def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_tractogram, args.in_transfo])
assert_outputs_exist(parser, args, args.out_tractogram)
if args.verbose:
log_level = logging.INFO
logging.basicConfig(level=log_level)
wb_file = load_tractogram_with_reference(parser, args, args.in_tractogram)
wb_streamlines = wb_file.streamlines
model_file = load_tractogram_with_reference(parser, args, args.in_model)
transfo = load_matrix_in_any_format(args.in_transfo)
if args.inverse:
transfo = np.linalg.inv(load_matrix_in_any_format(args.in_transfo))
before, after = compute_distance_barycenters(wb_file, model_file, transfo)
if after > before:
logging.warning('The distance between volumes barycenter should be '
'lower after registration. Maybe try using/removing '
'--inverse.')
logging.info('Distance before: {}, Distance after: {}'.format(
np.round(before, 3), np.round(after, 3)))
model_streamlines = transform_streamlines(model_file.streamlines, transfo)
rng = np.random.RandomState(args.seed)
if args.in_pickle:
with open(args.in_pickle, 'rb') as infile:
cluster_map = pickle.load(infile)
reco_obj = RecoBundles(wb_streamlines,
cluster_map=cluster_map,
rng=rng,
verbose=args.verbose)
else:
reco_obj = RecoBundles(wb_streamlines,
clust_thr=args.tractogram_clustering_thr,
rng=rng,
verbose=args.verbose)
if args.out_pickle:
with open(args.out_pickle, 'wb') as outfile:
pickle.dump(reco_obj.cluster_map, outfile)
_, indices = reco_obj.recognize(ArraySequence(model_streamlines),
args.model_clustering_thr,
pruning_thr=args.pruning_thr,
slr_num_threads=args.slr_threads)
new_streamlines = wb_streamlines[indices]
new_data_per_streamlines = wb_file.data_per_streamline[indices]
new_data_per_points = wb_file.data_per_point[indices]
if not args.no_empty or new_streamlines:
sft = StatefulTractogram(new_streamlines,
wb_file.space_attributes,
Space.RASMM,
data_per_streamline=new_data_per_streamlines,
data_per_point=new_data_per_points)
save_tractogram(sft, args.out_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.moving_tractogram,
args.static_tractogram])
if args.only_rigid:
matrix_filename = os.path.splitext(args.out_name)[0] + '_rigid.txt'
else:
matrix_filename = os.path.splitext(args.out_name)[0] + '_affine.txt'
assert_outputs_exist(parser, args, matrix_filename, args.out_name)
sft_moving = load_tractogram_with_reference(parser, args,
args.moving_tractogram,
arg_name='moving_tractogram')
sft_static = load_tractogram_with_reference(parser, args,
args.static_tractogram,
arg_name='static_tractogram')
if args.only_rigid:
transformation_type = 'rigid'
else:
transformation_type = 'affine'
ret = whole_brain_slr(sft_moving.streamlines,
sft_static.streamlines,
x0=transformation_type,
maxiter=150,
verbose=args.verbose)
_, transfo, _, _ = ret
np.savetxt(matrix_filename, transfo)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser,
[args.moving_tractogram, args.static_tractogram])
if args.only_rigid:
matrix_filename = os.path.splitext(args.out_name)[0] + '_rigid.npy'
else:
matrix_filename = os.path.splitext(args.out_name)[0] + '_affine.npy'
assert_outputs_exist(parser, args, matrix_filename, args.out_name)
sft_moving = load_tractogram_with_reference(parser,
args,
args.moving_tractogram,
bbox_check=True,
argName='moving_tractogram')
sft_static = load_tractogram_with_reference(parser,
args,
args.static_tractogram,
bbox_check=True,
argName='static_tractogram')
register_tractogram(sft_moving, sft_static, args.only_rigid,
args.amount_to_load, matrix_filename, args.verbose)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_tractogram, args.transformation])
assert_outputs_exist(parser, args, args.output_name)
wb_file = load_tractogram_with_reference(parser, args, args.in_tractogram)
wb_streamlines = wb_file.streamlines
model_file = load_tractogram_with_reference(parser, args, args.in_model)
# Default transformation source is expected to be ANTs
transfo = np.loadtxt(args.transformation)
if args.inverse:
transfo = np.linalg.inv(np.loadtxt(args.transformation))
model_streamlines = ArraySequence(
transform_streamlines(model_file.streamlines, transfo))
rng = np.random.RandomState(args.seed)
if args.input_pickle:
with open(args.input_pickle, 'rb') as infile:
cluster_map = pickle.load(infile)
reco_obj = RecoBundles(wb_streamlines,
cluster_map=cluster_map,
rng=rng,
verbose=args.verbose)
else:
reco_obj = RecoBundles(wb_streamlines,
clust_thr=args.wb_clustering_thr,
rng=rng,
verbose=args.verbose)
if args.output_pickle:
with open(args.output_pickle, 'wb') as outfile:
pickle.dump(reco_obj.cluster_map, outfile)
_, indices = reco_obj.recognize(model_streamlines,
args.model_clustering_thr,
pruning_thr=args.pruning_thr,
slr_num_threads=args.slr_threads)
new_streamlines = wb_streamlines[indices]
new_data_per_streamlines = wb_file.data_per_streamline[indices]
new_data_per_points = wb_file.data_per_point[indices]
if not args.no_empty or new_streamlines:
sft = StatefulTractogram(new_streamlines,
wb_file,
Space.RASMM,
data_per_streamline=new_data_per_streamlines,
data_per_point=new_data_per_points)
save_tractogram(sft, args.output_name)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser,
[args.in_bundle, args.in_centroid],
optional=args.reference)
assert_outputs_exist(parser, args, args.out_map)
sft_bundle = load_tractogram_with_reference(parser, args, args.in_bundle)
sft_centroid = load_tractogram_with_reference(parser, args,
args.in_centroid)
if not len(sft_bundle.streamlines):
logging.error('Empty bundle file {}. '
'Skipping'.format(args.in_bundle))
raise ValueError
if not len(sft_centroid.streamlines):
logging.error('Centroid file {} should contain one streamline. '
'Skipping'.format(args.in_centroid))
raise ValueError
sft_bundle.to_vox()
bundle_streamlines_vox = sft_bundle.streamlines
bundle_streamlines_vox._data *= args.upsample
sft_centroid.to_vox()
centroid_streamlines_vox = sft_centroid.streamlines
centroid_streamlines_vox._data *= args.upsample
upsampled_shape = [s * args.upsample for s in sft_bundle.dimensions]
tdi_mask = compute_tract_counts_map(bundle_streamlines_vox,
upsampled_shape) > 0
tdi_mask_nzr = np.nonzero(tdi_mask)
tdi_mask_nzr_ind = np.transpose(tdi_mask_nzr)
min_dist_ind, _ = min_dist_to_centroid(tdi_mask_nzr_ind,
centroid_streamlines_vox[0])
# Save the (upscaled) labels mask
labels_mask = np.zeros(tdi_mask.shape)
labels_mask[tdi_mask_nzr] = min_dist_ind + 1 # 0 is background value
rescaled_affine = sft_bundle.affine
rescaled_affine[:3, :3] /= args.upsample
labels_img = nib.Nifti1Image(labels_mask, rescaled_affine)
upsampled_spacing = sft_bundle.voxel_sizes / args.upsample
labels_img.header.set_zooms(upsampled_spacing)
nib.save(labels_img, args.out_map)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_bundles)
output_streamlines_filename = '{}streamlines.trk'.format(
args.output_prefix)
output_voxels_filename = '{}voxels.nii.gz'.format(args.output_prefix)
assert_outputs_exist(parser, args,
[output_voxels_filename, output_streamlines_filename])
if not 0 <= args.ratio_voxels <= 1 or not 0 <= args.ratio_streamlines <= 1:
parser.error('Ratios must be between 0 and 1.')
fusion_streamlines = []
if args.reference:
reference_file = args.reference
else:
reference_file = args.in_bundles[0]
sft_list = []
for name in args.in_bundles:
tmp_sft = load_tractogram_with_reference(parser, args, name)
tmp_sft.to_vox()
tmp_sft.to_corner()
if not is_header_compatible(reference_file, tmp_sft):
raise ValueError('Headers are not compatible.')
sft_list.append(tmp_sft)
fusion_streamlines.append(tmp_sft.streamlines)
fusion_streamlines, _ = union_robust(fusion_streamlines)
transformation, dimensions, _, _ = get_reference_info(reference_file)
volume = np.zeros(dimensions)
streamlines_vote = dok_matrix(
(len(fusion_streamlines), len(args.in_bundles)))
for i in range(len(args.in_bundles)):
sft = sft_list[i]
binary = compute_tract_counts_map(sft.streamlines, dimensions)
volume[binary > 0] += 1
if args.same_tractogram:
_, indices = intersection_robust(
[fusion_streamlines, sft.streamlines])
streamlines_vote[list(indices), [i]] += 1
if args.same_tractogram:
real_indices = []
ratio_value = int(args.ratio_streamlines * len(args.in_bundles))
real_indices = np.where(
np.sum(streamlines_vote, axis=1) >= ratio_value)[0]
new_sft = StatefulTractogram.from_sft(fusion_streamlines[real_indices],
sft_list[0])
save_tractogram(new_sft, output_streamlines_filename)
volume[volume < int(args.ratio_voxels * len(args.in_bundles))] = 0
volume[volume > 0] = 1
nib.save(nib.Nifti1Image(volume.astype(np.uint8), transformation),
output_voxels_filename)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram, args.reference)
assert_outputs_exist(parser, args, args.out_tractogram)
sft = load_tractogram_with_reference(parser,
args,
args.in_tractogram,
bbox_check=False)
ori_len = len(sft)
sft.remove_invalid_streamlines()
indices = []
if args.remove_single_point:
# Will try to do a PR in Dipy
indices = [i for i in range(len(sft)) if len(sft.streamlines[i]) <= 1]
if args.remove_overlapping_points:
for i in range(len(sft)):
norm = np.linalg.norm(np.gradient(sft.streamlines[i], axis=0),
axis=1)
if (norm < 0.001).any():
indices.append(i)
indices = np.setdiff1d(range(len(sft)), indices)
new_sft = StatefulTractogram.from_sft(
sft.streamlines[indices],
sft,
data_per_point=sft.data_per_point[indices],
data_per_streamline=sft.data_per_streamline[indices])
logging.warning('Removed {} invalid streamlines.'.format(ori_len -
len(new_sft)))
save_tractogram(new_sft, args.out_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_bundle] + args.metrics,
optional=args.reference)
assert_same_resolution(args.metrics)
metrics = [nib.load(metric) for metric in args.metrics]
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
sft.to_vox()
sft.to_corner()
bundle_stats = get_bundle_metrics_mean_std(sft.streamlines,
metrics,
args.density_weighting)
bundle_name, _ = os.path.splitext(os.path.basename(args.in_bundle))
stats = {bundle_name: {}}
for metric, (mean, std) in zip(metrics, bundle_stats):
metric_name = split_name_with_nii(
os.path.basename(metric.get_filename()))[0]
stats[bundle_name][metric_name] = {
'mean': mean,
'std': std
}
print(json.dumps(stats, indent=args.indent, sort_keys=args.sort_keys))
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser,
[args.in_bundle, args.in_bingham, args.in_lobe_metric])
assert_outputs_exist(parser, args, [args.out_mean_map])
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
bingham_img = nib.load(args.in_bingham)
metric_img = nib.load(args.in_lobe_metric)
if bingham_img.shape[-2] != metric_img.shape[-1]:
parser.error('Dimension mismatch between Bingham coefficients '
'and lobe-specific metric image.')
metric_mean_map =\
lobe_specific_metric_map_along_streamlines(sft,
bingham_img.get_fdata(),
metric_img.get_fdata(),
args.max_theta,
args.length_weighting)
nib.Nifti1Image(metric_mean_map.astype(np.float32),
bingham_img.affine).to_filename(args.out_mean_map)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram)
assert_outputs_exist(parser, args, [], optional=args.output_centroids)
if args.output_clusters_dir:
assert_output_dirs_exist_and_empty(parser,
args,
args.output_clusters_dir,
create_dir=True)
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
streamlines = sft.streamlines
thresholds = [40, 30, 20, args.dist_thresh]
clusters = qbx_and_merge(streamlines,
thresholds,
nb_pts=args.nb_points,
verbose=False)
for i, cluster in enumerate(clusters):
if len(cluster.indices) > 1:
cluster_streamlines = itemgetter(*cluster.indices)(streamlines)
else:
cluster_streamlines = streamlines[cluster.indices]
new_sft = StatefulTractogram(cluster_streamlines, sft, Space.RASMM)
save_tractogram(
new_sft,
os.path.join(args.output_clusters_dir, 'cluster_{}.trk'.format(i)))
if args.output_centroids:
new_sft = StatefulTractogram(clusters.centroids, sft, Space.RASMM)
save_tractogram(new_sft, args.output_centroids)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(
parser,
[args.in_moving_tractogram, args.in_target_file, args.in_transfo],
args.in_deformation)
assert_outputs_exist(parser, args, args.out_tractogram)
moving_sft = load_tractogram_with_reference(parser,
args,
args.in_moving_tractogram,
bbox_check=False)
transfo = load_matrix_in_any_format(args.in_transfo)
deformation_data = None
if args.in_deformation is not None:
deformation_data = np.squeeze(
nib.load(args.in_deformation).get_fdata(dtype=np.float32))
new_sft = transform_warp_streamlines(moving_sft,
transfo,
args.in_target_file,
inverse=args.inverse,
deformation_data=deformation_data,
remove_invalid=args.remove_invalid,
cut_invalid=args.cut_invalid)
if args.keep_invalid:
if not new_sft.is_bbox_in_vox_valid():
logging.warning('Saving tractogram with invalid streamlines.')
save_tractogram(new_sft, args.out_tractogram, bbox_valid_check=False)
else:
save_tractogram(new_sft, args.out_tractogram)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram)
assert_outputs_exist(parser, args, args.out_tractogram)
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
new_streamlines, new_per_point, new_per_streamline = filter_streamlines_by_length(
sft, args.minL, args.maxL)
new_sft = StatefulTractogram(new_streamlines,
sft,
Space.RASMM,
data_per_streamline=new_per_streamline,
data_per_point=new_per_point)
if not new_streamlines:
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(new_sft, args.out_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)
if not args.out_tractogram.endswith('.trk'):
parser.error('Output file needs to end with .trk.')
if len(args.color) == 7:
args.color = '0x' + args.color.lstrip('#')
if len(args.color) == 8:
color_int = int(args.color, 0)
red = color_int >> 16
green = (color_int & 0x00FF00) >> 8
blue = color_int & 0x0000FF
else:
parser.error('Hexadecimal RGB color should be formatted as "#RRGGBB"'
' or 0xRRGGBB.')
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
sft.data_per_point["color"] = [np.tile([red, green, blue],
(len(i), 1)) for i in sft.streamlines]
sft = StatefulTractogram.from_sft(sft.streamlines, sft,
data_per_point=sft.data_per_point)
save_tractogram(sft, args.out_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)
log_level = logging.WARNING
if args.verbose:
log_level = logging.DEBUG
logging.basicConfig(level=log_level)
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
smoothed_streamlines = []
for streamline in sft.streamlines:
if args.gaussian:
tmp_streamlines = smooth_line_gaussian(streamline, args.gaussian)
else:
tmp_streamlines = smooth_line_spline(streamline, args.spline[0],
args.spline[1])
if args.error_rate:
smoothed_streamlines.append(
compress_streamlines(tmp_streamlines, args.error_rate))
smoothed_sft = StatefulTractogram.from_sft(
smoothed_streamlines, sft, data_per_streamline=sft.data_per_streamline)
save_tractogram(smoothed_sft, args.out_tractogram)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_bundle, optional=args.reference)
assert_outputs_exist(parser, args, args.out_img)
max_ = np.iinfo(np.int16).max
if args.binary is not None and (args.binary <= 0 or args.binary > max_):
parser.error(
'The value of --binary ({}) '
'must be greater than 0 and smaller or equal to {}'.format(
args.binary, max_))
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
sft.to_vox()
sft.to_corner()
streamlines = sft.streamlines
transformation, dimensions, _, _ = sft.space_attributes
streamline_count = compute_tract_counts_map(streamlines, dimensions)
if args.binary is not None:
streamline_count[streamline_count > 0] = args.binary
nib.save(
nib.Nifti1Image(streamline_count.astype(np.int16), transformation),
args.out_img)
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 load_data(parser, args, path):
logging.info('Loading streamlines from {0}.'.format(path))
sft = load_tractogram_with_reference(parser, args, path)
streamlines = list(sft.streamlines)
data_per_streamline = sft.data_per_streamline
data_per_point = sft.data_per_point
return streamlines, data_per_streamline, data_per_point
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()
swap = args.swap
assert_inputs_exist(parser, args.in_bundle, args.reference)
assert_outputs_exist(parser, args,
[args.endpoints_map_head, args.endpoints_map_tail])
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
sft.to_vox()
if len(sft.streamlines) == 0:
logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
return
transfo, dim, _, _ = sft.space_attributes
endpoints_map_head = np.zeros(dim)
endpoints_map_tail = np.zeros(dim)
head_name = args.endpoints_map_head
tail_name = args.endpoints_map_tail
if swap:
head_name = args.endpoints_map_tail
tail_name = args.endpoints_map_head
for streamline in sft.streamlines:
xyz = streamline[0, :].astype(int)
endpoints_map_head[xyz[0], xyz[1], xyz[2]] += 1
xyz = streamline[-1, :].astype(int)
endpoints_map_tail[xyz[0], xyz[1], xyz[2]] += 1
nib.save(nib.Nifti1Image(endpoints_map_head, transfo), head_name)
nib.save(nib.Nifti1Image(endpoints_map_tail, transfo), tail_name)
bundle_name, _ = os.path.splitext(os.path.basename(args.in_bundle))
bundle_name_head = bundle_name + '_head'
bundle_name_tail = bundle_name + '_tail'
if swap:
bundle_name_head = bundle_name + '_tail'
bundle_name_tail = bundle_name + '_head'
stats = {
bundle_name_head: {
'count': np.count_nonzero(endpoints_map_head)
},
bundle_name_tail: {
'count': np.count_nonzero(endpoints_map_tail)
}
}
print(json.dumps(stats, indent=args.indent))
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()
swap = args.swap
assert_inputs_exist(parser, args.in_bundle, args.reference)
assert_outputs_exist(parser, args,
[args.endpoints_map_head, args.endpoints_map_tail])
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
sft.to_vox()
sft.to_corner()
if len(sft.streamlines) == 0:
logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
return
transfo, dim, _, _ = sft.space_attributes
head_name = args.endpoints_map_head
tail_name = args.endpoints_map_tail
if swap:
head_name = args.endpoints_map_tail
tail_name = args.endpoints_map_head
endpoints_map_head, endpoints_map_tail = \
get_head_tail_density_maps(sft.streamlines, dim)
if args.binary:
endpoints_map_head = (endpoints_map_head > 0).astype(np.int16)
endpoints_map_tail = (endpoints_map_tail > 0).astype(np.int16)
nib.save(nib.Nifti1Image(endpoints_map_head, transfo), head_name)
nib.save(nib.Nifti1Image(endpoints_map_tail, transfo), tail_name)
bundle_name, _ = os.path.splitext(os.path.basename(args.in_bundle))
bundle_name_head = bundle_name + '_head'
bundle_name_tail = bundle_name + '_tail'
if swap:
bundle_name_head = bundle_name + '_tail'
bundle_name_tail = bundle_name + '_head'
stats = {
bundle_name_head: {
'count': np.count_nonzero(endpoints_map_head)
},
bundle_name_tail: {
'count': np.count_nonzero(endpoints_map_tail)
}
}
print(json.dumps(stats, indent=args.indent))
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 compute_gt_masks(gt_bundles, parser, args):
"""
Compute ground-truth masks. If the ground-truth is
already a mask, load it. If the ground-truth is a
bundle, compute the mask.
Parameters
----------
gt_bundles: list
List of either StatefulTractograms or niftis.
parser: ArgumentParser
Argument parser which handles the script's arguments.
args: Namespace
List of arguments passed to the script.
Returns
-------
mask_1: numpy.ndarray
"Head" of the mask.
mask_2: numpy.ndarray
"Tail" of the mask.
"""
gt_bundle_masks = []
gt_bundle_inv_masks = []
for gt_bundle in args.gt_bundles:
# Support ground truth as streamlines or masks
# Will be converted to binary masks immediately
_, ext = split_name_with_nii(gt_bundle)
if ext in ['.gz', '.nii.gz']:
gt_img = nib.load(gt_bundle)
gt_mask = get_data_as_mask(gt_img)
affine = gt_img.affine
dimensions = gt_mask.shape
else:
gt_sft = load_tractogram_with_reference(parser,
args,
gt_bundle,
bbox_check=False)
gt_sft.to_vox()
gt_sft.to_corner()
affine, dimensions, _, _ = gt_sft.space_attributes
gt_mask = compute_tract_counts_map(gt_sft.streamlines,
dimensions).astype(np.int16)
gt_inv_mask = np.zeros(dimensions, dtype=np.int16)
gt_inv_mask[gt_mask == 0] = 1
gt_mask[gt_mask > 0] = 1
gt_bundle_masks.append(gt_mask)
gt_bundle_inv_masks.append(gt_inv_mask)
return gt_bundle_masks, gt_bundle_inv_masks, affine, dimensions
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)
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
new_sft = get_subset_streamlines(sft, args.max_num_streamlines, args.seed)
save_tractogram(new_sft, args.out_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)
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
sft.to_vox()
sft.to_corner()
new_sft = flip_sft(sft, args.axes)
save_tractogram(new_sft, args.out_tractogram)
def main():
parser = _build_args_parser()
args = parser.parse_args()
assert_inputs_exist(parser, args.in_tractogram, args.reference)
assert_outputs_exist(parser, args, args.output_name)
sft = load_tractogram_with_reference(parser,
args,
args.in_tractogram,
bbox_check=False)
sft.remove_invalid_streamlines()
save_tractogram(sft, args.output_name)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_bundle, args.in_centroid])
assert_outputs_exist(parser, args,
[args.output_label, args.output_distance])
is_header_compatible(args.in_bundle, args.in_centroid)
sft_bundle = load_tractogram_with_reference(parser, args, args.in_bundle)
sft_centroid = load_tractogram_with_reference(parser, args,
args.in_centroid)
if not len(sft_bundle.streamlines):
logging.error('Empty bundle file {}. Skipping'.format(args.in_bundle))
raise ValueError
if not len(sft_centroid.streamlines):
logging.error('Empty centroid streamline file {}. Skipping'.format(
args.centroid_streamline))
raise ValueError
min_dist_label, min_dist = min_dist_to_centroid(
sft_bundle.streamlines.data, sft_centroid.streamlines.data)
min_dist_label += 1
# Save assignment in a compressed numpy file
# You can load this file and access its data using
# f = np.load('someFile.npz')
# assignment = f['arr_0']
np.savez_compressed(args.output_label, min_dist_label)
# Save distance in a compressed numpy file
# You can load this file and access its data using
# f = np.load('someFile.npz')
# distance = f['arr_0']
np.savez_compressed(args.output_distance, min_dist)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.INFO)
assert_inputs_exist(parser, [args.in_tractogram, args.in_mask])
assert_outputs_exist(parser, args, args.out_tractogram)
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
if args.step_size is not None:
sft = resample_streamlines_step_size(sft, args.step_size)
mask_img = nib.load(args.in_mask)
binary_mask = get_data_as_mask(mask_img)
if not is_header_compatible(sft, mask_img):
parser.error('Incompatible header between the tractogram and mask.')
bundle_disjoint, _ = ndi.label(binary_mask)
unique, count = np.unique(bundle_disjoint, return_counts=True)
if args.biggest_blob:
val = unique[np.argmax(count[1:]) + 1]
binary_mask[bundle_disjoint != val] = 0
unique = [0, val]
if len(unique) == 2:
logging.info('The provided mask has 1 entity '
'cut_outside_of_mask_streamlines function selected.')
new_sft = cut_outside_of_mask_streamlines(sft, binary_mask)
elif len(unique) == 3:
logging.info('The provided mask has 2 entity '
'cut_between_masks_streamlines function selected.')
new_sft = cut_between_masks_streamlines(sft, binary_mask)
else:
logging.error('The provided mask has more than 2 entities. Cannot cut '
'between >2.')
return
if len(new_sft) == 0:
logging.warning('No streamline intersected the provided mask. '
'Saving empty tractogram.')
elif args.error_rate is not None:
compressed_strs = [
compress_streamlines(s, args.error_rate)
for s in new_sft.streamlines
]
new_sft = StatefulTractogram.from_sft(compressed_strs, sft)
save_tractogram(new_sft, args.out_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, args.save_rejected)
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
# Silencing SFT's logger if our logging is in DEBUG mode, because it
# typically produces a lot of outputs!
set_sft_logger_level('WARNING')
if args.min_x == 0 and np.isinf(args.max_x) and \
args.min_y == 0 and np.isinf(args.max_y) and \
args.min_z == 0 and np.isinf(args.max_z):
logging.warning("You have not specified min or max in any direction. "
"Output will simply be a copy of your input!")
sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
computed_rejected_sft = args.save_rejected is not None
new_sft, indices, rejected_sft = \
filter_streamlines_by_total_length_per_dim(
sft, [args.min_x, args.max_x], [args.min_y, args.max_y],
[args.min_z, args.max_z], args.use_abs, computed_rejected_sft)
if args.display_counts:
sc_bf = len(sft.streamlines)
sc_af = len(new_sft.streamlines)
print(
json.dumps(
{
'streamline_count_before_filtering': int(sc_bf),
'streamline_count_after_filtering': int(sc_af)
},
indent=args.indent))
if len(new_sft.streamlines) == 0:
if args.no_empty:
logging.debug("The file {} won't be written "
"(0 streamline).".format(args.out_tractogram))
else:
logging.debug('The file {} contains 0 streamline'.format(
args.out_tractogram))
save_tractogram(new_sft, args.out_tractogram)
if computed_rejected_sft:
save_tractogram(rejected_sft, args.save_rejected)
def main():
parser = _build_arg_parser()
args = parser.parse_args()
assert_inputs_exist(parser, [args.in_bundle] + args.in_metrics)
assert_output_dirs_exist_and_empty(parser, args,
args.out_folder,
create_dir=True)
assert_same_resolution(args.in_metrics)
sft = load_tractogram_with_reference(parser, args, args.in_bundle)
sft.to_vox()
sft.to_corner()
if len(sft.streamlines) == 0:
logging.warning('Empty bundle file {}. Skipping'.format(args.bundle))
return
mins, maxs, indices = _process_streamlines(sft.streamlines)
metrics = [nib.load(metric) for metric in args.in_metrics]
for metric in metrics:
data = metric.get_fdata(dtype=np.float32)
endpoint_metric_map = np.zeros(metric.shape)
count = np.zeros(metric.shape)
for cur_min, cur_max, cur_ind, orig_s in zip(mins, maxs,
indices,
sft.streamlines):
streamline_mean = _compute_streamline_mean(cur_ind,
cur_min,
cur_max,
data)
xyz = orig_s[0, :].astype(int)
endpoint_metric_map[xyz[0], xyz[1], xyz[2]] += streamline_mean
count[xyz[0], xyz[1], xyz[2]] += 1
xyz = orig_s[-1, :].astype(int)
endpoint_metric_map[xyz[0], xyz[1], xyz[2]] += streamline_mean
count[xyz[0], xyz[1], xyz[2]] += 1
endpoint_metric_map[count != 0] /= count[count != 0]
metric_fname, ext = split_name_with_nii(
os.path.basename(metric.get_filename()))
nib.save(nib.Nifti1Image(endpoint_metric_map, metric.affine,
metric.header),
os.path.join(args.out_folder,
'{}_endpoints_metric{}'.format(metric_fname,
ext)))