Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
78 commits
Select commit Hold shift + click to select a range
261cb04
Modifications to register exemplar IVAS/APSuite concepts for the atom…
atomprobe-tc Jan 26, 2025
8cfc492
make nxdl causing many changes because change of year and changes in …
atomprobe-tc Jan 26, 2025
3dce2b0
Updates during dev of pynxtools_apm parser for APSuite
atomprobe-tc Jan 27, 2025
e0648fe
Edits in reply to issues spotted when using cameca examples in NOMAD
atomprobe-tc Jan 28, 2025
c162e9f
further edits
atomprobe-tc Jan 28, 2025
3b983b6
Moved location of number of ions
atomprobe-tc Jan 28, 2025
bd675f4
Refactored storing of event types
atomprobe-tc Jan 30, 2025
f6e55a9
Added instrument types
atomprobe-tc Jan 30, 2025
bc2622c
Refactoring to remove the base class NXreflectron as that will likely…
atomprobe-tc Jan 31, 2025
f87c859
Refactoring to remove the base class NXapm_volt_and_bowl as that will…
atomprobe-tc Jan 31, 2025
e58b66e
Refactoring to remove the base class NXapm_sim as that was not detail…
atomprobe-tc Jan 31, 2025
0c5228d
Remove accidentally recreated NXapm_volt_and_bowl.yaml
atomprobe-tc Jan 31, 2025
77979ed
Refactoring to remove the base class NXapm_hit_finding that detailed …
atomprobe-tc Jan 31, 2025
a860287
Refactoring to remove the base class NXevent_data_apm_set as it was o…
atomprobe-tc Jan 31, 2025
8846f36
BREAKING REFACTORING, resolve the error-prone repetition of concepts …
atomprobe-tc Jan 31, 2025
44c3eda
Implementation of the afore-mentioned BREAKING REFACTORING for NXapm_…
atomprobe-tc Jan 31, 2025
ef786b7
Finished refactoring of NXapm
atomprobe-tc Jan 31, 2025
65cec29
Cleaning the APM landing page of the documentation and tests
atomprobe-tc Jan 31, 2025
b74acd8
Fixes of NOMAD APM example
atomprobe-tc Feb 1, 2025
cc3dc40
run_number now NX_UINT
atomprobe-tc Feb 1, 2025
d93f5b5
Implementing additions for bugfixes when parsing config and results f…
atomprobe-tc Feb 7, 2025
a79703b
Updated NXmicrostructure_score_config appdef, next step, update resul…
atomprobe-tc Feb 15, 2025
417519a
Updated score_results and microstructure
atomprobe-tc Feb 15, 2025
536e271
Generated NXDL files
atomprobe-tc Feb 15, 2025
36ba122
Minor edits score config
atomprobe-tc Feb 16, 2025
c274ae5
Finalizing NXmicrostructure_score using newest nyaml
atomprobe-tc Feb 24, 2025
dc331be
Updated NXem_calorimetry based on NIAC changes
atomprobe-tc Feb 24, 2025
724ad11
Edits on em_calorimetry
atomprobe-tc Feb 26, 2025
6277f77
Reverting copyright end year back to 2024
atomprobe-tc Mar 7, 2025
d4c77c7
Reverting copyright end year back to 2024
atomprobe-tc Mar 7, 2025
bd8274a
Reverting copyright end year back to 2024
atomprobe-tc Mar 7, 2025
cac3fb0
Reverting copyright end year back to 2024
atomprobe-tc Mar 7, 2025
0bb04fe
Syncing up with niac changes on NIAC PR #1531 which promotes csg to b…
atomprobe-tc Mar 9, 2025
6f5961b
Cherry pick from NIAC issue1531_nxcsg 7a52e09a
atomprobe-tc Mar 9, 2025
67b0adf
Syncing up with niac changes on fairmat PR #1422 which promotes apm t…
atomprobe-tc Mar 9, 2025
b47ebd8
Removal of classes for which the discussions with NIAC suggested thei…
atomprobe-tc Mar 9, 2025
3d550ac
Syncing up base classes for apm with #1422 f719fe0e
atomprobe-tc Mar 9, 2025
86bb923
Syncing up base classes for apm with #1422 f719fe0e, cs classes
atomprobe-tc Mar 9, 2025
687e017
Syncing up base classes for apm with #1422 f719fe0e, remaining base c…
atomprobe-tc Mar 9, 2025
ad61763
Update apm docs and renamed NXrotation_set to NXrotations, unfortunat…
atomprobe-tc Mar 9, 2025
1e9dc7a
Wrapping up syncing of classes for apm, cherry-picked changes on docu…
atomprobe-tc Mar 9, 2025
960890c
Syncing up with niac changes on fairmat PR #1421 which promotes cg to…
atomprobe-tc Mar 9, 2025
796f30b
Syncing up with niac changes on fairmat PR #1421 which promotes cg to…
atomprobe-tc Mar 9, 2025
0ac8ed5
Syncing up with niac changes on fairmat PR #1421 which promotes cg to…
atomprobe-tc Mar 9, 2025
f39d3c5
Update docs to remove non-cg-related classes, which should be moved i…
atomprobe-tc Mar 9, 2025
f441a99
Syncing up with niac changes on fairmat PR #1421, introducing concept…
atomprobe-tc Mar 9, 2025
8168db8
Syncing up with NIAC changes on PR #1423 em, applications directory
atomprobe-tc Mar 10, 2025
5458e8b
Syncing up with NIAC changes on PR #1423 em, applications directory, …
atomprobe-tc Mar 10, 2025
abe07be
Syncing up with NIAC changes on PR #1423 em, baseclasses, promoting f…
atomprobe-tc Mar 10, 2025
7c604f2
Syncing up with NIAC changes on PR #1423 non-em, generic classes that…
atomprobe-tc Mar 10, 2025
dbbcb73
Syncing up with NIAC changes on PR #1423 em, removal of base classes …
atomprobe-tc Mar 10, 2025
b872544
Syncing up with NIAC changes on PR #1423 em, cherry-picking base clas…
atomprobe-tc Mar 10, 2025
1c9042a
Syncing up with NIAC changes on PR #1423 em, cherry-picking base clas…
atomprobe-tc Mar 10, 2025
d60e1d1
Syncing up with NIAC changes on PR #1423 em, cherry-picking base clas…
atomprobe-tc Mar 10, 2025
7cbb892
Syncing up with NIAC changes on PR #1423 em, removal of old baseclass…
atomprobe-tc Mar 10, 2025
3b81a5a
Fixing of references in the manual to classes that were removed durin…
atomprobe-tc Mar 11, 2025
771662a
Merge branch 'fairmat' into niac_changes_merge_fairmat
atomprobe-tc Mar 11, 2025
a070a03
Firstly, ran make clean, secondly, ran make nyaml to regenerate nyaml…
atomprobe-tc Mar 11, 2025
3b8b547
Deactivated for now tests only on NXem to focus on building the docum…
atomprobe-tc Mar 11, 2025
5e200b8
Fixes related to cases where in some places still NXidentifier, NXser…
atomprobe-tc Mar 11, 2025
62802b7
Reintroduced ellipsometry-structure but that should be checked agains…
atomprobe-tc Mar 11, 2025
0cc829b
Suggestion from Lukas move proposed classes back to contributed as th…
atomprobe-tc Mar 11, 2025
618d731
Suggestions from Lukas on specific files to use for the manual and sp…
atomprobe-tc Mar 11, 2025
0f924c4
Fixes on manual source domain-specific rsts
atomprobe-tc Mar 11, 2025
bce7aa2
Refactored prefixID nameType partials to implicit nameType anys and C…
atomprobe-tc Mar 12, 2025
8cc2cf0
Fixes on suggestions for instance name prefixes and implementation of…
atomprobe-tc Mar 12, 2025
565b802
Fixes on suggestions for instance name prefixes and implementation of…
atomprobe-tc Mar 12, 2025
a3f7260
Merge branch 'fairmat' into niac_changes_merge_fairmat
atomprobe-tc Mar 12, 2025
5b4904e
Fix NXcg_primitive not mentioned in manual
atomprobe-tc Mar 12, 2025
7556ca0
Fix issues that were with the README.md turning out inconsistent to t…
atomprobe-tc Mar 12, 2025
b0c329c
Remaining swoppings of concept names with keyword identifier and iden…
atomprobe-tc Mar 12, 2025
88d6641
manual one more reversion for index I/O examples
atomprobe-tc Mar 12, 2025
0eb5f04
is_simulation for specimen
atomprobe-tc Mar 12, 2025
c6af308
Move remaining base classes back to contributed
atomprobe-tc Mar 13, 2025
31a863b
Merge branch 'fairmat' into niac_changes_merge_fairmat
atomprobe-tc Mar 13, 2025
9a5474e
A few more fixes on nameType
atomprobe-tc Mar 13, 2025
bf0de5b
Rerunning nyaml with nyaml v0.2.2
atomprobe-tc Mar 13, 2025
623dfcd
Revert Makefile to its original state and checked that docs is buildi…
atomprobe-tc Mar 13, 2025
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Empty file modified README.md
100755 → 100644
Empty file.
16 changes: 8 additions & 8 deletions contributed_definitions/NXaberration.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
# Copyright (C) 2014-2025 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
Expand All @@ -27,19 +27,19 @@
</doc>
<field name="magnitude" type="NX_NUMBER" units="NX_ANY">
<doc>
Value of the aberration coefficient.
Magnitude of the aberration
</doc>
</field>
<field name="uncertainty" type="NX_NUMBER" units="NX_ANY">
<field name="magnitude_errors" type="NX_NUMBER" units="NX_ANY">
<doc>
Uncertainty of the value of the aberration coefficient
according to uncertainty_model.
Uncertainty of the magnitude of the aberration
</doc>
</field>
<field name="uncertainty_model" type="NX_CHAR">
<field name="magnitude_errors_model" type="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.
</doc>
</field>
<field name="delta_time" type="NX_NUMBER" units="NX_TIME">
Expand Down
1,242 changes: 738 additions & 504 deletions contributed_definitions/NXapm.nxdl.xml

Large diffs are not rendered by default.

10 changes: 5 additions & 5 deletions contributed_definitions/NXapm_compositionspace_config.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
<!--
# NeXus - Neutron and X-ray Common Data Format
#
# Copyright (C) 2024-2025 NeXus International Advisory Committee (NIAC)
# Copyright (C) 2025-2025 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
Expand All @@ -29,7 +29,7 @@

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.
</doc>
<!--by default for appdefs the value of the exists keyword is required unless it is explicitly specified differently-->
<group type="NXentry" minOccurs="1" maxOccurs="1">
Expand All @@ -40,7 +40,7 @@
</enumeration>
</field>
<group name="config" type="NXobject">
<field name="analysis_identifier" type="NX_UINT" recommended="true"/>
<field name="identifier_analysis" type="NX_UINT" recommended="true"/>
<group name="reconstruction" type="NXnote">
<doc>
Specification of the tomographic reconstruction used for this analysis.
Expand All @@ -51,7 +51,7 @@
to use for this analysis.
</doc>
<field name="type" type="NX_CHAR" optional="true"/>
<field name="path" type="NX_CHAR"/>
<field name="file_path" type="NX_CHAR"/>
<field name="checksum" type="NX_CHAR" recommended="true"/>
<field name="algorithm" type="NX_CHAR" recommended="true"/>
<field name="position" type="NX_CHAR">
Expand All @@ -75,7 +75,7 @@
iontype is unknown_type. The value 0 is also reserved for voxels that lie outside the dataset.
</doc>
<field name="type" type="NX_CHAR" optional="true"/>
<field name="identifier" type="NX_CHAR"/>
<field name="file_path" type="NX_CHAR"/>
<field name="checksum" type="NX_CHAR" recommended="true"/>
<field name="algorithm" type="NX_CHAR" recommended="true"/>
<field name="ranging_definitions" type="NX_CHAR">
Expand Down
225 changes: 130 additions & 95 deletions contributed_definitions/NXapm_compositionspace_results.nxdl.xml

Large diffs are not rendered by default.

147 changes: 0 additions & 147 deletions contributed_definitions/NXapm_hit_finding.nxdl.xml

This file was deleted.

Loading