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

Jump to bottom

Rename PointCloud -> PointCloudDataFrame #232

Merged
merged 1 commit into from
Sep 30, 2024
Merged

Rename PointCloud -> PointCloudDataFrame #232

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
4 changes: 2 additions & 2 deletions python-spec/src/somacore/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
from .spatial import GeometryDataFrame
from .spatial import ImageProperties
from .spatial import MultiscaleImage
from .spatial import PointCloud
from .spatial import PointCloudDataFrame
from .spatial import SpatialRead
from .types import ContextBase

Expand Down Expand Up @@ -72,7 +72,7 @@
"ImageProperties",
"MultiscaleImage",
"GeometryDataFrame",
"PointCloud",
"PointCloudDataFrame",
"BatchSize",
"IOfN",
"ResultOrder",
Expand Down
14 changes: 7 additions & 7 deletions python-spec/src/somacore/ephemeral/collections.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ class Collection( # type: ignore[misc] # __eq__ false positive

_BasicAbstractScene = scene.Scene[
spatial.MultiscaleImage,
spatial.PointCloud,
spatial.PointCloudDataFrame,
spatial.GeometryDataFrame,
base.SOMAObject,
]
Expand Down Expand Up @@ -200,7 +200,7 @@ def add_multiscale_image(
) -> spatial.MultiscaleImage:
raise NotImplementedError()

def add_new_point_cloud(
def add_new_point_cloud_dataframe(
self,
key: str,
subcollection: Union[str, Sequence[str]],
Expand All @@ -212,7 +212,7 @@ def add_new_point_cloud(
axis_names: Sequence[str] = ("x", "y"),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
) -> spatial.PointCloud:
) -> spatial.PointCloudDataFrame:
raise NotImplementedError()

def set_transform_to_geometry_dataframe(
Expand All @@ -235,14 +235,14 @@ def set_transform_to_multiscale_image(
) -> spatial.MultiscaleImage:
raise NotImplementedError()

def set_transform_to_point_cloud(
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,
) -> spatial.PointCloud:
) -> spatial.PointCloudDataFrame:
raise NotImplementedError()

def get_transform_from_geometry_dataframe(
Expand All @@ -259,7 +259,7 @@ def get_transform_from_multiscale_image(
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_from_point_cloud(
def get_transform_from_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
) -> coordinates.CoordinateTransform:
raise NotImplementedError()
Expand All @@ -278,7 +278,7 @@ def get_transform_to_multiscale_image(
) -> coordinates.CoordinateTransform:
raise NotImplementedError()

def get_transform_to_point_cloud(
def get_transform_to_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
) -> coordinates.CoordinateTransform:
raise NotImplementedError()
Expand Down
38 changes: 21 additions & 17 deletions python-spec/src/somacore/scene.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,9 @@
_MultiscaleImage = TypeVar("_MultiscaleImage", bound=spatial.MultiscaleImage)
"""A particular implementation of a multiscale image."""

_PointCloud = TypeVar("_PointCloud", bound=spatial.PointCloud)
_PointCloudDataFrame = TypeVar(
"_PointCloudDataFrame", bound=spatial.PointCloudDataFrame
)
"""A particular implementation of a point cloud."""

_GeometryDataFrame = TypeVar("_GeometryDataFrame", bound=spatial.GeometryDataFrame)
Expand All @@ -28,7 +30,7 @@

class Scene(
collection.BaseCollection[_RootSO],
Generic[_MultiscaleImage, _PointCloud, _GeometryDataFrame, _RootSO],
Generic[_MultiscaleImage, _PointCloudDataFrame, _GeometryDataFrame, _RootSO],
):
"""A collection subtype representing spatial assets that can all be stored
on a single coordinate space.
Expand All @@ -45,7 +47,7 @@ class Scene(
# ImplBaseCollection[ImplSOMAObject],
# somacore.Scene[
# ImplMultiscaleImage,
# ImplPointCloud,
# ImplPointCloudDataFrame,
# ImplGeometryDataFrame,
# ImplSOMAObject,
# ],
Expand All @@ -61,19 +63,21 @@ class Scene(
Lifecycle: experimental
"""

obsl = _mixin.item[collection.Collection[Union[_PointCloud, _GeometryDataFrame]]]()
obsl = _mixin.item[
collection.Collection[Union[_PointCloudDataFrame, _GeometryDataFrame]]
]()
"""A collection of observation location data.

This collection exists to store any spatial data in the scene that joins on the obs
``soma_joinid``. Each dataframe in ``obsl`` can be either a PointCloud
``soma_joinid``. Each dataframe in ``obsl`` can be either a PointCloudDataFrame
or a GeometryDataFrame.

Lifecycle: experimental
"""

varl = _mixin.item[
collection.Collection[
collection.Collection[Union[_PointCloud, _GeometryDataFrame]]
collection.Collection[Union[_PointCloudDataFrame, _GeometryDataFrame]]
]
]()
"""A collection of collections of variable location data.
Expand All @@ -83,7 +87,7 @@ class Scene(
collection maps from measurement name to a collection of dataframes.

Each dataframe in a ``varl`` subcollection can be either a GeometryDataFrame or a
PointCloud.
PointCloudDataFrame.

Lifecycle: experimental
"""
Expand Down Expand Up @@ -161,7 +165,7 @@ def add_multiscale_image(
"""Adds a ``MultiscaleImage`` to the scene and sets a coordinate transform
between the scene and the dataframe.

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

Args:
Expand All @@ -178,7 +182,7 @@ def add_multiscale_image(
raise NotImplementedError()

@abc.abstractmethod
def add_new_point_cloud(
def add_new_point_cloud_dataframe(
self,
key: str,
subcollection: Union[str, Sequence[str]],
Expand All @@ -190,11 +194,11 @@ def add_new_point_cloud(
axis_names: Sequence[str] = ("x", "y"),
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
) -> _PointCloud:
) -> _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.PointCloud.create`.
Parameters are as in :meth:`spatial.PointCloudDataFrame.create`.
See :meth:`add_new_collection` for details about child URIs.

Args:
Expand All @@ -204,7 +208,7 @@ def add_new_point_cloud(
dataframe is stored in. Defaults to ``'obsl'``.

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

Lifecycle: experimental
"""
Expand Down Expand Up @@ -279,14 +283,14 @@ def set_transform_to_multiscale_image(
raise NotImplementedError()

@abc.abstractmethod
def set_transform_to_point_cloud(
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,
) -> _PointCloud:
) -> _PointCloudDataFrame:
"""Adds the coordinate transform for the scene coordinate space to
a point cloud stored in the scene.

Expand All @@ -295,7 +299,7 @@ def set_transform_to_point_cloud(
to set a transform for a point named `transcripts` in the `var/RNA`
collection::

scene.set_transformation_for_point_cloud(
scene.set_transformation_for_point_cloud_dataframe(
'transcripts', transform, subcollection=['var', 'RNA'],
)

Expand Down Expand Up @@ -361,7 +365,7 @@ def get_transform_from_multiscale_image(
raise NotImplementedError()

@abc.abstractmethod
def get_transform_from_point_cloud(
def get_transform_from_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the requested point cloud to
Expand Down Expand Up @@ -425,7 +429,7 @@ def get_transform_to_multiscale_image(
raise NotImplementedError()

@abc.abstractmethod
def get_transform_to_point_cloud(
def get_transform_to_point_cloud_dataframe(
self, key: str, *, subcollection: str = "obsl"
) -> coordinates.CoordinateTransform:
"""Returns the coordinate transformation from the scene to a requested
Expand Down
16 changes: 9 additions & 7 deletions python-spec/src/somacore/spatial.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,18 +34,20 @@
_ReadData = TypeVar("_ReadData")


class PointCloud(base.SOMAObject, metaclass=abc.ABCMeta):
"""A specialized SOMA DataFrame for storing collections of points in multi-dimensional space.
class PointCloudDataFrame(base.SOMAObject, metaclass=abc.ABCMeta):
"""A specialized SOMA DataFrame for storing collections of points in
multi-dimensional space.

The ``PointCloud`` class is designed to efficiently store and query point data, where each
point is represented by coordinates in one or more spatial dimensions (e.g., x, y, z) and
may have additional columns for associated attributes.
The ``PointCloudDataFrame`` class is designed to efficiently store and query point
data, where each point is represented by coordinates in one or more spatial
dimensions (e.g., x, y, z) and may have additional columns for associated
attributes.

Lifecycle: experimental
"""

__slots__ = ()
soma_type: Final = "SOMAPointCloud" # type: ignore[misc]
soma_type: Final = "SOMAPointCloudDataFrame" # type: ignore[misc]

@classmethod
@abc.abstractmethod
Expand All @@ -60,7 +62,7 @@ def create(
platform_config: Optional[options.PlatformConfig] = None,
context: Optional[Any] = None,
) -> Self:
"""Creates a new ``PointCloud`` at the given URI.
"""Creates a new ``PointCloudDataFrame`` at the given URI.

The schema of the created point cloud will include a column named
``soma_joinid`` of type ``pyarrow.int64``, with negative values disallowed, and
Expand Down
Loading