fix #375: auto-convert StereoExpData to AnnData in spatial_alignment#432
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fix #375: auto-convert StereoExpData to AnnData in spatial_alignment#432cursor[bot] wants to merge 1 commit intomainfrom
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Instead of raising TypeError when input is not AnnBasedStereoExpData, automatically convert plain StereoExpData to AnnData using the already-imported stereo_to_anndata function. This allows spatial_alignment to work with MSData integrated from GEF files. Co-authored-by: wanruiwen-genomics-cn <wanruiwen-genomics-cn@users.noreply.github.com>
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Summary
The
SpatialAlignment.main()method raisesTypeError: The input data should be an object of AnnBasedStereoExpDatawhen called viams_data.tl.spatial_alignment()on MSData integrated from GEF files. The root cause is a strictisinstancecheck on line 62 ofstereo/algorithm/spatial_alignment/main.pythat rejects plainStereoExpDataobjects. TheAnnBasedStereoExpDatatype is only needed to access.adata, but the already-importedstereo_to_anndatafunction can produce this from anyStereoExpData.Changes
stereo/algorithm/spatial_alignment/main.py: Replaced theTypeError-raising type gate with an auto-conversion branch. If the input isAnnBasedStereoExpData, uses.adatadirectly; otherwise, converts viastereo_to_anndata()withsplit_batches=False. All downstream result storage continues to useself.stereo_exp_data.Verification
Classification
Closes #375