Data formats (advanced)

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[source]#

alias of RasterFormatV03

class spatialdata._io.format.RasterFormatV01[source]#

Bases: FormatV04, CoordinateMixinV01

Formatter for raster data.

init_store(path, mode='r')[source]#

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)[source]#

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[source]#

alias of ShapesFormatV03

class spatialdata._io.format.ShapesFormatV01[source]#

Bases: FormatV04

Formatter for shapes.

init_store(path, mode='r')[source]#

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)[source]#

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[source]#

Bases: FormatV04

Formatter for shapes.

init_store(path, mode='r')[source]#

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)[source]#

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[source]#

alias of PointsFormatV02

class spatialdata._io.format.PointsFormatV01[source]#

Bases: FormatV04, PointsAttrsMixinV01

Formatter for points.

init_store(path, mode='r')[source]#

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)[source]#

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[source]#

alias of TablesFormatV02

class spatialdata._io.format.TablesFormatV01[source]#

Bases: FormatV04

Formatter for the table.

init_store(path, mode='r')[source]#

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)[source]#

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