def test_smoke_convertall(tmpdir):
runner(
("-f convertall -c dcm2niix -o %s -b --datalad "
"-s fmap_acq-3mm -d %s/{subject}/*"
% (tmpdir, TESTS_DATA_PATH)
).split(' ')
)
def test_ls(stdout):
args = (
"-f reproin --command ls --files %s"
% (TESTS_DATA_PATH)
).split(' ')
runner(args)
out = stdout.getvalue()
assert 'StudySessionInfo(locator=' in out
assert 'Halchenko/Yarik/950_bids_test4' in out
def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
is_bids = True if heuristic == 'reproin' else False
arg = "--random-seed 1 -f %s -c dcm2niix -o %s" \
% (heuristic, tmpdir)
if is_bids:
arg += " -b"
arg += " --datalad "
args = (
arg + invocation
).split(' ')
# Test some safeguards
if invocation == "--files %s" % TESTS_DATA_PATH:
# Multiple subjects must not be specified -- only a single one could
# be overridden from the command line
with pytest.raises(ValueError):
runner(args + ['--subjects', 'sub1', 'sub2'])
if heuristic != 'reproin':
# none other heuristic has mighty infotoids atm
with pytest.raises(NotImplementedError):
runner(args)
return
runner(args)
ds = Dataset(str(tmpdir))
assert ds.is_installed()
assert not ds.repo.dirty
head = ds.repo.get_hexsha()
# and if we rerun -- should fail
lgr.info(
"RERUNNING, expecting to FAIL since the same everything "
"and -c specified so we did conversion already"
)
with pytest.raises(RuntimeError):
runner(args)
# but there should be nothing new
assert not ds.repo.dirty
assert head == ds.repo.get_hexsha()
# unless we pass 'overwrite' flag
runner(args + ['--overwrite'])
# but result should be exactly the same, so it still should be clean
# and at the same commit
assert ds.is_installed()
assert not ds.repo.dirty
assert head == ds.repo.get_hexsha()
def test_scout_conversion(tmpdir):
tmppath = tmpdir.strpath
args = ("-b -f reproin --files %s" %
(TESTS_DATA_PATH)).split(' ') + ['-o', tmppath]
runner(args)
assert not op.exists(
pjoin(
tmppath,
'Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/anat'
))
assert op.exists(
pjoin(
tmppath,
'Halchenko/Yarik/950_bids_test4/sourcedata/sub-phantom1sid1/'
'ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz'
))
def test_scans_keys_reproin(tmpdir, invocation):
args = "-f reproin -c dcm2niix -o %s -b " % (tmpdir)
args += invocation
runner(args.split())
# for now check it exists
scans_keys = glob(pjoin(tmpdir.strpath, '*/*/*/*/*/*.tsv'))
assert(len(scans_keys) == 1)
with open(scans_keys[0]) as f:
reader = csv.reader(f, delimiter='\t')
for i, row in enumerate(reader):
if i == 0:
assert(row == ['filename', 'acq_time', 'operator', 'randstr'])
assert(len(row) == 4)
if i != 0:
assert(os.path.exists(pjoin(dirname(scans_keys[0]), row[0])))
assert(re.match(
'^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}$',
row[1]))
def test_scout_conversion(tmpdir):
tmppath = tmpdir.strpath
args = (
"-b -f reproin --files %s"
% (TESTS_DATA_PATH)
).split(' ') + ['-o', tmppath]
runner(args)
assert not op.exists(pjoin(
tmppath,
'Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/anat'))
assert op.exists(pjoin(
tmppath,
'Halchenko/Yarik/950_bids_test4/sourcedata/sub-phantom1sid1/'
'ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz'
)
)
def test_populate_bids_templates(tmpdir):
populate_bids_templates(
str(tmpdir),
defaults={'Acknowledgements': 'something'})
for f in "README", "dataset_description.json", "CHANGES":
# Just test that we have created them and they all have stuff TODO
assert "TODO" in tmpdir.join(f).read()
description_file = tmpdir.join('dataset_description.json')
assert "something" in description_file.read()
# it should also be available as a command
os.unlink(str(description_file))
runner([
'--command', 'populate-templates', '-f', 'convertall',
'--files', str(tmpdir)
])
assert "something" not in description_file.read()
assert "TODO" in description_file.read()
def test_notop(tmpdir, bidsoptions):
tmppath = tmpdir.strpath
args = ("-f reproin --files %s" %
(TESTS_DATA_PATH)).split(' ') + ['-o', tmppath] + ['-b'
] + bidsoptions
runner(args)
assert op.exists(pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4'))
for fname in [
'CHANGES', 'dataset_description.json', 'participants.tsv',
'README', 'participants.json'
]:
if 'notop' in bidsoptions:
assert not op.exists(
pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4', fname))
else:
assert op.exists(
pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4', fname))
def test_scans_keys_reproin(tmpdir, invocation):
args = "-f reproin -c dcm2niix -o %s -b " % (tmpdir)
args += invocation
runner(args.split())
# for now check it exists
scans_keys = glob(pjoin(tmpdir.strpath, '*/*/*/*/*/*.tsv'))
assert (len(scans_keys) == 1)
with open(scans_keys[0]) as f:
reader = csv.reader(f, delimiter='\t')
for i, row in enumerate(reader):
if i == 0:
assert (row == ['filename', 'acq_time', 'operator', 'randstr'])
assert (len(row) == 4)
if i != 0:
assert (os.path.exists(pjoin(dirname(scans_keys[0]), row[0])))
assert (re.match(
'^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}$',
row[1]))
def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
is_bids = True if heuristic == 'reproin' else False
arg = "--random-seed 1 -f %s -c dcm2niix -o %s" \
% (heuristic, tmpdir)
if is_bids:
arg += " -b"
arg += " --datalad "
args = (arg + invocation).split(' ')
# Test some safeguards
if invocation == "--files %s" % TESTS_DATA_PATH:
# Multiple subjects must not be specified -- only a single one could
# be overridden from the command line
with pytest.raises(ValueError):
runner(args + ['--subjects', 'sub1', 'sub2'])
if heuristic != 'reproin':
# none other heuristic has mighty infotoids atm
with pytest.raises(NotImplementedError):
runner(args)
return
runner(args)
ds = Dataset(str(tmpdir))
assert ds.is_installed()
assert not ds.repo.dirty
head = ds.repo.get_hexsha()
# and if we rerun -- should fail
lgr.info("RERUNNING, expecting to FAIL since the same everything "
"and -c specified so we did conversion already")
with pytest.raises(RuntimeError):
runner(args)
# but there should be nothing new
assert not ds.repo.dirty
assert head == ds.repo.get_hexsha()
# unless we pass 'overwrite' flag
runner(args + ['--overwrite'])
# but result should be exactly the same, so it still should be clean
# and at the same commit
assert ds.is_installed()
assert not ds.repo.dirty
assert head == ds.repo.get_hexsha()
def test_conversion(tmpdir, subject, heuristic):
tmpdir.chdir()
datadir = fetch_data(tmpdir.strpath, subject)
outdir = tmpdir.mkdir('out').strpath
args = gen_heudiconv_args(datadir, outdir, subject, heuristic)
runner(args) # run conversion
# verify functionals were converted
assert glob('{}/{}/func/*'.format(outdir, subject)) == \
glob('{}/{}/func/*'.format(datadir, subject))
# compare some json metadata
json_ = '{}/task-rest_acq-24mm64sl1000tr32te600dyn_bold.json'.format
orig, conv = (json.load(open(json_(datadir))),
json.load(open(json_(outdir))))
keys = ['EchoTime', 'MagneticFieldStrength', 'Manufacturer', 'SliceTiming']
for key in keys:
assert orig[key] == conv[key]
def test_scout_conversion(tmpdir):
tmppath = tmpdir.strpath
args = ("-b -f reproin --files %s" %
(TESTS_DATA_PATH)).split(' ') + ['-o', tmppath]
runner(args)
dspath = Path(tmppath) / 'Halchenko/Yarik/950_bids_test4'
sespath = dspath / 'sub-phantom1sid1/ses-localizer'
assert not (sespath / 'anat').exists()
assert (dspath / 'sourcedata/sub-phantom1sid1/ses-localizer/'
'anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz').exists()
# Let's do some basic checks on produced files
j = load_json(sespath /
'fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json')
# We store HeuDiConv version in each produced .json file
# TODO: test that we are not somehow overwritting that version in existing
# files which we have not produced in a particular run.
assert j[HEUDICONV_VERSION_JSON_KEY] == __version__
def test_cache(tmpdir):
tmppath = tmpdir.strpath
args = ("-f convertall --files %s/axasc35.dcm -s S01" %
(TESTS_DATA_PATH)).split(' ') + ['-o', tmppath]
runner(args)
cachedir = (tmpdir / '.heudiconv' / 'S01' / 'info')
assert cachedir.exists()
# check individual files
assert (cachedir / 'heuristic.py').exists()
assert (cachedir / 'filegroup.json').exists()
assert (cachedir / 'dicominfo.tsv').exists()
assert (cachedir / 'S01.auto.txt').exists()
assert (cachedir / 'S01.edit.txt').exists()
# check dicominfo has "time" as last column:
with open(str(cachedir / 'dicominfo.tsv'), 'r') as f:
cols = f.readline().split()
assert cols[26] == "time"
def test_conversion(tmpdir, subject, heuristic):
tmpdir.chdir()
try:
datadir = fetch_data(tmpdir.strpath, subject)
except IncompleteResultsError as exc:
pytest.skip("Failed to fetch test data: %s" % str(exc))
outdir = tmpdir.mkdir('out').strpath
args = gen_heudiconv_args(datadir, outdir, subject, heuristic)
runner(args) # run conversion
# verify functionals were converted
assert glob('{}/{}/func/*'.format(outdir, subject)) == \
glob('{}/{}/func/*'.format(datadir, subject))
# compare some json metadata
json_ = '{}/task-rest_acq-24mm64sl1000tr32te600dyn_bold.json'.format
orig, conv = (json.load(open(json_(datadir))),
json.load(open(json_(outdir))))
keys = ['EchoTime', 'MagneticFieldStrength', 'Manufacturer', 'SliceTiming']
for key in keys:
assert orig[key] == conv[key]
def test_grouping(tmpdir, subject):
dicoms = [
op.join(TESTS_DATA_PATH, fl) for fl in ['axasc35.dcm', 'phantom.dcm']
]
# ensure DICOMs are different studies
studyuids = {
dcm.read_file(fl, stop_before_pixels=True).StudyInstanceUID for fl
in dicoms
}
assert len(studyuids) == len(dicoms)
# symlink to common location
outdir = tmpdir.mkdir('out')
datadir = tmpdir.mkdir(subject)
for fl in dicoms:
os.symlink(fl, (datadir / op.basename(fl)).strpath)
template = op.join("{subject}/*.dcm")
hargs = gen_heudiconv_args(
tmpdir.strpath,
outdir.strpath,
subject,
'convertall.py',
template=template
)
with pytest.raises(AssertionError):
runner(hargs)
# group all found DICOMs under subject, despite conflicts
hargs += ["-g", "all"]
runner(hargs)
assert len([fl for fl in outdir.visit(fil='run0*')]) == 4
tsv = (outdir / 'participants.tsv')
assert tsv.check()
lines = tsv.open().readlines()
assert len(lines) == 2
assert lines[1].split('\t')[0] == 'sub-{}'.format(subject)
def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
is_bids = True if heuristic == 'dbic_bids' else False
arg = "-f heuristics/%s.py -c dcm2niix -o %s" % (heuristic, tmpdir)
if is_bids:
arg += " -b"
arg += " --datalad "
args = (
arg + invocation
).split(' ')
if heuristic != 'dbic_bids' and invocation == '--files tests/data':
# none other heuristic has mighty infotoids atm
with pytest.raises(NotImplementedError):
runner(args)
return
runner(args)
ds = Dataset(str(tmpdir))
assert ds.is_installed()
assert not ds.repo.dirty
head = ds.repo.get_hexsha()
# and if we rerun -- should fail
if heuristic != 'dbic_bids' and invocation != '--files tests/data':
# those guys -- they just plow through it ATM without failing, i.e.
# the logic is to reprocess
runner(args)
# don't raise error by rerun...
# else:
# with pytest.raises(RuntimeError):
# runner(args)
# but there should be nothing new
assert not ds.repo.dirty
assert head == ds.repo.get_hexsha()
# unless we pass 'overwrite' flag
runner(args + ['--overwrite'])
# but result should be exactly the same, so it still should be clean
# and at the same commit
assert ds.is_installed()
assert not ds.repo.dirty
assert head == ds.repo.get_hexsha()
def test_ls(stdout):
args = "-f heuristics/dbic_bids.py --command ls --files tests/data".split(' ')
runner(args)
out = stdout.getvalue()
assert 'StudySessionInfo(locator=' in out
assert 'Halchenko/Yarik/950_bids_test4' in out
def test_smoke_convertall(tmpdir):
runner(("-f convertall -c dcm2niix -o %s -b --datalad "
"-s fmap_acq-3mm -d %s/{subject}/*" %
(tmpdir, TESTS_DATA_PATH)).split(' '))
def test_main_help(stdout):
with pytest.raises(SystemExit):
runner(['--help'])
assert stdout.getvalue().startswith("usage: ")
def test_main_version(std):
with pytest.raises(SystemExit):
runner(['--version'])
assert std.getvalue().rstrip() == __version__
def test_smoke_converall(tmpdir):
runner(
("-f heuristics/convertall.py -c dcm2niix -o %s -b --datalad "
"-s fmap_acq-3mm -d tests/data/{subject}/*" % tmpdir).split(' ')
)
