file_tr

gistfile1.txt

import pickle
import psycopg2 as py

# Replace this with your mimic iii database details
conn = py.connect(
    "dbname = 'mimic' user = 'root' host = 'localhost' port='5432' password = 'postgres'")

cur = conn.cursor()
cur.execute("""select hadm_id from admissions""")
list_adm_id = cur.fetchall()

cur.execute("select hadm_id, admission_type, trunc(extract(epoch from " +
            "dischtime- admittime)/3600), hospital_expire_flag from admissions")
length_of_stay = cur.fetchall()
pickle.dump(length_of_stay, open('adm_type_los_mortality.p', 'wb'))

# SpO2 - 646, 220277
# HR - 211, 220045
# RR - 618, 615, 220210, 224690
# SBP - 51,442,455,6701,220179,220050
# DBP - 8368,8440,8441,8555,220180,220051
# EtCO2 - 1817, 228640
# Temp(F) - 223761,678
# Temp(C) - 223762,676
# TGCS - 198, 226755, 227013
# CRR - 3348
# Urine Output - 43647, 43053, 43171, 43173, 43333, 43347,
# 43348, 43355, 43365, 43373, 43374, 43379, 43380, 43431,
# 43519, 43522, 43537, 43576, 43583, 43589, 43638, 43654,
# 43811, 43812, 43856, 44706, 45304, 227519,
# FiO2 - 2981, 3420, 3422, 223835,
# Glucose - 807,811,1529,3745,3744,225664,220621,226537
# pH - 780, 860, 1126, 1673, 3839, 4202, 4753, 6003, 220274, 220734, 223830, 228243,

data = []
vitals = []
ids = []
# print("Sp02")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN "
            + str(ids) + " and (itemid =" + str(646) +
            "or itemid =" + str(220277) + ")order by charttime")
vitals.append(cur.fetchall())

# Heart Rate
# print("HR")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(211) +
            "or itemid =" + str(220045) + ")order by charttime")
vitals.append(cur.fetchall())

# Respiratory Rate
# print("RR")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(618) +
            "or itemid =" + str(615) + "or itemid =" + str(220210) +
            "or itemid =" + str(224690) + ")order by charttime")
vitals.append(cur.fetchall())

# Systolic Blood Pressure
# print("SBP")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(51) +
            "or itemid =" + str(442) + "or itemid =" + str(455) +
            "or itemid =" + str(6701) + "or itemid =" + str(220179) +
            "or itemid =" + str(220050) + ")order by charttime")
vitals.append(cur.fetchall())

# Diastolic Blood Pressure
# print("DBP")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(8368) +
            "or itemid =" + str(8440) + "or itemid =" + str(8441) +
            "or itemid =" + str(8555) + "or itemid =" + str(220180) +
            "or itemid =" + str(220051) + ")order by charttime")
vitals.append(cur.fetchall())

# End-tidal carbon dioxide
# print("EtC02")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids)  + " and (itemid =" + str(1817) +
            "or itemid =" + str(228640) + ")order by charttime")
vitals.append(cur.fetchall())

# Temperature
# print("Temp")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(678) +
            "or itemid =" + str(223761) + ")order by charttime")
vitals.append(cur.fetchall())
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(676) +
            "or itemid =" + str(223762) + ")order by charttime")
vitals.append(cur.fetchall())

# Total Glasgow coma score
# print("TGCS")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN "
            + str(ids) + " and (itemid =" + str(198) +
            "or itemid =" + str(226755) + "or itemid =" + str(227013)
            + ")order by charttime")
vitals.append(cur.fetchall())

# Peripheral capillary refill rate
# print("CRR")
cur.execute("select charttime, value from chartevents where hadm_id IN"
            + str(ids)  + " and itemid =" + str(3348) +
            "order by charttime")
vitals.append(cur.fetchall())
cur.execute("select charttime, value from chartevents where hadm_id IN"
            + str(list_adm_id[id][0]) + " and (itemid =" + str(115) +
            "or itemid = 223951) order by charttime")
vitals.append(cur.fetchall())
cur.execute("select charttime, value from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(8377) +
            "or itemid = 224308) order by charttime")
vitals.append(cur.fetchall())

# Urine output 43647, 43053, 43171, 43173, 43333, 43347, 43348, 43355, 43365, 43373, 43374, 43379
# print("UO")
cur.execute("select charttime, VALUE from outputevents where hadm_id IN "
            + str(ids) + " and ( itemid = 40405 or itemid =" +
            " 40428 or itemid = 41857 or itemid = 42001 or itemid = 42362 or itemid =" +
            " 42676 or itemid = 43171 or itemid = 43173 or itemid = 42042 or itemid =" +
            " 42068 or itemid = 42111 or itemid = 42119 or itemid = 40715 or itemid =" +
            " 40056 or itemid = 40061 or itemid = 40085 or itemid = 40094 or itemid =" +
            " 40096 or itemid = 43897 or itemid = 43931 or itemid = 43966 or itemid =" +
            " 44080 or itemid = 44103 or itemid = 44132 or itemid = 44237 or itemid =" +
            " 43348 or itemid =" +
            " 43355 or itemid = 43365 or itemid = 43372 or itemid = 43373 or itemid =" +
            " 43374 or itemid = 43379 or itemid = 43380 or itemid = 43431 or itemid =" +
            " 43462 or itemid = 43522 or itemid = 44706 or itemid = 44911 or itemid =" +
            " 44925 or itemid = 42810 or itemid = 42859 or itemid = 43093 or itemid =" +
            " 44325 or itemid = 44506 or itemid = 43856 or itemid = 45304 or itemid =" +
            " 46532 or itemid = 46578 or itemid = 46658 or itemid = 46748 or itemid =" +
            " 40651 or itemid = 40055 or itemid = 40057 or itemid = 40065 or itemid =" +
            " 40069 or itemid = 44752 or itemid = 44824 or itemid = 44837 or itemid =" +
            " 43576 or itemid = 43589 or itemid = 43633 or itemid = 43811 or itemid =" +
            " 43812 or itemid = 46177 or itemid = 46727 or itemid = 46804 or itemid =" +
            " 43987 or itemid = 44051 or itemid = 44253 or itemid = 44278 or itemid =" +
            " 46180 or itemid = 45804 or itemid = 45841 or itemid = 45927 or itemid =" +
            " 42592 or itemid = 42666 or itemid = 42765 or itemid = 42892 or itemid =" +
            " 43053 or itemid = 43057 or itemid = 42130 or itemid = 41922 or itemid =" +
            " 40473 or itemid = 43333 or itemid = 43347 or itemid = 44684 or itemid =" +
            " 44834 or itemid = 43638 or itemid = 43654 or itemid = 43519 or itemid =" +
            " 43537 or itemid = 42366 or itemid = 45991 or itemid = 43583 or itemid =" +
            " 43647) order by charttime ")
vitals.append(cur.fetchall())

# Fraction inspired oxygen
# print("Fi02")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(2981) +
            "or itemid =" + str(3420) + "or itemid =" + str(3422) +
            "or itemid =" + str(223835) + ")order by charttime")
vitals.append(cur.fetchall())

# Glucose 807,811,1529,3745,3744,225664,220621,226537
# print("Glucose")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(807) +
            "or itemid =" + str(811) + "or itemid =" + str(1529) +
            "or itemid =" + str(3745) + "or itemid =" + str(3744) +
            "or itemid =" + str(225664) + "or itemid =" + str(220621) +
            "or itemid =" + str(226537) + ")order by charttime")
vitals.append(cur.fetchall())

# pH 780, 860, 1126, 1673, 3839, 4202, 4753, 6003, 220274, 220734, 223830, 228243,
# print("pH")
cur.execute("select charttime, valuenum from chartevents where hadm_id IN"
            + str(ids) + " and (itemid =" + str(780) +
            "or itemid =" + str(860) + "or itemid =" + str(1126) +
            "or itemid =" + str(1673) + "or itemid =" + str(3839) +
            "or itemid =" + str(4202) + "or itemid =" + str(4753) +
            "or itemid =" + str(6003) + "and itemid =" + str(220274) +
            "or itemid =" + str(220734) + "or itemid =" + str(223830) +
            "or itemid =" + str(228243) + ") order by charttime")
vitals.append(cur.fetchall())
data.append(vitals)
pickle.dump(data, open('vitals_records.p', 'wb'))