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 concatxfm(atob, btoc, atoc):
"""Use ``convert_xfm`` to concatenate two affines. Note that the
order of the input matrices is the opposite of the order expected
by ``convert_xfm``.
:arg atob: Input matrix, transforming from "A" to "B".
:arg btoc: Input matrix, transforming from "B" to "C".
:arg atoc: Output matrix, transforming from "A" to "C".
"""
asrt.assertFileExists(atob, btoc)
cmd = ['convert_xfm', '-omat', atoc, '-concat', btoc, atob]
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 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_assertFileExists():
with tempdir.tempdir():
open('file.txt', 'wt').close()
os.makedirs(op.join('path', 'to', 'some', 'dir'))
open(op.join('path', 'to', 'file.txt'), 'wt').close()
assertions.assertFileExists('file.txt')
assertions.assertFileExists(op.join('path', 'to', 'some', 'dir'))
assertions.assertFileExists(op.join('path', 'to', 'file.txt'))
assertions.assertFileExists('file.txt', op.join('path'))
with pytest.raises(AssertionError):
assertions.assertFileExists(op.join('not', 'a', 'directory'))
with pytest.raises(AssertionError):
assertions.assertFileExists('notafile.txt')
with pytest.raises(AssertionError):
assertions.assertFileExists('file.txt', 'notafile.txt')
def test_disabled():
with assertions.disabled():
assertions.assertFileExists('NOT', 'A', 'FILE', 'NO', 'WAY')
assertions.assertIsNifti('boo.txt')
def invxfm(inmat, omat):
"""Use ``convert_xfm`` to invert an affine."""
asrt.assertFileExists(inmat)
return ['convert_xfm', '-omat', omat, '-inverse', inmat]
def func():
asrt.assertFileExists('file')
return ['echo', 'hello']
