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Don't write into the location of the dummy pixel_indices coordinate #107

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Mar 29, 2021
Merged

Don't write into the location of the dummy pixel_indices coordinate #107

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6 changes: 3 additions & 3 deletions skan/csr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -316,7 +316,7 @@ class Skeleton:
`keep_images` is True. This is useful for visualization.
"""
def __init__(self, skeleton_image, *, spacing=1, source_image=None,
_buffer_size_offset=None, keep_images=True,
_buffer_size_offset=None, keep_images=True,
unique_junctions=True):
graph, coords, degrees = skeleton_to_csgraph(skeleton_image,
spacing=spacing,
Expand Down Expand Up @@ -608,8 +608,8 @@ def skeleton_to_csgraph(skel, *, spacing=1, value_is_height=False,
pixel_indices = np.concatenate(([[0.] * ndim],
np.transpose(np.nonzero(skel))), axis=0)
skelint = np.zeros(skel.shape, dtype=int)
skelint[tuple(pixel_indices.T.astype(int))] = \
np.arange(pixel_indices.shape[0])
skelint[tuple(pixel_indices[1:].T.astype(int))] = \
np.arange(pixel_indices.shape[0])[1:]

degree_kernel = np.ones((3,) * ndim)
degree_kernel[(1,) * ndim] = 0 # remove centre pixel
Expand Down