parser.add_argument('-lh_mask', type=str, default=None, help='input left surface mask array')
# option
parser.add_argument('-report', type=str, default=None, help='output intersection report')
args = parser.parse_args()
rh_lines = get_streamlines(load_streamlines_poyldata(args.rh_tracking))
lh_lines = get_streamlines(load_streamlines_poyldata(args.lh_tracking))
lines = [rh_lines, lh_lines]
print "Read .vtk surface file"
rh_mesh = TriMesh_Vtk(args.rh_surface, None)
lh_mesh = TriMesh_Vtk(args.lh_surface, None)
tris = [rh_mesh.get_triangles(), lh_mesh.get_triangles()]
vts = [rh_mesh.get_vertices(), lh_mesh.get_vertices()]
print "Generate OBB-Tree"
#tree = vtk.vtkModifiedBSPTree()
rh_tree = vtk.vtkOBBTree()
rh_tree.SetDataSet(rh_mesh.get_polydata())
rh_tree.BuildLocator()
lh_tree = vtk.vtkOBBTree()
lh_tree.SetDataSet(lh_mesh.get_polydata())
lh_tree.BuildLocator()
tree = [rh_tree, lh_tree]
# report info [rh, lh]
start_count = [len(rh_lines), len(lh_lines)]
saved_flow = "testflow.dat" #files names sphere_file_name = "../data/test_mesh/sphere.obj" cube_file_name = "../data/test_mesh/cube_simple.obj" torus_file_name = "../data/test_mesh/torus.obj" spot_file_name = "../data/test_mesh/spot.obj" brain_file_name = "../data/brain_mesh/100307_smooth_lh.vtk" # Init Sphere s_mesh = TriMesh_Vtk(sphere_file_name, None) s_vshape0 = s_mesh.get_nb_vertices() # Display sphere sphere_tmf = TriMeshFlow_Vtk(s_mesh.get_triangles(), s_mesh.get_vertices()) sphere_tmf.display() # Umbrella sphere sphere_tmf.laplacian_smooth(100, 1, l2_dist_weighted=False, area_weighted=False, backward_step=False, flow_file=saved_flow) sphere_tmf.set_vertices_flow_from_memmap(saved_flow, 100, s_vshape0) sphere_tmf.display() sphere_tmf.display_vertices_flow() # L2 weighted sphere_tmf.set_vertices_flow(s_mesh.get_vertices()) sphere_tmf.laplacian_smooth(100, 1, l2_dist_weighted=True, area_weighted=False, backward_step=False, flow_file=saved_flow) sphere_tmf.set_vertices_flow_from_memmap(saved_flow, 100, s_vshape0) sphere_tmf.display() sphere_tmf.display_vertices_flow()
# by Etienne St-Onge 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
# by [email protected] import numpy as np from trimeshpy.trimesh_class import TriMesh from trimeshpy.trimesh_vtk import TriMesh_Vtk file_name = "../data/test_mesh/cube_simple.obj" #file_name = "../data/test_mesh/sphere.obj" #file_name = "../data/test_mesh/torus.obj" mesh = TriMesh_Vtk(file_name, None) triangles = mesh.get_triangles() vertices = mesh.get_vertices() tri_mesh = TriMesh(triangles, vertices) print tri_mesh.get_nb_triangles(), tri_mesh.get_nb_vertices() bool_tests = True current_test = True """CONNECTIVITY MATRIX""" # test vertex connectivity vv_matrix = tri_mesh.edge_map(False) current_test = np.alltrue(vv_matrix.todense() == vv_matrix.T.todense()) print current_test, ": connectivity is symmetric" bool_tests = bool_tests and current_test # test triangles vertex connectivity tv_matrix = tri_mesh.triangle_vertex_map() nb_triangles_per_points = tri_mesh.nb_triangles_per_vertex() current_test = np.alltrue(tv_matrix.sum(1) == 3)
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)
volume_nib = nib.load(nii_name)
if not args.no_lps:
voxel_space = nib.aff2axcodes(volume_nib.get_affine())
new_vertice = mesh.get_vertices()
# voxel_space -> LPS
print str(voxel_space), "-to-> LPS"
if voxel_space[0] != 'L':
new_vertice[:,0] = -new_vertice[:,0]
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.tx is not None or args.ty is not None or args.tz is not None :
translate2 = [0.0, 0.0, 0.0]
if args.tx is not None:
translate2[0] = args.tx
parser.add_argument('-max_nb_step', type=int, default=100, help='nb step for surface tracking interpolation')
parser.add_argument('-compression', type=float, default=None, help='compression toll (no-compression by default, but 0.01 is dipy default)')
args = parser.parse_args()
### weight correctly the ending triangle !
print " loading files!"
intersect = np.load(args.intersection)
surf_id = np.load(args.surf_idx)
tracto_polydata = load_streamlines_poyldata(args.tracto_cut)
tracto = get_streamlines(tracto_polydata)
rh_mesh = TriMesh_Vtk(args.rh_surface, None)
rh_vts = rh_mesh.get_vertices()
rh_tris = rh_mesh.get_triangles()
lh_mesh = TriMesh_Vtk(args.lh_surface, None)
lh_vts = lh_mesh.get_vertices()
lh_tris = lh_mesh.get_triangles()
rh_info = np.load(args.rh_flow_info)
lh_info = np.load(args.lh_flow_info)
rh_flow = np.memmap(args.rh_flow_file, dtype=np.float64, mode='r',
shape=(rh_info[0], rh_vts.shape[0], rh_vts.shape[1]))
lh_flow = np.memmap(args.lh_flow_file, dtype=np.float64, mode='r',
shape=(rh_info[0], lh_vts.shape[0], lh_vts.shape[1]))
# by Etienne St-Onge
import trimeshpy
from trimeshpy.trimesh_vtk import TriMesh_Vtk
from trimeshpy.trimeshflow_vtk import TriMeshFlow_Vtk
# Init Sphere
s_mesh = TriMesh_Vtk(trimeshpy.data.sphere, None)
s_vshape0 = s_mesh.get_nb_vertices()
# Display sphere
sphere_tmf = TriMeshFlow_Vtk(s_mesh.get_triangles(), s_mesh.get_vertices())
sphere_tmf.display()
NB_STEP_SPHERE = 100
# Umbrella sphere
sphere_tmf.laplacian_smooth(NB_STEP_SPHERE,
1,
l2_dist_weighted=False,
area_weighted=False,
backward_step=False,
flow_file=trimeshpy.data.output_test_flow)
sphere_tmf.set_vertices_flow_from_memmap(trimeshpy.data.output_test_flow,
NB_STEP_SPHERE, s_vshape0)
sphere_tmf.display()
sphere_tmf.display_vertices_flow()
# L2 weighted
sphere_tmf.set_vertices_flow(s_mesh.get_vertices())
sphere_tmf.laplacian_smooth(NB_STEP_SPHERE,
1,
