using for loop to install conda package
This commit is contained in:
95
.CondaPkg/env/Lib/site-packages/skimage/segmentation/_expand_labels.py
vendored
Normal file
95
.CondaPkg/env/Lib/site-packages/skimage/segmentation/_expand_labels.py
vendored
Normal file
@@ -0,0 +1,95 @@
|
||||
import numpy as np
|
||||
from scipy.ndimage import distance_transform_edt
|
||||
|
||||
|
||||
def expand_labels(label_image, distance=1):
|
||||
"""Expand labels in label image by ``distance`` pixels without overlapping.
|
||||
|
||||
Given a label image, ``expand_labels`` grows label regions (connected components)
|
||||
outwards by up to ``distance`` pixels without overflowing into neighboring regions.
|
||||
More specifically, each background pixel that is within Euclidean distance
|
||||
of <= ``distance`` pixels of a connected component is assigned the label of that
|
||||
connected component.
|
||||
Where multiple connected components are within ``distance`` pixels of a background
|
||||
pixel, the label value of the closest connected component will be assigned (see
|
||||
Notes for the case of multiple labels at equal distance).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
label_image : ndarray of dtype int
|
||||
label image
|
||||
distance : float
|
||||
Euclidean distance in pixels by which to grow the labels. Default is one.
|
||||
|
||||
Returns
|
||||
-------
|
||||
enlarged_labels : ndarray of dtype int
|
||||
Labeled array, where all connected regions have been enlarged
|
||||
|
||||
Notes
|
||||
-----
|
||||
Where labels are spaced more than ``distance`` pixels are apart, this is
|
||||
equivalent to a morphological dilation with a disc or hyperball of radius ``distance``.
|
||||
However, in contrast to a morphological dilation, ``expand_labels`` will
|
||||
not expand a label region into a neighboring region.
|
||||
|
||||
This implementation of ``expand_labels`` is derived from CellProfiler [1]_, where
|
||||
it is known as module "IdentifySecondaryObjects (Distance-N)" [2]_.
|
||||
|
||||
There is an important edge case when a pixel has the same distance to
|
||||
multiple regions, as it is not defined which region expands into that
|
||||
space. Here, the exact behavior depends on the upstream implementation
|
||||
of ``scipy.ndimage.distance_transform_edt``.
|
||||
|
||||
See Also
|
||||
--------
|
||||
:func:`skimage.measure.label`, :func:`skimage.segmentation.watershed`, :func:`skimage.morphology.dilation`
|
||||
|
||||
References
|
||||
----------
|
||||
.. [1] https://cellprofiler.org
|
||||
.. [2] https://github.com/CellProfiler/CellProfiler/blob/082930ea95add7b72243a4fa3d39ae5145995e9c/cellprofiler/modules/identifysecondaryobjects.py#L559
|
||||
|
||||
Examples
|
||||
--------
|
||||
>>> labels = np.array([0, 1, 0, 0, 0, 0, 2])
|
||||
>>> expand_labels(labels, distance=1)
|
||||
array([1, 1, 1, 0, 0, 2, 2])
|
||||
|
||||
Labels will not overwrite each other:
|
||||
|
||||
>>> expand_labels(labels, distance=3)
|
||||
array([1, 1, 1, 1, 2, 2, 2])
|
||||
|
||||
In case of ties, behavior is undefined, but currently resolves to the
|
||||
label closest to ``(0,) * ndim`` in lexicographical order.
|
||||
|
||||
>>> labels_tied = np.array([0, 1, 0, 2, 0])
|
||||
>>> expand_labels(labels_tied, 1)
|
||||
array([1, 1, 1, 2, 2])
|
||||
>>> labels2d = np.array(
|
||||
... [[0, 1, 0, 0],
|
||||
... [2, 0, 0, 0],
|
||||
... [0, 3, 0, 0]]
|
||||
... )
|
||||
>>> expand_labels(labels2d, 1)
|
||||
array([[2, 1, 1, 0],
|
||||
[2, 2, 0, 0],
|
||||
[2, 3, 3, 0]])
|
||||
"""
|
||||
|
||||
distances, nearest_label_coords = distance_transform_edt(
|
||||
label_image == 0, return_indices=True
|
||||
)
|
||||
labels_out = np.zeros_like(label_image)
|
||||
dilate_mask = distances <= distance
|
||||
# build the coordinates to find nearest labels,
|
||||
# in contrast to [1] this implementation supports label arrays
|
||||
# of any dimension
|
||||
masked_nearest_label_coords = [
|
||||
dimension_indices[dilate_mask]
|
||||
for dimension_indices in nearest_label_coords
|
||||
]
|
||||
nearest_labels = label_image[tuple(masked_nearest_label_coords)]
|
||||
labels_out[dilate_mask] = nearest_labels
|
||||
return labels_out
|
||||
Reference in New Issue
Block a user