Update task_cohort.py
Browse files- task_cohort.py +121 -1
task_cohort.py
CHANGED
@@ -2,11 +2,131 @@ import os
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import sys
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import yaml
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import time
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from .check_config import check_config_file
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from .day_intervals_cohort_v22 import *
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from .data_generation_icu_modify import *
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from .data_generation_modify import *
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def task_cohort(task, mimic_path, config_path):
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sys.path.append('./preprocessing/day_intervals_preproc')
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sys.path.append('./utils')
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import sys
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import yaml
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import time
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from .day_intervals_cohort_v22 import *
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from .data_generation_icu_modify import *
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from .data_generation_modify import *
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import yaml
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import sys
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def check_config_file(task,config_file):
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with open(config_file) as f:
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config = yaml.safe_load(f)
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if task=='Phenotype':
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disease_label = config['disease_label']
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else :
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disease_label = ""
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time = config['timePrediction']
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label = task
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timeW = config['timeWindow']
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include=int(timeW.split()[1])
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bucket = config['timebucket']
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radimp = config['radimp']
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predW = config['predW']
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disease_filter = config['disease_filter']
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icu_no_icu = config['icu_no_icu']
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groupingDiag = config['groupingDiag']
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assert( icu_no_icu in ['ICU','Non-ICU' ], "Chossen data should be one of the following: ICU, Non-ICU")
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data_icu = icu_no_icu=='ICU'
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if data_icu:
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chart_flag = config['chart']
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output_flag = config['output']
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select_chart = config['select_chart']
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lab_flag = False
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select_lab = False
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else:
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lab_flag =config['lab']
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select_lab = config['select_lab']
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groupingMed = config['groupingMed']
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groupingProc = config['groupingProc']
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chart_flag = False
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output_flag = False
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select_chart = False
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diag_flag= config['diagnosis']
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proc_flag = config['proc']
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meds_flag = config['meds']
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select_diag= config['select_diag']
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select_med= config['select_med']
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select_proc= config['select_proc']
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select_out = config['select_out']
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outlier_removal=config['outlier_removal']
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thresh=config['outlier']
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left_thresh=config['left_outlier']
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if data_icu:
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assert (isinstance(select_diag,bool) and isinstance(select_med,bool) and isinstance(select_proc,bool) and isinstance(select_out,bool) and isinstance(select_chart,bool), " select_diag, select_chart, select_med, select_proc, select_out should be boolean")
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assert (isinstance(chart_flag,bool) and isinstance(output_flag,bool) and isinstance(diag_flag,bool) and isinstance(proc_flag,bool) and isinstance(meds_flag,bool), "chart_flag, output_flag, diag_flag, proc_flag, meds_flag should be boolean")
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else:
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assert (isinstance(select_diag,bool) and isinstance(select_med,bool) and isinstance(select_proc,bool) and isinstance(select_out,bool) and isinstance(select_lab,bool), " select_diag, select_lab, select_med, select_proc, select_out should be boolean")
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assert (isinstance(lab_flag,bool) and isinstance(diag_flag,bool) and isinstance(proc_flag,bool) and isinstance(meds_flag,bool), "lab_flag, diag_flag, proc_flag, meds_flag should be boolean")
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if task=='Phenotype':
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if disease_label=='Heart Failure':
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label='Readmission'
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time=30
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disease_label='I50'
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elif disease_label=='CAD':
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label='Readmission'
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time=30
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disease_label='I25'
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elif disease_label=='CKD':
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label='Readmission'
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time=30
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disease_label='N18'
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elif disease_label=='COPD':
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label='Readmission'
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time=30
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disease_label='J44'
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else :
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raise ValueError('Disease label not correct provide one in the list: Heart Failure, CAD, CKD, COPD')
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predW=0
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assert (timeW[0]=='Last' and include<=72 and include>=24, "Time window should be between Last 24 and Last 72")
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elif task=='Mortality':
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time=0
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label= 'Mortality'
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assert (predW<=8 and predW>=2, "Prediction window should be between 2 and 8")
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assert (timeW[0]=='Fisrt' and include<=72 and include>=24, "Time window should be between First 24 and First 72")
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elif task=='Length_of_Stay':
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label= 'Length of Stay'
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assert (timeW[0]=='Fisrt' and include<=72 and include>=24, "Time window should be between Fisrt 24 and Fisrt 72")
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assert (time<=10 and time>=1, "Length of stay should be between 1 and 10")
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predW=0
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elif task=='Readmission':
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label= 'Readmission'
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assert (timeW[0]=='Last' and include<=72 and include>=24, "Time window should be between Last 24 and Last 72")
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assert (time<=150 and time>=10 and time%10==0, "Readmission window should be between 10 and 150 with a step of 10")
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predW=0
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else:
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raise ValueError('Task not correct')
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assert( disease_filter in ['Heart Failure','COPD','CKD','CAD',""], "Disease filter should be one of the following: Heart Failure, COPD, CKD, CAD or empty")
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assert( groupingDiag in ['Convert ICD-9 to ICD-10 and group ICD-10 codes','Keep both ICD-9 and ICD-10 codes','Convert ICD-9 to ICD-10 codes'], "Grouping ICD should be one of the following: Convert ICD-9 to ICD-10 and group ICD-10 codes, Keep both ICD-9 and ICD-10 codes, Convert ICD-9 to ICD-10 codes")
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assert (bucket<=6 and bucket>=1 and isinstance(bucket, int), "Time bucket should be between 1 and 6 and an integer")
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assert (radimp in ['No Imputation', 'forward fill and mean','forward fill and median'], "imputation should be one of the following: No Imputation, forward fill and mean, forward fill and median")
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if chart_flag:
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assert (left_thresh>=0 and left_thresh<=10 and isinstance(left_thresh, int), "Left outlier threshold should be between 0 and 10 and an integer")
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assert (thresh>=90 and thresh<=99 and isinstance(thresh, int), "Outlier threshold should be between 90 and 99 and an integer")
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assert (outlier_removal in ['No outlier detection','Impute Outlier (default:98)','Remove outliers (default:98)'], "Outlier removal should be one of the following: No outlier detection, Impute Outlier (default:98), Remove outliers (default:98)")
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if lab_flag:
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assert (left_thresh>=0 and left_thresh<=10 and isinstance(left_thresh, int), "Left outlier threshold should be between 0 and 10 and an integer")
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assert (thresh>=90 and thresh<=99 and isinstance(thresh, int), "Outlier threshold should be between 90 and 99 and an integer")
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assert (outlier_removal in ['No outlier detection','Impute Outlier (default:98)','Remove outliers (default:98)'], "Outlier removal should be one of the following: No outlier detection, Impute Outlier (default:98), Remove outliers (default:98)")
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assert (groupingProc in ['ICD-9 and ICD-10','ICD-10'], "Grouping procedure should be one of the following: ICD-9 and ICD-10, ICD-10")
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assert (groupingMed in ['Yes','No'], "Do you want to group Medication codes to use Non propietary names? : Grouping medication should be one of the following: Yes, No")
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return label, time, disease_label, predW
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def task_cohort(task, mimic_path, config_path):
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sys.path.append('./preprocessing/day_intervals_preproc')
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sys.path.append('./utils')
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