def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Path to the input file.')
p.add_argument('out_sh', help='File name for averaged signal.')
p.add_argument('--out_sym',
default=None,
help='Name of optional symmetric output. [%(default)s]')
add_sh_basis_args(p)
p.add_argument('--sphere',
default='repulsion724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. '
'[%(default)s]')
p.add_argument('--sharpness',
default=1.0,
type=float,
help='Specify sharpness factor to use for weighted average.'
' [%(default)s]')
p.add_argument('--sigma',
default=1.0,
type=float,
help='Sigma of the gaussian to use. [%(default)s]')
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
epilog=EPILOG,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Input SH image.')
p.add_argument('--mask', default='', help='Optional mask.')
# outputs
p.add_argument('--cos_asym_map',
default='',
help='Output asymmetry map using cos similarity.')
p.add_argument('--odd_power_map', default='', help='Output odd power map.')
p.add_argument('--peaks',
default='',
help='Output filename for the extracted peaks.')
p.add_argument('--peak_values',
default='',
help='Output filename for the extracted peaks values.')
p.add_argument('--peak_indices',
default='',
help='Output filename for the generated peaks indices on '
'the sphere.')
p.add_argument('--nupeaks',
default='',
help='Output filename for the nupeaks file.')
p.add_argument('--not_all',
action='store_true',
help='If set, only saves the files specified using the '
'file flags [%(default)s].')
p.add_argument('--at',
dest='a_threshold',
type=float,
default='0.0',
help='Absolute threshold on fODF amplitude. This '
'value should be set to\napproximately 1.5 to 2 times '
'the maximum fODF amplitude in isotropic voxels\n'
'(ie. ventricles).\n'
'Use compute_fodf_max_in_ventricles.py to find the '
'maximal value.\n'
'See [Dell\'Acqua et al HBM 2013] [%(default)s].')
p.add_argument('--rt',
dest='r_threshold',
type=float,
default='0.1',
help='Relative threshold on fODF amplitude in percentage '
'[%(default)s].')
p.add_argument('--sphere',
default='symmetric724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere to use for peak directions estimation '
'[%(default)s].')
add_processes_arg(p)
add_sh_basis_args(p)
add_overwrite_arg(p)
return p
def add_sphere_arg(parser, symmetric_only=False, default='symmetric724'):
spheres = sorted(SPHERE_FILES.keys())
if symmetric_only:
spheres = [s for s in spheres if 'symmetric' in s]
if 'symmetric' not in default:
raise ValueError("Default cannot be {} if you only accept "
"symmetric spheres.".format(default))
parser.add_argument('--sphere',
choices=spheres,
default=default,
help='Dipy sphere; set of possible directions.')
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
# Positional arguments
p.add_argument('in_bingham', help='Input SH image file.')
# Window configuration options
p.add_argument('--slice_index',
type=int,
help='Index of the slice to visualize along a given axis. '
'Defaults to middle of volume.')
p.add_argument('--win_dims',
nargs=2,
metavar=('WIDTH', 'HEIGHT'),
default=(768, 768),
type=int,
help='The dimensions for the vtk window. [%(default)s]')
p.add_argument('--interactor',
default='trackball',
choices={'image', 'trackball'},
help='Specify interactor mode for vtk window. '
'[%(default)s]')
p.add_argument('--axis_name',
default='axial',
type=str,
choices={'axial', 'coronal', 'sagittal'},
help='Name of the axis to visualize. [%(default)s]')
p.add_argument('--silent',
action='store_true',
help='Disable interactive visualization.')
p.add_argument('--output', help='Path to output file.')
add_overwrite_arg(p)
p.add_argument('--sphere',
default='symmetric362',
choices=sorted(SPHERE_FILES.keys()),
help='Name of the sphere used to reconstruct SF. '
'[%(default)s]')
p.add_argument('--color_per_lobe',
action='store_true',
help='Color each bingham distribution with a '
'different color. [%(default)s]')
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Path of the SH volume.')
p.add_argument('out_sf',
help='Name of the output SF file to save (bvals/bvecs will '
'be automatically named when necessary).')
# Sphere vs bvecs choice for SF
directions = p.add_mutually_exclusive_group(required=True)
directions.add_argument('--sphere',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. ')
directions.add_argument(
'--in_bvec', help="Directions used for the SH to SF projection.")
p.add_argument('--dtype',
default="float32",
choices=["float32", "float64"],
help="Datatype to use for SF computation and output array."
"'[%(default)s]'")
# Optional args for a DWI-like volume
p.add_argument('--in_bval',
help='b-value file, in FSL format, '
'used to assign a b-value to the '
'output SF and generate a `.bval` file.')
p.add_argument('--in_b0',
help='b0 volume to concatenate to the '
'final SF volume.')
p.add_argument('--out_bval', help="Optional output bval file.")
p.add_argument('--out_bvec', help="Optional output bvec file.")
p.add_argument('--b0_scaling',
action="store_true",
help="Scale resulting SF by the b0 image.")
add_sh_basis_args(p)
p.add_argument('--full_basis',
action="store_true",
help="If true, use a full basis for the input SH "
"coefficients.")
add_processes_arg(p)
add_overwrite_arg(p)
add_force_b0_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh', help='Path to the input file.')
p.add_argument('out_sh', help='File name for averaged signal.')
p.add_argument('--out_asymmetry',
default='asym_map.nii.gz',
help='File name for asymmetry map. Can only be outputed'
' when the output SH basis is full. [%(default)s]')
p.add_argument('--sh_order',
default=8,
type=int,
help='SH order of the input. [%(default)s]')
add_sh_basis_args(p)
p.add_argument('--sphere',
default='repulsion724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. '
'[%(default)s]')
p.add_argument('--sharpness',
default=1.0,
type=float,
help='Specify sharpness factor to use for weighted average.'
' [%(default)s]')
p.add_argument('--sigma',
default=1.0,
type=float,
help='Sigma of the gaussian to use. [%(default)s]')
p.add_argument('--out_sym',
action='store_true',
help='If set, saves output in symmetric SH basis.')
add_verbose_arg(p)
add_overwrite_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
p.add_argument('in_sh',
help='Path to the input file.')
p.add_argument('out_sh',
help='File name for averaged signal.')
add_sh_basis_args(p)
p.add_argument('--out_sym', default=None,
help='Name of optional symmetric output. [%(default)s]')
p.add_argument('--sphere', default='repulsion724',
choices=sorted(SPHERE_FILES.keys()),
help='Sphere used for the SH to SF projection. '
'[%(default)s]')
p.add_argument('--sigma_angular', default=1.0, type=float,
help='Standard deviation for angular distance.'
' [%(default)s]')
p.add_argument('--sigma_spatial', default=1.0, type=float,
help='Standard deviation for spatial distance.'
' [%(default)s]')
p.add_argument('--sigma_range', default=1.0, type=float,
help='Standard deviation for range filter.'
' [%(default)s]')
p.add_argument('--use_gpu', action='store_true',
help='Use GPU for computation.')
add_verbose_arg(p)
add_overwrite_arg(p)
add_processes_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
p._optionals.title = 'Generic options'
p.add_argument('sh_file',
help='Spherical harmonic file. \n'
'(isotropic resolution, nifti, see --basis).')
p.add_argument('seed_file',
help='Seeding mask (isotropic resolution, nifti).')
p.add_argument('mask_file',
help='Seeding mask(isotropic resolution, nifti).\n' +
'Tracking will stop outside this mask')
p.add_argument('output_file',
help='Streamline output file (must be trk or tck).')
track_g = p.add_argument_group('Tracking options')
track_g.add_argument(
'--algo',
default='prob',
choices=['det', 'prob'],
help='Algorithm to use (must be "det" or "prob"). [%(default)s]')
track_g.add_argument('--step',
dest='step_size',
type=float,
default=0.5,
help='Step size in mm. [%(default)s]')
track_g.add_argument(
'--min_length',
type=float,
default=10.,
help='Minimum length of a streamline in mm. [%(default)s]')
track_g.add_argument(
'--max_length',
type=float,
default=300.,
help='Maximum length of a streamline in mm. [%(default)s]')
track_g.add_argument(
'--theta',
type=float,
help='Maximum angle between 2 steps. ["eudx"=60, det"=45, "prob"=20]')
track_g.add_argument(
'--sfthres',
dest='sf_threshold',
type=float,
default=0.1,
help='Spherical function relative threshold. [%(default)s]')
add_sh_basis_args(track_g)
seed_group = p.add_argument_group(
'Seeding options', 'When no option is provided, uses --npv 1.')
seed_sub_exclusive = seed_group.add_mutually_exclusive_group()
seed_sub_exclusive.add_argument('--npv',
type=int,
help='Number of seeds per voxel.')
seed_sub_exclusive.add_argument('--nt',
type=int,
help='Total number of seeds to use.')
p.add_argument('--sphere',
choices=sorted(SPHERE_FILES.keys()),
default='symmetric724',
help='Set of directions to be used for tracking')
out_g = p.add_argument_group('Output options')
out_g.add_argument(
'--compress',
type=float,
help='If set, will compress streamlines. The parameter\nvalue is the '
'distance threshold. A rule of thumb\nis to set it to 0.1mm for '
'deterministic\nstreamlines and 0.2mm for probabilitic '
'streamlines.')
out_g.add_argument('--seed',
type=int,
help='Random number generator seed.')
add_overwrite_arg(out_g)
log_g = p.add_argument_group('Logging options')
add_verbose(log_g)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
p._optionals.title = 'Generic options'
p.add_argument('in_sh',
help='Spherical harmonic file (.nii.gz) OR \n'
'peaks/evecs (.nii.gz) for EUDX tracking.')
p.add_argument('in_seed', help='Seeding mask (.nii.gz).')
p.add_argument('in_mask',
help='Seeding mask (.nii.gz).\n'
'Tracking will stop outside this mask.')
p.add_argument('out_tractogram',
help='Tractogram output file (must be .trk or .tck).')
track_g = p.add_argument_group('Tracking options')
track_g.add_argument('--algo',
default='prob',
choices=['det', 'prob', 'eudx'],
help='Algorithm to use [%(default)s]')
track_g.add_argument('--step',
dest='step_size',
type=float,
default=0.5,
help='Step size in mm. [%(default)s]')
track_g.add_argument('--min_length',
type=float,
default=10.,
help='Minimum length of a streamline in mm. '
'[%(default)s]')
track_g.add_argument('--max_length',
type=float,
default=300.,
help='Maximum length of a streamline in mm. '
'[%(default)s]')
track_g.add_argument('--theta',
type=float,
help='Maximum angle between 2 steps.\n'
'["eudx"=60, "det"=45, "prob"=20]')
track_g.add_argument('--sfthres',
dest='sf_threshold',
type=float,
default=0.1,
help='Spherical function relative threshold. '
'[%(default)s]')
add_sh_basis_args(track_g)
seed_group = p.add_argument_group(
'Seeding options', 'When no option is provided, uses --npv 1.')
seed_sub_exclusive = seed_group.add_mutually_exclusive_group()
seed_sub_exclusive.add_argument('--npv',
type=int,
help='Number of seeds per voxel.')
seed_sub_exclusive.add_argument('--nt',
type=int,
help='Total number of seeds to use.')
p.add_argument('--sphere',
choices=sorted(SPHERE_FILES.keys()),
default='symmetric724',
help='Set of directions to be used for tracking.')
out_g = p.add_argument_group('Output options')
out_g.add_argument('--compress',
type=float,
help='If set, will compress streamlines.\n'
'The parameter value is the distance threshold.')
out_g.add_argument('--seed',
type=int,
help='Random number generator seed.')
add_overwrite_arg(out_g)
out_g.add_argument('--save_seeds',
action='store_true',
help='If set, save the seeds used for the tracking \n '
'in the data_per_streamline property.')
log_g = p.add_argument_group('Logging options')
add_verbose_arg(log_g)
return p
def test_sphere_dtypes():
for sphere_name, sphere_path in SPHERE_FILES.items():
sphere_data = np.load(sphere_path)
npt.assert_equal(sphere_data['vertices'].dtype, np.float64)
def _build_arg_parser():
parser = argparse.ArgumentParser(
description='Dipy-based local tracking on fiber ODF (fODF)',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
'type',
choices=[DETERMINISTIC, PROBABILISTIC, EUDX],
help='Tracking type (deterministic, probabilistic or EuDX based on '
'fODF peaks)')
parser.add_argument('sh_file', help='Spherical Harmonic file')
parser.add_argument('seed_file', help='Seeding mask')
parser.add_argument(
'mask_file',
help='Tracking mask. Tracking will stop outside this mask')
parser.add_argument('output_file', help='Streamline output file (TRK)')
seed_group = parser.add_mutually_exclusive_group()
seed_group.add_argument('--npv',
default=5,
type=int,
help='Number of seeds per voxel')
seed_group.add_argument('--nts',
default=argparse.SUPPRESS,
type=int,
help='Total number of seeds. Replaces --npv')
deviation_angle_group = parser.add_mutually_exclusive_group()
deviation_angle_group.add_argument(
'--theta',
default=argparse.SUPPRESS,
help='Maximum angle between 2 steps. [{}=45.0, {}=20.0, {}=60.0]'
''.format(DETERMINISTIC, PROBABILISTIC, EUDX))
deviation_angle_group.add_argument(
'--curvature',
type=float,
default=argparse.SUPPRESS,
help='Minimum radius of curvature R in mm. Replaces --theta')
parser.add_argument('--step_size',
default=0.5,
type=float,
help='Step size used for tracking')
parser.add_argument('--sphere',
choices=sorted(SPHERE_FILES.keys()),
default='symmetric724',
help='Set of directions to be used for tracking')
parser.add_argument(
'--basis',
default='fibernav',
choices=['mrtrix', 'fibernav'],
help='Basis used for the spherical harmonic coefficients')
parser.add_argument('--sf_thres',
type=float,
default=0.1,
help='Spherical function relative threshold')
parser.add_argument('--min_len',
type=float,
default=10,
help='Minimum length of a streamline in mm')
parser.add_argument('--max_len',
type=float,
default=300,
help='Maximum length of a streamline in mm')
parser.add_argument('--compress_streamlines',
action='store_true',
help='If set, compress streamlines on-the-fly')
parser.add_argument(
'--tolerance_error',
type=float,
default=0.1,
help='Tolerance error in mm. A rule of thumb is to set it to 0.1mm '
'for deterministic streamlines and 0.2mm for probabilitic '
'streamlines.')
parser.add_argument('--seed',
type=int,
default=None,
help='Random number generator seed')
add_overwrite_arg(parser)
return parser