Is ImageJ memory-leaky?

[Pedro J CamelloDr Pedro J Camello]

I´m trying to use ratio Plus plugin to generate a stack calculating
ratio between two stacks. My problem is that I use several hundreds of
images and ImageJ is out of memory too easily (I have allocated 450 Mb f
RAM). I say "too easily" because the same original stacks can generate a
third stack of images in Metafluor Analyst withou memory problems, so
that increasing amount of RAM is not the best solution

Thanks

[Albert Cardona]

Pedro,

ImageJ is not leaky that I know of, at all. Memory issues have to do with how
the java virtual machine works. This is not so different from C/C++: memory
has to be released at some point or your virtual machine will run out of RAM
space before it occurs to it to run a garbage collector.

So I recommend you insert code into your plugin that:

1) checks how much memory is available
2) if not enough for what you want to do, release it by calling in a
while(true) loop the garbage collector until enough memory has been released.
3) proceed with whatever memory-consuming task

ImageJ has in the ij.IJ class methods to tests the amount of available memory;
if you want to do it manually check the java.lang.System class

If this does not address your problem because your plugin actually uses all
that filled-up memory, try dynamic loading/unloading of memory: release what
you don't need at the moment and then reload it when it is needed. This way I
manage to deal with 6 GB of images at the same time in a 512Mb RAM machine.


Albert
--


Albert Cardona
Institute of Neuroinformatics     Tel : [phone]
University/ETH Zurich             Fax : [phone]
Winterthurerstrasse 190           acardona (at) ini phys ethz ch
Zurich 8057, Switzerland          www.ini.unizh.ch

[Gabriel Landini]

On Wednesday 14 September 2005 10:24, Albert Cardona wrote:
> So I recommend you insert code into your plugin that:
> 2) if not enough for what you want to do, release it by calling in a
> while(true) loop the garbage collector until enough memory has been
> released.

What is the code to do this?
Many thanks,

G.

[Albert Cardona]

Mr. G,

The code to release memory is a simple call to the garbage collector. You can
run a test for 10 iterations (a while(true) loop is rather dangerous unless
carefully planned) :

//define the minimum ammount of free memory you need:
int min_free_memory = 50; //in percentage of total

int i =0;
for (; i<10; i++) {
        // run garbage collector:
        System.gc();
        // check for free memory:
 int free_memory = 100 - (IJ.currentMemory() * 100 / IJ.maxMemory());
 if (free_memory >= min_free_memory) {
                break;
        }
}

if (10 == i) {
       IJ.log("Failed to release enough memory.");
}



Albert Cardona
Institute of Neuroinformatics     Tel : [phone]
University/ETH Zurich             Fax : [phone]
Winterthurerstrasse 190           acardona (at) ini phys ethz ch
Zurich 8057, Switzerland          www.ini.unizh.ch

[Gabriel Landini]

On Wednesday 14 September 2005 12:49, Albert Cardona wrote:
> The code to release memory is a simple call to the garbage collector. You
> can run a test for 10 iterations (a while(true) loop is rather dangerous
> unless carefully planned) :

Many thanks, this is very useful.
Cheers,

Gabriel

[Pedro J CamelloDr Pedro J Camello]

Many thanks, Albert

regarding your last paragraph

_/If this does not address your problem because your plugin actually uses all
that filled-up memory, try dynamic loading/unloading of memory: release what
you don't need at the moment and then reload it when it is needed. This way I
manage to deal with 6 GB of images at the same time in a 512Mb RAM machine.
/_

 could you please explain how to do it /grosso modo? /(I´m afraid  in
the next months I´ll need to handle big stacks)




Albert Cardona wrote:

>Pedro,
>
>ImageJ is not leaky that I know of, at all. Memory issues have to do with how
>the java virtual machine works. This is not so different from C/C++: memory
>has to be released at some point or your virtual machine will run out of RAM
>space before it occurs to it to run a garbage collector.
>
>So I recommend you insert code into your plugin that:
>
>1) checks how much memory is available
>2) if not enough for what you want to do, release it by calling in a
>while(true) loop the garbage collector until enough memory has been released.
>3) proceed with whatever memory-consuming task
>
>ImageJ has in the ij.IJ class methods to tests the amount of available memory;
>if you want to do it manually check the java.lang.System class
>
>If this does not address your problem because your plugin actually uses all
>that filled-up memory, try dynamic loading/unloading of memory: release what
>you don't need at the moment and then reload it when it is needed. This way I
>manage to deal with 6 GB of images at the same time in a 512Mb RAM machine.
>
>
>Albert
>  
>

[Albert Cardona]

Pedro,

There are many ways to dynamically load/unload RAM memory, in this case
images. A very nice and straightforward example is found in the
Virtual_Stack_Opener.java plugin by Wayne, at
http://rsb.info.nih.gov/ij/plugins/virtual-opener.html

The way I do it for my purposes is to wrap the object to be loaded/unloaded in
a wrapper class to which all calls to that object are piped. So when the
object is required, the wrapper class first makes some space by telling the
cache to do so, loads it either from scratch (as the files in the Virtual
Stack Opener) or from the cache, and then sends it to the cache for storing.
The cache keeps a first-in-first-out queue of the objects and self-regulates
itself to make space, releasing as many of the least-used objects first (the
older ones in the queue) as needed.

Hope it helps.

Albert
--


Albert Cardona
Institute of Neuroinformatics     Tel : [phone]
University/ETH Zurich             Fax : [phone]
Winterthurerstrasse 190           acardona (at) ini phys ethz ch
Zurich 8057, Switzerland          www.ini.unizh.ch