Пример #1
0
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
Пример #2
0
                           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)