# extracting separate episodes
for i in range(stays.shape[0]):
stay_id = stays.ICUSTAY_ID.iloc[i]
intime = stays.INTIME.iloc[i]
outtime = stays.OUTTIME.iloc[i]
episode = get_events_for_stay(timeseries, stay_id, intime, outtime)
if episode.shape[0] == 0:
# no data for this episode
continue
episode = add_hours_elpased_to_events(
episode, intime).set_index('HOURS').sort_index(axis=0)
if stay_id in episodic_data.index:
episodic_data.loc[stay_id,
'Weight'] = get_first_valid_from_timeseries(
episode, 'Weight')
episodic_data.loc[stay_id,
'Height'] = get_first_valid_from_timeseries(
episode, 'Height')
episodic_data.loc[episodic_data.index == stay_id].to_csv(
os.path.join(args.subjects_root_path, subject_dir,
'episode{}.csv'.format(i + 1)),
index_label='Icustay')
columns = list(episode.columns)
columns_sorted = sorted(columns,
key=(lambda x: "" if x == "Hours" else x))
episode = episode[columns_sorted]
episode.to_csv(os.path.join(args.subjects_root_path, subject_dir,
'episode{}_timeseries.csv'.format(i + 1)),
index_label='Hours')
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)
# extracting separate episodes
for i in range(stays.shape[0]):
stay_id = stays.ICUSTAY_ID.iloc[i]
intime = stays.INTIME.iloc[i].date()
outtime = stays.OUTTIME.iloc[i].date()
episode = get_events_for_stay(timeseries, stay_id, intime, outtime)
if episode.shape[0] == 0:
# no data for this episode
continue
episode = add_hours_elpased_to_events(episode, intime).set_index('HOURS').sort_index(axis=0)
if stay_id in episodic_data.index:
episodic_data.loc[stay_id, 'Weight'] = get_first_valid_from_timeseries(episode, 'Weight')
episodic_data.loc[stay_id, 'Height'] = get_first_valid_from_timeseries(episode, 'Height')
episodic_data.loc[episodic_data.index == stay_id].to_csv(os.path.join(args.subjects_root_path, subject_dir,
'episode{}.csv'.format(i+1)),
index_label='Icustay')
columns = list(episode.columns)
columns_sorted = sorted(columns, key=(lambda x: "" if x == "Hours" else x))
episode = episode[columns_sorted]
episode.to_csv(os.path.join(args.subjects_root_path, subject_dir, 'episode{}_timeseries.csv'.format(i+1)),
index_label='Hours')
for i in range(stays.shape[0]):
stay_id = stays.ICUSTAY_ID.iloc[i]
sys.stdout.write(' {}'.format(stay_id))
sys.stdout.flush()
intime = stays.INTIME.iloc[i]
outtime = stays.OUTTIME.iloc[i]
episode = get_events_for_stay(timeseries, stay_id, intime, outtime)
if episode.shape[0] == 0:
sys.stdout.write(' (no data!)')
sys.stdout.flush()
continue
episode = add_hours_elpased_to_events(
episode, intime).set_index('HOURS').sort_index(axis=0)
episodic_data.Weight.ix[stay_id] = get_first_valid_from_timeseries(
episode, 'Weight')
episodic_data.Height.ix[stay_id] = get_first_valid_from_timeseries(
episode, 'Height')
episodic_data.ix[episodic_data.index == stay_id].to_csv(
os.path.join(args.subjects_root_path, subject_dir,
'episode{}.csv'.format(i + 1)),
index_label='Icustay')
columns = list(episode.columns)
columns_sorted = sorted(columns,
key=(lambda x: "" if x == "Hours" else x))
episode = episode[columns_sorted]
episode.to_csv(os.path.join(args.subjects_root_path, subject_dir,
'episode{}_timeseries.csv'.format(i + 1)),
index_label='Hours')
sys.stdout.write(' DONE!\n')
if events.shape[0] == 0:
sys.stdout.write('no valid events!\n')
continue
timeseries = convert_events_to_timeseries(events, variables=variables)
sys.stdout.write('extracting separate episodes...')
sys.stdout.flush()
for i in range(stays.shape[0]):
stay_id = stays.ICUSTAY_ID.iloc[i]
sys.stdout.write(' {}'.format(stay_id))
sys.stdout.flush()
intime = stays.INTIME.iloc[i]
outtime = stays.OUTTIME.iloc[i]
episode = get_events_for_stay(timeseries, stay_id, intime, outtime)
if episode.shape[0] == 0:
sys.stdout.write(' (no data!)')
sys.stdout.flush()
continue
episode = add_hours_elpased_to_events(episode, intime).set_index('HOURS').sort_index(axis=0)
episodic_data.Weight.ix[stay_id] = get_first_valid_from_timeseries(episode, 'Weight')
episodic_data.Height.ix[stay_id] = get_first_valid_from_timeseries(episode, 'Height')
episodic_data.ix[episodic_data.index==stay_id].to_csv(os.path.join(args.subjects_root_path, subject_dir, 'episode{}.csv'.format(i+1)), index_label='Icustay')
columns = list(episode.columns)
columns_sorted = sorted(columns, key=(lambda x: "" if x == "Hours" else x))
episode = episode[columns_sorted]
episode.to_csv(os.path.join(args.subjects_root_path, subject_dir, 'episode{}_timeseries.csv'.format(i+1)), index_label='Hours')
sys.stdout.write(' DONE!\n')