spatialdata.models.Labels2DModel#

class spatialdata.models.Labels2DModel(*args, **kwargs)#

Attributes table#

Methods table#

parse(*args, **kwargs)

Validate (or parse) raster data.

to_json(**dumps_kws)

validate(data)

Validate data.

Attributes#

Labels2DModel.ATTRS_KEY = 'spatialdata_attrs'#
Labels2DModel.array_type = <xarray_schema.components.ArrayTypeSchema object>#
Labels2DModel.attrs = <xarray_schema.components.AttrsSchema object>#
Labels2DModel.checks#
Labels2DModel.chunks#
Labels2DModel.coords#
Labels2DModel.dims = <xarray_schema.components.DimsSchema object>#
Labels2DModel.dtype#
Labels2DModel.json#
Labels2DModel.name#
Labels2DModel.shape#

Methods#

classmethod Labels2DModel.parse(*args, **kwargs)#

Validate (or parse) raster data.

Parameters:
  • data – Data to validate (or parse). The shape of the data should be c(z)yx for 2D (3D) images and (z)yx for 2D ( 3D) labels. If you have a 2D image with shape yx, you can use numpy.expand_dims() (or an equivalent function) to add a channel dimension.

  • dims – Dimensions of the data (e.g. [‘c’, ‘y’, ‘x’] for 2D image data). If the data is a xarray.DataArray, the dimensions can also be inferred from the data. If the dimensions are not in the order (c)(z)yx, the data will be transposed to match the order.

  • transformations – Dictionary of transformations to apply to the data. The key is the name of the target coordinate system, the value is the transformation to apply. By default, a single Identity transformation mapping to the "global" coordinate system is applied.

  • scale_factors – Scale factors to apply to construct a multiscale image (datatree.DataTree). If None, a xarray.DataArray is returned instead. Importantly, each scale factor is relative to the previous scale factor. For example, if the scale factors are [2, 2, 2], the returned multiscale image will have 4 scales. The original image and then the 2x, 4x and 8x downsampled images.

  • method – Method to use for multiscale downsampling. Please refer to multiscale_spatial_image.to_multiscale.

  • chunks – Chunks to use for dask array.

  • kwargs (Any) – Additional arguments for to_spatial_image(). In particular the c_coords kwargs argument (an iterable) can be used to set the channel coordinates for image data. c_coords is not available for labels data as labels do not have channels.

Return type:

DataArray | DataTree

Returns:

: xarray.DataArray or datatree.DataTree

Notes

RGB images

If you have an image with 3 or 4 channels and you want to interpret it as an RGB or RGB(A) image, you can use the c_coords argument to specify the channel coordinates as ["r", "g", "b"] or ["r", "g", "b", "a"].

You can also pass the rgb argument to kwargs to automatically set the c_coords to ["r", "g", "b"]. Please refer to to_spatial_image() for more information. Note: if you set rgb=None in kwargs, 3-4 channel images will be interpreted automatically as RGB(A) images.

Labels2DModel.to_json(**dumps_kws)#
Return type:

str

Labels2DModel.validate(data)#

Validate data.

Parameters:

data (Any) – Data to validate.

Raises:

ValueError – If data is not valid.

Return type:

None