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add remote write support + cleanup#973

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melonora merged 7 commits into from
Aug 22, 2025
Merged

add remote write support + cleanup #973

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77c5bbe
refactor StoreLike to types
melonora Aug 20, 2025
4d12f4f
support remote write points and shapes
melonora Aug 20, 2025
fed71af
cleanup
melonora Aug 20, 2025
edf30a7
add additional remote write support
melonora Aug 22, 2025
e8fcb61
update dependency ome-zarr
melonora Aug 22, 2025
a2acd48
revert update dependency
melonora Aug 22, 2025
db41db0
support remote write tables
melonora Aug 22, 2025
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10 changes: 1 addition & 9 deletions src/spatialdata/_core/query/relational_query.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
"""
Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
match_element_to_table : Function to match a spatial element to a table.
join_spatialelement_table : General function, to join spatial elements with a table with more control.
"""
if table_name is None:
warnings.warn(
"Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
"Please provide the name of the table as argument to table_name.",
DeprecationWarning,
stacklevel=2,
)
table_name = "table"
_, table = join_spatialelement_table(
sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
)
Expand Down
119 changes: 37 additions & 82 deletions src/spatialdata/_core/spatialdata.py
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
Image2DModel,
Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
)

def _get_groups_for_element(
self, zarr_path: Path, element_type: str, element_name: str
self, zarr_path: StoreLike, element_type: str, element_name: str
) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
"""
Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
:class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
:class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
"""
from spatialdata._io._utils import _open_zarr_store

if isinstance(file_path, str):
file_path = Path(file_path)
self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
self._validate_all_elements()
if isinstance(file_path, Path):
# TODO: also validate remote paths
self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
self._validate_all_elements()

store = parse_url(file_path, mode="w").store
store = _open_zarr_store(file_path, mode="w")
zarr_group = zarr.group(store=store, overwrite=overwrite)
self.write_attrs(zarr_group=zarr_group)
store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
def _write_element(
self,
element: SpatialElement | AnnData,
zarr_container_path: Path,
zarr_container_path: StoreLike,
element_type: str,
element_name: str,
overwrite: bool,
format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
) -> None:
if not isinstance(zarr_container_path, Path):
if not isinstance(zarr_container_path, StoreLike):
raise ValueError(
f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
f"zarr_container_path must be a 'StoreLike' object "
f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
)
if isinstance(zarr_container_path, Path):
file_path_of_element = zarr_container_path / element_type / element_name
self._validate_can_safely_write_to_path(
file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
)
file_path_of_element = zarr_container_path / element_type / element_name
self._validate_can_safely_write_to_path(
file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
)

root_group, element_type_group, _ = self._get_groups_for_element(
zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

parsed = _parse_formats(formats=format)

# We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
if element_type == "images":
write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
elif element_type == "labels":
write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
elif element_type == "points":
write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
write_points(
points=element,
group=element_type_group,
name=element_name,
zarr_container_path=zarr_container_path,
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,
zarr_container_path=zarr_container_path,
format=parsed["shapes"],
)
elif element_type == "tables":
write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
-------
The table.
"""
warnings.warn(
"Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
DeprecationWarning,
stacklevel=2,
)
# Isinstance will still return table if anndata has 0 rows.
if isinstance(self.tables.get("table"), AnnData):
return self.tables["table"]
return None
raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

@table.setter
def table(self, table: AnnData) -> None:
warnings.warn(
"Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
DeprecationWarning,
stacklevel=2,
)
TableModel().validate(table)
if self.tables.get("table") is not None:
raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
self.tables["table"] = table
raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

@table.deleter
def table(self) -> None:
"""Delete the table."""
warnings.warn(
"del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
DeprecationWarning,
stacklevel=2,
)
if self.tables.get("table"):
del self.tables["table"]
else:
# More informative than the error in the zarr library.
raise KeyError("table with name 'table' not present in the SpatialData object.")
raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

@staticmethod
def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

return read_zarr(file_path, selection=selection)

def add_image(
self,
name: str,
image: DataArray | DataTree,
storage_options: JSONDict | list[JSONDict] | None = None,
overwrite: bool = False,
) -> None:
"""Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
_error_message_add_element()

def add_labels(
self,
name: str,
labels: DataArray | DataTree,
storage_options: JSONDict | list[JSONDict] | None = None,
overwrite: bool = False,
) -> None:
"""Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
_error_message_add_element()

def add_points(
self,
name: str,
points: DaskDataFrame,
overwrite: bool = False,
) -> None:
"""Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
_error_message_add_element()

def add_shapes(
self,
name: str,
shapes: GeoDataFrame,
overwrite: bool = False,
) -> None:
"""Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
_error_message_add_element()

@property
def images(self) -> Images:
"""Return images as a Dict of name to image data."""
Expand Down
6 changes: 2 additions & 4 deletions src/spatialdata/_io/_utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
# TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
if isinstance(path, str | Path):
Expand Down
7 changes: 5 additions & 2 deletions src/spatialdata/_io/io_points.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
_get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
points: DaskDataFrame,
group: zarr.Group,
name: str,
zarr_container_path: StoreLike,
group_type: str = "ngff:points",
format: Format = CurrentPointsFormat(),
) -> None:
axes = get_axes_names(points)
t = _get_transformations(points)

points_groups = group.require_group(name)
path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
store = points_groups._store
path = zarr_container_path / points_groups.path / "points.parquet"

# The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
# 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
c = c.cat.as_known()
points[column_name] = c

points.to_parquet(path)
points.to_parquet(path, filesystem=getattr(store, "fs", None))

attrs = format.attrs_to_dict(points.attrs)
attrs["version"] = format.spatialdata_format_version
Expand Down
9 changes: 7 additions & 2 deletions src/spatialdata/_io/io_shapes.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
shapes: GeoDataFrame,
group: zarr.Group,
name: str,
zarr_container_path: StoreLike,
group_type: str = "ngff:shapes",
format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
attrs = format.attrs_to_dict(geometry)
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)
store = shapes_group._store
path = zarr_container_path / shapes_group.path / "shapes.parquet"

# Geopandas only allows path-like objects for local filesystems and not remote ones.
shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

attrs = format.attrs_to_dict(shapes.attrs)
attrs["version"] = format.spatialdata_format_version
Expand Down
4 changes: 2 additions & 2 deletions src/spatialdata/_io/io_zarr.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
BadFileHandleMethod,
StoreLike,
_create_upath,
_open_zarr_store,
handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
"""
# stay in sync with ome v4 format spec:
# https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
store = _open_zarr_store(path, normalize_keys=False)
return _read_multiscale(store, raster_type="image")


Expand Down
9 changes: 7 additions & 2 deletions src/spatialdata/_types.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group
2 changes: 1 addition & 1 deletion tests/conftest.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
table = TableModel.parse(
table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
)
sdata.table = table
sdata["table"] = table
return sdata


Expand Down
2 changes: 1 addition & 1 deletion tests/core/operations/test_spatialdata_operations.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
adata = full_sdata["table"]
del adata.uns[TableModel.ATTRS_KEY]
del full_sdata.tables["table"]
full_sdata.table = TableModel.parse(
full_sdata["table"] = TableModel.parse(
adata,
region=["circles", "poly"],
region_key="annotated_shapes",
Expand Down
8 changes: 6 additions & 2 deletions tests/core/query/test_relational_query.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
matched_table = match_table_to_element(
sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
)
arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
sdata_query_aggregation["values_circles"].index = arr
matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
matched_table_reversed = match_table_to_element(
sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
)
assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

# TODO: add tests for labels
Expand Down
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add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
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add remote write support + cleanup#973

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 Merged

melonora
merged 7 commits into

from

Aug 22, 2025
 Merged


add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

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

9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


Expand Down

9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

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Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


Expand Down

2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
Expand Down

8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
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 Merged

melonora
merged 7 commits into

from

Aug 22, 2025
 Merged


add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

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

9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


Expand Down

9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

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Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


Expand Down

2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
Expand Down

8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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var __re = new RegExp('^' + ".*" + '
add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
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 Merged

melonora
merged 7 commits into

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Aug 22, 2025
 Merged


add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

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

9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


Expand Down

9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


Expand Down

2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
Expand Down

8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
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add remote write support + cleanup#973

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melonora
merged 7 commits into

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Aug 22, 2025
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add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

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

9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


Expand Down

9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


Expand Down

2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
Expand Down

8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
Skip to content
add remote write support + cleanup#973

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 Merged

melonora
merged 7 commits into

from

Aug 22, 2025
 Merged


add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

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

9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


Expand Down

9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


Expand Down

2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
Expand Down

8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
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 Merged

melonora
merged 7 commits into

from

Aug 22, 2025
 Merged


add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

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

9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


Expand Down

9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


Expand Down

2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
Expand Down

8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
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pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
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function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
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// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
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observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
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add remote write support + cleanup by melonora · Pull Request #973 · scverse/spatialdata · GitHub
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 Merged

melonora
merged 7 commits into

from

Aug 22, 2025
 Merged


add remote write support + cleanup
#973
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77c5bbe

refactor StoreLike to types


melonora Aug 20, 2025
4d12f4f

support remote write points and shapes


melonora Aug 20, 2025
fed71af

cleanup


melonora Aug 20, 2025
edf30a7

add additional remote write support


melonora Aug 22, 2025
e8fcb61

update dependency ome-zarr


melonora Aug 22, 2025
a2acd48

revert update dependency


melonora Aug 22, 2025
db41db0

support remote write tables


melonora Aug 22, 2025

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10 changes: 1 addition & 9 deletions
src/spatialdata/_core/query/relational_query.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -716,7 +716,7 @@ def _call_join(
 return elements_dict, table


def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str = "table") -> AnnData:
def match_table_to_element(sdata: SpatialData, element_name: str, table_name: str) -> AnnData:
 """
 Filter the table and reorders the rows to match the instances (rows/labels) of the specified SpatialElement.

Expand All@@ -738,14 +738,6 @@ def match_table_to_element(sdata: SpatialData, element_name: str, table_name: st
 match_element_to_table : Function to match a spatial element to a table.
 join_spatialelement_table : General function, to join spatial elements with a table with more control.
 """
 if table_name is None:
 warnings.warn(
 "Assumption of table with name `table` being present is being deprecated in SpatialData v0.1. "
 "Please provide the name of the table as argument to table_name.",
 DeprecationWarning,
 stacklevel=2,
 )
 table_name = "table"
 _, table = join_spatialelement_table(
 sdata=sdata, spatial_element_names=element_name, table_name=table_name, how="left", match_rows="left"
 )
Expand Down

119 changes: 37 additions & 82 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,7 +17,6 @@
from dask.delayed import Delayed
from geopandas import GeoDataFrame
from ome_zarr.io import parse_url
from ome_zarr.types import JSONDict
from shapely import MultiPolygon, Polygon
from xarray import DataArray, DataTree

Expand All@@ -30,8 +29,8 @@
 validate_table_attr_keys,
)
from spatialdata._logging import logger
from spatialdata._types import ArrayLike, Raster_T
from spatialdata._utils import _deprecation_alias, _error_message_add_element
from spatialdata._types import ArrayLike, Raster_T, StoreLike
from spatialdata._utils import _deprecation_alias
from spatialdata.models import (
 Image2DModel,
 Image3DModel,
Expand DownExpand Up@@ -598,7 +597,7 @@ def path(self, value: Path | None) -> None:
 )

 def _get_groups_for_element(
 self, zarr_path: Path, element_type: str, element_name: str
 self, zarr_path: StoreLike, element_type: str, element_name: str
 ) -> tuple[zarr.Group, zarr.Group, zarr.Group]:
 """
 Get the Zarr groups for the root, element_type and element for a specific element.
Expand DownExpand Up@@ -1205,12 +1204,16 @@ def write(
 :class:`~spatialdata._io.format.CurrentRasterFormat`, :class:`~spatialdata._io.format.CurrentShapesFormat`,
 :class:`~spatialdata._io.format.CurrentPointsFormat`, :class:`~spatialdata._io.format.CurrentTablesFormat`.
 """
 from spatialdata._io._utils import _open_zarr_store

 if isinstance(file_path, str):
 file_path = Path(file_path)
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()
 if isinstance(file_path, Path):
 # TODO: also validate remote paths
 self._validate_can_safely_write_to_path(file_path, overwrite=overwrite)
 self._validate_all_elements()

 store = parse_url(file_path, mode="w").store
 store = _open_zarr_store(file_path, mode="w")
 zarr_group = zarr.group(store=store, overwrite=overwrite)
 self.write_attrs(zarr_group=zarr_group)
 store.close()
Expand All@@ -1236,20 +1239,22 @@ def write(
 def _write_element(
 self,
 element: SpatialElement | AnnData,
 zarr_container_path: Path,
 zarr_container_path: StoreLike,
 element_type: str,
 element_name: str,
 overwrite: bool,
 format: SpatialDataFormat | list[SpatialDataFormat] | None = None,
 ) -> None:
 if not isinstance(zarr_container_path, Path):
 if not isinstance(zarr_container_path, StoreLike):
 raise ValueError(
 f"zarr_container_path must be a Path object, type(zarr_container_path) = {type(zarr_container_path)}."
 f"zarr_container_path must be a 'StoreLike' object "
 f"(str | Path | UPath | zarr.storage.StoreLike | zarr.Group), got: {type(zarr_container_path)}."
 )
 if isinstance(zarr_container_path, Path):
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )
 file_path_of_element = zarr_container_path / element_type / element_name
 self._validate_can_safely_write_to_path(
 file_path=file_path_of_element, overwrite=overwrite, saving_an_element=True
 )

 root_group, element_type_group, _ = self._get_groups_for_element(
 zarr_path=zarr_container_path, element_type=element_type, element_name=element_name
Expand All@@ -1259,14 +1264,27 @@ def _write_element(

 parsed = _parse_formats(formats=format)

 # We pass on zarr_container_path to ensure proper paths when writing to remote system even when on windows.
 if element_type == "images":
 write_image(image=element, group=element_type_group, name=element_name, format=parsed["raster"])
 elif element_type == "labels":
 write_labels(labels=element, group=root_group, name=element_name, format=parsed["raster"])
 elif element_type == "points":
 write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
 write_points(
 points=element,
 group=element_type_group,
 name=element_name,
 zarr_container_path=zarr_container_path,
 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,
 zarr_container_path=zarr_container_path,
 format=parsed["shapes"],
 )
 elif element_type == "tables":
 write_table(table=element, group=element_type_group, name=element_name, format=parsed["tables"])
 else:
Expand DownExpand Up@@ -1797,41 +1815,16 @@ def table(self) -> None | AnnData:
 -------
 The table.
 """
 warnings.warn(
 "Table accessor will be deprecated with SpatialData version 0.1, use sdata.tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 # Isinstance will still return table if anndata has 0 rows.
 if isinstance(self.tables.get("table"), AnnData):
 return self.tables["table"]
 return None
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.setter
 def table(self, table: AnnData) -> None:
 warnings.warn(
 "Table setter will be deprecated with SpatialData version 0.1, use tables instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 TableModel().validate(table)
 if self.tables.get("table") is not None:
 raise ValueError("The table already exists. Use del sdata.tables['table'] to remove it first.")
 self.tables["table"] = table
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @table.deleter
 def table(self) -> None:
 """Delete the table."""
 warnings.warn(
 "del sdata.table will be deprecated with SpatialData version 0.1, use del sdata.tables['table'] instead.",
 DeprecationWarning,
 stacklevel=2,
 )
 if self.tables.get("table"):
 del self.tables["table"]
 else:
 # More informative than the error in the zarr library.
 raise KeyError("table with name 'table' not present in the SpatialData object.")
 raise AttributeError("The property 'table' is deprecated. use '.tables' instead.")

 @staticmethod
 def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialData:
Expand All@@ -1853,44 +1846,6 @@ def read(file_path: Path | str, selection: tuple[str] | None = None) -> SpatialD

 return read_zarr(file_path, selection=selection)

 def add_image(
 self,
 name: str,
 image: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = image` instead.""" # noqa: D401
 _error_message_add_element()

 def add_labels(
 self,
 name: str,
 labels: DataArray | DataTree,
 storage_options: JSONDict | list[JSONDict] | None = None,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = labels` instead.""" # noqa: D401
 _error_message_add_element()

 def add_points(
 self,
 name: str,
 points: DaskDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = points` instead.""" # noqa: D401
 _error_message_add_element()

 def add_shapes(
 self,
 name: str,
 shapes: GeoDataFrame,
 overwrite: bool = False,
 ) -> None:
 """Deprecated. Use `sdata[name] = shapes` instead.""" # noqa: D401
 _error_message_add_element()

 @property
 def images(self) -> Images:
 """Return images as a Dict of name to image data."""
Expand Down

6 changes: 2 additions & 4 deletions
src/spatialdata/_io/_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -11,7 +11,7 @@
from enum import Enum
from functools import singledispatch
from pathlib import Path
from typing import Any, Literal, TypeAlias
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand All@@ -24,6 +24,7 @@
from zarr.storage import FSStore

from spatialdata._core.spatialdata import SpatialData
from spatialdata._types import StoreLike
from spatialdata._utils import get_pyramid_levels
from spatialdata.models._utils import (
 MappingToCoordinateSystem_t,
Expand DownExpand Up@@ -386,9 +387,6 @@ def save_transformations(sdata: SpatialData) -> None:
 sdata.write_transformations()


StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group


def _open_zarr_store(path: StoreLike, **kwargs: Any) -> zarr.storage.BaseStore:
 # TODO: ensure kwargs like mode are enforced everywhere and passed correctly to the store
 if isinstance(path, str | Path):
Expand Down

7 changes: 5 additions & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,6 +12,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentPointsFormat, PointsFormats, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import get_axes_names
from spatialdata.transformations._utils import (
 _get_transformations,
Expand DownExpand Up@@ -44,14 +45,16 @@ def write_points(
 points: DaskDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:points",
 format: Format = CurrentPointsFormat(),
) -> None:
 axes = get_axes_names(points)
 t = _get_transformations(points)

 points_groups = group.require_group(name)
 path = Path(points_groups._store.path) / points_groups.path / "points.parquet"
 store = points_groups._store
 path = zarr_container_path / points_groups.path / "points.parquet"

 # The following code iterates through all columns in the 'points' DataFrame. If the column's datatype is
 # 'category', it checks whether the categories of this column are known. If not, it explicitly converts the
Expand All@@ -64,7 +67,7 @@ def write_points(
 c = c.cat.as_known()
 points[column_name] = c

 points.to_parquet(path)
 points.to_parquet(path, filesystem=getattr(store, "fs", None))

 attrs = format.attrs_to_dict(points.attrs)
 attrs["version"] = format.spatialdata_format_version
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9 changes: 7 additions & 2 deletions
src/spatialdata/_io/io_shapes.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -13,6 +13,7 @@
 overwrite_coordinate_transformations_non_raster,
)
from spatialdata._io.format import CurrentShapesFormat, ShapesFormats, ShapesFormatV01, ShapesFormatV02, _parse_version
from spatialdata._types import StoreLike
from spatialdata.models import ShapesModel, get_axes_names
from spatialdata.transformations._utils import _get_transformations, _set_transformations

Expand DownExpand Up@@ -55,6 +56,7 @@ def write_shapes(
 shapes: GeoDataFrame,
 group: zarr.Group,
 name: str,
 zarr_container_path: StoreLike,
 group_type: str = "ngff:shapes",
 format: Format = CurrentShapesFormat(),
) -> None:
Expand DownExpand Up@@ -82,8 +84,11 @@ def write_shapes(
 attrs = format.attrs_to_dict(geometry)
 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)
 store = shapes_group._store
 path = zarr_container_path / shapes_group.path / "shapes.parquet"

 # Geopandas only allows path-like objects for local filesystems and not remote ones.
 shapes.to_parquet(str(path), filesystem=getattr(store, "fs", None))

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

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,7 +14,6 @@
from spatialdata._core.spatialdata import SpatialData
from spatialdata._io._utils import (
 BadFileHandleMethod,
 StoreLike,
 _create_upath,
 _open_zarr_store,
 handle_read_errors,
Expand All@@ -25,6 +24,7 @@
from spatialdata._io.io_shapes import _read_shapes
from spatialdata._io.io_table import _read_table
from spatialdata._logging import logger
from spatialdata._types import StoreLike


def is_hidden_zarr_entry(name: str) -> bool:
Expand All@@ -46,7 +46,7 @@ def read_image_element(path: StoreLike) -> DataArray | DataTree:
 """
 # stay in sync with ome v4 format spec:
 # https://github.com/ome/ome-zarr-py/blob/7d1ae35c97/ome_zarr/format.py#L189-L192
 store = _open_zarr_store(path, dimension_separator="/", normalize_keys=False)
 store = _open_zarr_store(path, normalize_keys=False)
 return _read_multiscale(store, raster_type="image")


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9 changes: 7 additions & 2 deletions
src/spatialdata/_types.py

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Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
from typing import Any
from pathlib import Path
from typing import Any, TypeAlias

import numpy as np
import zarr
from upath import UPath
from xarray import DataArray, DataTree

__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T"]
__all__ = ["ArrayLike", "ColorLike", "DTypeLike", "Raster_T", "StoreLike"]

from numpy.typing import DTypeLike, NDArray

Expand All@@ -12,3 +15,5 @@

Raster_T = DataArray | DataTree
ColorLike = tuple[float, ...] | str

StoreLike: TypeAlias = str | Path | UPath | zarr.storage.StoreLike | zarr.Group

2 changes: 1 addition & 1 deletion
tests/conftest.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -440,7 +440,7 @@ def _make_sdata_for_testing_querying_and_aggretation() -> SpatialData:
 table = TableModel.parse(
 table, region=["values_circles", "values_polygons"], region_key="region", instance_key="instance_id"
 )
 sdata.table = table
 sdata["table"] = table
 return sdata


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2 changes: 1 addition & 1 deletion
tests/core/operations/test_spatialdata_operations.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -174,7 +174,7 @@ def test_filter_by_coordinate_system_also_table(full_sdata: SpatialData) -> None
 adata = full_sdata["table"]
 del adata.uns[TableModel.ATTRS_KEY]
 del full_sdata.tables["table"]
 full_sdata.table = TableModel.parse(
 full_sdata["table"] = TableModel.parse(
 adata,
 region=["circles", "poly"],
 region_key="annotated_shapes",
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8 changes: 6 additions & 2 deletions
tests/core/query/test_relational_query.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,10 +15,14 @@


def test_match_table_to_element(sdata_query_aggregation):
 matched_table = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 arr = np.array(list(reversed(sdata_query_aggregation["values_circles"].index)))
 sdata_query_aggregation["values_circles"].index = arr
 matched_table_reversed = match_table_to_element(sdata=sdata_query_aggregation, element_name="values_circles")
 matched_table_reversed = match_table_to_element(
 sdata=sdata_query_aggregation, element_name="values_circles", table_name="table"
 )
 assert matched_table.obs.index.tolist() == list(reversed(matched_table_reversed.obs.index.tolist()))

 # TODO: add tests for labels
Expand Down
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