Added subset API; fix behavior with zero-len table

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented
 

CHANGELOG.md

@@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- added SpatialData.subset() API
+
 ### Fixed
 
 #### Minor

src/spatialdata/_core/query/spatial_query.py

@@ -266,6 +266,8 @@ def _(
  new_elements[element_type] = queried_elements
 
  table = _filter_table_by_elements(sdata.table, new_elements) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
  return SpatialData(**new_elements, table=table)
 
 
@@ -641,6 +643,8 @@ def _polygon_query(
 
  if filter_table and sdata.table is not None:
  table = _filter_table_by_elements(sdata.table, {"shapes": new_shapes, "points": new_points})
+ if table is not None and len(table) == 0:
+ table = None
  else:
  table = sdata.table
  return SpatialData(shapes=new_shapes, points=new_points, images=new_images, table=table)
@@ -749,5 +753,7 @@ def polygon_query(
  geodataframes[k] = vv
 
  table = _filter_table_by_elements(sdata.table, {"shapes": geodataframes}) if filter_table else sdata.table
+ if len(table) == 0:
+ table = None
 
  return SpatialData(shapes=geodataframes, table=table)

src/spatialdata/_core/spatialdata.py

@@ -1124,6 +1124,33 @@ def init_from_elements(cls, elements: dict[str, SpatialElement], table: AnnData
  elements_dict.setdefault(element_type, {})[name] = element
  return cls(**elements_dict, table=table)
 
+ def subset(self, element_names: list[str], filter_table: bool = True) -> SpatialData:
+ """
+ Subset the SpatialData object.
+
+ Parameters
+ ----------
+ element_names
+ The names of the element_names to subset.
+ filter_table
+ If True (default), the table is filtered to only contain rows that are annotating regions
+ contained within the element_names.
+
+ Returns
+ -------
+ The subsetted SpatialData object.
+ """
+ from spatialdata._core.query.relational_query import _filter_table_by_elements
+
+ elements_dict: dict[str, SpatialElement] = {}
+ for element_type, element_name, element in self._gen_elements():
+ if element_name in element_names:
+ elements_dict.setdefault(element_type, {})[element_name] = element
+ table = _filter_table_by_elements(self.table, elements_dict=elements_dict) if filter_table else self.table
+ if len(table) == 0:
+ table = None
+ return SpatialData(**elements_dict, table=table)
+
  def __getitem__(self, item: str) -> SpatialElement:
  """
  Return the element with the given name.

tests/core/operations/test_spatialdata_operations.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy as np
 import pytest
 from anndata import AnnData
@@ -123,8 +125,8 @@ def _assert_elements_left_to_right_seem_identical(sdata0: SpatialData, sdata1: S
  raise TypeError(f"Unsupported type {type(element)}")
 
 
-def _assert_tables_seem_identical(table0: AnnData, table1: AnnData) -> None:
- assert table0.shape == table1.shape
+def _assert_tables_seem_identical(table0: AnnData | None, table1: AnnData | None) -> None:
+ assert table0 is None and table1 is None or table0.shape == table1.shape
 
 
 def _assert_spatialdata_objects_seem_identical(sdata0: SpatialData, sdata1: SpatialData) -> None:
@@ -360,3 +362,27 @@ def test_init_from_elements(full_sdata: SpatialData) -> None:
  sdata = SpatialData.init_from_elements(all_elements, table=full_sdata.table)
  for element_type in ["images", "labels", "points", "shapes"]:
  assert set(getattr(sdata, element_type).keys()) == set(getattr(full_sdata, element_type).keys())
+
+
+def test_subset(full_sdata: SpatialData) -> None:
+ element_names = ["image2d", "labels2d", "points_0", "circles", "poly"]
+ subset0 = full_sdata.subset(element_names)
+ unique_names = set()
+ for _, k, _ in subset0._gen_elements():
+ unique_names.add(k)
+ assert "image3d_xarray" in full_sdata.images
+ assert unique_names == set(element_names)
+ assert subset0.table is None
+
+ adata = AnnData(
+ shape=(10, 0),
+ obs={"region": ["circles"] * 5 + ["poly"] * 5, "instance_id": [0, 1, 2, 3, 4, "a", "b", "c", "d", "e"]},
+ )
+ del full_sdata.table
+ full_sdata.table = TableModel.parse(
+ adata, region=["circles", "poly"], region_key="region", instance_key="instance_id"
+ )
+ subset1 = full_sdata.subset(["poly"])
+ assert subset1.table is not None
+ assert len(subset1.table) == 5
+ assert subset1.table.obs["region"].unique().tolist() == ["poly"]

tests/core/query/test_spatial_query.py

@@ -364,7 +364,7 @@ def test_polygon_query_points(sdata_query_aggregation):
  queried = polygon_query(sdata, polygons=polygon, target_coordinate_system="global", shapes=False, points=True)
  points = queried["points"].compute()
  assert len(points) == 6
- assert len(queried.table) == 0
+ assert queried.table is None
 
  # TODO: the case of querying points with multiple polygons is not currently implemented