From 19d2949ae45e0c340de5ee05be6e8b31926fbe7f Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 4 Mar 2018 12:15:00 +0000
Subject: [PATCH] unit tests for wrapper functions, and more for wrapperutils
---
tests/__init__.py | 26 ++--
tests/test_wrappers.py | 265 +++++++++++++++++++++++++++++++++++++
tests/test_wrapperutils.py | 40 +++++-
3 files changed, 311 insertions(+), 20 deletions(-)
create mode 100644 tests/test_wrappers.py
diff --git a/tests/__init__.py b/tests/__init__.py
index 13d510658..723ed0f1d 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -21,29 +21,27 @@ import nibabel as nib
from six import StringIO
-import fsl.data.image as fslimage
+import fsl.data.image as fslimage
+from fsl.utils.tempdir import tempdir
+from fsl.utils.platform import platform as fslplatform
logging.getLogger().setLevel(logging.WARNING)
-
@contextlib.contextmanager
-def tempdir():
- """Returnsa context manager which creates and returns a temporary
- directory, and then deletes it on exit.
- """
+def mockFSLDIR():
- testdir = tempfile.mkdtemp()
- prevdir = os.getcwd()
- try:
-
- os.chdir(testdir)
- yield testdir
+ oldval = fslplatform.fsldir
+ try:
+ with tempdir() as td:
+ fsldir = op.join(td, 'fsl')
+ os.makedirs(fsldir)
+ fslplatform.fsldir = fsldir
+ yield fsldir
finally:
- os.chdir(prevdir)
- shutil.rmtree(testdir)
+ fslplatform.fsldir = oldval
def touch(fname):
diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py
new file mode 100644
index 000000000..1e366a166
--- /dev/null
+++ b/tests/test_wrappers.py
@@ -0,0 +1,265 @@
+#!/usr/bin/env python
+#
+# test_wrappers.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import os.path as op
+import itertools as it
+
+import fsl.wrappers as fw
+import fsl.utils.assertions as asrt
+import fsl.utils.run as run
+
+from . import mockFSLDIR
+
+
+def checkResult(cmd, base, args):
+ """We can't control the order in which command line args are generated,
+ so we need to test all possible orderings.
+
+ :arg cmd: Generated command
+ :arg base: Beginning of expected command
+ :arg args: Sequence of expected arguments
+ """
+ permutations = it.permutations(args, len(args))
+ possible = [' '.join([base] + list(p)) for p in permutations]
+
+ return any([cmd == p for p in possible])
+
+
+def test_bet():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() 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'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_robustfov():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ rfov = op.join(fsldir, 'bin', 'robustfov')
+ result = fw.robustfov('input', 'output', b=180)
+ expected = (rfov + ' -i input', ('-r output', '-b 180'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_eddy_cuda():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ eddy = op.join(fsldir, 'bin', 'eddy_cuda')
+ result = fw.eddy_cuda('imain', 'mask', 'index', 'acqp',
+ 'bvecs', 'bvals', 'out', dont_mask_output=True)
+ expected = (eddy, ('--imain=imain',
+ '--mask=mask',
+ '--index=index',
+ '--acqp=acqp',
+ '--bvecs=bvecs',
+ '--bvals=bvals',
+ '--out=out',
+ '--dont_mask_output'))
+
+ assert checkResult(result.output[0], *expected)
+
+
+def test_topup():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ topup = op.join(fsldir, 'bin', 'topup')
+ result = fw.topup('imain', 'datain', minmet=1)
+ expected = topup + ' --imain=imain --datain=datain --minmet=1'
+ assert result.output[0] == expected
+
+
+def test_flirt():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ flirt = op.join(fsldir, 'bin', 'flirt')
+ result = fw.flirt('src', 'ref', usesqform=True, anglerep='euler')
+ expected = (flirt + ' -in src -ref ref',
+ ('-usesqform', '-anglerep euler'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_applyxfm():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ flirt = op.join(fsldir, 'bin', 'flirt')
+ result = fw.applyxfm('src', 'ref', 'mat', 'out', interp='trilinear')
+ expected = (flirt + ' -in src -ref ref',
+ ('-applyxfm',
+ '-out out',
+ '-init mat',
+ '-interp trilinear'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_invxfm():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
+ result = fw.invxfm('mat', 'output')
+ expected = cnvxfm + ' -omat output -inverse mat'
+ assert result.output[0] == expected
+
+
+def test_concatxfm():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
+ result = fw.concatxfm('mat1', 'mat2', 'output')
+ expected = cnvxfm + ' -omat output -concat mat2 mat1'
+ assert result.output[0] == expected
+
+
+def test_mcflirt():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ mcflirt = op.join(fsldir, 'bin', 'mcflirt')
+ result = fw.mcflirt('input', out='output', cost='normcorr', dof=12)
+ expected = (mcflirt + ' -in input',
+ ('-out output',
+ '-cost normcorr',
+ '-dof 12'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_fnirt():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ fnirt = op.join(fsldir, 'bin', 'fnirt')
+ result = fw.fnirt('src', 'ref', iout='iout', fout='fout',
+ subsamp=(8, 6, 4, 2))
+ 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:
+ 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'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_invwarp():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ invwarp = op.join(fsldir, 'bin', 'invwarp')
+ result = fw.invwarp('warp', 'ref', 'out',
+ rel=True, noconstraint=True)
+ expected = (invwarp + ' --warp=warp --ref=ref --out=out',
+ ('--rel', '--noconstraint'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_convertwarp():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ cnvwarp = op.join(fsldir, 'bin', 'convertwarp')
+ result = fw.convertwarp('out', 'ref', absout=True, jacobian=True)
+ expected = (cnvwarp + ' --ref=ref --out=out',
+ ('--absout', '--jacobian'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_fugue():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ fugue = op.join(fsldir, 'bin', 'fugue')
+ result = fw.fugue(input='input', warp='warp',
+ median=True, dwell=10)
+ expected = (fugue, ('--in=input',
+ '--warp=warp',
+ '--median',
+ '--dwell=10'))
+ assert checkResult(result.output[0], *expected)
+
+
+
+def test_sigloss():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ sigloss = op.join(fsldir, 'bin', 'sigloss')
+ result = fw.sigloss('input', 'sigloss', mask='mask', te=0.5)
+ expected = (sigloss + ' --in input --sigloss sigloss',
+ ('--mask mask', '--te 0.5'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_melodic():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ melodic = op.join(fsldir, 'bin', 'melodic')
+ result = fw.melodic('input', dim=50, mask='mask', Oall=True)
+ expected = (melodic + ' --in=input',
+ ('--dim=50', '--mask=mask', '--Oall'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_fsl_regfilt():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ regfilt = op.join(fsldir, 'bin', 'fsl_regfilt')
+ result = fw.fsl_regfilt('input', 'output', 'design',
+ filter=(1, 2, 3, 4), vn=True)
+ expected = (regfilt + ' --in=input --out=output --design=design',
+ ('--filter=1,2,3,4', '--vn'))
+ assert checkResult(result.output[0], *expected)
+
+
+
+def test_fslreorient2std():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ r2std = op.join(fsldir, 'bin', 'fslreorient2std')
+ result = fw.fslreorient2std('input', 'output')
+ expected = r2std + ' input output'
+ assert result.output[0] == expected
+
+
+def test_fslroi():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ fslroi = op.join(fsldir, 'bin', 'fslroi')
+
+ result = fw.fslroi('input', 'output', 1, 10)
+ expected = fslroi + ' input output 1 10'
+ assert result.output[0] == expected
+
+ result = fw.fslroi('input', 'output', 1, 10, 2, 20, 3, 30)
+ expected = fslroi + ' input output 1 10 2 20 3 30'
+ assert result.output[0] == expected
+
+ result = fw.fslroi('input', 'output', 1, 10, 2, 20, 3, 30, 4, 40)
+ expected = fslroi + ' input output 1 10 2 20 3 30 4 40'
+ assert result.output[0] == expected
+
+
+def test_slicer():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() 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'
+ assert result.output[0] == expected
+
+
+def test_cluster():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ cluster = op.join(fsldir, 'bin', 'cluster')
+ result = fw.cluster('input', 'thresh',
+ fractional=True, osize='osize')
+ expected = (cluster + ' --in=input --thresh=thresh',
+ ('--fractional', '--osize=osize'))
+ assert checkResult(result.output[0], *expected)
+
+
+def test_fslmaths():
+ with asrt.disabled(), run.dryrun(), mockFSLDIR() as fsldir:
+ cmd = op.join(fsldir, 'bin', 'fslmaths')
+ result = fw.fslmaths('input') \
+ .abs().bin().binv().recip().Tmean().Tstd().Tmin().Tmax() \
+ .fillh().ero().dilM().dilF().add('addim').sub('subim') \
+ .mul('mulim').div('divim').mas('masim').rem('remim') \
+ .thr('thrim').uthr('uthrim').inm('inmim').bptf(1, 10).run('output')
+
+ expected = [cmd, 'input',
+ '-abs', '-bin', '-binv', '-recip', '-Tmean', '-Tstd',
+ '-Tmin', '-Tmax', '-fillh', '-ero', '-dilM', '-dilF',
+ '-add addim', '-sub subim', '-mul mulim', '-div divim',
+ '-mas masim', '-rem remim', '-thr thrim', '-uthr uthrim',
+ '-inm inmim', '-bptf 1 10', 'output']
+ expected = ' '.join(expected)
+
+ assert result.output[0] == expected
+
+ # TODO test LOAD output
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 658909ae9..ef5a6fd4f 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -5,8 +5,9 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-import os
-import shlex
+import os.path as op
+import os
+import shlex
import pytest
@@ -14,9 +15,13 @@ import numpy as np
import nibabel as nib
import fsl.utils.tempdir as tempdir
+import fsl.utils.run as run
import fsl.wrappers.wrapperutils as wutils
+from . import mockFSLDIR
+
+
def test_applyArgStyle():
kwargs = {
@@ -160,10 +165,6 @@ def test_namedPositionals():
result = wutils.namedPositionals(func, args)
assert list(result) == list(expected)
-# TODO
-# - test _FileOrImage LOAD tuple order
-
-
def test_fileOrArray():
@@ -231,6 +232,7 @@ def test_fileOrImage():
img1 = nib.nifti1.Nifti1Image(np.array([[1, 2], [ 3, 4]]), np.eye(4))
img2 = nib.nifti1.Nifti1Image(np.array([[5, 6], [ 7, 8]]), np.eye(4))
+ img3 = nib.nifti1.Nifti1Image(np.array([[1, 2], [ 3, 4]]), np.eye(4))
expected = np.array([[5, 12], [21, 32]])
nib.save(img1, 'img1.nii')
nib.save(img2, 'img2.nii')
@@ -271,6 +273,12 @@ def test_fileOrImage():
result = func(img1, img2=img2, output=wutils.LOAD)['output']
assert np.all(result.get_data() == expected)
+ # in-memory image, file, file
+ result = func(img3, img2='img2.nii', output='output.nii')
+ assert np.all(nib.load('output.nii').get_data() == expected)
+ os.remove('output.nii')
+
+
def test_chained_fileOrImageAndArray():
@wutils.fileOrImage('image')
@@ -291,3 +299,23 @@ def test_chained_fileOrImageAndArray():
func('image.nii', array)
func( image, 'array.txt')
func( image, array)
+
+
+def test_cmdwrapper():
+ @wutils.cmdwrapper
+ def func(a, b):
+ return ['func', str(a), str(b)]
+
+ with run.dryrun():
+ assert func(1, 2)[0] == 'func 1 2'
+
+
+
+def test_fslwrapper():
+ @wutils.fslwrapper
+ def func(a, b):
+ return ['func', str(a), str(b)]
+
+ with run.dryrun(), mockFSLDIR() as fsldir:
+ expected = '{} 1 2'.format(op.join(fsldir, 'bin', 'func'))
+ assert func(1, 2)[0] == expected
--
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