def build_args_p():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
p.add_argument('operation',
choices=OPERATIONS.keys(),
metavar='OPERATION',
help='The type of operation to be performed on the '
'streamlines. Must\nbe one of the following: '
'%(choices)s.')
p.add_argument('inputs',
metavar='INPUT_FILES',
nargs='+',
help='The list of files that contain the ' +
'streamlines to operate on.')
p.add_argument('output',
metavar='OUTPUT_FILE',
help='The file where the remaining streamlines '
'are saved.')
add_reference(p)
p.add_argument('--precision',
'-p',
metavar='NUMBER_OF_DECIMALS',
type=int,
help='The precision used when comparing streamlines.')
p.add_argument('--no_metadata',
'-n',
action='store_true',
help='Strip the streamline metadata from the output.')
p.add_argument('--save_metadata_indices',
'-m',
action='store_true',
help='Save streamline indices to metadata. Has no '
'effect if --no-data\nis present. Will '
'overwrite \'ids\' metadata if already present.')
p.add_argument('--save_indices',
'-s',
metavar='OUTPUT_INDEX_FILE',
help='Save the streamline indices to the supplied '
'json file.')
p.add_argument(
'--no-bbox-check',
action='store_true',
help='Avoid check if all streamline coordinates are within '
'proper bounding box in voxel space.\nWARNING: By using this option '
'ill-formatted tractograms are not being detected.')
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _buildArgsParser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=DESCRIPTION)
p.add_argument('in_tractogram', help='Path of the input tractogram file.')
p.add_argument('out_tractogram',
help='Path of the output tractogram file.')
add_reference(p)
p.add_argument('--drawn_roi',
nargs=3,
action='append',
metavar=('ROI_NAME', 'MODE', 'CRITERIA'),
help='Filename of a hand drawn ROI (.nii or .nii.gz).')
p.add_argument('--atlas_roi',
nargs=4,
action='append',
metavar=('ROI_NAME', 'ID', 'MODE', 'CRITERIA'),
help='Filename of an atlas (.nii or .nii.gz).')
p.add_argument('--bdo',
dest='bdo',
nargs=3,
action='append',
metavar=('BDO_NAME', 'MODE', 'CRITERIA'),
help='Filename of a bounding box (bdo) file from MI-Brain.')
p.add_argument('--x_plane',
nargs=3,
action='append',
metavar=('PLANE', 'MODE', 'CRITERIA'),
help='Slice number in X, in voxel space.')
p.add_argument('--y_plane',
nargs=3,
action='append',
metavar=('PLANE', 'MODE', 'CRITERIA'),
help='Slice number in Y, in voxel space.')
p.add_argument('--z_plane',
nargs=3,
action='append',
metavar=('PLANE', 'MODE', 'CRITERIA'),
help='Slice number in Z, in voxel space.')
p.add_argument('--filtering_list',
help='Text file containing one rule per line\n'
'(i.e. drawn_roi mask.nii.gz both_ends include).')
p.add_argument('--no_empty',
action='store_true',
help='Do not write file if there is no streamline.')
add_verbose(p)
add_overwrite_arg(p)
return p
def _build_args_parser():
p = argparse.ArgumentParser(
formatter_class=argparse.RawTextHelpFormatter,
description=__doc__,
epilog="""Garyfallidis, E., Côté, M. A., Rheault, F., ... &
Descoteaux, M. (2018). Recognition of white matter
bundles using local and global streamline-based registration and
clustering. NeuroImage, 170, 283-295.""")
p.add_argument('in_tractogram',
help='Input tractogram filename (trk or tck).')
p.add_argument('in_model',
help='Model to use for recognition (trk or tck).')
p.add_argument('transformation',
help='4x4 transformation to bring the model onto \n'
'the input tractogram')
p.add_argument('output_name',
help='Output tractogram filename.')
add_reference(p)
p.add_argument('--wb_clustering_thr', type=float, default=8,
help='Clustering threshold used for the whole brain '
'[%(default)smm].')
p.add_argument('--model_clustering_thr', type=float, default=4,
help='Clustering threshold used for the model '
'[%(default)smm].')
p.add_argument('--pruning_thr', type=float, default=6,
help='MDF threshold used for final streamlines selection '
'[%(default)smm].')
p.add_argument('--slr_threads', type=int, default=None,
help='Number of threads for SLR [all].')
p.add_argument('--seed', type=int, default=None,
help='Random number generator seed [%(default)s].')
p.add_argument('--inverse', action='store_true',
help='Use the inverse transformation.')
p.add_argument('--no_empty', action='store_true',
help='Do not write file if there is no streamline.')
group = p.add_mutually_exclusive_group()
group.add_argument('--input_pickle',
help='Input pickle clusters map file.\n'
'Will override the wb_clustering_thr parameter.')
group.add_argument('--output_pickle',
help='Output pickle clusters map file.')
add_verbose(p)
add_overwrite_arg(p)
return p
def _build_args_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_tractogram',
metavar='IN_TRACTOGRAM',
help='Tractogram filename. Format must be one of \n'
'trk, tck, vtk, fib, dpy')
p.add_argument('output_name',
metavar='OUTPUT_NAME',
help='Output filename. Format must be one of \n'
'trk, tck, vtk, fib, dpy')
add_reference(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=DESCRIPTION,
epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('tract_filename', help='Input streamlines file.')
add_reference(p)
p.add_argument('--sphere',
default='repulsion724',
help='sphere used for the angular discretization.')
p.add_argument('--mask', help='Use the given mask')
p.add_argument('--out_mask', help='Mask showing where TDI > 0.')
p.add_argument('--out_lw_tdi', help='Output length-weighted TDI map.')
p.add_argument('--out_lw_todi', help='Output length-weighted TODI map.')
p.add_argument('--out_lw_todi_sh',
help='Output length-weighted TODI map, '
'with SH coefficient.')
p.add_argument('--sh_order',
type=int,
default=8,
help='Order of the original SH.')
p.add_argument('--sh_normed', action='store_true', help='Normalize sh.')
p.add_argument('--smooth',
action='store_true',
help='Smooth todi (angular and spatial).')
add_sh_basis_args(p)
add_overwrite_arg(p)
return p