Merge pull request scverse#133 from melonora/main

make obs names unique

CHANGELOG.md

@@ -14,6 +14,11 @@ and this project adheres to [Semantic Versioning][].
 
 -   (Xenium) support reading multi-polygon selection files from the Xenium Explorer
 
+### Fixed
+
+-   (Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique.
+    obs_names_make_unique is now called internally to enforce unique index values allowing for join operations.
+
 ## [0.1.2] - 2024-03-30
 
 ### Added

src/spatialdata_io/readers/visium.py

@@ -168,6 +168,12 @@ def visium(
     adata.obs.drop(columns=[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y], inplace=True)
     adata.obs["spot_id"] = np.arange(len(adata))
     adata.var_names_make_unique()
+
+    if not adata.obs_names.is_unique:
+        logger.info("Non-unique obs names detected, calling `obs_names_make_unique`.")
+        # This is required for napari-spatialdata because of the join operation that would otherwise fail
+        adata.obs_names_make_unique()
+
     if (path / "spatial" / VisiumKeys.SCALEFACTORS_FILE).exists() or (
         scalefactors_file is not None and (path / scalefactors_file).exists()
     ):

src/spatialdata_io/readers/visium_hd.py

@@ -227,6 +227,7 @@ def load_image(path: Path, suffix: str, scale_factors: list[int] | None = None)
         # parse table
         adata.obs[VisiumHDKeys.REGION_KEY] = shapes_name
         adata.obs[VisiumHDKeys.REGION_KEY] = adata.obs[VisiumHDKeys.REGION_KEY].astype("category")
+
         tables[bin_size_str] = TableModel.parse(
             adata,
             region=shapes_name,