Esempio n. 1
0
def main():
    parser = _build_arg_parser()
    args = parser.parse_args()

    if args.verbose:
        logging.basicConfig(level=logging.INFO)

    assert_gradients_filenames_valid(parser, args.mrtrix_enc, 'mrtrix')
    assert_gradients_filenames_valid(parser, [args.fsl_bval, args.fsl_bvec],
                                     'fsl')
    assert_outputs_exist(parser, args, [args.fsl_bval, args.fsl_bvec])

    mrtrix2fsl(args.mrtrix_enc, args.fsl_bval, args.fsl_bvec)
Esempio n. 2
0
def main():
    parser = _build_arg_parser()
    args = parser.parse_args()
    assert_inputs_exist(parser, args.gradient_sampling_file)

    if args.verbose:
        logging.basicConfig(level=logging.INFO)

    if len(args.gradient_sampling_file) == 2:
        assert_gradients_filenames_valid(parser, args.gradient_sampling_file,
                                         'fsl')
    elif len(args.gradient_sampling_file) == 1:
        basename, ext = os.path.splitext(args.gradient_sampling_file[0])
        if ext in ['.bvec', '.bvecs', '.bvals', '.bval']:
            parser.error('You should input two files for fsl format (.bvec '
                         'and .bval).')
        else:
            assert_gradients_filenames_valid(parser,
                                             args.gradient_sampling_file,
                                             'mrtrix')
    else:
        parser.error('Depending on the gradient format you should have '
                     'two files for FSL format and one file for MRtrix')

    out_basename = None

    proj = args.enable_proj
    each = args.plot_shells

    if not (proj or each):
        parser.error('Select at least one type of rendering (proj or each).')

    if len(args.gradient_sampling_file) == 2:
        gradient_sampling_files = args.gradient_sampling_file
        gradient_sampling_files.sort()  # [bval, bvec]
        # bvecs/bvals (FSL) format, X Y Z AND b (or transpose)
        points = np.genfromtxt(gradient_sampling_files[1])
        if points.shape[0] == 3:
            points = points.T
        bvals = np.genfromtxt(gradient_sampling_files[0])
        centroids, shell_idx = identify_shells(bvals)
    else:
        # MRtrix format X, Y, Z, b
        gradient_sampling_file = args.gradient_sampling_file[0]
        tmp = np.genfromtxt(gradient_sampling_file, delimiter=' ')
        points = tmp[:, :3]
        bvals = tmp[:, 3]
        centroids, shell_idx = identify_shells(bvals)

    if args.out_basename:
        out_basename, ext = os.path.splitext(args.out_basename)
        possible_output_paths = [
            out_basename + '_shell_' + str(i) + '.png' for i in centroids
        ]
        possible_output_paths.append(out_basename + '.png')
        assert_outputs_exist(parser, args, possible_output_paths)

    for idx, b0 in enumerate(centroids[centroids < 40]):
        shell_idx[shell_idx == idx] = -1
        centroids = np.delete(centroids, np.where(centroids == b0))

    if len(shell_idx[shell_idx == -1]) > 0:
        shell_idx[shell_idx != -1] -= 1

    sym = args.enable_sym
    sph = args.enable_sph
    same = args.same_color

    ms = build_ms_from_shell_idx(points, shell_idx)
    if proj:
        plot_proj_shell(ms,
                        use_sym=sym,
                        use_sphere=sph,
                        same_color=same,
                        rad=0.025,
                        opacity=args.opacity,
                        ofile=out_basename,
                        ores=(args.res, args.res))
    if each:
        plot_each_shell(ms,
                        centroids,
                        plot_sym_vecs=sym,
                        use_sphere=sph,
                        same_color=same,
                        rad=0.025,
                        opacity=args.opacity,
                        ofile=out_basename,
                        ores=(args.res, args.res))