added data_shuffling flag and debugged run

run.py

@@ -360,35 +360,34 @@ if __name__ == '__main__':
             data_parameters['data_directory'], data_parameters['train_percentage'], data_parameters['validation_percentage'])
         update_shuffling_flag('settings.ini')
         # TODO: This might also be a very good point to add cross-validation later
-    else:
 
-        if arguments.mode == 'train':
-            train(data_parameters, training_parameters,
-                  network_parameters, misc_parameters)
-
-        # NOTE: THE EVAL FUNCTIONS HAVE NOT YET BEEN DEBUGGED (16/04/20)
-
-        elif arguments.mode == 'evaluate-score':
-            evaluate_score(training_parameters,
-                           network_parameters, misc_parameters, evaluation_parameters)
-        elif arguments.mode == 'evaluate-mapping':
-            logging.basicConfig(filename='evaluate-mapping-error.log')
-            if arguments.settings_path is not None:
-                settings_evaluation = Settings(arguments.settings_path)
-            else:
-                settings_evaluation = Settings('settings_evaluation.ini')
-            mapping_evaluation_parameters = settings_evaluation['MAPPING']
-            evaluate_mapping(mapping_evaluation_parameters)
-        elif arguments.mode == 'clear-experiments':
-            shutil.rmtree(os.path.join(
-                misc_parameters['experiments_directory'], training_parameters['experiment_name']))
-            shutil.rmtree(os.path.join(
-                misc_parameters['logs_directory'], training_parameters['experiment_name']))
-            print('Cleared the current experiments and logs directory successfully!')
-        elif arguments.mode == 'clear-everything':
-            delete_files(misc_parameters['experiments_directory'])
-            delete_files(misc_parameters['logs_directory'])
-            print('Cleared the current experiments and logs directory successfully!')
+    if arguments.mode == 'train':
+        train(data_parameters, training_parameters,
+                network_parameters, misc_parameters)
+
+    # NOTE: THE EVAL FUNCTIONS HAVE NOT YET BEEN DEBUGGED (16/04/20)
+
+    elif arguments.mode == 'evaluate-score':
+        evaluate_score(training_parameters,
+                        network_parameters, misc_parameters, evaluation_parameters)
+    elif arguments.mode == 'evaluate-mapping':
+        logging.basicConfig(filename='evaluate-mapping-error.log')
+        if arguments.settings_path is not None:
+            settings_evaluation = Settings(arguments.settings_path)
         else:
-            raise ValueError(
-                'Invalid mode value! Only supports: train, evaluate-score, evaluate-mapping, clear-experiments and clear-everything')
+            settings_evaluation = Settings('settings_evaluation.ini')
+        mapping_evaluation_parameters = settings_evaluation['MAPPING']
+        evaluate_mapping(mapping_evaluation_parameters)
+    elif arguments.mode == 'clear-experiments':
+        shutil.rmtree(os.path.join(
+            misc_parameters['experiments_directory'], training_parameters['experiment_name']))
+        shutil.rmtree(os.path.join(
+            misc_parameters['logs_directory'], training_parameters['experiment_name']))
+        print('Cleared the current experiments and logs directory successfully!')
+    elif arguments.mode == 'clear-everything':
+        delete_files(misc_parameters['experiments_directory'])
+        delete_files(misc_parameters['logs_directory'])
+        print('Cleared the current experiments and logs directory successfully!')
+    else:
+        raise ValueError(
+            'Invalid mode value! Only supports: train, evaluate-score, evaluate-mapping, clear-experiments and clear-everything')

settings.ini

 [DATA]
 data_directory = "../well/win-biobank/projects/imaging/data/data3/subjectsAll/"
-data_split_flag = False
+data_split_flag = True
 train_percentage = 90
 validation_percentage = 5
 train_list = "train.txt"