def test_Vec_reg():
vrg = fsl.VecReg()
# make sure command gets called
assert vrg.cmd == 'vecreg'
# test raising error with mandatory args absent
with pytest.raises(ValueError):
vrg.run()
# .inputs based parameters setting
vrg.inputs.infile = 'infile'
vrg.inputs.outfile = 'outfile'
vrg.inputs.refVolName = 'MNI152'
vrg.inputs.affineTmat = 'tmat.mat'
assert vrg.cmdline == 'vecreg -i infile -o outfile -r MNI152 -t tmat.mat'
# .run based parameter setting
vrg2 = fsl.VecReg(infile='infile2',
outfile='outfile2',
refVolName='MNI152',
affineTmat='tmat2.mat',
brainMask='nodif_brain_mask')
actualCmdline = sorted(vrg2.cmdline.split())
cmd = 'vecreg -i infile2 -o outfile2 -r MNI152 -t tmat2.mat -m nodif_brain_mask'
desiredCmdline = sorted(cmd.split())
assert actualCmdline == desiredCmdline
vrg3 = fsl.VecReg()
results = vrg3.run(infile='infile3',
outfile='outfile3',
refVolName='MNI152',
affineTmat='tmat3.mat',)
assert results.runtime.cmdline == \
'vecreg -i infile3 -o outfile3 -r MNI152 -t tmat3.mat'
assert results.runtime.returncode != 0
assert results.interface.inputs.infile == 'infile3'
assert results.interface.inputs.outfile == 'outfile3'
assert results.interface.inputs.refVolName == 'MNI152'
assert results.interface.inputs.affineTmat == 'tmat3.mat'
# test arguments for opt_map
opt_map = {'verbose': ('-v', True),
'helpDoc': ('-h', True),
'tensor': ('--tensor', True),
'affineTmat': ('-t Tmat', 'Tmat'),
'warpFile': ('-w wrpFile', 'wrpFile'),
'interpolation': ('--interp=sinc', 'sinc'),
'brainMask': ('-m mask', 'mask')}
for name, settings in list(opt_map.items()):
vrg4 = fsl.VecReg(infile='infile', outfile='outfile',
refVolName='MNI152', **{name: settings[1]})
assert vrg4.cmdline == vrg4.cmd + \
' -i infile -o outfile -r MNI152 ' + settings[0]
def test_vecreg():
input_map = dict(
affine_mat=dict(argstr='-t %s', ),
args=dict(argstr='%s', ),
environ=dict(),
in_file=dict(
mandatory=True,
argstr='-i %s',
),
interpolation=dict(argstr='--interp=%s', ),
mask=dict(argstr='-m %s', ),
out_file=dict(argstr='-o %s', ),
output_type=dict(),
ref_mask=dict(argstr='--refmask=%s', ),
ref_vol=dict(
mandatory=True,
argstr='-r %s',
),
rotation_mat=dict(argstr='--rotmat=%s', ),
rotation_warp=dict(argstr='--rotwarp=%s', ),
warp_field=dict(argstr='-w %s', ),
)
instance = fsl.VecReg()
for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(instance.inputs.traits()[key],
metakey), value
def test_Vec_reg():
vrg = fsl.VecReg()
# make sure command gets called
assert vrg.cmd == "vecreg"
# test raising error with mandatory args absent
with pytest.raises(ValueError):
vrg.run()
# .inputs based parameters setting
vrg.inputs.infile = "infile"
vrg.inputs.outfile = "outfile"
vrg.inputs.refVolName = "MNI152"
vrg.inputs.affineTmat = "tmat.mat"
assert vrg.cmdline == "vecreg -i infile -o outfile -r MNI152 -t tmat.mat"
# .run based parameter setting
vrg2 = fsl.VecReg(
infile="infile2",
outfile="outfile2",
refVolName="MNI152",
affineTmat="tmat2.mat",
brainMask="nodif_brain_mask",
)
actualCmdline = sorted(vrg2.cmdline.split())
cmd = "vecreg -i infile2 -o outfile2 -r MNI152 -t tmat2.mat -m nodif_brain_mask"
desiredCmdline = sorted(cmd.split())
assert actualCmdline == desiredCmdline
vrg3 = fsl.VecReg()
results = vrg3.run(
infile="infile3",
outfile="outfile3",
refVolName="MNI152",
affineTmat="tmat3.mat",
)
assert (results.runtime.cmdline ==
"vecreg -i infile3 -o outfile3 -r MNI152 -t tmat3.mat")
assert results.runtime.returncode != 0
assert results.interface.inputs.infile == "infile3"
assert results.interface.inputs.outfile == "outfile3"
assert results.interface.inputs.refVolName == "MNI152"
assert results.interface.inputs.affineTmat == "tmat3.mat"
# test arguments for opt_map
opt_map = {
"verbose": ("-v", True),
"helpDoc": ("-h", True),
"tensor": ("--tensor", True),
"affineTmat": ("-t Tmat", "Tmat"),
"warpFile": ("-w wrpFile", "wrpFile"),
"interpolation": ("--interp=sinc", "sinc"),
"brainMask": ("-m mask", "mask"),
}
for name, settings in list(opt_map.items()):
vrg4 = fsl.VecReg(infile="infile",
outfile="outfile",
refVolName="MNI152",
**{name: settings[1]})
assert (vrg4.cmdline == vrg4.cmd + " -i infile -o outfile -r MNI152 " +
settings[0])