def streams_to_connmat(filename, seeds_per_voxel=1, thr=[0.25, 0.5, 0.75]):
streams, hdr = nib.trackvis.read(filename)
streamlines = [s[0] for s in streams]
# show_streamlines(streamlines, opacity=0.5)
rois, affine = get_train_rois()
mat, srois, ratio = connectivity_matrix(streamlines, rois)
golden_mat = np.load('train_connmat.npy')
lr = []
for i in range(1, 41):
lr.append(np.sum(rois == i))
lr = seeds_per_voxel * np.array(lr, dtype='f8')
mat /= lr
mat += mat.T
golden_mat += golden_mat.T
conn_mats = []
diffs = []
for th in thr:
conn_mat = mat > th
conn_mats.append(conn_mat)
diffs.append(np.sum(np.abs(conn_mat - golden_mat)))
return mat, conn_mats, diffs, ratio
opacity=opacity)
fvtk.add(ren, line_actor)
if r is None:
fvtk.show(ren)
else:
return ren
if __name__ == '__main__':
from load_data import get_train_gt_fibers
streamlines, radii = get_train_gt_fibers()
show_gt_streamlines(streamlines, radii, 'orient', None)
from load_data import get_train_rois
rois, affine = get_train_rois()
streamlines = [s + np.array([24.5, 24.5, 24.5]) for s in streamlines]
from conn_mat import connectivity_matrix
mat, srois, ratio = connectivity_matrix(streamlines, rois)
np.save('train_connmat.npy', mat)