Em, APM, CG, Microstructure for preparing the next pynxtools and NOMAD release#400
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mkuehbach
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Jul 28, 2025
mkuehbach
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- EM
- APM
- Computational geometry
- Microstructure
…eserved NeXus keyword versus renaming many of these to index_offset, indices_*
…se NX_POSINT, NX_UINT, harmonizing that all index and indices use NX_INT
…plus proofreading
…x is present writing tsl and mtex
…per decision of the NIAC nexusformat#1423 (comment)
…r thinking further about grouping NXevent_data instance or not I thought it could also be a valid argument that as why should the standard force people to not have thousands of groups ending up at the same level of the hierarchy. Clearly, there is nothing which prevents sb from doing this for the example of HDF5 but performance-wise this is problematic, there are multiple examples even in commercial microscope software solutions where indeed HDF5 files with thousands and more groups at the same level are stored using HDF5, while there is overhead involved in this and searching by humans might be ineffective it is still a valid HDF5 file according to the HDF5 data model. Also NeXus with allowing an (NXentry) de facto allows to make an instance where thousands of e.g. entry1, entry2, ... are stored in the same HDF5 file also here no attempt has been made to build another group to just suggest strongly that people avoid this practice. Therefore, I removed one layer of indentation within NXem_measurement so that in an instance one now can have instrument, event1, event2, .. It is a design issue with NeXus that when we accept and wish that one cannot use NXobject as a plain structuring element but at the same time does not wish ones content to become at the schema level already non verified like when using an NXcollection there is no practice to group content other than making a new base class such for the sake of it holding the grouping.
…oot of an app or class def
…Type: any with docstring Instances should by nameType partial and prefixID, lot 1, apm and cg
…sion with the NIAC when specifically as documented in https://github.com/nexusformat/definitions/pull/1415/files
…starting with the inline comments, next step, address remaining comments that were made directly in the PR discussion
…s_computer, ii) review remaining large EM base classes
…pdefs and baseclasses where inconsistent with those from the NIAC on their current main ecc9361
… will start in two days and wont change fundamentally once voting starts) back changes for em proposal evaluating against fairmat-2024-em branch commit 54f6d29
… also updated all XML headers from discouraged single to double straight quotes, all nyamls reprocessed clean
… concepts in NXtransformations should be checked) changes from optical spectroscopy evaluated against fairmat-2024-optical_spectroscopy 6bba40f
…n ancestor commits to this commit added either as they were accepted from the NIAC main or as they are speculatively assumed - to not further block modifications to the software tools - there are no remaining appdef changes that might still need some old FAIRamt contributed definitions. Therefore, this commit removes all yaml and nxdl files from all those classes that are no longer developed that have been promoted already to the base classes or appdefs or some classes which are no longer developed further, reasons were: i) removed because obsolete: NXion,roi,sample_component_set, ii) removed postpone for future: NXlab_electro...,lab_sample..., microstructure_gragles_..., microstructure_imm..., iii) remove promoted to appdef NXapm,ellipsometry,em,optical_spectroscopy,raman, iv) remove because promoted to base class, remaining of the removed
… from 2025/07/17 as seen by the updated fairmat-2024-em branch for which the voting started today, next steps, a few touches on remaining contributed definitions
…r per feature composition reporting
This was referenced Jul 28, 2025
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lukaspie
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Jul 28, 2025
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Some small questions, rest looks good.
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Branch not deleted yet as still used until new pynxtools version made |
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