api.md

API

.. module:: spatialdata

SpatialData

The SpatialData class.

.. autosummary::
    :toctree: generated

    SpatialData

Operations

Operations on SpatialData objects.

.. autosummary::
    :toctree: generated

    bounding_box_query
    polygon_query
    get_values
    get_extent
    match_table_to_element
    concatenate
    transform
    rasterize
    aggregate

Operations Utilities

.. autosummary::
    :toctree: generated

    unpad_raster
    are_extents_equal

Models

The elements (building-blocks) that consitute SpatialData.

.. currentmodule:: spatialdata.models

.. autosummary::
    :toctree: generated

    Image2DModel
    Image3DModel
    Labels2DModel
    Labels3DModel
    ShapesModel
    PointsModel
    TableModel

Models Utilities

.. currentmodule:: spatialdata.models

.. autosummary::
    :toctree: generated

    get_model
    SpatialElement
    get_axes_names
    get_spatial_axes
    points_geopandas_to_dask_dataframe
    points_dask_dataframe_to_geopandas

Transformations

The transformations that can be defined between elements and coordinate systems in SpatialData.

.. currentmodule:: spatialdata.transformations

.. autosummary::
    :toctree: generated

    BaseTransformation
    Identity
    MapAxis
    Translation
    Scale
    Affine
    Sequence

Transformations Utilities

.. currentmodule:: spatialdata.transformations

.. autosummary::
    :toctree: generated

    get_transformation
    set_transformation
    remove_transformation
    get_transformation_between_coordinate_systems
    get_transformation_between_landmarks
    align_elements_using_landmarks
    remove_transformations_to_coordinate_system

DataLoader

.. currentmodule:: spatialdata.dataloader

.. autosummary::
    :toctree: generated

    ImageTilesDataset

Input/Output

.. currentmodule:: spatialdata

.. autosummary::
    :toctree: generated

    read_zarr
    save_transformations
    get_dask_backing_files