Skip wasted cs-level table copy in render_shapes/render_labels (#680)

Author: timtreis

src/spatialdata_plot/pl/render.py

@@ -411,9 +411,11 @@ def _render_shapes(
 
     _check_obs_var_shadow(sdata, element, col_for_color, render_params.table_name)
 
+    # filter_tables=False: join_spatialelement_table below overwrites the table,
+    # so the cs-level sparse copy is wasted work.
     sdata_filt = sdata.filter_by_coordinate_system(
         coordinate_system=coordinate_system,
-        filter_tables=bool(render_params.table_name),
+        filter_tables=False,
     )
 
     table_name = render_params.table_name
@@ -425,18 +427,28 @@ def _render_shapes(
 
         # Workaround for upstream spatialdata bug (scverse/spatialdata#1099):
         # join_spatialelement_table calls table.obs.reset_index() which fails when
-        # the obs index name matches an existing column (e.g. "EntityID" in Merfish data).
-        # Temporarily drop the conflicting index name for the join, then restore it.
+        # the obs index name matches an existing column (e.g. "EntityID" in Merfish
+        # data). When that collision is present, the obs index may also be a
+        # non-RangeIndex of int dtype, which AnnData's `_normalize_index` rejects
+        # when the join indexes back into the table. Temporarily swap to a clean
+        # RangeIndex / drop the conflicting name; restore on exit.
         _obs = sdata[table_name].obs
         _saved_index_name = _obs.index.name
-        if _saved_index_name is not None and _saved_index_name in _obs.columns:
+        _saved_index: pd.Index | None = None
+        _name_collides = _saved_index_name is not None and _saved_index_name in _obs.columns
+        if _name_collides and not isinstance(_obs.index, pd.RangeIndex):
+            _saved_index = _obs.index
+            _obs.index = pd.RangeIndex(len(_obs))
+        elif _name_collides:
             _obs.index.name = None
 
         try:
             element_dict, joined_table = join_spatialelement_table(
                 sdata, spatial_element_names=element, table_name=table_name, how="inner"
             )
         finally:
+            if _saved_index is not None:
+                _obs.index = _saved_index
             _obs.index.name = _saved_index_name
         sdata_filt[element] = shapes = element_dict[element]
         joined_table.uns["spatialdata_attrs"]["region"] = (
@@ -1748,9 +1760,11 @@ def _render_labels(
 
     _check_obs_var_shadow(sdata, element, col_for_color, table_name)
 
+    # filter_tables=False: match_table_to_element below already filters per
+    # element, so the cs-level sparse copy is wasted work.
     sdata_filt = sdata.filter_by_coordinate_system(
         coordinate_system=coordinate_system,
-        filter_tables=bool(table_name),
+        filter_tables=False,
     )
 
     label = sdata_filt.labels[element]