removed manual garbage collection management (resolves #2125)

cellprofiler/analysis.py

@@ -5,7 +5,6 @@
 import Queue
 import cStringIO as StringIO
 import collections
-import gc
 import logging
 import multiprocessing
 import os

cellprofiler/modules/tests/test_exporttodatabase.py

@@ -2,7 +2,6 @@
 '''
 
 import base64
-import gc
 import numpy as np
 import os
 import PIL.Image as PILImage
@@ -1822,7 +1821,6 @@ def callback_handler(caller, event):
             module.directory.custom_path = output_dir
 
             def finally_fn():
-                gc.collect()
                 for filename in os.listdir(output_dir):
                     os.remove(os.path.join(output_dir, filename))
 

cellprofiler/modules/tests/test_loadimages.py

@@ -2,7 +2,6 @@
 """
 
 import base64
-import gc
 import glob
 import hashlib
 import os

cellprofiler/modules/tests/test_mergeoutputfiles.py

@@ -1,6 +1,5 @@
 '''test_mergeoutputfiles.py - test the MergeOutputFiles module'''
 
-import gc
 import os
 import tempfile
 import unittest
@@ -29,7 +28,6 @@ def execute_merge_files(self, mm):
 
         M.MergeOutputFiles.merge_files(output_file, [x[1] for x in input_files])
         m = cpmeas.load_measurements(output_file)
-        gc.collect()
         os.close(output_fd)
         os.remove(output_file)
         for fd, filename in input_files:

cellprofiler/modules/tests/test_untangleworms.py

@@ -3,7 +3,6 @@
 import StringIO
 import base64
 import bioformats
-import gc
 import os
 import tempfile
 import unittest
@@ -273,7 +272,6 @@ def setUp(self):
         self.filename = tempfile.mktemp(".mat")
 
     def tearDown(self):
-        gc.collect()
         if os.path.exists(self.filename):
             os.remove(self.filename)
 

cellprofiler/pipeline.py

@@ -4,7 +4,6 @@
 
 import bisect
 import csv
-import gc
 import hashlib
 import json
 import logging
@@ -1831,7 +1830,6 @@ def group(workspace):
                 should_write_measurements = True
                 grids = None
                 for module in self.modules():
-                    gc.collect()
                     if module.should_stop_writing_measurements():
                         should_write_measurements = False
                     else:
@@ -1980,7 +1978,6 @@ def run_image_set(self, measurements, image_set_number,
         should_write_measurements = True
         for module in self.modules():
             print "Running module", module.module_name, module.module_num
-            gc.collect()
             if module.should_stop_writing_measurements():
                 should_write_measurements = False
             workspace = cpw.Workspace(self,

cellprofiler/tests/test_measurements.py

@@ -2,7 +2,6 @@
 """
 
 import base64
-import gc
 import os
 import sys
 import tempfile
@@ -784,7 +783,6 @@ def test_13_01_load_matlab(self):
             self.assertEqual(len(values), 1)
             self.assertAlmostEqual(values[0], 34.580433355219959)
         finally:
-            gc.collect()
             if m is not None:
                 del m
             os.unlink(name)

cellprofiler/worker.py

@@ -122,7 +122,6 @@ def aw_parse_args():
 import random
 import zmq
 import cStringIO as StringIO
-import gc
 import traceback
 from weakref import WeakSet
 
@@ -397,7 +396,6 @@ def do_job(self, job):
             if should_process:
                 abort = False
                 for image_set_number in image_set_numbers:
-                    gc.collect()
                     try:
                         self.pipeline_listener.image_set_number = image_set_number
                         last_workspace = current_pipeline.run_image_set(