def __init__(self, track_file, label_file=None):
""" Create a new tractogram.
"""
self.tracks = loadtxt(track_file)
if label_file is None:
self.labels = [0, ] * self.shape()
else:
self.labels = {}
with open(label_file) as open_file:
clusters = json.load(open_file)
for clusterid, clusteritem in clusters.items():
for trkindex in clusteritem["indices"]:
self.labels[trkindex] = clusterid
self.length = [None, ] * self.shape()
def __init__(self, track_file, label_file=None):
""" Create a new tractogram.
"""
self.tracks = loadtxt(track_file)
if label_file is None:
self.labels = [
0,
] * self.shape()
else:
self.labels = {}
with open(label_file) as open_file:
clusters = json.load(open_file)
for clusterid, clusteritem in clusters.items():
for trkindex in clusteritem["indices"]:
self.labels[trkindex] = clusterid
self.length = [
None,
] * self.shape()
track_file = os.path.join(track_outdir, "fibers.txt")
if not os.path.isdir(track_outdir):
os.mkdir(track_outdir)
if not os.path.isfile(track_file):
deterministic(diffusion_file,
bvecs_file,
bvals_file,
track_outdir,
mask_file=mask_file,
order=4,
nb_seeds_per_voxel=nb_seeds_per_voxel,
step=0.5,
fmt="%.4f")
if use_vtk:
tracks = loadtxt(track_file)
actor = pvtk.line(tracks, scalar=1)
pvtk.add(ren, actor)
pvtk.record(ren, qcdir, "fibers", az_ang=45, n_frames=2)
pvtk.clear(ren)
connect_outdir = os.path.join(outdir, "det_region_connectivity")
if not os.path.isdir(connect_outdir):
os.mkdir(connect_outdir)
if len(os.listdir(connect_outdir)) == 0:
if use_t1_space:
proba_file, network_file = anatomical_connectivity_matrix(
track_file,
label_file,
t1_file,
fa_file,
if not os.path.isdir(track_outdir):
os.mkdir(track_outdir)
if not os.path.isfile(track_file):
deterministic(
diffusion_file,
bvecs_file,
bvals_file,
track_outdir,
mask_file=mask_file,
order=4,
nb_seeds_per_voxel=nb_seeds_per_voxel,
step=0.5,
fmt="%.4f")
if use_vtk:
tracks = loadtxt(track_file)
actor = pvtk.line(tracks, scalar=1)
pvtk.add(ren, actor)
pvtk.record(ren, qcdir, "fibers", az_ang=45, n_frames=2)
pvtk.clear(ren)
connect_outdir = os.path.join(outdir, "det_region_connectivity")
if not os.path.isdir(connect_outdir):
os.mkdir(connect_outdir)
if len(os.listdir(connect_outdir)) == 0:
if use_t1_space:
proba_file, network_file = anatomical_connectivity_matrix(
track_file,
label_file,
t1_file,
