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src/spatialdata_io/readers/xenium.py

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -390,15 +390,14 @@ def _get_labels_and_indices_mapping(
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# this information will probably be available in the `label_id` column for version > 2.0.0 (see public
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# release notes mentioned above)
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real_label_index = _get_unique_label_values_as_index(labels)
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real_label_index = _get_unique_label_values_as_index(labels).values
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# background removal
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if real_label_index[0] == 0:
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real_label_index = real_label_index[1:]
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if version < packaging.version.parse("2.0.0"):
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expected_label_index = z["seg_mask_value"][...]
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real_label_index = _get_unique_label_values_as_index(labels).values
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if not np.array_equal(expected_label_index, real_label_index):
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raise ValueError(

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