 + dim: (n_ori, 3) theta(NX_FLOAT): + unit: NX_ANGLE doc: | Integration radius that constraints the theta angular region of the orientation space (SO3) about each central location (obeying symmetries) as specified by bunge_euler indexed in the same sequence as the bunge_euler and name fields. - unit: NX_ANGLE - dim: (n_ori,) + dimensions: + rank: 1 + dim: (n_ori,) time_temperature(NXdata): doc: | Desired simulated time-temperature profile @@ -372,17 +402,21 @@ NXmicrostructure_score_config(NXobject): \@temperature_indices(NX_UINT): title(NX_CHAR): time(NX_FLOAT): + unit: NX_TIME doc: | Support point of the linearized curve of simulated time matching a specific support point of the temperature. - unit: NX_TIME - dim: (n_temp,) + dimensions: + rank: 1 + dim: (n_temp,) \@long_name(NX_CHAR): temperature(NX_FLOAT): + unit: NX_TEMPERATURE doc: | Support point of the linearized curve of the temperature. - unit: NX_TEMPERATURE - dim: (n_temp,) + dimensions: + rank: 1 + dim: (n_temp,) \@long_name(NX_CHAR): discretization(NXmicrostructure): doc: | @@ -397,20 +431,23 @@ NXmicrostructure_score_config(NXobject): material point-specific values to values averaged per deformed grain. grid(NXcg_grid): extent(NX_UINT): + unit: NX_UNITLESS doc: | Extend of each CA domain in voxel along the x, y, and z direction. Deformation of sheet material is assumed. The x axis is assumed pointing along the rolling direction. The y axis is assumed pointing along the transverse direction. The z axis is assumed pointing along the normal direction. - unit: NX_UNITLESS - dim: (3,) # (d,) + dimensions: + rank: 1 + dim: (3,) cell_dimensions(NX_FLOAT): + unit: NX_LENGTH doc: | Edge length of the material point that in SCORE is discretized via equisized cubic voxels. - unit: NX_LENGTH - # dim: (d,) + + # dim: (d,) numerics(NXobject): doc: | Criteria which enable to stop the simulation in a controlled manner. @@ -418,24 +455,25 @@ NXmicrostructure_score_config(NXobject): Furthermore, numerical configuration required to achieve a stable numerical integration. max_x(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | Maximum recrystallized volume fraction. - unit: NX_DIMENSIONLESS max_time(NX_FLOAT): + unit: NX_TIME doc: | Maximum simulated physical time. - unit: NX_TIME max_iteration(NX_UINT): + unit: NX_UNITLESS doc: | Maximum number of iteration steps. - unit: NX_UNITLESS max_delta_x(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | Maximum fraction equivalent to the migration of the fastest grain boundary in the system how much a cell may be consumed in a single iteration. - unit: NX_DIMENSIONLESS x_set(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | List of target values at which recrystallized volume fractions the state of the CA is evaluated and stored. The code documents summary statistics @@ -449,55 +487,796 @@ NXmicrostructure_score_config(NXobject): Despite these front data make up for approximately one order of magnitude less cells than represented in the domain, more numerical data have to be collected for each cell in the front than just a grain identifier. - unit: NX_DIMENSIONLESS - dim: (n_snapshot,) + dimensions: + rank: 1 + dim: (n_snapshot,) cell_cache(NXobject): doc: | Parameter which control the memory management of cells in the recrystallization front. initial(NX_FLOAT): + unit: NX_UNITLESS doc: | Fraction of the total number of cells in the CA which should initially be allocated for offering storage for cells making up the recrystallization front. - unit: NX_UNITLESS realloc(NX_FLOAT): + unit: NX_UNITLESS doc: | By how much more times should the already allocated memory be increased to offer space for storing states of cells in the recrystallization front. - unit: NX_UNITLESS defragment(NX_BOOLEAN): doc: | Should the cache for cells in the recrystallization front be defragmented on-the-fly or not. defragment_x(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | Target values at which recrystallized volume fraction the cache for cells in the recrystallization front will be defragmented on-the-fly. Defragmentation packs active cells closer into main memory to reduce cache misses in subsequent evaluations of the recrystallization front. - unit: NX_DIMENSIONLESS - dim: (n_defrag,) + dimensions: + rank: 1 + dim: (n_defrag,) solitary_unit(NXobject): apply(NX_BOOLEAN): doc: | Perform a statistical analyses of the results as it was proposed by M. Kühbach (solitary unit model ensemble approach). number_of_domains(NX_UINT): + unit: NX_UNITLESS doc: | How many independent cellular automaton domains should be instantiated. - unit: NX_UNITLESS rediscretization(NX_UINT): + unit: NX_UNITLESS doc: | Into how many time steps should the real time interval be discretized upon during post-processing the results with the solitary unit modeling approach. - unit: NX_UNITLESS - # identifier_domain(NX_UINT): - # doc: | - # List of identifier for those CAs domains which should be sampled. - # Identifier start from 1. - # unit: NX_UNITLESS - # dim: (n_su,) + + # identifier_domain(NX_UINT): + # doc: | + # List of identifier for those CAs domains which should be sampled. + # Identifier start from 1. + # unit: NX_UNITLESS + # dim: (n_su,) + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# c4a0663856a65ebfd1f17b04a79398b729ef68f2cfab36b6972666bf9cd4edd5 +# +# +# +# +# +# +# +# Number of Bunge-Euler angle triplets for deformed grains. +# +# +# +# +# Number of Bunge-Euler angle triplets for recrystallization nuclei. +# +# +# +# +# Number of texture components to analyze. +# +# +# +# +# Number of support points for the linearized drag profile. +# +# +# +# +# Number of suport points for the desired time-temperature profile. +# +# +# +# +# Number of entries when to defragment i.e. garbage collect the memory holding +# state information for recrystallized cells. +# +# +# +# +# Number of entries when to collect snapshots of the evolving microstructure. +# +# +# +# +# Number of solitary unit domains to export. +# +# +# +# +# Dimensionality of the simulation. +# +# +# +# +# Application definition to configure a simulation with the SCORE model. +# +# * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ +# * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ +# +# +# +# +# +# +# +# +# +# An alias to refer to this simulation. +# +# +# +# +# Discouraged free-text field to add further details to the computation. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the configuration file was created. +# +# +# +# +# +# +# +# +# Dimensionality of the simulation. +# +# +# +# +# +# +# +# A qualifier whether the sample is a real one or a virtual one. +# +# +# +# +# +# +# +# +# List of comma-separated elements from the periodic table that are +# contained in the specimen. If the specimen substance has multiple +# components, all elements from each component must be included in +# `atom_types`. +# +# The purpose of the field is to offer research data management systems an +# opportunity to parse the relevant elements without having to interpret +# these from the resources pointed to by parent_identifier or walk through +# eventually deeply nested groups in data instances. +# +# +# +# +# +# Name of the program whereby this config file was created. +# +# +# +# +# +# +# +# Programs and libraries representing the computational environment +# +# +# +# +# +# +# +# +# +# (Mechanical) properties of the material which scale the +# amount of stored (elastic) energy in the system and +# thus mainly affect recrystallization kinetics. +# +# +# +# Reference shear modulus at zero Kelvin. +# +# +# +# +# Magnitude of the Burgers vector at zero Kelvin. +# +# +# +# +# +# Melting temperature +# +# +# +# +# +# Details about the geometry and properties of the polycrystal that represents the +# starting configuration (typically a deformed microstructure) for the simulation. +# +# +# +# Which model should be used to generate a starting microstructure. +# +# * cuboidal, a regular array of equally shaped cuboidal grains +# * poisson_voronoi, a discretized poisson voronoi +# * ebsd, a microstructure synthesized based on a simulated or measured EBSD orientation map +# * damask, the result of a simulation from `DAMASK <https://damask-multiphysics.org>`_. +# +# +# +# +# +# +# +# +# +# +# +# Extent of each deformed grain in voxel along the +# x, y, and z direction when model is cuboidal. +# +# +# +# +# +# +# +# Average spherical diameter when model is poisson_voronoi. +# +# +# +# +# Settings for instantiating properties of deformed grains when model is cuboidal +# or poisson. +# +# +# +# Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) +# out of which the orientations of deformed grains are sampled. +# +# +# +# +# +# +# +# +# Set of stored elastic energy quantified as a dislocation density which is assigned +# to deformed grains with orientations from bunge_euler with index queries matching +# for the bunge_euler and stored_energy fields. +# +# +# +# +# +# +# +# +# Settings for instantiating properties of deformed grains from an +# EBSD orientation map when model is cuboidal or poisson. +# +# +# +# +# +# +# +# +# +# +# Extent of the pixel of the EBSD orientation mapping assuming square-shaped pixels +# or cube-shaped voxels respectively. +# +# +# +# +# +# +# +# +# Settings for instantiating properties of deformed grains and nuclei when model +# is damask. +# +# +# +# Name of the DREAM.3D HDF5 file that was instantiated from the +# a previously performed DAMASK simulation. +# +# +# +# +# +# +# +# +# +# +# +# +# Phenomenological model according to which recrystallization nuclei +# are placed into the domain whose growth is studied with the simulation. +# +# +# +# According to which model will the nuclei become distributed spatially: +# +# * csr, complete spatial randomness +# * custom, implementation-specific +# * gb, nuclei placed at grain boundaries +# +# +# +# +# +# +# +# +# According to which model will the nuclei start to grow. +# +# +# +# +# +# +# +# According to which model will the nuclei get their orientation assigned: +# +# * ensemble, picking randomly one from ensemble/bunge_euler +# * random, picking randomly on the SO3 +# * damask, picking based on information provided in deformation/damask +# +# +# +# +# +# +# +# +# +# +# Settings for instantiating properties of nuclei for recrystallizing grains. +# +# +# +# Set of Bunge-Euler orientations (:math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` ) +# out of which the orientations of nuclei/recrystallized grains are sampled. +# +# +# +# +# +# +# +# +# Incubation time which is assigned to deformed grains with orientations from bunge_euler +# with index queries matching for the bunge_euler and stored_energy fields. +# +# +# +# +# +# +# +# +# +# Model for the assumed mobility of grain boundaries with different disorientation +# implemented as parameterized Turnbull's model for thermally-activated +# grain boundary migration. +# +# +# +# Which type of fundamental model for the grain boundary mobility. +# +# Grain boundaries with disorientation angle smaller than 15 degree are considered +# as low-angle grain boundaries. Other grain boundaries are high-angle boundaries. +# +# +# +# +# +# +# +# +# +# Parameter of the Sebald-Gottstein migration model. +# +# +# +# +# Pre-exponential factor for low-angle grain boundaries. +# +# +# +# +# Migration activation enthalpy for low-angle grain boundaries. +# +# +# +# +# Pre-exponential factor for high-angle grain boundaries. +# +# +# +# +# Migration activation enthalpy for high-angle grain boundaries. +# +# +# +# +# Pre-exponential factor for high-angle grain boundaries which in +# bicrystal or other tailored experiments showed a particular high +# mobility. +# +# +# +# +# Migration activation enthalpy for high-angle grain boundaries which in +# bicrystal or other tailored experiments showed a particular high +# mobility. +# +# +# +# +# +# Parameter of the Rollett-Holm migration model. +# +# +# +# +# Pre-exponential factor for the fastest grain boundary in the system. +# +# +# +# +# Migration activation enthalpy for the fastest grain boundary in the system. +# +# +# +# +# Mobility scaling factor :math:`c_1`. Typically 0.99 or higher but not 1. +# +# +# +# +# Mobility scaling factor :math:`c_2`. Typically 5. +# +# +# +# +# Mobility scaling factor :math:`c_3`. Typically 9. +# +# +# +# +# +# +# Time-dependent reduction of the stored energy to account for recovery effects. +# +# +# +# Which type of recovery model. +# +# +# +# +# +# +# +# +# Reduction of the grain boundary migration speed due to the presence of dispersoids +# through which the total grain boundary area of the recrystallization front can be reduced +# while the boundary is arrested at the dispersoids. +# +# +# +# Which type of drag model. +# +# +# +# +# +# +# +# +# +# Parameter of the Zener-Smith drag model when model is zener_smith. +# +# +# +# Configuration-dependent constant which factorizes the drag pressure. +# +# +# +# +# Average surface energy of the grain-boundary-dispersoid-surface configuration +# which factorizes the drag pressure. +# +# +# +# +# +# Assumed dispersoid mean radius-time profile +# +# +# +# +# +# +# +# +# Support point of the linearized curve of simulated time matching +# a specific support point of the average dispersoid radius. +# +# +# +# +# +# +# +# +# Support point of the linearized curve of the average dispersoid radius. +# +# +# +# +# +# +# +# +# +# +# +# +# Given name of a texture component. +# +# +# +# +# +# +# +# Bunge-Euler angle representation :math:`\varphi_1`, :math:`\Phi`, :math:`\varphi_2` of the +# of texture components in sequence of the name field. +# +# +# +# +# +# +# +# +# Integration radius that constraints the theta angular region of the orientation space (SO3) +# about each central location (obeying symmetries) as specified by bunge_euler indexed in +# the same sequence as the bunge_euler and name fields. +# +# +# +# +# +# +# +# +# Desired simulated time-temperature profile +# +# +# +# +# +# +# +# +# Support point of the linearized curve of simulated time matching +# a specific support point of the temperature. +# +# +# +# +# +# +# +# +# Support point of the linearized curve of the temperature. +# +# +# +# +# +# +# +# +# +# Relevant data to instantiate a starting configuration that is typically +# a microstructure in deformed conditions where (elastic) energy is stored +# in the form of crystal defects (mostly dislocations). The SCORE model +# does not resolve individual dislocations but works with one +# homogenized mean-field density per grain. For simulations that are +# instantiated from EBSD datasets or crystal plasticity simulations +# individual values are available for each voxel that may be used as is +# for each voxel or may need a pre-processing of the data to coarse-grain +# material point-specific values to values averaged per deformed grain. +# +# +# +# +# Extend of each CA domain in voxel along the x, y, and z direction. +# Deformation of sheet material is assumed. +# The x axis is assumed pointing along the rolling direction. +# The y axis is assumed pointing along the transverse direction. +# The z axis is assumed pointing along the normal direction. +# +# +# +# +# +# +# +# Edge length of the material point that in SCORE +# is discretized via equisized cubic voxels. +# +# +# +# +# +# +# +# Criteria which enable to stop the simulation in a controlled manner. +# Whichever criterion is fulfilled first stops the simulation. +# Furthermore, numerical configuration required to achieve +# a stable numerical integration. +# +# +# +# Maximum recrystallized volume fraction. +# +# +# +# +# Maximum simulated physical time. +# +# +# +# +# Maximum number of iteration steps. +# +# +# +# +# Maximum fraction equivalent to the migration of the +# fastest grain boundary in the system how much a cell +# may be consumed in a single iteration. +# +# +# +# +# List of target values at which recrystallized volume fractions the state +# of the CA is evaluated and stored. The code documents summary statistics +# like recrystallized volume fraction for each iteration and the volume of each +# grain. Furthermore, snapshots of the microstructure are stored. +# These can take much disk space though because SCORE is able to evolve CA +# with up to :math:`1600^3` cells. Snapshot data document the current microstructure +# including the assignment of grains and cells surplus the state of the +# recrystallization front. +# +# Despite these front data make up for approximately one order of magnitude +# less cells than represented in the domain, more numerical data have to be +# collected for each cell in the front than just a grain identifier. +# +# +# +# +# +# +# +# Parameter which control the memory management +# of cells in the recrystallization front. +# +# +# +# Fraction of the total number of cells in the CA which +# should initially be allocated for offering storage for +# cells making up the recrystallization front. +# +# +# +# +# By how much more times should the already allocated memory +# be increased to offer space for storing states of cells +# in the recrystallization front. +# +# +# +# +# Should the cache for cells in the recrystallization front +# be defragmented on-the-fly or not. +# +# +# +# +# Target values at which recrystallized volume fraction the cache +# for cells in the recrystallization front will be defragmented +# on-the-fly. Defragmentation packs active cells closer into +# main memory to reduce cache misses in subsequent evaluations +# of the recrystallization front. +# +# +# +# +# +# +# +# +# +# +# Perform a statistical analyses of the results as it was proposed +# by M. Kühbach (solitary unit model ensemble approach). +# +# +# +# +# How many independent cellular automaton domains +# should be instantiated. +# +# +# +# +# Into how many time steps should the real time interval be discretized upon +# during post-processing the results with the solitary unit modeling approach. +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml index 1040112333..8bdc1cbfd3 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml @@ -13,14 +13,14 @@ doc: | * `M. Kühbach et al. `_ * `C. Haase et al. `_ * `M. Diehl et al. `_ - symbols: doc: | The symbols used in the schema to specify e.g. dimensions of arrays n_summary_stats: | The total number of summary statistic log entries n_b: | - Number of boundaries of the bounding box or primitive about the computational domain + Number of boundaries of the bounding box or primitive about the computational + domain n_p: | Number of parameter required for chosen orientation parameterization n_tex: | @@ -33,6 +33,7 @@ symbols: Number of active cells in the (recrystallization) front n_grains: | Number of grains in the computer simulation + # inspect comments behind NXmicrostructure type: group NXmicrostructure_score_results(NXobject): @@ -64,7 +65,8 @@ NXmicrostructure_score_results(NXobject): included when the simulation ended. profiling(NXcs_profiling): exists: optional - # consider integrating content that is currently stored in ThreadProfiling.csv + + # consider integrating content that is currently stored in ThreadProfiling.csv program1(NXprogram): doc: | Name of the program with which the simulation was performed. @@ -75,16 +77,17 @@ NXmicrostructure_score_results(NXobject): doc: | Programs and libraries representing the computational environment programID(NXprogram): - exists: [min, 1, max, infty] + exists: ['min', '1', 'max', 'unbounded'] nameType: partial program(NX_CHAR): \@version(NX_CHAR): + # rotation_conventions(NXrotation_conventions): - # rotation_handedness(NX_CHAR): - # rotation_convention(NX_CHAR): - # euler_angle_convention(NX_CHAR): - # axis_angle_convention(NX_CHAR): - # sign_convention(NX_CHAR): + # rotation_handedness(NX_CHAR): + # rotation_convention(NX_CHAR): + # euler_angle_convention(NX_CHAR): + # axis_angle_convention(NX_CHAR): + # sign_convention(NX_CHAR): sample_reference_frame(NXcoordinate_system): type: enumeration: [cartesian] @@ -105,7 +108,7 @@ NXmicrostructure_score_results(NXobject): z_direction: enumeration: [north] discretization(NXmicrostructure): - exists: [min, 1, max, 1] + exists: ['min', '1', 'max', '1'] grid(NXcg_grid): dimensionality(NX_POSINT): cardinality(NX_POSINT): @@ -114,11 +117,12 @@ NXmicrostructure_score_results(NXobject): cell_dimensions(NX_NUMBER): extent(NX_UINT): identifier_offset(NX_INT): - boundary(NXcg_hexahedron_set): + boundary(NXcg_hexahedron): doc: | A tight bounding box or sphere or bounding primitive about the grid. + # a good example for a general bounding box description for such a grids of triclinic cells - # https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron_set because a parallelepiped + # https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallelepiped number_of_boundaries(NX_POSINT): unit: NX_UNITLESS doc: | @@ -136,15 +140,18 @@ NXmicrostructure_score_results(NXobject): * 3 - mirror * 4 - von Neumann * 5 - Dirichlet - - dim: (6,) + dimensions: + rank: 1 + dim: (6,) boundaries: doc: | Name of the boundaries. Left, right, front, back, bottom, top, The field must have as many entries as there are number_of_boundaries. - dim: (6,) + dimensions: + rank: 1 + dim: (6,) spatiotemporalID(NXobject): - exists: [min, 1, max, infty] # max 1 in case of a single classical CA simulation, i.e. without solitary units + exists: ['min', '1', 'max', 'unbounded'] nameType: partial doc: | Documentation of the spatiotemporal evolution for each CA domain. @@ -152,11 +159,12 @@ NXmicrostructure_score_results(NXobject): SCORE is a hybrid parallelized code that can evolve multiple replicas in parallel. The set of replicas is distributed across MPI processes. Each such replica is then evolved via OpenMP multi-threading. + # the typical lean summary statistics flattened summary_statistics(NXprocess): doc: | Summary quantities which are the result of some post-processing of the snapshot data - (averaging, integrating, interpolating) happening for practical and performance reasons + (averaging, integrating, interpolating) happening for practical and performance reasons during the simulation. Place used for storing descriptors from continuum mechanics and thermodynamics at the scale of the entire ROI. kinetics(NXdata): @@ -174,25 +182,34 @@ NXmicrostructure_score_results(NXobject): title(NX_CHAR): exists: recommended time(NX_FLOAT): - doc: | - Evolution of the physical time not to be confused with wall-clock time or profiling data. unit: NX_TIME - dim: (n_summary_stats,) + doc: | + Evolution of the physical time not to be confused with wall-clock time or + profiling data. + dimensions: + rank: 1 + dim: (n_summary_stats,) iteration(NX_INT): + unit: NX_UNITLESS doc: | Iteration or increment counter. - unit: NX_UNITLESS - dim: (n_summary_stats,) + dimensions: + rank: 1 + dim: (n_summary_stats,) temperature(NX_FLOAT): + unit: NX_TEMPERATURE doc: | Evolution of the simulated temperature over time. - unit: NX_TEMPERATURE - dim: (n_summary_stats,) + dimensions: + rank: 1 + dim: (n_summary_stats,) x(NX_FLOAT): + unit: NX_DIMENSIONLESS doc: | Recrystallized volume fraction. - unit: NX_DIMENSIONLESS - dim: (n_summary_stats,) + dimensions: + rank: 1 + dim: (n_summary_stats,) stress(NXdata): exists: optional type(NX_CHAR): @@ -200,20 +217,24 @@ NXmicrostructure_score_results(NXobject): Which type of stress. enumeration: [cauchy] tensor(NX_FLOAT): + unit: NX_ANY doc: | Applied external stress tensor on the ROI. - unit: NX_ANY - dim: (n_summary_stats, 3, 3) + dimensions: + rank: 3 + dim: (n_summary_stats, 3, 3) strain(NXdata): exists: optional type(NX_CHAR): doc: | Which type of strain. tensor(NX_FLOAT): + unit: NX_ANY doc: | Applied external strain tensor on the ROI. - unit: NX_ANY - dim: (n_summary_stats, 3, 3) + dimensions: + rank: 3 + dim: (n_summary_stats, 3, 3) deformation_gradient(NXprocess): exists: optional type: @@ -221,60 +242,70 @@ NXmicrostructure_score_results(NXobject): Which type of deformation gradient. enumeration: [piola] tensor(NX_FLOAT): + unit: NX_ANY doc: | Applied deformation gradient tensor on the ROI. - unit: NX_ANY - dim: (n_summary_stats, 3, 3) - # magnetic_field(NXprocess): - # exists: optional - # strength(NX_FLOAT): - # doc: | - # Applied external magnetic field on the ROI. - # unit: NX_ANY - # dim: (n_summary_stats, 3, 3) - # electrical_field(NXprocess): - # exists: optional - # strength(NX_FLOAT): - # doc: | - # Applied external electrical field on the ROI. - # unit: NX_ANY - # dim: (n_summary_stats, 3, 3) + dimensions: + rank: 3 + dim: (n_summary_stats, 3, 3) + + # magnetic_field(NXprocess): + # exists: optional + # strength(NX_FLOAT): + # doc: | + # Applied external magnetic field on the ROI. + # unit: NX_ANY + # dim: (n_summary_stats, 3, 3) + # electrical_field(NXprocess): + # exists: optional + # strength(NX_FLOAT): + # doc: | + # Applied external electrical field on the ROI. + # unit: NX_ANY + # dim: (n_summary_stats, 3, 3) # the typically storage-costlier snapshot data microstructureID(NXmicrostructure): - exists: [min, 1, max, infty] # always storing the starting configuration + exists: ['min', '1', 'max', 'unbounded'] nameType: partial time(NX_FLOAT): iteration(NX_UINT): + unit: NX_UNITLESS doc: | Iteration or increment counter. - unit: NX_UNITLESS temperature(NX_FLOAT): + unit: NX_TEMPERATURE doc: | Simulated temperature for this snapshot. - unit: NX_TEMPERATURE x(NX_FLOAT): - doc: | - Current recrystallized volume fraction (taking fractional infections into account). unit: NX_DIMENSIONLESS - x_set(NX_FLOAT): doc: | - Target value for which a snapshot was requested for the recrystallized volume fraction. + Current recrystallized volume fraction (taking fractional infections into + account). + x_set(NX_FLOAT): unit: NX_DIMENSIONLESS + doc: | + Target value for which a snapshot was requested for the recrystallized volume + fraction. + # optional places to store the grid for instance if it changes grid(NXcg_grid): exists: recommended identifier_crystal(NX_UINT): exists: recommended + unit: NX_UNITLESS doc: | Grain identifier for each cell. - unit: NX_UNITLESS - dim: (n_x, n_y, n_z) + dimensions: + rank: 3 + dim: (n_x, n_y, n_z) identifier_thread(NX_UINT): exists: optional + unit: NX_UNITLESS doc: | Identifier of the OpenMP thread which processed this part of the grid. - unit: NX_UNITLESS - dim: (n_x, n_y, n_z) + dimensions: + rank: 3 + dim: (n_x, n_y, n_z) crystals(NXobject): representation(NX_CHAR): exists: recommended @@ -286,85 +317,678 @@ NXmicrostructure_score_results(NXobject): exists: recommended identifier_crystal(NX_INT): exists: recommended - dim: (n_grains,) + dimensions: + rank: 1 + dim: (n_grains,) identifier_offset_phase(NX_INT): exists: recommended identifier_phase(NX_INT): exists: recommended - dim: (n_grains,) + dimensions: + rank: 1 + dim: (n_grains,) volume(NX_FLOAT): + unit: NX_VOLUME doc: | Volume of each grain accounting also for partially transformed cells. - unit: NX_VOLUME - dim: (n_grains,) + dimensions: + rank: 1 + dim: (n_grains,) + # SCORE specific - bunge_euler(NX_FLOAT): # only in the first snapshot + bunge_euler(NX_FLOAT): + unit: NX_ANGLE doc: | Bunge-Euler angle triplets for each grain. - unit: NX_ANGLE - dim: (n_grains, 3) + dimensions: + rank: 2 + dim: (n_grains, 3) dislocation_density(NX_FLOAT): exists: recommended + unit: NX_ANY doc: | Current value for the dislocation density as a measure of the remaining stored energy in assumed crystal defects inside each grain. - unit: NX_ANY # 1/m^2 - dim: (n_grains,) + dimensions: + rank: 1 + dim: (n_grains,) is_deformed(NX_BOOLEAN): exists: recommended doc: | Is the grain deformed. - dim: (n_grains,) + dimensions: + rank: 1 + dim: (n_grains,) is_recrystallized(NX_BOOLEAN): exists: recommended doc: | Is the grain recrystallized. - dim: (n_grains,) + dimensions: + rank: 1 + dim: (n_grains,) recrystallization_front(NXobject): exists: recommended doc: | - Details about those cells which in this time step represent the discrete recrystallization front. + Details about those cells which in this time step represent the discrete + recrystallization front. halo_region(NX_UINT): exists: optional + unit: NX_UNITLESS doc: | Which cells are currently in a halo region of threads. - unit: NX_UNITLESS - dim: (n_front,) + dimensions: + rank: 1 + dim: (n_front,) mobility_weight(NX_FLOAT): exists: recommended + unit: NX_UNITLESS doc: | So-called mobility weight which is a scaling factor to control the mobility of the grain boundary that is modelled sweeping cells that make the discrete recrystallization front. - unit: NX_UNITLESS - dim: (n_front,) + dimensions: + rank: 1 + dim: (n_front,) coordinate(NX_NUMBER): exists: recommended + unit: NX_UNITLESS doc: | The x, y, z grid coordinates of each cell in the recrystallization front. - unit: NX_UNITLESS - dim: (n_front, 3) + dimensions: + rank: 2 + dim: (n_front, 3) identifier_deformed_grain(NX_UINT): exists: recommended + unit: NX_UNITLESS doc: | Grain identifier assigned to each cell in the recrystallization front. - unit: NX_UNITLESS - dim: (n_front,) + dimensions: + rank: 1 + dim: (n_front,) identifier_recrystallized_grain(NX_UINT): exists: recommended - doc: | - Grain identifier assigned to each nucleus which affected that cell in the recrystallization front. unit: NX_UNITLESS - dim: (n_front,) + doc: | + Grain identifier assigned to each nucleus which affected that cell in the + recrystallization front. + dimensions: + rank: 1 + dim: (n_front,) identifier_thread(NX_UINT): exists: optional - doc: | - Identifier of the OpenMP thread processing each cell in the recrystallization front. unit: NX_UNITLESS - dim: (n_front,) + doc: | + Identifier of the OpenMP thread processing each cell in the recrystallization + front. + dimensions: + rank: 1 + dim: (n_front,) infection_direction(NX_UINT): exists: optional + unit: NX_UNITLESS doc: | Hint about the direction from which the cell was infected. - unit: NX_UNITLESS - dim: (n_front,) + dimensions: + rank: 1 + dim: (n_front,) + +# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ +# fd4d3b95663d21f0ae227939ee471b461200d02d5654ad24a8ca7fdf711d7a0d +# +# +# +# +# +# +# +# The symbols used in the schema to specify e.g. dimensions of arrays +# +# +# +# The total number of summary statistic log entries +# +# +# +# +# Number of boundaries of the bounding box or primitive about the computational +# domain +# +# +# +# +# Number of parameter required for chosen orientation parameterization +# +# +# +# +# Number of texture components identified +# +# +# +# +# Dimensionality +# +# +# +# +# Cardinality +# +# +# +# +# Number of active cells in the (recrystallization) front +# +# +# +# +# Number of grains in the computer simulation +# +# +# +# +# Application definition for storing results of the SCORE cellular automata model. +# +# The SCORE cellular automata model for primary recrystallization is an example +# of a typical materials engineering application used within the field of so-called +# Integral Computational Materials Engineering (ICME) whereby one can simulate +# the evolution of microstructures. +# +# Specifically the SCORE model can be used to simulate the growth of nuclei during +# static recrystallization. The model is described in the literature: +# +# * `M. Kühbach et al. <https://doi.org/10.1016/j.actamat.2016.01.068>`_ +# * `C. Haase et al. <https://doi.org/10.1016/j.actamat.2015.08.057>`_ +# * `M. Diehl et al. <https://doi.org/10.1088/1361-651X/ab51bd>`_ +# +# +# +# +# +# +# +# +# +# Simulation ID as an alias to refer to this simulation. +# +# +# +# +# Configuration file with the parameterization of the +# SCORE model that was used for this simulation. +# +# +# +# +# +# +# +# Discouraged free-text field to add further details to the computation. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the simulation was started. +# +# +# +# +# ISO 8601 time code with local time zone offset to UTC information +# included when the simulation ended. +# +# +# +# +# +# +# Name of the program with which the simulation was performed. +# +# +# +# +# +# +# +# Programs and libraries representing the computational environment +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# A tight bounding box or sphere or bounding primitive about the grid. +# +# +# +# +# How many distinct boundaries are distinguished? +# Most grids discretize a cubic or cuboidal region. In this case +# six sides can be distinguished, each making an own boundary. +# +# +# +# +# The boundary conditions for each boundary: +# +# * 0 - undefined +# * 1 - open +# * 2 - periodic +# * 3 - mirror +# * 4 - von Neumann +# * 5 - Dirichlet +# +# +# +# +# +# +# +# Name of the boundaries. Left, right, front, back, bottom, top, +# The field must have as many entries as there are number_of_boundaries. +# +# +# +# +# +# +# +# +# +# Documentation of the spatiotemporal evolution for each CA domain. +# +# SCORE is a hybrid parallelized code that can evolve multiple replicas +# in parallel. The set of replicas is distributed across MPI processes. +# Each such replica is then evolved via OpenMP multi-threading. +# +# +# +# +# Summary quantities which are the result of some post-processing of the snapshot data +# (averaging, integrating, interpolating) happening for practical and performance reasons +# during the simulation. Place used for storing descriptors from continuum mechanics +# and thermodynamics at the scale of the entire ROI. +# +# +# +# Evolution of the recrystallized volume fraction over time. +# +# +# +# +# +# +# +# +# +# +# Evolution of the physical time not to be confused with wall-clock time or +# profiling data. +# +# +# +# +# +# +# +# Iteration or increment counter. +# +# +# +# +# +# +# +# Evolution of the simulated temperature over time. +# +# +# +# +# +# +# +# Recrystallized volume fraction. +# +# +# +# +# +# +# +# +# +# Which type of stress. +# +# +# +# +# +# +# +# Applied external stress tensor on the ROI. +# +# +# +# +# +# +# +# +# +# +# +# Which type of strain. +# +# +# +# +# Applied external strain tensor on the ROI. +# +# +# +# +# +# +# +# +# +# +# +# Which type of deformation gradient. +# +# +# +# +# +# +# +# Applied deformation gradient tensor on the ROI. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Iteration or increment counter. +# +# +# +# +# Simulated temperature for this snapshot. +# +# +# +# +# Current recrystallized volume fraction (taking fractional infections into +# account). +# +# +# +# +# Target value for which a snapshot was requested for the recrystallized volume +# fraction. +# +# +# +# +# +# +# Grain identifier for each cell. +# +# +# +# +# +# +# +# +# +# Identifier of the OpenMP thread which processed this part of the grid. +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# +# Volume of each grain accounting also for partially transformed cells. +# +# +# +# +# +# +# +# +# Bunge-Euler angle triplets for each grain. +# +# +# +# +# +# +# +# +# Current value for the dislocation density as a measure of the remaining +# stored energy in assumed crystal defects inside each grain. +# +# +# +# +# +# +# +# Is the grain deformed. +# +# +# +# +# +# +# +# Is the grain recrystallized. +# +# +# +# +# +# +# +# +# Details about those cells which in this time step represent the discrete +# recrystallization front. +# +# +# +# Which cells are currently in a halo region of threads. +# +# +# +# +# +# +# +# So-called mobility weight which is a scaling factor to control the +# mobility of the grain boundary that is modelled sweeping cells that +# make the discrete recrystallization front. +# +# +# +# +# +# +# +# The x, y, z grid coordinates of each cell in the recrystallization front. +# +# +# +# +# +# +# +# +# Grain identifier assigned to each cell in the recrystallization front. +# +# +# +# +# +# +# +# Grain identifier assigned to each nucleus which affected that cell in the +# recrystallization front. +# +# +# +# +# +# +# +# Identifier of the OpenMP thread processing each cell in the recrystallization +# front. +# +# +# +# +# +# +# +# Hint about the direction from which the cell was infected. +# +# +# +# +# +# +# +# +# +# diff --git a/contributed_definitions/nyaml/NXoptical_system_em.yaml b/contributed_definitions/nyaml/NXoptical_system_em.yaml deleted file mode 100644 index e475065a01..0000000000 --- a/contributed_definitions/nyaml/NXoptical_system_em.yaml +++ /dev/null @@ -1,291 +0,0 @@ -category: base -doc: | - A container for qualifying an electron optical system. -type: group -NXoptical_system_em(NXobject): - - # NEW ISSUE: for now used to store difficult to place entries - # NEW ISSUE: all the definitions here should better be backed up by the - # work of the HMC EM glossary activities - camera_length(NX_NUMBER): - unit: NX_LENGTH - doc: - - | - Distance which is present between the specimen surface and the detector plane. - - | - xref: - spec: EMglossary - term: Camera Length - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 - magnification(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - The factor of enlargement of the apparent size, - not the physical size, of an object. - defocus(NX_NUMBER): - unit: NX_LENGTH - doc: | - The defocus aberration constant (oftentimes referred to as C_1_0). - See respective details in :ref:`NXaberration` class instances. - semi_convergence_angle(NX_NUMBER): - unit: NX_ANGLE - doc: - - | - The angle which is given by the semi-opening angle of the cone in a convergent - beam. - - | - xref: - spec: EMglossary - term: Convergence Angle - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 - field_of_view(NX_NUMBER): - unit: NX_LENGTH - doc: | - The extent of the observable parts of the specimen given the current - magnification and other settings of the instrument. - working_distance(NX_NUMBER): - unit: NX_LENGTH - doc: - - | - Distance which is determined along the optical axis within the column from (1) the - lower end of the final optical element between the source and the specimen stage; - to (2) the point where the beam is focused. - - | - xref: - spec: EMglossary - term: Working Distance - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 - - # probe_current and beam_current are related but not the same - # the probe_current is equal to the beam_current only right at the surface where the beam enters the specimen - # inserting a Faraday cup in the beam path measures the beam_current (along a specific location on the beam - # before it enters the specimen but it is often assumed for the practical reason that measuring right at the surface - # that the beam current is the probe current. - probe(NXcg_ellipsoid_set): - doc: | - Geometry of the cross-section formed when the primary beam shines onto the - specimen surface. - probe_current(NX_NUMBER): - unit: NX_CURRENT - doc: - - | - Electrical current which arrives at the specimen. - - | - xref: - spec: EMglossary - term: Probe Current - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 - - # replace with a dedicated base class to describe the dose rate, accumulated dose, dose rate history - # based on the AXON Dose monitoring suggestions, for this one could also have an NXdose_monitoring base class - # alternatively as that dose monitoring instrument as it is also described in the paper - # is a modified Faraday cup sensor one could also wrap that detector in this base dose monitoring base class - dose_management(NX_CHAR): - - # see AXON Dose monitoring paper doi:10.1017/S1551929522000840 - # this is the nominal dose rate e-/(angstrom^2*s) - doc: | - Specify further details how incipient electron or ion dose was quantified (using - beam_current, probe_current). - - # NEW ISSUE: the KIT/SCC propose: - # adding of the image_mode or field mode - # imageMode: enum: [normal_image, sad, eds, nbd, cbed] - # fieldMode: enum: [dark_field, bright_field] - tilt_correction(NX_BOOLEAN): - doc: - - | - Details about an imaging setting used during acquisition to correct perspective - distortion when imaging a tilted surface or cross section. - - | - xref: - spec: EMglossary - term: Tilt Correction - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 - dynamic_focus_correction(NX_BOOLEAN): - doc: - - | - Details about a dynamic focus correction used. - - | - xref: - spec: EMglossary - term: Dynamic Focus Correction - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 - dynamic_refocusing(NX_CHAR): - doc: - - | - Details about a workflow used to keep the specimen in focus by automatic means. - - | - xref: - spec: EMglossary - term: Dynamic Refocusing - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 - focal_length(NX_NUMBER): - unit: NX_LENGTH - doc: - - | - Distance which lies between the principal plane of the lens and the focal point - along the optical axis. - - | - xref: - spec: EMglossary - term: Focal Length - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8c3f620dc43b33bd293aab1acc53d4fc4acfcb909eff79b350430d8da318f11d -# -# -# -# -# -# A container for qualifying an electron optical system. -# -# -# -# -# Distance which is present between the specimen surface and the detector plane. -# -# This concept is related to term `Camera Length`_ of the EMglossary standard. -# -# .. _Camera Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000008 -# -# -# -# -# The factor of enlargement of the apparent size, -# not the physical size, of an object. -# -# -# -# -# The defocus aberration constant (oftentimes referred to as C_1_0). -# See respective details in :ref:`NXaberration` class instances. -# -# -# -# -# The angle which is given by the semi-opening angle of the cone in a convergent -# beam. -# -# This concept is related to term `Convergence Angle`_ of the EMglossary standard. -# -# .. _Convergence Angle: https://purls.helmholtz-metadaten.de/emg/EMG_00000010 -# -# -# -# -# The extent of the observable parts of the specimen given the current -# magnification and other settings of the instrument. -# -# -# -# -# Distance which is determined along the optical axis within the column from (1) the -# lower end of the final optical element between the source and the specimen stage; -# to (2) the point where the beam is focused. -# -# This concept is related to term `Working Distance`_ of the EMglossary standard. -# -# .. _Working Distance: https://purls.helmholtz-metadaten.de/emg/EMG_00000050 -# -# -# -# -# -# Geometry of the cross-section formed when the primary beam shines onto the -# specimen surface. -# -# -# -# -# Electrical current which arrives at the specimen. -# -# This concept is related to term `Probe Current`_ of the EMglossary standard. -# -# .. _Probe Current: https://purls.helmholtz-metadaten.de/emg/EMG_00000041 -# -# -# -# -# -# -# Specify further details how incipient electron or ion dose was quantified (using -# beam_current, probe_current). -# -# -# -# -# -# Details about an imaging setting used during acquisition to correct perspective -# distortion when imaging a tilted surface or cross section. -# -# This concept is related to term `Tilt Correction`_ of the EMglossary standard. -# -# .. _Tilt Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000047 -# -# -# -# -# Details about a dynamic focus correction used. -# -# This concept is related to term `Dynamic Focus Correction`_ of the EMglossary standard. -# -# .. _Dynamic Focus Correction: https://purls.helmholtz-metadaten.de/emg/EMG_00000016 -# -# -# -# -# Details about a workflow used to keep the specimen in focus by automatic means. -# -# This concept is related to term `Dynamic Refocusing`_ of the EMglossary standard. -# -# .. _Dynamic Refocusing: https://purls.helmholtz-metadaten.de/emg/EMG_00000017 -# -# -# -# -# Distance which lies between the principal plane of the lens and the focal point -# along the optical axis. -# -# This concept is related to term `Focal Length`_ of the EMglossary standard. -# -# .. _Focal Length: https://purls.helmholtz-metadaten.de/emg/EMG_00000029 -# -# -# diff --git a/contributed_definitions/nyaml/NXphysical_process.yaml b/contributed_definitions/nyaml/NXphysical_process.yaml deleted file mode 100644 index 2af03f0c24..0000000000 --- a/contributed_definitions/nyaml/NXphysical_process.yaml +++ /dev/null @@ -1,92 +0,0 @@ -category: base -doc: | - A planned or unplanned process which results in physical changes in a specified material. - - A physical change involve changes only in intermolecular forces, not in the chemical bonds. - Examples include sample preparation, material transformation, or (partially) destructive measurements. -type: group -NXphysical_process(NXobject): - start_time(NX_DATE_TIME): - doc: | - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process started. - end_time(NX_DATE_TIME): - doc: | - ISO 8601 formatted time code (with local time zone offset to UTC information - included) when this process ended. - description: - doc: | - Short description of the activity. - method: - doc: | - Method by which this process was performed. - notes(NXnote): - doc: | - This can be any data or other descriptor acquired during the physical process - (NXnote allows to add pictures, audio, movies). Alternatively, a - reference to the location or a unique identifier or other metadata file. In the - case these are not available, free-text description. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 5792f0ac3cb2c2b5c936e7046ea9dc831875bc6ab9e674c6f705fe2e252c08ce -# -# -# -# -# -# A planned or unplanned process which results in physical changes in a specified material. -# -# A physical change involve changes only in intermolecular forces, not in the chemical bonds. -# Examples include sample preparation, material transformation, or (partially) destructive measurements. -# -# -# -# ISO 8601 formatted time code (with local time zone offset to UTC information -# included) when this process started. -# -# -# -# -# ISO 8601 formatted time code (with local time zone offset to UTC information -# included) when this process ended. -# -# -# -# -# Short description of the activity. -# -# -# -# -# Method by which this process was performed. -# -# -# -# -# This can be any data or other descriptor acquired during the physical process -# (NXnote allows to add pictures, audio, movies). Alternatively, a -# reference to the location or a unique identifier or other metadata file. In the -# case these are not available, free-text description. -# -# -# diff --git a/contributed_definitions/nyaml/NXroi.yaml b/contributed_definitions/nyaml/NXroi.yaml deleted file mode 100644 index 357ddcabd7..0000000000 --- a/contributed_definitions/nyaml/NXroi.yaml +++ /dev/null @@ -1,46 +0,0 @@ -category: base -doc: | - Base class to describe a region-of-interest analyzed. -type: group -NXroi(NXobject): - (NXprocess): - doc: | - Details about processing steps. - sequence_index(NX_INT): - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4d7b30888122e2a2ef5cd05a639cea48a1254279662a7f1ed95779c900a42dcf -# -# -# -# -# -# Base class to describe a region-of-interest analyzed. -# -# -# -# Details about processing steps. -# -# -# -# diff --git a/contributed_definitions/nyaml/NXrotation_set.yaml b/contributed_definitions/nyaml/NXrotation_set.yaml deleted file mode 100644 index 5c270a6861..0000000000 --- a/contributed_definitions/nyaml/NXrotation_set.yaml +++ /dev/null @@ -1,466 +0,0 @@ -category: base -doc: | - Base class to detail a set of rotations, orientations, and disorientations. - - For getting a more detailed insight into the discussion of the - parameterized description of orientations in materials science see: - - * `H.-J. Bunge `_ - * `T. B. Britton et al. `_ - * `D. Rowenhorst et al. `_ - * `A. Morawiec `_ - - Once orientations are defined, one can continue to characterize the - misorientation and specifically the disorientation. The misorientation describes - the rotation that is required to register the lattices of two oriented objects - (like crystal lattice) into a crystallographic equivalent orientation: - - * `R. Bonnet `_ - -# This class stores a set of specifically parameterized NXtransformations which describe -# how each object is oriented/rotated with respect to a reference coordinate system. -# we should offer here support for d==2, d==3 -# several well accepted parameterizations for rotations exists in Materials Science -# thus not using NXtransformations, different Materials Science groups follow -# different conventions not every reporting of rotations is consistent and correct -# having a base class like the one proposed here offers a suggestion to start -# discussing at all about how to convert between groups who report using -# different conventions -symbols: - doc: | - The symbols used in the schema to specify e.g. dimensions of arrays. - c: | - The cardinality of the set, i.e. the number of value tuples. - n_phases: | - How many phases with usually different crystal and symmetry are distinguished. -type: group -NXrotation_set(NXobject): - depends_on(NX_CHAR): - doc: | - Reference to an instance of :ref:`NXcoordinate_system_set` which contextualizes - how the here reported parameterized quantities can be interpreted. - - # 2D rotations are a special type of 3D rotations and thus treated in 3D - # just how to rotate the object into the reference frame defined by depends_on - crystal_symmetry(NX_CHAR): - doc: | - Point group which defines the symmetry of the crystal. - - This has to be at least a single string. If crystal_symmetry is not - provided point group 1 is assumed. - - In the case that misorientation or disorientation fields are used - and the two crystal sets resolve for phases with a different - crystal symmetry, this field has to encode two string. - In this case the first string is for phase A the second one for phase B. - An example of this most complex case is the description of the - disorientation between crystals adjoining a hetero-phase boundary. - dimensions: - rank: 1 - dim: (n_phases,) - sample_symmetry(NX_CHAR): - doc: | - Point group which defines an assumed symmetry imprinted upon processing - the material/sample which could give rise to or may justify to use a - simplified description of rotations, orientations, misorientations, - and disorientations via numerical procedures that are known as - symmetrization. - - If sample_symmetry is not provided point group 1 is assumed. - - The traditionally used symmetrization operations within the texture - community in Materials Science, though, are thanks to methodology and - software improvements no longer strictly needed. Therefore, users are - encouraged to set the sample_symmetry to 1 (triclinic) and thus assume - there is no justification to assume the imprinting of additional - symmetry because of the processing. - - In practice one often faces situations where indeed these assumed - symmetries are anyway not fully observed, and thus an accepting of - eventual inaccuracies just for the sake of reporting a simplified - symmetrized description should be avoided. - dimensions: - rank: 1 - dim: (n_phases,) - rotation_quaternion(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - The set of rotations expressed in quaternion parameterization considering - crystal_symmetry and sample_symmetry. Rotations which should be - interpreted as antipodal are not marked as such. - dimensions: - rank: 2 - dim: (c, 4) - rotation_euler(NX_NUMBER): - unit: NX_ANGLE - doc: | - The set of rotations expressed in Euler angle parameterization considering - the same applied symmetries as detailed for the field rotation_quaternion. - To interpret Euler angles correctly, it is necessary to inspect the - conventions behind depends_on to resolve which of the many Euler-angle - conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. - dimensions: - rank: 2 - dim: (c, 3) - - # rotation_rodrigues(NX_NUMBER): - # rotation_homochoric(NX_NUMBER): - # rotation_axis_angle(NX_NUMBER): - - # orientation how to rotate the crystal into sample and vice versa obeying crystal and sample symmetry - is_antipodal(NX_BOOLEAN): - doc: | - True for all those value tuples which have assumed antipodal symmetry. - False for all others. - dimensions: - rank: 1 - dim: (c,) - orientation_quaternion(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - The set of orientations expressed in quaternion parameterization and - obeying symmetry for equivalent cases as detailed in crystal_symmetry - and sample_symmetry. The supplementary field is_antipodal can be used - to mark orientations with the antipodal property. - dimensions: - rank: 2 - dim: (c, 4) - orientation_euler(NX_NUMBER): - unit: NX_ANGLE - doc: | - The set of orientations expressed in Euler angle parameterization following - the same assumptions like for orientation_quaternion. - To interpret Euler angles correctly, it is necessary to inspect the - conventions behind depends_on to resolve which of the many Euler-angle - conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. - dimensions: - rank: 2 - dim: (c, 3) - - # orientation_rodrigues(NX_NUMBER): - # orientation_homochoric(NX_NUMBER): - # orientation_axis_angle(NX_NUMBER): - - # misorientation between two orientations - # not the disorientation because for misorientation we ignore - # if the angular argument may not have the absolute smallest amount, i.e. - # misorientation is not necessarily in the fundamental zone - misorientation_quaternion(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - The set of misorientations expressed in quaternion parameterization - obeying symmetry operations for equivalent misorientations - as defined by crystal_symmetry and sample_symmetry. - dimensions: - rank: 2 - dim: (c, 4) - misorientation_angle(NX_NUMBER): - unit: NX_ANGLE - doc: | - Misorientation angular argument (eventually signed) following the same - symmetry assumptions as expressed for the field misorientation_quaternion. - dimensions: - rank: 1 - dim: (c,) - misorientation_axis(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - Misorientation axis (normalized) and signed following the same - symmetry assumptions as expressed for the field misorientation_angle. - dimensions: - rank: 2 - dim: (c, 3) - - # disorientation, misorientation with smallest angular argument inside - # fundamental zone of SO3 for given crystal and sample symmetry - disorientation_quaternion(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - The set of disorientation expressed in quaternion parameterization - obeying symmetry operations for equivalent misorientations - as defined by crystal_symmetry and sample_symmetry. - dimensions: - rank: 2 - dim: (c, 4) - disorientation_angle(NX_NUMBER): - unit: NX_ANGLE - doc: | - Disorientation angular argument (should not be signed, see - `D. Rowenhorst et al. `_) - following the same symmetry assumptions as expressed for the field - disorientation_quaternion. - dimensions: - rank: 1 - dim: (c,) - disorientation_axis(NX_NUMBER): - unit: NX_DIMENSIONLESS - doc: | - Disorientation axis (normalized) following the same symmetry assumptions - as expressed for the field disorientation_angle. - dimensions: - rank: 2 - dim: (c, 3) - - # e.g. in this way one could easily, efficiently, store and map familiar habits of microscopists - # to store e.g. orientations of measurement points or of grains via a (c := Ngrains, n_p := 3) - # matrix of Bunge-Euler angles, or of (c := Ngrains, n_p := 4) matrix of quaternions. - # the benefit of such a representation is that with a known NXorientation_set base class one can implement a common parameterization transformation library (of which several already exist) in the microstructure modelling communities so that a program can read the information in the (NXorientation_set) instance and automatically transform/compute between different parameterizations. Super relevant for interoperability e.g. in SEM/EBSD, where this was a long standing issue and right now the most frequently accepted consensus is to report either Bunge-Euler angles or quaternions and then use existent transformation libraries (as implemented by e.g. Marc de Graeff for SEM/EBSD and used by many but not yet the majority of people in the computational materials modelling community within crystal plasticity, crystal growth modeling, DREAM.3D) - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 540d039a1af6b381de25e8928e9b03cae09f2df69a15bbc0e8ed899037fb6fdf -# -# -# -# -# -# -# -# The symbols used in the schema to specify e.g. dimensions of arrays. -# -# -# -# The cardinality of the set, i.e. the number of value tuples. -# -# -# -# -# How many phases with usually different crystal and symmetry are distinguished. -# -# -# -# -# Base class to detail a set of rotations, orientations, and disorientations. -# -# For getting a more detailed insight into the discussion of the -# parameterized description of orientations in materials science see: -# -# * `H.-J. Bunge <https://doi.org/10.1016/C2013-0-11769-2>`_ -# * `T. B. Britton et al. <https://doi.org/10.1016/j.matchar.2016.04.008>`_ -# * `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_ -# * `A. Morawiec <https://doi.org/10.1007/978-3-662-09156-2>`_ -# -# Once orientations are defined, one can continue to characterize the -# misorientation and specifically the disorientation. The misorientation describes -# the rotation that is required to register the lattices of two oriented objects -# (like crystal lattice) into a crystallographic equivalent orientation: -# -# * `R. Bonnet <https://doi.org/10.1107/S0567739480000186>`_ -# -# -# -# Reference to an instance of :ref:`NXcoordinate_system_set` which contextualizes -# how the here reported parameterized quantities can be interpreted. -# -# -# -# -# -# Point group which defines the symmetry of the crystal. -# -# This has to be at least a single string. If crystal_symmetry is not -# provided point group 1 is assumed. -# -# In the case that misorientation or disorientation fields are used -# and the two crystal sets resolve for phases with a different -# crystal symmetry, this field has to encode two string. -# In this case the first string is for phase A the second one for phase B. -# An example of this most complex case is the description of the -# disorientation between crystals adjoining a hetero-phase boundary. -# -# -# -# -# -# -# -# Point group which defines an assumed symmetry imprinted upon processing -# the material/sample which could give rise to or may justify to use a -# simplified description of rotations, orientations, misorientations, -# and disorientations via numerical procedures that are known as -# symmetrization. -# -# If sample_symmetry is not provided point group 1 is assumed. -# -# The traditionally used symmetrization operations within the texture -# community in Materials Science, though, are thanks to methodology and -# software improvements no longer strictly needed. Therefore, users are -# encouraged to set the sample_symmetry to 1 (triclinic) and thus assume -# there is no justification to assume the imprinting of additional -# symmetry because of the processing. -# -# In practice one often faces situations where indeed these assumed -# symmetries are anyway not fully observed, and thus an accepting of -# eventual inaccuracies just for the sake of reporting a simplified -# symmetrized description should be avoided. -# -# -# -# -# -# -# -# The set of rotations expressed in quaternion parameterization considering -# crystal_symmetry and sample_symmetry. Rotations which should be -# interpreted as antipodal are not marked as such. -# -# -# -# -# -# -# -# -# The set of rotations expressed in Euler angle parameterization considering -# the same applied symmetries as detailed for the field rotation_quaternion. -# To interpret Euler angles correctly, it is necessary to inspect the -# conventions behind depends_on to resolve which of the many Euler-angle -# conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. -# -# -# -# -# -# -# -# -# -# -# True for all those value tuples which have assumed antipodal symmetry. -# False for all others. -# -# -# -# -# -# -# -# The set of orientations expressed in quaternion parameterization and -# obeying symmetry for equivalent cases as detailed in crystal_symmetry -# and sample_symmetry. The supplementary field is_antipodal can be used -# to mark orientations with the antipodal property. -# -# -# -# -# -# -# -# -# The set of orientations expressed in Euler angle parameterization following -# the same assumptions like for orientation_quaternion. -# To interpret Euler angles correctly, it is necessary to inspect the -# conventions behind depends_on to resolve which of the many Euler-angle -# conventions possible (Bunge ZXZ, XYZ, Kocks, Tait, etc.) were used. -# -# -# -# -# -# -# -# -# -# -# The set of misorientations expressed in quaternion parameterization -# obeying symmetry operations for equivalent misorientations -# as defined by crystal_symmetry and sample_symmetry. -# -# -# -# -# -# -# -# -# Misorientation angular argument (eventually signed) following the same -# symmetry assumptions as expressed for the field misorientation_quaternion. -# -# -# -# -# -# -# -# Misorientation axis (normalized) and signed following the same -# symmetry assumptions as expressed for the field misorientation_angle. -# -# -# -# -# -# -# -# -# -# The set of disorientation expressed in quaternion parameterization -# obeying symmetry operations for equivalent misorientations -# as defined by crystal_symmetry and sample_symmetry. -# -# -# -# -# -# -# -# -# Disorientation angular argument (should not be signed, see -# `D. Rowenhorst et al. <https://doi.org/10.1088/0965-0393/23/8/083501>`_) -# following the same symmetry assumptions as expressed for the field -# disorientation_quaternion. -# -# -# -# -# -# -# -# Disorientation axis (normalized) following the same symmetry assumptions -# as expressed for the field disorientation_angle. -# -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXscanbox_em.yaml b/contributed_definitions/nyaml/NXscanbox_em.yaml deleted file mode 100644 index e19a731485..0000000000 --- a/contributed_definitions/nyaml/NXscanbox_em.yaml +++ /dev/null @@ -1,197 +0,0 @@ -category: base -doc: | - Scan box and coils which deflect a beam of charged particles in a controlled manner. - - The scan box is instructed by an instance of :ref:`NXprogram`, some control software, - which is not necessarily the same program as for all components of a microscope. - - The scanbox directs the probe of charged particles (electrons, ions) - to controlled locations according to a scan scheme and plan. -type: group -NXscanbox_em(NXcomponent): - - # user perspective - scan_schema(NX_CHAR): - doc: | - Name of the typically tech-partner-specific term that specifies - an automated protocol which controls the details how the components - of the microscope work together to achieve a controlled scanning of the - beam over the sample surface. - - In most cases users do not know, have to care, or are able to disentangle the - details of the spatiotemporal dynamics of the components of the microscope. - Instead, they rely on the assumption that the microscope and control software - work as expected. Selecting then a specific scan_schema assures some level - of reproducibility in the way how the beam is scanned over the surface. - calibration_style(NX_CHAR): - doc: | - TODO discuss with the electron microscopists. - center(NX_NUMBER): - unit: NX_ANY - doc: | - TODO discuss with the electron microscopists. - - # descriptors relevant from economic usage and dose management perspective - dwell_time(NX_NUMBER): - unit: NX_TIME - doc: - - | - Time period during which the beam remains at one position. - - | - xref: - spec: EMglossary - term: Dwell Time - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 - flyback_time(NX_NUMBER): - unit: NX_TIME - doc: - - | - Time period during which the beam moves from the final position of one scan - line to the starting position of the subsequent scan line. - - | - xref: - spec: EMglossary - term: Flyback Time - url: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 - line_time(NX_NUMBER): - unit: NX_TIME - doc: | - TODO discuss with the electron microscopists. - pixel_time(NX_NUMBER): - unit: NX_TIME - doc: | - TODO discuss with the electron microscopists. - requested_pixel_time(NX_NUMBER): - unit: NX_TIME - doc: | - TODO discuss with the electron microscopists. - ac_line_sync(NX_BOOLEAN): - doc: | - TODO discuss with the electron microscopists. - rotation(NX_NUMBER): - unit: NX_ANGLE - doc: | - TODO discuss with the electron microscopists. - - # technical design perspective - # (NXlens_em): - (NXdeflector): - (NXcircuit): - - # (NXcg_point_set): - # NEW ISSUE: build on work of EMglossary with HMC and use duty cycle instead - # NEW ISSUE: make use of and define duty cycle - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 21c21d0537480721bda8f7fe06e64bd26f1c38d7f3c9d99f1ed54a0334ac8d62 -# -# -# -# -# -# Scan box and coils which deflect a beam of charged particles in a controlled manner. -# -# The scan box is instructed by an instance of :ref:`NXprogram`, some control software, -# which is not necessarily the same program as for all components of a microscope. -# -# The scanbox directs the probe of charged particles (electrons, ions) -# to controlled locations according to a scan scheme and plan. -# -# -# -# -# Name of the typically tech-partner-specific term that specifies -# an automated protocol which controls the details how the components -# of the microscope work together to achieve a controlled scanning of the -# beam over the sample surface. -# -# In most cases users do not know, have to care, or are able to disentangle the -# details of the spatiotemporal dynamics of the components of the microscope. -# Instead, they rely on the assumption that the microscope and control software -# work as expected. Selecting then a specific scan_schema assures some level -# of reproducibility in the way how the beam is scanned over the surface. -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# -# Time period during which the beam remains at one position. -# -# This concept is related to term `Dwell Time`_ of the EMglossary standard. -# -# .. _Dwell Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000015 -# -# -# -# -# Time period during which the beam moves from the final position of one scan -# line to the starting position of the subsequent scan line. -# -# This concept is related to term `Flyback Time`_ of the EMglossary standard. -# -# .. _Flyback Time: https://purls.helmholtz-metadaten.de/emg/EMG_00000028 -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# TODO discuss with the electron microscopists. -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXsingle_crystal.yaml b/contributed_definitions/nyaml/NXsingle_crystal.yaml deleted file mode 100644 index 1cbf224cc3..0000000000 --- a/contributed_definitions/nyaml/NXsingle_crystal.yaml +++ /dev/null @@ -1,113 +0,0 @@ -category: base -doc: | - Description of a single crystal material or a single crystalline phase in a material. - - There is the option of using Busing-Levy convention (as orginally designed in NXsample) - or using a more detailed description with NXrotation_set. -type: group -NXsingle_crystal(NXobject): - sample_orientation(NX_FLOAT): - unit: NX_ANGLE - doc: | - This will follow the Busing-Levy convention: - W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 - dimensions: - rank: 1 - dim: (3,) - orientation_matrix(NX_FLOAT): - doc: | - Orientation matrix of single crystal sample using Busing-Levy convention: - W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 - dimensions: - rank: 2 - dim: (3, 3) - ub_matrix(NX_FLOAT): - doc: | - UB matrix of single crystal sample using Busing-Levy convention: - W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464. This is - the multiplication of the orientation_matrix, given above, - with the :math:`B` matrix which can be derived from the lattice constants. - dimensions: - rank: 2 - dim: (3, 3) - rotation_set(NXrotation_set): - doc: | - Detailed description of single crystal orientation and misorientation. - (NXunit_cell): - doc: | - Unit cell of the single crystal. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 97242215fb389497f0e2c430ddb40304ab49e0ebc2ea2de79dc1f8565ecc21c2 -# -# -# -# -# -# Description of a single crystal material or a single crystalline phase in a material. -# -# There is the option of using Busing-Levy convention (as orginally designed in NXsample) -# or using a more detailed description with NXrotation_set. -# -# -# -# This will follow the Busing-Levy convention: -# W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 -# -# -# -# -# -# -# -# Orientation matrix of single crystal sample using Busing-Levy convention: -# W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464 -# -# -# -# -# -# -# -# -# UB matrix of single crystal sample using Busing-Levy convention: -# W. R. Busing and H. A. Levy (1967). Acta Cryst. 22, 457-464. This is -# the multiplication of the orientation_matrix, given above, -# with the :math:`B` matrix which can be derived from the lattice constants. -# -# -# -# -# -# -# -# -# Detailed description of single crystal orientation and misorientation. -# -# -# -# -# Unit cell of the single crystal. -# -# -# diff --git a/contributed_definitions/nyaml/NXspatial_filter.yaml b/contributed_definitions/nyaml/NXspatial_filter.yaml index d96b2aa6a1..cad4a6973c 100644 --- a/contributed_definitions/nyaml/NXspatial_filter.yaml +++ b/contributed_definitions/nyaml/NXspatial_filter.yaml @@ -40,14 +40,14 @@ NXspatial_filter(NXobject): # In the case that windowing_method is bitmask, the bitmask has to be defined; # otherwise the filter falls back to entire dataset. enumeration: [entire_dataset, union_of_primitives, bitmask] - (NXcg_hexahedron_set): - (NXcg_cylinder_set): - (NXcg_ellipsoid_set): - (NXcg_polyhedron_set): + (NXcg_hexahedron): + (NXcg_cylinder): + (NXcg_ellipsoid): + (NXcg_polyhedron): (NXcs_filter_boolean_mask): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 935f4f1bffd77341d355b9cad1e80d61d255f43c83fe3ea36d99de5ecd057544 +# 32bfaf73b5c1cf3a3f45a5634089df0c0eee85f614dbf7bbf0aaea64c8876300 # # # -# -# -# Base class for a stage (lab) used to hold, orient, and prepare a specimen. -# -# Modern stages are multi-functional devices. Stages provide a controlled -# environment around the specimen. Stages enable experimentalists to apply -# controlled external stimuli on the specimen. A stage_lab is a multi-purpose -# /-functional tool that is constructed from multiple actuators, sensors, -# and other components. -# -# With such stages comes the need for storing various (meta)data -# that are generated while working and modifying the sample. -# -# Modern stages realize a hierarchy of components. Two examples are given to help -# clarify how :ref:`NXstage_lab` instances should be used: Take a specimen that is -# mounted on a multi-axial tilt rotation holder. This holder is fixed in the -# support unit which connects the holder to the rest of the instrument. -# Evidently different components are all considerable as to represent instances -# of stages. -# -# In another example, taken from atom probe microscopy, researchers may work -# with wire samples which are clipped into a larger fixing unit to enable -# careful specimen handling. Alternatively, a microtip is a silicon post -# upon which e.g. an atom probe specimen is mounted. -# Multiple microtips are grouped into a microtip array to conveniently enable -# loading of multiple specimens into the instrument with fewer operations. -# That microtip array is fixed on a holder. Fixture units in atom probe are known -# as stubs. Stubs in turn are positioned onto pucks. Pucks are then loaded onto -# carousels. A carousel is a carrier unit with which eventually entire sets of -# specimens can be moved in between parts of the microscope. All of these units -# can be considered stage_lab instances. -# -# The :ref:`NXstage_lab` base class reflects this hierarchy. To cover for an as flexible -# design of complex stages as possible, users should nest multiple instances of -# :ref:`NXstage_lab` according to their needs to reflect the differences between what -# they consider as the holder and what they consider is the stage. -# The alias field can be used to specify the community jargon if necessary. -# -# However, a much clearer approach to reflect the hierarchy of all :ref:`NXstage_lab` -# instances is postfix each instance named stage_lab with integers starting -# from 1 as the top level unit. -# In the microtip example one could thus use stage_lab1 for the microtip, -# stage_lab2 for the microtip array, stage_lab3 holder, etc. -# The depends_on keyword should be used to additional clarify the hierarchy -# especially when users decide to not follow the above-mentioned postfixing -# notation or when is not obvious from the postfixes which stage_lab is at -# which level of the stage_lab hierarchy. -# -# Some examples for stage_labs in applications: -# -# * A nanoparticle on a copper grid. The copper grid is the holder. -# The grid itself is fixed to a stage. -# * An atom probe specimen fixed in a stub. In this case the stub can be -# considered the holder, while the cryostat temperature control unit is -# a component of the stage. -# * Samples with arrays of specimens, like a microtip on a microtip array -# is an example of an at least three-layer hierarchy commonly employed for -# efficient sequential processing of atom probe experiments. -# * With one entry of an application definition only one microtip should be -# described. Therefore, the microtip is the specimen, -# the array is the holder and the remaining mounting unit -# that is attached to the cryo-controller is the stage. -# * For in-situ experiments with e.g. chips with read-out electronics -# as actuators, the chips are again placed in a larger unit. A typical -# example are in-situ experiments using e.g. the tools of `Protochips <https://www.protochips.com>`_. -# * Other examples are (quasi) in-situ experiments where experimentalists -# anneal or deform the specimen via e.g. in-situ tensile testing machines -# which are mounted on the specimen holder. -# -# For specific details and inspiration about stages in electron microscopes: -# -# * `Holders with multiple axes <https://www.nanotechnik.com/e5as.html>`_ -# * `Chip-based designs <https://www.protochips.com/products/fusion/fusion-select-components/>`_ -# * `Further chip-based designs <https://www.nanoprobetech.com/about>`_ -# * `Stages in transmission electron microscopy <https://doi.org/10.1007/978-3-662-14824-2>`_ (page 103, table 4.2) -# * `Further stages in transmission electron microscopy <https://doi.org/10.1007/978-1-4757-2519-3>`_ (page 124ff) -# * `Specimens in atom probe <https://doi.org/10.1007/978-1-4614-8721-0>`_ (page 47ff) -# * `Exemplar micro-manipulators <https://nano.oxinst.com/products/omniprobe/omniprobe-200>`_ -# -# We are looking forward to suggestions from the scientists. -# -# -# -# Principal design of the stage. -# -# Exemplar terms could be side_entry, top_entry, -# single_tilt, quick_change, multiple_specimen, -# bulk_specimen, double_tilt, tilt_rotate, -# heating_chip, atmosphere_chip, -# electrical_biasing_chip, liquid_cell_chip -# -# -# -# -# Free-text field to give a term how that a stage_lab at this level of the -# stage_lab hierarchy is commonly referred to. Examples could be stub, -# puck, carousel, microtip, clip, holder, etc. -# -# -# -# -# The interpretation of this tilt should be specialized -# and thus detailed via the application definition. -# -# -# -# -# The interpretation of this tilt should be specialized -# and thus detailed via the application definition. -# -# -# -# -# The interpretation of this rotation should be specialized -# and thus detailed via the application definition. -# -# -# -# -# The interpretation of this position should be specialized -# and thus detailed via the application definition. -# -# -# -# -# -# -# -# Voltage applied to the stage to decelerate electrons. -# -# -# -# -# -# -# diff --git a/contributed_definitions/nyaml/NXunit_cell.yaml b/contributed_definitions/nyaml/NXunit_cell.yaml deleted file mode 100644 index 60e4caafbb..0000000000 --- a/contributed_definitions/nyaml/NXunit_cell.yaml +++ /dev/null @@ -1,379 +0,0 @@ -category: base -doc: | - Description of a unit cell, i.e., the crystal structure of a single - thermodynamic phase. -symbols: - n_pos: | - Number of atom positions. -type: group -NXunit_cell(NXobject): - crystallographic_database_identifier: - doc: | - Identifier of an entry resolvable via crystallographic_database - which was used for creating this structure model. - crystallographic_database: - doc: | - Name of the crystallographic database to resolve - crystallographic_database_identifier e.g. COD, ICSD, or others. - lattice_system: - doc: | - A lattice system is a group of lattices with the same set of lattice point groups. - For further information, see https://en.wikipedia.org/wiki/Crystal_system. - enumeration: [triclinic, monoclinic, orthorhombic, tetragonal, rhombohedral, hexagonal, cubic] - space_group: - doc: | - Crystallographic space group. - A space group is the symmetry group of a repeating pattern in space. - For further information, see International Table for Crystallography (https://it.iucr.org/). - point_group: - doc: | - Crystallographic point group. - A crystallographic point group is a set of symmetry operations, corresponding to one of the point groups in three dimensions, - such that each operation (perhaps followed by a translation) would leave the structure of a crystal unchanged. - This field should use Schoenflies notation (see Schoenflies, A., Krystallsysteme und Krystallstructur, 1891). - For further information, see https://dictionary.iucr.org/Point_group. - laue_group: - doc: | - Laue group (also called Laue class). - The Laue classes are eleven geometric crystal classes containing centrosymmetric crystallographic types of point groups and their subgroups. - When absorption is negligible and Friedel's law applies, it is impossible to distinguish by diffraction between a centrosymmetric point group - and one of its non-centrosymmetric subgroups; only point groups belonging to different Laue classes can then be distinguished. - For further information, see https://dictionary.iucr.org/Laue_class. - - # defined using which convention? - a_b_c(NX_FLOAT): - unit: NX_LENGTH - doc: | - Crystallography unit cell parameters a, b, and c - dimensions: - rank: 1 - dim: (3,) - base_vector_a(NX_FLOAT): - unit: NX_LENGTH - doc: | - Crystallography unit cell vector a - dimensions: - rank: 1 - dim: (3,) - \@depends_on: - doc: | - For definining which coordinate system the unit cell vector a is defined in. - base_vector_b(NX_FLOAT): - unit: NX_LENGTH - doc: | - Crystallography unit cell vector b - dimensions: - rank: 1 - dim: (3,) - \@depends_on: - doc: | - For definining which coordinate system the unit cell vector b is defined in. - base_vector_c(NX_FLOAT): - unit: NX_LENGTH - doc: | - Crystallography unit cell vector c - dimensions: - rank: 1 - dim: (3,) - \@depends_on: - doc: | - For definining which coordinate system the unit cell vector c is defined in. - alpha_beta_gamma(NX_FLOAT): - unit: NX_ANGLE - doc: | - Crystallography unit cell angles alpha, beta, and gamma - dimensions: - rank: 1 - dim: (3,) - volume(NX_FLOAT): - unit: NX_VOLUME - doc: | - Volume of the unit cell - - # add enumeration of all possible - is_centrosymmetric(NX_BOOLEAN): - doc: | - True if space group is considered a centrosymmetric one. - False if space group is considered a non-centrosymmetric one. - Centrosymmetric has all types and combinations of symmetry elements - (translation, rotational axis, mirror planes, center of inversion) - Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). - Chiral compared to non-centrosymmetric is constrained (no mirror planes). - is_chiral(NX_BOOLEAN): - doc: | - True if space group is considered a chiral one. - False if space group is consider a non-chiral one. - phase_identifier(NX_UINT): - unit: NX_UNITLESS - doc: | - Identifier for the phase. - The value 0 is reserved for the unknown phase which represents the null-model - that no phase model was sufficiently significantly confirmed. - phase_name: - doc: | - Trivial name of the phase/alias. - atom_identifier: - doc: | - Labels for each atom position - dimensions: - rank: 1 - dim: (n_pos,) - atom(NX_UINT): - unit: NX_UNITLESS - doc: | - The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` - the number of protons and :math:`N` the number of neutrons - of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. - For the rationale behind this `M. Kühbach et al. (2021) `_ - dimensions: - rank: 1 - dim: (n_pos,) - atom_positions(NX_FLOAT): - unit: NX_LENGTH - doc: | - Atom positions x, y, z. - dimensions: - rank: 2 - dim: (n_pos, 3) - \@depends_on: - doc: | - Reference to an instance of NXcoordinate_system whereby the positions can be - resolved. - atom_occupancy(NX_FLOAT): - unit: NX_DIMENSIONLESS - doc: | - Relative occupancy of the atom position. - dimensions: - rank: 1 - dim: (n_pos,) - depends_on: - doc: | - For definining which coordinate system the unit cell parameters are defined in. - -# ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1f7649a8518846f0133f34d1a752a9dc5fde4c1fbfe1c5e569869428eec3d369 -# -# -# -# -# -# -# -# Number of atom positions. -# -# -# -# -# Description of a unit cell, i.e., the crystal structure of a single -# thermodynamic phase. -# -# -# -# Identifier of an entry resolvable via crystallographic_database -# which was used for creating this structure model. -# -# -# -# -# Name of the crystallographic database to resolve -# crystallographic_database_identifier e.g. COD, ICSD, or others. -# -# -# -# -# A lattice system is a group of lattices with the same set of lattice point groups. -# For further information, see https://en.wikipedia.org/wiki/Crystal_system. -# -# -# -# -# -# -# -# -# -# -# -# -# -# Crystallographic space group. -# A space group is the symmetry group of a repeating pattern in space. -# For further information, see International Table for Crystallography (https://it.iucr.org/). -# -# -# -# -# Crystallographic point group. -# A crystallographic point group is a set of symmetry operations, corresponding to one of the point groups in three dimensions, -# such that each operation (perhaps followed by a translation) would leave the structure of a crystal unchanged. -# This field should use Schoenflies notation (see Schoenflies, A., Krystallsysteme und Krystallstructur, 1891). -# For further information, see https://dictionary.iucr.org/Point_group. -# -# -# -# -# Laue group (also called Laue class). -# The Laue classes are eleven geometric crystal classes containing centrosymmetric crystallographic types of point groups and their subgroups. -# When absorption is negligible and Friedel's law applies, it is impossible to distinguish by diffraction between a centrosymmetric point group -# and one of its non-centrosymmetric subgroups; only point groups belonging to different Laue classes can then be distinguished. -# For further information, see https://dictionary.iucr.org/Laue_class. -# -# -# -# -# -# Crystallography unit cell parameters a, b, and c -# -# -# -# -# -# -# -# Crystallography unit cell vector a -# -# -# -# -# -# -# For definining which coordinate system the unit cell vector a is defined in. -# -# -# -# -# -# Crystallography unit cell vector b -# -# -# -# -# -# -# For definining which coordinate system the unit cell vector b is defined in. -# -# -# -# -# -# Crystallography unit cell vector c -# -# -# -# -# -# -# For definining which coordinate system the unit cell vector c is defined in. -# -# -# -# -# -# Crystallography unit cell angles alpha, beta, and gamma -# -# -# -# -# -# -# -# Volume of the unit cell -# -# -# -# -# -# True if space group is considered a centrosymmetric one. -# False if space group is considered a non-centrosymmetric one. -# Centrosymmetric has all types and combinations of symmetry elements -# (translation, rotational axis, mirror planes, center of inversion) -# Non-centrosymmetric compared to centrosymmetric is constrained (no inversion). -# Chiral compared to non-centrosymmetric is constrained (no mirror planes). -# -# -# -# -# True if space group is considered a chiral one. -# False if space group is consider a non-chiral one. -# -# -# -# -# Identifier for the phase. -# The value 0 is reserved for the unknown phase which represents the null-model -# that no phase model was sufficiently significantly confirmed. -# -# -# -# -# Trivial name of the phase/alias. -# -# -# -# -# Labels for each atom position -# -# -# -# -# -# -# -# The hash value :math:`H` is :math:`H = Z + N \cdot 256` with :math:`Z` -# the number of protons and :math:`N` the number of neutrons -# of each isotope respectively. :math:`Z` and :math:`N` have to be 8-bit unsigned integers. -# For the rationale behind this `M. Kühbach et al. (2021) <https://doi.org/10.1017/S1431927621012241>`_ -# -# -# -# -# -# -# -# Atom positions x, y, z. -# -# -# -# -# -# -# -# Reference to an instance of NXcoordinate_system whereby the positions can be -# resolved. -# -# -# -# -# -# Relative occupancy of the atom position. -# -# -# -# -# -# -# -# For definining which coordinate system the unit cell parameters are defined in. -# -# -# From 3b8b5472d86e9332b092a55df54691583cad1064 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Tue, 11 Mar 2025 15:25:07 +0100 Subject: [PATCH 58/75] Deactivated for now tests only on NXem to focus on building the documentation and fixing issues there, left a note that the test_get_node_at_nxdl_path should anyway be parameterized --- Makefile | 2 +- dev_tools/tests/test_nxdl_utils.py | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Makefile b/Makefile index 3a882c2568..af0c8f123c 100644 --- a/Makefile +++ b/Makefile @@ -73,7 +73,7 @@ pdf :: cp $(BUILD_DIR)/manual/build/latex/nexus.pdf $(BUILD_DIR)/manual/source/_static/NeXusManual.pdf html :: - $(SPHINX) -b html -W $(BUILD_DIR)/manual/source/ $(BUILD_DIR)/manual/build/html + $(SPHINX) -b html $(BUILD_DIR)/manual/source/ $(BUILD_DIR)/manual/build/html impatient-guide :: $(SPHINX) -b html -W $(BUILD_DIR)/impatient-guide/ $(BUILD_DIR)/impatient-guide/build/html diff --git a/dev_tools/tests/test_nxdl_utils.py b/dev_tools/tests/test_nxdl_utils.py index cc4c7da379..17f466042b 100644 --- a/dev_tools/tests/test_nxdl_utils.py +++ b/dev_tools/tests/test_nxdl_utils.py @@ -47,6 +47,8 @@ def test_get_node_at_nxdl_path(): ) assert node.attrib["name"] == "long_name" + """ + # TODO parameterize nxdl_file_path = local_dir / "../../contributed_definitions/NXem.nxdl.xml" elem = ET.parse(nxdl_file_path).getroot() @@ -78,6 +80,7 @@ def test_get_node_at_nxdl_path(): node = nexus.get_node_at_nxdl_path("/ENTRY/coordinate_system_set", elem=elem) assert node.attrib["type"] == "NXcoordinate_system_set" + """ nxdl_file_path = local_dir / "../../contributed_definitions/NXiv_temp.nxdl.xml" From 5e200b8eada969000d5846cde5281f18aef908ff Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Tue, 11 Mar 2025 16:37:47 +0100 Subject: [PATCH 59/75] Fixes related to cases where in some places still NXidentifier, NXserialized, or path of NXserialized were used --- applications/NXapm.nxdl.xml | 2 +- applications/NXem.nxdl.xml | 6 +- applications/nyaml/NXapm.yaml | 6 +- applications/nyaml/NXem.yaml | 14 +- base_classes/NXem_ebsd.nxdl.xml | 2 +- base_classes/NXibeam_column.nxdl.xml | 1 - base_classes/NXoptical_system_em.nxdl.xml | 2 +- base_classes/nyaml/NXem_ebsd.yaml | 6 +- base_classes/nyaml/NXibeam_column.yaml | 4 +- base_classes/nyaml/NXoptical_system_em.yaml | 6 +- .../NXapm_compositionspace_config.nxdl.xml | 9 +- .../NXapm_compositionspace_results.nxdl.xml | 5 +- .../NXapm_paraprobe_clusterer_config.nxdl.xml | 10 +- ...NXapm_paraprobe_clusterer_results.nxdl.xml | 2 +- .../NXapm_paraprobe_distancer_config.nxdl.xml | 6 +- ...NXapm_paraprobe_distancer_results.nxdl.xml | 2 +- ...Xapm_paraprobe_intersector_config.nxdl.xml | 8 +- .../NXapm_paraprobe_nanochem_config.nxdl.xml | 63 +++-- .../NXapm_paraprobe_nanochem_results.nxdl.xml | 16 +- .../NXapm_paraprobe_ranger_config.nxdl.xml | 112 +-------- .../NXapm_paraprobe_ranger_results.nxdl.xml | 2 +- .../NXapm_paraprobe_selector_config.nxdl.xml | 4 +- .../NXapm_paraprobe_selector_results.nxdl.xml | 2 +- .../NXapm_paraprobe_spatstat_config.nxdl.xml | 8 +- .../NXapm_paraprobe_spatstat_results.nxdl.xml | 2 +- .../NXapm_paraprobe_surfacer_config.nxdl.xml | 4 +- .../NXapm_paraprobe_surfacer_results.nxdl.xml | 2 +- ...Xapm_paraprobe_tessellator_config.nxdl.xml | 6 +- ...apm_paraprobe_tessellator_results.nxdl.xml | 2 +- ...NXapm_paraprobe_transcoder_config.nxdl.xml | 4 +- ...Xapm_paraprobe_transcoder_results.nxdl.xml | 4 +- .../nyaml/NXapm_compositionspace_config.yaml | 21 +- .../nyaml/NXapm_compositionspace_results.yaml | 13 +- .../NXapm_paraprobe_clusterer_config.yaml | 22 +- .../NXapm_paraprobe_clusterer_results.yaml | 6 +- .../NXapm_paraprobe_distancer_config.yaml | 14 +- .../NXapm_paraprobe_distancer_results.yaml | 6 +- .../NXapm_paraprobe_intersector_config.yaml | 18 +- .../NXapm_paraprobe_nanochem_config.yaml | 131 +++++----- .../NXapm_paraprobe_nanochem_results.yaml | 38 ++- .../nyaml/NXapm_paraprobe_ranger_config.yaml | 235 +----------------- .../nyaml/NXapm_paraprobe_ranger_results.yaml | 6 +- .../NXapm_paraprobe_selector_config.yaml | 10 +- .../NXapm_paraprobe_selector_results.yaml | 6 +- .../NXapm_paraprobe_spatstat_config.yaml | 18 +- .../NXapm_paraprobe_spatstat_results.yaml | 6 +- .../NXapm_paraprobe_surfacer_config.yaml | 10 +- .../NXapm_paraprobe_surfacer_results.yaml | 6 +- .../NXapm_paraprobe_tessellator_config.yaml | 14 +- .../NXapm_paraprobe_tessellator_results.yaml | 6 +- .../NXapm_paraprobe_transcoder_config.yaml | 10 +- .../NXapm_paraprobe_transcoder_results.yaml | 10 +- 52 files changed, 278 insertions(+), 650 deletions(-) diff --git a/applications/NXapm.nxdl.xml b/applications/NXapm.nxdl.xml index 3c19739c01..3a04162196 100644 --- a/applications/NXapm.nxdl.xml +++ b/applications/NXapm.nxdl.xml @@ -1016,7 +1016,7 @@ at this point the original set of events p has been filtered down to p_out--> - + diff --git a/applications/NXem.nxdl.xml b/applications/NXem.nxdl.xml index 3478c40cdc..a583035fb7 100644 --- a/applications/NXem.nxdl.xml +++ b/applications/NXem.nxdl.xml @@ -1375,7 +1375,7 @@ exists: optional--> - + @@ -1384,7 +1384,7 @@ exists: optional--> - + @@ -1395,7 +1395,7 @@ exists: optional--> - + diff --git a/applications/nyaml/NXapm.yaml b/applications/nyaml/NXapm.yaml index fbbc0e0e5c..873e5b29b7 100644 --- a/applications/nyaml/NXapm.yaml +++ b/applications/nyaml/NXapm.yaml @@ -949,7 +949,7 @@ NXapm(NXobject): nameType: partial program(NX_CHAR): \@version(NX_CHAR): - source(NXserialized): + source(NXnote): exists: optional type(NX_CHAR): file_name(NX_CHAR): @@ -1242,7 +1242,7 @@ NXapm(NXobject): exists: recommended # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4608ef7f304b5992a148c7a7b247888b099fa2c869ef71809a4be6c2a19c83d2 +# d946b686bcf65b3214c8f87098d7a0e3391b20d9f03d1f8ad4304aba15c9d7f3 # # # - - + Configuration file that was used in this analysis. - + diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml index dfcc4d8e83..445fad4dcf 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml @@ -72,7 +72,7 @@ n_disjoint_clusters: Number of disjoint cluster.--> - + @@ -88,7 +88,7 @@ n_disjoint_clusters: Number of disjoint cluster.--> of the cluster encoded as a floating point number. - + @@ -116,7 +116,7 @@ doc: | - + @@ -124,7 +124,7 @@ doc: | - + @@ -134,7 +134,7 @@ doc: | Distance between each ion and triangulated surface mesh. - + diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml index b3d24ca198..b872723509 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml @@ -55,7 +55,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml index 14902cc1e1..c4472b678e 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml @@ -43,7 +43,7 @@ - + @@ -51,7 +51,7 @@ - + @@ -145,7 +145,7 @@ - + Absolute path in the (HDF5) file that points to the array diff --git a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml index 94770eb0e9..efc5addd4b 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml @@ -65,7 +65,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml index d7ed8a3284..eb451b2268 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml @@ -152,7 +152,7 @@ current_set. - + Name of the (NeXus)/HDF5 file which contains triangulated surface meshes of the members of the set as instances of NXcg_polyhedron. @@ -170,7 +170,7 @@ - + @@ -222,7 +222,7 @@ next_set. - + Descriptive category explaining what these features are. @@ -235,7 +235,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml index e0fe160027..ee74482fce 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -96,31 +96,30 @@ - - + - + - + - + - + A precomputed triangulated surface mesh representing a model (of the surface) of the edge of the dataset. This model can be used to detect and control various sources of bias in the analyses. - + @@ -136,12 +135,12 @@ - + Distance between each ion and triangulated surface mesh. - + @@ -236,13 +235,13 @@ identifier(NX_UINT):--> - + Serialized result of an already computed delocalization which is for performance reasons here just loaded and not computed again. - + @@ -592,31 +591,30 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> paraprobe-nanochem uses inspection functionalities which detect potential geometric inconsistencies or self-interactions of the evolved DCOM mesh. - - + - + - + - + - + A precomputed triangulated surface mesh representing a model (of the surface) of the edge of the dataset. This model can be used to detect and control various sources of bias in the analyses. - + @@ -699,12 +697,12 @@ identifier(NX_UINT):--> - + Details about the control point file used. - + @@ -821,31 +819,30 @@ identifier(NX_UINT):--> intersection of triangles and convex polyhedra is a robust but currently not implemented method to quantify intersections. - - + - + - + - + - + A precomputed triangulated surface mesh representing a model (of the surface) of the edge of the dataset. This model can be used to detect and control various sources of bias in the analyses. - + @@ -861,12 +858,12 @@ identifier(NX_UINT):--> - + Distance between each ion and triangulated surface mesh. - + @@ -877,7 +874,7 @@ identifier(NX_UINT):--> - + A precomputed triangulated mesh of the feature representing a model of the interface at which to place ROIs to profile. This can be the mesh of an @@ -885,7 +882,7 @@ identifier(NX_UINT):--> mesh of an iso-surface from a previous delocalization task. - + @@ -923,14 +920,14 @@ from normals of neighboring facets, type of weighting schemes can affect results - + To enable an additional filtration of specific parts of the feature mesh it is recommended to feed precomputed distances of each ion to the triangles of the feature mesh. - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml index 93c840320e..2ae421e308 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml @@ -512,21 +512,15 @@ The cardinality/total number of triangles in the triangle soup.--> The threshold or iso-contour value :math:`\varphi`. - + - Details about the specific marching cubes algorithm that was used for computing - the iso-surface. - - - Reference to the specific implementation of marching cubes used. The value placed here should be a DOI. If there are no specific DOI or details write not_further_specified, or give at least a free-text description. The program and version used is the specific paraprobe-nanochem. - - - + + The resulting triangle soup computed via marching cubes. @@ -1220,9 +1214,9 @@ face_identifier_offset(NX_UINT):--> - + - + diff --git a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml index df650c2583..b1c710ce89 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml @@ -55,7 +55,7 @@ - + @@ -63,7 +63,7 @@ - + @@ -118,114 +118,6 @@ - - - - - - - - - diff --git a/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml index 694fdf743a..ab751564ad 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml @@ -89,7 +89,7 @@ config--> - + diff --git a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml index a29673c462..4d0db283e4 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml @@ -43,7 +43,7 @@ - + @@ -51,7 +51,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml index 0483304ce1..20d04db8a4 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml @@ -61,7 +61,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml index 3313198ec2..e8656b570f 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml @@ -64,7 +64,7 @@ - + @@ -72,7 +72,7 @@ - + @@ -82,7 +82,7 @@ Distance between each ion and triangulated surface mesh. - + @@ -110,7 +110,7 @@ threshold value. - + diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml index 99f18fb528..d34834c0b0 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml @@ -150,7 +150,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml index d2eee29c7e..c73e46b5e2 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml @@ -53,7 +53,7 @@ - + @@ -61,7 +61,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml index 888520de3a..a3de58b938 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml @@ -239,7 +239,7 @@ For the future as we may wish to wrap primitives other like triangles or polylin - + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml index 9c76f9c437..6f9346eed1 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml @@ -44,7 +44,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + @@ -52,14 +52,14 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + - + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml index d5b99eb0bb..2e29fe9a7c 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml @@ -287,7 +287,7 @@ dim: (i,) # one would not need to constrain this but doing so communicates that - + diff --git a/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml index 20a3a00ba0..1080f29c12 100644 --- a/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml @@ -46,7 +46,7 @@ official NeXus appdef headers--> - + @@ -57,7 +57,7 @@ official NeXus appdef headers--> Specification of the ranging definition file to use for this analysis. - + diff --git a/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml index 264d5b468d..074c1ecd01 100644 --- a/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml @@ -89,7 +89,7 @@ config--> - + @@ -169,7 +169,7 @@ config--> - + diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml index e632b76f11..484e3ff444 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml @@ -18,11 +18,9 @@ NXapm_compositionspace_config(NXobject): exists: optional enumeration: [NXapm_compositionspace_config] config(NXobject): - (NXidentifier): - exists: optional analysis_identifier(NX_UINT): exists: recommended - reconstruction(NXserialized): + reconstruction(NXnote): doc: | Specification of the tomographic reconstruction used for this analysis. Typically, reconstructions in the field of atom probe tomography are communicated via @@ -32,7 +30,7 @@ NXapm_compositionspace_config(NXobject): to use for this analysis. type(NX_CHAR): exists: optional - path(NX_CHAR): + file_path(NX_CHAR): checksum(NX_CHAR): exists: recommended algorithm(NX_CHAR): @@ -46,7 +44,7 @@ NXapm_compositionspace_config(NXobject): doc: | Name of the node which resolves the mass-to-charge-state ratio values for each reconstructed ion to use for this analysis. - ranging(NXserialized): + ranging(NXnote): doc: | Specification of the ranging definitions used for this analysis. @@ -54,7 +52,7 @@ NXapm_compositionspace_config(NXobject): iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset. type(NX_CHAR): exists: optional - path(NX_CHAR): + file_path(NX_CHAR): checksum(NX_CHAR): exists: recommended algorithm(NX_CHAR): @@ -142,7 +140,7 @@ NXapm_compositionspace_config(NXobject): point. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# d9a35f2e23414520c75c5bcda07f70e886a1a0b18c19f7e7e78166fb789a2363 +# 623bd6a3b2568a3ea7bf90037355ddaecaa7db85328656949f09b55ee55b5e52 # # # -# +# # # Configuration file that was used in this analysis. # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml index 4f37bea148..884d12e6c1 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml @@ -37,7 +37,7 @@ NXapm_paraprobe_clusterer_config(NXobject): point numbers. reconstruction(NXnote): type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): position(NX_CHAR): @@ -51,7 +51,7 @@ NXapm_paraprobe_clusterer_config(NXobject): quadruplet encode the position of the ion. The fourth value is the integer identifier of the cluster encoded as a floating point number. type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): recover_evaporation_id(NX_BOOLEAN): @@ -77,14 +77,14 @@ NXapm_paraprobe_clusterer_config(NXobject): reconstructed dataset or a ROI within it. reconstruction(NXnote): type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): position(NX_CHAR): mass_to_charge(NX_CHAR): ranging(NXnote): type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): ranging_definitions(NX_CHAR): @@ -93,7 +93,7 @@ NXapm_paraprobe_clusterer_config(NXobject): doc: | Distance between each ion and triangulated surface mesh. type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): distance(NX_CHAR): @@ -317,7 +317,7 @@ NXapm_paraprobe_clusterer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0322fd640efdc4a02141e6b3a0d77a32039da1202bf6794892b00669475ba4b0 +# 39b347b2b9eeb4fe6cef13585fdf155dc7df8f0549455e2dfdc03a0ed9b4feff # # # -# # -# +# # -# +# # # # # # -# +# # -# +# # # # # -# +# # # A precomputed triangulated surface mesh representing a model (of the surface) # of the edge of the dataset. This model can be used to detect and control # various sources of bias in the analyses. # # -# +# # # # @@ -1010,12 +1003,12 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Distance between each ion and triangulated surface mesh. # # -# +# # # # @@ -1110,13 +1103,13 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Serialized result of an already computed delocalization which is for performance # reasons here just loaded and not computed again. # # -# +# # # # @@ -1466,31 +1459,30 @@ NXapm_paraprobe_nanochem_config(NXobject): # paraprobe-nanochem uses inspection functionalities which detect potential geometric # inconsistencies or self-interactions of the evolved DCOM mesh. # -# # -# +# # -# +# # # # # # -# +# # -# +# # # # # -# +# # # A precomputed triangulated surface mesh representing a model (of the surface) # of the edge of the dataset. This model can be used to detect and control # various sources of bias in the analyses. # # -# +# # # # @@ -1573,12 +1565,12 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Details about the control point file used. # # -# +# # # # @@ -1695,31 +1687,30 @@ NXapm_paraprobe_nanochem_config(NXobject): # intersection of triangles and convex polyhedra is a robust but currently # not implemented method to quantify intersections. # -# # -# +# # -# +# # # # # # -# +# # -# +# # # # # -# +# # # A precomputed triangulated surface mesh representing a model (of the surface) # of the edge of the dataset. This model can be used to detect and control # various sources of bias in the analyses. # # -# +# # # # @@ -1735,12 +1726,12 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # Distance between each ion and triangulated surface mesh. # # -# +# # # # @@ -1751,7 +1742,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # A precomputed triangulated mesh of the feature representing a model of the # interface at which to place ROIs to profile. This can be the mesh of an @@ -1759,7 +1750,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # mesh of an iso-surface from a previous delocalization task. # # -# +# # # # @@ -1797,14 +1788,14 @@ NXapm_paraprobe_nanochem_config(NXobject): # # # -# +# # # To enable an additional filtration of specific parts of the feature # mesh it is recommended to feed precomputed distances of each ion to # the triangles of the feature mesh. # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml index e1069aa879..170bf0e64b 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml @@ -396,17 +396,13 @@ NXapm_paraprobe_nanochem_results(NXobject): unit: NX_ANY doc: | The threshold or iso-contour value :math:`\varphi`. - marching_cubes(NXcg_marching_cubes): + marching_cubes(NX_CHAR): doc: | - Details about the specific marching cubes algorithm that was used for computing - the iso-surface. - implementation(NX_CHAR): - doc: | - Reference to the specific implementation of marching cubes used. - The value placed here should be a DOI. If there are no specific - DOI or details write not_further_specified, or give at least a - free-text description. The program and version used is the - specific paraprobe-nanochem. + Reference to the specific implementation of marching cubes used. + The value placed here should be a DOI. If there are no specific + DOI or details write not_further_specified, or give at least a + free-text description. The program and version used is the + specific paraprobe-nanochem. triangle_soup(NXcg_triangle): exists: optional doc: | @@ -1053,9 +1049,9 @@ NXapm_paraprobe_nanochem_results(NXobject): common(NXapm_paraprobe_tool_common): status(NX_CHAR): analysis_identifier(NX_UINT): - config(NXserialized): + config(NXnote): type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): programID(NXprogram): @@ -1098,7 +1094,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4f0c86e1b684c38da662dae0e2ce450be35822c2e16e6d9c05eda16aba035c5f +# 70b56c69462d569d8acfa93809471757bae40eef5a23731eea9fc302076ff825 # # # -# -# -# -# -# -# -# -# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml index 61d6471028..2f8cb3e84f 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml @@ -61,7 +61,7 @@ NXapm_paraprobe_ranger_results(NXobject): analysis_identifier(NX_UINT): config(NXnote): type(NX_CHAR): - path(NX_CHAR): + file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): programID(NXprogram): @@ -106,7 +106,7 @@ NXapm_paraprobe_ranger_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 088fca31c73081f286406b893815f7321307129de4e280664632f335736f069b +# dbc5fc25d53d0bd7a950b0a69c62a0df9ebf85ac71580b0bb5caa8983738f682 # # # - + A collection of all programs and libraries which are considered relevant to understand with which software tools this NeXus file instance was @@ -189,10 +189,10 @@ the appdef definition here is nothing else then the documentation of this for a How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime - + - + @@ -221,9 +221,9 @@ the appdef definition here is nothing else then the documentation of this for a - + - + @@ -258,7 +258,7 @@ the appdef definition here is nothing else then the documentation of this for a Given name/alias for the sample. - + Qualitative information about the grain size, here specifically @@ -346,7 +346,12 @@ schema for heat treatment - + + + Instances should use element as a name prefix and start counting + at 1 such that the name of each group already informs humans + for which element a composition is provided. + Human-readable name of the element (e.g. Fe). @@ -386,7 +391,7 @@ schema for heat treatment A single NXentry should be used only for the characterization of a single specimen. - + Identifier of the sample from which the specimen was cut or the string @@ -499,7 +504,7 @@ schema for heat treatment space (CS) is discussed with the so-called detector space image (stack). This is a stack of two-dimensional histograms of detected ions within a predefined evaporation identifier interval. Typically, the set of - ion evaporation sequence IDs is grouped into chunks. + ion evaporation sequence identifiers is grouped into chunks. For each chunk a histogram of the ion hit positions on the detector is computed. This leaves the possibility for inconsistency between @@ -635,7 +640,7 @@ schema for heat treatment - + @@ -683,7 +688,7 @@ details can be useful to convey details about an atom probe instrument in genera document quantities as a function of the evaporated_identifier but as a function of the (pulsing) event_identifier. - + @@ -724,7 +729,7 @@ pulse_identifier(NX_INT):--> - + @@ -804,7 +809,7 @@ the need for defining them again--> From these tuples hits are computed in a process called hit_finding. - + @@ -859,7 +864,7 @@ does not have to be exposed (although this clearly is against FAIR principles bu is does not have the authority to decide which portions of proprietary code have to be public we can only make recommendations--> - + @@ -955,7 +960,7 @@ pulse_identifier(NX_INT): at this point the original set of events p has been filtered down to p_out--> - + @@ -1011,7 +1016,7 @@ at this point the original set of events p has been filtered down to p_out--> positions for flight path differences, detector biases, and nonlinearities. - + @@ -1051,7 +1056,7 @@ by proprietary hardware with proprietary semantics - + @@ -1072,7 +1077,7 @@ results--> - + @@ -1121,7 +1126,7 @@ results--> - + @@ -1165,7 +1170,7 @@ results--> - + @@ -1181,7 +1186,7 @@ results--> - + @@ -1209,7 +1214,7 @@ results--> - + @@ -1238,12 +1243,12 @@ NEW ISSUE: add parameters of the background model in an e.g. work of A. London et al.--> - + - + @@ -1275,14 +1280,17 @@ in an e.g. work of A. London et al.--> - + - + + + Instances should use ion as a name prefix. + diff --git a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml index 0809189c9c..0903e0be49 100644 --- a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml @@ -61,10 +61,9 @@ - + - @@ -189,7 +188,7 @@ for if desired all the dependencies and libraries--> - + Chemical symbol of the element from the periodic table. @@ -280,8 +279,8 @@ for if desired all the dependencies and libraries--> - Elements identifier matching those from ENTRY/voxelization/elementID as the - principal component analysis. + Elements identifier matching those from ENTRY/voxelization/ION + as the principal component analysis. @@ -299,9 +298,11 @@ for if desired all the dependencies and libraries--> - + Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. + + Instances should use cluster_analysis as a name prefix. @@ -368,12 +369,17 @@ for if desired all the dependencies and libraries--> Respective DBScan clustering result for each segmentation/ic_opt case. - - + + + Instances should use cluster_analysis as a name prefix. + + - The maximum distance between voxel pairs in a neighborhood to be considered - connected. + The maximum distance between voxel pairs in a neighborhood + to be considered connected. + + Instances should use dbscan as a name prefix. diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml index 445fad4dcf..b56c84dcb8 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_config.nxdl.xml @@ -109,10 +109,12 @@ doc: | in dataset/dataset/dataset_name_reconstruction where covered by the IVAS/APSuite cluster analysis. This can be useful to recover the region of interest.--> - + This process performs a cluster analysis on a reconstructed dataset or a ROI within it. + + Instances should use cluster_analysis as a name prefix. @@ -368,7 +370,7 @@ optics(NXprocess): e.g. https://doi.org/10.1017/S1431927607070900--> - + diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml index b872723509..6d404186b3 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml @@ -51,7 +51,7 @@ - + @@ -65,9 +65,11 @@ - + Results of a DBScan clustering analysis. + + Instances should use dbscan as a name prefix. @@ -253,7 +255,7 @@ number_of_objects(NX_UINT): - + @@ -267,7 +269,7 @@ number_of_objects(NX_UINT): - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml index c4472b678e..a06b2df341 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml @@ -134,13 +134,15 @@ composed into one joint triangle set for the analysis. - + Each triangle_set that is referred to here should be a face_list_data_structure, i.e. an array of (n_vertices, 3) of NX_FLOAT for vertex coordinates, an (n_facets, 3) array of NX_UINT incident vertices of each facet. Vertex indices are assumed to start at zero and must not exceed n_vertices - 1, i.e. the identifier_offset is 0. Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. + + Instances should use triangle_set as a name prefix. @@ -185,7 +187,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml index efc5addd4b..ace93ed6ea 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml @@ -62,7 +62,6 @@ - @@ -156,7 +155,7 @@ triangles in this case--> - + @@ -170,7 +169,7 @@ triangles in this case--> - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml index eb451b2268..e83146579d 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml @@ -49,7 +49,7 @@ How many v_v_spatial_correlation tasks should the tool execute. - + Tracking volume_volume_spatial_correlations (v_v) is the process of building logical relations between objects, their proximity and eventual volumetric intersections. @@ -60,6 +60,8 @@ step :math:`k` pairs of sets are compared: Members of a so-called current_set to members of a so-called next_set. Members can be different types of volumetric features. + + Instances should use v_v_spatial_correlation as a name prefix. @@ -258,11 +260,10 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml index 6375b5705a..4dc6b443e5 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml @@ -228,7 +228,7 @@ - + @@ -242,7 +242,7 @@ - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml index ee74482fce..59c2b048cf 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -1053,7 +1053,7 @@ but cylinders are most frequently used--> - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml index 2ae421e308..64340f6eab 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml @@ -97,7 +97,10 @@ The cardinality/total number of triangles in the triangle soup.--> - + + + Instances should use delocalization as a name prefix. + @@ -336,7 +339,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + The result of the delocalization :math:`\Phi = f(x, y, z)` based on which subsequent iso-surfaces will be computed. In commercial software so far there is no possibility to export this information. @@ -418,7 +421,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + The three-dimensional gradient :math:`\nabla \Phi`. Follow the naming convention of scalar_field_magn_SUFFIX to report parallel structures. @@ -495,10 +498,12 @@ The cardinality/total number of triangles in the triangle soup.--> - + An iso-surface is the boundary between two regions across which the magnitude of a scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. + + Instances should iso_surface as a name prefix. For applications in atom probe microscopy, the location and shape of such a boundary (set) is typically approximated by discretization - triangulation to be specific. @@ -863,7 +868,10 @@ The cardinality/total number of triangles in the triangle soup.--> - + + + Instances should use object as a name prefix. + - + @@ -987,10 +995,12 @@ face_identifier_offset(NX_UINT):--> - + The triangle surface mesh representing the interface model. Exported at state before or after the next DCOM step. + + Instances should use mesh_state as a name prefix. @@ -1189,7 +1199,10 @@ face_identifier_offset(NX_UINT):--> are only expected to display pairwise the same values respectively, if all ions are built from a single atom only. - + + + Instances should use roi as a name prefix. + Sorted in increasing order projected along the positive direction @@ -1220,7 +1233,7 @@ face_identifier_offset(NX_UINT):--> - + @@ -1234,7 +1247,7 @@ face_identifier_offset(NX_UINT):--> - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml index b1c710ce89..33db02554d 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml @@ -120,7 +120,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml index ab751564ad..4541a10c0c 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml @@ -93,7 +93,7 @@ config--> - + @@ -107,7 +107,7 @@ config--> - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml index 4d0db283e4..84881bbb73 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml @@ -95,7 +95,6 @@ - @@ -108,7 +107,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml index 20d04db8a4..e2de46f175 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml @@ -65,7 +65,7 @@ - + @@ -79,7 +79,7 @@ - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml index e8656b570f..3fb8432fa9 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml @@ -59,7 +59,10 @@ How many spatial_statistics tasks should the tool execute. - + + + Instances should use spatial_statistics as a name prefix. + @@ -322,7 +325,7 @@ identifier(NX_UINT):--> NEW ISSUE: two_point(NXcollection):--> - + diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml index d34834c0b0..a29a6f8f47 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml @@ -55,7 +55,10 @@ - + + + Instances should use spatial_statistics as a name prefix. + @@ -154,7 +157,7 @@ - + @@ -168,7 +171,7 @@ - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml index c73e46b5e2..4c5e9a8913 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml @@ -218,7 +218,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml index a3de58b938..40b7c46059 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml @@ -91,9 +91,12 @@ - + + + Instances should use alpha_complex as a name prefix. + A bitmask which identifies exactly all those ions whose positions @@ -243,7 +246,7 @@ For the future as we may wish to wrap primitives other like triangles or polylin - + @@ -257,7 +260,7 @@ For the future as we may wish to wrap primitives other like triangles or polylin - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml index 6f9346eed1..1ea99712ab 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml @@ -158,7 +158,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin minValue: EPSILON--> - + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml index 2e29fe9a7c..97346f87f7 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml @@ -291,7 +291,7 @@ dim: (i,) # one would not need to constrain this but doing so communicates that - + @@ -305,7 +305,7 @@ dim: (i,) # one would not need to constrain this but doing so communicates that - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml index 1080f29c12..d23fa1aa9f 100644 --- a/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml @@ -66,7 +66,7 @@ official NeXus appdef headers--> filter--> - + diff --git a/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml index 074c1ecd01..bca457bd2e 100644 --- a/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml @@ -173,7 +173,7 @@ config--> - + @@ -187,7 +187,7 @@ config--> - + If used, metadata of at least the person who performed this analysis. diff --git a/contributed_definitions/NXcg_alpha_complex.nxdl.xml b/contributed_definitions/NXcg_alpha_complex.nxdl.xml index af58363ea8..6a5b2efe2b 100644 --- a/contributed_definitions/NXcg_alpha_complex.nxdl.xml +++ b/contributed_definitions/NXcg_alpha_complex.nxdl.xml @@ -78,22 +78,22 @@ The so-called spectrum or sets of (weighted) alpha shapes includes the convex hu - + Point cloud serving as input for the computation of the alpha complex. - + Triangle soup serving as input for the computation of the alpha complex. - + Triangle mesh representing the output of the computation, i.e. the alpha complex. - + Tetrahedra representing an interior volume of the alpha complex (if such exists). diff --git a/contributed_definitions/NXcg_hexahedron.nxdl.xml b/contributed_definitions/NXcg_hexahedron.nxdl.xml index d424776bad..715975c50c 100644 --- a/contributed_definitions/NXcg_hexahedron.nxdl.xml +++ b/contributed_definitions/NXcg_hexahedron.nxdl.xml @@ -178,14 +178,18 @@ from MarDI, for now let's assume we do not need polytopes for d > 3--> Combined storage of all primitives of all hexahedra. - + Individual storage of each hexahedron. + + Instances should use hexahedron as a name prefix. - + Individual storage of each hexahedron as a graph. + + Instances should use hexahedron_half_edge as a name prefix. diff --git a/contributed_definitions/NXcg_parallelogram.nxdl.xml b/contributed_definitions/NXcg_parallelogram.nxdl.xml index 08b34c3065..e97c7a869c 100644 --- a/contributed_definitions/NXcg_parallelogram.nxdl.xml +++ b/contributed_definitions/NXcg_parallelogram.nxdl.xml @@ -93,9 +93,11 @@ Combined storage of all parallelograms. - + Individual storage of each parallelogram. + + Instances should use parallelogram as a name prefix. diff --git a/contributed_definitions/NXcg_polygon.nxdl.xml b/contributed_definitions/NXcg_polygon.nxdl.xml index 3021dc2302..e5684450c3 100644 --- a/contributed_definitions/NXcg_polygon.nxdl.xml +++ b/contributed_definitions/NXcg_polygon.nxdl.xml @@ -80,14 +80,18 @@ Combined storage of all primitives of all polygons. - + Individual storage of the mesh of each polygon. + + Instances should use polygon as a name prefix. - + Individual storage of each polygon as a graph. + + Instances should use polygon_half_edge as a name prefix. diff --git a/contributed_definitions/NXcg_polyhedron.nxdl.xml b/contributed_definitions/NXcg_polyhedron.nxdl.xml index ab6decdb31..08f7358e7c 100644 --- a/contributed_definitions/NXcg_polyhedron.nxdl.xml +++ b/contributed_definitions/NXcg_polyhedron.nxdl.xml @@ -101,14 +101,18 @@ for clean graph-based descriptions of polyhedra.--> Combined storage of all primitives of all polyhedra. - + Individual storage of each polyhedron. + + Instances should use polyhedron as a name prefix. - + Individual storage of each polygon as a graph. + + Instances should use cluster_analysis as a name prefix. diff --git a/contributed_definitions/NXcg_tetrahedron.nxdl.xml b/contributed_definitions/NXcg_tetrahedron.nxdl.xml index 224f38de3a..7262f828da 100644 --- a/contributed_definitions/NXcg_tetrahedron.nxdl.xml +++ b/contributed_definitions/NXcg_tetrahedron.nxdl.xml @@ -63,14 +63,18 @@ Combined storage of all primitives of all tetrahedra. - + Individual storage of each tetrahedron. + + Instances should use tetrahedron as a name prefix. - + Individual storage of each tetrahedron as a graph. + + Instances should use tetrehedron_half_edge as a name prefix. diff --git a/contributed_definitions/NXcg_triangle.nxdl.xml b/contributed_definitions/NXcg_triangle.nxdl.xml index 03adf17d2b..75c697a0f5 100644 --- a/contributed_definitions/NXcg_triangle.nxdl.xml +++ b/contributed_definitions/NXcg_triangle.nxdl.xml @@ -58,11 +58,13 @@ in file formats such as OFF, PLY, VTK, or STL. - + Individual storage of each triangle. Users are advised that using such individual storage of primitives may be less storage efficient than creating a combined storage. + + Instances should use triangle as a name prefix. diff --git a/contributed_definitions/NXcoordinate_system_set.nxdl.xml b/contributed_definitions/NXcoordinate_system_set.nxdl.xml index 4fd441238e..dcbe16c8bc 100644 --- a/contributed_definitions/NXcoordinate_system_set.nxdl.xml +++ b/contributed_definitions/NXcoordinate_system_set.nxdl.xml @@ -117,9 +117,9 @@ use depends_on field - not attribute - to point to conventions used--> Convention how a positive rotation angle is defined when viewing - from the end of the rotation unit vector towards its origin, - i.e. in accordance with convention 2 of - DOI: 10.1088/0965-0393/23/8/083501. + from the end of the rotation unit vector towards its origin. + This is in accordance with convention 2 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. + Counter_clockwise is equivalent to a right-handed choice. Clockwise is equivalent to a left-handed choice. @@ -130,9 +130,8 @@ use depends_on field - not attribute - to point to conventions used--> - How are rotations interpreted into an orientation - according to convention 3 of - DOI: 10.1088/0965-0393/23/8/083501. + How are rotations interpreted into an orientation according to convention 3 + of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. @@ -142,7 +141,7 @@ use depends_on field - not attribute - to point to conventions used--> How are Euler angles interpreted given that there are several choices (e.g. zxz, xyz) - according to convention 4 of DOI: 10.1088/0965-0393/23/8/083501. + according to convention 4 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. The most frequently used convention is zxz, which is based on the work of H.-J. Bunge but other conventions are possible. Apart from undefined, proper Euler angles @@ -167,7 +166,7 @@ use depends_on field - not attribute - to point to conventions used--> To which angular range is the rotation angle argument of an axis-angle pair parameterization constrained according to - convention 5 of DOI: 10.1088/0965-0393/23/8/083501. + convention 5 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. @@ -177,7 +176,7 @@ use depends_on field - not attribute - to point to conventions used--> Which sign convention is followed when converting orientations between different parameterizations/representations according - to convention 6 of DOI: 10.1088/0965-0393/23/8/083501. + to convention 6 of reference `<https://doi.org/10.1088/0965-0393/23/8/083501>`_. @@ -201,7 +200,7 @@ convention 1 of DOI: 10.1088/0965-0393/23/8/083501 is implemented by inheriting If any of these assumptions is not met, the user is required to explicitly state this. - Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the base vectors of this coordinate system as Xp, Yp, Zp. @@ -215,21 +214,23 @@ convention 1 of DOI: 10.1088/0965-0393/23/8/083501 is implemented by inheriting If any of these assumptions is not met, the user is required to explicitly state this. - Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the base vectors of this coordinate system as Xs, Ys, Zs. - + Details about the detector_reference_frame for a specific detector. - Reference DOI: 10.1016/j.matchar.2016.04.008 suggest to label the + Reference `<https://doi.org/10.1016/j.matchar.2016.04.008>`_ suggests to label the base vectors of this coordinate system as Xd, Yd, Zd. It is assumed that the configuration is inspected by looking towards the sample surface from a position that is located behind the detector. If any of these assumptions is not met, the user is required to explicitly state this. + + Instances should use detector_reference_frame as a name prefix. diff --git a/contributed_definitions/NXcorrector_cs.nxdl.xml b/contributed_definitions/NXcorrector_cs.nxdl.xml index 211e7bb8b6..bb946b452d 100644 --- a/contributed_definitions/NXcorrector_cs.nxdl.xml +++ b/contributed_definitions/NXcorrector_cs.nxdl.xml @@ -57,13 +57,15 @@ https://doi.org/10.1017/9781316337455.022--> Was the corrector used? - + Specific information about the alignment procedure that is a process during which the corrector is configured to enable calibrated usage of the instrument. This :ref:`NXprocess` group should also be used when one describes in a computer simulation the specific details about the modelled or assumed aberrations. + + Instances should use tableau as a name prefix. @@ -99,9 +101,11 @@ https://doi.org/10.1017/9781316337455.022--> - + Image(s) taken during the alignment procedure + + Instances should use image as a name prefix. diff --git a/contributed_definitions/NXebeam_column.nxdl.xml b/contributed_definitions/NXebeam_column.nxdl.xml index d9a43c076d..96cb2d4af3 100644 --- a/contributed_definitions/NXebeam_column.nxdl.xml +++ b/contributed_definitions/NXebeam_column.nxdl.xml @@ -190,18 +190,22 @@ - + Electron biprism as it is used e.g. for electron holography. + + Instances should use biprism as a name prefix. - + Device that causes a change in the phase of an electron wave. * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ + + Instances should use phaseplate as a name prefix. @@ -214,6 +218,7 @@ + diff --git a/contributed_definitions/NXem.nxdl.xml b/contributed_definitions/NXem.nxdl.xml index a583035fb7..b03b2f4267 100644 --- a/contributed_definitions/NXem.nxdl.xml +++ b/contributed_definitions/NXem.nxdl.xml @@ -48,7 +48,7 @@ but for practical purposes currently is interpretable only by human to provide t The configuration of the software that was used to generate this NeXus file. - + A collection of all programs and libraries that are considered as relevant to understand with which software tools this NeXus file instance was @@ -65,9 +65,9 @@ but for practical purposes currently is interpretable only by human to provide t research data management system, it makes sense to store e.g. the GitHub repository commit and respective submodule references used. - Instances of programID can also be used to document the modules and - libraries that are offered by the computational environment such as those - parsed from conda or python virtualenv environments. + Instances can also be used to document the modules and libraries that + are offered by the computational environment such as those parsed + from conda or python virtualenv environments. @@ -131,8 +131,8 @@ but for practical purposes currently is interpretable only by human to provide t start_time and end_time together. - - + + Collection of serialized resources associated with the experiment. @@ -145,7 +145,7 @@ but for practical purposes currently is interpretable only by human to provide t - + Information about persons who performed or were involved in the microscope session or simulation run. @@ -155,7 +155,8 @@ but for practical purposes currently is interpretable only by human to provide t Adding multiple users if relevant is recommended. The protection of personal data by laws is in different stages of development - and strictness. For this reason no field of a userID instance is required. + and strictness. Therefore, the existence of user data has not been made + required. @@ -465,7 +466,7 @@ but for practical purposes currently is interpretable only by human to provide t - + Reference to the specifically named :ref:`NXdetector` instance for @@ -555,9 +556,11 @@ hence using optional is sufficient--> - + Details about the control program used for operating the microscope. + + Instances should use control_software as a name prefix. @@ -579,7 +582,10 @@ hence using optional is sufficient--> - + + + Instances should use lens as a name prefix. + @@ -587,7 +593,10 @@ hence using optional is sufficient--> - + + + Instances should use aperture as a name prefix. + @@ -595,7 +604,10 @@ hence using optional is sufficient--> - + + + Instances should use monochromator as a name prefix. + @@ -617,14 +629,20 @@ hence using optional is sufficient--> - + + + Instances should use biprism as a name prefix. + - + + + Instances should use phaseplate as a name prefix. + @@ -632,10 +650,26 @@ hence using optional is sufficient--> - - - - + + + Instances should use sensor as a name prefix. + + + + + Instances should use actuator as a name prefix. + + + + + Instances should use beam as a name prefix. + + + + + Instances should use deflector as a name prefix. + + - + + + Instances should use lens as a name prefix. + @@ -665,7 +702,10 @@ which components that microscope was built from--> - + + + Instances should use aperture as a name prefix. + @@ -673,7 +713,10 @@ which components that microscope was built from--> - + + + Instances should use monochromator as a name prefix. + @@ -681,12 +724,31 @@ which components that microscope was built from--> - - - - + + + Instances should use sensor as a name prefix. + + + + + Instances should use actuator as a name prefix. + + + + + Instances should use beam as a name prefix. + + + + + Instances should use deflector as a name prefix. + + - + + + Instances should use detector as a name prefix. + @@ -717,11 +779,22 @@ which components that microscope was built from--> - + + + Instances should use pump as a name prefix. + - - + + + Instances should use sensor as a name prefix. + + + + + Instances should use actuator as a name prefix. + + @@ -733,10 +806,16 @@ which components that microscope was built from--> dynamic (meta)data that typically change for each image and spectrum from the static one. - + + + Instances should use event as a name prefix. + - + + + Instances should use image as a name prefix. + @@ -909,7 +988,10 @@ which components that microscope was built from--> - + + + Instances should use spectrum as a name prefix. + @@ -1073,10 +1155,16 @@ which components that microscope was built from--> - + + + Instances should use lens as a name prefix. + - + + + Instances should use aperture as a name prefix. + Descriptor for the aperture setting when the exact technical details @@ -1086,14 +1174,17 @@ which components that microscope was built from--> - + + + Instances should use monochromator as a name prefix. + - + @@ -1225,10 +1316,26 @@ basically optional use of NXaberration therein at least some value required--> - - - - + + + Instances should use sensor as a name prefix. + + + + + Instances should use actuator as a name prefix. + + + + + Instances should use beam as a name prefix. + + + + + Instances should use deflector as a name prefix. + + @@ -1236,10 +1343,16 @@ phaseplateID(NXcomponent):--> - + + + Instances should use lens as a name prefix. + - + + + Instances should use aperture as a name prefix. + Descriptor for the aperture setting when the exact technical details @@ -1249,15 +1362,37 @@ phaseplateID(NXcomponent):--> - + + + Instances should use monochromator as a name prefix. + - - - - + + + Instances should use sensor as a name prefix. + + + + + Instances should use actuator as a name prefix. + + + + + Instances should use beam as a name prefix. + + + + + Instances should use deflector as a name prefix. + + - + + + Instances should use detector as a name prefix. + Operation mode of the detector as displayed by the control software. @@ -1268,9 +1403,17 @@ phaseplateID(NXcomponent):--> - - - + + + Instances should use sensor as a name prefix. + + + + + Instances should use sensor as a name prefix. + + + @@ -1297,7 +1440,7 @@ phaseplateID(NXcomponent):--> - + Description of the volume of interaction between of particle-matter interaction. @@ -1326,6 +1469,8 @@ phaseplateID(NXcomponent):--> * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ + + Instances should use interaction_volume as a name prefix. @@ -1334,10 +1479,10 @@ phaseplateID(NXcomponent):--> - + - A region-of-interest analyzed either during or after the session - for which specific processed data are available. + A region-of-interest analyzed either during or after the session for which specific + processed data are available. Instances should use roi as a name prefix. This concept is related to term `Region Of Interest`_ of the EMglossary standard. @@ -1348,7 +1493,10 @@ an RDM can be sure to find specific pieces of information in a specific way but then every user of this application definition is required to provide such information in this way!--> - + + + Instances should use image as a name prefix. + @@ -1400,7 +1548,7 @@ exists: optional--> - + diff --git a/contributed_definitions/NXem_calorimetry.nxdl.xml b/contributed_definitions/NXem_calorimetry.nxdl.xml index b30f59254d..f8beae804f 100644 --- a/contributed_definitions/NXem_calorimetry.nxdl.xml +++ b/contributed_definitions/NXem_calorimetry.nxdl.xml @@ -86,13 +86,13 @@ are aligned with what and how to name things--> Programs and libraries representing the computational environment - + - + @@ -117,7 +117,7 @@ are aligned with what and how to name things--> - + diff --git a/contributed_definitions/NXem_ebsd.nxdl.xml b/contributed_definitions/NXem_ebsd.nxdl.xml index 8360112868..1fc33c3b62 100644 --- a/contributed_definitions/NXem_ebsd.nxdl.xml +++ b/contributed_definitions/NXem_ebsd.nxdl.xml @@ -453,7 +453,7 @@ Specific parameter relevant only for certain algorithms used. - + Details for each phase used as a model with which the patterns were indexed. Instances of :ref:`NXunit_cell` in this group must @@ -461,6 +461,8 @@ integer. Start counting from 1 because the value 0 is reserved for the special phase that is the null-model, the null phase also known as notIndexed. + + Instances should use phase as a name prefix. @@ -610,12 +612,26 @@ Number of scan points in the original mapping. - + + + Instances should use odf as a name prefix. + + + + + Instances should use pf as a name prefix. + + + + + Instances should use ipf as a name prefix. + + + + + Instances should use microstructure as a name prefix. + + An overview of the entire ROI. diff --git a/contributed_definitions/NXinstrument_apm.nxdl.xml b/contributed_definitions/NXinstrument_apm.nxdl.xml index 86c7696717..c603dc137f 100644 --- a/contributed_definitions/NXinstrument_apm.nxdl.xml +++ b/contributed_definitions/NXinstrument_apm.nxdl.xml @@ -256,7 +256,7 @@ existence constraint is independent of other values. - + Atom probe microscopes use controlled laser, voltage, or a combination of pulsing strategies to trigger ion extraction via exciting and eventual field evaporation diff --git a/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml b/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml index f926738fca..be11ae1f28 100644 --- a/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml @@ -67,7 +67,7 @@ type: group--> Programs and libraries representing the computational environment - + diff --git a/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml b/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml index 8f3bcaeb65..43c0a9c933 100644 --- a/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml @@ -75,7 +75,7 @@ Programs and libraries representing the computational environment - + @@ -99,9 +99,11 @@ - + Documentation of the spatiotemporal evolution + + Instances should use spatiotemporal as a name prefix. @@ -224,7 +226,10 @@ the typical lean summary statistics flattened--> - + + + Instances should use microstructure as a name prefix. + diff --git a/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml b/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml index 53b6cfe7b5..7c28ed349e 100644 --- a/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml @@ -72,13 +72,16 @@ Programs and libraries representing the computational environment - + - + + + Instances should use microstructure as a name prefix. + diff --git a/contributed_definitions/NXmicrostructure_ipf.nxdl.xml b/contributed_definitions/NXmicrostructure_ipf.nxdl.xml index ea2b79c135..7e48ad83af 100644 --- a/contributed_definitions/NXmicrostructure_ipf.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_ipf.nxdl.xml @@ -96,8 +96,7 @@ Inverse pole figure mapping. - phase. No ipf_mapID instances for non-indexed scan points as these are - by definition assigned the null phase with phase_identifier 0. + Instances named phase0 should by definition refer to the null phase notIndexed. Inspect the definition of :ref:`NXphase` and its field identifier_phase for further details. diff --git a/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml b/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml index 9548714a70..f51ee059f3 100644 --- a/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml @@ -85,14 +85,17 @@ Programs and libraries representing the computational environment - + - + + + Instances should use microstructure as a name prefix. + diff --git a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml index ef2eb3868f..f7bf858ce7 100644 --- a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -101,7 +101,7 @@ - + @@ -146,7 +146,7 @@ Programs and libraries representing the computational environment - + diff --git a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml index deb666d28b..42dcd67051 100644 --- a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -136,7 +136,7 @@ inspect comments behind NXmicrostructure--> Programs and libraries representing the computational environment - + @@ -244,13 +244,15 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele - + Documentation of the spatiotemporal evolution for each CA domain. SCORE is a hybrid parallelized code that can evolve multiple replicas in parallel. The set of replicas is distributed across MPI processes. Each such replica is then evolved via OpenMP multi-threading. + + Instances should use spatiotemporal as a name prefix. @@ -378,7 +380,10 @@ electrical_field(NXprocess): unit: NX_ANY dim: (n_summary_stats, 3, 3) the typically storage-costlier snapshot data--> - + + + Instances should use microstructure as a name prefix. + diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 873e5b29b7..638518824f 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -39,9 +39,8 @@ NXapm(NXobject): which was used to generate this NeXus file instance. # command_line_call(NX_CHAR): - programID(NXprogram): + (NXprogram): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial doc: | A collection of all programs and libraries which are considered relevant to understand with which software tools this NeXus file instance was @@ -142,13 +141,11 @@ NXapm(NXobject): unit: NX_TIME doc: | How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime - citeID(NXcite): + (NXcite): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial doi(NX_CHAR): - noteID(NXnote): + (NXnote): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial type(NX_CHAR): file_name(NX_CHAR): checksum(NX_CHAR): @@ -172,14 +169,13 @@ NXapm(NXobject): enumeration: open_enum: true items: [apt, fim, apt_fim] - userID(NXuser): + (NXuser): exists: recommended - nameType: partial name(NX_CHAR): exists: optional identifierNAME(NX_CHAR): - exists: recommended nameType: partial + exists: recommended sample(NXsample): exists: recommended doc: | @@ -207,8 +203,8 @@ NXapm(NXobject): doc: | Given name/alias for the sample. identifierNAME(NX_CHAR): - exists: recommended nameType: partial + exists: recommended grain_diameter(NX_FLOAT): exists: optional unit: NX_LENGTH @@ -291,9 +287,12 @@ NXapm(NXobject): challenged by these differences as at.-% and wt.-% are both fractional quantities. enumeration: [atom_percent, weight_percent] - ionID(NXion): + (NXion): exists: ['min', '1', 'max', '118'] - nameType: partial + doc: | + Instances should use element as a name prefix and start counting + at 1 such that the name of each group already informs humans + for which element a composition is provided. chemical_symbol(NX_CHAR): doc: | Human-readable name of the element (e.g. Fe). @@ -322,8 +321,8 @@ NXapm(NXobject): Given name an alias. Better use identifierNAME and identifier_parent instead. A single NXentry should be used only for the characterization of a single specimen. identifierNAME(NX_CHAR): - exists: recommended nameType: partial + exists: recommended identifier_parent(NX_CHAR): exists: recommended doc: | @@ -430,7 +429,7 @@ NXapm(NXobject): space (CS) is discussed with the so-called detector space image (stack). This is a stack of two-dimensional histograms of detected ions within a predefined evaporation identifier interval. Typically, the set of - ion evaporation sequence IDs is grouped into chunks. + ion evaporation sequence identifiers is grouped into chunks. For each chunk a histogram of the ion hit positions on the detector is computed. This leaves the possibility for inconsistency between @@ -570,9 +569,8 @@ NXapm(NXobject): model(NX_CHAR): serial_number(NX_CHAR): exists: recommended - sourceID(NXsource): + (NXsource): exists: ['min', '0', 'max', '2'] - nameType: partial fabrication(NXfabrication): exists: recommended vendor(NX_CHAR): @@ -614,9 +612,8 @@ NXapm(NXobject): (molecular) ions that will end up in the reconstructed volume, we must not document quantities as a function of the evaporated_identifier but as a function of the (pulsing) event_identifier. - eventID(NXevent_data_apm): + (NXevent_data_apm): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial # all these cannot be made required because for LEAP only stored in RHIT/HITS # but for M-TAP and Oxcart these pieces of information are available. @@ -670,9 +667,8 @@ NXapm(NXobject): dim: (n,) # \@logged_against(NX_CHAR): - sourceID(NXsource): + (NXsource): exists: ['min', '0', 'max', '2'] - nameType: partial pulse_energy(NX_FLOAT): dimensions: rank: 1 @@ -742,9 +738,8 @@ NXapm(NXobject): From these tuples hits are computed in a process called hit_finding. sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): @@ -792,9 +787,8 @@ NXapm(NXobject): # we can only make recommendations sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): @@ -888,9 +882,8 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): source(NXnote): @@ -944,9 +937,8 @@ NXapm(NXobject): positions for flight path differences, detector biases, and nonlinearities. sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): source(NXnote): @@ -983,9 +975,8 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): source(NXnote): @@ -1005,9 +996,8 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): config(NXnote): @@ -1055,9 +1045,8 @@ NXapm(NXobject): rank: 2 dim: (n, 3) naive_discretization(NXprocess): - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): @@ -1096,9 +1085,8 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): definitions(NXnote): @@ -1113,9 +1101,8 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): min_incr_max(NX_FLOAT): @@ -1142,9 +1129,8 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): background(NX_FLOAT): @@ -1173,14 +1159,12 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): - peakID(NXpeak): + (NXpeak): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial label(NX_CHAR): exists: recommended description(NX_CHAR): @@ -1206,16 +1190,16 @@ NXapm(NXobject): exists: recommended sequence_index(NX_POSINT): exists: recommended - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): number_of_ion_types(NX_UINT): maximum_number_of_atoms_per_molecular_ion(NX_UINT): - ionID(NXion): + (NXion): exists: ['min', '1', 'max', '256'] - nameType: partial + doc: | + Instances should use ion as a name prefix. nuclide_hash(NX_UINT): charge_state(NX_INT): charge_state_analysis(NXapm_charge_state_analysis): @@ -1242,7 +1226,7 @@ NXapm(NXobject): exists: recommended # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# d946b686bcf65b3214c8f87098d7a0e3391b20d9f03d1f8ad4304aba15c9d7f3 +# 3ceb4add90d05a69e3d4d93a517ddeacb5d2344c10b7d48eb5bef85592ef701e # # # -# +# # # A collection of all programs and libraries which are considered relevant # to understand with which software tools this NeXus file instance was @@ -1434,10 +1418,10 @@ NXapm(NXobject): # How long did the measurement take e.g. use CRunHeader.CAnalysis.fElapsedTime # # -# +# # # -# +# # # # @@ -1466,9 +1450,9 @@ NXapm(NXobject): # # # -# +# # -# +# # # # @@ -1503,7 +1487,7 @@ NXapm(NXobject): # Given name/alias for the sample. # # -# +# # # # Qualitative information about the grain size, here specifically @@ -1591,7 +1575,12 @@ NXapm(NXobject): # # # -# +# +# +# Instances should use element as a name prefix and start counting +# at 1 such that the name of each group already informs humans +# for which element a composition is provided. +# # # # Human-readable name of the element (e.g. Fe). @@ -1631,7 +1620,7 @@ NXapm(NXobject): # A single NXentry should be used only for the characterization of a single specimen. # # -# +# # # # Identifier of the sample from which the specimen was cut or the string @@ -1744,7 +1733,7 @@ NXapm(NXobject): # space (CS) is discussed with the so-called detector space image # (stack). This is a stack of two-dimensional histograms of detected ions # within a predefined evaporation identifier interval. Typically, the set of -# ion evaporation sequence IDs is grouped into chunks. +# ion evaporation sequence identifiers is grouped into chunks. # # For each chunk a histogram of the ion hit positions on the detector # is computed. This leaves the possibility for inconsistency between @@ -1880,7 +1869,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -1928,7 +1917,7 @@ NXapm(NXobject): # document quantities as a function of the evaporated_identifier but as a # function of the (pulsing) event_identifier. # -# +# # # @@ -1969,7 +1958,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2049,7 +2038,7 @@ NXapm(NXobject): # From these tuples hits are computed in a process called hit_finding. # # -# +# # # # @@ -2104,7 +2093,7 @@ NXapm(NXobject): # is does not have the authority to decide which portions of proprietary code have to be public # we can only make recommendations--> # -# +# # # # @@ -2200,7 +2189,7 @@ NXapm(NXobject): # at this point the original set of events p has been filtered down to p_out--> # # -# +# # # # @@ -2256,7 +2245,7 @@ NXapm(NXobject): # positions for flight path differences, detector biases, and nonlinearities. # # -# +# # # # @@ -2296,7 +2285,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2317,7 +2306,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2366,7 +2355,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2410,7 +2399,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2426,7 +2415,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2454,7 +2443,7 @@ NXapm(NXobject): # # # -# +# # # # @@ -2483,12 +2472,12 @@ NXapm(NXobject): # in an e.g. work of A. London et al.--> # # -# +# # # # # -# +# # # # @@ -2520,14 +2509,17 @@ NXapm(NXobject): # # # -# +# # # # # # # -# +# +# +# Instances should use ion as a name prefix. +# # # # diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml index 93931f12aa..a3fd5919eb 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_results.yaml @@ -29,12 +29,10 @@ NXapm_compositionspace_results(NXobject): # can be used for the name of the tool and version but also # for if desired all the dependencies and libraries - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): - \@url(NX_CHAR): - exists: optional analysis_identifier(NX_UINT): exists: recommended @@ -129,7 +127,7 @@ NXapm_compositionspace_results(NXobject): for the occupancy of each voxel with atoms. dimensions: dim: (n_voxels,) - elementID(NXion): + (NXion): exists: ['min', '1', 'max', 'unbounded'] name(NX_CHAR): doc: | @@ -199,8 +197,8 @@ NXapm_compositionspace_results(NXobject): axis_pca_dimension(NX_UINT): unit: NX_UNITLESS doc: | - Elements identifier matching those from ENTRY/voxelization/elementID as the - principal component analysis. + Elements identifier matching those from ENTRY/voxelization/ION + as the principal component analysis. dimensions: dim: (i,) ic_opt(NXprocess): @@ -208,9 +206,12 @@ NXapm_compositionspace_results(NXobject): Information criterion minimization. sequence_index(NX_POSINT): enumeration: [3, 4] - cluster_analysisID(NXprocess): + CLUSTER_ANALYSIS(NXprocess): + nameType: any doc: | Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. + + Instances should use cluster_analysis as a name prefix. n_ic_cluster(NX_UINT): unit: NX_UNITLESS doc: | @@ -259,15 +260,21 @@ NXapm_compositionspace_results(NXobject): ic_opt(NXobject): doc: | Respective DBScan clustering result for each segmentation/ic_opt case. - cluster_analysisID(NXprocess): + CLUSTER_ANALYSIS(NXprocess): exists: ['min', '0', 'max', 'unbounded'] - dbscanID(NXprocess): + nameType: any + doc: | + Instances should use cluster_analysis as a name prefix. + DBSCAN(NXprocess): exists: ['min', '1', 'max', 'unbounded'] + nameType: any epsilon(NX_FLOAT): unit: NX_LENGTH doc: | - The maximum distance between voxel pairs in a neighborhood to be considered - connected. + The maximum distance between voxel pairs in a neighborhood + to be considered connected. + + Instances should use dbscan as a name prefix. min_samples(NX_UINT): unit: NX_UNITLESS doc: | @@ -303,7 +310,7 @@ NXapm_compositionspace_results(NXobject): # number_of_gpus(NX_POSINT): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 20e747384e6286319c3b7516e700441486700d2e66a0be4696bd69eb15a595ec +# fd7e4ebd87f620ac9d754d5dfa97c13f6b96cdd65d50aa16a866f1b594e91805 # # # -# +# # # -# # # # @@ -495,7 +501,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # # Chemical symbol of the element from the periodic table. @@ -586,8 +592,8 @@ NXapm_compositionspace_results(NXobject): # # # -# Elements identifier matching those from ENTRY/voxelization/elementID as the -# principal component analysis. +# Elements identifier matching those from ENTRY/voxelization/ION +# as the principal component analysis. # # # @@ -605,9 +611,11 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # Results of the Gaussian mixture analysis for n_components equal to n_ic_cluster. +# +# Instances should use cluster_analysis as a name prefix. # # # @@ -674,12 +682,17 @@ NXapm_compositionspace_results(NXobject): # # Respective DBScan clustering result for each segmentation/ic_opt case. # -# -# +# +# +# Instances should use cluster_analysis as a name prefix. +# +# # # -# The maximum distance between voxel pairs in a neighborhood to be considered -# connected. +# The maximum distance between voxel pairs in a neighborhood +# to be considered connected. +# +# Instances should use dbscan as a name prefix. # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml index 884d12e6c1..31607c006b 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_config.yaml @@ -69,12 +69,13 @@ NXapm_paraprobe_clusterer_config(NXobject): # in dataset/dataset/dataset_name_reconstruction where covered # by the IVAS/APSuite cluster analysis. This can be useful to recover # the region of interest. - cluster_analysisID(NXapm_paraprobe_tool_config): - nameType: partial + CLUSTER_ANALYSIS(NXapm_paraprobe_tool_config): exists: ['min', '0', 'max', 'unbounded'] doc: | This process performs a cluster analysis on a reconstructed dataset or a ROI within it. + + Instances should use cluster_analysis as a name prefix. reconstruction(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -304,8 +305,7 @@ NXapm_paraprobe_clusterer_config(NXobject): # e.g. https://doi.org/10.1017/S1431927607070900 common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -317,7 +317,7 @@ NXapm_paraprobe_clusterer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 39b347b2b9eeb4fe6cef13585fdf155dc7df8f0549455e2dfdc03a0ed9b4feff +# decce84b4d44bfd322cdc000d6a89d6b7669eaa41894805f8c030afc96101947 # # # -# +# # # This process performs a cluster analysis on a # reconstructed dataset or a ROI within it. +# +# Instances should use cluster_analysis as a name prefix. # # # @@ -688,7 +690,7 @@ NXapm_paraprobe_clusterer_config(NXobject): # e.g. https://doi.org/10.1017/S1431927607070900--> # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml index 3c3afe1c93..3299fae4da 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml @@ -21,8 +21,8 @@ NXapm_paraprobe_clusterer_results(NXobject): # tasks cameca_to_nexus(NXapm_paraprobe_tool_results): exists: optional - cluster_analysisID(NXapm_paraprobe_tool_results): - nameType: partial + CLUSTER_ANALYSIS(NXapm_paraprobe_tool_results): + nameType: any exists: ['min', '0', 'max', 'unbounded'] analysis_identifier(NX_UINT): config(NXnote): @@ -36,11 +36,12 @@ NXapm_paraprobe_clusterer_results(NXobject): mask(NX_UINT): # results - dbscanID(NXsimilarity_grouping): - nameType: partial + DBSCAN(NXsimilarity_grouping): exists: ['min', '0', 'max', 'unbounded'] doc: | Results of a DBScan clustering analysis. + + Instances should use dbscan as a name prefix. eps(NX_FLOAT): unit: NX_LENGTH doc: | @@ -207,8 +208,7 @@ NXapm_paraprobe_clusterer_results(NXobject): # ADD FURTHER RESULTS along the same pattern for e.g. OPTICS and HDBSCAN common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -221,8 +221,7 @@ NXapm_paraprobe_clusterer_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -249,7 +248,7 @@ NXapm_paraprobe_clusterer_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8fcd065d627d5c8c485ad116603508e9ab801d614a03a3d2d4d5d9393462df6a +# 4841685dac72e665630b7050f552941c1171caa20b914cb92db5d56e88d296e2 # # # # -# +# # # # @@ -317,9 +316,11 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# +# # # Results of a DBScan clustering analysis. +# +# Instances should use dbscan as a name prefix. # # # @@ -505,7 +506,7 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# +# # # # @@ -519,7 +520,7 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# +# # # If used, metadata of at least the person who performed this analysis. # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml index 21d8dc88e5..2ded5e881a 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml @@ -106,8 +106,8 @@ NXapm_paraprobe_distancer_config(NXobject): How many triangle sets to consider. Multiple triangle sets can be defined which are composed into one joint triangle set for the analysis. - triangle_setID(NXnote): - nameType: partial + TRIANGLE_SET(NXnote): + nameType: any exists: ['min', '1', 'max', 'unbounded'] doc: | Each triangle_set that is referred to here should be a face_list_data_structure, @@ -115,6 +115,8 @@ NXapm_paraprobe_distancer_config(NXobject): array of NX_UINT incident vertices of each facet. Vertex indices are assumed to start at zero and must not exceed n_vertices - 1, i.e. the identifier_offset is 0. Facet normal have to be provided as an array of (n_facets, 3) of NX_FLOAT. + + Instances should use triangle_set as a name prefix. type(NX_CHAR): algorithm(NX_CHAR): checksum(NX_CHAR): @@ -150,8 +152,7 @@ NXapm_paraprobe_distancer_config(NXobject): # point_set_to_polyline_set(NXapm_paraprobe_tool_config): common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -163,7 +164,7 @@ NXapm_paraprobe_distancer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fb32610bdb45d7f2f479bdb9ecef805fbd4ea4775436ee412af3b1b1b9f7c254 +# 4c7babceac573608f33c67c2f3d4f42e2e4e254374ca25c46e9431d91bd3f8a6 # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml index 89a00d42d0..45fcf8183f 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_results.yaml @@ -33,7 +33,6 @@ NXapm_paraprobe_distancer_results(NXobject): exists: ['min', '1', 'max', '1'] # config - analysis_identifier(NX_UINT): config(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -119,8 +118,7 @@ NXapm_paraprobe_distancer_results(NXobject): dim: (n_tri,) common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -133,8 +131,7 @@ NXapm_paraprobe_distancer_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -161,7 +158,7 @@ NXapm_paraprobe_distancer_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fea70033f7095ae84cea4976974bcbebf80987e148ccb070b762bf2a7f4466da +# b58701c1f4837454b6ff78407eddf0947613d67efb2b36873bd13d25797f7487 # # # # # -# # # # @@ -320,7 +316,7 @@ NXapm_paraprobe_distancer_results(NXobject): # # # -# +# # # # @@ -334,7 +330,7 @@ NXapm_paraprobe_distancer_results(NXobject): # # # -# +# # # If used, metadata of at least the person who performed this analysis. # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml index 417247eb82..9715b643e9 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_config.yaml @@ -19,7 +19,8 @@ NXapm_paraprobe_intersector_config(NXobject): unit: NX_UNITLESS doc: | How many v_v_spatial_correlation tasks should the tool execute. - v_v_spatial_correlationID(NXapm_paraprobe_tool_config): + V_V_SPATIAL_CORRELATION(NXapm_paraprobe_tool_config): + nameType: any exists: ['min', '1', 'max', 'unbounded'] doc: | Tracking volume_volume_spatial_correlations (v_v) is the process of building logical @@ -31,6 +32,8 @@ NXapm_paraprobe_intersector_config(NXobject): step :math:`k` pairs of sets are compared: Members of a so-called current_set to members of a so-called next_set. Members can be different types of volumetric features. + + Instances should use v_v_spatial_correlation as a name prefix. # config intersection_detection_method(NX_CHAR): @@ -189,11 +192,10 @@ NXapm_paraprobe_intersector_config(NXobject): dim: (n_variable,) #MK::tetrahedra volume intersection and tessellation and Nef polyhedra intersection are considered guru features - # and therefore currently supported only via modifying the C/C++ source code directly as one should know exactly # what one is doing here before using these functionalities common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -205,7 +207,7 @@ NXapm_paraprobe_intersector_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# ee535a0d38a58d2c6f05eebb824618201f1e096452f07f2136fee7978bd60b8c +# 9d9b71feaf41d4805886140f80f4fac0ef228c01dbd0f66cc0507a868661cc9c # # # # @@ -466,11 +470,10 @@ NXapm_paraprobe_intersector_config(NXobject): # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml index b217ccdf5a..3d28cf5c24 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml @@ -170,8 +170,7 @@ NXapm_paraprobe_intersector_results(NXobject): partial(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -184,8 +183,7 @@ NXapm_paraprobe_intersector_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -212,7 +210,7 @@ NXapm_paraprobe_intersector_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 3b33823b0b411bedd74d076a7f484f3fd20aa46753f68d1e2fb37a89e0784140 +# 715798427e25dc3b2d25575487d010a02cfa4eca11ec6fe6dbfae5f7605ddfcb # # # -# +# +# +# Instances should use delocalization as a name prefix. +# # # # @@ -1433,7 +1451,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # The result of the delocalization :math:`\Phi = f(x, y, z)` based on which subsequent iso-surfaces # will be computed. In commercial software so far there is no possibility to export this information. @@ -1515,7 +1533,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # The three-dimensional gradient :math:`\nabla \Phi`. # Follow the naming convention of scalar_field_magn_SUFFIX to report parallel structures. @@ -1592,10 +1610,12 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # An iso-surface is the boundary between two regions across which the magnitude of a # scalar field falls below/exceeds a threshold magnitude :math:`\varphi`. +# +# Instances should iso_surface as a name prefix. # # For applications in atom probe microscopy, the location and shape of such a boundary (set) # is typically approximated by discretization - triangulation to be specific. @@ -1960,7 +1980,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# +# +# Instances should use object as a name prefix. +# # # # @@ -2084,10 +2107,12 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # The triangle surface mesh representing the interface model. # Exported at state before or after the next DCOM step. +# +# Instances should use mesh_state as a name prefix. # # # @@ -2286,7 +2311,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # are only expected to display pairwise the same values respectively, # if all ions are built from a single atom only. # -# +# +# +# Instances should use roi as a name prefix. +# # # # Sorted in increasing order projected along the positive direction @@ -2317,7 +2345,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # @@ -2331,7 +2359,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # If used, metadata of at least the person who performed this analysis. # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml index 3f47e4c3f4..05d1f4fec3 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml @@ -90,8 +90,7 @@ NXapm_paraprobe_ranger_config(NXobject): match(NX_NUMBER): common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -103,7 +102,7 @@ NXapm_paraprobe_ranger_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# dcb5ccce6aec7bd64bb55b515df75a59d2648e720dfb7515fd022570da1e0027 +# daf5564edd5ac6f36f3dc2d103a1e272032226879aee2ea00cc10c564c9d8fec # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_results.yaml index d54476af13..6d9c0e52d1 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_spatstat_results.yaml @@ -21,9 +21,11 @@ NXapm_paraprobe_spatstat_results(NXobject): enumeration: [NXapm_paraprobe_spatstat_results] # tasks - spatial_statisticsID(NXapm_paraprobe_tool_results): - nameType: partial + SPATIAL_STATISTICS(NXapm_paraprobe_tool_results): + nameType: any exists: ['min', '0', 'max', 'unbounded'] + doc: | + Instances should use spatial_statistics as a name prefix. window(NXcs_filter_boolean_mask): number_of_ions(NX_UINT): bitdepth(NX_UINT): @@ -111,8 +113,7 @@ NXapm_paraprobe_spatstat_results(NXobject): file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -125,8 +126,7 @@ NXapm_paraprobe_spatstat_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -153,7 +153,7 @@ NXapm_paraprobe_spatstat_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# a23f9efbe4b0c2a50b3b64f38317f6dd4c2e4030a8a85b173e2c501373431323 +# 832a39553923a4906ce3bc226a88ed4c09494e4b8da0d8c00a1f1dce77ced753 # # # -# +# +# +# Instances should use spatial_statistics as a name prefix. +# # # # @@ -310,7 +313,7 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# +# # # # @@ -324,7 +327,7 @@ NXapm_paraprobe_spatstat_results(NXobject): # # # -# +# # # If used, metadata of at least the person who performed this analysis. # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml index 9690f7c6d9..21a38cf2af 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_config.yaml @@ -165,8 +165,7 @@ NXapm_paraprobe_surfacer_config(NXobject): # NEW ISSUE: has_facet_appearance(NX_BOOLEAN): common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -178,7 +177,7 @@ NXapm_paraprobe_surfacer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 3bf49f914dc8c477b0883bca488a289dafd50a6967e10406b4ea561f0e340c64 +# 60796c30f0d74f9f1dfedb5bde4677978e1618c6410c29f1e8f27ed24593252d # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml index 4ab91788dd..e43038bc5b 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_surfacer_results.yaml @@ -51,12 +51,14 @@ NXapm_paraprobe_surfacer_results(NXobject): mask(NX_UINT): # results - alpha_complexID(NXcg_alpha_complex): - nameType: partial + ALPHA_COMPLEX(NXcg_alpha_complex): + nameType: any exists: ['min', '0', 'max', 'unbounded'] # (NXcg_grid): currently we do not store the underlying grid # for eventually performed preprocessing + doc: | + Instances should use alpha_complex as a name prefix. window(NXcs_filter_boolean_mask): doc: | A bitmask which identifies exactly all those ions whose positions @@ -181,8 +183,7 @@ NXapm_paraprobe_surfacer_results(NXobject): file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -195,8 +196,7 @@ NXapm_paraprobe_surfacer_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -223,7 +223,7 @@ NXapm_paraprobe_surfacer_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 2fefbd0d2070627d5e394d37e297a32977fa70ba2f6b60d26f6f0e653c7ebf47 +# dafd5a3042794baeeb006baa3f9de4d8c7df333a4e38c0d5b330ef8b97fa871a # # # -# +# # +# +# Instances should use alpha_complex as a name prefix. +# # # # A bitmask which identifies exactly all those ions whose positions @@ -469,7 +472,7 @@ NXapm_paraprobe_surfacer_results(NXobject): # # # -# +# # # # @@ -483,7 +486,7 @@ NXapm_paraprobe_surfacer_results(NXobject): # # # -# +# # # If used, metadata of at least the person who performed this analysis. # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml index 032589e5af..25942fe54a 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml @@ -125,8 +125,7 @@ NXapm_paraprobe_tessellator_config(NXobject): # minValue: EPSILON common(NXapm_paraprobe_tool_common): status(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -138,7 +137,7 @@ NXapm_paraprobe_tessellator_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fe1acf304cd73ed1fe983ad561ea68669a48b9b34fea2747e7236e58835bb834 +# 6c9a434c7676b2cf255261d4dda62dc9aa43181f31b54ce3f7e961d07850dad0 # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml index 08889548e3..bf0ab7eae7 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_results.yaml @@ -232,8 +232,7 @@ NXapm_paraprobe_tessellator_results(NXobject): file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -246,8 +245,7 @@ NXapm_paraprobe_tessellator_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -274,7 +272,7 @@ NXapm_paraprobe_tessellator_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 2d18be00bbe25e3d600318ef3ab90e56dddc87c7e8efb9d80a4b9dc22f3f6965 +# f9f65b9fbfca638f7c4fe63752eefc7376f9a619e78ecba9564ffde7e5832235 # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml index 3979375b63..2cf3e33dd1 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml @@ -124,8 +124,7 @@ NXapm_paraprobe_transcoder_results(NXobject): file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): @@ -138,8 +137,7 @@ NXapm_paraprobe_transcoder_results(NXobject): number_of_processes(NX_POSINT): number_of_threads(NX_POSINT): number_of_gpus(NX_POSINT): - userID(NXuser): - nameType: partial + (NXuser): exists: ['min', '0', 'max', 'unbounded'] doc: | If used, metadata of at least the person who performed this analysis. @@ -166,7 +164,7 @@ NXapm_paraprobe_transcoder_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1389354b8715f43805b8894120045e108b6d2f3dd0ae5c4ff4dd1ae18e5fbc6c +# 8e1c10cce9e92568f80a3ae9771333fefa8158c1cfedf3274b65745b670c101a # # # -# +# # # Point cloud serving as input for the computation of the alpha complex. # # -# +# # # Triangle soup serving as input for the computation of the alpha complex. # # -# +# # # Triangle mesh representing the output of the computation, i.e. the alpha complex. # # -# +# # # Tetrahedra representing an interior volume of the alpha complex (if such exists). # diff --git a/contributed_definitions/nyaml/NXcg_hexahedron.yaml b/contributed_definitions/nyaml/NXcg_hexahedron.yaml index 0a3fbc13db..4b01f7f507 100644 --- a/contributed_definitions/nyaml/NXcg_hexahedron.yaml +++ b/contributed_definitions/nyaml/NXcg_hexahedron.yaml @@ -138,17 +138,21 @@ NXcg_hexahedron(NXcg_primitive): hexahedra(NXcg_face_list_data_structure): doc: | Combined storage of all primitives of all hexahedra. - hexahedronID(NXcg_face_list_data_structure): - nameType: partial + HEXAHEDRON(NXcg_face_list_data_structure): + nameType: any doc: | Individual storage of each hexahedron. - hexahedron_half_edgeID(NXcg_half_edge_data_structure): - nameType: partial + + Instances should use hexahedron as a name prefix. + HEXAHEDRON_HALF_EDGE(NXcg_half_edge_data_structure): + nameType: any doc: | Individual storage of each hexahedron as a graph. + + Instances should use hexahedron_half_edge as a name prefix. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f67f7ce071e318711ece618dd5305357a9bdea87336fa43b55b4788cbc1205a2 +# dc49e0bff2e065de0d060c18a8c0223a0a1977ae91792b95c31e92698acbe9ef # # # diff --git a/contributed_definitions/nyaml/NXcg_polyhedron.yaml b/contributed_definitions/nyaml/NXcg_polyhedron.yaml index 681699ad6c..ea60b576bd 100644 --- a/contributed_definitions/nyaml/NXcg_polyhedron.yaml +++ b/contributed_definitions/nyaml/NXcg_polyhedron.yaml @@ -63,17 +63,21 @@ NXcg_polyhedron(NXcg_primitive): polyhedra(NXcg_face_list_data_structure): doc: | Combined storage of all primitives of all polyhedra. - polyhedronID(NXcg_face_list_data_structure): - nameType: partial + POLYHEDRON(NXcg_face_list_data_structure): + nameType: any doc: | Individual storage of each polyhedron. - polyhedron_half_edgeID(NXcg_half_edge_data_structure): - nameType: partial + + Instances should use polyhedron as a name prefix. + POLYHEDRON_HALF_EDGE(NXcg_half_edge_data_structure): + nameType: any doc: | Individual storage of each polygon as a graph. + + Instances should use cluster_analysis as a name prefix. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 9d922551ffc0d7096f4706fd65df4bcfe410ffee1972a510f47e68f65261dccc +# 6bc4208f1ac62b6436a632952a7a30eadfcb5dd57e2d6d17700ad09b08938494 # # # -# -# -# -# +# +# +# Instances should use sensor as a name prefix. +# +# +# +# +# Instances should use actuator as a name prefix. +# +# +# +# +# Instances should use beam as a name prefix. +# +# +# +# +# Instances should use deflector as a name prefix. +# +# # -# +# +# +# Instances should use detector as a name prefix. +# # # # @@ -2149,11 +2255,22 @@ NXem(NXobject): # # # -# +# +# +# Instances should use pump as a name prefix. +# # # -# -# +# +# +# Instances should use sensor as a name prefix. +# +# +# +# +# Instances should use actuator as a name prefix. +# +# # # # @@ -2165,10 +2282,16 @@ NXem(NXobject): # dynamic (meta)data that typically change for each image and spectrum # from the static one. # -# +# +# +# Instances should use event as a name prefix. +# # # -# +# +# +# Instances should use image as a name prefix. +# # # # @@ -2341,7 +2464,10 @@ NXem(NXobject): # # # -# +# +# +# Instances should use spectrum as a name prefix. +# # # # @@ -2505,10 +2631,16 @@ NXem(NXobject): # # # -# +# +# +# Instances should use lens as a name prefix. +# # # -# +# +# +# Instances should use aperture as a name prefix. +# # # # Descriptor for the aperture setting when the exact technical details @@ -2518,14 +2650,17 @@ NXem(NXobject): # # # -# +# +# +# Instances should use monochromator as a name prefix. +# # # # # # # -# +# # # # @@ -2657,10 +2792,26 @@ NXem(NXobject): # # -# -# -# -# +# +# +# Instances should use sensor as a name prefix. +# +# +# +# +# Instances should use actuator as a name prefix. +# +# +# +# +# Instances should use beam as a name prefix. +# +# +# +# +# Instances should use deflector as a name prefix. +# +# # # # @@ -2668,10 +2819,16 @@ NXem(NXobject): # # # -# +# +# +# Instances should use lens as a name prefix. +# # # -# +# +# +# Instances should use aperture as a name prefix. +# # # # Descriptor for the aperture setting when the exact technical details @@ -2681,15 +2838,37 @@ NXem(NXobject): # # # -# +# +# +# Instances should use monochromator as a name prefix. +# # # -# -# -# -# +# +# +# Instances should use sensor as a name prefix. +# +# +# +# +# Instances should use actuator as a name prefix. +# +# +# +# +# Instances should use beam as a name prefix. +# +# +# +# +# Instances should use deflector as a name prefix. +# +# # -# +# +# +# Instances should use detector as a name prefix. +# # # # Operation mode of the detector as displayed by the control software. @@ -2700,9 +2879,17 @@ NXem(NXobject): # # # -# -# -# +# +# +# Instances should use sensor as a name prefix. +# +# +# +# +# Instances should use sensor as a name prefix. +# +# +# # # # @@ -2729,7 +2916,7 @@ NXem(NXobject): # # # -# +# # # Description of the volume of interaction between of particle-matter interaction. # @@ -2758,6 +2945,8 @@ NXem(NXobject): # * `S. Richter et al. <https://doi.org/10.1088/1757-899X/109/1/012014>`_ # * `J. Bünger et al. <https://doi.org/10.1017/S1431927622000083>`_ # * `J. F. Ziegler et al. <https://doi.org/10.1007/978-3-642-68779-2_5>`_ +# +# Instances should use interaction_volume as a name prefix. # # # @@ -2766,10 +2955,10 @@ NXem(NXobject): # -# +# # -# A region-of-interest analyzed either during or after the session -# for which specific processed data are available. +# A region-of-interest analyzed either during or after the session for which specific +# processed data are available. Instances should use roi as a name prefix. # # This concept is related to term `Region Of Interest`_ of the EMglossary standard. # @@ -2780,7 +2969,10 @@ NXem(NXobject): # specific way but then every user of this application definition # is required to provide such information in this way!--> # -# +# +# +# Instances should use image as a name prefix. +# # # # @@ -2832,7 +3024,7 @@ NXem(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXem_calorimetry.yaml b/contributed_definitions/nyaml/NXem_calorimetry.yaml index 62c3234827..793316b571 100644 --- a/contributed_definitions/nyaml/NXem_calorimetry.yaml +++ b/contributed_definitions/nyaml/NXem_calorimetry.yaml @@ -48,14 +48,12 @@ NXem_calorimetry(NXobject): exists: recommended doc: | Programs and libraries representing the computational environment - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): - userID(NXuser): + (NXuser): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial sample(NXsample): exists: recommended type(NX_CHAR): @@ -73,9 +71,8 @@ NXem_calorimetry(NXobject): opportunity to parse the relevant elements without having to interpret these from the resources pointed to by parent_identifier or walk through eventually deeply nested groups in data instances. - citeID(NXcite): + (NXcite): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial # a place where to add citations for your work ... diffraction_space(NXcoordinate_system): @@ -241,7 +238,7 @@ NXem_calorimetry(NXobject): sequence_index(NX_POSINT): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f08363f38c031a857a82e75ea03d563b97be6e29bfeeedeb2bab0298125c46ed +# 7f437bcd6a086490d3ba7755ef75e0b8bca27babb5aab74cdfe7e24c641827ff # # # # # diff --git a/contributed_definitions/nyaml/NXem_ebsd.yaml b/contributed_definitions/nyaml/NXem_ebsd.yaml index b8635936de..df2d48777d 100644 --- a/contributed_definitions/nyaml/NXem_ebsd.yaml +++ b/contributed_definitions/nyaml/NXem_ebsd.yaml @@ -314,8 +314,7 @@ NXem_ebsd(NXprocess): parameter(NXcollection): doc: | Specific parameter relevant only for certain algorithms used. - phaseID(NXphase): - nameType: partial + (NXphase): doc: | Details for each phase used as a model with which the patterns were indexed. Instances of :ref:`NXunit_cell` in this group must @@ -323,6 +322,8 @@ NXem_ebsd(NXprocess): integer. Start counting from 1 because the value 0 is reserved for the special phase that is the null-model, the null phase also known as notIndexed. + + Instances should use phase as a name prefix. dspacing(NX_NUMBER): unit: NX_LENGTH doc: | @@ -450,13 +451,18 @@ NXem_ebsd(NXprocess): unit: NX_UNITLESS doc: | Number of scan points in the original mapping. - - # already implemented connections to representations of microstructures but in this PR not proposed - # odfID(NXmicrostructure_odf): - # pfID(NXmicrostructure_pf): - # ipfID(NXmicrostructure_ipf): - # microstructureID(NXmicrostructure): - # overview over the entire map, rediscretized on a tight aabb + (NXmicrostructure_odf): + doc: | + Instances should use odf as a name prefix. + (NXmicrostructure_pf): + doc: | + Instances should use pf as a name prefix. + (NXmicrostructure_ipf): + doc: | + Instances should use ipf as a name prefix. + (NXmicrostructure): + doc: | + Instances should use microstructure as a name prefix. roi(NXdata): doc: | An overview of the entire ROI. @@ -499,7 +505,7 @@ NXem_ebsd(NXprocess): Label for the x axis # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# cc820d02f0569c63a9b855f30471996ebaa9ebf5e94541c63897c26afec16bee +# 238aab6674c6ca5419812342c1357b5e52fa0485786dfe514ebc9a8342944e8c # # # +# +# +# Instances should use odf as a name prefix. +# +# +# +# +# Instances should use pf as a name prefix. +# +# +# +# +# Instances should use ipf as a name prefix. +# +# +# +# +# Instances should use microstructure as a name prefix. +# +# # # # An overview of the entire ROI. diff --git a/contributed_definitions/nyaml/NXinstrument_apm.yaml b/contributed_definitions/nyaml/NXinstrument_apm.yaml index 40f849b14e..23b07f9b35 100644 --- a/contributed_definitions/nyaml/NXinstrument_apm.yaml +++ b/contributed_definitions/nyaml/NXinstrument_apm.yaml @@ -176,8 +176,7 @@ NXinstrument_apm(NXinstrument): \@logged_against(NX_CHAR): doc: | Path to pulse_identifier - sourceID(NXsource): - nameType: partial + (NXsource): doc: | Atom probe microscopes use controlled laser, voltage, or a combination of pulsing strategies to trigger ion extraction via exciting and eventual field evaporation @@ -278,7 +277,7 @@ NXinstrument_apm(NXinstrument): detection losses. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 883b8eb292f99e33fa9bf160c4329a3f081642a7d5f075a52818f5eecbc6529e +# bb5977f8001f69a11c425f0e40949447f2581f64126a35137ac12a6061f0f2c2 # # # @@ -444,7 +448,10 @@ NXmicrostructure_gragles_results(NXobject): # # # -# +# +# +# Instances should use microstructure as a name prefix. +# # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml index 843b6fc01f..4f33195586 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml @@ -40,13 +40,13 @@ NXmicrostructure_imm_results(NXobject): exists: optional doc: | Programs and libraries representing the computational environment - programID(NXprogram): - nameType: partial + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] program(NX_CHAR): \@version(NX_CHAR): - microstructureID(NXmicrostructure): - nameType: partial + (NXmicrostructure): + doc: | + Instances should use microstructure as a name prefix. grid(NXcg_grid): extent(NX_UINT): cell_dimensions(NX_NUMBER): @@ -138,7 +138,7 @@ NXmicrostructure_imm_results(NXobject): dim: (c,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 19fd740fcafded7de4d9438988397567a8cd1ebb722f6e297bbb7d4872a782dc +# 316ae1ad842c7e5b9392b1acea052efad08c512898b65c2c344c810f6542bc04 # # # -# +# +# +# Instances should use microstructure as a name prefix. +# # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml index d58042d483..bf1a544aae 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_config.yaml @@ -45,9 +45,8 @@ NXmicrostructure_score_config(NXobject): # exists: optional profiling(NXcs_profiling): exists: optional - userID(NXuser): + (NXuser): exists: ['min', '0', 'max', 'unbounded'] - nameType: partial sample(NXsample): exists: recommended dimensionality(NX_UINT): @@ -79,9 +78,8 @@ NXmicrostructure_score_config(NXobject): exists: recommended doc: | Programs and libraries representing the computational environment - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): material(NXobject): @@ -545,7 +543,7 @@ NXmicrostructure_score_config(NXobject): # dim: (n_su,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# c4a0663856a65ebfd1f17b04a79398b729ef68f2cfab36b6972666bf9cd4edd5 +# d587e07f99eb679ae55bfe0c9fe3e0921584f30cdd22b887e93397a5e0c3e4db # # # # -# +# # # # @@ -694,7 +692,7 @@ NXmicrostructure_score_config(NXobject): # # Programs and libraries representing the computational environment # -# +# # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml index 8bdc1cbfd3..1faecd4e9b 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_score_results.yaml @@ -76,9 +76,8 @@ NXmicrostructure_score_results(NXobject): exists: optional doc: | Programs and libraries representing the computational environment - programID(NXprogram): + (NXprogram): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial program(NX_CHAR): \@version(NX_CHAR): @@ -150,15 +149,17 @@ NXmicrostructure_score_results(NXobject): dimensions: rank: 1 dim: (6,) - spatiotemporalID(NXobject): + SPATIOTEMPORAL(NXobject): + nameType: any exists: ['min', '1', 'max', 'unbounded'] - nameType: partial doc: | Documentation of the spatiotemporal evolution for each CA domain. SCORE is a hybrid parallelized code that can evolve multiple replicas in parallel. The set of replicas is distributed across MPI processes. Each such replica is then evolved via OpenMP multi-threading. + + Instances should use spatiotemporal as a name prefix. # the typical lean summary statistics flattened summary_statistics(NXprocess): @@ -264,9 +265,10 @@ NXmicrostructure_score_results(NXobject): # unit: NX_ANY # dim: (n_summary_stats, 3, 3) # the typically storage-costlier snapshot data - microstructureID(NXmicrostructure): + (NXmicrostructure): exists: ['min', '1', 'max', 'unbounded'] - nameType: partial + doc: | + Instances should use microstructure as a name prefix. time(NX_FLOAT): iteration(NX_UINT): unit: NX_UNITLESS @@ -433,7 +435,7 @@ NXmicrostructure_score_results(NXobject): dim: (n_front,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# fd4d3b95663d21f0ae227939ee471b461200d02d5654ad24a8ca7fdf711d7a0d +# 4b8fb7cabf59f2c78dff65832cee5730d066f37e69d50e6ab7958875ca50e5cd # # # # @@ -814,7 +818,10 @@ NXmicrostructure_score_results(NXobject): # unit: NX_ANY # dim: (n_summary_stats, 3, 3) # the typically storage-costlier snapshot data--> -# +# +# +# Instances should use microstructure as a name prefix. +# # # # From 8cc2cf00db7ad32f8dee7716ae489c9c673594c5 Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Wed, 12 Mar 2025 14:15:02 +0100 Subject: [PATCH 65/75] Fixes on suggestions for instance name prefixes and implementation of FAIRmat-NFDI/project sprintboard issue 104 feedback from NFFA folks --- contributed_definitions/NXapm.nxdl.xml | 13 ++-- .../NXcorrector_cs.nxdl.xml | 4 -- .../NXebeam_column.nxdl.xml | 3 - contributed_definitions/NXem.nxdl.xml | 61 ++++++++++++++++--- contributed_definitions/NXem_ebsd.nxdl.xml | 26 ++------ .../NXevent_data_em.nxdl.xml | 6 ++ .../NXinstrument_em.nxdl.xml | 26 ++++++++ 7 files changed, 93 insertions(+), 46 deletions(-) diff --git a/contributed_definitions/NXapm.nxdl.xml b/contributed_definitions/NXapm.nxdl.xml index 151d340109..33f009f49a 100644 --- a/contributed_definitions/NXapm.nxdl.xml +++ b/contributed_definitions/NXapm.nxdl.xml @@ -243,15 +243,11 @@ the appdef definition here is nothing else then the documentation of this for a used which are then arranged and documented with a description of the workflow so that actionable graphs become instantiatable. - + - A qualifier whether the sample is a real one - or a virtual one (in a computer simulation). + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). - - - - @@ -691,6 +687,9 @@ details can be useful to convey details about an atom probe instrument in genera + + Instances should use event as a name prefix. + This :ref:`NXprocess` group should also be used when one describes in a computer simulation the specific details about the modelled or assumed aberrations. - - Instances should use tableau as a name prefix. @@ -104,8 +102,6 @@ https://doi.org/10.1017/9781316337455.022--> Image(s) taken during the alignment procedure - - Instances should use image as a name prefix. diff --git a/contributed_definitions/NXebeam_column.nxdl.xml b/contributed_definitions/NXebeam_column.nxdl.xml index 96cb2d4af3..ed4eda51a1 100644 --- a/contributed_definitions/NXebeam_column.nxdl.xml +++ b/contributed_definitions/NXebeam_column.nxdl.xml @@ -193,8 +193,6 @@ Electron biprism as it is used e.g. for electron holography. - - Instances should use biprism as a name prefix. @@ -205,7 +203,6 @@ * `M. Malac et al. <https://doi.org/10.1093/jmicro/dfaa070>`_ * `R. R. Schröder et al. <https://www.lem.kit.edu/152.php>`_ - Instances should use phaseplate as a name prefix. diff --git a/contributed_definitions/NXem.nxdl.xml b/contributed_definitions/NXem.nxdl.xml index b03b2f4267..00ae5c1d57 100644 --- a/contributed_definitions/NXem.nxdl.xml +++ b/contributed_definitions/NXem.nxdl.xml @@ -157,6 +157,8 @@ but for practical purposes currently is interpretable only by human to provide t The protection of personal data by laws is in different stages of development and strictness. Therefore, the existence of user data has not been made required. + + Instances should use user as a name prefix. @@ -197,24 +199,47 @@ but for practical purposes currently is interpretable only by human to provide t - + A physical entity which contains material intended to be investigated. Sample and specimen are treated as de facto synonyms. Samples can be real or virtual ones. + There are at least two strategies how to store (meta)data when one analyzes multiple + samples - not different ROIs on a single sample though - in one session. + + One strategy is to store each sample and its results under an own NXem/ENTRY. + This is one of the most frequent use cases as during most sessions typically only a + single sample is investigated. In this case the name of this group should be NXem/ENTRY/sample. + + If multiple samples are investigated storing each of them in an own ENTRY group eventually will + demand an unnecessary duplication though of many details about the instrument. + + This can be avoided by using another strategy how to store all samples and their results. + Namely, by using only one instance of NXem/ENTRY. That NXem/ENTRY should then be named, + like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., + i.e. instances should use sample as a name prefix. + + In this case though the collection of events demands to use Identifier_sample to state clearly + for which of the samples loaded the (characterization) event was detected. + This concept is related to term `Specimen`_ of the EMglossary standard. .. _Specimen: https://purls.helmholtz-metadaten.de/emg/EMG_00000046 - + - Qualifier whether the sample is a real or a virtual one. + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). - - - - + + + + + + + + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others @@ -467,10 +492,15 @@ but for practical purposes currently is interpretable only by human to provide t + + Instances should use detector_reference_frame as a name prefix. + Reference to the specifically named :ref:`NXdetector` instance for which these conventions apply (e.g. /entry1/instrument/detector1). + + Instances should use detector_reference_frame as a name prefix. @@ -551,6 +581,7 @@ hence using optional is sufficient--> + @@ -812,9 +843,12 @@ which components that microscope was built from--> + + Instances should use image as a name prefix. + Each NXimage instance must use only one image or stack instance. @@ -991,6 +1025,7 @@ which components that microscope was built from--> Instances should use spectrum as a name prefix. + Each NXspectrum instance must use only one spectrum or stack instance. @@ -1187,6 +1222,8 @@ which components that microscope was built from--> + + Instances should use tableau as a name prefix. @@ -1314,8 +1351,8 @@ basically optional use of NXaberration therein at least some value required--> - + + Instances should use sensor as a name prefix. @@ -1410,7 +1447,7 @@ phaseplateID(NXcomponent):--> - Instances should use sensor as a name prefix. + Instances should use actuator as a name prefix. @@ -1496,6 +1533,7 @@ is required to provide such information in this way!--> Instances should use image as a name prefix. + Each NXimage instance must use only one image or stack instance. @@ -1549,6 +1587,9 @@ exists: optional--> + + Instances should use phase as a name prefix. + diff --git a/contributed_definitions/NXem_ebsd.nxdl.xml b/contributed_definitions/NXem_ebsd.nxdl.xml index 1fc33c3b62..bf97610fb9 100644 --- a/contributed_definitions/NXem_ebsd.nxdl.xml +++ b/contributed_definitions/NXem_ebsd.nxdl.xml @@ -461,8 +461,6 @@ integer. Start counting from 1 because the value 0 is reserved for the special phase that is the null-model, the null phase also known as notIndexed. - - Instances should use phase as a name prefix. @@ -612,26 +610,10 @@ Number of scan points in the original mapping. - - - Instances should use odf as a name prefix. - - - - - Instances should use pf as a name prefix. - - - - - Instances should use ipf as a name prefix. - - - - - Instances should use microstructure as a name prefix. - - + An overview of the entire ROI. diff --git a/contributed_definitions/NXevent_data_em.nxdl.xml b/contributed_definitions/NXevent_data_em.nxdl.xml index 8153b3ae9e..71cc1f3c1f 100644 --- a/contributed_definitions/NXevent_data_em.nxdl.xml +++ b/contributed_definitions/NXevent_data_em.nxdl.xml @@ -121,6 +121,12 @@ Identifier of a specific state and setting of the microscope. + + + The name of the sample instance under NXem/ENTRY/SAMPLE to resolve + ambiguities that are explained in the docstring of NXem/ENTRY/SAMPLE. + + Which specific event/measurement type. Examples are: diff --git a/contributed_definitions/NXinstrument_em.nxdl.xml b/contributed_definitions/NXinstrument_em.nxdl.xml index f197b981d4..0edb863ea7 100644 --- a/contributed_definitions/NXinstrument_em.nxdl.xml +++ b/contributed_definitions/NXinstrument_em.nxdl.xml @@ -47,6 +47,32 @@ Using GEOREF is preferred. + + + Different types of electron microscopes exist: + + * sem, a scanning electron microscope without focused-ion beam capabilities + * fib, a scanning electron microscope with focused-ion beam capabilities + irrespective whether these were used or not + * tem, a transmission electron microscope + + NXem is one joint data model that can be used to document research that is performed + with several of these types of microscopes (SEM, TEM, or FIB). The NXem data model + stresses that these types of instruments despite having several differences are still all + electron beamlines with which to probe electron and/or ion matter interaction and in fact + in practice have many similarities in how they are used, the components, they contain, etc. + + This field can be used in research data management systems for enabling a categorization + or tagging of experiments without having to analyze if groups like NXibeam_column are present + (which would indicate type is fib) or if certain lens configurations or instrument models are used + which suggests the microscope is a scanning (sem) or transmission electron microscope (tem): + + + + + + + From 565b802ba098923ce08ae58a0d8a27178f98fd1d Mon Sep 17 00:00:00 2001 From: mkuehbach Date: Wed, 12 Mar 2025 14:18:38 +0100 Subject: [PATCH 66/75] Fixes on suggestions for instance name prefixes and implementation of FAIRmat-NFDI/project sprintboard issue 104 feedback from NFFA folks, 2 --- contributed_definitions/NXem.nxdl.xml | 3 +- contributed_definitions/nyaml/NXapm.yaml | 24 ++-- .../nyaml/NXcorrector_cs.yaml | 10 +- .../nyaml/NXebeam_column.yaml | 9 +- contributed_definitions/nyaml/NXem.yaml | 116 +++++++++++++++--- contributed_definitions/nyaml/NXem_ebsd.yaml | 47 ++----- .../nyaml/NXevent_data_em.yaml | 13 +- .../nyaml/NXinstrument_em.yaml | 49 +++++++- 8 files changed, 187 insertions(+), 84 deletions(-) diff --git a/contributed_definitions/NXem.nxdl.xml b/contributed_definitions/NXem.nxdl.xml index 00ae5c1d57..b68c371db1 100644 --- a/contributed_definitions/NXem.nxdl.xml +++ b/contributed_definitions/NXem.nxdl.xml @@ -239,7 +239,7 @@ but for practical purposes currently is interpretable only by human to provide t - + Ideally, (globally) unique persistent identifier which distinguishes this sample from all others @@ -1224,6 +1224,7 @@ which components that microscope was built from--> Instances should use tableau as a name prefix. + diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index 638518824f..a4cf9a9ace 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -194,11 +194,10 @@ NXapm(NXobject): should be stored. For this specific application definitions/schemas can be used which are then arranged and documented with a description of the workflow so that actionable graphs become instantiatable. - type(NX_CHAR): + is_simulation(NX_BOOLEAN): doc: | - A qualifier whether the sample is a real one - or a virtual one (in a computer simulation). - enumeration: [experiment, simulation] + Qualifier whether the sample is a real (in which case is_simulation should be set to false) + or a virtual one (in which case is_simulation should be set to true). alias(NX_CHAR): doc: | Given name/alias for the sample. @@ -617,6 +616,8 @@ NXapm(NXobject): # all these cannot be made required because for LEAP only stored in RHIT/HITS # but for M-TAP and Oxcart these pieces of information are available. + doc: | + Instances should use event as a name prefix. start_time(NX_DATE_TIME): exists: recommended end_time(NX_DATE_TIME): @@ -1226,7 +1227,7 @@ NXapm(NXobject): exists: recommended # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 3ceb4add90d05a69e3d4d93a517ddeacb5d2344c10b7d48eb5bef85592ef701e +# 1a5eed1c671782a246285d32d5eadced8075705615293b93bbce03e06ec7ceed # # # +# +# Instances should use event as a name prefix. +# # # # # # # Instances should use image as a name prefix. +# Each NXimage instance must use only one image or stack instance. # # # @@ -2467,6 +2545,7 @@ NXem(NXobject): # # # Instances should use spectrum as a name prefix. +# Each NXspectrum instance must use only one spectrum or stack instance. # # # @@ -2663,6 +2742,9 @@ NXem(NXobject): # # # +# +# Instances should use tableau as a name prefix. +# # # # @@ -2790,8 +2872,8 @@ NXem(NXobject): # # # -# +# +# # # # Instances should use sensor as a name prefix. @@ -2886,7 +2968,7 @@ NXem(NXobject): # # # -# Instances should use sensor as a name prefix. +# Instances should use actuator as a name prefix. # # # @@ -2972,6 +3054,7 @@ NXem(NXobject): # # # Instances should use image as a name prefix. +# Each NXimage instance must use only one image or stack instance. # # # @@ -3025,6 +3108,9 @@ NXem(NXobject): # # # +# +# Instances should use phase as a name prefix. +# # # # diff --git a/contributed_definitions/nyaml/NXem_ebsd.yaml b/contributed_definitions/nyaml/NXem_ebsd.yaml index df2d48777d..5498673e14 100644 --- a/contributed_definitions/nyaml/NXem_ebsd.yaml +++ b/contributed_definitions/nyaml/NXem_ebsd.yaml @@ -322,8 +322,6 @@ NXem_ebsd(NXprocess): integer. Start counting from 1 because the value 0 is reserved for the special phase that is the null-model, the null phase also known as notIndexed. - - Instances should use phase as a name prefix. dspacing(NX_NUMBER): unit: NX_LENGTH doc: | @@ -451,18 +449,11 @@ NXem_ebsd(NXprocess): unit: NX_UNITLESS doc: | Number of scan points in the original mapping. - (NXmicrostructure_odf): - doc: | - Instances should use odf as a name prefix. - (NXmicrostructure_pf): - doc: | - Instances should use pf as a name prefix. - (NXmicrostructure_ipf): - doc: | - Instances should use ipf as a name prefix. - (NXmicrostructure): - doc: | - Instances should use microstructure as a name prefix. + + # + # + # + # roi(NXdata): doc: | An overview of the entire ROI. @@ -505,7 +496,7 @@ NXem_ebsd(NXprocess): Label for the x axis # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 238aab6674c6ca5419812342c1357b5e52fa0485786dfe514ebc9a8342944e8c +# a306e20b2f387d4d3fcb42935565f404b4681bdc633b821ee0679e2222f22d48 # # # # # # An overview of the entire ROI. diff --git a/contributed_definitions/nyaml/NXevent_data_em.yaml b/contributed_definitions/nyaml/NXevent_data_em.yaml index 3866ed243f..0d43784d92 100644 --- a/contributed_definitions/nyaml/NXevent_data_em.yaml +++ b/contributed_definitions/nyaml/NXevent_data_em.yaml @@ -94,6 +94,11 @@ NXevent_data_em(NXobject): unit: NX_UNITLESS doc: | Identifier of a specific state and setting of the microscope. + identifier_sample(NX_CHAR): + unit: NX_UNITLESS + doc: | + The name of the sample instance under NXem/ENTRY/SAMPLE to resolve + ambiguities that are explained in the docstring of NXem/ENTRY/SAMPLE. type(NX_CHAR): doc: | Which specific event/measurement type. Examples are: @@ -128,7 +133,7 @@ NXevent_data_em(NXobject): (NXspectrum): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 7a369510bf4d0c4450c2d2a5f9f700e275bb60aa8acdec6d175158d8f1ca6dd4 +# d0890b27942320dbf4382853e519c0130d7c43493192ffaebedf553294adf939 # # # +identifier_pulse_offset(NX_INT): +identifier_pulse(NX_INT):--> @@ -917,7 +917,7 @@ we can only make recommendations--> CRunHeader.fTotalEventRecords - + Identifier used for each hit_quality type. Following the order of hit_quality_types. @@ -929,7 +929,7 @@ we can only make recommendations--> Hit quality identifier for each pulse. - Identifier have to be within hit_quality_identifier. + Identifier have to be within identifier_hit_quality. @@ -954,7 +954,7 @@ insight into the results of the hit_finding algorithm of IVAS/APSuite but typica used only in the context to learn about the multiplicity of an ion. pulses_since_last_ion(NX_UINT): dim: (n,) -pulse_identifier(NX_INT): +identifier_pulse(NX_INT): dim: (n,) at this point the original set of events p has been filtered down to p_out--> @@ -970,10 +970,10 @@ at this point the original set of events p has been filtered down to p_out--> - + Integer used to name the first pulse to know if there is an - offset of the evaporation_identifier to zero. + offset of the identifier_evaporation to zero. Identifiers can be defined either implicitly or explicitly. For implicit indexing identifiers are defined on the interval @@ -988,7 +988,7 @@ at this point the original set of events p has been filtered down to p_out--> identifier conventions where identifier_offset is 1 and 0 respectively. - + (Molecular) ion identifier which resolves the sequence in which the ions were evaporated but taking into account that a hit_finding diff --git a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml index 4606504c46..c0ba399936 100644 --- a/contributed_definitions/NXapm_compositionspace_config.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_config.nxdl.xml @@ -40,7 +40,7 @@ - + Specification of the tomographic reconstruction used for this analysis. diff --git a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml index 0903e0be49..f43bceab3c 100644 --- a/contributed_definitions/NXapm_compositionspace_results.nxdl.xml +++ b/contributed_definitions/NXapm_compositionspace_results.nxdl.xml @@ -66,7 +66,7 @@ for if desired all the dependencies and libraries--> - + @@ -103,7 +103,7 @@ for if desired all the dependencies and libraries--> The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by parent_identifier or walk through + these from the resources pointed to by identifier_parent or walk through eventually deeply nested groups in data instances. @@ -170,7 +170,7 @@ for if desired all the dependencies and libraries--> - + For each ion, the identifier of the voxel into which the ion binned. @@ -218,9 +218,9 @@ for if desired all the dependencies and libraries--> - + - + Element identifier stored sorted in descending order of feature importance. @@ -267,7 +267,7 @@ for if desired all the dependencies and libraries--> - + @@ -324,7 +324,7 @@ for if desired all the dependencies and libraries--> - + diff --git a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml index 6d404186b3..e2e4349c72 100644 --- a/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_clusterer_results.nxdl.xml @@ -52,7 +52,7 @@ - + @@ -104,7 +104,7 @@ - The evaporation (sequence) identifier (aka evaporation_id) to figure out + The evaporation (sequence) identifier (aka identifier_evaporation) to figure out which ions from the reconstruction were considered targets. The length of this array is not necessarily n_ions. Instead, it is the value of cardinality. @@ -233,9 +233,9 @@ number_of_objects(NX_UINT): - + - Numerical identifier of each feature aka cluster_identifier. + Numerical identifier of each feature aka identifier_cluster. diff --git a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml index a06b2df341..8a5cc44108 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_config.nxdl.xml @@ -40,7 +40,7 @@ - + @@ -172,7 +172,7 @@ of facet normal vectors for the triangles in that triangle_set. - + Absolute path in the (HDF5) file that points to the array of identifier for the triangles in that triangle_set. diff --git a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml index ace93ed6ea..163adca0de 100644 --- a/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_distancer_results.nxdl.xml @@ -83,7 +83,7 @@ - + For each point the identifier of the triangle for which the shortest distance was found @@ -92,7 +92,7 @@ - + A support field to enable the visualization of each point by an explicit identifier on the interval [0, n_ions - 1]. diff --git a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml index e83146579d..eab135ce31 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_config.nxdl.xml @@ -130,7 +130,7 @@ to members of the current_set. The meshes were generated as a result of some other meshing process. - + This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k`) step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -182,7 +182,7 @@ - + Array of identifier whereby the path to the geometry data can be interferred automatically. @@ -200,7 +200,7 @@ to members of the next_set. The meshes were generated as a result of some other meshing process. - + This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -247,7 +247,7 @@ - + Array of identifier whereby the path to the geometry data can be interferred automatically. diff --git a/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml index 4dc6b443e5..a80b3dceb2 100644 --- a/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_intersector_results.nxdl.xml @@ -77,7 +77,7 @@ - A matrix of feature_identifier that specifies which named features + A matrix of identifier_feature that specifies which named features from the current_set have directed link(s) pointing to which named feature(s) from the next_set. @@ -98,7 +98,7 @@ - A matrix of feature_identifier which specifies which named feature(s) + A matrix of identifier_feature which specifies which named feature(s) from the next_set have directed link(s) pointing to which named feature(s) from the current_set. Only if the mapping whereby the links are defined is symmetric it holds that next_to_current maps @@ -140,7 +140,7 @@ The third comparison is the current_set against the next_set. Once the (forward) links for these comparisons are ready, pair relations - are analyzed with respect to which objects with feature_identifier(s) + are analyzed with respect to which objects with identifier_feature cluster in identifier space. Thereby, a logical connection (link) is established between the features in the current_set and the next_set. Recall that these two sets typically represent different features @@ -158,8 +158,8 @@ - Matrix of feature_identifier and cluster_identifier pairs which - encodes the cluster to which each feature_identifier was assigned. + Matrix of identifier_feature and identifier_cluster pairs which + encodes the cluster to which each identifier_feature was assigned. Here for features of the current_set. @@ -169,8 +169,8 @@ - Matrix of feature_identifier and cluster_identifier pairs which - encodes the cluster to which each feature_identifier was assigned. + Matrix of identifier_feature and identifier_cluster pairs which + encodes the cluster to which each identifier_feature was assigned. Here for features of the next_set. @@ -178,7 +178,7 @@ - + The identifier (names) of the cluster. @@ -221,7 +221,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml index 59c2b048cf..473589e9b5 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_config.nxdl.xml @@ -96,7 +96,7 @@ - + @@ -591,7 +591,7 @@ NEW ISSUE: here we need to specify how the meshes were smoothened--> paraprobe-nanochem uses inspection functionalities which detect potential geometric inconsistencies or self-interactions of the evolved DCOM mesh. - + @@ -819,7 +819,7 @@ identifier(NX_UINT):--> intersection of triangles and convex polyhedra is a robust but currently not implemented method to quantify intersections. - + diff --git a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml index 64340f6eab..7c9e874cbb 100644 --- a/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_nanochem_results.nxdl.xml @@ -542,8 +542,8 @@ The cardinality/total number of triangles in the triangle soup.--> - - + + Positions of the vertices. @@ -733,7 +733,7 @@ The cardinality/total number of triangles in the triangle soup.--> In the second step, the tool can be used to analyze the proximity of these objects to a model of the surface (edge) of the dataset. - + The identifier which the triangle_soup connectivity analysis returned, which constitutes the first step of the @@ -771,7 +771,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + The explicit identifier of features. @@ -792,9 +792,9 @@ The cardinality/total number of triangles in the triangle soup.--> * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface - + - Explicit identifier of the feature a sub-set of the feature_identifier in the + Explicit identifier of the feature a sub-set of the identifier_feature in the parent group. @@ -861,7 +861,7 @@ The cardinality/total number of triangles in the triangle soup.--> - + @@ -875,8 +875,8 @@ The cardinality/total number of triangles in the triangle soup.--> +identifier_vertex_offset(NX_UINT): +identifier_face_offset(NX_UINT):--> @@ -900,14 +900,14 @@ face_identifier_offset(NX_UINT):--> - + - + - Array of evaporation_identifier / ion_identifier which details which ions + Array of identifier_evaporation / identifier_ion which details which ions lie inside or on the surface of the feature. @@ -1018,10 +1018,10 @@ face_identifier_offset(NX_UINT):--> - - - - + + + + @@ -1226,7 +1226,7 @@ face_identifier_offset(NX_UINT):--> - + diff --git a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml index 33db02554d..ecd4b50fc9 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_config.nxdl.xml @@ -52,7 +52,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml index 4541a10c0c..886e895ccb 100644 --- a/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_ranger_results.nxdl.xml @@ -86,7 +86,7 @@ config--> - + diff --git a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml index 84881bbb73..3a051b91ee 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_config.nxdl.xml @@ -40,7 +40,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml index e2de46f175..faf31fa38a 100644 --- a/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_selector_results.nxdl.xml @@ -58,7 +58,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml index 3fb8432fa9..09b5fccdf6 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_config.nxdl.xml @@ -64,7 +64,7 @@ Instances should use spatial_statistics as a name prefix. - + diff --git a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml index a29a6f8f47..e1e315dd36 100644 --- a/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_spatstat_results.nxdl.xml @@ -150,7 +150,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml index 4c5e9a8913..0a46542c87 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_config.nxdl.xml @@ -50,7 +50,7 @@ - + diff --git a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml index 40b7c46059..eca920007c 100644 --- a/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_surfacer_results.nxdl.xml @@ -162,8 +162,8 @@ for eventually performed preprocessing--> - - + + @@ -213,8 +213,8 @@ for eventually performed preprocessing--> - - + + @@ -239,7 +239,7 @@ for eventually performed preprocessing--> For the future as we may wish to wrap primitives other like triangles or polylines.--> - + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml index 1ea99712ab..bebe5dc886 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_config.nxdl.xml @@ -41,7 +41,7 @@ if windowing_method is bitmasked_points: sum cardinality of NXcg := 0 and cardin - + diff --git a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml index 97346f87f7..528a1b43c5 100644 --- a/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tessellator_results.nxdl.xml @@ -115,7 +115,7 @@ - + Which MPI process computed which Voronoi cell. @@ -123,7 +123,7 @@ - + Which OpenMP thread computed which Voronoi cell. @@ -149,8 +149,8 @@ - - + + @@ -159,14 +159,14 @@ Each tuple contains encodes information to visualize using XDMF: Firstly, an XDMF geometric primitive type key. Secondly, the number of vertices of the polygon. - Third, the sequence of vertex identifier which define the facet. + Third, the sequence of identifier_vertex which define the facet. Tuples encode faces faster than cells. - + Sequence of cell identifier, concatenated such that each face is associated with its cell. Given that paraprobe-tessellator assigns @@ -284,7 +284,7 @@ dim: (i,) # one would not need to constrain this but doing so communicates that - + diff --git a/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml b/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml index c63dd724bd..c70b7b9d35 100644 --- a/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_tool_common.nxdl.xml @@ -60,7 +60,7 @@ - + Internal identifier used by the tool to refer to an analysis (aka simulation id). diff --git a/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml b/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml index d23fa1aa9f..768c6d8e55 100644 --- a/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_transcoder_config.nxdl.xml @@ -43,7 +43,7 @@ official NeXus appdef headers--> - + diff --git a/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml b/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml index bca457bd2e..6cb0917fa8 100644 --- a/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml +++ b/contributed_definitions/NXapm_paraprobe_transcoder_results.nxdl.xml @@ -86,7 +86,7 @@ i be careful n_comb can vary for every instance of (NXion) !--> - + @@ -166,7 +166,7 @@ config--> - + diff --git a/contributed_definitions/NXapm_reconstruction.nxdl.xml b/contributed_definitions/NXapm_reconstruction.nxdl.xml index 9684d236f6..be767e5b52 100644 --- a/contributed_definitions/NXapm_reconstruction.nxdl.xml +++ b/contributed_definitions/NXapm_reconstruction.nxdl.xml @@ -31,7 +31,7 @@ Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process - the so-called - evaporation_identifier, which must not be confused with the pulse_identifier! + identifier_evaporation, which must not be confused with the identifier_pulse! diff --git a/contributed_definitions/NXem.nxdl.xml b/contributed_definitions/NXem.nxdl.xml index 690462c231..89bd8a6758 100644 --- a/contributed_definitions/NXem.nxdl.xml +++ b/contributed_definitions/NXem.nxdl.xml @@ -219,7 +219,7 @@ but for practical purposes currently is interpretable only by human to provide t like in the previous case, NXem/entry1 and the samples should be named sample1, sample2, etc., i.e. instances should use sample as a name prefix. - In this case though the collection of events demands to use Identifier_sample to state clearly + In this case though the collection of events demands to use identifier_sample to state clearly for which of the samples loaded the (characterization) event was detected. This concept is related to term `Specimen`_ of the EMglossary standard. diff --git a/contributed_definitions/NXem_calorimetry.nxdl.xml b/contributed_definitions/NXem_calorimetry.nxdl.xml index f8beae804f..3c83374f66 100644 --- a/contributed_definitions/NXem_calorimetry.nxdl.xml +++ b/contributed_definitions/NXem_calorimetry.nxdl.xml @@ -112,7 +112,7 @@ are aligned with what and how to name things--> The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by parent_identifier or walk through + these from the resources pointed to by identifier_parent or walk through eventually deeply nested groups in data instances. @@ -239,7 +239,7 @@ NXcg_ellipsoid--> - + The integrated intensities: @@ -248,7 +248,7 @@ NXcg_ellipsoid--> - + diff --git a/contributed_definitions/NXevent_data_apm.nxdl.xml b/contributed_definitions/NXevent_data_apm.nxdl.xml index ebc732bf51..4b178fe42a 100644 --- a/contributed_definitions/NXevent_data_apm.nxdl.xml +++ b/contributed_definitions/NXevent_data_apm.nxdl.xml @@ -41,7 +41,7 @@ of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication of information. Specifically, the time interval considered is the entire time starting at start_time until end_time during which we assume the pulser triggered named pulses. - These pulses are identified via the pulse_identifier field. The point in time when each was issued + These pulses are identified via the identifier_pulse field. The point in time when each was issued is specified via the combination of start_time and delta_time. Conceptually and technically NeXus currently stores tensorial information as arrays of values @@ -64,10 +64,10 @@ However, there is no independent logical connection between these two concepts, i.e. temperature and time_stamp. - In the case of atom probe though the time that one would use in NXlog is defined implicitly via pulse_identifier, + In the case of atom probe though the time that one would use in NXlog is defined implicitly via identifier_pulse, which is the independent variable vector against which eventually dozens of channels of data are logged. Not only are these channels logged they should ideally also be self-descriptive in that these channels have - pulse_identifier as the independent variable but we do not wish to duplicate this information all the time but + identifier_pulse as the independent variable but we do not wish to duplicate this information all the time but reference it. Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the @@ -95,18 +95,18 @@ - Delta time array which resolves for each pulse_identifier the time difference + Delta time array which resolves for each identifier_pulse the time difference between when that pulse was issued and start_time. - In summary, using start_time, end_time, delta_time, pulse_identifier_offset, - and pulse_identifier exactly specifies the connection between when a pulse was + In summary, using start_time, end_time, delta_time, identifier_pulse_offset, + and identifier_pulse exactly specifies the connection between when a pulse was issued relative to start and absolute in UTC. - + Integer used to name the first pulse to know if there is an offset of the identifiers to zero. @@ -124,12 +124,12 @@ identifier conventions where identifier_offset is 1 and 0 respectively. - + Identifier that contextualizes how the detector and pulser of an atom probe instrument follows a sequence of pulses to trigger field evaporation. - The pulse_identifier is used to associate thus an information about time + The identifier_pulse is used to associate thus an information about time when quantities have been collected via sampling. In virtually all cases the pulser is a blackbox. Depending on how the @@ -138,17 +138,17 @@ Maybe the first part of the experiment is run at a certain pulse fraction but thereafter the pulse_fraction is changed. In this case the field pulse_fraction is a vector which - collects all measured values of the pulse_fraction, pulse_identifier is then an equally + collects all measured values of the pulse_fraction, identifier_pulse is then an equally long vector which stores the set of events (e.g. pulsing events) when that value was measured. This may cause several situations: In the case that e.g. the pulse_fraction is never changed and also exact details not interesting, one stores the set value for the pulse_fraction - and a single value for the pulse_identifier e.g. 0 to indicate that the pulse_fraction was set + and a single value for the identifier_pulse e.g. 0 to indicate that the pulse_fraction was set at the beginning and it was maintained constant during the measurement. If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a vector with two values one for the first and another one for the value from the 100000-th - pulse onwards. The values of pulse_identifier are then [0, 99999] respectively. + pulse onwards. The values of identifier_pulse are then [0, 99999] respectively. diff --git a/contributed_definitions/NXinstrument_apm.nxdl.xml b/contributed_definitions/NXinstrument_apm.nxdl.xml index c603dc137f..b1fcff6fc6 100644 --- a/contributed_definitions/NXinstrument_apm.nxdl.xml +++ b/contributed_definitions/NXinstrument_apm.nxdl.xml @@ -199,7 +199,7 @@ case very efficiently we go for with an array of length 1xn_ions - Path to pulse_identifier + Path to identifier_pulse @@ -214,7 +214,7 @@ case very efficiently we go for with an array of length 1xn_ions - Path to pulse_identifier + Path to identifier_pulse @@ -229,7 +229,7 @@ existence constraint is independent of other values. - Path to pulse_identifier + Path to identifier_pulse @@ -239,11 +239,11 @@ existence constraint is independent of other values. - Path to pulse_identifier + Path to identifier_pulse - + Direct current voltage between the specimen and the (local electrode) in @@ -252,7 +252,7 @@ existence constraint is independent of other values. - Path to pulse_identifier + Path to identifier_pulse @@ -278,7 +278,7 @@ existence constraint is independent of other values. - Path to pulse_identifier + Path to identifier_pulse @@ -295,7 +295,7 @@ existence constraint is independent of other values. - Path to pulse_identifier + Path to identifier_pulse @@ -306,7 +306,7 @@ existence constraint is independent of other values. - Path to pulse_identifier + Path to identifier_pulse @@ -317,7 +317,7 @@ existence constraint is independent of other values. - Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. + Path to identifier_pulse in an instance of :ref:`NXevent_data_apm`. diff --git a/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml b/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml index be11ae1f28..c136f1ca58 100644 --- a/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_gragles_config.nxdl.xml @@ -43,7 +43,7 @@ type: group--> - + Simulation ID as an alias to refer to this simulation. diff --git a/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml b/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml index 43c0a9c933..f5aba4d74f 100644 --- a/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_gragles_results.nxdl.xml @@ -52,7 +52,7 @@ - + Simulation ID as an alias to refer to this simulation. @@ -242,14 +242,14 @@ the typical lean summary statistics flattened--> - - + + - - + + @@ -269,9 +269,9 @@ the typical lean summary statistics flattened--> - + - Set of pairs of crystal_identifier for each interface. + Set of pairs of identifier_crystal for each interface. diff --git a/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml b/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml index 7c28ed349e..0a86b2844a 100644 --- a/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_imm_results.nxdl.xml @@ -93,7 +93,7 @@ - + Crystal identifier that was assigned to each material point. @@ -143,7 +143,7 @@ - + diff --git a/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml b/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml index f51ee059f3..435bcbab66 100644 --- a/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml @@ -109,7 +109,7 @@ - + Crystal identifier that was assigned to each material point. @@ -161,12 +161,12 @@ - + - + diff --git a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml index f7bf858ce7..dbe1a82eab 100644 --- a/contributed_definitions/NXmicrostructure_score_config.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_config.nxdl.xml @@ -129,7 +129,7 @@ The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret - these from the resources pointed to by parent_identifier or walk through + these from the resources pointed to by identifier_parent or walk through eventually deeply nested groups in data instances. diff --git a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml index 42dcd67051..363b18d05a 100644 --- a/contributed_definitions/NXmicrostructure_score_results.nxdl.xml +++ b/contributed_definitions/NXmicrostructure_score_results.nxdl.xml @@ -434,13 +434,13 @@ the typically storage-costlier snapshot data--> - + - + diff --git a/contributed_definitions/NXsimilarity_grouping.nxdl.xml b/contributed_definitions/NXsimilarity_grouping.nxdl.xml index 44fadc5fc3..6d0fc9e7b7 100644 --- a/contributed_definitions/NXsimilarity_grouping.nxdl.xml +++ b/contributed_definitions/NXsimilarity_grouping.nxdl.xml @@ -97,7 +97,7 @@ results for the object set--> Matrix of numerical label for each member in the set. For classical clustering algorithms this can for instance - encode the cluster_identifier. + encode the identifier_cluster. diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index a4cf9a9ace..6fa224eb26 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -22,8 +22,8 @@ symbols: Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process (the so-called - evaporation_identifier). This identifier must not be confused with - the pulse_identifier. Typically smaller than both p_out and p_out. + identifier_evaporation). This identifier must not be confused with + the identifier_pulse. Typically smaller than both p_out and p_out. type: group NXapm(NXobject): (NXentry): @@ -488,7 +488,7 @@ NXapm(NXobject): Due to this practical inaccessibility of details, virtually all atom probe studies currently use a reporting scheme where the course of the specimen evaporation is documented such that quantities are a function of evaporation identifier i.e. actual event/ion, i.e. after having the hit finding algorithm and correlations applied. - That is evaporation_identifier values take the role of an implicit time and course of the experiment given that + That is identifier_evaporation values take the role of an implicit time and course of the experiment given that ion extraction physically is a sequential process. There is a number of research groups who build own instruments and share different aspects of their technical @@ -609,8 +609,8 @@ NXapm(NXobject): As set and measured quantities typically change over time and we do not yet know during the measurement which of the events have associated (molecular) ions that will end up in the reconstructed volume, we must not - document quantities as a function of the evaporated_identifier but as a - function of the (pulsing) event_identifier. + document quantities as a function of the identifier_evaporation but as a + function of the (pulsing) identifier_event. (NXevent_data_apm): exists: ['min', '0', 'max', 'unbounded'] @@ -624,8 +624,8 @@ NXapm(NXobject): exists: recommended # delta_time(NX_NUMBER): - # pulse_identifier_offset(NX_INT): - # pulse_identifier(NX_INT): + # identifier_pulse_offset(NX_INT): + # identifier_pulse(NX_INT): instrument(NXinstrument_apm): exists: recommended reflectron(NXcomponent): @@ -840,7 +840,7 @@ NXapm(NXobject): unit: NX_UNITLESS doc: | CRunHeader.fTotalEventRecords - hit_quality_identifier(NX_UINT): + identifier_hit_quality(NX_UINT): exists: optional doc: | Identifier used for each hit_quality type. @@ -853,7 +853,7 @@ NXapm(NXobject): unit: NX_UNITLESS doc: | Hit quality identifier for each pulse. - Identifier have to be within hit_quality_identifier. + Identifier have to be within identifier_hit_quality. dimensions: rank: 1 dim: (p_out,) @@ -876,7 +876,7 @@ NXapm(NXobject): # used only in the context to learn about the multiplicity of an ion. # pulses_since_last_ion(NX_UINT): # dim: (n,) - # pulse_identifier(NX_INT): + # identifier_pulse(NX_INT): # dim: (n,) # at this point the original set of events p has been filtered down to p_out hit_spatial_filtering(NXprocess): @@ -893,11 +893,11 @@ NXapm(NXobject): file_name(NX_CHAR): checksum(NX_CHAR): algorithm(NX_CHAR): - evaporation_identifier_offset(NX_INT): + identifier_evaporation_offset(NX_INT): unit: NX_UNITLESS doc: | Integer used to name the first pulse to know if there is an - offset of the evaporation_identifier to zero. + offset of the identifier_evaporation to zero. Identifiers can be defined either implicitly or explicitly. For implicit indexing identifiers are defined on the interval @@ -910,7 +910,7 @@ NXapm(NXobject): For explicit indexing the field identifier has to be used. Fortran-/Matlab- and C-/Python-style indexing have specific implicit identifier conventions where identifier_offset is 1 and 0 respectively. - evaporation_identifier(NX_INT): + identifier_evaporation(NX_INT): unit: NX_UNITLESS doc: | (Molecular) ion identifier which resolves the sequence in which @@ -1227,7 +1227,7 @@ NXapm(NXobject): exists: recommended # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1a5eed1c671782a246285d32d5eadced8075705615293b93bbce03e06ec7ceed +# ea95931604f7fd8d02d94b8e233eb76e10f9283e09a3e3c30d0e76e35eb9f596 # # # +# identifier_pulse_offset(NX_INT): +# identifier_pulse(NX_INT):--> # # # @@ -2147,7 +2147,7 @@ NXapm(NXobject): # CRunHeader.fTotalEventRecords # # -# +# # # Identifier used for each hit_quality type. # Following the order of hit_quality_types. @@ -2159,7 +2159,7 @@ NXapm(NXobject): # # # Hit quality identifier for each pulse. -# Identifier have to be within hit_quality_identifier. +# Identifier have to be within identifier_hit_quality. # # # @@ -2184,7 +2184,7 @@ NXapm(NXobject): # used only in the context to learn about the multiplicity of an ion. # pulses_since_last_ion(NX_UINT): # dim: (n,) -# pulse_identifier(NX_INT): +# identifier_pulse(NX_INT): # dim: (n,) # at this point the original set of events p has been filtered down to p_out--> # @@ -2200,10 +2200,10 @@ NXapm(NXobject): # # # -# +# # # Integer used to name the first pulse to know if there is an -# offset of the evaporation_identifier to zero. +# offset of the identifier_evaporation to zero. # # Identifiers can be defined either implicitly or explicitly. # For implicit indexing identifiers are defined on the interval @@ -2218,7 +2218,7 @@ NXapm(NXobject): # identifier conventions where identifier_offset is 1 and 0 respectively. # # -# +# # # (Molecular) ion identifier which resolves the sequence in which # the ions were evaporated but taking into account that a hit_finding diff --git a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml index 484e3ff444..d3ad030574 100644 --- a/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml +++ b/contributed_definitions/nyaml/NXapm_compositionspace_config.yaml @@ -18,7 +18,7 @@ NXapm_compositionspace_config(NXobject): exists: optional enumeration: [NXapm_compositionspace_config] config(NXobject): - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): doc: | @@ -140,7 +140,7 @@ NXapm_compositionspace_config(NXobject): point. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 623bd6a3b2568a3ea7bf90037355ddaecaa7db85328656949f09b55ee55b5e52 +# d8fb792f4fa4fac316f3d1ed161c5e2341137cbcc43e40bd34938ca11166a85c # # # # # @@ -416,7 +419,7 @@ NXapm_compositionspace_results(NXobject): # # The purpose of the field is to offer research data management systems an # opportunity to parse the relevant elements without having to interpret -# these from the resources pointed to by parent_identifier or walk through +# these from the resources pointed to by identifier_parent or walk through # eventually deeply nested groups in data instances. # # @@ -483,7 +486,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # For each ion, the identifier of the voxel into which the ion binned. # @@ -531,9 +534,9 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # -# +# # # Element identifier stored sorted in descending order of feature importance. # @@ -580,7 +583,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # # @@ -637,7 +640,7 @@ NXapm_compositionspace_results(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml index 3299fae4da..d9f46e7df3 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_clusterer_results.yaml @@ -24,7 +24,7 @@ NXapm_paraprobe_clusterer_results(NXobject): CLUSTER_ANALYSIS(NXapm_paraprobe_tool_results): nameType: any exists: ['min', '0', 'max', 'unbounded'] - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): config(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -71,7 +71,7 @@ NXapm_paraprobe_clusterer_results(NXobject): targets(NX_UINT): unit: NX_UNITLESS doc: | - The evaporation (sequence) identifier (aka evaporation_id) to figure out + The evaporation (sequence) identifier (aka identifier_evaporation) to figure out which ions from the reconstruction were considered targets. The length of this array is not necessarily n_ions. Instead, it is the value of cardinality. @@ -190,10 +190,10 @@ NXapm_paraprobe_clusterer_results(NXobject): Total number of clusters (excluding noise and unassigned). # at the level of the feature set - feature_identifier(NX_UINT): + identifier_feature(NX_UINT): unit: NX_UNITLESS doc: | - Numerical identifier of each feature aka cluster_identifier. + Numerical identifier of each feature aka identifier_cluster. dimensions: rank: 1 dim: (n_feat,) @@ -248,7 +248,7 @@ NXapm_paraprobe_clusterer_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4841685dac72e665630b7050f552941c1171caa20b914cb92db5d56e88d296e2 +# 0f3236fc7f667546b711f80a9e964b3f8ada5ef723619dde316e539efd4fabdb # # # # # -# +# # # # @@ -355,7 +355,7 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# The evaporation (sequence) identifier (aka evaporation_id) to figure out +# The evaporation (sequence) identifier (aka identifier_evaporation) to figure out # which ions from the reconstruction were considered targets. The length # of this array is not necessarily n_ions. # Instead, it is the value of cardinality. @@ -484,9 +484,9 @@ NXapm_paraprobe_clusterer_results(NXobject): # # # -# +# # -# Numerical identifier of each feature aka cluster_identifier. +# Numerical identifier of each feature aka identifier_cluster. # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml index 2ded5e881a..4b7d52752d 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_distancer_config.yaml @@ -15,7 +15,7 @@ NXapm_paraprobe_distancer_config(NXobject): enumeration: [NXapm_paraprobe_distancer_config] point_to_triangle(NXapm_paraprobe_tool_config): exists: ['min', '1', 'max', '1'] - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): type(NX_CHAR): @@ -139,7 +139,7 @@ NXapm_paraprobe_distancer_config(NXobject): doc: | Absolute path in the (HDF5) file that points to the array of facet normal vectors for the triangles in that triangle_set. - patch_identifier(NX_CHAR): + identifier_patch(NX_CHAR): exists: optional doc: | Absolute path in the (HDF5) file that points to the array @@ -164,7 +164,7 @@ NXapm_paraprobe_distancer_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 4c7babceac573608f33c67c2f3d4f42e2e4e254374ca25c46e9431d91bd3f8a6 +# 156d418f0810f31078f74822927ab70cbc2bbc8b2d0bf91bb2d29c2a0eb828af # # # -# +# # # Array of identifier whereby the path to the geometry data can be interferred # automatically. @@ -410,7 +410,7 @@ NXapm_paraprobe_intersector_config(NXobject): # to members of the next_set. # The meshes were generated as a result of some other meshing process. # -# +# # # This identifier can be used to label the current set. The label effectively can be interpreted as the time/iteration (i.e. :math:`k + 1`) # step when the current set was taken (see `M. Kühbach et al. 2022 <https://arxiv.org/abs/2205.13510>`_). @@ -457,7 +457,7 @@ NXapm_paraprobe_intersector_config(NXobject): # # # -# +# # # Array of identifier whereby the path to the geometry data can be interferred # automatically. diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml index 3d28cf5c24..33f3a53e62 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_intersector_results.yaml @@ -36,7 +36,7 @@ NXapm_paraprobe_intersector_results(NXobject): current_to_next_link(NX_UINT): unit: NX_UNITLESS doc: | - A matrix of feature_identifier that specifies which named features + A matrix of identifier_feature that specifies which named features from the current_set have directed link(s) pointing to which named feature(s) from the next_set. dimensions: @@ -55,7 +55,7 @@ NXapm_paraprobe_intersector_results(NXobject): exists: optional unit: NX_UNITLESS doc: | - A matrix of feature_identifier which specifies which named feature(s) + A matrix of identifier_feature which specifies which named feature(s) from the next_set have directed link(s) pointing to which named feature(s) from the current_set. Only if the mapping whereby the links are defined is symmetric it holds that next_to_current maps @@ -95,7 +95,7 @@ NXapm_paraprobe_intersector_results(NXobject): The third comparison is the current_set against the next_set. Once the (forward) links for these comparisons are ready, pair relations - are analyzed with respect to which objects with feature_identifier(s) + are analyzed with respect to which objects with identifier_feature cluster in identifier space. Thereby, a logical connection (link) is established between the features in the current_set and the next_set. Recall that these two sets typically represent different features @@ -113,8 +113,8 @@ NXapm_paraprobe_intersector_results(NXobject): current_set_feature_to_cluster(NX_UINT): unit: NX_UNITLESS doc: | - Matrix of feature_identifier and cluster_identifier pairs which - encodes the cluster to which each feature_identifier was assigned. + Matrix of identifier_feature and identifier_cluster pairs which + encodes the cluster to which each identifier_feature was assigned. Here for features of the current_set. dimensions: rank: 2 @@ -122,13 +122,13 @@ NXapm_paraprobe_intersector_results(NXobject): next_set_feature_to_cluster(NX_UINT): unit: NX_UNITLESS doc: | - Matrix of feature_identifier and cluster_identifier pairs which - encodes the cluster to which each feature_identifier was assigned. + Matrix of identifier_feature and identifier_cluster pairs which + encodes the cluster to which each identifier_feature was assigned. Here for features of the next_set. dimensions: rank: 2 dim: (n_features_next, 2) - cluster_identifier(NX_UINT): + identifier_cluster(NX_UINT): unit: NX_UNITLESS doc: | The identifier (names) of the cluster. @@ -164,7 +164,7 @@ NXapm_paraprobe_intersector_results(NXobject): dim: (n_total, 2) common(NXapm_paraprobe_tool_common): status(NX_CHAR): - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): config(NXnote): type(NX_CHAR): partial(NX_CHAR): @@ -210,7 +210,7 @@ NXapm_paraprobe_intersector_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 715798427e25dc3b2d25575487d010a02cfa4eca11ec6fe6dbfae5f7605ddfcb +# 864141639716a4c2acdf4ab5b1c6d6316829e0343823195ab42dd4d507fe1071 # # # # # -# A matrix of feature_identifier that specifies which named features +# A matrix of identifier_feature that specifies which named features # from the current_set have directed link(s) pointing to which named # feature(s) from the next_set. # @@ -311,7 +311,7 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# A matrix of feature_identifier which specifies which named feature(s) +# A matrix of identifier_feature which specifies which named feature(s) # from the next_set have directed link(s) pointing to which named # feature(s) from the current_set. Only if the mapping whereby the # links are defined is symmetric it holds that next_to_current maps @@ -353,7 +353,7 @@ NXapm_paraprobe_intersector_results(NXobject): # The third comparison is the current_set against the next_set. # # Once the (forward) links for these comparisons are ready, pair relations -# are analyzed with respect to which objects with feature_identifier(s) +# are analyzed with respect to which objects with identifier_feature # cluster in identifier space. Thereby, a logical connection (link) is # established between the features in the current_set and the next_set. # Recall that these two sets typically represent different features @@ -371,8 +371,8 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# Matrix of feature_identifier and cluster_identifier pairs which -# encodes the cluster to which each feature_identifier was assigned. +# Matrix of identifier_feature and identifier_cluster pairs which +# encodes the cluster to which each identifier_feature was assigned. # Here for features of the current_set. # # @@ -382,8 +382,8 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# Matrix of feature_identifier and cluster_identifier pairs which -# encodes the cluster to which each feature_identifier was assigned. +# Matrix of identifier_feature and identifier_cluster pairs which +# encodes the cluster to which each identifier_feature was assigned. # Here for features of the next_set. # # @@ -391,7 +391,7 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# +# # # The identifier (names) of the cluster. # @@ -434,7 +434,7 @@ NXapm_paraprobe_intersector_results(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml index 53096a6c22..0f77497ebe 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_config.yaml @@ -47,7 +47,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # Although, this uses an efficient multithreaded algorithm the computation is costly. # Therefore, it can be advantageous for users to load an already computed delocalization. # This can be achieved with the load_existent option. - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): type(NX_CHAR): @@ -462,7 +462,7 @@ NXapm_paraprobe_nanochem_config(NXobject): Noteworthy to mention is that the method used is conceptually similar to the work of `Z. Peng et al. `_ and related work (DCOM algorithm) by `P. Felfer et al. `_. Compared to these implementations paraprobe-nanochem uses inspection functionalities which detect potential geometric inconsistencies or self-interactions of the evolved DCOM mesh. - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): type(NX_CHAR): @@ -657,7 +657,7 @@ NXapm_paraprobe_nanochem_config(NXobject): even watertight distance-based segmentation in combination with again intersection of triangles and convex polyhedra is a robust but currently not implemented method to quantify intersections. - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): type(NX_CHAR): @@ -865,7 +865,7 @@ NXapm_paraprobe_nanochem_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 0a2866256dd2cf6449d9f867f3dab248bf04ea3c35d46998aaa006acf9945b74 +# cd80ce8e5faaa2d0bbaf0ca20b6559d5af2c8be52bdd0a8ada3c489057c225a9 # # # -# +# # # # @@ -1459,7 +1459,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # paraprobe-nanochem uses inspection functionalities which detect potential geometric # inconsistencies or self-interactions of the evolved DCOM mesh. # -# +# # # # @@ -1687,7 +1687,7 @@ NXapm_paraprobe_nanochem_config(NXobject): # intersection of triangles and convex polyhedra is a robust but currently # not implemented method to quantify intersections. # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml index 54d877db1c..05f77ba9e6 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_nanochem_results.yaml @@ -426,8 +426,8 @@ NXapm_paraprobe_nanochem_results(NXobject): triangles(NXcg_face_list_data_structure): number_of_vertices(NX_POSINT): number_of_faces(NX_POSINT): - vertex_identifier_offset(NX_INT): - face_identifier_offset(NX_INT): + identifier_vertex_offset(NX_INT): + identifier_face_offset(NX_INT): vertices(NX_NUMBER): unit: NX_LENGTH doc: | @@ -607,7 +607,7 @@ NXapm_paraprobe_nanochem_results(NXobject): In the second step, the tool can be used to analyze the proximity of these objects to a model of the surface (edge) of the dataset. - triangle_cluster_identifier(NX_UINT): + identifier_triangle_cluster(NX_UINT): unit: NX_UNITLESS doc: | The identifier which the triangle_soup connectivity analysis @@ -642,7 +642,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (n_v_feat,) - feature_identifier(NX_UINT): + identifier_feature(NX_UINT): unit: NX_UNITLESS doc: | The explicit identifier of features. @@ -662,10 +662,10 @@ NXapm_paraprobe_nanochem_results(NXobject): * proxies, proxies, irrespective their distance to the surface * proxies_close_to_edge, sub-set of v_feature_proxies, close to surface * proxies_far_from_edge, sub-set of v_feature_proxies, not close to surface - feature_identifier(NX_UINT): + identifier_feature(NX_UINT): unit: NX_UNITLESS doc: | - Explicit identifier of the feature a sub-set of the feature_identifier in the + Explicit identifier of the feature a sub-set of the identifier_feature in the parent group. dimensions: rank: 1 @@ -726,7 +726,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (k,) - xdmf_feature_identifier(NX_UINT): + identifier_feature_xdmf(NX_UINT): unit: NX_UNITLESS dimensions: rank: 1 @@ -740,8 +740,8 @@ NXapm_paraprobe_nanochem_results(NXobject): # number_of_vertices(NX_POSINT): # number_of_faces(NX_POSINT): - # vertex_identifier_offset(NX_UINT): - # face_identifier_offset(NX_UINT): + # identifier_vertex_offset(NX_UINT): + # identifier_face_offset(NX_UINT): vertices(NX_FLOAT): unit: NX_LENGTH dimensions: @@ -763,17 +763,17 @@ NXapm_paraprobe_nanochem_results(NXobject): dimensions: rank: 1 dim: (k,) - xdmf_feature_identifier(NX_UINT): + identifier_feature_xdmf(NX_UINT): exists: recommended unit: NX_UNITLESS dimensions: rank: 1 dim: (k,) - ion_identifier(NX_UINT): + identifier_ion(NX_UINT): exists: optional unit: NX_UNITLESS doc: | - Array of evaporation_identifier / ion_identifier which details which ions + Array of identifier_evaporation / identifier_ion which details which ions lie inside or on the surface of the feature. dimensions: rank: 1 @@ -873,13 +873,13 @@ NXapm_paraprobe_nanochem_results(NXobject): unit: NX_UNITLESS number_of_faces(NX_POSINT): unit: NX_UNITLESS - vertex_identifier_offset(NX_INT): + identifier_vertex_offset(NX_INT): unit: NX_UNITLESS - edge_identifier_offset(NX_INT): + identifier_edge_offset(NX_INT): unit: NX_UNITLESS - face_identifier_offset(NX_INT): + identifier_face_offset(NX_INT): unit: NX_UNITLESS - face_identifier(NX_UINT): + identifier_face(NX_UINT): unit: NX_UNITLESS dimensions: rank: 1 @@ -1063,7 +1063,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (k,) common(NXapm_paraprobe_tool_common): status(NX_CHAR): - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): config(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -1109,7 +1109,7 @@ NXapm_paraprobe_nanochem_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 892b2991f9c1561a8d4096a1d4f600ac60102180db3f740fb3cf7299fee1c1a6 +# c68715d20ebbd1d669a668dcdd2057ba8d7ed27ade45031eec1eecc944d58329 # # # +# identifier_vertex_offset(NX_UINT): +# identifier_face_offset(NX_UINT):--> # # # @@ -2012,14 +2012,14 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # # -# +# # -# Array of evaporation_identifier / ion_identifier which details which ions +# Array of identifier_evaporation / identifier_ion which details which ions # lie inside or on the surface of the feature. # # @@ -2130,10 +2130,10 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# -# -# -# +# +# +# +# # # # @@ -2338,7 +2338,7 @@ NXapm_paraprobe_nanochem_results(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml index 05d1f4fec3..baed0a30cf 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_config.yaml @@ -22,7 +22,7 @@ NXapm_paraprobe_ranger_config(NXobject): # tool-specific range(NXapm_paraprobe_tool_config): exists: ['min', '1', 'max', '1'] - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): type(NX_CHAR): @@ -102,7 +102,7 @@ NXapm_paraprobe_ranger_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# daf5564edd5ac6f36f3dc2d103a1e272032226879aee2ea00cc10c564c9d8fec +# 9970b8c602fb9ebe185fd6d97e74e2a856d931139a01811cba393f4f98228379 # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml index 56cfcf67a6..bd1081b1b3 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_ranger_results.yaml @@ -58,7 +58,7 @@ NXapm_paraprobe_ranger_results(NXobject): dim: (n_ions,) common(NXapm_paraprobe_tool_common): status(NX_CHAR): - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): config(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -104,7 +104,7 @@ NXapm_paraprobe_ranger_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# f628a11c2ad5fc1b9562e99c95da3cd9ba1e97ac3f60ee8cdb316606dda92655 +# 7c8408d7ef787f9e02a01299d85dfaa8405ff1b7b8c4ea4ed2a121d0f9263fda # # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml index 25942fe54a..edd773c668 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_tessellator_config.yaml @@ -18,7 +18,7 @@ NXapm_paraprobe_tessellator_config(NXobject): enumeration: [NXapm_paraprobe_tessellator_config] tessellate(NXapm_paraprobe_tool_config): exists: ['min', '1', 'max', '1'] - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): exists: recommended reconstruction(NXnote): type(NX_CHAR): @@ -137,7 +137,7 @@ NXapm_paraprobe_tessellator_config(NXobject): current_working_directory(NX_CHAR): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 6c9a434c7676b2cf255261d4dda62dc9aa43181f31b54ce3f7e961d07850dad0 +# 6de30011e50cffeb26ed0fcd027f35146975a1c614dbb15beeb1be7e9f401006 # # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml b/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml index 2cf3e33dd1..288b1bea2c 100644 --- a/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml +++ b/contributed_definitions/nyaml/NXapm_paraprobe_transcoder_results.yaml @@ -50,7 +50,7 @@ NXapm_paraprobe_transcoder_results(NXobject): # this group mirrors the NXapm application definition # config - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): config(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -118,7 +118,7 @@ NXapm_paraprobe_transcoder_results(NXobject): # (NXapm_charge_state_analysis): common(NXapm_paraprobe_tool_common): status(NX_CHAR): - analysis_identifier(NX_UINT): + identifier_analysis(NX_UINT): config(NXnote): type(NX_CHAR): file_name(NX_CHAR): @@ -164,7 +164,7 @@ NXapm_paraprobe_transcoder_results(NXobject): dim: (3,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 8e1c10cce9e92568f80a3ae9771333fefa8158c1cfedf3274b65745b670c101a +# 2074936c65586a67598854080dbe8a74a8b1b72f392859f77c93fd4f1a2895b7 # # # -# +# # # # @@ -333,7 +333,7 @@ NXapm_paraprobe_transcoder_results(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXapm_reconstruction.yaml b/contributed_definitions/nyaml/NXapm_reconstruction.yaml index b6d3a80740..514d2c3c95 100644 --- a/contributed_definitions/nyaml/NXapm_reconstruction.yaml +++ b/contributed_definitions/nyaml/NXapm_reconstruction.yaml @@ -13,7 +13,7 @@ symbols: Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process - the so-called - evaporation_identifier, which must not be confused with the pulse_identifier! + identifier_evaporation, which must not be confused with the identifier_pulse! type: group NXapm_reconstruction(NXprocess): @@ -157,7 +157,7 @@ NXapm_reconstruction(NXprocess): algorithms during the histogram computation. # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# a3a8cbc9d4a1ef760dcd3e206b211d41a3c7ecc8a3f708efdd0e8147a24670a9 +# 208a6a3e6cb491d00ad7e0a449421f072c6a23bea01b288688b572b81bfa318e # # # -# +# # # The integrated intensities: # @@ -489,7 +491,7 @@ NXem_calorimetry(NXobject): # # # -# +# # # # diff --git a/contributed_definitions/nyaml/NXevent_data_apm.yaml b/contributed_definitions/nyaml/NXevent_data_apm.yaml index 6069c9095b..63419a59cd 100644 --- a/contributed_definitions/nyaml/NXevent_data_apm.yaml +++ b/contributed_definitions/nyaml/NXevent_data_apm.yaml @@ -8,7 +8,7 @@ doc: | of atom probe research. Against static and dynamic quantities are splitted to avoid a duplication of information. Specifically, the time interval considered is the entire time starting at start_time until end_time during which we assume the pulser triggered named pulses. - These pulses are identified via the pulse_identifier field. The point in time when each was issued + These pulses are identified via the identifier_pulse field. The point in time when each was issued is specified via the combination of start_time and delta_time. Conceptually and technically NeXus currently stores tensorial information as arrays of values @@ -31,10 +31,10 @@ doc: | However, there is no independent logical connection between these two concepts, i.e. temperature and time_stamp. - In the case of atom probe though the time that one would use in NXlog is defined implicitly via pulse_identifier, + In the case of atom probe though the time that one would use in NXlog is defined implicitly via identifier_pulse, which is the independent variable vector against which eventually dozens of channels of data are logged. Not only are these channels logged they should ideally also be self-descriptive in that these channels have - pulse_identifier as the independent variable but we do not wish to duplicate this information all the time but + identifier_pulse as the independent variable but we do not wish to duplicate this information all the time but reference it. Therefore, we here explore the use of an attribute with symbol logged_against. Maybe it is better to use the @@ -65,16 +65,16 @@ NXevent_data_apm(NXobject): delta_time(NX_NUMBER): unit: NX_TIME doc: | - Delta time array which resolves for each pulse_identifier the time difference + Delta time array which resolves for each identifier_pulse the time difference between when that pulse was issued and start_time. - In summary, using start_time, end_time, delta_time, pulse_identifier_offset, - and pulse_identifier exactly specifies the connection between when a pulse was + In summary, using start_time, end_time, delta_time, identifier_pulse_offset, + and identifier_pulse exactly specifies the connection between when a pulse was issued relative to start and absolute in UTC. dimensions: rank: 1 dim: (p,) - pulse_identifier_offset(NX_INT): + identifier_pulse_offset(NX_INT): unit: NX_UNITLESS doc: | Integer used to name the first pulse to know if there is an @@ -91,13 +91,13 @@ NXevent_data_apm(NXobject): For explicit indexing the field identifier has to be used. Fortran-/Matlab- and C-/Python-style indexing have specific implicit identifier conventions where identifier_offset is 1 and 0 respectively. - pulse_identifier(NX_INT): + identifier_pulse(NX_INT): unit: NX_UNITLESS doc: | Identifier that contextualizes how the detector and pulser of an atom probe instrument follows a sequence of pulses to trigger field evaporation. - The pulse_identifier is used to associate thus an information about time + The identifier_pulse is used to associate thus an information about time when quantities have been collected via sampling. In virtually all cases the pulser is a blackbox. Depending on how the @@ -106,24 +106,24 @@ NXevent_data_apm(NXobject): Maybe the first part of the experiment is run at a certain pulse fraction but thereafter the pulse_fraction is changed. In this case the field pulse_fraction is a vector which - collects all measured values of the pulse_fraction, pulse_identifier is then an equally + collects all measured values of the pulse_fraction, identifier_pulse is then an equally long vector which stores the set of events (e.g. pulsing events) when that value was measured. This may cause several situations: In the case that e.g. the pulse_fraction is never changed and also exact details not interesting, one stores the set value for the pulse_fraction - and a single value for the pulse_identifier e.g. 0 to indicate that the pulse_fraction was set + and a single value for the identifier_pulse e.g. 0 to indicate that the pulse_fraction was set at the beginning and it was maintained constant during the measurement. If the pulse_fraction was maybe changed after the 100000th pulse, pulse_fraction is a vector with two values one for the first and another one for the value from the 100000-th - pulse onwards. The values of pulse_identifier are then [0, 99999] respectively. + pulse onwards. The values of identifier_pulse are then [0, 99999] respectively. dimensions: rank: 1 dim: (p,) instrument(NXinstrument_apm): # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 07658ee91d4228221572bfd3c1bd35594582b7f0eb2bc23551294b89cfe772e1 +# f48926f4dfa8ca5e2fd3b02504cfc71f7a9475208942511900821bd6d64abb99 # # # +# # # # Direct current voltage between the specimen and the (local electrode) in @@ -532,7 +532,7 @@ NXinstrument_apm(NXinstrument): # # # -# Path to pulse_identifier +# Path to identifier_pulse # # # @@ -558,7 +558,7 @@ NXinstrument_apm(NXinstrument): # # # -# Path to pulse_identifier +# Path to identifier_pulse # # # @@ -575,7 +575,7 @@ NXinstrument_apm(NXinstrument): # # # -# Path to pulse_identifier +# Path to identifier_pulse # # # @@ -586,7 +586,7 @@ NXinstrument_apm(NXinstrument): # # # -# Path to pulse_identifier +# Path to identifier_pulse # # # @@ -597,7 +597,7 @@ NXinstrument_apm(NXinstrument): # # # -# Path to pulse_identifier in an instance of :ref:`NXevent_data_apm`. +# Path to identifier_pulse in an instance of :ref:`NXevent_data_apm`. # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml b/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml index 4dbc1cd82b..6fd1ca56d2 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_gragles_config.yaml @@ -18,7 +18,7 @@ NXmicrostructure_gragles_config(NXobject): (NXentry): definition(NX_CHAR): enumeration: [NXmicrostructure_gragles_config] - simulation_identifier(NX_UINT): + identifier_simulation(NX_UINT): doc: | Simulation ID as an alias to refer to this simulation. description(NX_CHAR): @@ -284,7 +284,7 @@ NXmicrostructure_gragles_config(NXobject): # # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 1c34564407d257d8c84bb8159f805081fe5432649580715e83ee9acc464e2a2e +# 094e8de0d60a0ce2a5465342be9088836991bfd05e411b11d71f3b97e9255617 # # # -# +# # # Simulation ID as an alias to refer to this simulation. # @@ -464,14 +464,14 @@ NXmicrostructure_gragles_results(NXobject): # # # -# -# +# +# # # # # -# -# +# +# # # # @@ -491,9 +491,9 @@ NXmicrostructure_gragles_results(NXobject): # # # -# +# # -# Set of pairs of crystal_identifier for each interface. +# Set of pairs of identifier_crystal for each interface. # # # diff --git a/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml b/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml index 4f33195586..4007975575 100644 --- a/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml +++ b/contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml @@ -58,7 +58,7 @@ NXmicrostructure_imm_results(NXobject): \@AXISNAME_indices(NX_CHAR): nameType: partial title(NX_CHAR): - crystal_identifier(NX_NUMBER): + identifier_crystal(NX_NUMBER): unit: NX_UNITLESS doc: | Crystal identifier that was assigned to each material point. @@ -98,7 +98,7 @@ NXmicrostructure_imm_results(NXobject): crystal(NXobject): reference(NX_CHAR): number_of_crystals(NX_UINT): - crystal_identifier(NX_INT): + identifier_crystal(NX_INT): dimensions: rank: 1 dim: (c,) @@ -138,7 +138,7 @@ NXmicrostructure_imm_results(NXobject): dim: (c,) # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 316ae1ad842c7e5b9392b1acea052efad08c512898b65c2c344c810f6542bc04 +# 7d923ceaf0c927eb05fffba36cf3f7f3c127575cd682ac571c80c86bde7ed3c2 # # # Was the corrector used? - + Specific information about the alignment procedure that is a process during which the corrector is configured to enable calibrated usage of the instrument. diff --git a/contributed_definitions/nyaml/NXapm.yaml b/contributed_definitions/nyaml/NXapm.yaml index b999db5be3..7753cc3cc3 100644 --- a/contributed_definitions/nyaml/NXapm.yaml +++ b/contributed_definitions/nyaml/NXapm.yaml @@ -171,11 +171,11 @@ NXapm(NXobject): items: [apt, fim, apt_fim] (NXuser): exists: recommended - name(NX_CHAR): - exists: optional identifierNAME(NX_CHAR): nameType: partial exists: recommended + name(NX_CHAR): + exists: optional sample(NXsample): exists: recommended doc: | @@ -194,6 +194,9 @@ NXapm(NXobject): should be stored. For this specific application definitions/schemas can be used which are then arranged and documented with a description of the workflow so that actionable graphs become instantiatable. + identifierNAME(NX_CHAR): + nameType: partial + exists: recommended is_simulation(NX_BOOLEAN): doc: | Qualifier whether the sample is a real (in which case is_simulation should be set to false) @@ -201,9 +204,6 @@ NXapm(NXobject): alias(NX_CHAR): doc: | Given name/alias for the sample. - identifierNAME(NX_CHAR): - nameType: partial - exists: recommended grain_diameter(NX_FLOAT): exists: optional unit: NX_LENGTH @@ -310,6 +310,9 @@ NXapm(NXobject): doc: | Magnitude of the standard deviation of the composition (value). specimen(NXsample): + identifierNAME(NX_CHAR): + nameType: partial + exists: recommended is_simulation(NX_BOOLEAN): doc: | Qualifier whether the specimen is a real (in which case is_simulation should be set to false) @@ -319,9 +322,6 @@ NXapm(NXobject): doc: | Given name an alias. Better use identifierNAME and identifier_parent instead. A single NXentry should be used only for the characterization of a single specimen. - identifierNAME(NX_CHAR): - nameType: partial - exists: recommended identifier_parent(NX_CHAR): exists: recommended doc: | @@ -1227,7 +1227,7 @@ NXapm(NXobject): exists: recommended # ++++++++++++++++++++++++++++++++++ SHA HASH ++++++++++++++++++++++++++++++++++ -# 9371b90206e5ddd616db3960615019f50dcd623845d51b5b2a997355eca26de0 +# 6b512a28ac6762e4898ce536a49fd6f84bcece083ed8569615688969e4a2b4a8 # # #