From 9ba484dd4e58dccbcd74d431c1f4b81b28440b87 Mon Sep 17 00:00:00 2001 From: Atsushi Takayama Date: Mon, 9 May 2022 12:11:45 +0900 Subject: [PATCH 1/2] Fill hadm_id for records in pivoted_vital.csv --- code/preprocessing/generate_sepsis_variables.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/code/preprocessing/generate_sepsis_variables.py b/code/preprocessing/generate_sepsis_variables.py index 633146b..ec82e24 100644 --- a/code/preprocessing/generate_sepsis_variables.py +++ b/code/preprocessing/generate_sepsis_variables.py @@ -162,6 +162,12 @@ 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: @@ -197,6 +203,7 @@ 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" From 53c66eb9798d0204f874f7ba294f0e1f8c366c40 Mon Sep 17 00:00:00 2001 From: Atsushi Takayama Date: Mon, 9 May 2022 12:33:29 +0900 Subject: [PATCH 2/2] Support Python 3 --- code/preprocessing/generate_sepsis_variables.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/code/preprocessing/generate_sepsis_variables.py b/code/preprocessing/generate_sepsis_variables.py index ec82e24..8c08821 100644 --- a/code/preprocessing/generate_sepsis_variables.py +++ b/code/preprocessing/generate_sepsis_variables.py @@ -4,8 +4,6 @@ import sys -reload(sys) -sys.setdefaultencoding('utf8') import os import sys