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Move docstring updates
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@jp-dark
jp-dark committed Sep 18, 2024
1 parent 7ccefb6 commit 462678a
Showing 1 changed file with 22 additions and 28 deletions.
50 changes: 22 additions & 28 deletions python-spec/src/somacore/spatialdata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,22 +97,23 @@ def read_region(
value_filter: Optional[str] = None,
platform_config: Optional[options.PlatformConfig] = None,
) -> "SpatialRead[data.ReadIter[pa.Table]]":
"""Reads a user-defined slice of data into Arrow tables.
"""Reads a data intersecting an user-defined region into a
:class:`SpatialRead` with data in Arrow tables.
TODO: Add details about the requested input region.
TODO: Add details about the output SpatialReadIter.
Args:
region: for each index dimension, which rows to read or a single shape.
Defaults to ``()``, meaning no constraint -- all IDs.
region: The region to query. May be a box in the form
[x_min, y_min, x_max, y_max] (for 2D images), a box in the form
[x_min, y_min, z_min, x_max, y_max, z_max] (for 3D images), or
a shapely Geometry.
column_names: the named columns to read and return.
Defaults to ``None``, meaning no constraint -- all column names.
extra_coords: a name to coordinate mapping non-spatial index columns.
Defaults to selecting entire region for non-spatial coordinates.
transform: coordinate transform to apply to results.
transform: An optional coordinate transform that provides desribes the
Defaults to ``None``, meaning an identity transform.
region_coord_space: the coordinate space of the region being read.
Defaults to ``None``, coordinate space will be infer from transform.
region_coord_space: An optional coordinate space for the region being read.
Defaults to ``None``, coordinate space will be inferred from transform.
batch_size: The size of batched reads.
Defaults to `unbatched`.
partitions: If present, specifies that this is part of
Expand All @@ -125,7 +126,7 @@ def read_region(
for the particular SOMA implementation for details.
Returns:
A :class:`ReadIter` of :class:`pa.Table`s.
A :class:`SpatialRead` with :class:`ReadIter` of :class:`pa.Table`s data.
Lifecycle: experimental
"""
Expand Down Expand Up @@ -229,20 +230,16 @@ def create(
Args:
uri: The URI where the dataframe will be created.
schema: Arrow schema defining the per-column schema. This schema
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.
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
coorespond to the names of axes of the the coordinate space the points
are defined on.
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.
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 @@ -299,21 +296,17 @@ def create(
Args:
uri: The URI where the dataframe will be created.
schema: Arrow schema defining the per-column schema. This schema
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.
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
coorespond to the names of the axes of the coordinate space the
geometries are defined on.
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 @@ -425,8 +418,8 @@ def read_region(
result_order: options.ResultOrderStr = _RO_AUTO,
platform_config: Optional[options.PlatformConfig] = None,
) -> "SpatialRead[Union[pa.Tensor, pa.Table]]":
"""Reads a user-defined region into a :class:`SpatialRead` with
:class:`pa.Tensor` or :class:`pa.Table` data.
"""Reads a user-defined region into a :class:`SpatialRead` with data in
either an Arrow tensor or table.
Reads the bounding box of the input region from the requested image level. If
``create_mask=True``, this will return a :class:`SpatialRead` with the image
Expand All @@ -444,9 +437,10 @@ def read_region(
to read.
transform: An optional coordinate transform that provides desribes the
transformation from the provided region to the reference level fo this
image.
region_coord_space: An optional coordinate space for the region being
read. The axis names must match the input axis names of the transform.
image. Defaults to ``None``.
region_coord_space: An optional coordinate space for the region being read.
The axis names must match the input axis names of the transform.
Defaults to ``None``, coordinate space will be inferred from transform.
create_mask: If ``True``, return a bitmask for the pixels in the returned
data that intersect the region.
result_order: the order to return results, specified as a
Expand Down

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