FAIRmat-NFDI / pynxtools-spm

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• 69-integrate-north-tools-as-a-cicd-part
• AddCruftStructure
• ApplyNorth
• BrukerFile
• CollectDataFromZenodo
• DimensionEdgeInstrumentPublish
• ExampleUPloadTask
• FixApp
• FixAxisName
• FixInvalidateConceptInFlt
• FixTest
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• UpdateDocs
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• ZenodoUploadsAndSpmImagePublish
• adjust-to-new-pynx-read-output
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• dataconverter-deprecated
• fixNoneString
• main
• nomad-tests
• release_2_3

Build # 32974612526

Build Type

push

github

Committed by web-flow

Commit Message

Read Bruker NanoScope .spm with gwyddionpy instead of pySPM (#99)

pySPM was pulled in as a direct git reference to a fork, which PyPI rejects
outright ("400 Can't have direct dependency"), and every pySPM release caps
requires-python at <3.13. Gwyddion's `nanoscope` importer reads the format
too, and gwyddionpy is already a dependency for the SPMLab .flt reader, so
SpmBruker now builds on it and pySPM is dropped from pyproject.toml.

gwyddionpy returns SI values with Gwyddion's unconditional vertical flip
applied and merges every header section into one flat per-channel dict, so
the parser:

- takes the image arrays from gwyddionpy and reads the ASCII header itself,
  preserving the /File/, /Equipment_list/, /Scanner_list/ and
  /Scan/<channel>/<direction>/ key layout the config files address;
- identifies each layer from `@2:Image Data` and `Line Direction` rather
  than from gwyddionpy's channel labels;
- converts each layer back to its own unit with a factor derived from the
  sensitivity named by the layer's `@2:Z scale`, including the factor 1000
  for the channels whose Z scale is written in millivolts.

The migration is output-neutral: all 119 tests pass against the committed
reference NeXus files, and the conversion examples reproduce their run log.

Reading the header directly also fixes the truncation of /File/* and
/Equipment_list/* values to their first character; no config refers to
those paths, so the generated files are unaffected.

Coverage Stats

371 of 375 relevant lines covered (98.93%)

0.99 hits per line