Posted by
Cédric Messaoudi on
Dec 14, 2009; 10:28am
URL: http://imagej.273.s1.nabble.com/increasing-memory-allocation-via-Java-code-tp3689982p3689986.html
I have to point out that the jvm from sun (on windows, I didn't check on
linux) has a small limitation of memory on multi core/cpu systems.
On my dual core cpu in my laptop with 8 GB of RAM, I am able to start ImageJ
with the option -Xmx5000m but when trying to allocate a volume of 4 GB I
have an out of memory error. It seems that the jvm from sun is dividing
actual RAM memory by the number of cores. Would it be possible to other
people to test this issue?
Trying BEA jvm (jrockit) allowed me some time ago to solve this problem.
Actually I mostly use virtual stack to open very big dataset, so it not a
problem from my part to use the jvm from sun.
Regards,
Cédric
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Cédric MESSAOUDI
Institut Curie - INSERM U759 Laboratoire d'Imagerie Intégrative
Bât 112, Centre Universitaire d'Orsay
91405 Orsay CEDEX
France
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[hidden email]
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-----Message d'origine-----
De : ImageJ Interest Group [mailto:
[hidden email]] De la part de Pang,
Zhengyu (GE, Research)
Envoyé : vendredi 11 décembre 2009 15:44
À :
[hidden email]
Objet : Re: what is real max memory limit of ImageJ ?
Franklin,
Size of image is different from size of image stored in the memory. JPEG
image size is much smaller than TIFF, but when it is loaded to memory,
it is same as TIFF file.
In your application, I wonder if you close images once you are done with
those image. Just use close(), then your computer could free up the
space.
Hopefully it helps.
Zhengyu
Dr. Zhengyu Pang
Biochemistry and Biological Engineering Laboratory
General Electric Company Global Research
GE Imagination at work
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
Franklin Shaffer
Sent: Friday, December 11, 2009 9:12 AM
To:
[hidden email]
Subject: what is real max memory limit of ImageJ ?
I am doing particle recognition and tracking of images on high speed
videos. I break the hs video up into images, then load the image
sequence into ImageJ.
I put 64 GB of RAM in a very fast PC (HP Z800). I try to load a
sequence of 50,000 image files, but I get a memory error after it loads
about 40,000. The total combined size of all of the 50,000 images is 20
GB. But I have 64 GB of RAM, and I have the memory limit set in ImageJ
as 50 GB.
So if I tell ImageJ to use 50 GB of RAM, why is it giving memory errors
when I try to load 20 GB of images ?
ImageJ is an excellent code for cell/particle analysis, so I want to
continue using it.
Thank you all for building ImageJ!
Frank Shaffer
Research Engineer, National Energy Technology Laboratory, US.
[hidden email]
>>> "Roy Wollman" <
[hidden email]> 10/30/2009 9:47 PM >>>
Hi All,
I'm trying to import few of the ImageJ classes to use within matlab.
Matlab has great java support which basically means that I can create
objects on the command line (e.g. stk=imp.createEmptyStack();).
However, the maximal memory allocation is too low. Since I'm running on
a OS-X with 64-bit and lots of memory I want to increase the maximal
memory allocation. I already don't so in the standalone
ImageJ64 application and it works great.
Here is the matlab code I'm using:
javaaddpath
/Applications/ImageJ/ImageJ64.app/Contents/Resources/Java/ij.jar
import ij.*;
mem=ij.plugin.Memory;
mem.run('');
Than I get the menu in which I change the total memory but.... I get the
following message:
ImageJ is unable to change the memory limit. For more information, refer
to the installation notes at
http://rsb.info.nih.gov/ij/docs/install/
The ImageJ application (ImageJ.app) was not found.
Current limit: 189MB
Since the java objects are created within matlab its not my job to worry
about memory management but matlab's problem. Is there another way to
increase the limit or just disable the memory limit altogether?
Thanks,
Roy