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Xenium Reader now filters out invalid polygons #283

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Xenium Reader now filters out invalid polygons #283

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9ac2d92
now removing faulty IDs
timtreis Feb 27, 2025
1abd69a
updated action
timtreis Mar 22, 2025
c0dcf5e
Merge branch 'main' into bugfix/issue245-linearring
LucaMarconato Jan 8, 2026
2e228cf
wip support for polygons with 3 vertices without filtering
LucaMarconato Jan 8, 2026
9768bfd
fix
LucaMarconato Jan 8, 2026
57a1cb2
ehapes in xenium remove constrain on representation
LucaMarconato Jan 9, 2026
091c5f3
fix formatting
LucaMarconato Jan 9, 2026
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8 changes: 2 additions & 6 deletions src/spatialdata_io/readers/xenium.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,7 @@
import logging
import os
import re
import tempfile
import warnings
import zipfile
from pathlib import Path
from types import MappingProxyType
from typing import TYPE_CHECKING, Any
Expand Down Expand Up @@ -418,9 +416,6 @@ def _get_polygons(
n_jobs: int,
idx: ArrayLike | None = None,
) -> GeoDataFrame:
def _poly(arr: ArrayLike) -> Polygon:
return Polygon(arr[:-1])

# seems to be faster than pd.read_parquet
df = pq.read_table(path / file).to_pandas()

Expand All @@ -429,8 +424,9 @@ def _poly(arr: ArrayLike) -> Polygon:
# convert the index to str since we will compare it with an AnnData object, where the index is a str
index.index = index.index.astype(str)
index = _decode_cell_id_column(index)

out = Parallel(n_jobs=n_jobs)(
delayed(_poly)(i.to_numpy())
delayed(Polygon)(i.to_numpy())
for _, i in group_by[[XeniumKeys.BOUNDARIES_VERTEX_X, XeniumKeys.BOUNDARIES_VERTEX_Y]]
)
geo_df = GeoDataFrame({"geometry": out})
Expand Down
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