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[python] Update Scene add_* methods #236

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merged 6 commits into from
Oct 16, 2024
Merged

[python] Update Scene add_* methods #236

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3322f13
Update Scene `add_*` methods
jp-dark Oct 16, 2024
98d8b38
Remove `platform_config` from `Scene` `add_new_*` methods
jp-dark Oct 16, 2024
4a49dcb
Change examples in docs to be things that go in varl
jp-dark Oct 16, 2024
20680fa
Fix typo in docstring
jp-dark Oct 16, 2024
accb814
Make `transform` a kwarg and fix more docstrings
jp-dark Oct 16, 2024
4126d4b
Update args docstring order to match method definition
jp-dark Oct 16, 2024
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45 changes: 3 additions & 42 deletions python-spec/src/somacore/ephemeral/collections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,10 @@
NoReturn,
Optional,
Sequence,
Tuple,
TypeVar,
Union,
)

import pyarrow as pa
from typing_extensions import Literal, Self

from .. import base
Expand Down Expand Up @@ -167,51 +165,14 @@ def coordinate_space(self) -> coordinates.CoordinateSpace:
def coordinate_space(self, value: coordinates.CoordinateSpace) -> None:
raise NotImplementedError()

def add_geometry_dataframe(
self,
key: str,
subcollection: Union[str, Sequence[str]],
transform: Optional[coordinates.CoordinateTransform],
*,
uri: str,
schema: pa.Schema,
index_column_names: Sequence[str] = (
options.SOMA_JOINID,
options.SOMA_GEOMETRY,
),
axis_names: Sequence[str] = ("x", "y"),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
context: Optional[Any] = None,
) -> spatial.GeometryDataFrame:
def add_new_geometry_dataframe(self, *args, **kwargs) -> spatial.GeometryDataFrame:
raise NotImplementedError()

def add_multiscale_image(
self,
key: str,
subcollection: Union[str, Sequence[str]],
transform: Optional[coordinates.CoordinateTransform],
*,
uri: str,
type: pa.DataType,
reference_level_shape: Sequence[int],
axis_names: Sequence[str] = ("c", "x", "y"),
axis_types: Sequence[str] = ("channel", "height", "width"),
) -> spatial.MultiscaleImage:
def add_new_multiscale_image(self, *args, **kwargs) -> spatial.MultiscaleImage:
raise NotImplementedError()

def add_new_point_cloud_dataframe(
self,
key: str,
subcollection: Union[str, Sequence[str]],
transform: Optional[coordinates.CoordinateTransform],
*,
uri: Optional[str] = None,
schema: pa.Schema,
index_column_names: Sequence[str] = (options.SOMA_JOINID,),
axis_names: Sequence[str] = ("x", "y"),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
self, *args, **kwargs
) -> spatial.PointCloudDataFrame:
raise NotImplementedError()

Expand Down
85 changes: 45 additions & 40 deletions python-spec/src/somacore/scene.py
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Original file line number Diff line number Diff line change
@@ -1,16 +1,14 @@
"""Implementation of the SOMA scene collection for spatial data"""

import abc
from typing import Any, Generic, Optional, Sequence, Tuple, TypeVar, Union
from typing import Generic, Optional, Sequence, TypeVar, Union

import pyarrow as pa
from typing_extensions import Final

from . import _mixin
from . import base
from . import collection
from . import coordinates
from . import options
from . import spatial

_MultiscaleImage = TypeVar("_MultiscaleImage", bound=spatial.MultiscaleImage)
Expand Down Expand Up @@ -107,40 +105,38 @@ def coordinate_space(self, value: coordinates.CoordinateSpace) -> None:
raise NotImplementedError()

@abc.abstractmethod
def add_geometry_dataframe(
def add_new_geometry_dataframe(
self,
key: str,
subcollection: Union[str, Sequence[str]],
transform: Optional[coordinates.CoordinateTransform],
*,
uri: str,
schema: pa.Schema,
index_column_names: Sequence[str] = (
options.SOMA_JOINID,
options.SOMA_GEOMETRY,
),
axis_names: Sequence[str] = ("x", "y"),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
context: Optional[Any] = None,
transform: Optional[coordinates.CoordinateTransform],
uri: Optional[str] = ...,
**kwargs,
) -> _GeometryDataFrame:
"""Adds a ``GeometryDataFrame`` to the scene and sets a coordinate transform
between the scene and the dataframe.

If the subcollection the geometry dataframe is inside of is more than one
layer deep, the input should be provided as a sequence of names. For example,
to set the transformation to a geometry dataframe named "transcripts" in
the "var/RNA" collection::
If the subcollection the geometry dataframe will be created inside of is more
than one layer deep, the input should be provided as a sequence of names. For
example, to add a new geometry dataframe named "transcripts" in the "var/RNA"
collection::

scene.add_geometry_dataframe(
'cell_boundaries', subcollection=['var', 'RNA'], **kwargs
scene.add_new_geometry_dataframe(
'transcripts', subcollection=['var', 'RNA'], **kwargs
)

See :meth:`add_new_collection` for details about child URIs.

Args:
key: The name of the geometry dataframe.
transform: The coordinate transformation from the scene to the dataframe.
subcollection: The name, or sequence of names, of the subcollection the
dataframe is stored in. Defaults to ``'obsl'``.
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.
kwargs: Additional keyword arugments as specified in
:meth:`spatial.GeometryDataFrame.create`.

Returns:
The newly create ``GeometryDataFrame``, opened for writing.
Expand All @@ -150,29 +146,29 @@ def add_geometry_dataframe(
raise NotImplementedError()

@abc.abstractmethod
def add_multiscale_image(
def add_new_multiscale_image(
self,
key: str,
subcollection: Union[str, Sequence[str]],
transform: Optional[coordinates.CoordinateTransform],
*,
uri: str,
type: pa.DataType,
reference_level_shape: Sequence[int],
axis_names: Sequence[str] = ("c", "y", "x"),
axis_types: Sequence[str] = ("channel", "height", "width"),
transform: Optional[coordinates.CoordinateTransform],
uri: Optional[str] = ...,
**kwargs,
) -> _MultiscaleImage:
"""Adds a ``MultiscaleImage`` to the scene and sets a coordinate transform
between the scene and the dataframe.

Parameters are as in :meth:`spatial.PointCloudDataFrame.create`.
See :meth:`add_new_collection` for details about child URIs.

Args:
key: The name of the multiscale image.
transform: The coordinate transformation from the scene to the dataframe.
subcollection: The name, or sequence of names, of the subcollection the
dataframe is stored in. Defaults to ``'obsl'``.
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.
kwargs: Additional keyword arugments as specified in
:meth:`spatial.MultiscaleImage.create`.

Returns:
The newly create ``MultiscaleImage``, opened for writing.
Expand All @@ -186,26 +182,35 @@ def add_new_point_cloud_dataframe(
self,
key: str,
subcollection: Union[str, Sequence[str]],
transform: Optional[coordinates.CoordinateTransform],
*,
uri: Optional[str] = None,
schema: pa.Schema,
index_column_names: Sequence[str] = (options.SOMA_JOINID,),
axis_names: Sequence[str] = ("x", "y"),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
transform: Optional[coordinates.CoordinateTransform],
uri: Optional[str] = ...,
**kwargs,
) -> _PointCloudDataFrame:
"""Adds a point cloud to the scene and sets a coordinate transform
between the scene and the dataframe.

Parameters are as in :meth:`spatial.PointCloudDataFrame.create`.
If the subcollection the point cloud dataframe will be added to is more than
one layer deep, the input should be provided as a sequence of names. For
example, to add a new point cloud dataframe named "transcripts" to the
"var/RNA" collection::

scene.add_new_point_cloud_dataframe(
'transcripts', subcollection=['var', 'RNA'], **kwargs
)


See :meth:`add_new_collection` for details about child URIs.

Args:
key: The name of the point cloud dataframe.
transform: The coordinate transformation from the scene to the dataframe.
subcollection: The name, or sequence of names, of the subcollection the
dataframe is stored in. Defaults to ``'obsl'``.
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.
kwargs: Additional keyword arugments as specified in
:meth:`spatial.PointCloudDataFrame.create`.

Returns:
The newly created ``PointCloudDataFrame``, opened for writing.
Expand Down
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