T = img.affine[:3,3]
z = img.header.get_zooms()
mid_point = np.array(img.shape, dtype=np.float)/2.0
# Input assert
assert not(args.ir and args.r), "--ir or --r option"
assert not(args.it and args.t), "--it or --t option"
assert not(args.im and args.m and args.imz and args.mz ), "--m,im,mz or imz option"
assert not(args.tr and args.itr and args.tir and args.itir), "--tr,itr,tir or itir option"
mesh = TriMesh_Vtk(surface_file_in, None)
if args.test :
tranfo = [-2,33,12]
mesh.set_vertices(mesh.vertices_translation(tranfo))
print "test : " + str(tranfo)
#todo nii rotation before or after translation?!?!?!
if args.r :
tranfo = R
mesh.set_vertices(mesh.vertices_rotation(tranfo))
print "r : " + str(tranfo)
elif args.ir :
tranfo = R.T
mesh.set_vertices(mesh.vertices_rotation(R))
print "ir : " + str(tranfo)
# nii translation
if args.t:
tranfo = T
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 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)
if args.json is not None:
json_file = args.json
else:
json_file = "se_script_config.json"
with open(json_file) as data_file:
config = json.load(data_file)
rh_mesh = TriMesh_Vtk(args.rh_surface, None)
lh_mesh = TriMesh_Vtk(args.lh_surface, None)
run = config["run"]
if run["translate"]:
t = fsf.get_xras_translation(args.mask)
rh_mesh.set_vertices(rh_mesh.vertices_translation(t))
lh_mesh.set_vertices(lh_mesh.vertices_translation(t))
print "xras translation", t
if run["space"]:
if config["space"]["auto"]:
vox = fsf.get_nifti_voxel_space(args.mask)
world = fsf.get_nifti_voxel_space(args.mask)
else:
vox = config["space"]["vox"]
world = config["space"]["world"]
rh_mesh = fsf.vox_to_world(rh_mesh, vox, world)
lh_mesh = fsf.vox_to_world(lh_mesh, vox, world)
if args.world_lps:
rotation = volume_nib.get_affine()[:3,:3]
translation = volume_nib.get_affine()[:3,3]
voxel_space = nib.aff2axcodes(volume_nib.get_affine())
new_vertice = vertices.dot(rotation)
new_vertice = new_vertice + translation
# 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.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)
# Find freesurfer transformation
transform_command_line = "mri_info --cras " + nii_name + " --o " + temp_file_dir
print "run :", transform_command_line
os.system(transform_command_line)
print "read :", temp_file_dir
open_file = open(temp_file_dir, 'r')
center_ras = open_file.read()
open_file.close()
os.remove(temp_file_dir)
os.rmdir(temp_dir)
print center_ras
translate = np.array([float(x) for x in center_ras.split()])# temp HACK
mesh.set_vertices(mesh.vertices_translation(translate))
print "cras", translate
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:
mesh.display() """ from scipy.spatial import Delaunay # Triangulate parameter space to determine the triangles #tri = mtri.Triangulation(u, v) tri = Delaunay(vertices) delaunay_triangles = np.vstack((tri.simplices[:,0:3], np.roll(tri.simplices,2,axis=1)[:,0:3])) mesh.set_triangles(tri.simplices[:,0:3]) mesh.display() """ """ #pre-smooth 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() """
