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Update Scene subcollection API #239

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merged 2 commits into from
Oct 30, 2024
Merged

Update Scene subcollection API #239

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be1f842
Update Scene subcollection API
jp-dark Oct 25, 2024
6e385b8
Fix linters
jp-dark Oct 25, 2024
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43 changes: 9 additions & 34 deletions python-spec/src/somacore/ephemeral/collections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,7 @@
Iterator,
NoReturn,
Optional,
Sequence,
TypeVar,
Union,
)

from typing_extensions import Literal, Self
Expand Down Expand Up @@ -177,70 +175,47 @@ def add_new_point_cloud_dataframe(
raise NotImplementedError()

def set_transform_to_geometry_dataframe(
self,
key: str,
transform: coordinates.CoordinateTransform,
*,
subcollection: Union[str, Sequence[str]] = "obsl",
coordinate_space: Optional[coordinates.CoordinateSpace] = None,
self, *args, **kwargs
) -> spatial.GeometryDataFrame:
raise NotImplementedError()

def set_transform_to_multiscale_image(
self,
key: str,
transform: coordinates.CoordinateTransform,
*,
subcollection: Union[str, Sequence[str]] = "img",
coordinate_space: Optional[coordinates.CoordinateSpace] = None,
self, *args, **kwargs
) -> spatial.MultiscaleImage:
raise NotImplementedError()

def set_transform_to_point_cloud_dataframe(
self,
key: str,
transform: coordinates.CoordinateTransform,
*,
subcollection: Union[str, Sequence[str]] = "obsl",
coordinate_space: Optional[coordinates.CoordinateSpace] = None,
self, *args, **kwargs
) -> spatial.PointCloudDataFrame:
raise NotImplementedError()

def get_transform_from_geometry_dataframe(
self, key: str, *, subcollection: Union[str, Sequence[str]] = "obsl"
self, *args, **kwargs
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_from_multiscale_image(
self,
key: str,
*,
subcollection: str = "img",
level: Optional[Union[str, int]] = None,
self, *args, **kwargs
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_from_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
self, *args, **kwargs
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_to_geometry_dataframe(
self, key: str, *, subcollection: Union[str, Sequence[str]] = "obsl"
self, *args, **kwargs
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_to_multiscale_image(
self,
key: str,
*,
subcollection: str = "img",
level: Optional[Union[str, int]] = None,
self, *args, **kwargs
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_to_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
self, *args, **kwargs
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

Expand Down
36 changes: 18 additions & 18 deletions python-spec/src/somacore/scene.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ def add_new_geometry_dataframe(
Args:
key: The name of the geometry dataframe.
subcollection: The name, or sequence of names, of the subcollection the
dataframe is stored in. Defaults to ``'obsl'``.
dataframe is stored in.
transform: The coordinate transformation from the scene to the dataframe.
uri: If provided, overrides the default URI what would be used to create
this object. This may be aboslution or relative.
Expand Down Expand Up @@ -163,7 +163,7 @@ def add_new_multiscale_image(
Args:
key: The name of the multiscale image.
subcollection: The name, or sequence of names, of the subcollection the
dataframe is stored in. Defaults to ``'obsl'``.
dataframe is stored in.
transform: The coordinate transformation from the scene to the dataframe.
uri: If provided, overrides the default URI what would be used to create
this object. This may be aboslution or relative.
Expand Down Expand Up @@ -205,7 +205,7 @@ def add_new_point_cloud_dataframe(
Args:
key: The name of the point cloud dataframe.
subcollection: The name, or sequence of names, of the subcollection the
dataframe is stored in. Defaults to ``'obsl'``.
dataframe is stored in.
transform: The coordinate transformation from the scene to the dataframe.
uri: If provided, overrides the default URI what would be used to create
this object. This may be aboslution or relative.
Expand All @@ -223,9 +223,9 @@ def add_new_point_cloud_dataframe(
def set_transform_to_geometry_dataframe(
self,
key: str,
transform: coordinates.CoordinateTransform,
*,
subcollection: Union[str, Sequence[str]] = "obsl",
*,
transform: coordinates.CoordinateTransform,
coordinate_space: Optional[coordinates.CoordinateSpace] = None,
) -> _GeometryDataFrame:
"""Adds the coordinate transform for the scene coordinate space to
Expand Down Expand Up @@ -259,9 +259,9 @@ def set_transform_to_geometry_dataframe(
def set_transform_to_multiscale_image(
self,
key: str,
transform: coordinates.CoordinateTransform,
*,
subcollection: Union[str, Sequence[str]] = "img",
*,
transform: coordinates.CoordinateTransform,
coordinate_space: Optional[coordinates.CoordinateSpace] = None,
) -> _MultiscaleImage:
"""Adds the coordinate transform for the scene coordinate space to
Expand All @@ -273,10 +273,10 @@ def set_transform_to_multiscale_image(

Args:
key: The name of the multiscale image.
transform: The coordinate transformation from the scene to the reference
level of the multiscale image.
subcollection: The name, or sequence of names, of the subcollection the
image is stored in. Defaults to ``'img'``.
transform: The coordinate transformation from the scene to the reference
level of the multiscale image.
coordinate_space: Optional coordinate space for the image. This will
replace the existing coordinate space of the multiscale image.

Expand All @@ -291,9 +291,9 @@ def set_transform_to_multiscale_image(
def set_transform_to_point_cloud_dataframe(
self,
key: str,
transform: coordinates.CoordinateTransform,
*,
subcollection: Union[str, Sequence[str]] = "obsl",
*,
transform: coordinates.CoordinateTransform,
coordinate_space: Optional[coordinates.CoordinateSpace] = None,
) -> _PointCloudDataFrame:
"""Adds the coordinate transform for the scene coordinate space to
Expand All @@ -310,9 +310,9 @@ def set_transform_to_point_cloud_dataframe(

Args:
key: The name of the point cloud.
transform: The coordinate transformation from the scene to the point cloud.
subcollection: The name, or sequence of names, of the subcollection the
point cloud is stored in. Defaults to ``'obsl'``.
transform: The coordinate transformation from the scene to the point cloud.
coordinate_space: Optional coordinate space for the point cloud. This will
replace the existing coordinate space of the point cloud. Defaults to
``None``.
Expand All @@ -326,7 +326,7 @@ def set_transform_to_point_cloud_dataframe(

@abc.abstractmethod
def get_transform_from_geometry_dataframe(
self, key: str, *, subcollection: Union[str, Sequence[str]] = "obsl"
self, key: str, subcollection: Union[str, Sequence[str]] = "obsl"
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the requested geometry dataframe
to the scene.
Expand All @@ -347,8 +347,8 @@ def get_transform_from_geometry_dataframe(
def get_transform_from_multiscale_image(
self,
key: str,
*,
subcollection: str = "img",
*,
level: Optional[Union[str, int]] = None,
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the requested multiscale image to
Expand All @@ -371,7 +371,7 @@ def get_transform_from_multiscale_image(

@abc.abstractmethod
def get_transform_from_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
self, key: str, subcollection: str = "obsl"
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the requested point cloud to
the scene.
Expand All @@ -390,7 +390,7 @@ def get_transform_from_point_cloud_dataframe(

@abc.abstractmethod
def get_transform_to_geometry_dataframe(
self, key: str, *, subcollection: Union[str, Sequence[str]] = "obsl"
self, key: str, subcollection: Union[str, Sequence[str]] = "obsl"
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the scene to a requested
geometery dataframe.
Expand All @@ -411,8 +411,8 @@ def get_transform_to_geometry_dataframe(
def get_transform_to_multiscale_image(
self,
key: str,
*,
subcollection: str = "img",
*,
level: Optional[Union[str, int]] = None,
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the scene to a requested
Expand All @@ -435,7 +435,7 @@ def get_transform_to_multiscale_image(

@abc.abstractmethod
def get_transform_to_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
self, key: str, subcollection: str = "obsl"
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the scene to a requested
point cloud.
Expand Down
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