def get_laus125_ts_labels():
laus125_labels_lh = [
line.rstrip()
for line in open(op.join(root_path, 'fmri_laus125_lh.txt'))
]
laus125_labels_rh = [
line.rstrip()
for line in open(op.join(root_path, 'fmri_laus125_rh.txt'))
]
laus125_labels_lh = [s + '-lh' for s in laus125_labels_lh]
laus125_labels_rh = [s + '-rh' for s in laus125_labels_rh]
laus125_labels = np.array(laus125_labels_lh + laus125_labels_rh)
utils.write_list_to_file(laus125_labels,
op.join(root_path, 'linda_laus125_order.txt'))
return laus125_labels
def run_on_subjects(args, main_func, subjects_itr=None, subject_func=None):
if subjects_itr is None:
subjects_itr = args.subject
subjects_flags, subjects_errors = {}, {}
args = init_args(args)
for tup in subjects_itr:
subject = get_subject(tup, subject_func)
utils.make_dir(op.join(MMVT_DIR, subject, 'mmvt'))
remote_subject_dir = utils.build_remote_subject_dir(
args.remote_subject_dir, subject)
logging.info(args)
print(
'****************************************************************')
print('subject: {}, atlas: {}'.format(subject, args.atlas))
print('remote dir: {}'.format(remote_subject_dir))
print(
'****************************************************************')
os.environ['SUBJECT'] = subject
flags = dict()
try:
# if utils.should_run(args, 'prepare_subject_folder'):
# I think we always want to run this
# *) Prepare the local subject's folder
flags['prepare_subject_folder'] = prepare_subject_folder(
subject, remote_subject_dir, args)
if not flags['prepare_subject_folder'] and not args.ignore_missing:
ans = input('Do you wish to continue (y/n)? ')
if not au.is_true(ans):
continue
flags['prepare_subject_folder'] = True
flags = main_func(tup, remote_subject_dir, args, flags)
subjects_flags[subject] = flags
except:
subjects_errors[subject] = traceback.format_exc()
print('Error in subject {}'.format(subject))
print(traceback.format_exc())
errors = defaultdict(list)
ret = True
good_subjects, bad_subjects = [], []
logs_fol = utils.make_dir(op.join(MMVT_DIR, subject, 'logs'))
logging.basicConfig(filename=op.join(logs_fol, 'preproc.log'),
level=logging.DEBUG)
for subject, flags in subjects_flags.items():
print('subject {}:'.format(subject))
logging.info('subject {}:'.format(subject))
for flag_type, val in flags.items():
print('{}: {}'.format(flag_type, val))
logging.info('{}: {}'.format(flag_type, val))
if not val:
errors[subject].append(flag_type)
if len(errors) > 0:
ret = False
print('Errors:')
logging.info('Errors:')
for subject, error in errors.items():
print('{}: {}'.format(subject, error))
logging.info('{}: {}'.format(subject, error))
for subject in subjects_flags.keys():
if len(errors[subject]) == 0:
good_subjects.append(subject)
else:
bad_subjects.append(subject)
print('Good subjects:\n {}'.format(good_subjects))
logging.info('Good subjects:\n {}'.format(good_subjects))
print('Bad subjects:\n {}'.format(bad_subjects))
logging.info('Good subjects:\n {}'.format(good_subjects))
utils.write_list_to_file(
good_subjects, op.join(utils.get_logs_fol(), 'good_subjects.txt'))
utils.write_list_to_file(bad_subjects,
op.join(utils.get_logs_fol(), 'bad_subjects.txt'))
return ret