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Replace Image2DCollection with MultiscaleImage in Python and C++ #2946

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merged 14 commits into from
Sep 5, 2024

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@jp-dark jp-dark commented Aug 30, 2024

This PR cleans up the multiscale image pyramid class. It includes the following:

  • Merge ImageCollection and Image2DCollection into a single class
  • Rename new class to MultiscaleImage
  • Remove Collection methods from MultiscaleImage (e.g. ability to add subcollections, sparse arrays, etc.)
  • Add checking that all images have the same number of channels
  • Add checks for number of dimensions (NotImplemented for more than 2 spatial dimensions + 1 channel dimension for now)
  • Add method to get transformations from image levels
  • Update image name in experimental Visium ingestor

@jp-dark jp-dark marked this pull request as draft August 30, 2024 20:15
This required refactoring `BaseCollection` so `MultiscaleImage` and
`BaseCollection` both inherit from a new `SOMAGroup`, but
`MultiscaleImage` does not inherit the collection-specific methods.
@jp-dark jp-dark marked this pull request as ready for review September 4, 2024 19:00
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codecov bot commented Sep 4, 2024

Codecov Report

Attention: Patch coverage is 57.48299% with 125 lines in your changes missing coverage. Please review.

Project coverage is 80.08%. Comparing base (6fb2894) to head (0ec09bf).
Report is 2 commits behind head on spatial.

Additional details and impacted files
@@             Coverage Diff             @@
##           spatial    #2946      +/-   ##
===========================================
+ Coverage    80.05%   80.08%   +0.02%     
===========================================
  Files           45       46       +1     
  Lines         4719     4755      +36     
===========================================
+ Hits          3778     3808      +30     
- Misses         941      947       +6     
Flag Coverage Δ
python 80.08% <57.48%> (+0.02%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components Coverage Δ
python_api 80.08% <57.48%> (+0.02%) ⬆️
libtiledbsoma ∅ <ø> (∅)

@jp-dark jp-dark merged commit 275cd71 into spatial Sep 5, 2024
35 checks passed
@jp-dark jp-dark deleted the dark/multiscaleimage branch September 5, 2024 13:54
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