Fix write validation against empty transformations#1118

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Merged
LucaMarconato merged 3 commits into from
May 7, 2026
Merged

Fix write validation against empty transformations #1118

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aea89c5
Fix write validation not catching empty (rather than None) transforma…
LucaMarconato May 7, 2026
2f18304
Move empty-transformation validation into model validate() methods
LucaMarconato May 7, 2026
8c42cbe
Move empty-transformation validation into model validate() methods
LucaMarconato May 7, 2026
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1 change: 1 addition & 0 deletions docs/api/models_utils.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down
5 changes: 5 additions & 0 deletions src/spatialdata/_core/spatialdata.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
if parsed_formats is None:
parsed_formats = _parse_formats(formats=parsed_formats)

if element_type != "tables":
from spatialdata.models import validate_element

validate_element(element)

if element_type == "images":
write_image(
image=element,
Expand Down
3 changes: 1 addition & 2 deletions src/spatialdata/_io/io_points.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
"""
axes = get_axes_names(points)
transformations = _get_transformations(points)
assert transformations is not None # mypy: validate_element() in _write_element guarantees this

store_root = group.store_path.store.root
path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
axes=list(axes),
attrs=attrs,
)
if transformations is None:
raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)
6 changes: 2 additions & 4 deletions src/spatialdata/_io/io_raster.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

data = raster_data.data
transformations = _get_transformations(raster_data)
if transformations is None:
raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
assert transformations is not None # mypy: validate_element() in _write_element guarantees this
input_axes: tuple[str, ...] = tuple(raster_data.dims)
parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
assert len(d) == 1
xdata = d.values().__iter__().__next__()
transformations = _get_transformations_xarray(xdata)
if transformations is None:
raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
assert transformations is not None # mypy: validate_element() in _write_element guarantees this

parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
storage_options = _prepare_storage_options(storage_options)
Expand Down
3 changes: 1 addition & 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@@ -100,8 +100,7 @@ def write_shapes(

axes = get_axes_names(shapes)
transformations = _get_transformations(shapes)
if transformations is None:
raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
assert transformations is not None # mypy: validate_element() in _write_element guarantees this
if isinstance(element_format, ShapesFormatV01):
attrs = _write_shapes_v01(shapes, group, element_format)
elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down
2 changes: 2 additions & 0 deletions src/spatialdata/models/__init__.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
TableModel,
get_model,
get_table_keys,
validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
"points_dask_dataframe_to_geopandas",
"check_target_region_column_symmetry",
"get_table_keys",
"validate_element",
"get_channel_names",
"set_channel_names",
"force_2d",
Expand Down
32 changes: 32 additions & 0 deletions src/spatialdata/models/models.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
f"No transformation found for `{data}`. At least one transformation is required for "
f"raster elements, e.g. images, labels."
)
if len(parsed_transform) == 0:
raise ValueError(
f"The transformations dict for `{data}` is empty. At least one transformation is required for "
f"raster elements, e.g. images, labels."
)

@classmethod
def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
)
if cls.TRANSFORM_KEY not in data.attrs:
raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
if not data.attrs[cls.TRANSFORM_KEY]:
raise ValueError(
f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
f"At least one transformation is required." + SUGGESTION
)
if len(data) > 0:
n = data.geometry.iloc[0]._ndim
if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
raise ValueError(
f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
)
if not data.attrs[cls.TRANSFORM_KEY]:
raise ValueError(
f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
f"At least one transformation is required." + SUGGESTION
)
if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
"""
Validate a spatial element against its model schema.

Parameters
----------
e
The spatial element to validate.

Raises
------
ValueError
If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
"""
get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
"""
Get the table keys giving information about what spatial element is annotated.
Expand Down
26 changes: 26 additions & 0 deletions tests/core/operations/test_transform.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

transform(points, transformation=t0, maintain_positioning=True)
transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
"element_fixture,kwargs",
[
("image2d", {"images": {}}),
("image2d_multiscale", {"images": {}}),
("labels2d", {"labels": {}}),
("labels2d_multiscale", {"labels": {}}),
("circles", {"shapes": {}}),
("points_0", {"points": {}}),
],
)
def test_write_fails_after_removing_all_transformations(
full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
"""Writing should fail when all transformations are removed from an element already in a SpatialData."""
# Build a valid SpatialData first (passes __setitem__ validation)
container_key = next(iter(kwargs))
sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

# Mutate in-place after construction, bypassing __setitem__ validation
remove_transformation(sdata[element_fixture], remove_all=True)

with pytest.raises(ValueError, match="transform"):
sdata.write(tmp_path / "sdata.zarr")
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Fix write validation against empty transformations#1118

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 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
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aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_shapes.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
Expand Down

32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
Expand Down

26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fix write validation against empty transformations#1118

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Already on GitHub?
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 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
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aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand Down

3 changes: 1 addition & 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@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
Expand Down

32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
Expand Down

26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fix write validation against empty transformations#1118

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 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
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aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
Expand Down

32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
Expand Down

26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Fix write validation against empty transformations#1118

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
Show file tree
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3 commits


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Hold shift + click to select a range
aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
Expand Down

32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
Expand Down

26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fix write validation against empty transformations#1118

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 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
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aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
Expand Down

32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
Expand Down

26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Fix write validation against empty transformations#1118

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Already on GitHub?
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to your account

 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
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aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
Expand Down

5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand Down

3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_shapes.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
Expand Down

2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
Expand Down

32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
Expand Down

26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
Loading

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

Skip to content
Fix write validation against empty transformations#1118

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

LucaMarconato
merged 3 commits into

from

May 7, 2026
 Merged


Fix write validation against empty transformations
#1118
Show file tree
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Hold shift + click to select a range
aea89c5

Fix write validation not catching empty (rather than None) transforma…


LucaMarconato May 7, 2026
2f18304

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026
8c42cbe

Move empty-transformation validation into model validate() methods


LucaMarconato May 7, 2026

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1 change: 1 addition & 0 deletions
docs/api/models_utils.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -4,6 +4,7 @@
.. currentmodule:: spatialdata.models

.. autofunction:: get_model
.. autofunction:: validate_element
.. autodata:: SpatialElement
.. autofunction:: get_axes_names
.. autofunction:: get_spatial_axes
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5 changes: 5 additions & 0 deletions
src/spatialdata/_core/spatialdata.py

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Expand Up@@ -1225,6 +1225,11 @@ def _write_element(
 if parsed_formats is None:
 parsed_formats = _parse_formats(formats=parsed_formats)

 if element_type != "tables":
 from spatialdata.models import validate_element

 validate_element(element)

 if element_type == "images":
 write_image(
 image=element,
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3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_points.py

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Expand Up@@ -67,6 +67,7 @@ def write_points(
 """
 axes = get_axes_names(points)
 transformations = _get_transformations(points)
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 store_root = group.store_path.store.root
 path = store_root / group.path / "points.parquet"
Expand DownExpand Up@@ -95,6 +96,4 @@ def write_points(
 axes=list(axes),
 attrs=attrs,
 )
 if transformations is None:
 raise ValueError(f"No transformations specified for element '{group.basename}'. Cannot write.")
 overwrite_coordinate_transformations_non_raster(group=group, axes=axes, transformations=transformations)

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

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Expand Up@@ -369,8 +369,7 @@ def _write_raster_dataarray(

 data = raster_data.data
 transformations = _get_transformations(raster_data)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 input_axes: tuple[str, ...] = tuple(raster_data.dims)
 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
Expand DownExpand Up@@ -439,8 +438,7 @@ def _write_raster_datatree(
 assert len(d) == 1
 xdata = d.values().__iter__().__next__()
 transformations = _get_transformations_xarray(xdata)
 if transformations is None:
 raise ValueError(f"{element_name} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this

 parsed_axes = _get_valid_axes(axes=list(input_axes), fmt=raster_format)
 storage_options = _prepare_storage_options(storage_options)
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3 changes: 1 addition & 2 deletions
src/spatialdata/_io/io_shapes.py

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Expand Up@@ -100,8 +100,7 @@ def write_shapes(

 axes = get_axes_names(shapes)
 transformations = _get_transformations(shapes)
 if transformations is None:
 raise ValueError(f"{group.basename} does not have any transformations and can therefore not be written.")
 assert transformations is not None # mypy: validate_element() in _write_element guarantees this
 if isinstance(element_format, ShapesFormatV01):
 attrs = _write_shapes_v01(shapes, group, element_format)
 elif isinstance(element_format, ShapesFormatV02 | ShapesFormatV03):
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2 changes: 2 additions & 0 deletions
src/spatialdata/models/__init__.py

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Expand Up@@ -27,6 +27,7 @@
 TableModel,
 get_model,
 get_table_keys,
 validate_element,
)

__all__ = [
Expand All@@ -51,6 +52,7 @@
 "points_dask_dataframe_to_geopandas",
 "check_target_region_column_symmetry",
 "get_table_keys",
 "validate_element",
 "get_channel_names",
 "set_channel_names",
 "force_2d",
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32 changes: 32 additions & 0 deletions
src/spatialdata/models/models.py

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Expand Up@@ -347,6 +347,11 @@ def _check_transforms_present(cls, data: DataArray | DataTree) -> None:
 f"No transformation found for `{data}`. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )
 if len(parsed_transform) == 0:
 raise ValueError(
 f"The transformations dict for `{data}` is empty. At least one transformation is required for "
 f"raster elements, e.g. images, labels."
 )

 @classmethod
 def _check_chunk_size_not_too_large(cls, data: DataArray | DataTree) -> None:
Expand DownExpand Up@@ -479,6 +484,11 @@ def validate(cls, data: GeoDataFrame) -> None:
 )
 if cls.TRANSFORM_KEY not in data.attrs:
 raise ValueError(f":class:`geopandas.GeoDataFrame` does not contain `{TRANSFORM_KEY}`." + SUGGESTION)
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":class:`geopandas.GeoDataFrame` has an empty `{TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if len(data) > 0:
 n = data.geometry.iloc[0]._ndim
 if n != 2:
Expand DownExpand Up@@ -672,6 +682,11 @@ def validate(cls, data: DaskDataFrame) -> None:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` does not contain `{cls.TRANSFORM_KEY}`." + SUGGESTION
 )
 if not data.attrs[cls.TRANSFORM_KEY]:
 raise ValueError(
 f":attr:`dask.dataframe.core.DataFrame.attrs` has an empty `{cls.TRANSFORM_KEY}` dict. "
 f"At least one transformation is required." + SUGGESTION
 )
 if ATTRS_KEY in data.attrs and "feature_key" in data.attrs[ATTRS_KEY]:
 feature_key = data.attrs[ATTRS_KEY][cls.FEATURE_KEY]
 if feature_key not in data.columns:
Expand DownExpand Up@@ -1293,6 +1308,23 @@ def _validate_and_return(
 raise TypeError(f"Unsupported type {type(e)}")


def validate_element(e: SpatialElement) -> None:
 """
 Validate a spatial element against its model schema.

 Parameters
 ----------
 e
 The spatial element to validate.

 Raises
 ------
 ValueError
 If the element is invalid (e.g. missing or empty transformations, wrong dtypes).
 """
 get_model(e, validate=True)


def get_table_keys(table: AnnData) -> tuple[str | list[str], str, str]:
 """
 Get the table keys giving information about what spatial element is annotated.
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26 changes: 26 additions & 0 deletions
tests/core/operations/test_transform.py

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Expand Up@@ -796,3 +796,29 @@ def test_transform_until_0_0_15(points):

 transform(points, transformation=t0, maintain_positioning=True)
 transform(points, to_coordinate_system="global", maintain_positioning=True)


@pytest.mark.parametrize(
 "element_fixture,kwargs",
 [
 ("image2d", {"images": {}}),
 ("image2d_multiscale", {"images": {}}),
 ("labels2d", {"labels": {}}),
 ("labels2d_multiscale", {"labels": {}}),
 ("circles", {"shapes": {}}),
 ("points_0", {"points": {}}),
 ],
)
def test_write_fails_after_removing_all_transformations(
 full_sdata: SpatialData, tmp_path: Path, element_fixture: str, kwargs: dict
) -> None:
 """Writing should fail when all transformations are removed from an element already in a SpatialData."""
 # Build a valid SpatialData first (passes __setitem__ validation)
 container_key = next(iter(kwargs))
 sdata = SpatialData(**{container_key: {element_fixture: full_sdata[element_fixture]}})

 # Mutate in-place after construction, bypassing __setitem__ validation
 remove_transformation(sdata[element_fixture], remove_all=True)

 with pytest.raises(ValueError, match="transform"):
 sdata.write(tmp_path / "sdata.zarr")
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