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Ray's suggestion to the NXem PR #1423 (how the NIAC sees it) #402

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12 changes: 6 additions & 6 deletions applications/NXapm.nxdl.xml
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<symbol name="p">
<doc>
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
instance of :ref:`NXapm_event_data`. 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 dataset.
</doc>
Expand Down Expand Up @@ -149,7 +149,7 @@
or a new file. Removing the specimen from the instrument is an interruption. Changing evaporation conditions
while the specimen is remains in the analysis_chamber and resuming thereafter the measurement
is not considered as an interruption. It is a common strategy to probe the evaporation process for different
instrument parameters. Each individual collection should then though be stored in an own NXevent_data_apm
instrument parameters. Each individual collection should then though be stored in an own NXapm_event_data
group. Parking the specimen to the buffer_chamber and resuming the measurement at a later stage is an interruption.
During a run, the microscope is used for a certain amount of time to characterize a single specimen.
- The groups ``sample`` and ``specimen`` provide concepts for storing metadata about the sample and the specimen,
Expand Down Expand Up @@ -340,7 +340,7 @@

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.
purpose the :ref:`NXapm_event_data` instance should be used.
</doc>
</field>
<field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand Down Expand Up @@ -740,7 +740,7 @@
<group name="measurement" type="NXapm_measurement" optional="true">
<field name="status" type="NX_CHAR" recommended="true"/>
<field name="quality" type="NX_CHAR" recommended="true"/>
<group name="instrument" type="NXinstrument_apm">
<group name="instrument" type="NXapm_instrument">
<field name="type" type="NX_CHAR" recommended="true"/>
<field name="location" type="NX_CHAR" recommended="true"/>
<field name="flight_path" type="NX_FLOAT" recommended="true"/>
Expand Down Expand Up @@ -832,10 +832,10 @@
</group>
</group>
</group>
<group name="eventID" type="NXevent_data_apm" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="eventID" type="NXapm_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<field name="start_time" type="NX_DATE_TIME" recommended="true"/>
<field name="end_time" type="NX_DATE_TIME" recommended="true"/>
<group name="instrument" type="NXinstrument_apm" recommended="true">
<group name="instrument" type="NXapm_instrument" recommended="true">
<group name="reflectron" type="NXcomponent" recommended="true">
<field name="voltage" type="NX_FLOAT"/>
</group>
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12 changes: 6 additions & 6 deletions applications/NXem.nxdl.xml
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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.
of respective :ref:`NXem_event_data` instances.
</doc>
</field>
<field name="end_time" type="NX_DATE_TIME" recommended="true">
Expand Down Expand Up @@ -422,7 +422,7 @@
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 connected to individual :ref:`NXevent_data_em`
region-of-interest connected to individual :ref:`NXem_event_data`
instances can provide a cleaner description of the relevant details.
</doc>
</field>
Expand Down Expand Up @@ -747,8 +747,8 @@
</field>
</group>
<group name="measurement" type="NXem_measurement" optional="true">
<!--voltage like all other dynamic quantities should better be placed in instances of NXevent_data_em-->
<group name="instrument" type="NXinstrument_em">
<!--voltage like all other dynamic quantities should better be placed in instances of NXem_event_data-->
<group name="instrument" type="NXem_instrument">
<field name="name" type="NX_CHAR" recommended="true"/>
<field name="location" type="NX_CHAR" recommended="true"/>
<field name="type" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -976,7 +976,7 @@
<group name="sensorID" type="NXsensor" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
<group name="actuatorID" type="NXactuator" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
</group>
<group name="eventID" type="NXevent_data_em" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<group name="eventID" type="NXem_event_data" nameType="partial" minOccurs="0" maxOccurs="unbounded">
<field name="start_time" type="NX_DATE_TIME" recommended="true"/>
<field name="end_time" type="NX_DATE_TIME" recommended="true"/>
<field name="identifier_sample" type="NX_CHAR" recommended="true"/>
Expand Down Expand Up @@ -1341,7 +1341,7 @@
</field>
</group>
</group>
<group name="instrument" type="NXinstrument_em" recommended="true">
<group name="instrument" type="NXem_instrument" recommended="true">
<group name="ebeam_column" type="NXebeam_column">
<field name="operation_mode" type="NX_CHAR" recommended="true"/>
<group name="electron_source" type="NXsource" optional="true">
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4 changes: 3 additions & 1 deletion base_classes/NXaberration.nxdl.xml
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<doc>
Quantified aberration coefficient in an aberration_model.

For an introduction in the aberrations in electron microscopy
For an introduction in the details about aberrations with relevance for electron microscopy
see `R. Dunin-Borkowski et al. &lt;https://doi.org/10.1017/9781316337455.022&gt;`_ and
`S. J. Pennycock and P. D. Nellist &lt;https://doi.org/10.1007/978-1-4419-7200-2&gt;`_ (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 &lt;https://www.globalsino.com/EM/page3740.html&gt;`_ an introduction.

The use of the base class is not restricted to electron microscopy but can also be useful for classical optics.
</doc>
<field name="magnitude" type="NX_NUMBER" units="NX_ANY">
<doc>
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6 changes: 3 additions & 3 deletions base_classes/NXevent_data_apm.nxdl.xml → base_classes/NXapm_event_data.nxdl.xml
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#
# For further information, see http://www.nexusformat.org
-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXevent_data_apm" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXapm_event_data" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<symbols>
<doc>
The symbols used in the schema to specify e.g. dimensions of arrays.
Expand All @@ -37,7 +37,7 @@

Having at least one instance for an instance of NXapm is recommended.

This base class applies the concept of the :ref:`NXevent_data_em` base class to the specific needs
This base class applies the concept of the :ref:`NXem_event_data` base class to the specific needs
of atom probe research. Again static and dynamic quantities are split 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 pulses.
Expand Down Expand Up @@ -110,7 +110,7 @@
<dim index="1" value="p"/>
</dimensions>
</field>
<group name="instrument" type="NXinstrument_apm">
<group name="instrument" type="NXapm_instrument">
<doc>
Place to store dynamic metadata of the instrument to document as close as possible
the state of the instrument during the event, i.e. in between start_time and end_time.
Expand Down
12 changes: 6 additions & 6 deletions base_classes/NXinstrument_apm.nxdl.xml → base_classes/NXapm_instrument.nxdl.xml
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<!--
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
file required, while NXapm_instrument can be used directly for the static and the dynamic
or volatile (meta)data.-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXinstrument_apm" extends="NXinstrument" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXapm_instrument" extends="NXinstrument" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<symbols>
<doc>
The symbols used in the schema to specify e.g. dimensions of arrays.
</doc>
<symbol name="p">
<doc>
Number of pulses collected in between start_time and end_time
inside a parent instance of :ref:`NXevent_data_apm`.
inside a parent instance of :ref:`NXapm_event_data`.
</doc>
</symbol>
</symbols>
Expand All @@ -44,7 +44,7 @@ or volatile (meta)data.-->

For collecting data and experiments which are simulations of an atom probe
microscope or a session with such instrument use the :ref:`NXapm` application definition
and the :ref:`NXevent_data_apm` groups it provides.
and the :ref:`NXapm_event_data` groups it provides.

This base class implements the concept of :ref:`NXapm` whereby (meta)data are distinguished
whether these typically change during a session, so-called dynamic, or not, so-called static metadata.
Expand Down Expand Up @@ -194,7 +194,7 @@ or volatile (meta)data.-->
<doc>
Laser- and/or voltage-pulsing device to trigger ion removal.

When the base class NXinstrument_apm is used in the NXapm
When the base class NXapm_instrument is used in the NXapm
application definition, the values for the following fields:

* pulse_frequency
Expand All @@ -208,7 +208,7 @@ or volatile (meta)data.-->
* spot_position

should be recorded in the order of, and assumed associated,
with the pulse_id in an instance of :ref:`NXevent_data_apm`.
with the pulse_id in an instance of :ref:`NXapm_event_data`.
</doc>
<!--technical design-->
<group name="fabrication" type="NXfabrication"/>
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4 changes: 2 additions & 2 deletions base_classes/NXapm_measurement.nxdl.xml
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field of a CamecaRoot ROOT file.
</doc>
</field>
<group type="NXinstrument_apm"/>
<group type="NXevent_data_apm"/>
<group type="NXapm_instrument"/>
<group type="NXapm_event_data"/>
</definition>
21 changes: 15 additions & 6 deletions base_classes/NXcorrector_cs.nxdl.xml
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Expand Up @@ -33,15 +33,15 @@
</symbol>
</symbols>
<doc>
Base class for a corrector reducing (spherical) aberrations in electron microscopy.
Base class for a corrector reducing (spherical) aberrations of an electron optical setup.

Different technology partners use different conventions and
models for quantifying the aberration coefficients.

Correctors in an electron microscope are composed of multiple lenses
and multipole stigmators. Their technical details are specific for the
technology partner as well as microscope. Most technical details are
proprietary knowledge.
Aberration correction components are especially important for (scanning)
transmission electron microscopy. Composed of multiple lenses and multipole stigmators,
their technical details are specific for the technology partner as well as
the microscope and instrument. Most technical details are proprietary knowledge.

If one component corrects for multiple types of aberrations (like it is the case
reported here `CEOS &lt;https://www.ceos-gmbh.de/en/research/electrostat&gt;`_) follow this
Expand All @@ -50,6 +50,14 @@
* 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

Although this base class currently provides concepts that are foremost used in
the field of electron microscopy using this base class is not restricted to this
research field. NXcorrector_cs can also serve as a container to detail, in
combination with :ref:`NXaberration`, about measured aberrations in classical optics.
In optics, though, the difference is that the design of the :ref:NXoptical_lens`
itself (e.g., using aspheric lenses or combinations of lenses) enables to
reduce spherical aberrations.
</doc>
<!--user perspective-->
<field name="applied" type="NX_BOOLEAN">
Expand All @@ -63,7 +71,7 @@
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.
simulation the specific details about the modeled or assumed aberrations.
</doc>
<field name="description" type="NX_CHAR">
<doc>
Expand Down Expand Up @@ -164,6 +172,7 @@
<group name="c_5_6_b" type="NXaberration"/>
</group>
<group type="NXelectromagnetic_lens"/>
<group type="NXoptical_lens"/>
<group type="NXaperture"/>
<group type="NXdeflector"/>
</definition>
4 changes: 2 additions & 2 deletions base_classes/NXebeam_column.nxdl.xml
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<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
The idea behind defining :ref:`NXebeam_column` as an own base class vs. adding these
concepts in :ref:`NXem_instrument` is that the electron beam generating component
might be worthwhile to use also in other types of experiments.
</doc>
<field name="operation_mode" type="NX_CHAR">
Expand Down
10 changes: 5 additions & 5 deletions base_classes/NXevent_data_em.nxdl.xml → base_classes/NXem_event_data.nxdl.xml
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#
# For further information, see http://www.nexusformat.org
-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXevent_data_em" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXem_event_data" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<doc>
Base class to store state and (meta)data of events for electron microscopy.

Expand All @@ -48,7 +48,7 @@
data of the instrument state can be stored and documented in an representation
that facilitates interoperability. This is the idea behind this base class.

:ref:`NXevent_data_em` represents an instance to describe and serialize flexibly
:ref:`NXem_event_data` 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 it.
Examples of such tasks are the collecting of data (images and spectra) or
Expand All @@ -59,7 +59,7 @@
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:
:ref:`NXem_event_data` 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.
Expand Down Expand Up @@ -94,7 +94,7 @@
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 also warrants to document the time-dependent details of individual components
of the microscope via the here implemented class :ref:`NXevent_data_em`.
of the microscope via the here implemented class :ref:`NXem_event_data`.
</doc>
<field name="start_time" type="NX_DATE_TIME">
<doc>
Expand Down Expand Up @@ -151,7 +151,7 @@
</doc>
</field>
<group type="NXuser"/>
<group type="NXinstrument_em"/>
<group type="NXem_instrument"/>
<group type="NXimage"/>
<group type="NXspectrum"/>
</definition>
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