Source code for fsl.wrappers.fast

#
# fast.py - Wrapper for the FSL fast command.
#
# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
#         Paul McCarthy <pauldmccarthy@gmail.com>
#
"""This module provides the :func:`fast` function, a wrapper for the FSL
`FAST <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST>`_ command.
"""


import six

import fsl.utils.assertions as asrt
from . import wrapperutils  as wutils


[docs]@wutils.fileOrImage('imgs', 'A', 's', 'manualseg', outprefix='out') @wutils.fileOrArray('a') @wutils.fslwrapper def fast(imgs, out='fast', **kwargs): """Wrapper for the ``fast`` command. :arg imgs: Input image(s) :arg out: Output basename :arg n_classes: Number of tissue classes (corresponds to the ``--class`` command line option) """ if isinstance(imgs, six.string_types): imgs = [imgs] asrt.assertIsNifti(*imgs) valmap = { 'nobias' : wutils.SHOW_IF_TRUE, 'N' : wutils.SHOW_IF_TRUE, 'verbose' : wutils.SHOW_IF_TRUE, 'v' : wutils.SHOW_IF_TRUE, 'Prior' : wutils.SHOW_IF_TRUE, 'P' : wutils.SHOW_IF_TRUE, 'segments' : wutils.SHOW_IF_TRUE, 'nopve' : wutils.SHOW_IF_TRUE, 'g' : wutils.SHOW_IF_TRUE, 'b' : wutils.SHOW_IF_TRUE, 'B' : wutils.SHOW_IF_TRUE, 'p' : wutils.SHOW_IF_TRUE, } argmap = { 'n_classes' : 'class', } cmd = ['fast', '-v', '--out=%s' % out] cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs) cmd += imgs return cmd