I have a strange memory problem with JAVA:
I wrote a pipeline that processes all the images in a directory. In some directories I have “small” images (1000 X 1000) and in others I have “big” images (12000 X 12000).
When I use the GUI of CellProfiler, it works flawlessly on both small and large images (I work on the “big PC of the lab” with 64 GB and I gave 60GB to Java in CellProfiler preferences).
But when I run CellProfiler with a batch file, it works perfectly for small images but I get: “JavaException: Java heap space” for large images.
Can you tell me why it works like a charm when I use the GUI and not when I use command line mode and how to allow the batch version to do what the GUI session does.
Thks a lot
Some additional information:
PC: i7 8700k, 64 GB ram
My batch command:
cd C: / Program Files (x86) / CellProfiler /
cellprofiler -p C: \ Users \ home \ Desktop \ Super_macro \ arrives_petit \ super_macro_1.cppipe -c -r -i C: \ Users \ home \ Desktop \ Super_macro \ arrives_small \ FIJI_results / OK_10K / -o C: \ Users \ home \ Desktop \ Super_macro \ arrivee_petit \ CP_results