for subject_dir in tqdm(os.listdir(args.subjects_root_path),
desc='Iterating over subjects'):
dn = os.path.join(args.subjects_root_path, subject_dir)
try:
subject_id = int(subject_dir)
if not os.path.isdir(dn):
raise Exception
except:
continue
try:
# reading tables of this subject
stays = read_stays(os.path.join(args.subjects_root_path, subject_dir))
diagnoses = read_diagnoses(
os.path.join(args.subjects_root_path, subject_dir))
events = read_events(os.path.join(args.subjects_root_path,
subject_dir))
except:
sys.stderr.write(
'Error reading from disk for subject: {}\n'.format(subject_id))
continue
episodic_data = assemble_episodic_data(stays, diagnoses)
# cleaning and converting to time series
events = map_itemids_to_variables(events, var_map)
events = clean_events(events)
if events.shape[0] == 0:
# no valid events for this subject
continue
timeseries = convert_events_to_timeseries(events, variables=variables)
dn = os.path.join(args.subjects_root_path, subject_dir)
try:
subject_id = int(subject_dir)
if not os.path.isdir(dn):
raise Exception
except:
continue
sys.stdout.write('Subject {}: '.format(subject_id))
sys.stdout.flush()
try:
sys.stdout.write('reading...')
sys.stdout.flush()
stays = read_stays(os.path.join(args.subjects_root_path, subject_dir))
diagnoses = read_diagnoses(os.path.join(args.subjects_root_path, subject_dir))
events = read_events(os.path.join(args.subjects_root_path, subject_dir))
except:
sys.stdout.write('error reading from disk!\n')
continue
else:
sys.stdout.write('got {0} stays, {1} diagnoses, {2} events...'.format(stays.shape[0], diagnoses.shape[0], events.shape[0]))
sys.stdout.flush()
episodic_data = assemble_episodic_data(stays, diagnoses)
sys.stdout.write('cleaning and converting to time series...')
sys.stdout.flush()
events = map_itemids_to_variables(events, var_map)
events = clean_events(events)
if events.shape[0] == 0:
sys.stdout.write('no valid events!\n')