Thank you for the very useful program.
I am occasionally getting java.lang.OutOfMemoryError exceptions about the Java heap space. I would expect this to be a fatal error, but for some reason the pipeline processing continues and even completes. Why isn’t it a fatal error (somehow CellProfiler recovers?) and are the results to be trusted?
I am using r11710 on Windows 7 64 bit with 16 GB RAM. The relevant excerpt from log is below:
Wed May 15 12:17:38 2013: Image # 1, module LoadImages # 1: 4.37 sec (bg)
Exception in thread "Thread-16" java.lang.OutOfMemoryError: Java heap space
Traceback (most recent call last):
File "cellprofiler\modules\loadimages.pyc", line 2759, in provide_image
File "cellprofiler\modules\loadimages.pyc", line 2928, in load_using_bioformat
File "cellprofiler\utilities\jutil.pyc", line 439, in method
File "cellprofiler\utilities\jutil.pyc", line 377, in call
JavaException: Java heap space
Wed May 15 12:17:42 2013: Image # 1, module ColorToGray # 2: 3.99 sec (bg)