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Small fixes to new spatial classes #231

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merged 4 commits into from
Sep 30, 2024
Merged

Small fixes to new spatial classes #231

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73ea945
Fix params for `add_multiscale_image`
jp-dark Sep 30, 2024
0accb79
Update `coordinate_space` property to not be optional
jp-dark Sep 30, 2024
c941cc0
Update ephemeral Scene class to match Scene API
jp-dark Sep 30, 2024
c8b0ae5
Remove non-existant class from __all__
jp-dark Sep 30, 2024
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2 changes: 1 addition & 1 deletion python-spec/src/somacore/ephemeral/collections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,9 +194,9 @@ def add_multiscale_image(
*,
uri: str,
type: pa.DataType,
image_type: str = "CYX", # TODO: Replace this arg after PR #219 is merged
reference_level_shape: Sequence[int],
axis_names: Sequence[str] = ("c", "x", "y"),
axis_types: Sequence[str] = ("channel", "height", "width"),
) -> spatial.MultiscaleImage:
raise NotImplementedError()

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2 changes: 1 addition & 1 deletion python-spec/src/somacore/scene.py
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Expand Up @@ -154,9 +154,9 @@ def add_multiscale_image(
*,
uri: str,
type: pa.DataType,
image_type: str = "CYX", # TODO: Replace this arg after PR #219 is merged
reference_level_shape: Sequence[int],
axis_names: Sequence[str] = ("c", "x", "y"),
axis_types: Sequence[str] = ("channel", "height", "width"),
) -> _MultiscaleImage:
"""Adds a ``MultiscaleImage`` to the scene and sets a coordinate transform
between the scene and the dataframe.
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6 changes: 3 additions & 3 deletions python-spec/src/somacore/spatial.py
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Expand Up @@ -224,7 +224,7 @@ def index_column_names(self) -> Tuple[str, ...]:

@property
@abc.abstractmethod
def coordinate_space(self) -> Optional[coordinates.CoordinateSpace]:
def coordinate_space(self) -> coordinates.CoordinateSpace:
"""Coordinate space for this point cloud.

Lifecycle: experimental
Expand Down Expand Up @@ -470,7 +470,7 @@ def axis_names(self) -> Tuple[str, ...]:

@property
@abc.abstractmethod
def coordinate_space(self) -> Optional[coordinates.CoordinateSpace]:
def coordinate_space(self) -> coordinates.CoordinateSpace:
"""Coordinate space for this geometry dataframe.

Lifecycle: experimental
Expand Down Expand Up @@ -639,7 +639,7 @@ def axis_names(self) -> Tuple[str, ...]:

@property
@abc.abstractmethod
def coordinate_space(self) -> Optional[coordinates.CoordinateSpace]:
def coordinate_space(self) -> coordinates.CoordinateSpace:
"""Coordinate space for this multiscale image.

Lifecycle: experimental
Expand Down
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