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,