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Fairmat 2024: proposal on photoemission spectroscopy (MPES) #1424

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Fairmat 2024: proposal on photoemission spectroscopy (MPES) #1424

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Commits on Jul 9, 2024

  1. small modifications to clarify NXmpes

    @lukaspie
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  2. Base class refactoring for NXms proposal removing too small base clas… 

    …ses by definitions in appdefs
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  3. Following @lukaspie suggestion to rename the base classes related to … 

    …NXms with NXmicrostructure to avoid confusing the symbol convention with mass spectrometry as the abbreviation NXms may suggest
    @atomprobe-tc
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  4. remove changes to polarization in NXbeam

    @lukaspie
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  5. remove changes to final_polarization in NXbeam

    @lukaspie
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  6. Removed remaining references to NXms and renamed NXslip_system_set

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  7. Removed the two tiny base classes NXmicrostructure_snapshot and *_set

    @atomprobe-tc
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  8. Refactored NXmicrostructure_feature_set to map to NXmicrostructure_re… 

    …con and eventually make this NXmicrostructure
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  9. Removed NXmicrostructure_recon

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  10. Fix documentation generation

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  11. Continuing on NXmicrostructure

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Commits on Jul 10, 2024

  1. Finished NXmicrostructure

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  2. Fix docs CI to only keep orphan branch

    @lukaspie
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  3. Finalized data model for NXmicrostructure_imm

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  4. Finished data model example for NXmicrostructure_kanapy

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  5. add step to remove build artifacts

    @lukaspie
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  6. Activate .github/workflows/fairmat-build-pages.yaml 

    Co-authored-by: Florian Dobener <[email protected]>
    @lukaspie @domna
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  7. readd units to NXbeam polarization

    @lukaspie
    lukaspie committed Jul 10, 2024
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  8. move existing docs before making orphan branch

    @lukaspie
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  9. reactivate ci workflow

    @lukaspie
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  10. modify moving of existing docs

    @lukaspie
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  11. remove commented CI code that is not needed anymore

    @lukaspie
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  12. Merge pull request #268 from FAIRmat-NFDI/237-repository-extremely-large 

    Fix docs CI to only keep orphan branch
    @lukaspie
    lukaspie authored Jul 10, 2024
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Commits on Jul 11, 2024

  1. Opened NXem_conventions for usage in methods other than electron micr… 

    …oscopy
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  2. Consolidated based classes related to NXem_conventions into NXcoordin… 

    …ate_system_set because that is what these conventions only talk about
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  3. Refactored NXmicrostructure_score_config

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  4. Refactored NXmicrostructure_gragles_config

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  5. Even make html runs through locally

    @atomprobe-tc
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  6. remove _source build artifacts before docs deployment

    @lukaspie
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  7. Merge pull request #266 from FAIRmat-NFDI/mpes-clarifications 

    Small modifications to clarify NXmpes
    @lukaspie
    lukaspie authored Jul 11, 2024
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  8. Merge pull request #269 from FAIRmat-NFDI/remove-build-artifacts-duri… 

    …ng-deployment

Remove _sources build artifacts before docs deployment
    @lukaspie
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  9. Finished NXmicrostructure_score_results and hope that commenting out … 

    …the rollett-holm formula fixes the build error with latex, locally at least it does
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  10. Fixed the too stiff name of microstructure1

    @atomprobe-tc
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  11. Initial version of NXmicrostructure_gragles_results

    @atomprobe-tc
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  12. Fixed grammar issue

    @atomprobe-tc
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  13. Finished NXmicrostructure_gragles_results

    mkuehbach committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Implemented suggestions from @lukaspie

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  2. nxdl

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Commits on Jul 15, 2024

  1. NXdata linking of signal (#205) 

    * 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]>
    @domna @lukaspie
    domna and lukaspie authored Jul 15, 2024
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  2. Merge branch 'fairmat' into sprint22_microstructure

    @atomprobe-tc
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  3. Merge branch 'fairmat' into sprint22_corrector

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Commits on Jul 16, 2024

  1. Roll back changes to NXmpes/instrument/pressure_gauge

    @lukaspie
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  2. Merge pull request #271 from FAIRmat-NFDI/mpes-pressure-gauge 

    Roll back changes to NXmpes/instrument/pressure_gauge
    @lukaspie
    lukaspie authored Jul 16, 2024
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Commits on Jul 19, 2024

  1. fix 2theta and use NXobject instead of collection.

    @RubelMozumder
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Commits on Jul 22, 2024

  1. reproducibity check.

    @RubelMozumder
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  2. Merge pull request #272 from FAIRmat-NFDI/XRD_2thta_fix 

    fix 2theta and use NXobject instead of collection.
    @RubelMozumder
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Commits on Jul 23, 2024

  1. add radius to NXenergydispersion

    @lukaspie
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  2. Merge pull request #273 from FAIRmat-NFDI/add-energydispersion-radius 

    Add radius to NXenergydispersion
    @lukaspie
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Commits on Jul 26, 2024

  1. Xrd modification (#274) 

    * 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]>
    @RubelMozumder @domna
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Commits on Jul 30, 2024

  1. Merge branch 'fairmat' into sprint22_microstructure

    @atomprobe-tc
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  2. Merge branch 'fairmat' into sprint22_corrector

    @atomprobe-tc
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  3. Merge pull request #275 from FAIRmat-NFDI/sprint22_corrector 

    Replacement for closed #270
    @mkuehbach
    mkuehbach authored Jul 30, 2024
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  4. Implementing suggestions from lukaspie

    @atomprobe-tc
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  5. Refactored NXcoordinate_system_em_ebsd into NXem_ebsd

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  6. Merge branch 'sprint23_em_v3' into sprint22_microstructure

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  7. Merge pull request #276 from FAIRmat-NFDI/sprint22_microstructure 

    Replacement for #267
    @mkuehbach
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Commits on Aug 6, 2024

  1. Fix naming bug for monochromator_em

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Commits on Aug 9, 2024

  1. Bug fixes in images and spectrum and renaming of groups, refining pre… 

    …cision of concept image and how this is connected to tilings
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Commits on Aug 13, 2024

  1. Add circuit to component

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  2. Adding routine tests for py3.12

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  3. Added circuit and corrected laziness error

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  4. Editing NXem for aberrations in event data

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  5. Extension of Doc for Optical spectroscopy and Raman

    Ron Hildebrandt authored and Ron Hildebrandt committed Aug 13, 2024
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  6. Update webpage for optical spectroscopy

    Ron Hildebrandt authored and Ron Hildebrandt committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. Further simplification of where and how to store aberrations

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  2. change ellips name to optical spec

    Ron Hildebrandt authored and Ron Hildebrandt committed Aug 14, 2024
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  3. Use something from lensID

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  4. Correcting units for complex aberrations

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  5. Removed mandatory model for aberrations as clear for naming conventio… 

    …ns used
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Commits on Aug 16, 2024

  1. Reference Rafal for aberration function

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Commits on Aug 20, 2024

  1. Fixed time(NX_TIME) bug

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Commits on Aug 26, 2024

  1. fix_renaming_of_ellipsometry_to_optical_spec

    Ron Hildebrandt authored and Ron Hildebrandt committed Aug 26, 2024
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  2. add missed links

    Ron Hildebrandt authored and Ron Hildebrandt committed Aug 26, 2024
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  3. add missing #### in title...

    Ron Hildebrandt authored and Ron Hildebrandt committed Aug 26, 2024
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Commits on Aug 28, 2024

  1. Merge pull request #279 from FAIRmat-NFDI/update_optical_spec_website 

    Update optical spec website to include optical spectroscopy and raman
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Commits on Aug 30, 2024

  1. Merge branch 'fairmat' into sprint23_em_v3

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  2. Clarified issues with depends_on, fixed typo pID for pfID in NXem_ebsd

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  3. Hooked in examples for usage of NXem_ebsd and NXem_eds into NXem

    @atomprobe-tc
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  4. Merge pull request #223 from FAIRmat-NFDI/namefit-docs 

    Add edge cases to namefit documentation
    @lukaspie
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  5. Last cleaning for depends_on on this feature branch

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  6. <<<<Merge branch 'fairmat' into sprint23_em_v3

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  7. Initial draft of NXmpes_xps sub app-def

    @lukaspie
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  8. Prepare NXmpes_xps for extending NXmpes

    @lukaspie
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  9. Removed information already given in base classes

    @lukaspie
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  10. Removed some unneeded comments

    @lukaspie
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  11. Add description of instrument orientation 

    - Angle between beam and sample normal-> needed for determination of probing depth
- Angle between beam and analyzer axes -> needed for data analysis
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  12. Move orientation of instrument parts 

    Instead of having two fields on the instrument for the angle between beam and sample and the angle between beam and analyser, this information is stored in depends_on and NXtransformations in NXinstrument and NXsample, respectively.
    @lukaspie
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  13. Update transmission function information 

     - The transmission function contains an additional NXnote field "file" describing the file in which the TF data is stored.
    @lukaspie
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  14. Update documentation, add comments for discussion

    @lukaspie
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  15. Initial draft of NXmpes_xps sub app-def

    @lukaspie
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  16. Prepare NXmpes_xps for extending NXmpes

    @lukaspie
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  17. Removed information already given in base classes

    @lukaspie
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  18. Removed some unneeded comments

    @lukaspie
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  19. Add description of instrument orientation 

    - Angle between beam and sample normal-> needed for determination of probing depth
- Angle between beam and analyzer axes -> needed for data analysis
    @lukaspie
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  20. Move orientation of instrument parts 

    Instead of having two fields on the instrument for the angle between beam and sample and the angle between beam and analyser, this information is stored in depends_on and NXtransformations in NXinstrument and NXsample, respectively.
    @lukaspie
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  21. Update transmission function information 

     - The transmission function contains an additional NXnote field "file" describing the file in which the TF data is stored.
    @lukaspie
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  22. Update documentation, add comments for discussion

    @lukaspie
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  23. fix NXmpes yaml

    @lukaspie
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  24. update to current NXmpes status

    @lukaspie
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  25. refine NXtransformations

    @lukaspie
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  26. add coordinate system and coordinate_system_set

    @lukaspie
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  27. Adds mpes_xps to mpes structure

    @domna @lukaspie
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  28. rename to NXxps

    @lukaspie
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  29. initial attempt at modeling XPS peak fitting

    @lukaspie
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  30. add lineshape to NXpeak

    @lukaspie
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  31. update lineshape in NXpeak

    @lukaspie
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  32. add NXbackground to NXfit_region

    @lukaspie
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  33. add fitting method to NXpeak_model

    @lukaspie
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  34. remove NXtransformations from NXcoordinate_system

    @lukaspie
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  35. restructure NXfit with background and peaks

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  36. change to NXcoordinate_system_set, use NXfit in NXxps

    @lukaspie
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  37. add fit_function and parameters

    @lukaspie
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  38. use NXfit_function for peaks and backgrounds

    @lukaspie
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  39. use NXdata in NXfit

    @lukaspie
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  40. use new peak fitting in NXxps

    @lukaspie
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  41. add missing class name in NXxps

    @lukaspie
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  42. remove underscores from variable names in NXfit

    @lukaspie
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  43. update nyamls

    @lukaspie
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  44. switch axes docs in NXfit

    @lukaspie
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  45. use old nyaml dim notation for now

    @lukaspie
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  46. fix math notation

    @lukaspie
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  47. make nxdls

    @lukaspie
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  48. regenerate with nyaml==0.0.8

    @lukaspie
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  49. make NXfit, NXpeak multi-dimensional

    @lukaspie
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  50. redefine XPS coordinate system, small changes to XPS peak fitting

    @lukaspie
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  51. required energy axis in XPS

    @lukaspie
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  52. fix dimensions issues

    @lukaspie
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  53. regenerate NXxps

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  54. make energy an NX_NUMBER

    @lukaspie
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  55. remove unneeded depends_on enumerations

    @lukaspie
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  56. align symbols across all fit-related definitions

    @lukaspie
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  57. remove single and repeated parameters in fit

    @lukaspie
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  58. fix dimensions in NXpeak and NXfit_background

    @lukaspie
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  59. use globlal_fit and error_function in NXfit, fix dimensions

    @lukaspie
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  60. docstring fixes in NXfit

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  61. NXfit extends NXprocess

    @lukaspie
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  62. fix math notation in NXfit_function

    @lukaspie
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  63. fix link in NXfit_function

    @lukaspie
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  64. change requiredness for formulas in XPS fit

    @lukaspie
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  65. small fixes for links

    @lukaspie
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  66. fix issues with manual build

    @lukaspie
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  67. fix math notation

    @lukaspie
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  68. more math fixes

    @lukaspie
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  69. regenerate NXxps and NXpeak nxdl files

    @lukaspie
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  70. fix rebasing issues

    @lukaspie
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  71. make NXpeak spectrum-independent

    @lukaspie
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  72. fix rebase conflicts

    @lukaspie
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  73. fix nyaml-nxdl inconsistency

    @lukaspie
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Commits on Sep 3, 2024

  1. add notes from both workshops

    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 3, 2024
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  2. added make nxdl and make local

    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 3, 2024
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  3. lowercase enumeration, source_type todo added, doc for ellipsometry_type

    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 3, 2024
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  4. HOW LONG? does it take to learn to make nxdl and local before commiti… 

    …ng >.<
    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Fixes in EM

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  2. Merging NXem_adf into NXem_img, enabling microstructure reconstructio… 

    …ns as dependants of specific method results, introduction of NXatom_set to discuss generalization of NXion towards enabling descriptions of groups of atoms, also to lias with FAIRmat Area C
    @atomprobe-tc
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  3. Removal of non-standardized assumption that i, j, k can be used as co… 

    …unter variables in case one does not know the actual dimensions but one is sure it is not a scalar
    @atomprobe-tc
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Commits on Sep 6, 2024

  1. add missing elements in ellipsometry from specialized NXlens_opt

    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 6, 2024
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  2. Add todo notes for beamsize and shape description

    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 6, 2024
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  3. typo and note for possible rework/reconsideration of NXfabrication

    Ron Hildebrandt authored and Ron Hildebrandt committed Sep 6, 2024
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Commits on Sep 9, 2024

  1. Merge pull request #282 from FAIRmat-NFDI/add_workshop_notes_from_ell… 

    …ip_and_raman

Most changes here are just notes - Many todos were added, which have to be included for a future rework.
    @RonHildebrandt
    RonHildebrandt authored Sep 9, 2024
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  2. Merge branch 'fairmat' into sprint23_em_v3

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  3. Suggestions from lukaspie

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Commits on Sep 10, 2024

  1. Fixes apm

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  2. Added undefined enum in NXidentifier

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Commits on Sep 11, 2024

  1. Merge pull request #170 from FAIRmat-NFDI/158-xps-peak-fitting-in-nexus 

    Description of peak fitting (e.g., in XPS)
    @lukaspie
    lukaspie authored Sep 11, 2024
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  2. <Merge branch 'fairmat' into sprint23_em_v3

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  3. Merge pull request #278 from FAIRmat-NFDI/sprint23_em_v3 

    Sprint23 EM v3 and microstructure replacing #267 and #270
    @mkuehbach
    mkuehbach authored Sep 11, 2024
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  4. use NXidentifier in NXsample and NXfabrication

    @lukaspie
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  5. rename sample name in NXoptical spectroscopy

    @lukaspie
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  6. make ellipsometer_type optional

    @lukaspie
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  7. NXidentifier in NXoptical_spectroscopy instrument

    @lukaspie
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  8. remove NXsample name docs from NXoptical_spectroscopy

    @lukaspie
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  9. add serial_number to NXfabrication

    @lukaspie
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  10. use NXidentifier in NXmpes

    @lukaspie
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  11. use NXidentifier consistently across all our contributed definitions

    @lukaspie
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  12. decode binary strings in nxdl_utils.py

    @rettigl @lukaspie
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  13. add function for decoding

    @rettigl @lukaspie
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  14. use NXidentifier in NXentry

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  15. Merge pull request #283 from FAIRmat-NFDI/convert_binary_strings 

    decode binary strings in nxdl_utils.py
    @lukaspie
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  16. small changes to NXbeam and NXmonochromator

    @lukaspie
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  17. Merge pull request #285 from FAIRmat-NFDI/small-nxbeam-changes 

    Small changes to NXbeam and NXmonochromator
    @lukaspie
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  18. typo fixes

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  19. Merge pull request #284 from FAIRmat-NFDI/use-nx-identifier 

    Use NXidentifier more consistently
    @lukaspie
    lukaspie authored Sep 11, 2024
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  20. proper string decoding

    @lukaspie
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  21. remove unneeded imports

    @lukaspie
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  22. black formatting

    @lukaspie
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  23. remove code and move to pynxtools

    @lukaspie
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  24. remove unneeded requirements

    @lukaspie
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  25. escape black check

    @lukaspie
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  26. ignore flake8 issue

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  27. isort imports

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Commits on Sep 12, 2024

  1. use less strict version of str decoding

    @lukaspie
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  2. slightly enhanced version of str decoding, test

    @lukaspie
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  3. remove flake error catching

    @lukaspie
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  4. reset requirements.txt

    @lukaspie
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  5. reformatting

    @lukaspie
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  6. remove strict type checking

    @lukaspie
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  7. add support for list of bytes

    @lukaspie
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  8. formatting

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Commits on Sep 13, 2024

  1. Merge pull request #286 from FAIRmat-NFDI/strict-string-check 

    Modify byte decoding
    @lukaspie
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  2. add pulse_delay to NXbeam

    @lukaspie
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  3. recreate nyaml file

    @lukaspie
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  4. Merge pull request #288 from FAIRmat-NFDI/pulse-delay-in-nxbeam 

    pulse_delay in NXbeam
    @lukaspie
    lukaspie authored Sep 13, 2024
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Commits on Sep 16, 2024

  1. Merge branch 'nexusformat/deifinitions/main' into fairmat-2024

    @lukaspie
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  2. regenerate nyaml files

    @lukaspie
    lukaspie committed Sep 16, 2024
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  3. various small fixes are merging main and fairmat

    @lukaspie
    lukaspie committed Sep 16, 2024
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  4. fix string No in NXelectron_level

    @lukaspie
    lukaspie committed Sep 16, 2024
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  5. remove unused MANIFEST.in

    @lukaspie
    lukaspie committed Sep 16, 2024
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  6. manually reset NXem yaml file

    @lukaspie
    lukaspie committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. format base classes and applications in accordance to existing NIAC v… 

    …ersion
    @lukaspie
    lukaspie committed Sep 17, 2024
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  2. revert changes to NXtransformations docs

    @lukaspie
    lukaspie committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. add CSS tweak to hide summary

    @lukaspie
    lukaspie committed Sep 18, 2024
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  2. add css file

    @lukaspie
    lukaspie committed Sep 18, 2024
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  3. Merge pull request #293 from FAIRmat-NFDI/add-ccs-tweak-to-hide-summary 

    Add CSS tweak to hide summary
    @lukaspie
    lukaspie authored Sep 18, 2024
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Commits on Sep 19, 2024

  1. Suggestions from Lukas

    @atomprobe-tc
    atomprobe-tc committed Sep 19, 2024
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  2. fix dev_tools tests 

    black code style
    @lukaspie
    lukaspie committed Sep 19, 2024
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  3. remove use of details_summary_hide

    @lukaspie
    lukaspie committed Sep 19, 2024
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  4. change refs in NXarpes

    @lukaspie
    lukaspie committed Sep 19, 2024
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  5. move doc bundles to applications and base_classes

    @lukaspie
    lukaspie committed Sep 19, 2024
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  6. Merge commit '09aa5191d2e327d74f54e20aac091c94661b90fe' into fairmat-… 

    …2024
    @lukaspie
    lukaspie committed Sep 19, 2024
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  7. Reverting the proposal that NXmicrostructure is not just proposed for… 

    … contributed but implicitly as a dependency of NXem, NXem_ebsd, NXem_img proposed for voting and acceptance
    @atomprobe-tc
    atomprobe-tc committed Sep 19, 2024
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  8. Merge commit '5ac17fba2c96b83b3aa40446ba3f57b877be93bf' into fairmat-… 

    …2024
    @lukaspie
    lukaspie committed Sep 19, 2024
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  9. Revert one more microstructure

    @atomprobe-tc
    atomprobe-tc committed Sep 19, 2024
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  10. Merge commit '4e485a6cb4b185da158439b6e6c726e628eb1740' into fairmat-… 

    …2024
    @lukaspie
    lukaspie committed Sep 19, 2024
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  11. move new definitions to application and base_classes

    @lukaspie
    lukaspie committed Sep 19, 2024
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  12. small update to mpes-structure

    @lukaspie
    lukaspie committed Sep 19, 2024
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Commits on Sep 20, 2024

  1. update category for NXxrd.nxdl. (#296)

    @RubelMozumder
    RubelMozumder authored Sep 20, 2024
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  2. remove fairmat-specific files

    @lukaspie
    lukaspie committed Sep 20, 2024
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  3. remove nyaml files

    @lukaspie
    lukaspie committed Sep 20, 2024
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  4. move NXdata_mpes* classes back to contributed

    @lukaspie
    lukaspie committed Sep 20, 2024
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  5. revert small changes to the dev_tools 

    black formatting

isort dev_tools
    @lukaspie
    lukaspie committed Sep 20, 2024
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  6. change docs in NXcircuit

    @lukaspie
    lukaspie committed Sep 20, 2024
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  7. pull out modifications for fairmat-2024-mpes

    @lukaspie
    lukaspie committed Sep 20, 2024
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Commits on Sep 24, 2024

  1. remove classes from contributed that have been moved to base_classes 

    remove classes from contributed that have been moved to base_classes
    @lukaspie
    lukaspie committed Sep 24, 2024
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  2. bring in multiline doc handling

    @lukaspie
    lukaspie committed Sep 24, 2024
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  3. update type in NXsource

    @lukaspie
    lukaspie committed Sep 24, 2024
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Commits on Sep 29, 2024

  1. Merge commit '56e3ce5949752c5b096621116fae5b8bc98fad51' into fairmat-… 

    …2024-mpes
    @lukaspie
    lukaspie committed Sep 29, 2024
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  2. add merged NXaperture

    @lukaspie
    lukaspie committed Sep 29, 2024
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Commits on Oct 8, 2024

  1. remove unneeded base classes

    @lukaspie
    lukaspie committed Oct 8, 2024
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  2. use NXparameters in NXfit_function

    @lukaspie
    lukaspie committed Oct 8, 2024
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  3. workshopping ideas to get rid of NXprocess_mpes

    @lukaspie
    lukaspie committed Oct 8, 2024
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  4. bring in NXdata_mpes* classes

    @lukaspie
    lukaspie committed Oct 8, 2024
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Commits on Oct 16, 2024

  1. bring in changes to NXdata

    @lukaspie
    lukaspie committed Oct 16, 2024
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  2. Merge branch 'main' into fairmat-2024-mpes

    @lukaspie
    lukaspie committed Oct 16, 2024
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  3. reorder attributes in NXxps

    @lukaspie
    lukaspie committed Oct 16, 2024
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  4. units in NXfit_function

    @lukaspie
    lukaspie committed Oct 16, 2024
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  5. typo fix

    @lukaspie
    lukaspie committed Oct 16, 2024
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Commits on Nov 27, 2024

  1. small updates to NXxps and NXfit base classes

    @lukaspie
    lukaspie committed Nov 27, 2024
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  2. Merge remote-tracking branch 'upstream/main' into fairmat-2024-mpes

    @lukaspie
    lukaspie committed Nov 27, 2024
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  3. bring in NXdata from base class branch

    @lukaspie
    lukaspie committed Nov 27, 2024
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  4. remove unneeded file

    @lukaspie
    lukaspie committed Nov 27, 2024
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