Update metadata convention

[jlaehne]

Description of the change

Adapt the metadata structure according to the discussion in #2095

Progress of the PR

• update metadata documentation,
• Update occurences where metadata is accessed in HyperSpy,
• Create PR in RosettaSciIO to reflect the changes in the metadata structure,
• Check that tests are running on all ends,
• add an changelog entry in the upcoming_changes folder (see upcoming_changes/README.rst),
• Check formatting changelog entry in the readthedocs doc build of this PR (link in github checks)
• ready for review.

[codecov]

Codecov Report

Base: 80.60% // Head: 80.60% // No change to project coverage 👍

Coverage data is based on head (ada3a4c) compared to base (da5a683).
Patch has no changes to coverable lines.

Additional details and impacted files

@@                 Coverage Diff                 @@
##           RELEASE_next_major    #3093   +/-   ##
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  Coverage               80.60%   80.60%           
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  Files                     176      176           
  Lines                   24476    24476           
  Branches                 5383     5383           
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  Hits                    19729    19729           
  Misses                   3421     3421           
  Partials                 1326     1326           

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[jlaehne]

In hyperspy/rosettasciio#89 (comment) it was suggested to actually migrate to the NeXus metadata convention for electron microscopy, developed in the meantime, instead of improving our custom-scheme.

I'm copying in @sem-geologist @jordiferrero @CSSFrancis, as they were involved in the discussion in #2095.

[jlaehne]

The main difference between the current proposal and the Nexus definition seems to be to me that the information I proposed to put in source actually moves another level up and directly resides in instrument, but some of the parameters we currently have there then go into the subnodes EBEAM_COLUMN and OPTICAL_SYSTEM_EM.

A rough overview is given in the following, though in the details the structure would need to be more thorougly revised.

Current proposal, which tried to be more generic concerning type of experiment (e.g. allowing also a laser as source without using a different definition):

├── Acquisition_instrument
│   ├── Source
│   │   ├── source_type
│   │   ├── beam_current (nA)
│   │   ├── beam_energy (keV)
│   │   ├── ...
│   │   ├── Stage
│   │   │   ├── rotation (º)
│   │   │   ├── ...
│   │   └── working_distance (mm)
│   ├── Detector
│   │   ├── ...

NeXus scheme (selected components), which is again more EM specific:

├── em_lab - NXinstrument
│   ├── EBAM_COLUMN - NXebeam_column
│   │   ├── probe (e.g. electrons)
│   │   ├── voltage (kV)
│   │   └── ...
│   ├── OPTICAL_SYSTEM_EM - NXoptical_system_em
│   │   ├── working_distance (mm)
│   │   └── ...
│   ├── Stage - NXStage
│   │   ├── rotation (º)
│   │   └── ...
│   ├── Detector - NXdetector
│   │   ├── ...

[ericpre]

I am wondering if we should keep the metadata, as they are for HyperSpy 2.0 but plan for HyperSpy 3.0. Using the nexus definition for electron microscopy seems to be a very good option but it would take some time to do correctly. We need to get HyperSpy 2.0 released sooner than later and HyperSpy 3.0 could be focused solely on metadata changes.

[ericpre]

Re-opening because this has been closed automatically by mistake!