def test_loadSeries():
# test a pre-CRC and a post-CRC version
for version in ('1.0.20190410', '1.0.20190902'):
with install_dcm2niix(version):
datafile = op.join(datadir, 'example_dicom.tbz2')
with tarfile.open(datafile) as f:
f.extractall()
dcmdir = os.getcwd()
series = fsldcm.scanDir(dcmdir)
expShape = (512, 512, 1)
explens = [1, 1]
for s, explen in zip(series, explens):
imgs = fsldcm.loadSeries(s)
assert len(imgs) == explen
for img in imgs:
assert img.dicomDir == dcmdir
assert img.shape == expShape
assert img[:].shape == expShape
assert img.getMeta('PatientName') == 'MCCARTHY_PAUL' or \
img.getMeta('PatientName') == 'MCCARTHY_PAUL_2'
assert 'PatientName' in img.metaKeys()
assert 'MCCARTHY_PAUL' in img.metaValues() or \
'MCCARTHY_PAUL_2' in img.metaValues()
assert ('PatientName', 'MCCARTHY_PAUL') in img.metaItems() or \
('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems()
def test_scanDir():
with install_dcm2niix():
series = fsldcm.scanDir('.')
assert len(series) == 0
datafile = op.join(datadir, 'example_dicom.tbz2')
with tarfile.open(datafile) as f:
f.extractall()
series = fsldcm.scanDir('.')
assert len(series) == 2
for s in series:
assert (s['PatientName'] == 'MCCARTHY_PAUL' or
s['PatientName'] == 'MCCARTHY_PAUL_2')
def scan():
try:
series.extend(fsldcm.scanDir(dcmdir))
if len(series) == 0:
raise Exception('Could not find any DICOM '
'data series in {}'.format(dcmdir))
except Exception as e:
series.append(e)
def test_disabled():
with mock.patch('fsl.data.dicom.enabled', return_value=False):
with pytest.raises(RuntimeError):
fsldcm.scanDir('.')
with pytest.raises(RuntimeError):
fsldcm.loadSeries({})