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cache skeleton_image shape for path_label_image #210

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merged 4 commits into from
Oct 3, 2023
Merged

cache skeleton_image shape for path_label_image #210

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f687678
cache skeleton_image shape for path_label_image
jarodhanko-crafco Aug 9, 2023
7c730ec
revert csr
jarodhanko-crafco Aug 9, 2023
81e98e0
make changes again since diff was messed up
jarodhanko-crafco Aug 9, 2023
f1f9f66
Add test for path_label_image (fails on main)
jni Oct 3, 2023
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3 changes: 2 additions & 1 deletion src/skan/csr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -513,6 +513,7 @@ def __init__(
self.distances = np.empty(self.n_paths, dtype=float)
self._distances_initialized = False
self.skeleton_image = None
self.skeleton_shape = skeleton_image.shape
self.source_image = None
self.degrees = np.diff(self.graph.indptr)
self.spacing = (
Expand Down Expand Up @@ -618,7 +619,7 @@ def path_label_image(self):
Image of the same shape as self.skeleton_image where each pixel
has the value of its branch id + 1.
"""
image_out = np.zeros(self.skeleton_image.shape, dtype=int)
image_out = np.zeros(self.skeleton_shape, dtype=int)
for i in range(self.n_paths):
coords_to_wipe = self.path_coordinates(i)
coords_idxs = tuple(np.round(coords_to_wipe).astype(int).T)
Expand Down