Skip to content
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.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Small fixes to new spatial classes #231

Merged
merged 4 commits into from
Sep 30, 2024
Merged

Small fixes to new spatial classes #231

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion python-spec/src/somacore/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,6 @@
"Scene",
"ImageProperties",
"MultiscaleImage",
"SpatialDataFrame",
"GeometryDataFrame",
"PointCloud",
"BatchSize",
Expand Down
2 changes: 1 addition & 1 deletion python-spec/src/somacore/ephemeral/collections.py
View file
Open in desktop
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()

Expand Down
2 changes: 1 addition & 1 deletion python-spec/src/somacore/scene.py
View file
Open in desktop
Original file line number Diff line number Diff line change
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.
Expand Down
6 changes: 3 additions & 3 deletions python-spec/src/somacore/spatial.py
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Loading