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Merge pull request #354 from scverse/fix/steinbock
fix steinbock
2 parents 06400c4 + a2bb7fc commit 26fb99b

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src/spatialdata_io/readers/steinbock.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -77,7 +77,7 @@ def steinbock(
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image_models_kwargs,
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)
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80-
adata = ad.read(path / SteinbockKeys.CELLS_FILE)
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adata = ad.read_h5ad(path / SteinbockKeys.CELLS_FILE)
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idx = adata.obs.index.str.split(" ").map(lambda x: int(x[1]))
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regions = adata.obs.image.str.replace(".tiff", "", regex=False)
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regions = regions.apply(lambda x: f"{x}_labels")
@@ -101,7 +101,7 @@ def steinbock(
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raise ValueError("Samples in table and images are inconsistent, please check.")
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table = TableModel.parse(adata, region=regions.unique().tolist(), region_key="region", instance_key="cell_id")
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return SpatialData(images=images, labels=labels, table=table)
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return SpatialData(images=images, labels=labels, tables={"table": table})
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def _get_images(

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