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)
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))