def layout_ds005_multi_derivs():
data_dir = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(data_dir)
deriv_dir1 = join(get_test_data_path(), 'ds005_derivs')
deriv_dir2 = join(data_dir, 'derivatives', 'events')
layout.add_derivatives([deriv_dir1, deriv_dir2])
return layout
def layout_ds005_multi_derivs():
data_dir = join(get_test_data_path(), 'ds005')
layout = BIDSLayout(data_dir)
deriv_dir1 = join(get_test_data_path(), 'ds005_derivs')
deriv_dir2 = join(data_dir, 'derivatives', 'events')
layout.add_derivatives([deriv_dir1, deriv_dir2])
return layout
def layout_ds005_multi_derivs(request, db_dir):
data_dir = join(get_test_data_path(), 'ds005')
database_path = str(db_dir / request.param) if request.param else None
layout = BIDSLayout(data_dir, database_path=database_path)
deriv_dir1 = join(get_test_data_path(), 'ds005_derivs')
deriv_dir2 = join(data_dir, 'derivatives', 'events')
layout.add_derivatives([deriv_dir1, deriv_dir2])
return layout
def get_files():
DSET_DIR = op.abspath('/home/data/nbc/external-datasets/ds001491/')
layout = BIDSLayout(DSET_DIR)
layout.add_derivatives(
'/home/data/nbc/external-datasets/ds001491/derivatives/afni-step1/')
task = 'images'
info = {}
for sub in sorted(layout.get_subjects()):
print(sub)
sub_info = {'files': [], 'echo_times': []}
for echo in sorted(layout.get_echoes(subject=sub, task=task)):
raw_files = layout.get(subject=sub,
task=task,
echo=echo,
extensions='.nii.gz')
preproc_files = layout.get(subject=sub,
task=task,
root='afni-step1',
extensions='.nii.gz')
# For some reason pybids doesn't index echo in derivatives
preproc_files = [
p for p in preproc_files
if 'echo-{0}'.format(echo) in p.filename
]
if len(preproc_files) != 1:
print(preproc_files)
raise Exception('BAD')
# Replace filename with path when using new version of bids
sub_info['files'].append(preproc_files[0].path)
metadata = raw_files[0].metadata
sub_info['echo_times'].append(metadata['EchoTime'])
info[sub] = sub_info
with open('preproc_files.json', 'w') as fo:
json.dump(info, fo, indent=4, sort_keys=True)
