Update Mimic4Dataset.py

Mimic4Dataset.py

@@ -136,36 +136,24 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
         if self.config.name == 'Length of Stay' and self.config_path is None : self.config_path = _CONFIG_URLS['los'] 
         if self.config.name == 'Mortality' and self.config_path is None : self.config_path = _CONFIG_URLS['mortality']
 
+        #move to parent directory of mimic data
         version = self.mimic_path.split('/')[-1]
         m = self.mimic_path.split('/')[-2]
         s='/'+m+'/'+version
         dir = self.mimic_path.replace(s,'')
-        print('3 : '+os.getcwd())
         os.chdir(dir)
-        print('0 : '+os.getcwd())
 
 
         #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 = os.path.abspath('MIMIC-IV-Data-Pipeline-main')
+            path_bench = dir+'MIMIC-IV-Data-Pipeline-main'
         else:
             repodir = os.getcwd()
             path_bench = repodir+'/MIMIC-IV-Data-Pipeline-main'
             subprocess.run(["git", "clone", repo_url, path_bench])
         os.chdir(path_bench)
         print('1 : '+ os.getcwd())
-        
-        
-        #move data to mimic-iv folder
-        #if not os.path.exists(path_bench+'/mimic-iv'):
-            #os.makedirs(path_bench+'/mimic-iv')
-            #os.chdir(self.mimic_path.replace(version,''))
-            #print('2 : '+os.getcwd())
-            #shutil.move('/'+version, path_bench+'/mimic-iv/'+version)
-        self.mimic_path = './'+s
-        #os.chdir(path_bench)
-        print('3 : '+os.getcwd())
 
         #download config file if not custom
         if self.config_path[0:4] == 'http':
@@ -175,34 +163,32 @@ class Mimic4Dataset(datasets.GeneratorBasedBuilder):
             file_path = self.config_path
 
         #create config folder
-        if not os.path.exists(path_bench+'/config'):
-            os.makedirs(path_bench+'/config')
+        if not os.path.exists('./config'):
+            os.makedirs('config')
         #save config file in config folder
-        conf=path_bench+'/config/'+file_path.split('/')[-1]
+        conf='./config/'+file_path.split('/')[-1]
         if not os.path.exists(conf):
-            shutil.move(file_path, path_bench+'/config')
+            shutil.move(file_path,'./config')
 
         #downloads modules from hub
-        if not os.path.exists(path_bench+'/model/data_generation_icu_modify.py'):
+        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, path_bench+'/model')
+            shutil.move(file_path, './model')
 
-        if not os.path.exists(path_bench+'/preprocessing/day_intervals_preproc/day_intervals_cohort_v22.py'):
+        if not os.path.exists('./preprocessing/day_intervals_preproc/day_intervals_cohort_v22.py'):
             file_path, head = urlretrieve(_DAY_INT, "day_intervals_cohort_v22.py")
-            shutil.move(file_path, path_bench+'/preprocessing/day_intervals_preproc')
+            shutil.move(file_path, './preprocessing/day_intervals_preproc')
         
-        if not os.path.exists(path_bench+'/cohort.py'):
+        if not os.path.exists('./cohort.py'):
             file_path, head = urlretrieve(_COHORT, "cohort.py")
-            shutil.move(file_path, path_bench)
+            shutil.move(file_path, './')
         
-        data_dir = path_bench + "/data/dataDic"
+        data_dir = "./data/dataDic"
         sys.path.append(path_bench)
         config = self.config_path.split('/')[-1]
         script = 'python cohort.py '+ self.config.name +" "+ self.mimic_path+ " "+path_bench+ " "+config
         os.system(script)
-        root = path_bench.replace('/MIMIC-IV-Data-Pipeline-main',"")
-        os.chdir(root)
-        print(os.getcwd())
+        print('last pos'+os.getcwd())
         return [
             datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": data_dir}),
         ]