def create_cpac_data_config(bids_dir,
participant_label=None,
aws_input_creds=None,
skip_bids_validator=False):
from bids_utils import collect_bids_files_configs, bids_gen_cpac_sublist
print("Parsing {0}..".format(bids_dir))
(file_paths, config) = collect_bids_files_configs(bids_dir,
aws_input_creds)
if participant_label:
file_paths = [
file_path for file_path in file_paths
if any(participant_label in file_path
for participant_label in participant_labels)
]
if not file_paths:
print("Did not find data for {0}".format(", ".join(participant_label)))
sys.exit(1)
raise_error = not skip_bids_validator
sub_list = bids_gen_cpac_sublist(bids_dir,
file_paths,
config,
aws_input_creds,
raise_error=raise_error)
if not sub_list:
print("Did not find data in {0}".format(bids_dir))
sys.exit(1)
return sub_list
def test_gen_bids_sublist(bids_dir, test_yml, creds_path, dbg=False):
(img_files, config) = collect_bids_files_configs(bids_dir, creds_path)
print("Found %d config files for %d image files" %
(len(config), len(img_files)))
sublist = bids_gen_cpac_sublist(bids_dir, img_files, config, creds_path,
dbg)
with open(test_yml, "w") as ofd:
yaml.dump(sublist, ofd, encoding='utf-8')
sublist = bids_gen_cpac_sublist(bids_dir, img_files, None, creds_path, dbg)
test_yml = test_yml.replace(".yml", "_no_param.yml")
with open(test_yml, "w") as ofd:
yaml.dump(sublist, ofd, encoding='utf-8')
assert sublist
if 'sub-' not in pt:
pt = 'sub-' + pt
pt_file_paths += [fp for fp in file_paths if pt in fp]
file_paths = pt_file_paths
if not file_paths:
print("Did not find any files to process")
sys.exit(1)
# TODO: once CPAC is updated to use per-scan parameters from subject list,
# change the 3rd arguement to the config dict returned from
# collect_bids_files_configs
sub_list = bids_gen_cpac_sublist(args.bids_dir, file_paths, [],
args.aws_input_creds)
if not sub_list:
print("Did not find data in {0}".format(args.bids_dir))
sys.exit(1)
else:
# load the file as a check to make sure it is available and readable
sub_list = yaml.load(open(os.path.realpath(args.data_config_file), 'r'))
if args.participant_label:
t_sub_list = []
for sub_dict in sub_list:
if sub_dict["participant_id"] in args.participant_label or \
sub_dict["participant_id"].replace("sub-", "") in args.participant_label:
t_sub_list.append(sub_dict)
file_paths = [
file_path for file_path in file_paths
if any(participant_label in file_path
for participant_label in participant_labels)
]
if not file_paths:
print("Did not find data for {0}".format(", ".join(
args.participant_label)))
sys.exit(1)
raise_error = not args.skip_bids_validator
sub_list = bids_gen_cpac_sublist(args.bids_dir,
file_paths,
config,
args.aws_input_creds,
raise_error=raise_error)
if not sub_list:
print("Did not find data in {0}".format(args.bids_dir))
sys.exit(1)
else:
# load the file as a check to make sure it is available and readable
sub_list = load_yaml_config(args.data_config_file,
args.aws_input_creds)
if args.participant_label:
sub_list = [
pt_file_paths = []
for pt in args.participant_label:
if 'sub-' not in pt:
pt = 'sub-' + pt
pt_file_paths += [fp for fp in file_paths if pt in fp]
file_paths = pt_file_paths
if not file_paths:
print("Did not find any files to process")
sys.exit(1)
sub_list = bids_gen_cpac_sublist(args.bids_dir, file_paths, config,
args.aws_input_creds)
if not sub_list:
print("Did not find data in {0}".format(args.bids_dir))
sys.exit(1)
else:
# load the file as a check to make sure it is available and readable
sub_list = load_yaml_config(args.data_config_file, args.aws_input_creds)
if args.participant_label:
t_sub_list = []
for sub_dict in sub_list:
if sub_dict["subject_id"] in args.participant_label or \
sub_dict["subject_id"].replace("sub-", "") in args.participant_label:
t_sub_list.append(sub_dict)
