def unif_resample(x,n,tol=1,deg=3):
x = np.atleast_2d(x)
x = mu.remove_duplicate_rows(x)
dl = mu.norms(x[1:] - x[:-1],1)
l = np.cumsum(np.r_[0,dl])
(tck,_) = si.splprep(x.T,k=deg,s = tol**2*len(x),u=l)
newu = np.linspace(0,l[-1],n)
return np.array(si.splev(newu,tck)).T
def unif_resample(x,n,tol=0,deg=None):
if deg is None: deg = min(3, len(x) - 1)
x = np.atleast_2d(x)
x = math_utils.remove_duplicate_rows(x)
dl = math_utils.norms(x[1:] - x[:-1],1)
l = np.cumsum(np.r_[0,dl])
(tck,_) = si.splprep(x.T,k=deg,s = tol**2*len(x),u=l)
newu = np.linspace(0,l[-1],n)
return np.array(si.splev(newu,tck)).T
def unif_resample(x,n,weights,tol=.001,deg=3):
x = np.atleast_2d(x)
weights = np.atleast_2d(weights)
x = mu.remove_duplicate_rows(x)
x_scaled = x * weights
dl = mu.norms(x_scaled[1:] - x_scaled[:-1],1)
l = np.cumsum(np.r_[0,dl])
(tck,_) = si.splprep(x_scaled.T,k=deg,s = tol**2*len(x),u=l)
newu = np.linspace(0,l[-1],n)
out_scaled = np.array(si.splev(newu,tck)).T
out = out_scaled/weights
return out
def find_path_through_point_cloud(xyzs, plotting = False):
xyzs = np.asarray(xyzs).reshape(-1,3)
S = skeletonize_point_cloud(xyzs)
segs = get_segments(S)
if plotting:
from mayavi import mlab
mlab.figure(1); mlab.clf()
plot_graph_3d(S)
S,segs = prune_skeleton(S, segs)
if plotting:
from mayavi import mlab
mlab.figure(3); mlab.clf()
plot_graph_3d(S)
segs3d = [np.array([S.node[i]["xyz"] for i in seg]) for seg in segs]
if plotting: plot_paths_2d(segs3d)
C = make_cost_matrix(segs3d)
PG = make_path_graph(C, [len(path) for path in segs3d])
(score, nodes) = longest_path_through_segment_graph(PG)
print nodes
total_path = []
for node in nodes[::2]:
if node%2 == 0: total_path.extend(segs[node//2])
else: total_path.extend(segs[node//2][::-1])
total_path_3d = math_utils.remove_duplicate_rows(np.array([S.node[i]["xyz"] for i in total_path]))
total_path_3d = unif_resample(total_path_3d, n = 100, tol=.01) # tolerance of 1mm
if plotting:
mlab.figure(2); mlab.clf()
for seg in segs3d:
x,y,z = np.array(seg).T
mlab.plot3d(x,y,z,color=(0,1,0),tube_radius=.001)
x,y,z = np.array(total_path_3d).T
mlab.plot3d(x,y,z,color=(1,0,0),tube_radius=.01,opacity=.2)
x,y,z = np.array(xyzs).reshape(-1,3).T
mlab.points3d(x,y,z,scale_factor=.01,opacity=.1,color=(0,0,1))
return total_path_3d