def test_getMeanFile():
paths = [
'analysis.ica/melodic_IC.nii.gz', 'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix', 'analysis.ica/mean.nii.gz'
]
paths = [op.join(*p.split('/')) for p in paths]
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
expected = op.join(testdir, 'analysis.ica', 'mean.nii.gz')
assert mela.getMeanFile(meldir) == expected
paths = [
'analysis.ica/melodic_IC.nii.gz', 'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix', 'analysis.ica/mean.txt'
]
paths = [op.join(*p.split('/')) for p in paths]
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
with pytest.raises(fslpath.PathError):
mela.getMeanFile(meldir)
def test_MelodicImage_create():
# non existent
with pytest.raises(Exception):
meli.MelodicImage('badfile')
# bad file
paths = [
'analysis.ica/melodic_IC.nii.gz', 'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix'
]
with tests.testdir(paths) as testdir:
path = op.join(testdir, 'analysis.ica/melodic_IC.nii.gz')
with pytest.raises(Exception):
meli.MelodicImage(path)
with tests.testdir() as testdir:
meldir = _create_dummy_melodic_analysis(testdir)
icfile = op.join(meldir, 'melodic_IC.nii.gz')
icfilenosuf = op.join(meldir, 'melodic_IC')
# Should be able to specify the
# melodic dir, or the IC image
meli.MelodicImage(meldir)
meli.MelodicImage(icfile)
meli.MelodicImage(icfilenosuf)
def test_MelodicImage_create():
# non existent
with pytest.raises(Exception):
meli.MelodicImage('badfile')
# bad file
paths = [
'analysis.ica/melodic_IC.nii.gz', 'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix'
]
paths = [op.join(*p.split('/')) for p in paths]
with tests.testdir(paths) as testdir:
path = op.join(testdir, 'analysis.ica', 'melodic_IC.nii.gz')
with pytest.raises(Exception):
meli.MelodicImage(path)
for ic_prefix in ['melodic_IC', 'melodic_oIC']:
with tests.testdir() as testdir:
meldir = _create_dummy_melodic_analysis(testdir,
ic_prefix=ic_prefix)
icfile = op.join(meldir, '{}.nii.gz'.format(ic_prefix))
icfilenosuf = op.join(meldir, ic_prefix)
# Should be able to specify the
# melodic dir, or the IC image
i = meli.MelodicImage(meldir)
i = meli.MelodicImage(icfile)
i = meli.MelodicImage(icfilenosuf)
i = None
def test_MelodicImage_tr():
# If data file not present, tr should default to 1.0
with tests.testdir() as testdir:
meldir = _create_dummy_melodic_analysis(testdir, with_data=False)
img = meli.MelodicImage(meldir)
assert img.tr == 1
# Otherwise, it should be set to the datafile tr
with tests.testdir() as testdir:
meldir = _create_dummy_melodic_analysis(testdir, tr=5)
img = meli.MelodicImage(meldir)
assert img.tr == 5
# The TR can be updated
with tests.testdir() as testdir:
cbCalled = [False]
def trChanged(*a):
cbCalled[0] = True
meldir = _create_dummy_melodic_analysis(testdir, with_data=False)
img = meli.MelodicImage(meldir)
img.register('cbname', trChanged, topic='tr')
img.tr = 8
assert cbCalled[0]
assert img.tr == 8
def test_isFEATDir():
# We need these files for a directory
# to be considered a FEAT directory
paths = ['analysis.feat/filtered_func_data.nii.gz',
'analysis.feat/design.fsf',
'analysis.feat/design.mat',
'analysis.feat/design.con']
with tests.testdir(paths) as testdir:
assert featanalysis.isFEATDir(op.join(testdir, 'analysis.feat'))
# If the directory does not end in .feat,
# then it's not a feat directory
with tests.testdir([p.replace('feat', 'bleat') for p in paths]) as testdir:
assert not featanalysis.isFEATDir(op.join(testdir, 'analysis.bleat'))
# If the directory doesn't exist, then
# it's not a feat directory
assert not featanalysis.isFEATDir('nonexistent.feat')
# If any of the above files are not
# present, it is not a FEAT directory
perms = it.chain(it.combinations(paths, 1),
it.combinations(paths, 2),
it.combinations(paths, 3))
for p in perms:
with tests.testdir(p) as testdir:
assert not featanalysis.isFEATDir(
op.join(testdir, 'analysis.feat'))
def test_getAnalysisDir():
paths = [
'analysis.ica/melodic_IC.nii.gz', 'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix'
]
testpaths = [
'analysis.ica/melodic_IC.nii.gz', 'analysis.ica/log.txt',
'analysis.ica/stats/thresh_zstat1.nii.gz',
'analysis.ica/report/00index.html'
]
with tests.testdir(paths) as testdir:
expected = op.join(testdir, 'analysis.ica')
for tp in testpaths:
assert mela.getAnalysisDir(op.join(testdir, tp)) == expected
paths = [
'analysis.ica/melodic_blob.nii.gz', 'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix'
]
with tests.testdir(paths) as testdir:
for tp in testpaths:
assert mela.getAnalysisDir(op.join(testdir, tp)) is None
def test_hasStats():
with tests.testdir(['analysis.feat/stats/zstat1.nii.gz']) as testdir:
featdir = op.join(testdir, 'analysis.feat')
assert featanalysis.hasStats(featdir)
with tests.testdir(['analysis.feat/stats/zstat1.txt']) as testdir:
featdir = op.join(testdir, 'analysis.feat')
assert not featanalysis.hasStats(featdir)
def test_getFTMixFile():
paths = ['analysis.ica/melodic_IC.nii.gz',
'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
expected = op.join(testdir, 'analysis.ica/melodic_FTmix')
assert mela.getFTMixFile(meldir) == expected
paths = ['analysis.ica/melodic_IC.ni.gz',
'analysis.ica/melodic_mix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
assert mela.getFTMixFile(meldir) is None
def test_init_writeOnExit():
atexit_funcs = []
def mock_atexit_register(func, *args, **kwargs):
atexit_funcs.append((func, args, kwargs))
testdata = {
'setting1': 123,
'setting2': 'Blahblah',
'setting3': [1, 2, ('three', 4)]
}
with tests.testdir() as testdir, \
mock.patch('fsl.utils.settings.atexit.register', mock_atexit_register):
s = settings.Settings('test', cfgdir=testdir)
for k, v in testdata.items():
s.write(k, v)
assert len(atexit_funcs) == 1
f, a, kwa = atexit_funcs[0]
f(*a, **kwa)
with open(op.join(testdir, 'config.pkl'), 'rb') as f:
readback = pickle.load(f)
assert testdata == readback
def test_listFiles():
ns1files = ['namespace1/setting1.txt',
'namespace1/setting2.txt',
'namespace1/setting3.txt']
ns2files = ['namespace2/setting1.txt',
'namespace2/setting2.txt',
'namespace2/setting3.txt']
with tests.testdir() as testdir:
s = settings.Settings(cfgid='test', cfgdir=testdir, writeOnExit=False)
assert s.listFiles() == []
for fn in ns1files + ns2files:
with s.writeFile(fn) as f:
f.write(fn)
assert list(sorted(s.listFiles())) == list(sorted(ns1files + ns2files))
assert list(sorted(s.listFiles('namespace1/*'))) == list(sorted(ns1files))
assert list(sorted(s.listFiles('namespace2/*'))) == list(sorted(ns2files))
assert list(sorted(s.listFiles('namespace?/*'))) == list(sorted(ns1files + ns2files))
assert list(sorted(s.listFiles('*.txt'))) == list(sorted(ns1files + ns2files))
assert list(sorted(s.listFiles('*/setting1.txt'))) == list(sorted([ns1files[0]] + [ns2files[0]]))
def test_loadSettings():
contents = """
set random_setting true
any lines that don't start with "set" should be ignored
# regardless of whether they are commented or not
set fmri(blah) 0.66
set something "quoted"
set somethingelse 'quotedagain'
set fmri_thing(no) none
# set comment commented out
set athing with spaces in the value
"""
expected = collections.OrderedDict((
('random_setting', 'true'),
('blah', '0.66'),
('something', 'quoted'),
('somethingelse', 'quotedagain'),
('fmri_thing(no)', 'none'),
('athing', 'with spaces in the value'),
))
contents = textwrap.dedent(contents).strip()
with pytest.raises(Exception):
featanalysis.loadSettings('no file')
with tests.testdir() as testdir:
featdir = op.join(testdir, 'analysis.feat')
designfsf = op.join(featdir, 'design.fsf')
tests.make_dummy_file(designfsf, contents)
assert featanalysis.loadSettings(featdir) == expected
assert featanalysis.loadFsf(designfsf) == expected
def test_clear():
testsettings = [('setting1', '1'), ('setting2', '2'), ('setting3', '3')]
testfiles = [('path/to/file1.txt', 'testfile1 contents'),
('path/to/another/file2.txt', 'testfile2 contents'),
('file3.txt', 'testfile3 contents')]
# TODO File
with tests.testdir() as testdir:
s = settings.Settings(cfgid='test', cfgdir=testdir, writeOnExit=False)
for k, v in testsettings:
s.write(k, v)
for p, c in testfiles:
with s.writeFile(p) as f:
f.write(c)
for k, v in testsettings:
assert s.read(k) == v
for p, c in testfiles:
assert s.readFile(p) == c
s.clear()
for k, v in testsettings:
assert s.read(k) is None
for p, c in testfiles:
assert s.readFile(p) is None
def test_loadLabelFile_customLabels():
included = [2, 3, 4, 5]
contents = '[{}]\n'.format([i + 1 for i in included])
defIncLabel = 'Unclassified noise'
defExcLabel = 'Signal'
with tests.testdir() as testdir:
fname = op.join(testdir, 'labels.txt')
with open(fname, 'wt') as f:
f.write(contents)
# Check default labels
_, labels = fixlabels.loadLabelFile(fname)
for i, ilbls in enumerate(labels):
assert len(ilbls) == 1
if i in included:
assert ilbls[0] == defIncLabel
else:
assert ilbls[0] == defExcLabel
# Check custom labels
incLabel = 'Included'
excLabel = 'Excluded label'
_, labels = fixlabels.loadLabelFile(fname,
includeLabel=incLabel,
excludeLabel=excLabel)
for i, ilbls in enumerate(labels):
assert len(ilbls) == 1
if i in included:
assert ilbls[0] == incLabel
else:
assert ilbls[0] == excLabel
def test_save():
expected = textwrap.dedent("""
1, Signal, Default mode, False
2, Unknown, False
3, Unclassified noise, True
4, Movement, True
[3, 4]
""").strip()
lbls = vollbls.VolumeLabels(4)
lbls.addLabel(0, 'Signal')
lbls.addLabel(0, 'Default mode')
lbls.addLabel(1, 'Unknown')
lbls.addLabel(2, 'Unclassified noise')
lbls.addLabel(3, 'Movement')
with tests.testdir() as testdir:
fname = op.join(testdir, 'labels.txt')
# Test saving without dirname
lbls.save(fname)
exp = '.\n{}'.format(expected)
with open(fname, 'rt') as f:
assert f.read().strip() == exp.strip()
# And with dirname
lbls.save(fname, 'path/to/analysis.ica')
exp = 'path/to/analysis.ica\n{}'.format(expected)
with open(fname, 'rt') as f:
assert f.read().strip() == exp.strip()
def test_load_aromafile():
contents = """2, 3, 5""".strip()
expected = [['unknown'], ['movement'], ['movement'], ['unknown'],
['movement']]
with tests.testdir() as testdir:
fname = op.join(testdir, 'labels.txt')
with open(fname, 'wt') as f:
f.write(contents)
# Too many labels in the file
lblobj = vollbls.VolumeLabels(3)
with pytest.raises(fixlbls.InvalidLabelFileError):
lblobj.load(fname)
# Not enough labels in the file -
# this is ok. Remaining labels
# should be given 'Unknown'
lblobj = vollbls.VolumeLabels(6)
lblobj.load(fname)
for i in range(4):
assert lblobj.getLabels(i) == expected[i]
assert lblobj.getLabels(5) == ['unknown']
# Right number of labels
lblobj = vollbls.VolumeLabels(5)
lblobj.load(fname)
for i in range(4):
assert lblobj.getLabels(i) == expected[i]
def test_DTIFitTensor():
with tests.testdir() as testdir:
with pytest.raises(Exception):
dtifit.DTIFitTensor(testdir)
v1file = op.join(testdir, 'dti_V1.nii')
v2file = op.join(testdir, 'dti_V2.nii')
v3file = op.join(testdir, 'dti_V3.nii')
l1file = op.join(testdir, 'dti_L1.nii')
l2file = op.join(testdir, 'dti_L2.nii')
l3file = op.join(testdir, 'dti_L3.nii')
v1 = tests.make_random_image(v1file, (5, 5, 5, 3)).get_data()
v2 = tests.make_random_image(v2file, (5, 5, 5, 3)).get_data()
v3 = tests.make_random_image(v3file, (5, 5, 5, 3)).get_data()
l1 = tests.make_random_image(l1file, (5, 5, 5)) .get_data()
l2 = tests.make_random_image(l2file, (5, 5, 5)) .get_data()
l3 = tests.make_random_image(l3file, (5, 5, 5)) .get_data()
dtiobj = dtifit.DTIFitTensor(testdir)
assert np.all(np.isclose(dtiobj.V1()[:], v1))
assert np.all(np.isclose(dtiobj.V2()[:], v2))
assert np.all(np.isclose(dtiobj.V3()[:], v3))
assert np.all(np.isclose(dtiobj.L1()[:], l1))
assert np.all(np.isclose(dtiobj.L2()[:], l2))
assert np.all(np.isclose(dtiobj.L3()[:], l3))
v1 = fslimage.Image(v1file)
assert np.all(np.isclose(dtiobj.voxToWorldMat, v1.voxToWorldMat))
assert np.all(np.isclose(dtiobj.shape[:3], v1.shape[:3]))
assert np.all(np.isclose(dtiobj.pixdim[:3], v1.pixdim[:3]))
def _test_image_indexed_read4D(threaded):
with tests.testdir() as testdir:
filename = op.join(testdir, 'image.nii.gz')
# Data range grows with volume
nvols = 50
data = np.zeros((50, 50, 50, nvols))
for vol in range(nvols):
data[..., vol] = vol
fslimage.Image(data).save(filename)
img = fslimage.Image(filename,
loadData=False,
calcRange=False,
indexed=True,
threaded=threaded)
# Test reading slice through
# 4D (e.g. voxel time course)
#
# n.b. This is SUPER SLOW!!
voxels = tests.random_voxels((50, 50, 50), 5)
for i, xyz in enumerate(voxels):
x, y, z = [int(v) for v in xyz]
data = img[x, y, z, :]
if threaded:
img.getImageWrapper().getTaskThread().waitUntilIdle()
assert np.all(data == np.arange(nvols))
def test_getDataFile():
testcases = [
([
'analysis.ica/filtfunc.ica/melodic_IC.nii.gz',
'analysis.ica/filtfunc.ica/melodic_mix',
'analysis.ica/filtfunc.ica/melodic_FTmix',
'analysis.ica/filtered_func_data.nii.gz'
], 'analysis.ica/filtfunc.ica',
'analysis.ica/filtered_func_data.nii.gz'),
([
'analysis.feat/filtfunc.ica/melodic_IC.nii.gz',
'analysis.feat/filtfunc.ica/melodic_mix',
'analysis.feat/filtfunc.ica/melodic_FTmix',
'analysis.feat/filtered_func_data.nii.gz'
], 'analysis.feat/filtfunc.ica',
'analysis.feat/filtered_func_data.nii.gz'),
(['no/analysis/dirs/here/melodic_IC.nii.gz'], 'no/analysis/dirs/here/',
None),
([
'analysis.feat/analysis.ica/melodic_IC.nii.gz',
'analysis.feat/analysis.ica/melodic_mix',
'analysis.feat/analysis.ica/melodic_FTmix'
], 'analysis.feat/analysis.ica', None),
]
for paths, meldir, expected in testcases:
paths = [op.join(*p.split('/')) for p in paths]
if expected is not None:
expected = op.join(*expected.split('/'))
with tests.testdir(paths) as testdir:
assert mela.getDataFile(meldir) == expected
def test_initialise():
# Assuming that initialise()
# has not yet been called
assert settings.read('nothing') is None
assert settings.read('nothing', 'default') == 'default'
settings.write('nothing', 'nothing')
settings.delete('nothing')
assert settings.readFile('nothing') is None
settings.writeFile('nothing', 'nothing')
settings.deleteFile('nothing')
assert settings.filePath() is None
assert settings.readAll() == {}
assert settings.listFiles() == []
settings.clear()
with tests.testdir() as testdir:
settings.initialise(cfgid='test', cfgdir=testdir, writeOnExit=False)
assert settings.settings.configID == 'test'
assert settings.settings.configDir == testdir
settings.write('setting', 'value')
assert settings.read('setting') == 'value'
assert settings.read('nothing') is None
def test_loadLabelFile_good():
for filecontents, expMelDir, expLabels, expIdxs in goodfiles:
with tests.testdir() as testdir:
if expMelDir is not None:
expMelDir = op.join(testdir, expMelDir)
fname = op.join(testdir, 'labels.txt')
with open(fname, 'wt') as f:
f.write(filecontents.strip())
resMelDir, resLabels = fixlabels.loadLabelFile(fname)
assert resMelDir == expMelDir
assert len(resLabels) == len(expLabels)
for exp, res in zip(expLabels, resLabels):
assert exp == res
resMelDir, resLabels, resIdxs = fixlabels.loadLabelFile(
fname, returnIndices=True)
assert resMelDir == expMelDir
assert resIdxs == expIdxs
assert len(resLabels) == len(expLabels)
for exp, res in zip(expLabels, resLabels):
assert exp == res
def test_writeConfigFile():
with tests.testdir() as testdir:
testdata = {
'setting1': 123,
'setting2': 'Blahblah',
'setting3': [1, 2, ('three', 4)]
}
s = settings.Settings(cfgid='test', cfgdir=testdir, writeOnExit=False)
for k, v in testdata.items():
s.write(k, v)
for k, v in testdata.items():
assert s.read(k) == v
s.writeConfigFile()
with open(op.join(testdir, 'config.pkl'), 'rb') as f:
readback = pickle.load(f)
assert testdata == readback
# should fail gracefuly
# if write is not possible
s = settings.Settings(cfgid='test', cfgdir=testdir, writeOnExit=False)
# testdir has been removed,
# but call should not crash
s.writeConfigFile()
def test_readall():
testsettings = [('namespace1.setting1', '1'),
('namespace1.setting2', '2'),
('namespace1.setting3', '3'),
('namespace2.setting1', '4'),
('namespace2.setting2', '5'),
('namespace2.setting3', '6')]
with tests.testdir() as testdir:
s = settings.Settings(cfgid='test', cfgdir=testdir, writeOnExit=False)
assert s.readAll() == {}
for k, v in testsettings:
s.write(k, v)
assert s.readAll() == dict(testsettings)
ns1 = [(k, v) for k, v in testsettings if k.startswith('namespace1')]
ns2 = [(k, v) for k, v in testsettings if k.startswith('namespace2')]
assert s.readAll('namespace1.*') == dict(ns1)
assert s.readAll('namespace2.*') == dict(ns2)
assert s.readAll('*setting*') == dict(testsettings)
def test_FEATImage_imageAccessors():
for featdir in TEST_ANALYSES.keys():
shape = TEST_ANALYSES[featdir]['shape']
xform = TEST_ANALYSES[featdir]['xform']
with tests.testdir() as testdir:
if 'realdata' not in featdir:
featdir = tests.make_mock_feat_analysis(
op.join(datadir, featdir), testdir, shape, xform)
else:
featdir = op.join(datadir, featdir)
shape4D = shape
shape = shape4D[:3]
fi = featimage.FEATImage(featdir)
nevs = fi.numEVs()
ncons = fi.numContrasts()
# Testing the FEATImage intenral cache
for i in range(2):
assert fi.getResiduals().shape == shape4D
for ev in range(nevs):
assert fi.getPE(ev).shape == shape
for con in range(ncons):
assert fi.getCOPE(con).shape == shape
assert fi.getZStats(con).shape == shape
assert fi.getClusterMask(con).shape == shape
def test_getClusterMaskFile():
testcases = [
([
'analysis.feat/cluster_mask_zstat1.nii.gz',
'analysis.feat/cluster_mask_zstat2.nii.gz'
], True),
(['analysis.feat/cluster_mask_zstat1.nii.gz'], True),
(['analysis.feat/cluster_mask_zstat0.nii.gz'], False),
(['analysis.feat/cluster_mask_zstat1.txt'], False),
]
for paths, shouldPass in testcases:
with tests.testdir(paths) as testdir:
featdir = op.join(testdir, 'analysis.feat')
for ci in range(len(paths)):
expect = op.join(featdir,
'cluster_mask_zstat{}.nii.gz'.format(ci + 1))
if shouldPass:
assert featanalysis.getClusterMaskFile(featdir,
ci) == expect
else:
with pytest.raises(fslpath.PathError):
featanalysis.getClusterMaskFile(featdir, ci)
def test_extra_atlases():
with tests.testdir() as testdir:
atlas1spec = _make_dummy_atlas(testdir, 'My atlas 1', 'myatlas1',
'MyAtlas1')
atlas2spec = _make_dummy_atlas(testdir, 'My atlas 2', 'myatlas2',
'MyAtlas2')
badspec = op.join(testdir, 'badSpec.xml')
with open(badspec, 'wt') as f:
f.write('Bwahahahah!')
extraAtlases = ':'.join([
'myatlas1={}'.format(atlas1spec), 'myatlas2={}'.format(atlas2spec),
'badatlas1=non-existent-path', 'badatlas2={}'.format(badspec)
])
with mock.patch('fsl.data.atlases.fslsettings.read',
return_value=extraAtlases), \
mock.patch('fsl.data.atlases.fslsettings.write',
return_value=None):
reg = atlases.registry
reg.rescanAtlases()
assert reg.hasAtlas('myatlas1')
assert reg.hasAtlas('myatlas2')
assert not reg.hasAtlas('badatlas1')
assert not reg.hasAtlas('badatlas2')
def test_getNumComponents():
paths = ['analysis.ica/melodic_IC.nii.gz',
'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
icfile = op.join(meldir, 'melodic_IC.nii.gz')
tests.make_random_image(icfile, (10, 10, 10, 17))
assert mela.getNumComponents(meldir) == 17
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
with pytest.raises(Exception):
mela.getNumComponents(meldir)
def test_readdefault():
with tests.testdir() as testdir:
s = settings.Settings(cfgid='test', cfgdir=testdir, writeOnExit=False)
assert s.read('non-existent') is None
assert s.read('non-existent', 'default') == 'default'
def test_getReportFile():
paths = ['analysis.ica/filtfunc.ica/melodic_IC.nii.gz',
'analysis.ica/filtfunc.ica/melodic_mix',
'analysis.ica/filtfunc.ica/melodic_FTmix',
'analysis.ica/report.html']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica/filtfunc.ica')
expected = op.join(testdir, 'analysis.ica/report.html')
assert op.abspath(mela.getReportFile(meldir)) == expected
paths = ['analysis.ica/filtfunc.ica/melodic_IC.ni.gz',
'analysis.ica/filtfunc.ica/melodic_mix',
'analysis.ica/filtfunc.ica/melodic_FTmix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
assert mela.getReportFile(meldir) is None
def test_getICFile():
paths = ['analysis.ica/melodic_IC.nii.gz',
'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
expected = op.join(testdir, 'analysis.ica/melodic_IC.nii.gz')
assert mela.getICFile(meldir) == expected
paths = ['analysis.ica/melodic_IC.txt',
'analysis.ica/melodic_mix',
'analysis.ica/melodic_FTmix']
with tests.testdir(paths) as testdir:
meldir = op.join(testdir, 'analysis.ica')
with pytest.raises(fslpath.PathError):
mela.getICFile(meldir)
def test_getDTIFitDataPrefix_and_isDTIFitPath():
def make_dtifit_dir(dir, prefix, suffixes):
for s in suffixes:
path = op.join(dir, '{}{}'.format(prefix, s))
with open(path, 'wt') as f:
f.write(path)
prefixes = ['dti', 'blob', 'random-prefix', '01234']
suffixes = [
'_V1.nii', '_V2.nii', '_V3.nii', '_L1.nii', '_L2.nii', '_L3.nii'
]
badSuffixes = [
'_V1.txt', '_V2.nii', '_V3.nii', '_L1.txt', '_L2.tar', '_L3.nii'
]
# Valid dtifit directories
with tests.testdir() as testdir:
for p in prefixes:
tests.cleardir(testdir)
make_dtifit_dir(testdir, p, suffixes)
assert dtifit.getDTIFitDataPrefix(testdir) == p
assert dtifit.isDTIFitPath(testdir)
# Invalid dtifit dir - one file missing
with tests.testdir() as testdir:
make_dtifit_dir(testdir, 'dti', suffixes[:-1])
assert dtifit.getDTIFitDataPrefix(testdir) is None
assert not dtifit.isDTIFitPath(testdir)
# Invalid dtifit dir - non-nifti files
with tests.testdir() as testdir:
make_dtifit_dir(testdir, 'dti', badSuffixes)
assert dtifit.getDTIFitDataPrefix(testdir) is None
assert not dtifit.isDTIFitPath(testdir)
# Ambiguous dtifit dir - multiple
# potential prefixes. Should return
# the first (alphabetical) one.
with tests.testdir() as testdir:
make_dtifit_dir(testdir, 'dti1', suffixes)
make_dtifit_dir(testdir, 'dti2', suffixes)
assert dtifit.getDTIFitDataPrefix(testdir) == 'dti1'
assert dtifit.isDTIFitPath(testdir)
