Update task_cohort.py

task_cohort.py

@@ -2,11 +2,131 @@ import os
 import sys
 import yaml
 import time
-from .check_config import check_config_file
 from .day_intervals_cohort_v22 import *
 from .data_generation_icu_modify import *
 from .data_generation_modify import *
+import yaml
+import sys
+
+def check_config_file(task,config_file):
+    with open(config_file) as f:
+        config = yaml.safe_load(f)
 
+    if task=='Phenotype':
+        disease_label =  config['disease_label']
+    else :
+        disease_label = ""
+    time = config['timePrediction']
+    label = task
+    timeW = config['timeWindow']
+    include=int(timeW.split()[1])
+    bucket = config['timebucket']
+    radimp = config['radimp']
+    predW = config['predW']
+    disease_filter = config['disease_filter']
+    icu_no_icu = config['icu_no_icu']
+    groupingDiag = config['groupingDiag']
+
+    assert( icu_no_icu in ['ICU','Non-ICU' ], "Chossen data should be one of the following: ICU, Non-ICU")
+    data_icu = icu_no_icu=='ICU'
+    
+    if data_icu:
+        chart_flag = config['chart']
+        output_flag = config['output']
+        select_chart = config['select_chart']
+        lab_flag = False
+        select_lab = False
+    else:
+        lab_flag =config['lab']
+        select_lab = config['select_lab']
+        groupingMed = config['groupingMed']
+        groupingProc = config['groupingProc']
+        chart_flag = False
+        output_flag = False
+        select_chart = False
+
+
+    diag_flag= config['diagnosis']
+    proc_flag = config['proc']
+    meds_flag = config['meds']
+    select_diag= config['select_diag']
+    select_med= config['select_med']
+    select_proc= config['select_proc']
+    select_out = config['select_out']
+
+    outlier_removal=config['outlier_removal']
+    thresh=config['outlier']
+    left_thresh=config['left_outlier']
+    
+    if data_icu:
+        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")
+        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")
+    
+    else:
+        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")
+        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")
+    
+    if task=='Phenotype':
+        if disease_label=='Heart Failure':
+            label='Readmission'
+            time=30
+            disease_label='I50'
+        elif disease_label=='CAD':
+            label='Readmission'
+            time=30
+            disease_label='I25'
+        elif disease_label=='CKD':
+            label='Readmission'
+            time=30
+            disease_label='N18'
+        elif disease_label=='COPD':
+            label='Readmission'
+            time=30
+            disease_label='J44'
+        else :
+            raise ValueError('Disease label not correct provide one in the list: Heart Failure, CAD, CKD, COPD')
+        predW=0
+        assert (timeW[0]=='Last' and include<=72 and include>=24, "Time window should be between Last 24 and Last 72")
+    
+    elif task=='Mortality':
+        time=0
+        label= 'Mortality'
+        assert (predW<=8 and predW>=2, "Prediction window should be between 2 and 8")
+        assert (timeW[0]=='Fisrt' and include<=72 and include>=24, "Time window should be between First 24 and First 72")
+    
+    elif task=='Length_of_Stay':
+        label= 'Length of Stay'
+        assert (timeW[0]=='Fisrt' and include<=72 and include>=24, "Time window should be between Fisrt 24 and Fisrt 72")
+        assert (time<=10 and time>=1, "Length of stay should be between 1 and 10")
+        predW=0
+    
+    elif task=='Readmission':
+        label= 'Readmission'
+        assert (timeW[0]=='Last' and include<=72 and include>=24, "Time window should be between Last 24 and Last 72")
+        assert (time<=150 and time>=10 and time%10==0, "Readmission window should be between 10 and 150 with a step of 10")
+        predW=0
+    
+    else:
+        raise ValueError('Task not correct')
+    
+    assert( disease_filter in ['Heart Failure','COPD','CKD','CAD',""], "Disease filter should be one of the following: Heart Failure, COPD, CKD, CAD or empty")
+    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")
+    assert (bucket<=6 and bucket>=1 and isinstance(bucket, int), "Time bucket should be between 1 and 6 and an integer")
+    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")
+    if chart_flag:
+        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")
+        assert (thresh>=90 and thresh<=99 and isinstance(thresh, int), "Outlier threshold should be between 90 and 99 and an integer")
+        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)")
+    if lab_flag:
+        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")
+        assert (thresh>=90 and thresh<=99 and isinstance(thresh, int), "Outlier threshold should be between 90 and 99 and an integer")
+        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)")
+        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")
+        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")
+
+    return label, time, disease_label, predW
+
+    
 def task_cohort(task, mimic_path, config_path):
     sys.path.append('./preprocessing/day_intervals_preproc')
     sys.path.append('./utils')