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Fix preprocessing #1

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Fix preprocessing #1

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9ba484d
Fill hadm_id for records in pivoted_vital.csv
edvakf May 9, 2022
53c66eb
Support Python 3
edvakf May 9, 2022
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9 changes: 7 additions & 2 deletions code/preprocessing/generate_sepsis_variables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@


import sys
reload(sys)
sys.setdefaultencoding('utf8')

import os
import sys
Expand Down Expand Up @@ -162,6 +160,12 @@ def merge_pivoted_data(csv_list):
line_dict['hadm_id'] = hadm_id
line_dict['charttime'] = line_dict['starttime']

if fi == 'pivoted_vital.csv':
icu_id = line_dict.get('icustay_id', 'xxx')
if icu_id not in icu_hadm_dict:
continue
hadm_id = str(icu_hadm_dict[icu_id])
line_dict['hadm_id'] = hadm_id

hadm_id = line_dict.get('hadm_id', 'xxx')
if hadm_id not in hadm_time_dict:
Expand Down Expand Up @@ -197,6 +201,7 @@ def merge_pivoted_data(csv_list):
wf.close()

else:
line = line.lower()
if fi == 'pivoted_sofa.csv':
sofa_head = ','.join(['time'] + line.replace('"', '').split(',')[4:])
# "icustay_id","hr","starttime","endtime","pao2fio2ratio_novent","pao2fio2ratio_vent","rate_epinephrine","rate_norepinephrine","rate_dopamine","rate_dobutamine","meanbp_min","gcs_min","urineoutput","bilirubin_max","creatinine_max","platelet_min","respiration","coagulation","liver","cardiovascular","cns","renal","respiration_24hours","coagulation_24hours","liver_24hours","cardiovascular_24hours","cns_24hours","renal_24hours","sofa_24hours"
Expand Down