A simple python module to skeletonize volumes given as numpy arrays.
conda config --add channels ukoethe
conda install -c funkey skeletopyze
Get this repository (and submodules):
git clone https://github.com/funkey/skeletopyze
cd skeletopyze
git submodule update --init
See the meta.yaml for build dependencies. Once fulfilled, build an install
with:
python setup.py install
import skeletopyze
import numpy as np
a = np.zeros((100,100,100), dtype=np.int32)
a[50,50,:] = 1
a[48:52,48:52,48:52] = 1
a[46:54,46:54,70:78] = 1
params = skeletopyze.Parameters()
print("Skeletonizing")
b = skeletopyze.get_skeleton_graph(a, params)
print("Skeleton contains nodes:")
for n in b.nodes():
print str(n) + ": " + "(%d, %d, %d), diameter %f"%(b.locations(n).x(), b.locations(n).y(), b.locations(n).z(), b.diameters(n))
print("Skeleton contains edges:")
for e in b.edges():
print (e.u, e.v)conda install conda-build\<2.0
conda config --add channels ukoethe
conda build --python 2.7 .
conda build --python 3.5 .
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