import argparse
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from trimeshpy.trimesh_vtk import load_streamlines_poyldata, get_streamlines
parser = argparse.ArgumentParser(description='lenghts stats')
parser.add_argument('-lengths', type=str, nargs='+', default=None, help='tractography length (.npy)')
parser.add_argument('-lengths', type=str, nargs='+', default=None, help='tractography surface connection idx (.npy)')
args = parser.parse_args()
streamlines_list = []
for filename in args.tracts:
streamlines_list.append(get_streamlines(load_streamlines_poyldata(filename)))
lines_length_list = []
for lines in streamlines_list:
lines_length = np.zeros([len(lines)], dtype=np.float)
for i in range(len(lines)):
dist = lines[i][:-1] - lines[i][1:]
lines_length[i] = np.sum(np.sqrt(np.sum(np.square(dist), axis=1)))
lines_length_list.append(lines_length)
#print np.average(lines_length)
#print np.var(lines_length)
histogram_list = []
color_list = ['lightcoral', 'darkred', 'lightgreen', 'darkgreen', 'skyblue', 'darkblue', 'khaki', 'y']
patches = []
fontsize=20
parser.add_argument('--fy1', action='store_true', default=False, help='flip x, from voxel_space')
parser.add_argument('--fz1', action='store_true', default=False, help='flip x, from voxel_space')
parser.add_argument('--fx2', action='store_true', default=False, help='flip x, from volume shape')
parser.add_argument('--fy2', action='store_true', default=False, help='flip x, from volume shape')
parser.add_argument('--fz2', action='store_true', default=False, help='flip x, from volume shape')
parser.add_argument('-tx', type=float, default=None, help='x translation')
parser.add_argument('-ty', type=float, default=None, help='y translation')
parser.add_argument('-tz', type=float, default=None, help='z translation')
args = parser.parse_args()
# get transform
nib_mask = nib.load(args.mask)
lines = get_streamlines(load_streamlines_poyldata(args.tract))
rotation = nib_mask.get_affine()[:3,:3]
inv_rotation = np.linalg.inv(rotation)
translation = nib_mask.get_affine()[:3,3]
scale = np.array(nib_mask.get_header().get_zooms())
voxel_space = nib.aff2axcodes(nib_mask.get_affine())
shape = nib_mask.get_data().shape
print shape
# transform
if not args.no_transfo:
if args.lps_ras:
print "LPS -> RAS"
print "Not implemented"
raise NotImplementedError()
parser.add_argument('rh_surface', type=str, default=None, help='input right surface')
parser.add_argument('lh_surface', type=str, default=None, help='input left surface')
parser.add_argument('output', type=str, default=None, help='output right tracking result .fib (VTK FORMAT)')
parser.add_argument('intersection', type=str, default=None, help='output points direction where flow stopped')
parser.add_argument('surf_idx_inter', type=str, default=None, help='output surface index for intersection')
parser.add_argument('-rh_mask', type=str, default=None, help='input right surface mask array')
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()
parser.add_argument('surf_idx', type=str, default=None, help='surface index intersection file')
parser.add_argument('output', type=str, default=None, help='tracking result .fib format')
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]))