def test_get_bids_files():
with InTemporaryDirectory():
bids_path = create_fake_bids_dataset(n_sub=10,
n_ses=2,
tasks=['localizer', 'main'],
n_runs=[1, 3])
# For each possible option of file selection we check that we
# recover the appropriate amount of files, as included in the
# fake bids dataset.
# 250 files in total related to subject images. Top level files like
# README not included
selection = get_bids_files(bids_path)
assert len(selection) == 250
# 160 bold files expected. .nii and .json files
selection = get_bids_files(bids_path, file_tag='bold')
assert len(selection) == 160
# Only 90 files are nii.gz. Bold and T1w files.
selection = get_bids_files(bids_path, file_type='nii.gz')
assert len(selection) == 90
# Only 25 files correspond to subject 01
selection = get_bids_files(bids_path, sub_label='01')
assert len(selection) == 25
# There are only 10 files in anat folders. One T1w per subject.
selection = get_bids_files(bids_path, modality_folder='anat')
assert len(selection) == 10
# 20 files corresponding to run 1 of session 2 of main task.
# 10 bold.nii.gz and 10 bold.json files. (10 subjects)
filters = [('task', 'main'), ('run', '01'), ('ses', '02')]
selection = get_bids_files(bids_path, file_tag='bold', filters=filters)
assert len(selection) == 20
# Get Top level folder files. Only 1 in this case, the README file.
selection = get_bids_files(bids_path, sub_folder=False)
assert len(selection) == 1
# 80 counfonds (4 runs per ses & sub), testing `fmriprep` >= 20.2 path
selection = get_bids_files(os.path.join(bids_path, 'derivatives'),
file_tag='desc-confounds_timeseries')
assert len(selection) == 80
with InTemporaryDirectory():
bids_path = create_fake_bids_dataset(n_sub=10,
n_ses=2,
tasks=['localizer', 'main'],
n_runs=[1, 3],
confounds_tag="desc-confounds_"
"regressors")
# 80 counfonds (4 runs per ses & sub), testing `fmriprep` >= 20.2 path
selection = get_bids_files(os.path.join(bids_path, 'derivatives'),
file_tag='desc-confounds_regressors')
assert len(selection) == 80
def test_first_level_models_from_bids():
with InTemporaryDirectory():
bids_path = create_fake_bids_dataset(n_sub=10,
n_ses=2,
tasks=['localizer', 'main'],
n_runs=[1, 3])
# test arguments are provided correctly
with pytest.raises(TypeError):
first_level_models_from_bids(2, 'main', 'MNI')
with pytest.raises(ValueError):
first_level_models_from_bids('lolo', 'main', 'MNI')
with pytest.raises(TypeError):
first_level_models_from_bids(bids_path, 2, 'MNI')
with pytest.raises(TypeError):
first_level_models_from_bids(bids_path,
'main',
'MNI',
model_init=[])
# test output is as expected
models, m_imgs, m_events, m_confounds = first_level_models_from_bids(
bids_path, 'main', 'MNI', [('desc', 'preproc')])
assert len(models) == len(m_imgs)
assert len(models) == len(m_events)
assert len(models) == len(m_confounds)
# test repeated run tag error when run tag is in filenames
# can arise when desc or space is present and not specified
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'main',
'T1w') # desc not specified
# test more than one ses file error when run tag is not in filenames
# can arise when desc or space is present and not specified
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'localizer',
'T1w') # desc not specified
# test issues with confound files. There should be only one confound
# file per img. An one per image or None. Case when one is missing
confound_files = get_bids_files(os.path.join(bids_path, 'derivatives'),
file_tag='desc-confounds_regressors')
os.remove(confound_files[-1])
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'main', 'MNI')
# test issues with event files
events_files = get_bids_files(bids_path, file_tag='events')
os.remove(events_files[0])
# one file missing
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'main', 'MNI')
for f in events_files[1:]:
os.remove(f)
# all files missing
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'main', 'MNI')
# In case different desc and spaces exist and are not selected we
# fail and ask for more specific information
shutil.rmtree(os.path.join(bids_path, 'derivatives'))
# issue if no derivatives folder is present
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'main', 'MNI')
# check runs are not repeated when ses field is not used
shutil.rmtree(bids_path)
bids_path = create_fake_bids_dataset(n_sub=10,
n_ses=1,
tasks=['localizer', 'main'],
n_runs=[1, 3],
no_session=True)
# test repeated run tag error when run tag is in filenames and not ses
# can arise when desc or space is present and not specified
with pytest.raises(ValueError):
first_level_models_from_bids(bids_path, 'main',
'T1w') # desc not specified
