def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_bundle)
assert_outputs_exist(parser, args, args.out_bundle, args.remaining_bundle)
if args.alpha <= 0 or args.alpha > 1:
parser.error('--alpha should be ]0, 1]')
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
if len(sft) == 0:
logging.warning("Bundle file contains no streamline")
return
check_tracts_same_format(
parser, [args.in_bundle, args.out_bundle, args.remaining_bundle])
outliers, inliers = remove_outliers(sft.streamlines, args.alpha)
inliers_sft = sft[inliers]
outliers_sfts = sft[outliers]
if len(inliers) == 0:
logging.warning("All streamlines are considered outliers."
"Please lower the --alpha parameter")
else:
save_tractogram(inliers_sft, args.out_bundle)
if len(outliers) == 0:
logging.warning("No outlier found. Please raise the --alpha parameter")
elif args.remaining_bundle:
save_tractogram(outliers_sfts, args.remaining_bundle)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_bundle)
assert_outputs_exist(parser, args, args.out_bundle, args.remaining_bundle)
if args.alpha <= 0 or args.alpha > 1:
parser.error('--alpha should be ]0, 1]')
tractogram = nib.streamlines.load(args.in_bundle)
if int(tractogram.header['nb_streamlines']) == 0:
logging.warning("Bundle file contains no streamline")
return
check_tracts_same_format(
parser, [args.in_bundle, args.out_bundle, args.remaining_bundle])
streamlines = tractogram.streamlines
summary = outliers_removal_using_hierarchical_quickbundles(streamlines)
outliers, inliers = prune(streamlines, args.alpha, summary)
inliers_streamlines = tractogram.streamlines[inliers]
inliers_data_per_streamline = tractogram.tractogram.data_per_streamline[
inliers]
inliers_data_per_point = tractogram.tractogram.data_per_point[inliers]
outliers_streamlines = tractogram.streamlines[outliers]
outliers_data_per_streamline = tractogram.tractogram.data_per_streamline[
outliers]
outliers_data_per_point = tractogram.tractogram.data_per_point[outliers]
if len(inliers_streamlines) == 0:
logging.warning("All streamlines are considered outliers."
"Please lower the --alpha parameter")
else:
inliers_tractogram = Tractogram(
inliers_streamlines,
affine_to_rasmm=np.eye(4),
data_per_streamline=inliers_data_per_streamline,
data_per_point=inliers_data_per_point)
nib.streamlines.save(inliers_tractogram,
args.out_bundle,
header=tractogram.header)
if len(outliers_streamlines) == 0:
logging.warning("No outlier found. Please raise the --alpha parameter")
elif args.remaining_bundle:
outlier_tractogram = Tractogram(
outliers_streamlines,
affine_to_rasmm=np.eye(4),
data_per_streamline=outliers_data_per_streamline,
data_per_point=outliers_data_per_point)
nib.streamlines.save(outlier_tractogram,
args.remaining_bundle,
header=tractogram.header)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram)
assert_outputs_exist(parser, args, args.out_tractogram,
optional=args.looping_tractogram)
check_tracts_same_format(parser, [args.in_tractogram, args.out_tractogram,
args.looping_tractogram])
if args.threshold <= 0:
parser.error('Threshold "{}" '.format(args.threshold) +
'must be greater than 0')
if args.angle <= 0:
parser.error('Angle "{}" '.format(args.angle) +
'must be greater than 0')
tractogram = load_tractogram_with_reference(
parser, args, args.in_tractogram)
streamlines = tractogram.streamlines
ids_c = []
ids_l = []
if len(streamlines) > 1:
ids_c = remove_loops_and_sharp_turns(
streamlines, args.angle, use_qb=args.qb,
qb_threshold=args.threshold)
ids_l = np.setdiff1d(np.arange(len(streamlines)), ids_c)
else:
parser.error(
'Zero or one streamline in {}'.format(args.in_tractogram) +
'. The file must have more than one streamline.')
if len(ids_c) > 0:
sft_c = filter_tractogram_data(tractogram, ids_c)
save_tractogram(sft_c, args.out_tractogram)
else:
logging.warning(
'No clean streamlines in {}'.format(args.in_tractogram))
if args.display_counts:
sc_bf = len(tractogram.streamlines)
sc_af = len(sft_c.streamlines)
print(json.dumps({'streamline_count_before_filtering': int(sc_bf),
'streamline_count_after_filtering': int(sc_af)},
indent=args.indent))
if len(ids_l) == 0:
logging.warning('No loops in {}'.format(args.in_tractogram))
elif args.looping_tractogram:
sft_l = filter_tractogram_data(tractogram, ids_l)
save_tractogram(sft_l, args.looping_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram)
assert_outputs_exist(parser,
args,
args.out_tractogram,
optional=args.remaining_tractogram)
check_tracts_same_format(
parser,
[args.in_tractogram, args.out_tractogram, args.remaining_tractogram])
if not (-1 <= args.minU <= 1 and -1 <= args.maxU <= 1):
parser.error('Min-Max ufactor "{},{}" '.format(args.minU, args.maxU) +
'must be between -1 and 1.')
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
ids_c = detect_ushape(sft, args.minU, args.maxU)
ids_l = np.setdiff1d(np.arange(len(sft.streamlines)), ids_c)
if len(ids_c) == 0:
if args.no_empty:
logging.debug("The file {} won't be written "
"(0 streamline).".format(args.out_tractogram))
return
logging.debug('The file {} contains 0 streamline.'.format(
args.out_tractogram))
save_tractogram(sft[ids_c], args.out_tractogram)
if args.display_counts:
sc_bf = len(sft.streamlines)
sc_af = len(ids_c)
print(
json.dumps(
{
'streamline_count_before_filtering': int(sc_bf),
'streamline_count_after_filtering': int(sc_af)
},
indent=args.indent))
if args.remaining_tractogram:
if len(ids_l) == 0:
if args.no_empty:
logging.debug("The file {} won't be written (0 streamline"
").".format(args.remaining_tractogram))
return
logging.warning('No remaining streamlines.')
save_tractogram(sft[ids_l], args.remaining_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram)
assert_outputs_exist(parser,
args,
args.out_tractogram,
optional=args.remaining_tractogram)
check_tracts_same_format(
parser,
[args.in_tractogram, args.out_tractogram, args.remaining_tractogram])
if args.threshold <= 0:
parser.error('Threshold "{}" '.format(args.threshold) +
'must be greater than 0')
if args.angle <= 0:
parser.error('Angle "{}" '.format(args.angle) +
'must be greater than 0')
tractogram = nib.streamlines.load(args.in_tractogram)
streamlines = tractogram.streamlines
streamlines_c = []
loops = []
if len(streamlines) > 1:
streamlines_c, loops = remove_loops_and_sharp_turns(
streamlines, args.angle, args.qb, args.threshold)
else:
parser.error(
'Zero or one streamline in {}'.format(args.in_tractogram) +
'. The file must have more than one streamline.')
if len(streamlines_c) > 0:
tractogram_c = nib.streamlines.Tractogram(streamlines_c,
affine_to_rasmm=np.eye(4))
nib.streamlines.save(tractogram_c,
args.out_tractogram,
header=tractogram.header)
else:
logging.warning('No clean streamlines in {}'.format(
args.in_tractogram))
if len(loops) == 0:
logging.warning('No loops in {}'.format(args.in_tractogram))
elif args.remaining_tractogram:
tractogram_l = nib.streamlines.Tractogram(loops,
affine_to_rasmm=np.eye(4))
nib.streamlines.save(tractogram_l,
args.remaining_tractogram,
header=tractogram.header)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram)
assert_outputs_exist(parser,
args,
args.out_tractogram,
optional=args.remaining_tractogram)
check_tracts_same_format(
parser,
[args.in_tractogram, args.out_tractogram, args.remaining_tractogram])
if not (-1 <= args.minU <= 1 and -1 <= args.maxU <= 1):
parser.error('Min-Max ufactor "{},{}" '.format(args.minU, args.maxU) +
'must be between -1 and 1.')
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
ids_c = []
ids_l = []
if len(sft.streamlines) > 1:
ids_c = detect_ushape(sft, args.minU, args.maxU)
ids_l = np.setdiff1d(np.arange(len(sft.streamlines)), ids_c)
else:
parser.error(
'Zero or one streamline in {}'.format(args.in_tractogram) +
'. The file must have more than one streamline.')
if len(ids_c) > 0:
save_tractogram(sft[ids_c], args.out_tractogram)
else:
logging.warning('No u-shape streamlines in {}'.format(
args.in_tractogram))
if args.display_counts:
sc_bf = len(sft.streamlines)
sc_af = len(ids_c)
print(
json.dumps(
{
'streamline_count_before_filtering': int(sc_bf),
'streamline_count_after_filtering': int(sc_af)
},
indent=args.indent))
if len(ids_l) == 0:
logging.warning('No remaining streamlines '
'in {}'.format(args.remaining_tractogram))
elif args.remaining_tractogram:
save_tractogram(sft[ids_l], args.remaining_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.tracts, args.ref_anat])
assert_outputs_exists(parser, args, [args.out])
check_tracts_support(parser, args.tracts, False)
check_tracts_same_format(parser, args.tracts, args.out)
# Deactivated for now.
# Tested implicitely with the 2 previous tracts checks.
# if not tc.is_supported(args.out):
# parser.error('Format of "{0}" not supported.'.format(args.out))
filter_points(args.tracts, args.ref_anat, args.out,
args.nifti_compliant_gen, args.for_nifti_compliant)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.tracts])
assert_outputs_exists(parser, args, [args.out])
check_tracts_support(parser, args.tracts, False)
check_tracts_same_format(parser, args.tracts, args.out)
if args.errorRate < 0.001 or args.errorRate > 1:
logging.warn(
'You are using an error rate of {}.\nWe recommend setting it '
'between 0.001 and 1.\n0.001 will do almost nothing to the tracts '
'while 1 will higly compress/linearize the tracts'.format(
args.errorRate))
compression_wrapper(args.tracts, args.out, args.errorRate)
