def test_AFQ_missing_files():
tmpdir = nbtmp.InTemporaryDirectory()
bids_path = tmpdir.name
with pytest.raises(
ValueError,
match="There must be a dataset_description.json in bids_path"):
api.AFQ(bids_path)
afd.to_bids_description(bids_path, **{
"Name": "Missing",
"Subjects": ["sub-01"]
})
with pytest.raises(
ValueError,
match=f"No non-json files recognized by pyBIDS in {bids_path}"):
api.AFQ(bids_path)
subses_folder = op.join(bids_path, "derivatives", "otherDeriv", 'sub-01',
'ses-01')
os.makedirs(subses_folder, exist_ok=True)
afd.to_bids_description(
op.join(bids_path, "derivatives", "otherDeriv"), **{
"Name": "Missing",
"PipelineDescription": {
"Name": "otherDeriv"
}
})
touch(op.join(subses_folder, "sub-01_ses-01_dwi.nii.gz"))
with pytest.raises(ValueError,
match="No non-json files recognized by pyBIDS" +
" in the pipeline: missingPipe"):
api.AFQ(bids_path, dmriprep="missingPipe")
os.mkdir(op.join(bids_path, "missingPipe"))
afd.to_bids_description(
op.join(bids_path, "missingPipe"), **{
"Name": "Missing",
"PipelineDescription": {
"Name": "missingPipe"
}
})
with pytest.raises(ValueError,
match="No non-json files recognized by pyBIDS" +
" in the pipeline: missingPipe"):
api.AFQ(bids_path, dmriprep="missingPipe")
afd.fetch_stanford_hardi_tractography()
bids_path = op.join(op.expanduser('~'), 'AFQ_data', 'stanford_hardi')
tractography_path = op.join(bids_path, 'derivatives', 'my_tractography')
sub_path = op.join(tractography_path, 'sub-01', 'ses-01', 'dwi')
os.makedirs(sub_path, exist_ok=True)
os.rename(
op.join(op.expanduser('~'), 'AFQ_data', 'stanford_hardi_tractography',
'full_segmented_cleaned_tractography.trk'),
op.join(sub_path, 'sub-01_ses-01-dwi_tractography.trk'))
afd.to_bids_description(
tractography_path, **{
"Name": "my_tractography",
"PipelineDescription": {
"Name": "my_tractography"
}
})
###########################################################################
# After we do that, our dataset folder should look like this:
#
# | stanford_hardi
# | ├── dataset_description.json
# | └── derivatives
# | ├── freesurfer
# | │ ├── dataset_description.json
# | │ └── sub-01
# | │ └── ses-01
# | │ └── anat
def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True):
subjects = ['sub-0%s' % (d + 1) for d in range(n_subjects)]
# Case where there are individual session folders within each subject's
# folder:
if n_sessions > 1:
# create data for n_sessions for each subject
if share_sessions:
sessions = ['ses-0%s' % (d + 1) for d in range(n_sessions)]
bids_dir = tempfile.mkdtemp()
afd.to_bids_description(
bids_dir, **{
"Name": "Dummy",
"Subjects": subjects,
"Sessions": sessions
})
dmriprep_dir = op.join(bids_dir, "derivatives", "dmriprep")
os.makedirs(dmriprep_dir)
afd.to_bids_description(
dmriprep_dir, **{
"Name": "Dummy",
"PipelineDescription": {
"Name": "synthetic"
}
})
for subject in subjects:
for session in sessions:
for modality in ['anat', 'dwi']:
os.makedirs(
op.join(dmriprep_dir, subject, session, modality))
# Make some dummy data:
create_dummy_data(dmriprep_dir, subject, session)
else:
# create different sessions for each subject
sessions = ['ses-0%s' % (d + 1) for d in range(n_subjects)]
bids_dir = tempfile.mkdtemp()
afd.to_bids_description(
bids_dir, **{
"Name": "Dummy",
"Subjects": subjects,
"Sessions": sessions
})
dmriprep_dir = op.join(bids_dir, "derivatives", "dmriprep")
os.makedirs(dmriprep_dir)
afd.to_bids_description(
dmriprep_dir, **{
"Name": "Dummy",
"PipelineDescription": {
"Name": "synthetic"
}
})
for d in range(n_subjects):
subject = subjects[d]
session = sessions[d]
for modality in ['anat', 'dwi']:
os.makedirs(
op.join(dmriprep_dir, subject, session, modality))
# Make some dummy data:
create_dummy_data(dmriprep_dir, subject, session)
else:
# Don't create session folders at all:
bids_dir = tempfile.mkdtemp()
afd.to_bids_description(bids_dir, **{
"Name": "Dummy",
"Subjects": subjects
})
dmriprep_dir = op.join(bids_dir, "derivatives", "dmriprep")
os.makedirs(dmriprep_dir)
afd.to_bids_description(
dmriprep_dir, **{
"Name": "Dummy",
"PipelineDescription": {
"Name": "synthetic"
}
})
for subject in subjects:
for modality in ['anat', 'dwi']:
os.makedirs(op.join(dmriprep_dir, subject, modality))
# Make some dummy data:
create_dummy_data(dmriprep_dir, subject)
return bids_dir