Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -39,6 +39,97 @@ _CONFIG_URLS = {'los' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/re
                 'readmission' : 'https://huggingface.co/datasets/thbndi/Mimic4Dataset/resolve/main/config/readmission.config'
         }
 
+
+
+def check_config(task,config_file):
+    with open(config_file) as f:
+        config = yaml.safe_load(f)
+
+    disease_label =  config['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']
+    groupingICD = config['groupingICD']
+
+    chart_flag = config['chart']
+    output_flag = config['output']
+    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']
+    select_chart = config['select_chart']
+
+    outlier_removal=config['outlier_removal']
+    thresh=config['outlier']
+    left_thresh=config['left_outlier']
+    
+    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")
+    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
+        disease_label=""
+        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':
+        disease_label=""
+        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':
+        disease_label=""
+        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( icu_no_icu in ['ICU'], "Dataset currently only supports ICU data")
+    assert( groupingICD 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)")
+
+    return label, time, disease_label, predW
+
 def create_vocab(file,task):
     with open ('./data/dict/'+task+'/'+file, 'rb') as fp:
         condVocab = pickle.load(fp)
@@ -392,14 +483,11 @@ def task_cohort(task, mimic_path, config_path):
     version = mimic_path.split('/')[-1][0]
     start = time.time()
     #----------------------------------------------config----------------------------------------------------
-    disease_label =  config['disease_label']
-    tim = config['time']
-    label = config['label']
-    timeW = config['timeW']
+    label, tim, disease_label, predW = check_config(task,config)
+    timeW = config['timeWindow']
     include=int(timeW.split()[1])
-    bucket = config['bucket']
+    bucket = config['timebucket']
     radimp = config['radimp']
-    predW = config['predW']
     diag_flag = config['diagnosis']
     out_flag = config['output']
     chart_flag = config['chart']
@@ -408,6 +496,14 @@ def task_cohort(task, mimic_path, config_path):
     disease_filter = config['disease_filter']
     icu_no_icu = config['icu_no_icu']
     groupingICD = config['groupingICD']
+
+    select_diag= config['select_diag']
+    select_med= config['select_med']
+    select_proc=  config['select_proc']
+    #select_lab= config['select_lab']
+    select_out= config['select_out']
+    select_chart=  config['select_chart']
+
     # -------------------------------------------------------------------------------------------------------------
 
     data_icu=icu_no_icu=="ICU"
@@ -437,9 +533,6 @@ def task_cohort(task, mimic_path, config_path):
     if data_icu :
         feature_selection_icu.feature_icu(cohort_output, version_path,diag_flag,out_flag,chart_flag,proc_flag,med_flag)
     #----------------------------------------------GROUPING-------------------------------------------------------
-    group_diag=False
-    group_med=False
-    group_proc=False
     if data_icu:
         if diag_flag:
             group_diag=groupingICD
@@ -449,13 +542,6 @@ def task_cohort(task, mimic_path, config_path):
         feature_selection_icu.generate_summary_icu(diag_flag,proc_flag,med_flag,out_flag,chart_flag)
     #----------------------------------------------FEATURE SELECTION---------------------------------------------
 
-    select_diag= config['select_diag']
-    select_med= config['select_med']
-    select_proc=  config['select_proc']
-    #select_lab= config['select_lab']
-    select_out= config['select_out']
-    select_chart=  config['select_chart']
-
     feature_selection_icu.features_selection_icu(cohort_output, diag_flag,proc_flag,med_flag,out_flag, chart_flag,select_diag,select_med,select_proc,select_out,select_chart)
     #---------------------------------------CLEANING OF FEATURES-----------------------------------------------
     thresh=0