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Fairmat 2024: proposal on electron microscopy (EM) #1423

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@lukaspie lukaspie commented Sep 24, 2024

  • Refactored version for NXem including feedback from the EM community
  • Refactoring of NXimage, NXspectrum_set base classes and examples for their usage
  • Examples for documenting method-specific results with some contextualization for processing EBSD as an example for diffraction, EDS for spectroscopy, as well as images
  • More complete representation of microscope components
  • Connection to all concepts within EMglossary community-agreed upon terminology set where it fits
  • Backed by example data converted to NeXus files using NXem for at least one example for each microscope manufacturer and thousands of cases for EBSD as a specific technique

This PR depends heavily on others that make changes to existing base classes or introduce base classes that are to be used outside of APM as well. Thus, it will be much smaller once the discussion on these PRs is done and this particular branch here has been rebased:
#1407 -> merged
#1408
#1410
#1412
#1413
#1414 -> merged
#1415
#1419
#1420 -> merged
#1486 -> merged

There are however several new base classes that are currently only used within NXapm that are introduced here:

  • NXaberration
  • NXcg_ellipsoid_set
  • NXcg_face_list_data_structure
  • NXcg_geodesic_mesh
  • NXcg_half_edge_data_structure
  • NXcg_primitive_set
  • NXcg_triangle_set
  • NXcg_triangulated_surface_mesh
  • NXcg_unit_normal_set
  • NXcorrector_cs
  • NXcrystal_structure
  • NXebeam_column
  • NXem_correlation
  • NXem_ebsd
  • NXem_eds
  • NXem_eels
  • NXem_img
  • NXem_method
  • NXem_msr
  • NXem_sim
  • NXevent_data_em
  • NXevent_data_em_set
  • NXibeam_column
  • NXinteraction_vol_em
  • NXoptical_system_em
  • NXscanbox_em
  • NXspectrum_set

For a full list of dependant changes, see #1465

lukaspie and others added 30 commits July 11, 2024 12:34
Small modifications to clarify NXmpes
…ng-deployment

Remove _sources build artifacts before docs deployment
…the rollett-holm formula fixes the build error with latex, locally at least it does
* Add depends for data field

* Use `@reference`

* use reference attribute in NXmpes and NXmpes_arpes

* change text style

* fix duplicated in reference attribute

---------

Co-authored-by: Lukas Pielsticker <[email protected]>
Roll back changes to NXmpes/instrument/pressure_gauge
fix 2theta and use NXobject instead of collection.
* Including scattering vector components perpendicular and parallel to the surface of the sample those are mainly used for RSM diffraction technique.

---------

Co-authored-by: Florian Dobener <[email protected]>
…cision of concept image and how this is connected to tilings
atomprobe-tc and others added 30 commits January 14, 2025 15:01
…ng of the fundamental matter based description of the FAIRmat proposal like changes to rename NXion to NXatom and possibly NXmicrostructure to NXsystem
…ture, groups. To increase the possibility for acceptance, the atom-probe-specific aspects of NXion now NXatom have been removed and will be reintroduced via NXapm_ion as a specialization of NXatom for usage in the field of atom probe
…, ii) NXstage_lab consolidation with NXmanipulator, and NXem appdef
…hich NXstage_lab will be replaced in NXem and NXapm appdefs via NXmanipulator from nexusformat#1424 augmented by remaining concepts and contextualizing top-level doc string from NXstage_lab pulled into the appdef. As a side effect thereby also docstring become more focused on the relevant techniques and a base class is not talking only with examples from atom probe
…h negotiation and coming to the conclusion that maybe indeed these base classes are tiny to warrant becoming part of the standard, instead NXcoordinate_system should be specialized in respective appdefs but the names sample_reference_frame, processing_reference_frame, and detector_reference_frame are good candidates
…e designing NXem iteratively and are now superseeded by better alternatives, NXaberration, NXcircuit, NXem_ebsd, NXimage, NXspectrum, editing of the EM-specific part of the documentation to document these changes
…Xapm, such that the same modular group of classes NXinstrument_em can be used in the NXem appdefs in both ENTRY.measurement.instrument, ENTRY.simulation.instrument, ENTRY.measurement.events, ENTRY.simulation.events
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NXem
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