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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
#1408
#1410
#1412
#1413
#1414
#1415
#1419
#1420 
#1486

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 4, 2024 16:51
…or_circuits

Cleaned the too many base classes for circuits and cleaned base classes for describing a computer
Make geometries and sourceTYPE recommended in NXxps
…NXms with NXmicrostructure to avoid confusing the symbol convention with mass spectrometry as the abbreviation NXms may suggest
…con and eventually make this NXmicrostructure
@lukaspie lukaspie force-pushed the fairmat-2024-em branch 2 times, most recently from 975d786 to d0c29fb Compare September 24, 2024 10:34
@sanbrock sanbrock mentioned this pull request Sep 29, 2024
@lukaspie lukaspie linked an issue Sep 29, 2024 that may be closed by this pull request
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NXem
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