MACSima: added reader

[berombau]

Redo of previous work in #156.

This tries to solve #155.

Lung_adc_demo

from spatialdata_io import macsima
sdata = macsima('./Lung_adc_demo', subset=1000)
sdata

Note that now the cycle information is added to a table and that the coordinate systems are named after the dataset.

SpatialData object
├── Images
│     └── 'Lung_adc_demo_image': DataTree[cyx] (116, 1000, 1000), (116, 500, 500)
└── Tables
      └── 'Lung_adc_demo_table': AnnData (0, 116)
with coordinate systems:
    ▸ 'Lung_adc_demo', with elements:
        Lung_adc_demo_image (Images)

For the LiverCellAtlas data, it stores all middle cycle nuclei channels in a different image and table.

SpatialData object
├── Images
│     ├── 'HumanLiverH36_image': DataTree[cyx] (102, 5772, 6621), (102, 2886, 3310), (102, 1443, 1655), (102, 721, 827)
│     └── 'HumanLiverH36_nuclei_image': DataTree[cyx] (50, 5772, 6621), (50, 2886, 3310), (50, 1443, 1655), (50, 721, 827)
└── Tables
      ├── 'HumanLiverH36_nuclei_table': AnnData (0, 50)
      └── 'HumanLiverH36_table': AnnData (0, 102)
with coordinate systems:
    ▸ 'HumanLiverH36', with elements:
        HumanLiverH36_image (Images), HumanLiverH36_nuclei_image (Images)

Parsing of raw data should be another PR. It differs in the handling of metadata for channels and cycles from https://gustaveroussy.github.io/sopa/api/io/#sopa.io.macsima @quentinblampey.

The channel naming is different (R{cycle} {marker} instead of {marker}{ (duplicate_number if duplicate markers)). I like both styles, so I'll try to add later style as well and add a parameter.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 27.35849% with 154 lines in your changes missing coverage. Please review.

Project coverage is 43.68%. Comparing base (ed60d9f) to head (c4f6cf7).
Report is 30 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/macsima.py	28.97%	125 Missing ⚠️
src/spatialdata_io/readers/_utils/_utils.py	17.14%	29 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #224      +/-   ##
==========================================
- Coverage   45.31%   43.68%   -1.63%     
==========================================
  Files          22       23       +1     
  Lines        2143     2353     +210     
==========================================
+ Hits          971     1028      +57     
- Misses       1172     1325     +153     

Files with missing lines	Coverage Δ
src/spatialdata_io/__init__.py	100.00% <100.00%> (ø)
src/spatialdata_io/readers/_utils/_utils.py	31.46% <17.14%> (-9.29%)	⬇️
src/spatialdata_io/readers/macsima.py	28.97% <28.97%> (ø)

[Copilot]

Copilot reviewed 6 out of 6 changed files in this pull request and generated 1 suggestion.

[LucaMarconato]

Great work @berombau! And it was a nice sprint today. Ready to merge!