def get_external_bids(scan_info, local_file):
"""Download an external T1 or T2 image.
Query flywheel to find the correct acquisition and get its BIDS
info. scan_info came from context.get_input('*_anatomy').
"""
modality = scan_info['object']['modality']
logger.info("Adding additional %s folder...", modality)
external_acq = fw.get(scan_info['hierarchy']['id'])
external_niftis = [f for f in external_acq.files if
f.name == scan_info['location']['name']]
if not len(external_niftis) == 1:
raise Exception("Unable to find location for extra %s" % modality)
nifti = external_niftis[0]
nifti_bids_path = bids_root / nifti.info['BIDS']['Path']
json_bids_path = str(nifti_bids_path).replace(
"nii.gz", ".json").replace(".nii", ".json")
# Warn if overwriting: Should never happen on purpose
if nifti_bids_path.exists():
logger.warning("Overwriting current T1w image...")
# Copy to / overwrite its place in BIDS
local_file.replace(nifti_bids_path)
# Download the sidecar
export.download_sidecar(nifti.info, json_bids_path)
assert PosixPath(json_bids_path).exists()
assert nifti_bids_path.exists()
path = "/flywheel/v0/output/bids_dataset/" + path
fname = nifti.info['BIDS']['Filename']
sidecar = nifti.info
if not os.path.exists(path):
os.makedirs(path)
if os.path.isfile("/".join([path, fname])):
logger.info("Overwriting current T1w image...")
os.remove("/".join([path, fname]))
t1_acq.download_file(nifti.name, "/".join([path, fname]))
sidecar_name = fname.replace('.nii.gz', '.json')
if os.path.isfile(path + sidecar_name):
os.remove(path + sidecar_name)
export.download_sidecar(sidecar, "/".join([path, sidecar_name]))
if t2_acq:
logger.info("Adding additional T2w folder...")
nifti = [f for f in t2_acq.files if '.nii' in f.name].pop()
path = nifti.info['BIDS']['Path']
path = "/flywheel/v0/output/bids_dataset/" + path
fname = nifti.info['BIDS']['Filename']
sidecar = nifti.info
if not os.path.exists(path):
os.makedirs(path)
if os.path.isfile("/".join([path, fname])):
logger.info("Overwriting current T2w image...")