Posted by
Olivier Burri on
Jul 19, 2013; 1:08pm
URL: http://imagej.273.s1.nabble.com/Out-of-Memory-Problems-tp5004033.html
Hi all,
We're running a simple script to resize extremely large images to a more manageable size for imageJ.
The original image is in the vicinity of 40'000x40'000 pixels
What the plugin does (In macro language)
1. Split the image in 4096x4096 chunks
2. Load a single chunk, resize it
3. Place this chunk in a stack
4. Close the loaded chunk and its scaled counterpart, leaving only the stack.
5. Repeat for all chunks
6. When done, make a montage of the stack.
This used to work just fine, but on a recent trial, imageJ ran out of memory (We have 32 Gb on the system, most of which is allocated to the JVM and ImageJ sees and uses it).
Normally we used no more than a few Gb per resize, but as we load the image, the memory usage goes way up (>10Gb) but still succeeds.
However, when we run the script again, instead of reusing the previously allocated memory, it keeps rising until an out of memory error.
We've tried just opening and closing the same image over and over and memory usage keeps climbing up to the Out of memory error as well, suggesting this does not come from the macro code itself.
Has something changed in the way ImageJ/Fiji handles garbage cleanup?
Thanks for any info!
Oli
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html