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"
#!/usr/bin/env python
import argparse
import numpy as np
from trimeshpy.trimesh_vtk import TriMesh_Vtk
parser = argparse.ArgumentParser(description='Surface transformation from RAS to LPS')
parser.add_argument('input', type=str, default=None, help='input RAS surface file name')
parser.add_argument('output', type=str, default=None, help='output LPS surface file name')
#args = parser.parse_args("brain_mesh/rhwhiteRAS.vtk brain_mesh/t1_PA000002.nii.gz".split())
args = parser.parse_args()
surface_file_in = args.input
surface_file_out = args.output
mesh = TriMesh_Vtk(surface_file_in, None)
mesh.update_polydata()
mesh.save(surface_file_out)
#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)
from trimeshpy.trimesh_vtk import TriMesh_Vtk file_name = "../data/brain_mesh/100307.obj" save_file = "../data/brain_mesh/100307.vtk" mesh1 = TriMesh_Vtk(file_name, None) mesh1.save(save_file)
if voxel_space[1] != 'P':
new_vertice[:,1] = -new_vertice[:,1]
if voxel_space[2] != 'S':
new_vertice[:,2] = -new_vertice[:,2]
mesh.set_vertices(new_vertice)
if args.fx or args.fy or args.fz:
flip = [-1 if args.fx else 1,
-1 if args.fy else 1,
-1 if args.fz else 1]
print "flip:", flip
f_triangles, f_vertices = mesh.flip_triangle_and_vertices(flip)
mesh.set_vertices(f_vertices)
mesh.set_triangles(f_triangles)
# smooth
if args.smooth is not None:
new_vertice = mesh.laplacian_smooth(1, args.smooth, l2_dist_weighted=False, area_weighted=False, backward_step=True)
mesh.set_vertices(new_vertice)
if args.out_surface is not None:
mesh.save(args.out_surface)
# view
if args.v:
mesh.update_polydata()
mesh.update_normals()
mesh.display()
if args.mask is not None:
np.save(args.end_points, end_vertices[mask])
else:
np.save(args.end_points, end_vertices)
if args.end_normal is not None:
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])
