if args.mask is not None:
mask = np.load(args.mask)
step_size = args.step_size * mask
else:
step_size = args.step_size
mesh = TriMesh_Vtk(surface_file_in, None)
smooth_vertices = mesh.laplacian_smooth(
nb_iter=args.nb_step,
diffusion_step=step_size,
l2_dist_weighted=args.dist_weighted,
area_weighted=args.area_weighted,
backward_step=not(args.forward_step),
flow_file=None)
smoothed_mesh = TriMesh_Vtk(mesh.get_triangles(), smooth_vertices)
# Save
smoothed_mesh.save(surface_file_out)
# Display
if args.vi:
mesh.display('input surface')
if args.vo:
smoothed_mesh.display('output surface')
#print "\n!!! Smooth surface Saved !!!\n"
import numpy as np import time import trimeshpy from trimeshpy.trimesh_vtk import TriMesh_Vtk from trimeshpy.trimeshflow_vtk import TriMeshFlow_Vtk from trimeshpy.vtk_util import lines_to_vtk_polydata, save_polydata # Test files file_name = trimeshpy.data.brain_lh mesh = TriMesh_Vtk(file_name, None) triangles = mesh.get_triangles() vertices = mesh.get_vertices() mesh.display(display_name="Trimeshpy: Initial Mesh") # pre-smooth vertices = mesh.laplacian_smooth(2, 10.0, l2_dist_weighted=False, area_weighted=False, backward_step=True, flow_file=None) mesh.set_vertices(vertices) mesh.display(display_name="Trimeshpy: Smoothed Mesh") tri_mesh_flow = TriMeshFlow_Vtk(triangles, vertices) # Test parameters nb_step = 10 diffusion_step = 10 saved_flow = trimeshpy.data.output_test_flow saved_fib = trimeshpy.data.output_test_fib # Test functions
#filter
if args.index is not None:
print args.index
mask = np.zeros([len(vts_label)], dtype=np.bool )
for index in args.index:
if index == -1:
print "selected region :", index, "None"
else:
print "selected region :", index, label_name[index]
mask = np.logical_or(mask, (vts_label == index))
if args.inverse_mask:
mask = ~mask
vts_color[~mask] = [0,0,0]
if args.white:
vts_color[mask] = [255,255,255]
mesh.update_polydata()
mesh.set_colors(vts_color)
if args.v:
mesh.display()
if args.out_surface is not None:
mesh.save(args.o)
if args.out_vts_mask is not None:
np.save(args.out_vts_mask, mask)
end_normal = end_mesh.vertices_normal(args.ed_not_normed, args.ed_not_weighted)
# save only not masked points
if args.mask is not None:
np.save(args.end_normal, end_normal[mask])
else:
np.save(args.end_normal, end_normal)
if args.end_surf is not None:
end_mesh.save(args.end_surf)
if args.info is not None:
info = np.array([args.nb_step, args.step_size], np.object)
np.save(args.info, info)
# display
if args.vi:
mesh.display('input surface')
if args.vo:
end_mesh.display('output surface')
if args.vf:
lines = np.swapaxes(flow, 0, 1)
actor = fvtk.line(lines, colors=[0.5,0,0.1])
ren = fvtk.ren()
fvtk.add(ren, actor)
fvtk.show(ren)
#print "\n !!! tracking Saved !!!\n"
