Use scanpy for reading matrixes

README.md

@@ -111,8 +111,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
 [link-docs]: https://spatialdata.scverse.org/projects/io/en/latest/
 [link-api]: https://spatialdata.scverse.org/projects/io/en/latest/api.html
 [link-cli]: https://spatialdata.scverse.org/projects/io/en/latest/cli.html
-
-[//]: # (numfocus-fiscal-sponsor-attribution)
+[//]: # "numfocus-fiscal-sponsor-attribution"
 
 spatialdata-io is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
 If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

src/spatialdata_io/readers/_utils/_utils.py

@@ -5,14 +5,13 @@
 from pathlib import Path
 from typing import Any, Union
 
+import scanpy as sc
 from anndata import AnnData, read_text
 from h5py import File
 from ome_types import from_tiff
 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/xenium.py

@@ -17,6 +17,7 @@
 import packaging.version
 import pandas as pd
 import pyarrow.parquet as pq
+import scanpy as sc
 import tifffile
 import zarr
 from anndata import AnnData
@@ -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()