From 8e1146b8e1bea3ca067008d53b2d9ea01d19ecb6 Mon Sep 17 00:00:00 2001
From: Ramon Correa <rlcorre@emory.edu>
Date: Mon, 5 Apr 2021 17:00:46 -0400
Subject: [PATCH] added call to process join and close to make sure pool is
 terminated.

modified one call of pool in line 348 to use core_count
---
 modules/png-extraction/ImageExtractor.py | 26 ++++++++++++------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/png-extraction/ImageExtractor.py b/modules/png-extraction/ImageExtractor.py
index 5e22212..8d33b1e 100644
--- a/modules/png-extraction/ImageExtractor.py
+++ b/modules/png-extraction/ImageExtractor.py
@@ -1,26 +1,24 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
-import numpy as np
-import pandas as pd
-import pydicom as dicom 
-import png, os, glob
-import PIL as pil
-from pprint import pprint
-import hashlib
+import os
+import glob 
 from shutil import copyfile
-import logging
-from multiprocessing import Pool
+import hashlib
 import json
 import sys
 import subprocess
+import logging
+from multiprocessing import Pool
 import pdb
+import time
 import pickle
+import numpy as np
+import pandas as pd
+import pydicom as dicom 
 #pydicom imports needed to handle data errrors
 from pydicom import config
 from pydicom import datadict
 from pydicom import values
-from subprocess import Popen
-import time
 
 with open('config.json', 'r') as f:
     niffler = json.load(f)
@@ -243,7 +241,7 @@ def fix_mismatch_callback(raw_elem, **kwargs):
                 pass
             else:
                 raw_elem = raw_elem._replace(VR=vr)
-                break  # I want to exit immediately after change is applied
+                break
     return raw_elem
 
 
@@ -347,7 +345,7 @@ def fix_mismatch(with_VRs=['PN', 'DS', 'IS']):
         filedata=data
         total = len(chunk)
         stamp = time.time()
-        p = Pool(os.cpu_count()) 
+        p = Pool(core_count) 
         res = p.imap_unordered(extract_images,range(len(filedata)))
         for out in res:
             (fmap,fail_path,err) = out
@@ -358,6 +356,8 @@ def fix_mismatch(with_VRs=['PN', 'DS', 'IS']):
                 logging.error(err_msg)
             else:
                 fm.write(fmap)
+        p.join()
+        p.close()
     fm.close()
     logging.info('Chunk run time: %s %s', time.time() - t_start, ' seconds!')