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3D Alpha Shape
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from scipy.spatial import Delaunay | |
import numpy as np | |
from collections import defaultdict | |
def alpha_shape_3D(pos, alpha): | |
""" | |
Compute the alpha shape (concave hull) of a set of 3D points. | |
Parameters: | |
pos - np.array of shape (n,3) points. | |
alpha - alpha value. | |
return | |
outer surface vertex indices, edge indices, and triangle indices | |
""" | |
tetra = Delaunay(pos) | |
# Find radius of the circumsphere. | |
# By definition, radius of the sphere fitting inside the tetrahedral needs | |
# to be smaller than alpha value | |
# http://mathworld.wolfram.com/Circumsphere.html | |
tetrapos = np.take(pos,tetra.vertices,axis=0) | |
normsq = np.sum(tetrapos**2,axis=2)[:,:,None] | |
ones = np.ones((tetrapos.shape[0],tetrapos.shape[1],1)) | |
a = np.linalg.det(np.concatenate((tetrapos,ones),axis=2)) | |
Dx = np.linalg.det(np.concatenate((normsq,tetrapos[:,:,[1,2]],ones),axis=2)) | |
Dy = -np.linalg.det(np.concatenate((normsq,tetrapos[:,:,[0,2]],ones),axis=2)) | |
Dz = np.linalg.det(np.concatenate((normsq,tetrapos[:,:,[0,1]],ones),axis=2)) | |
c = np.linalg.det(np.concatenate((normsq,tetrapos),axis=2)) | |
r = np.sqrt(Dx**2+Dy**2+Dz**2-4*a*c)/(2*np.abs(a)) | |
# Find tetrahedrals | |
tetras = tetra.vertices[r<alpha,:] | |
# triangles | |
TriComb = np.array([(0, 1, 2), (0, 1, 3), (0, 2, 3), (1, 2, 3)]) | |
Triangles = tetras[:,TriComb].reshape(-1,3) | |
Triangles = np.sort(Triangles,axis=1) | |
# Remove triangles that occurs twice, because they are within shapes | |
TrianglesDict = defaultdict(int) | |
for tri in Triangles:TrianglesDict[tuple(tri)] += 1 | |
Triangles=np.array([tri for tri in TrianglesDict if TrianglesDict[tri] ==1]) | |
#edges | |
EdgeComb=np.array([(0, 1), (0, 2), (1, 2)]) | |
Edges=Triangles[:,EdgeComb].reshape(-1,2) | |
Edges=np.sort(Edges,axis=1) | |
Edges=np.unique(Edges,axis=0) | |
Vertices = np.unique(Edges) | |
return Vertices,Edges,Triangles |
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