LabelImage

class starfish.morphology.LabelImage(label_image)[source]

Wraps an xarray that contains a 2D or 3D labeled image. Each axis is labeled with physical coordinate data.

Attributes
log

Returns a copy of the provenance data.

xarray

Returns the xarray that contains the label image and the physical coordinates.

Methods

from_label_array_and_ticks(array, …)

Constructs a LabelImage from an array containing the labels, a set of physical coordinates, and an optional log of how this label image came to be.

open_netcdf(path, pathlib.Path])

Load a label image saved as a netcdf file from disk.

to_netcdf(self, path, pathlib.Path])

Save the label image as a netcdf file.

classmethod from_label_array_and_ticks(array:numpy.ndarray, pixel_ticks:Union[Mapping[starfish.core.types._constants.Axes, Union[xarray.core.dataarray.DataArray, numpy.ndarray, Sequence[int]]], Mapping[str, Union[xarray.core.dataarray.DataArray, numpy.ndarray, Sequence[int]]], NoneType], physical_ticks:Union[Mapping[starfish.core.types._constants.Coordinates, Union[xarray.core.dataarray.DataArray, numpy.ndarray, Sequence[Union[int, float]]]], Mapping[str, Union[xarray.core.dataarray.DataArray, numpy.ndarray, Sequence[Union[int, float]]]]], log:Union[starfish.core.util.logging.Log, NoneType]) → 'LabelImage'[source]

Constructs a LabelImage from an array containing the labels, a set of physical coordinates, and an optional log of how this label image came to be.

Parameters
arraynp.ndarray

A 2D or 3D array containing the labels. The ordering of the axes must be Y, X for 2D images and ZPLANE, Y, X for 3D images.

pixel_ticksOptional[Union[Mapping[Axes, ArrayLike[int]], Mapping[str, ArrayLike[int]]]]

A map from the axis to the values for that axis. For any axis that exist in the array but not in pixel_coordinates, the pixel coordinates are assigned from 0..N-1, where N is the size along that axis.

physical_ticksUnion[Mapping[Coordinates, ArrayLike[Number]], Mapping[str,
ArrayLike[Number]]]

A map from the physical coordinate type to the values for axis. For 2D label images, X and Y physical coordinates must be provided. For 3D label images, Z physical coordinates must also be provided.

logOptional[Log]

A log of how this label image came to be.

Return type

LabelImage

property log

Returns a copy of the provenance data. Modifications to this copy will not affect the log stored on this label image.

Return type

Log

classmethod open_netcdf(path:Union[str, pathlib.Path]) → 'LabelImage'[source]

Load a label image saved as a netcdf file from disk.

Parameters
pathUnion[str, Path]

Path of the label image to instantiate from.

Returns
label_imageLabelImage

Label image from the path.

Return type

LabelImage

to_netcdf(self, path:Union[str, pathlib.Path])[source]

Save the label image as a netcdf file.

Parameters
pathUnion[str, Path]

Path of the netcdf file to write to.

property xarray

Returns the xarray that contains the label image and the physical coordinates.