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Replace axis_name with coordinate_space in spatial dataframes #237

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merged 3 commits into from
Oct 16, 2024
Merged

Replace axis_name with coordinate_space in spatial dataframes #237

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2df34fc
(WIP) Clean-up PointCloudDataFrame create parameters
jp-dark Oct 10, 2024
f08218e
Repace axis_name with coordinate_space in spatial dataframes
jp-dark Oct 15, 2024
d4d4f7c
Move `coordinate_space` before `index_column_names`
jp-dark Oct 16, 2024
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46 changes: 17 additions & 29 deletions python-spec/src/somacore/spatial.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,8 +56,11 @@ def create(
uri: str,
*,
schema: pa.Schema,
index_column_names: Sequence[str] = (options.SOMA_JOINID, "x", "y"),
axis_names: Sequence[str] = ("x", "y"),
coordinate_space: Union[Sequence[str], coordinates.CoordinateSpace] = (
"x",
"y",
),
index_column_names: Optional[Sequence[str]] = None,
domain: Optional[Sequence[Optional[Tuple[Any, Any]]]] = None,
platform_config: Optional[options.PlatformConfig] = None,
context: Optional[Any] = None,
Expand All @@ -77,12 +80,13 @@ def create(
must define all columns, including columns to be named as index
columns. If the schema includes types unsupported by the SOMA
implementation, an error will be raised.
coordinate_space: Either the coordinate space or the axis names for the
coordinate space the point cloud is defined on.
index_column_names: A list of column names to use as user-defined index
columns (e.g., ``['x', 'y']``). All named columns must exist in the
schema, and at least one index column name is required.
axis_names: An ordered list of axis column names that correspond to the
names of axes of the the coordinate space the points are defined on.
Must be the name of index columns.
columns (e.g., ``['x', 'y']``). Must include the axis names for all
axes in the coordinate space. May include the ``soma_joinid``.
Defaults to ``None`` which sets the index column names to be the
``soma_joinid`` followed by the axis names for the coordinate space.
domain: An optional sequence of tuples specifying the domain of each
index column. Each tuple should be a pair consisting of the minimum
and maximum values storable in the index column. If omitted entirely,
Expand Down Expand Up @@ -242,15 +246,6 @@ def coordinate_space(self, value: coordinates.CoordinateSpace) -> None:
"""
raise NotImplementedError()

@property
@abc.abstractmethod
def axis_names(self) -> Tuple[str, ...]:
"""The names of the axes of the coordinate space the data is defined on.

Lifecycle: experimental
"""
raise NotImplementedError()

@property
@abc.abstractmethod
def domain(self) -> Tuple[Tuple[Any, Any], ...]:
Expand Down Expand Up @@ -285,11 +280,14 @@ def create(
uri: str,
*,
schema: pa.Schema,
coordinate_space: Union[Sequence[str], coordinates.CoordinateSpace] = (
"x",
"y",
),
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,
Expand All @@ -311,13 +309,12 @@ def create(
must define all columns, including columns to be named as index
columns. If the schema includes types unsupported by the SOMA
implementation, an error will be raised.
coordinate_space: Either the coordinate space or the axis names for the
coordinate space the point cloud is defined on.
index_column_names: A list of column names to use as user-defined
index columns (e.g., ``['cell_type', 'tissue_type']``).
All named columns must exist in the schema, and at least one
index column name is required.
axis_names: An ordered list of axis column names that correspond to the
names of the axes of the coordinate space the geometries are defined
on.
domain: An optional sequence of tuples specifying the domain of each
index column. Two tuples must be provided for the ``soma_geometry``
column which store the width followed by the height. Each tuple should
Expand Down Expand Up @@ -461,15 +458,6 @@ def index_column_names(self) -> Tuple[str, ...]:
"""
raise NotImplementedError()

@property
@abc.abstractmethod
def axis_names(self) -> Tuple[str, ...]:
"""The names of the axes of the coordinate space the data is defined on.

Lifecycle: experimental
"""
raise NotImplementedError()

@property
@abc.abstractmethod
def coordinate_space(self) -> coordinates.CoordinateSpace:
Expand Down
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