Skip to content

TST: dcm2niix test fix #3058

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Sep 30, 2019
Merged

TST: dcm2niix test fix #3058

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
98e93a4
tst: create data directory prior to datalad install
mgxd Sep 30, 2019
5b30d5b
rf: clean up test
mgxd Sep 30, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
20 changes: 10 additions & 10 deletions nipype/interfaces/tests/test_extra_dcm2nii.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,42 +14,42 @@
DICOM_DIR = 'http://datasets-tests.datalad.org/dicoms/dcm2niix-tests'


def fetch_data(tmpdir, dicoms):
def fetch_data(datadir, dicoms):
"""Fetches some test DICOMs using datalad"""
data = os.path.join(tmpdir, 'data')
api.install(path=data, source=DICOM_DIR)
data = os.path.join(data, dicoms)
api.install(path=datadir, source=DICOM_DIR)
data = os.path.join(datadir, dicoms)
api.get(path=data)
return data

@pytest.mark.skipif(no_datalad, reason="Datalad required")
@pytest.mark.skipif(no_dcm2niix, reason="Dcm2niix required")
def test_dcm2niix_dwi(tmpdir):
tmpdir.chdir()
datadir = tmpdir.mkdir('data').strpath
try:
datadir = fetch_data(tmpdir.strpath, 'Siemens_Sag_DTI_20160825_145811')
dicoms = fetch_data(datadir, 'Siemens_Sag_DTI_20160825_145811')
except IncompleteResultsError as exc:
pytest.skip("Failed to fetch test data: %s" % str(exc))

def assert_dwi(eg, bids):
def assert_dwi(eg):
"Some assertions we will make"
assert eg.outputs.converted_files
assert eg.outputs.bvals
assert eg.outputs.bvecs
outputs = [y for x,y in eg.outputs.get().items()]
if bids:
if eg.inputs.get('bids_format'):
# ensure all outputs are of equal lengths
assert len(set(map(len, outputs))) == 1
else:
assert not eg.outputs.bids

dcm = Dcm2niix()
dcm.inputs.source_dir = datadir
dcm.inputs.source_dir = dicoms
dcm.inputs.out_filename = '%u%z'
assert_dwi(dcm.run(), True)
assert_dwi(dcm.run())

# now run specifying output directory and removing BIDS option
outdir = tmpdir.mkdir('conversion').strpath
dcm.inputs.output_dir = outdir
dcm.inputs.bids_format = False
assert_dwi(dcm.run(), False)
assert_dwi(dcm.run())