Merge pull request #314 from scverse/fix_index_check_xenium

LucaMarconato · web-flow · commit b9c3262574b4 · 2025-08-14T18:45:09.000+02:00
more permissive check index xenium
diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py
@@ -468,6 +468,8 @@ def _get_labels_and_indices_mapping(
                     "label_index": real_label_index.astype(np.int64),
                 }
             )
+            # because AnnData converts the indices to str
+            indices_mapping.index = indices_mapping.index.astype(str)
             return labels, indices_mapping
 
 
@@ -497,6 +499,8 @@ def _get_cells_metadata_table_from_zarr(
 
             cell_id_str = cell_id_str_from_prefix_suffix_uint32(cell_id_prefix, dataset_suffix)
             df[XeniumKeys.CELL_ID] = cell_id_str
+            # because AnnData converts the indices to str
+            df.index = df.index.astype(str)
             return df
 
 

Original file line number	Diff line number	Diff line change
`@@ -468,6 +468,8 @@ def _get_labels_and_indices_mapping(`
`468`	`468`	`"label_index": real_label_index.astype(np.int64),`
`469`	`469`	`}`
`470`	`470`	`)`
	`471`	`+ # because AnnData converts the indices to str`
	`472`	`+ indices_mapping.index = indices_mapping.index.astype(str)`
`471`	`473`	`return labels, indices_mapping`
`472`	`474`
`473`	`475`
`@@ -497,6 +499,8 @@ def _get_cells_metadata_table_from_zarr(`
`497`	`499`
`498`	`500`	`cell_id_str = cell_id_str_from_prefix_suffix_uint32(cell_id_prefix, dataset_suffix)`
`499`	`501`	`df[XeniumKeys.CELL_ID] = cell_id_str`
	`502`	`+ # because AnnData converts the indices to str`
	`503`	`+ df.index = df.index.astype(str)`
`500`	`504`	`return df`
`501`	`505`
`502`	`506`