def compute_patient_batches(configs):
pid_list = mlhc_io.read_list_from_file(configs["included_pid_path"])
pid_list = list(map(int, pid_list))
print("Number of PID stays in the database: {}".format(len(pid_list)))
batch_to_list_dict = {}
pid_to_batch_dict = {}
for batch_run_idx, base_idx in enumerate(range(0, len(pid_list), configs["batch_size_patients_per_file"])):
sub_pid_list = pid_list[base_idx:base_idx+configs["batch_size_patients_per_file"]]
batch_to_list_dict[batch_run_idx] = pid_list[base_idx:base_idx+configs["batch_size_patients_per_file"]]
for pid in sub_pid_list:
pid_to_batch_dict[pid] = batch_run_idx
pickle_obj = {"batch_to_lst": batch_to_list_dict, "pid_to_batch": pid_to_batch_dict}
with open(configs["output_path"], 'wb') as fp:
pickle.dump(pickle_obj, fp)
def filter_patients(configs):
pid_list = mlhc_io.read_list_from_file(configs["all_pid_stay_path"])
print("Number of PID stays in the database: {}".format(len(pid_list)))
included_patients = []
for pidx, pid in enumerate(pid_list):
if (pidx + 1) % 100 == 0:
print("PID: {}/{}".format(pidx + 1, len(pid_list)))
print("Included patient stays: {}/{}".format(\
len(included_patients), pidx+1))
df_vs = pd.read_hdf(configs["vital_per_table_path"],
mode='r',
where="patientunitstayid={}".format(pid))
df_vs.sort_values(by="observationoffset",
inplace=True,
kind="mergesort")
hr_col = df_vs[["observationoffset", "heartrate"]].dropna()
diffed_hr_col = hr_col["observationoffset"].diff()
min_ts = hr_col.observationoffset.min()
max_ts = hr_col.observationoffset.max()
segment_hours = (max_ts - min_ts) / 60.0
# Exclude stays longer than 30 days or shorter than 1 day
if np.isnan(segment_hours) or segment_hours < 24*configs[\
"min_length_days"] or segment_hours > configs[\
"max_length_days"]*24:
continue
max_disconnect_mins = int(diffed_hr_col.max())
# Exclude stays where the HR sensor is disconnected for more than 60
# minutes.
if max_disconnect_mins > configs["max_hr_disconnect_mins"]:
continue
included_patients.append(pid)
sorted_inc_pids = list(sorted(included_patients))
mlhc_io.write_list_to_file(configs["output_path"], sorted_inc_pids)
def save_variable_quantiles(configs):
''' Saves the quantiles of all variables in the LAB/VITAL SIGN tables'''
all_pids = mlhc_io.read_list_from_file(configs["included_pid_path"])
vital_per_variables = mlhc_io.read_list_from_file(\
configs["list_per_variables"])
vital_aper_variables = mlhc_io.read_list_from_file(\
configs["list_aper_variables"])
var_quantiles = {}
print("Lab table...")
df_lab = pd.read_hdf(configs["lab_table_path"], mode='r')
df_lab = df_lab[df_lab.patientunitstayid.isin(all_pids)]
print("Loaded lab table with {} rows".format(df_lab.shape[0]))
all_lab_vars = df_lab.labname.unique()
for lab_var in all_lab_vars:
print("Lab variable: {}".format(lab_var))
df_var = df_lab[df_lab.labname == lab_var]
var_quantiles["lab_" + lab_var] = []
for quantile in np.arange(0.01, 1.00, 0.01):
quant_val = df_var.labresult.quantile(quantile)
var_quantiles["lab_" + lab_var].append(quant_val)
print("List length: {}".format(len(var_quantiles["lab_" + lab_var])))
gc.collect()
print("Vital periodic table...")
found_eof = False
ct = 0
blk_sz = 1000000
df_cts = []
num_records = 0
while not found_eof:
df_ct = pd.read_hdf(configs["vital_per_path"],
mode='r',
start=ct * blk_sz,
stop=(ct + 1) * blk_sz)
if len(df_ct) != blk_sz:
found_eof = True
df_ct = df_ct[df_ct.patientunitstayid.isin(all_pids)]
df_cts.append(df_ct)
num_records += len(df_ct)
ct += 1
print("%d Vital periodic records loaded" % num_records)
df_vital_per = pd.concat(df_cts)
print("Loaded vital periodic table with {} rows".format(\
df_vital_per.shape[0]))
for per_var in vital_per_variables:
print("Periodic variable: {}".format(per_var))
df_col = df_vital_per[per_var]
var_quantiles["periodic_" + per_var] = []
for quantile in np.arange(0.01, 1.00, 0.01):
quant_val = df_col.quantile(quantile)
var_quantiles["periodic_" + per_var].append(quant_val)
print("List length: {}".format(\
len(var_quantiles["periodic_"+per_var])))
gc.collect()
print("Vital aperiodic table...")
df_vital_aper = pd.read_hdf(configs["vital_aper_path"], mode='r')
df_vital_aper = df_vital_aper[df_vital_aper.patientunitstayid.isin(\
all_pids)]
print("Loaded vital aperiodic table with {} rows".format(\
df_vital_aper.shape[0]))
for aper_var in vital_aper_variables:
print("Aperiodic variable: {}".format(aper_var))
df_col = df_vital_aper[aper_var]
var_quantiles["aperiodic_" + aper_var] = []
for quantile in np.arange(0.01, 1.00, 0.01):
quant_val = df_col.quantile(quantile)
var_quantiles["aperiodic_" + aper_var].append(quant_val)
print("List length: {}".format(\
len(var_quantiles["aperiodic_"+aper_var])))
gc.collect()
quantile_fp = open(configs["quantile_path"], mode='w')
json.dump(var_quantiles, quantile_fp)
quantile_fp.close()
def filter_variables(configs):
vital_variables = ["temperature", "sao2", "heartrate", "respiration", "cvp", "etco2", "systemicsystolic", "systemicdiastolic",
"systemicmean", "pasystolic", "padiastolic", "pamean", "st1", "st2", "st3", "icp"]
vital_aper_variables = ["noninvasivesystolic", "noninvasivediastolic", "noninvasivemean", "paop", "cardiacoutput", "cardiacinput", "svr",
"svri", "pvr", "pvri"]
ptable_path = os.path.join(configs["hdf_dir"], "patient.h5")
periodic_path = os.path.join(configs["hdf_dir"], "vitalPeriodic.h5")
aperiodic_path = os.path.join(configs["hdf_dir"], "vitalAperiodic.h5")
lab_path = os.path.join(configs["hdf_dir"], "lab.h5")
input_files = [periodic_path, aperiodic_path, lab_path]
output_files = [configs["output_selected_per_vars"], configs["output_selected_aper_vars"], configs["output_selected_lab_vars"]]
all_pids = list(map(int, mlhc_io.read_list_from_file(configs["included_pid_path"])))
var_obs_count_dict = {}
aper_var_obs_count_dict = {}
lab_var_obs_count_dict = {}
if configs["debug_mode"]:
base_size = 1000
else:
base_size = len(all_pids)
for pidx, pat in enumerate(all_pids):
if (pidx+1) % 1000 == 0:
print("Patient {}/{}".format(pidx+1, len(all_pids)))
if configs["debug_mode"]:
break
df_periodic = pd.read_hdf(periodic_path, mode='r', where="patientunitstayid={}".format(pat))
df_aperiodic = pd.read_hdf(aperiodic_path, mode='r', where="patientunitstayid={}".format(pat))
df_lab = pd.read_hdf(lab_path, mode='r', where="patientunitstayid={}".format(pat))[["labname", "labresult"]].dropna()
unique_lab_vars = list(map(lambda elem: elem.strip(), list(df_lab.labname.unique())))
for var in unique_lab_vars:
if var not in lab_var_obs_count_dict:
lab_var_obs_count_dict[var] = 0
lab_var_obs_count_dict[var] += 1
for var in vital_variables:
df_var = df_periodic[var].dropna()
if df_var.shape[0] > 0:
if var not in var_obs_count_dict:
var_obs_count_dict[var] = 0
var_obs_count_dict[var] += 1
for var in vital_aper_variables:
df_var = df_aperiodic[var].dropna()
if df_var.shape[0] > 0:
if var not in aper_var_obs_count_dict:
aper_var_obs_count_dict[var] = 0
aper_var_obs_count_dict[var] += 1
non_selected_vars = []
per_selected_vars = []
for var in sorted(var_obs_count_dict.keys()):
percentage = var_obs_count_dict[var]/base_size
if percentage >= configs["required_var_freq"]:
per_selected_vars.append(var)
else:
non_selected_vars.append(var)
non_selected_vars = []
aper_selected_vars = []
for var in sorted(aper_var_obs_count_dict.keys()):
percentage = aper_var_obs_count_dict[var]/base_size
if percentage >= configs["required_var_freq"]:
aper_selected_vars.append(var)
else:
non_selected_vars.append(var)
non_selected_vars = []
lab_selected_vars = []
for var in sorted(lab_var_obs_count_dict.keys()):
percentage = lab_var_obs_count_dict[var]/base_size
if percentage >= configs["required_var_freq"]:
lab_selected_vars.append(var)
else:
non_selected_vars.append(var)
mlhc_io.write_list_to_file(configs["output_selected_per_vars"], per_selected_vars)
mlhc_io.write_list_to_file(configs["output_selected_aper_vars"], aper_selected_vars)
mlhc_io.write_list_to_file(configs["output_selected_lab_vars"], lab_selected_vars)
for var in per_selected_vars:
print("Analyzing variable: {}".format(var))
df_var = pd.read_hdf(periodic_path, mode='r', columns=[var, "patientunitstayid"]).dropna()
df_var = df_var[df_var["patientunitstayid"].isin(all_pids)][var]
f, axarr = plt.subplots(2)
lower_cutoff = np.percentile(np.array(df_var), 0.1)
upper_cutoff = np.percentile(np.array(df_var), 99.9)
df_var.plot.hist(bins=100, ax=axarr[0], log=True, range=(lower_cutoff, upper_cutoff))
df_var.plot.box(ax=axarr[1], sym="", vert=False)
plt.clf()
gc.collect()
lower = np.percentile(np.array(df_var), 25)-5*sp_stats.iqr(np.array(df_var))
upper = np.percentile(np.array(df_var), 75)+5*sp_stats.iqr(np.array(df_var))
normal = np.median(np.array(df_var))
if configs["debug_mode"]:
break
for var in aper_selected_vars:
print("Analyzing variable: {}".format(var))
df_var = pd.read_hdf(aperiodic_path, mode='r', columns=[var, "patientunitstayid"]).dropna()
df_var = df_var[df_var["patientunitstayid"].isin(all_pids)][var]
f, axarr = plt.subplots(2)
lower_cutoff = np.percentile(np.array(df_var), 0.1)
upper_cutoff = np.percentile(np.array(df_var), 99.9)
df_var.plot.hist(bins=100, ax=axarr[0], log=True, range=(lower_cutoff, upper_cutoff))
df_var.plot.box(ax=axarr[1], sym="", vert=False)
plt.clf()
gc.collect()
lower = np.percentile(np.array(df_var), 25)-5*sp_stats.iqr(np.array(df_var))
upper = np.percentile(np.array(df_var), 75)+5*sp_stats.iqr(np.array(df_var))
normal = np.median(np.array(df_var))
if configs["debug_mode"]:
break
df_all_vars = pd.read_hdf(lab_path, mode='r', columns=["labname", "labresult", "patientunitstayid"]).dropna()
df_all_vars = df_all_vars[df_all_vars["patientunitstayid"].isin(all_pids)]
for var in lab_selected_vars:
print("Analyzing variable: {}".format(var))
df_var = df_all_vars[df_all_vars["labname"] == var]["labresult"]
f, axarr = plt.subplots(2)
lower_cutoff = np.percentile(np.array(df_var), 0.1)
upper_cutoff = np.percentile(np.array(df_var), 99.9)
df_var.plot.hist(bins=100, ax=axarr[0], range=(lower_cutoff, upper_cutoff), log=True)
df_var.plot.box(ax=axarr[1], sym="", vert=False)
plt.clf()
gc.collect()
lower = np.percentile(np.array(df_var), 25)-5*sp_stats.iqr(np.array(df_var))
upper = np.percentile(np.array(df_var), 75)+5*sp_stats.iqr(np.array(df_var))
normal = np.median(np.array(df_var))
if configs["debug_mode"]:
break
def save_variable_quantiles(configs):
''' Saves the quantiles of all variables in the LAB/VITAL SIGN tables'''
all_pids = mlhc_io.read_list_from_file(configs["included_pid_path"])
vital_per_variables = mlhc_io.read_list_from_file(
configs["list_per_variables"])
vital_aper_variables = mlhc_io.read_list_from_file(
configs["list_aper_variables"])
var_quantiles = {}
print("Lab table...")
df_lab = pd.read_hdf(configs["lab_table_path"], mode='r')
df_lab = df_lab[df_lab.patientunitstayid.isin(all_pids)]
print("Loaded lab table with {} rows".format(df_lab.shape[0]))
all_lab_vars = df_lab.labname.unique()
for lab_var in all_lab_vars:
print("Lab variable: {}".format(lab_var))
df_var = df_lab[df_lab.labname == lab_var]
var_quantiles["lab_" + lab_var] = []
for quantile in np.arange(0.01, 1.00, 0.01):
quant_val = df_var.labresult.quantile(quantile)
var_quantiles["lab_" + lab_var].append(quant_val)
print("List length: {}".format(len(var_quantiles["lab_" + lab_var])))
gc.collect()
print("Vital periodic table...")
df_vital_per = pd.read_hdf(configs["vital_per_path"], mode='r')
df_vital_per = df_vital_per[df_vital_per.patientunitstayid.isin(all_pids)]
print("Loaded vital periodic table with {} rows".format(
df_vital_per.shape[0]))
for per_var in vital_per_variables:
print("Periodic variable: {}".format(per_var))
df_col = df_vital_per[per_var]
var_quantiles["periodic_" + per_var] = []
for quantile in np.arange(0.01, 1.00, 0.01):
quant_val = df_col.quantile(quantile)
var_quantiles["periodic_" + per_var].append(quant_val)
print("List length: {}".format(
len(var_quantiles["periodic_" + per_var])))
gc.collect()
print("Vital aperiodic table...")
df_vital_aper = pd.read_hdf(configs["vital_aper_path"], mode='r')
df_vital_aper = df_vital_aper[df_vital_aper.patientunitstayid.isin(
all_pids)]
print("Loaded vital aperiodic table with {} rows".format(
df_vital_aper.shape[0]))
for aper_var in vital_aper_variables:
print("Aperiodic variable: {}".format(aper_var))
df_col = df_vital_aper[aper_var]
var_quantiles["aperiodic_" + aper_var] = []
for quantile in np.arange(0.01, 1.00, 0.01):
quant_val = df_col.quantile(quantile)
var_quantiles["aperiodic_" + aper_var].append(quant_val)
print("List length: {}".format(
len(var_quantiles["aperiodic_" + aper_var])))
gc.collect()
quantile_fp = open(configs["quantile_path"], mode='w')
json.dump(var_quantiles, quantile_fp)
quantile_fp.close()
