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Geometry encoding parameter for shapes #951

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Geometry encoding parameter for shapes #951

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22feee5
Geometry encoding parameter for shapes
keller-mark Jul 3, 2025
74690e4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 3, 2025
fc7d5ce
Update spatialdata.py
keller-mark Jul 18, 2025
76dd54e
Update io_shapes.py
keller-mark Jul 18, 2025
8680540
Update io_shapes.py
keller-mark Jul 18, 2025
5c0446e
Merge branch 'main' into keller-mark/geometry-encoding
keller-mark Sep 17, 2025
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11 changes: 10 additions & 1 deletion src/spatialdata/_core/spatialdata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1179,6 +1179,7 @@ def write(
overwrite: bool = False,
consolidate_metadata: bool = True,
format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
shapes_geometry_encoding: Literal["WKB", "geoarrow"] = "WKB",
) -> None:
"""
Write the `SpatialData` object to a Zarr store.
Expand Down Expand Up @@ -1223,6 +1224,7 @@ def write(
element_name=element_name,
overwrite=False,
format=format,
shapes_geometry_encoding=shapes_geometry_encoding,
)

if self.path != file_path:
Expand All @@ -1241,6 +1243,7 @@ def _write_element(
element_name: str,
overwrite: bool,
format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
shapes_geometry_encoding: Literal["WKB", "geoarrow"] = "WKB",
) -> None:
if not isinstance(zarr_container_path, Path):
raise ValueError(
Expand All @@ -1266,7 +1269,13 @@ def _write_element(
elif element_type == "points":
write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
elif element_type == "shapes":
write_shapes(shapes=element, group=element_type_group, name=element_name, format=parsed["shapes"])
write_shapes(
shapes=element,
group=element_type_group,
name=element_name,
format=parsed["shapes"],
geometry_encoding=shapes_geometry_encoding,
)
elif element_type == "tables":
write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
else:
Expand Down
4 changes: 3 additions & 1 deletion src/spatialdata/_io/io_shapes.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from collections.abc import MutableMapping
from pathlib import Path
from typing import Literal

import numpy as np
import zarr
Expand Down Expand Up @@ -68,6 +69,7 @@ def write_shapes(
name: str,
group_type: str = "ngff:shapes",
format: Format = CurrentShapesFormat(),
geometry_encoding: Literal["WKB", "geoarrow"] = "WKB",
) -> None:
import numcodecs

Expand All @@ -94,7 +96,7 @@ def write_shapes(
attrs["version"] = format.spatialdata_format_version
elif isinstance(format, ShapesFormatV02):
path = Path(shapes_group._store.path) / shapes_group.path / "shapes.parquet"
shapes.to_parquet(path)
shapes.to_parquet(path, geometry_encoding=geometry_encoding)

attrs = format.attrs_to_dict(shapes.attrs)
attrs["version"] = format.spatialdata_format_version
Expand Down
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