def process_episode(output_dir,
root_patient_folder,
episode_ind,
label_type,
pheno_map=None):
try:
episode_folder = os.path.join(root_patient_folder,
"episode" + str(episode_ind + 1))
episode = pd.read_csv(
os.path.join(root_patient_folder,
"episode" + str(episode_ind + 1) + ".csv"))
except:
print("episode csv file or folder missing for subject :" +
str(root_patient_folder))
return
stays = read_stays(root_patient_folder)
try:
subject_id = stays["SUBJECT_ID"].loc[stays["ICUSTAY_ID"] ==
episode.Icustay.iloc[0]].iloc[0]
hadm_id = stays["HADM_ID"].loc[stays["ICUSTAY_ID"] ==
episode.Icustay.iloc[0]].iloc[0]
except:
print("cannot match subject or admission for subject :" +
str(root_patient_folder))
return
pati_abrv = "pati." + str(subject_id) + "+" + str(hadm_id)
write_bio_edges(episode.Age[0], episode.Gender[0], episode.Ethnicity[0],
pati_abrv, output_dir)
write_diagnoses(root_patient_folder,
hadm_id,
output_dir,
type=label_type,
pheno_map=pheno_map)
for table in filter(lambda x: ".csv " not in x,
os.listdir(episode_folder)):
table_abrv_name = table_name_map[(table.split(".")[0].split("_")[0])]
if "timeseries" in table:
with open(os.path.join(episode_folder, table)) as tsfile:
ts_lines = tsfile.readlines()
write_seq_event(ts_lines, output_dir, pati_abrv, table_abrv_name)
else:
table_events = dataframe_from_csv(os.path.join(
episode_folder, table),
index_col=None)
write_static_event(table_events, output_dir, table_abrv_name)
var_map = read_itemid_to_variable_map(args.variable_map_file)
variables = var_map.VARIABLE.unique()
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:
for subject_dir in os.listdir(args.subjects_root_path):
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)
