def flirt(src, ref, **kwargs):
"""Wrapper for the ``flirt`` command.
The ``twod`` argument may be used in place of the ``2D`` command line
option.
"""
asrt.assertIsNifti(src, ref)
argmap = {'twod': '2D'}
valmap = {
'usesqform': wutils.SHOW_IF_TRUE,
'displayinit': wutils.SHOW_IF_TRUE,
'noresample': wutils.SHOW_IF_TRUE,
'forcescaling': wutils.SHOW_IF_TRUE,
'applyxfm': wutils.SHOW_IF_TRUE,
'nosearch': wutils.SHOW_IF_TRUE,
'noclamp': wutils.SHOW_IF_TRUE,
'noresampblur': wutils.SHOW_IF_TRUE,
'2D': wutils.SHOW_IF_TRUE,
'v': wutils.SHOW_IF_TRUE,
}
cmd = ['flirt', '-in', src, '-ref', ref]
cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
def melodic(input, **kwargs):
"""Wrapper for the ``melodic`` command."""
valmap = {
'Oall': wutils.SHOW_IF_TRUE,
'Ounmix': wutils.SHOW_IF_TRUE,
'Ostats': wutils.SHOW_IF_TRUE,
'Opca': wutils.SHOW_IF_TRUE,
'Owhite': wutils.SHOW_IF_TRUE,
'Oorig': wutils.SHOW_IF_TRUE,
'Omean': wutils.SHOW_IF_TRUE,
'verbose': wutils.SHOW_IF_TRUE,
'debug': wutils.SHOW_IF_TRUE,
'report': wutils.SHOW_IF_TRUE,
'CIFTI': wutils.SHOW_IF_TRUE,
'varnorm': wutils.SHOW_IF_TRUE,
'nomask': wutils.SHOW_IF_TRUE,
'nobet': wutils.SHOW_IF_TRUE,
'sep_vn': wutils.SHOW_IF_TRUE,
'disableMigp': wutils.SHOW_IF_TRUE,
'update_mask': wutils.HIDE_IF_TRUE,
'migp_shuffle': wutils.HIDE_IF_TRUE,
'no_mm': wutils.SHOW_IF_TRUE,
'logPower': wutils.SHOW_IF_TRUE,
}
asrt.assertIsNifti(input)
cmd = ['melodic', '--in={}'.format(input)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
def fslroi(input, output, *args):
"""Wrapper for the ``fslroi`` tool."""
asrt.assertIsNifti(input)
cmd = ['fslroi', input, output] + [str(a) for a in args]
return cmd
def preproc(*images):
"""Wrapper for the ``tbss_1_preproc`` command.
Usage: ``tbss_1_preproc(<image1>, <image2>, ...)``
"""
for img in images:
asrt.assertIsNifti(img)
return ["tbss_1_preproc"] + list(images)
def fnirt(src, **kwargs):
"""Wrapper for the ``fnirt`` command."""
asrt.assertIsNifti(src)
cmd = ['fnirt', '--in={}'.format(src)]
cmd += wutils.applyArgStyle('--=', **kwargs)
return cmd
def fslreorient2std(input, output=None):
"""Wrapper for the ``fsreorient2std`` tool."""
asrt.assertIsNifti(input)
cmd = ['fslreorient2std', input]
if output is not None:
cmd.append(output)
return cmd
def topup(imain, datain, **kwargs):
"""Wrapper for the ``topup`` command."""
valmap = {'verbose': wutils.SHOW_IF_TRUE}
asrt.assertFileExists(datain)
asrt.assertIsNifti(imain)
cmd = ['topup', '--imain={}'.format(imain), '--datain={}'.format(datain)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
def bet(input, output, **kwargs):
"""Wrapper for the ``bet`` command.
:arg mask: Generate a brain mask
:arg seg: If ``False``, a brain extracted image is not
generated.
:arg robust: Robust brain centre estimation
:arg fracintensity: Fractional intensity threshold
Refer to the ``bet`` command-line help for details on all arguments.
"""
asrt.assertIsNifti(input)
argmap = {
'mask': 'm',
'robust': 'R',
'fracintensity': 'f',
'seg': 'n',
'centre': 'c',
}
valmap = {
'm': wutils.SHOW_IF_TRUE,
'o': wutils.SHOW_IF_TRUE,
's': wutils.SHOW_IF_TRUE,
'n': wutils.HIDE_IF_TRUE,
't': wutils.SHOW_IF_TRUE,
'e': wutils.SHOW_IF_TRUE,
'R': wutils.SHOW_IF_TRUE,
'S': wutils.SHOW_IF_TRUE,
'B': wutils.SHOW_IF_TRUE,
'Z': wutils.SHOW_IF_TRUE,
'F': wutils.SHOW_IF_TRUE,
'A': wutils.SHOW_IF_TRUE,
'v': wutils.SHOW_IF_TRUE,
'd': wutils.SHOW_IF_TRUE,
}
cmd = ['bet', input, output]
# The 'centre' argument requires three co-ordinates and can't be passed
# as a single value, so needs to be handled separately. Assume it is
# passed as a Python sequence
centre = kwargs.pop("c", None)
if centre is not None:
cmd += [
'-c',
] + [str(v) for v in centre]
cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
def robustfov(input, output=None, **kwargs):
"""Wrapper for the ``robustfov`` command. """
asrt.assertIsNifti(input)
if output is not None:
kwargs.update({'output': output})
argmap = {'output': 'r', 'matrix': 'm'}
cmd = ['robustfov', '-i', input]
cmd += wutils.applyArgStyle('-', argmap=argmap, **kwargs)
return cmd
def applyxfm4D(src, ref, out, mat, **kwargs):
"""Wrapper for the ``applyxfm4D`` command. """
asrt.assertIsNifti(src, ref)
valmap = {
'singlematrix': wutils.SHOW_IF_TRUE,
'fourdigit': wutils.SHOW_IF_TRUE,
}
cmd = ['applyxfm4D', src, ref, out, mat]
cmd += wutils.applyArgStyle('-', valmap=valmap, **kwargs)
return cmd
def applytopup(imain, datain, index, **kwargs):
"""Wrapper for the ``applytopup`` command."""
valmap = {'verbose': wutils.SHOW_IF_TRUE}
asrt.assertFileExists(datain)
for fn in imain.split(','):
asrt.assertIsNifti(fn)
cmd = [
'applytopup',
'--imain={}'.format(imain),
'--inindex={}'.format(index),
'--datain={}'.format(datain),
]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
def fsl_regfilt(input, out, design, **kwargs):
"""Wrapper for the ``fsl_regfilt`` command. """
asrt.assertIsNifti(input, out)
valmap = {
'freqfilt': wutils.SHOW_IF_TRUE,
'freq_ic': wutils.HIDE_IF_TRUE,
'vn': wutils.SHOW_IF_TRUE,
'v': wutils.SHOW_IF_TRUE,
}
cmd = [
'fsl_regfilt', '--in={}'.format(input), '--out={}'.format(out),
'--design={}'.format(design)
]
cmd += wutils.applyArgStyle('--=', valsep=',', valmap=valmap, **kwargs)
return cmd
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
def mvntool(mvn, param, **kwargs):
"""
Wrapper for MVNTOOL.
:param mvn: Input MVN data
:param param: Parameter index (or name, but only if param-list is specified)
For other arguments, see command line tool for now
"""
asrt.assertIsNifti(mvn)
valmap = {
'write' : wutils.SHOW_IF_TRUE,
'new' : wutils.SHOW_IF_TRUE,
}
cmd = ['mvntool', '--input={}'.format(mvn), '--param={}'.format(param)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
def invwarp(warp, ref, out, **kwargs):
"""Wrapper for the ``invwarp`` command."""
valmap = {
'abs': wutils.SHOW_IF_TRUE,
'rel': wutils.SHOW_IF_TRUE,
'noconstraint': wutils.SHOW_IF_TRUE,
'debug': wutils.SHOW_IF_TRUE,
'verbose': wutils.SHOW_IF_TRUE,
}
asrt.assertIsNifti(warp, ref)
cmd = [
'invwarp', '--warp={}'.format(warp), '--ref={}'.format(ref),
'--out={}'.format(out)
]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
def epi_reg(epi, t1, t1brain, out='epi_reg', **kwargs):
"""Wrapper for the ``epi_reg`` command.
:arg epi: Input EPI image
:arg t1: Input wholehead T1 image
:arg t1brain: Input brain extracted T1 image
:arg out: Output name
"""
asrt.assertIsNifti(epi)
asrt.assertIsNifti(t1)
asrt.assertIsNifti(t1brain)
valmap = {
'nofmapreg': wutils.SHOW_IF_TRUE,
'noclean': wutils.SHOW_IF_TRUE,
'v': wutils.SHOW_IF_TRUE,
}
cmd = [
'epi_reg', '--epi=' + epi, '--t1=' + t1, '--t1brain=' + t1brain,
'--out=' + out
]
cmd += wutils.applyArgStyle('--=',
valmap=valmap,
singlechar_args=True,
**kwargs)
return cmd
def fsl_anat(img, out='fsl_anat', **kwargs):
"""Wrapper for the ``fsl_anat`` command.
:arg img: Input structural image
:arg out: Output directory name
"""
asrt.assertIsNifti(img)
valmap = {
'strongbias' : wutils.SHOW_IF_TRUE,
'weakbias' : wutils.SHOW_IF_TRUE,
'noreorient' : wutils.SHOW_IF_TRUE,
'nocrop' : wutils.SHOW_IF_TRUE,
'nobias' : wutils.SHOW_IF_TRUE,
'noreg' : wutils.SHOW_IF_TRUE,
'nononlinreg' : wutils.SHOW_IF_TRUE,
'noseg' : wutils.SHOW_IF_TRUE,
'nosubcortseg' : wutils.SHOW_IF_TRUE,
'nosearch' : wutils.SHOW_IF_TRUE,
'nocleanup' : wutils.SHOW_IF_TRUE,
}
argmap = {
}
img_type = kwargs.pop("img_type", "T1")
cmd = ['fsl_anat', '-i', img, '-o', out, '-t', img_type]
smoothing = kwargs.pop("bias_smoothing", None)
if smoothing is not None:
cmd += ['-s', str(smoothing)]
cmd += wutils.applyArgStyle('--=',
valmap=valmap,
argmap=argmap,
singlechar_args=True,
**kwargs)
return cmd
def mcflirt(infile, **kwargs):
"""Wrapper for the ``mcflirt`` command."""
asrt.assertIsNifti(infile)
argmap = {
'twod': '2d',
}
valmap = {
'2d': wutils.SHOW_IF_TRUE,
'gdt': wutils.SHOW_IF_TRUE,
'meanvol': wutils.SHOW_IF_TRUE,
'stats': wutils.SHOW_IF_TRUE,
'mats': wutils.SHOW_IF_TRUE,
'plots': wutils.SHOW_IF_TRUE,
'report': wutils.SHOW_IF_TRUE,
}
cmd = ['mcflirt', '-in', infile]
cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
def fnirtfileutils(src, **kwargs):
"""Wrapper for the ``fnirt`` command.
Compulsory arguments (You MUST set one or more of):
-i,--in filename of input coefficient volume (to be converted)
Optional arguments (You may optionally specify one or more of):
-r,--ref filename for reference volume
-o,--out filename for output (field/coef) volume - uses relative warp convention
-f,--outformat Output format [field spline], default=field
-w,--warpres Warp resolution (mm), only relevant when --outformat=spline
-k,--knotspace Knot-spacing (voxels), only relevant when --outformat=spline
-j,--jac filename for output (jacobian map) volume
-a,--withaff If set, the affine transform is included in the field/jacobian
-v,--verbose switch on diagnostic messages
-h,--help display this message
"""
asrt.assertIsNifti(src)
cmd = ['fnirtfileutils', '--in={}'.format(src)]
cmd += wutils.applyArgStyle('--=', **kwargs)
return cmd
def fslorient(input, **kwargs):
"""Wrapper for the ``fslorient`` tool."""
asrt.assertIsNifti(input)
valmap = {
'getorient': wutils.SHOW_IF_TRUE,
'getsform': wutils.SHOW_IF_TRUE,
'getqform': wutils.SHOW_IF_TRUE,
'getsformcode': wutils.SHOW_IF_TRUE,
'getqformcode': wutils.SHOW_IF_TRUE,
'copysform2qform': wutils.SHOW_IF_TRUE,
'copyqform2sform': wutils.SHOW_IF_TRUE,
'deleteorient': wutils.SHOW_IF_TRUE,
'forceradiological': wutils.SHOW_IF_TRUE,
'forceneurological': wutils.SHOW_IF_TRUE,
'swaporient': wutils.SHOW_IF_TRUE,
}
cmd = ['fslorient']
cmd += wutils.applyArgStyle('-', valsep=' ', valmap=valmap, **kwargs)
cmd += [input]
return cmd
def eddy_cuda(imain, mask, index, acqp, bvecs, bvals, out, **kwargs):
"""Wrapper for the ``eddy_cuda`` command."""
valmap = {
'fep': wutils.SHOW_IF_TRUE,
'initrand': wutils.SHOW_IF_TRUE,
'repol': wutils.SHOW_IF_TRUE,
'ol_pos': wutils.SHOW_IF_TRUE,
'ol_sqr': wutils.SHOW_IF_TRUE,
'dont_sep_offs_move': wutils.SHOW_IF_TRUE,
'dont_peas': wutils.SHOW_IF_TRUE,
'data_is_shelled': wutils.SHOW_IF_TRUE,
'b0_only': wutils.SHOW_IF_TRUE,
'dont_mask_output': wutils.SHOW_IF_TRUE,
'cnr_maps': wutils.SHOW_IF_TRUE,
'residuals': wutils.SHOW_IF_TRUE,
'estimate_move_by_susceptibility': wutils.SHOW_IF_TRUE,
'verbose': wutils.SHOW_IF_TRUE,
'very_verbose': wutils.SHOW_IF_TRUE,
}
asrt.assertFileExists(imain, mask, index, acqp, bvecs, bvals)
asrt.assertIsNifti(imain, mask)
kwargs.update({
'imain': imain,
'mask': mask,
'index': index,
'acqp': acqp,
'bvecs': bvecs,
'bvals': bvals,
'out': out
})
cmd = ['eddy_cuda'] + wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
def test_assertIsNifti():
with tempdir.tempdir():
analyze = make_random_image('analyze.img', imgtype=0)
nifti1 = make_random_image('nifti1.nii', imgtype=1)
nifti2 = make_random_image('nifti2.nii', imgtype=2)
with pytest.raises(AssertionError):
assertions.assertIsNifti(analyze)
with pytest.raises(AssertionError):
assertions.assertIsNifti('analyze.img')
assertions.assertIsNifti(nifti1)
assertions.assertIsNifti('nifti1.nii')
assertions.assertIsNifti(nifti2)
assertions.assertIsNifti('nifti2.nii')
assertions.assertIsNifti(nifti1, nifti2)
def test_disabled():
with assertions.disabled():
assertions.assertFileExists('NOT', 'A', 'FILE', 'NO', 'WAY')
assertions.assertIsNifti('boo.txt')
