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

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Merged
timtreis merged 2 commits into from
May 21, 2026
+19 −5
Merged

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

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9c5fb8f
Skip wasted cs-level table copy in render_shapes/render_labels
timtreis May 21, 2026
bb4c2e2
Trim comments, flatten nested if in EntityID workaround
timtreis May 21, 2026
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24 changes: 19 additions & 5 deletions src/spatialdata_plot/pl/render.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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"] = (
Expand Down Expand Up @@ -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]
Expand Down
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