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Fix shrink_labels for 1D face strips in 2D distributed segmentation #1480

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Fix shrink_labels for 1D face strips in 2D distributed segmentation #1480

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8 changes: 6 additions & 2 deletions cellpose/contrib/distributed_segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -882,8 +882,12 @@ def block_face_adjacency_graph(faces, nlabels):

def shrink_labels(plane, threshold):
"""Shrink labels in plane by some distance from their boundary"""
gradmag = np.linalg.norm(np.gradient(plane.squeeze()), axis=0)
shrunk_labels = np.copy(plane.squeeze())
squeezed = plane.squeeze()
grads = np.gradient(squeezed)
if not isinstance(grads, tuple):
grads = (grads,)
gradmag = np.linalg.norm(grads, axis=0)
shrunk_labels = np.copy(squeezed)
shrunk_labels[gradmag > 0] = 0
distances = scipy.ndimage.distance_transform_edt(shrunk_labels)
shrunk_labels[distances <= threshold] = 0
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