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small edit of the MCFLIRT tests #1979

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Merged
merged 1 commit into from
Apr 29, 2017
Merged

small edit of the MCFLIRT tests #1979

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15 changes: 14 additions & 1 deletion nipype/interfaces/fsl/tests/test_preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -324,6 +324,12 @@ def test_mcflirt(setup_flirt):
realcmd = 'mcflirt -in ' + infile + ' -out ' + outfile2
assert frt.cmdline == realcmd


@pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
def test_mcflirt_opt(setup_flirt):
tmpdir, infile, reffile = setup_flirt
_, nme = os.path.split(infile)

opt_map = {
'cost': ('-cost mutualinfo', 'mutualinfo'),
'bins': ('-bins 256', 256),
Expand All @@ -344,6 +350,9 @@ def test_mcflirt(setup_flirt):

for name, settings in list(opt_map.items()):
fnt = fsl.MCFLIRT(in_file=infile, **{name: settings[1]})
outfile = os.path.join(os.getcwd(), nme)
outfile = fnt._gen_fname(outfile, suffix='_mcf')
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Since these are always the same, they could go up under _, nme = os.path.split(infile), rather than be in the loop body.

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the first line could move, but outfile variable name would need to change because the second outfile has to be generated within the loop.


instr = '-in %s' % (infile)
outstr = '-out %s' % (outfile)
if name in ('init', 'cost', 'dof', 'mean_vol', 'bins'):
Expand All @@ -357,10 +366,14 @@ def test_mcflirt(setup_flirt):
outstr,
settings[0]])


@pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
def test_mcflirt_noinput():
# Test error is raised when missing required args
fnt = fsl.MCFLIRT()
with pytest.raises(ValueError):
with pytest.raises(ValueError) as excinfo:
fnt.run()
assert str(excinfo.value).startswith("MCFLIRT requires a value for input 'in_file'")

# test fnirt

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