Re: Memory matters, I think...

Posted by Mark R. Besonen on
URL: http://imagej.273.s1.nabble.com/Memory-matters-I-think-tp3701987p3701989.html

Hello Andy and others,

         I just bothered to investigate the newish "call" macro
function that I mentioned in my last message, and in fact, it is a
much more elegant solution than the kludge I pointed you to
originally.  Take a look at the CallJavaDemo.txt macro example
(http://rsb.info.nih.gov/ij/macros/CallJavaDemo.txt).  To provoke
garbage collection from within a macro nowadays is as simple as:

call("java.lang.System.gc");

         Sorry for steering you in the wrong direction initially--I'd
definitely suggest you use the "call" function instead nowadays.

Mark Besonen
UMass Geosciences



At 12:58 PM 7/27/2006, Mark R. Besonen wrote:

>Hello Andy,
>
>         Yes, there is a way to flush memory within a macro (to
> manually force the JVM to do "garbage collection").  The JVM is
> supposed to do garbage collection automatically when necessary, but
> as you have found it, it doesn't always do it.  So you can manually
> do an operation or process successfully, but then run into memory
> errors when you automate it via macro functions.
>
>         It is very easy to force garbage collection via a plugin,
> and perhaps with the newish "call" macro function, but I am pretty
> much macro-limited.  So last year when I ran into this problem, I
> prepared a small tool to help us macro-limited folks.  You can find
> more details in the mailing list archives, specifically topic 139
> in the archives from June 2005 (see
> https://list.nih.gov/cgi-bin/wa?A1=ind0506&L=imagej#139).
>
>         Curiously, you don't report that ImageJ actually gives you
> an "out of memory" error which is what I see.  But maybe things
> have changed with newer IJ versions.
>
>Mark Besonen
>UMass Geosciences
>
>
>
>
>At 12:22 PM 7/27/2006, you wrote:
>>Dear all,
>>
>>Is there any way to 'flush out' the memory at the start of a macro/for
>>loop?
>>
>>My macros keep coming up with problems that do not occur if I run things
>>manually in exactly the same routine!?
>>
>>For example, on some occasions, it says that run("Create Selection")
>>needs a thresholded/binary image. I have set this up correctly:
>>
>>    setAutoThreshold();
>>    run("Analyze Particles...", "size=5000-Infinity circularity=0.00-1.00
>>show=Masks exclude clear include");
>>    mask = getImageID;
>>    run("Copy");
>>    setPasteMode("AND");
>>    selectImage(img1);
>>    run("Paste");
>>    resetThreshold();
>>    selectImage(mask);
>>    run("Create Selection"); // requires 1.37j
>>
>>on other occasions, with the same dataset, it gets passed this point!?
>>
>>There's also a convex hull problem. Initially, I found that to run:
>>
>>    run("Enlarge...", "enlarge=0");
>>    run("Fit Spline");
>>
>>prior to:
>>
>>    run("Convex Hull");
>>
>>seems to solve the closed/polyline/polygon ROI problem. This, however,
>>is sometimes reoccurring?!
>>
>>Strange?! My only thought is that it is a memory problem...
>>
>>Cheers, Andy