From 4f3159f98039616c7b6fa1a49520f8f50209e6a3 Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Wed, 24 Oct 2018 19:31:35 +0100
Subject: [PATCH] Make sure command we are testing exists (as a dummy file) in
the mock FSLDIR Also, a couple of FNIRT fixes - Jacobian option is an image
and a couple of options that were previously compulsary are now optional
(because they are not required in certain circumstances)
---
tests/test_wrappers.py | 63 +++++++++++++++++++-------------------
tests/test_wrapperutils.py | 2 +-
2 files changed, 33 insertions(+), 32 deletions(-)
diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py
index af2a95fb6..b1517b32c 100644
--- a/tests/test_wrappers.py
+++ b/tests/test_wrappers.py
@@ -39,7 +39,7 @@ def checkResult(cmd, base, args, stripdir=None):
def test_bet():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('bet',)) as fsldir:
bet = op.join(fsldir, 'bin', 'bet')
result = fw.bet('input', 'output', mask=True, c=(10, 20, 30))
expected = (bet + ' input output', ('-m', '-c 10 20 30'))
@@ -47,7 +47,7 @@ def test_bet():
def test_robustfov():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('robustfov',)) as fsldir:
rfov = op.join(fsldir, 'bin', 'robustfov')
result = fw.robustfov('input', 'output', b=180)
expected = (rfov + ' -i input', ('-r output', '-b 180'))
@@ -55,7 +55,7 @@ def test_robustfov():
def test_eddy_cuda():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('eddy_cuda',)) as fsldir:
eddy = op.join(fsldir, 'bin', 'eddy_cuda')
result = fw.eddy_cuda('imain', 'mask', 'index', 'acqp',
'bvecs', 'bvals', 'out', dont_mask_output=True)
@@ -72,7 +72,7 @@ def test_eddy_cuda():
def test_topup():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('topup',)) as fsldir:
topup = op.join(fsldir, 'bin', 'topup')
result = fw.topup('imain', 'datain', minmet=1)
expected = topup + ' --imain=imain --datain=datain --minmet=1'
@@ -80,7 +80,7 @@ def test_topup():
def test_flirt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('flirt',)) as fsldir:
flirt = op.join(fsldir, 'bin', 'flirt')
result = fw.flirt('src', 'ref', usesqform=True, anglerep='euler')
expected = (flirt + ' -in src -ref ref',
@@ -89,7 +89,7 @@ def test_flirt():
def test_applyxfm():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('flirt',)) as fsldir:
flirt = op.join(fsldir, 'bin', 'flirt')
result = fw.applyxfm('src', 'ref', 'mat', 'out', interp='trilinear')
expected = (flirt + ' -in src -ref ref',
@@ -101,7 +101,7 @@ def test_applyxfm():
def test_invxfm():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('convert_xfm',)) as fsldir:
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.invxfm('mat', 'output')
expected = cnvxfm + ' -omat output -inverse mat'
@@ -109,7 +109,7 @@ def test_invxfm():
def test_concatxfm():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('convert_xfm',)) as fsldir:
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.concatxfm('mat1', 'mat2', 'output')
expected = cnvxfm + ' -omat output -concat mat2 mat1'
@@ -117,7 +117,7 @@ def test_concatxfm():
def test_mcflirt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('mcflirt',)) as fsldir:
mcflirt = op.join(fsldir, 'bin', 'mcflirt')
result = fw.mcflirt('input', out='output', cost='normcorr', dof=12)
expected = (mcflirt + ' -in input',
@@ -128,28 +128,29 @@ def test_mcflirt():
def test_fnirt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fnirt',)) as fsldir:
fnirt = op.join(fsldir, 'bin', 'fnirt')
- result = fw.fnirt('src', 'ref', iout='iout', fout='fout',
+ result = fw.fnirt('src', ref='ref', iout='iout', fout='fout',
subsamp=(8, 6, 4, 2))
- expected = (fnirt + ' --in=src --ref=ref',
- ('--iout=iout',
+ expected = (fnirt + ' --in=src',
+ ('--ref=ref',
+ '--iout=iout',
'--fout=fout',
'--subsamp=8,6,4,2'))
assert checkResult(result.output[0], *expected)
def test_applywarp():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('applywarp',)) as fsldir:
applywarp = op.join(fsldir, 'bin', 'applywarp')
- result = fw.applywarp('src', 'ref', 'out', 'warp', abs=True, super=True)
- expected = (applywarp + ' --in=src --ref=ref --out=out --warp=warp',
- ('--abs', '--super'))
+ result = fw.applywarp('src', 'ref', 'out', warp='warp', abs=True, super=True)
+ expected = (applywarp + ' --in=src --ref=ref --out=out',
+ ('--warp=warp', '--abs', '--super'))
assert checkResult(result.output[0], *expected)
def test_invwarp():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('invwarp',)) as fsldir:
invwarp = op.join(fsldir, 'bin', 'invwarp')
result = fw.invwarp('warp', 'ref', 'out',
rel=True, noconstraint=True)
@@ -159,16 +160,16 @@ def test_invwarp():
def test_convertwarp():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('convertwarp',)) as fsldir:
cnvwarp = op.join(fsldir, 'bin', 'convertwarp')
- result = fw.convertwarp('out', 'ref', absout=True, jacobian=True)
+ result = fw.convertwarp('out', 'ref', absout=True, jacobian='jacobian')
expected = (cnvwarp + ' --ref=ref --out=out',
- ('--absout', '--jacobian'))
+ ('--absout', '--jacobian=jacobian'))
assert checkResult(result.output[0], *expected)
def test_fugue():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fugue',)) as fsldir:
fugue = op.join(fsldir, 'bin', 'fugue')
result = fw.fugue(input='input', warp='warp',
median=True, dwell=10)
@@ -181,7 +182,7 @@ def test_fugue():
def test_sigloss():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('sigloss',)) as fsldir:
sigloss = op.join(fsldir, 'bin', 'sigloss')
result = fw.sigloss('input', 'sigloss', mask='mask', te=0.5)
expected = (sigloss + ' --in input --sigloss sigloss',
@@ -190,7 +191,7 @@ def test_sigloss():
def test_melodic():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('melodic',)) as fsldir:
melodic = op.join(fsldir, 'bin', 'melodic')
result = fw.melodic('input', dim=50, mask='mask', Oall=True)
expected = (melodic + ' --in=input',
@@ -199,7 +200,7 @@ def test_melodic():
def test_fsl_regfilt():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fsl_regfilt',)) as fsldir:
regfilt = op.join(fsldir, 'bin', 'fsl_regfilt')
result = fw.fsl_regfilt('input', 'output', 'design',
filter=(1, 2, 3, 4), vn=True)
@@ -210,7 +211,7 @@ def test_fsl_regfilt():
def test_fslreorient2std():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslreorient2std',)) as fsldir:
r2std = op.join(fsldir, 'bin', 'fslreorient2std')
result = fw.fslreorient2std('input', 'output')
expected = r2std + ' input output'
@@ -218,7 +219,7 @@ def test_fslreorient2std():
def test_fslroi():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslroi',)) as fsldir:
fslroi = op.join(fsldir, 'bin', 'fslroi')
result = fw.fslroi('input', 'output', 1, 10)
@@ -235,7 +236,7 @@ def test_fslroi():
def test_slicer():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('slicer',)) as fsldir:
slicer = op.join(fsldir, 'bin', 'slicer')
result = fw.slicer('input1', 'input2', i=(20, 100), x=(20, 'x.png'))
expected = slicer + ' input1 input2 -i 20 100 -x 20 x.png'
@@ -243,7 +244,7 @@ def test_slicer():
def test_cluster():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('cluster',)) as fsldir:
cluster = op.join(fsldir, 'bin', 'cluster')
result = fw.cluster('input', 'thresh',
fractional=True, osize='osize')
@@ -253,7 +254,7 @@ def test_cluster():
def test_fslmaths():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fslmaths',)) as fsldir:
cmd = op.join(fsldir, 'bin', 'fslmaths')
result = fw.fslmaths('input') \
.abs().bin().binv().recip().Tmean().Tstd().Tmin().Tmax() \
@@ -274,7 +275,7 @@ def test_fslmaths():
# TODO test LOAD output
def test_fast():
- with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ with asrt.disabled(), run.dryrun(), mockFSLDIR(bin=('fast',)) as fsldir:
cmd = op.join(fsldir, 'bin', 'fast')
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 29e569c9f..54cf16f4c 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -598,7 +598,7 @@ def test_fslwrapper():
def func(a, b):
return ['func', str(a), str(b)]
- with run.dryrun(), mockFSLDIR() as fsldir:
+ with run.dryrun(), mockFSLDIR(bin=('func',)) as fsldir:
expected = '{} 1 2'.format(op.join(fsldir, 'bin', 'func'))
assert func(1, 2)[0] == expected
--
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