changes for issue288

Author: cgeyskens

src/spatialdata_io/readers/_utils/_read_10x_h5.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+import scanpy as sc
 from collections.abc import Mapping
 from pathlib import Path
 from typing import Any, Union
@@ -11,8 +12,6 @@
 from ome_types.model import Pixels, UnitsLength
 from spatialdata._logging import logger
 
-from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
-
 PathLike = Union[os.PathLike, str]  # type:ignore[type-arg]
 
 
@@ -24,7 +23,7 @@ def _read_counts(
 ) -> tuple[AnnData, str]:
     path = Path(path)
     if counts_file.endswith(".h5"):
-        adata: AnnData = _read_10x_h5(path / counts_file, **kwargs)
+        adata: AnnData = sc.read_10x_h5(path / counts_file, **kwargs)
         with File(path / counts_file, mode="r") as f:
             attrs = dict(f.attrs)
             if library_id is None:

src/spatialdata_io/readers/_utils/_utils.py

@@ -19,6 +19,7 @@
 import pyarrow.parquet as pq
 import tifffile
 import zarr
+import scanpy as sc
 from anndata import AnnData
 from dask.dataframe import read_parquet
 from dask_image.imread import imread
@@ -42,7 +43,6 @@
 from spatialdata_io._constants._constants import XeniumKeys
 from spatialdata_io._docs import inject_docs
 from spatialdata_io._utils import deprecation_alias
-from spatialdata_io.readers._utils._read_10x_h5 import _read_10x_h5
 from spatialdata_io.readers._utils._utils import _initialize_raster_models_kwargs
 
 __all__ = ["xenium", "xenium_aligned_image", "xenium_explorer_selection"]
@@ -520,7 +520,7 @@ def _get_points(path: Path, specs: dict[str, Any]) -> Table:
 def _get_tables_and_circles(
     path: Path, cells_as_circles: bool, specs: dict[str, Any]
 ) -> AnnData | tuple[AnnData, AnnData]:
-    adata = _read_10x_h5(path / XeniumKeys.CELL_FEATURE_MATRIX_FILE)
+    adata = sc.read_10x_h5(path / XeniumKeys.CELL_FEATURE_MATRIX_FILE)
     metadata = pd.read_parquet(path / XeniumKeys.CELL_METADATA_FILE)
     np.testing.assert_array_equal(metadata.cell_id.astype(str), adata.obs_names.values)
     circ = metadata[[XeniumKeys.CELL_X, XeniumKeys.CELL_Y]].to_numpy()