Data formats (advanced)

The SpatialData format is defined as a set of versioned subclasses of ome_zarr.format.Format, one per type of element. The spatialdata.SpatialDataFormatType is a union type encompassing the possible valid formats. These format subclasses are useful to ensure backward compatibility whenever a major version change is introduced. We also provide pointers to the latest format.

spatialdata._io.format.CurrentRasterFormat

alias of RasterFormatV03

class spatialdata._io.format.RasterFormatV01

Bases: FormatV04, CoordinateMixinV01

Formatter for raster data.

init_store(path, mode='r')

Not ideal. Stores should remain hidden “dimension_separator” is specified at array creation time

Return type:

FsspecStore | LocalStore

validate_coordinate_transformations(ndim, nlevels, coordinate_transformations=None)

Validates that a list of dicts contains a ‘scale’ transformation

Raises ValueError if no ‘scale’ found or doesn’t match ndim.

Parameters:

ndim (int) – Number of image dimensions.

Return type:

None

spatialdata._io.format.CurrentShapesFormat

alias of ShapesFormatV03

class spatialdata._io.format.ShapesFormatV01

Bases: FormatV04

Formatter for shapes.

init_store(path, mode='r')

Not ideal. Stores should remain hidden “dimension_separator” is specified at array creation time

Return type:

FsspecStore | LocalStore

validate_coordinate_transformations(ndim, nlevels, coordinate_transformations=None)

Validates that a list of dicts contains a ‘scale’ transformation

Raises ValueError if no ‘scale’ found or doesn’t match ndim.

Parameters:

ndim (int) – Number of image dimensions.

Return type:

None

class spatialdata._io.format.ShapesFormatV02

Bases: FormatV04

Formatter for shapes.

init_store(path, mode='r')

Not ideal. Stores should remain hidden “dimension_separator” is specified at array creation time

Return type:

FsspecStore | LocalStore

validate_coordinate_transformations(ndim, nlevels, coordinate_transformations=None)

Validates that a list of dicts contains a ‘scale’ transformation

Raises ValueError if no ‘scale’ found or doesn’t match ndim.

Parameters:

ndim (int) – Number of image dimensions.

Return type:

None

spatialdata._io.format.CurrentPointsFormat

alias of PointsFormatV02

class spatialdata._io.format.PointsFormatV01

Bases: FormatV04, PointsAttrsMixinV01

Formatter for points.

init_store(path, mode='r')

Not ideal. Stores should remain hidden “dimension_separator” is specified at array creation time

Return type:

FsspecStore | LocalStore

validate_coordinate_transformations(ndim, nlevels, coordinate_transformations=None)

Validates that a list of dicts contains a ‘scale’ transformation

Raises ValueError if no ‘scale’ found or doesn’t match ndim.

Parameters:

ndim (int) – Number of image dimensions.

Return type:

None

spatialdata._io.format.CurrentTablesFormat

alias of TablesFormatV02

class spatialdata._io.format.TablesFormatV01

Bases: FormatV04

Formatter for the table.

init_store(path, mode='r')

Not ideal. Stores should remain hidden “dimension_separator” is specified at array creation time

Return type:

FsspecStore | LocalStore

validate_coordinate_transformations(ndim, nlevels, coordinate_transformations=None)

Validates that a list of dicts contains a ‘scale’ transformation

Raises ValueError if no ‘scale’ found or doesn’t match ndim.

Parameters:

ndim (int) – Number of image dimensions.

Return type:

None