def test_applyArgStyle_argmap_valmap():
argmap = {'a1': 'a', 'a2': 'b'}
valmap = {
'a': wutils.SHOW_IF_TRUE,
'b': wutils.HIDE_IF_TRUE,
}
# kwargs, expected
tests = [
({}, ['']),
({
'a1': False,
}, ['']),
({
'a1': True,
}, ['-a']),
({
'a2': False
}, ['-b']),
({
'a2': True
}, ['']),
({
'a1': False,
'a2': True
}, ['']),
({
'a1': True,
'a2': True
}, ['-a']),
({
'a1': False,
'a2': False
}, ['-b']),
({
'a1': False,
'a2': True
}, ['']),
({
'a1': True,
'a2': False
}, ['-a -b', '-b -a']),
({
'a1': True,
'a2': True
}, ['-a']),
]
for kwargs, expected in tests:
expected = [shlex.split(e) for e in expected]
assert wutils.applyArgStyle('-',
argmap=argmap,
valmap=valmap,
**kwargs) in expected
def test_applyArgStyle_default():
kwargs = {
'arg1': 'val',
'arg2': ['val1', 'val2'],
'a': 'val',
'b': ['val1', 'val2'],
}
exp = ['--arg1=val', '--arg2=val1,val2', '-a', 'val', '-b', 'val1', 'val2']
assert wutils.applyArgStyle(**kwargs) == exp
def test_applyArgStyle():
kwargs = {
'name': 'val',
'name2': ['val1', 'val2'],
'name3': 'val1 val2',
}
# these combinations of style+valsep should
# raise an error
with pytest.raises(ValueError):
wutils.applyArgStyle(style='-=', valsep=' ', **kwargs)
with pytest.raises(ValueError):
wutils.applyArgStyle(style='--=', valsep=' ', **kwargs)
# unsupported style/valsep
with pytest.raises(ValueError):
wutils.applyArgStyle('?', **kwargs)
with pytest.raises(ValueError):
wutils.applyArgStyle('-', valsep='b', **kwargs)
# style, valsep, expected_result.
tests = [
('-', ' ',
['-name', 'val', '-name2', 'val1', 'val2', '-name3', 'val1 val2']),
('-', '"',
['-name', 'val', '-name2', 'val1 val2', '-name3', 'val1 val2']),
('-', ',',
['-name', 'val', '-name2', 'val1,val2', '-name3', 'val1 val2']),
('--', ' ',
['--name', 'val', '--name2', 'val1', 'val2', '--name3', 'val1 val2']),
('--', '"',
['--name', 'val', '--name2', 'val1 val2', '--name3', 'val1 val2']),
('--', ',',
['--name', 'val', '--name2', 'val1,val2', '--name3', 'val1 val2']),
('-=', '"', ['-name=val', '-name2=val1 val2', '-name3=val1 val2']),
('-=', ',', ['-name=val', '-name2=val1,val2', '-name3=val1 val2']),
('--=', '"', ['--name=val', '--name2=val1 val2', '--name3=val1 val2']),
('--=', ',', ['--name=val', '--name2=val1,val2', '--name3=val1 val2']),
]
for style, valsep, exp in tests:
result = wutils.applyArgStyle(style, valsep=valsep, **kwargs)
assert result == exp
def test_applyArgStyle_charstyle():
kwargs = {
'n': 'val',
'm': ['val1', 'val2'],
'o': 'val1 val2',
}
# these combinations of charstyle+
# charsep should raise an error
with pytest.raises(ValueError):
wutils.applyArgStyle(charstyle='--=', charsep=' ', **kwargs)
with pytest.raises(ValueError):
wutils.applyArgStyle(charstyle='-=', charsep=' ', **kwargs)
# unsupported chrastyle/charsep
with pytest.raises(ValueError):
wutils.applyArgStyle(charstyle='?', **kwargs)
with pytest.raises(ValueError):
wutils.applyArgStyle('-', charsep='b', **kwargs)
# style, valsep, charstyle, charsep, expected_result.
# Order of arguments is not guaranteed
tests = [
('-', ' ', ['-n', 'val', '-m', 'val1', 'val2', '-o', 'val1 val2']),
('-', '"', ['-n', 'val', '-m', 'val1 val2', '-o', 'val1 val2']),
('-', ',', ['-n', 'val', '-m', 'val1,val2', '-o', 'val1 val2']),
('--', ' ', ['--n', 'val', '--m', 'val1', 'val2', '--o', 'val1 val2']),
('--', '"', ['--n', 'val', '--m', 'val1 val2', '--o', 'val1 val2']),
('--', ',', ['--n', 'val', '--m', 'val1,val2', '--o', 'val1 val2']),
('-=', '"', ['-n=val', '-m=val1 val2', '-o=val1 val2']),
('-=', ',', ['-n=val', '-m=val1,val2', '-o=val1 val2']),
('--=', '"', ['--n=val', '--m=val1 val2', '--o=val1 val2']),
('--=', ',', ['--n=val', '--m=val1,val2', '--o=val1 val2']),
]
for style, valsep, exp in tests:
result = wutils.applyArgStyle(charstyle=style,
charsep=valsep,
**kwargs)
assert result == exp
def test_applyArgStyle_argmap():
kwargs = {
'name1': 'val1',
'name2': 'val2',
}
argmap = {
'name1': 'n',
'name2': 'm',
}
# order not guaranteed
exp = [shlex.split('-n val1 -m val2'), shlex.split('-m val2 -n val1')]
assert wutils.applyArgStyle('-', argmap=argmap, **kwargs) in exp
def test_applyArgStyle():
kwargs = {
'name': 'val',
'name2': ['val1', 'val2'],
}
# these combinations of style+valsep should
# raise an error
with pytest.raises(ValueError):
wutils.applyArgStyle(style='-=', valsep=' ', **kwargs)
with pytest.raises(ValueError):
wutils.applyArgStyle(style='--=', valsep=' ', **kwargs)
# unsupported style/valsep
with pytest.raises(ValueError):
wutils.applyArgStyle('?', **kwargs)
with pytest.raises(ValueError):
wutils.applyArgStyle('-', valsep='b', **kwargs)
# style, valsep, expected_result.
# Order of arguments is not guaranteed
tests = [
('-', ' ', [' -name val', '-name2 val1 val2']),
('-', '"', [' -name val', '-name2 "val1 val2"']),
('-', ',', [' -name val', '-name2 val1,val2']),
('--', ' ', ['--name val', '--name2 val1 val2']),
('--', '"', ['--name val', '--name2 "val1 val2"']),
('--', ',', ['--name val', '--name2 val1,val2']),
('-=', '"', [' -name=val', '-name2="val1 val2"']),
('-=', ',', [' -name=val', '-name2=val1,val2']),
('--=', '"', ['--name=val', '--name2="val1 val2"']),
('--=', ',', ['--name=val', '--name2=val1,val2']),
]
for style, valsep, exp in tests:
exp = [shlex.split(e) for e in exp]
result = wutils.applyArgStyle(style, valsep=valsep, **kwargs)
assert result in (exp[0] + exp[1], exp[1] + exp[0])
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 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 epi_reg(**kwargs):
"""Wrapper for the ``epi_reg`` command.
Required options:
:arg epi: EPI image
:arg t1: T1 weighted image (wholehead)
:arg t1_brain: T1 weighted image (brain extracted)
:arg out: Output image name or LOAD to return in-memory image
Additional options:
:arg fmap: fieldmap image (in rad/s)
:arg fmapmag: fieldmap magnitude image - wholehead extracted
:arg fmapmagbrain: fieldmap magnitude image - brain extracted
:arg gdc: Gradient-distortion corection warpfield
:arg wmseg: white matter segmentation of T1 image
:arg echospacing: Effective EPI echo spacing (sometimes called dwell time) - in seconds
:arg pedir: Phase encoding direction, dir = x/y/z/-x/-y/-z
:arg weight: weighting image (in T1 space)
:arg nofmapreg: do not perform registration of fmap to T1 (use if fmap already registered)
"""
valmap = {
'nofmapreg': wutils.SHOW_IF_TRUE,
}
cmd = [
'epi_reg',
]
cmd += wutils.applyArgStyle('--=',
valmap=valmap,
singlechar_args=True,
**kwargs)
return cmd
def fslStats(inputFile, voxel, **kwargs):
cmd = ['fslstats', inputFile, "-k", voxel, "-m"]
return cmd + applyArgStyle('-', valmap={"v": SHOW_IF_TRUE}, **kwargs)