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Spectrum refactoring, Spectrum2DCollection (#305)
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A Spectrum2DCollection class is introduced, with a similar interface to Spectrum1DCollection.

- Common features of the two classes are broken out into a multiple-inheritance "mixin" class, so that Spectrum remains the common base of all spectra: Spectrum1D, Spectrum2D, Spectrum1DCollection and Spectrum2DCollection are all "children" on the same level and will not `isinstance` with each other.

- Some of the metadata handling has been refactored for legibility and robustness: select(), group_by() and internal methods

  - Some of this work uses toolz, which becomes a dependency for the main package. We don't anticipate that causing a lot of problems; it is a small, stable, pure-python library also available on conda-forge. Mantid core team were warned of this intention a month or two ago and seem happy enough.

- `iter_metadata` method is provided to allow iteration over spectrum indices (using enumerate) without the relatively slow overhead of creating new spectra (encounted when iterating over the collection object).

  - i.e. `list(collection.iter_metadata())` is much faster than `[spectrum.metadata for spectrum in collection]` because it avoids unnecessarily copying data and twiddling units.


Co-authored-by: Jacob Wilkins <46597752+oerc0122@users.noreply.github.com>
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@ajjackson @oerc0122
ajjackson and oerc0122 authored Sep 26, 2024
1 parent 8268881 commit ada9e25
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904 changes: 608 additions & 296 deletions euphonic/spectra.py
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3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -144,7 +144,8 @@ def run_setup():
'seekpath>=1.1.0',
'spglib>=1.9.4',
'pint>=0.22',
'threadpoolctl>=3.0.0'
'threadpoolctl>=3.0.0',
'toolz>=0.12.1',
],
extras_require={
'matplotlib': ['matplotlib>=3.8.0'],
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1 change: 1 addition & 0 deletions tests_and_analysis/minimum_euphonic_requirements.txt
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Expand Up @@ -7,3 +7,4 @@ matplotlib==3.8
h5py==3.6
PyYAML==6.0
threadpoolctl==3.0.0
toolz==0.12.1
267 changes: 267 additions & 0 deletions tests_and_analysis/test/data/spectrum2d/quartz_fuzzy_map_0.json
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