Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -569,8 +569,8 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             raise ValueError('Please provide a config file')
         
         version = self.mimic_path.split('/')[-1]
-        m = self.mimic_path.split('/')[-2]
-        s='/'+m+'/'+version
+        mimic_folder= self.mimic_path.split('/')[-2]
+        mimic_complete_path='/'+mimic_folder+'/'+version
         
         current_directory = os.getcwd()
         if os.path.exists(os.path.dirname(current_directory)+'/MIMIC-IV-Data-Pipeline-main'):
@@ -578,7 +578,7 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             os.chdir(dir)
         else:
             #move to parent directory of mimic data
-            dir = self.mimic_path.replace(s,'')
+            dir = self.mimic_path.replace(mimic_complete_path,'')
             if dir[-1]!='/':
                 dir=dir+'/'
             elif dir=='':
@@ -586,7 +586,7 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             parent_dir = os.path.dirname(self.mimic_path)
             os.chdir(parent_dir)
 
-        #clone git repo if doesnt exists
+        #####################clone git repo if doesnt exists
         repo_url='https://github.com/healthylaife/MIMIC-IV-Data-Pipeline'
         if os.path.exists('MIMIC-IV-Data-Pipeline-main'):
             path_bench = './MIMIC-IV-Data-Pipeline-main'
@@ -599,6 +599,7 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         os.chdir(path_bench)
         self.mimic_path = './mimic-iv/'+version
 
+        ####################Get configurations param
         #download config file if not custom
         if self.config_path[0:4] == 'http':
             c = self.config_path.split('/')[-1]
@@ -606,16 +607,18 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         else :
             file_path = self.config_path
 
-        #create config folder
         if not os.path.exists('./config'):
             os.makedirs('config')
         #save config file in config folder
         conf='./config/'+file_path.split('/')[-1]
-
         if not os.path.exists(conf):
             shutil.move(file_path,'./config')
+        with open(conf) as f:
+            config = yaml.safe_load(f)
+        feat_cond, feat_chart, feat_proc, feat_meds, feat_out = config['diagnosis'], config['chart'], config['proc'],  config['meds'], config['output']
 
-        #downloads modules from hub
+
+        #####################downloads modules from hub
         if not os.path.exists('./model/data_generation_icu_modify.py'):
             file_path, head = urlretrieve(_DATA_GEN, "data_generation_icu_modify.py")
             shutil.move(file_path, './model')
@@ -624,27 +627,14 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             file_path, head = urlretrieve(_DAY_INT, "day_intervals_cohort_v22.py")
             shutil.move(file_path, './preprocessing/day_intervals_preproc')
             
-        #file_path, head = urlretrieve(_COHORT, "cohort.py")
-        #if not os.path.exists('cohort.py'):
-        #    shutil.move(file_path, './')
-            
         data_dir = "./data/dict/"+self.config.name.replace(" ","_")+"/dataDic"
         sys.path.append(path_bench)
         config = self.config_path.split('/')[-1]
 
-        script = 'python cohort.py '+ self.config.name.replace(" ","_") +" "+ self.mimic_path+ " "+ " "+config
-        
-        #####################################CHANGE##########
-        #if not os.path.exists(data_dir) :
-        #os.system(script)  
+        #####################create task cohort
         task_cohort(self.config.name.replace(" ","_"),self.mimic_path,config)
-        #####################################CHANGE##########
-        
-        config_path='./config/'+config
-        with open(config_path) as f:
-            config = yaml.safe_load(f)
-        feat_cond, feat_chart, feat_proc, feat_meds, feat_out = config['diagnosis'], config['chart'], config['proc'],  config['meds'], config['output']
 
+        #####################Split data into train, test and val
         with open(data_dir, 'rb') as fp:
             dataDic = pickle.load(fp)
         data = pd.DataFrame.from_dict(dataDic)
@@ -669,7 +659,6 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         with open(test_path, 'wb') as f:
             pickle.dump(test_dic, f)
 
-        
         return feat_cond, feat_chart, feat_proc, feat_meds, feat_out, dict_dir
   
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