fix xenium index

quentinblampey · Jan 18, 2024 · 48d7d6f · 48d7d6f
1 parent c647f15
commit 48d7d6f
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Showing 3 changed files with 11 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
@@ -31,3 +31,4 @@ __pycache__/
 # other
 _version.py
 .code-workspace
+temp/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning][].
 
 -   (MERSCOPE) don't try to load unexisting elements #87
 -   (Visium) fixed axes ordering
+-   (Xenium) fixed index (fail on write)
 
 ## [0.0.9] - 2023-11-06
 

diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py
@@ -114,10 +114,15 @@ def xenium(
             XeniumKeys.NUCLEUS_BOUNDARIES_FILE,
             specs,
             n_jobs,
+            idx=table.obs[str(XeniumKeys.CELL_ID)].copy(),
         )
 
     polygons["cell_boundaries"] = _get_polygons(
-        path, XeniumKeys.CELL_BOUNDARIES_FILE, specs, n_jobs, idx=table.obs[str(XeniumKeys.CELL_ID)].copy()
+        path,
+        XeniumKeys.CELL_BOUNDARIES_FILE,
+        specs,
+        n_jobs,
+        idx=table.obs[str(XeniumKeys.CELL_ID)].copy(),
     )
 
     points = {}
@@ -194,6 +199,9 @@ def _get_tables_and_circles(
     metadata.drop([XeniumKeys.CELL_X, XeniumKeys.CELL_Y], axis=1, inplace=True)
     adata.obs = metadata
     adata.obs["region"] = specs["region"]
+    adata.obs["region"] = adata.obs["region"].astype("category")
+    if isinstance(adata.obs[XeniumKeys.CELL_ID].iloc[0], bytes):
+        adata.obs[XeniumKeys.CELL_ID] = adata.obs[XeniumKeys.CELL_ID].apply(lambda x: x.decode("utf-8"))
     table = TableModel.parse(adata, region=specs["region"], region_key="region", instance_key=str(XeniumKeys.CELL_ID))
     if cells_as_shapes:
         transform = Scale([1.0 / specs["pixel_size"], 1.0 / specs["pixel_size"]], axes=("x", "y"))