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)
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
# 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:
