def build_argparser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
add_mandatory_options_tracking(p)
track_g = add_tracking_options(p)
# If you need the sphere for your model:
add_sphere_arg(track_g, symmetric_only=False)
# As in scilpy:
add_seeding_options(p)
add_out_options(p)
add_logging_arg(p)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawTextHelpFormatter)
add_mandatory_options_tracking(p)
track_g = add_tracking_options(p)
track_g.add_argument('--algo', default='prob',
choices=['det', 'prob', 'eudx'],
help='Algorithm to use [%(default)s]')
add_sphere_arg(track_g, symmetric_only=True)
add_seeding_options(p)
out_g = add_out_options(p)
out_g.add_argument('--seed', type=int,
help='Random number generator seed.')
log_g = p.add_argument_group('Logging options')
add_verbose_arg(log_g)
return p
def _build_arg_parser():
p = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter,
description=__doc__)
add_mandatory_options_tracking(p)
track_g = add_tracking_options(p)
track_g.add_argument('--algo',
default='prob',
choices=['det', 'prob'],
help='Algorithm to use [%(default)s]')
add_sphere_arg(track_g, symmetric_only=False)
track_g.add_argument('--sfthres_init',
metavar='sf_th',
type=float,
default=0.5,
dest='sf_threshold_init',
help="Spherical function relative threshold value "
"for the \ninitial direction. [%(default)s]")
track_g.add_argument('--rk_order',
metavar="K",
type=int,
default=2,
choices=[1, 2, 4],
help="The order of the Runge-Kutta integration used "
"for the \nstep function [%(default)s]. As a "
"rule of thumb, doubling the rk_order \nwill "
"double the computation time in the worst case.")
track_g.add_argument('--max_invalid_length',
metavar='MAX',
type=float,
default=1,
help="Maximum length without valid direction, in mm. "
"[%(default)s]")
track_g.add_argument('--forward_only',
action='store_true',
help="If set, tracks in one direction only (forward) "
"given the \ninitial seed. The direction is "
"randomly drawn from the ODF.")
track_g.add_argument('--sh_interp',
default='trilinear',
choices=['nearest', 'trilinear'],
help="Spherical harmonic interpolation: "
"nearest-neighbor \nor trilinear. [%(default)s]")
track_g.add_argument('--mask_interp',
default='trilinear',
choices=['nearest', 'trilinear'],
help="Mask interpolation: nearest-neighbor or "
"trilinear. [%(default)s]")
add_seeding_options(p)
r_g = p.add_argument_group('Random seeding options')
r_g.add_argument('--rng_seed',
type=int,
default=0,
help='Initial value for the random number generator. '
'[%(default)s]')
r_g.add_argument('--skip',
type=int,
default=0,
help="Skip the first N random number. \n"
"Useful if you want to create new streamlines to "
"add to \na previously created tractogram with a "
"fixed --rng_seed.\nEx: If tractogram_1 was created "
"with -nt 1,000,000, \nyou can create tractogram_2 "
"with \n--skip 1,000,000.")
m_g = p.add_argument_group('Memory options')
add_processes_arg(m_g)
add_out_options(p)
add_verbose_arg(p)
return p