improve spatialdata file handling#171

Merged

sophiamaedler merged 14 commits intomainfrom

deprecate_cell_id_tracking

Feb 11, 2025

Commits on Feb 10, 2025

deprecate spLabels2DModel
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remove all occurances of .attrs["cell_ids"]
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[FIX] ensure channel names are preserved when reading input images from spatialdata object
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[FEATURE] make rechunking optional when reading from an existing spatialdata object
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adapt centers file naming convention so that each segmentation mask can have its own centers file
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[FIX] add support for calculating centers on multi-scaled segmentation masks
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[FIX] add center calculation to reading segmentation masks from spatialdata
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add center calculation to segmentation workflow
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[FEATURE] add method to automatically add an anndata object to the spatial data object
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[FIX] utilize filehandler.write_table_sdata method to reduce code overhead
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[FIX] bugs in write_table_sdata method
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ignore errors from shutil.rmtree call
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[LOG] add center calculation to log file
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[FIX] addresses #169, also adds short-term fix for #150
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