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
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]))
lines = np.asarray(lines)
L = {'lines': lines}
mat_file = ''.join([out_base, '.lines.mat'])
sio.savemat(file_name=mat_file, mdict=L)
# Compute length of flow lines
flow_lengths = flow_lengths(lines)
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))
