def voxelize(pts, polys, shape=(256, 256, 256), center=(128, 128, 128), mp=True):
from tvtk.api import tvtk
pd = tvtk.PolyData(points=pts + center + (0, 0, 0), polys=polys)
plane = tvtk.Planes(normals=[(0,0,1)], points=[(0,0,0)])
clip = tvtk.ClipPolyData(clip_function=plane, input=pd)
feats = tvtk.FeatureEdges(
manifold_edges=False,
non_manifold_edges=False,
feature_edges=False,
boundary_edges=True,
input=clip.output)
def func(i):
plane.points = [(0,0,i)]
feats.update()
vox = np.zeros(shape[:2][::-1], np.uint8)
if feats.output.number_of_lines > 0:
epts = feats.output.points.to_array()
edges = feats.output.lines.to_array().reshape(-1, 3)[:,1:]
for poly in trace_poly(edges):
vox += rasterize(epts[poly][:,:2]+[.5, .5], shape=shape[:2][::-1])
return vox % 2
if mp:
from . import mp
layers = mp.map(func, range(shape[2]))
else:
#layers = map(func, range(shape[2]))
layers = [func(x) for x in range(shape[2])] # python3 compatible
return np.array(layers).T
def _getmask(pia, wm, polys, shape):
from .. import polyutils
mask = sparse.csr_matrix((len(wm), np.prod(shape)))
from tvtk.api import tvtk
measure = tvtk.MassProperties()
planes = tvtk.PlaneCollection()
for norm in np.vstack([-np.eye(3), np.eye(3)]):
planes.append(tvtk.Plane(normal=norm))
ccs = tvtk.ClipClosedSurface(clipping_planes=planes)
feats = tvtk.FeatureEdges(boundary_edges=1,
non_manifold_edges=0,
manifold_edges=0,
feature_edges=0)
feats.set_input(ccs.output)
surf = polyutils.Surface(pia, polys)
for i, (pts, faces) in enumerate(surf.polyhedra(wm)):
if len(pts) > 0:
poly = tvtk.PolyData(points=pts, polys=faces)
measure.set_input(poly)
measure.update()
totalvol = measure.volume
ccs.set_input(poly)
measure.set_input(ccs.output)
bmin = pts.min(0).round().astype(int)
bmax = (pts.max(0).round() + 1).astype(int)
vidx = np.mgrid[bmin[0]:bmax[0], bmin[1]:bmax[1],
bmin[2]:bmax[2]]
for vox in vidx.reshape(3, -1).T:
try:
idx = np.ravel_multi_index(vox[::-1], shape)
for plane, m in zip(planes,
[.5, .5, .5, -.5, -.5, -.5]):
plane.origin = vox + m
ccs.update()
if ccs.output.number_of_cells > 2:
measure.update()
mask[i, idx] = measure.volume
except ValueError:
print('Voxel not in volume: (%d, %d, %d)' % tuple(vox))
mask.data[mask.indptr[i]:mask.indptr[i + 1]] /= mask[i].sum()
return mask