def flow_trajectories(vertices, triangles, flow_file, steps=10, timestep=5):
"""
Compute the positive mass stiffness surface flow of a surface mesh.
Parameters:
- - - - -
vertices: float array
list of vertices in mesh
triangles: int array
list of faces in mesh
flow_file: string
file (memory map) in which to save flow lines
steps: int
number of diffusion steps
timestep: int
diffusion time
"""
# initialize flow object
tri_mesh_flow = TriMeshFlow_Vtk(triangles, vertices)
# compute final flow surface
points = tri_mesh_flow.positive_mass_stiffness_smooth(steps,
timestep,
flow_file=flow_file)
# get flow trajectory for each mesh vertex
flow_lines = tri_mesh_flow.get_vertices_flow()
return flow_lines
help='Output base name.',
required=True,
type=str)
args = parser.parse_args()
# Load surface file
surface = nb.load(args.surface)
vertices = surface.darrays[0].data
triangles = surface.darrays[1].data
# Get diffusion step parameters
nb_step = args.diffusion_steps
nb_size = args.diffusion_size
tri_mesh_flow = TriMeshFlow_Vtk(triangles, vertices)
saved_flow = trimeshpy.data.output_test_flow
saved_fib = trimeshpy.data.output_test_fib
out_base = args.output_base
dat_file = ''.join([out_base, '.lines.dat'])
points = tri_mesh_flow.positive_mass_stiffness_smooth(nb_step,
nb_size,
flow_file=dat_file)
lines = np.memmap(dat_file,
dtype=np.float64,
mode='r',
shape=(nb_step, vertices.shape[0], vertices.shape[1]))
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()
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 start = time.time() #points = tri_mesh_flow.laplacian_smooth(nb_step, diffusion_step, l2_dist_weighted=False, area_weighted=False, backward_step=False, flow_file=saved_flow) #points = tri_mesh_flow.curvature_normal_smooth(nb_step, diffusion_step, area_weighted=True, backward_step=True, flow_file=saved_flow) #points = tri_mesh_flow.positive_curvature_normal_smooth(nb_step, diffusion_step, area_weighted=True, backward_step=True, flow_file=saved_flow) points = tri_mesh_flow.mass_stiffness_smooth(nb_step, diffusion_step, flow_file=saved_flow) #points = tri_mesh_flow.positive_mass_stiffness_smooth(nb_step, diffusion_step, flow_file=saved_flow) #points = tri_mesh_flow.volume_mass_stiffness_smooth(nb_step, diffusion_step, flow_file=saved_flow)
required=False, default='gifti', type=str, choices=['gifti','freesurfer'])
parser.add_argument('--nb', help='Number of smoothing iterations.',
required=True, type=int)
parser.add_argument('--ds', help='Number of diffusion steps.',
required=True, type=int)
args = parser.parse_args()
nb_step = args.nb
diffusion_step = args.ds
# Load surface file
if args.surface_type == 'gifti':
surface = nb.load(args.surface)
vertices = surface.darrays[0].data
triangles = surface.darrays[1].data
else:
vertices, triangles = nb.freesurfer.io.read_geometry(args.surface)
saved_flow = trimeshpy.data.output_test_flow
saved_fib = trimeshpy.data.output_test_fib
tri_mesh_flow = TriMeshFlow_Vtk(triangles, vertices)
start = time.time()
points = tri_mesh_flow.positive_mass_stiffness_smooth(
nb_step, diffusion_step, flow_file=saved_flow)
stop = time.time()
print('Total time: {:}'.format(start-stop))
# 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,
vertices = mesh.laplacian_smooth(2, 5.0, l2_dist_weighted=False, area_weighted=False, backward_step=True, flow_file=None) mesh.set_vertices(vertices) #mesh.display() # test colors curvature test_curv = mesh.vertices_cotan_curvature(False) color_curv = np.zeros([len(test_curv),3]) max_curv_color = 10000 color_curv[:,0] = np.maximum(-test_curv,0) * max_curv_color / np.abs(test_curv).max() color_curv[:,2] = np.maximum(test_curv,0) * max_curv_color / np.abs(test_curv).max() mesh.set_colors(color_curv) mesh.display() exit() """ tri_mesh_flow = TriMeshFlow_Vtk(triangles, vertices) print tri_mesh_flow.get_nb_vertices(), tri_mesh_flow.get_nb_triangles() # Test parameters nb_step = 10 diffusion_step = 1# saved_flow = "testflow.dat" # None saved_fib = "testflow.fib" # None # Test functions start = time.time() #points = tri_mesh_flow.laplacian_smooth(nb_step, diffusion_step, l2_dist_weighted=False, area_weighted=False, backward_step=False, flow_file=saved_flow) #points = tri_mesh_flow.curvature_normal_smooth(nb_step, diffusion_step, area_weighted=True, backward_step=True, flow_file=saved_flow) #points = tri_mesh_flow.positive_curvature_normal_smooth(nb_step, diffusion_step, area_weighted=True, backward_step=True, flow_file=saved_flow) #points = tri_mesh_flow.mass_stiffness_smooth(nb_step, diffusion_step, flow_file=saved_flow) #points = tri_mesh_flow.positive_mass_stiffness_smooth(nb_step, diffusion_step, flow_file=saved_flow)
