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[WIP] add macsima reader #156

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wants to merge 12 commits into from
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[WIP] add macsima reader #156

wants to merge 12 commits into from

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berombau
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@berombau berombau commented Jun 11, 2024

This tries to solve #155.

Lung_adc_demo

from spatialdata_io import macsima
sdata = macsima('./Lung_adc_demo', subset=1000)
sdata
SpatialData object with:
└── Images
      └── 'Lung_adc_demo': MultiscaleSpatialImage[cyx] (116, 1000, 1000), (116, 500, 500)
with coordinate systems:
▸ 'microns', with elements:
        Lung_adc_demo (Images)

Sill need to check on Liver cell atlas data and the parsing issue of the channel names.

@codecov-commenter
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codecov-commenter commented Jun 11, 2024

Codecov Report

Attention: Patch coverage is 21.47239% with 128 lines in your changes missing coverage. Please review.

Project coverage is 34.86%. Comparing base (cff4896) to head (e73cb1d).
Report is 2 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_io/readers/macsima.py 21.27% 74 Missing ⚠️
src/spatialdata_io/readers/_utils/_utils.py 14.28% 54 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #156       +/-   ##
===========================================
- Coverage   45.50%   34.86%   -10.65%     
===========================================
  Files          22       23        +1     
  Lines        2149     2312      +163     
===========================================
- Hits          978      806      -172     
- Misses       1171     1506      +335     
Files with missing lines Coverage Δ
src/spatialdata_io/__init__.py 100.00% <100.00%> (ø)
src/spatialdata_io/_constants/_constants.py 100.00% <100.00%> (ø)
src/spatialdata_io/readers/_utils/_utils.py 19.35% <14.28%> (-23.27%) ⬇️
src/spatialdata_io/readers/macsima.py 21.27% <21.27%> (ø)

... and 4 files with indirect coverage changes

@LucaMarconato
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@berombau excited to see this new reader! What the status/task list for this PR? Thanks for the info.

@berombau
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It's on my to-do list of things to wrap up by the end of next week before I go on holiday. I would want to change the code a little so it can also run on multiple folders. It should also work on a raw data output folder with some modifications from the other scripts. There is also a small bug in the channel parsing still.

@berombau berombau mentioned this pull request Oct 21, 2024
@berombau
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Close in favor of #224

@berombau berombau closed this Oct 22, 2024
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3 participants