Re: Out of Memory Problems

Posted by Hans Wurscht on Jul 25, 2013; 1:14pm
URL: http://imagej.273.s1.nabble.com/Out-of-Memory-Problems-tp5004033p5004139.html

Dear List,

I experience the same problem when using the doCommand in a macro:

openImage();

macro "open image in new thread"{
        newImage("Untitled", "8-bit white", 400, 400, 1);
       
}

function openImage(){
        setBatchMode(true);
        for(i=0;i<1000;i++){
                doCommand("open image in new thread");
                wait(100);
        }
        wait(3000);
        run("Close All");
        setBatchMode(false);
       
}

Once finished, you can see that the threads are terminated, but the
memory is not freed up.

Running the garbage collector from the menu does not help. I use the
doComand option to run some live analyis during timelapse recordings,
and this bug leads to an out of memory error and failue of the
analysis.

I tried IJ 1.47u, 1.48a with openJDK 6 / 7 on Ubuntu 12.04 32bit
without success.

Do you have any suggestions for me?

Thanks a lot,

Gabriel


On Jul 23, 2013, at 1:34 PM, Johannes Schindelin wrote:

> Hi Olivier,
>
> On Tue, 23 Jul 2013, Burri Olivier wrote:
>
>> I've tried loading a large dataset over and over through a macro (Load,
>> close loop) after updating Fiji And I still get the out of memory error.
>
> Well, this is my fault. For some reason, I failed to upload a new version
> of ij-legacy.jar when I said that I had. But now it worked, and this
> beautiful macro demonstrates that my fix works at least with the Clown
> sample (I was unable to run Plugins>Utilities>Monitor Memory... from the
> macro without blocking the rest of the commands, so please call that by
> hand before running it):

A macro can run Plugins>Utilities>Monitor Memory without blocking by
using the doCommand() macro function, which runs a menu command in a
separate thread. For example, this macro starts the Memory Monitor and
then opens and closes 5000 1MB images.

  setBatchMode(true);
  doCommand("Monitor Memory...");
  n = 5000;
  for (i = 0; i < n; i++) {
     showStatus((i+1)+"/"+n);
     newImage("Untitled", "8-bit ramp", 1024, 1024, 1);
     close();
  }

-wayne

> path = getDirectory("imagej") + "samples/clown.jpg";
> useBF = true;
> setBatchMode(true);
> for (i = 0; i < 100; i++) {
> if (useBF) {
> run("Bio-Formats", "open=[" + path + "] "
> + "autoscale color_mode=Default "
> + "view=Hyperstack stack_order=XYCZT");
> } else {
> open(path);
> }
> close();
> }
>
> For easy debugging and extensive testing, I also tried with "!true" for
> both useBF and setBatchMode(), and the issues that I could indeed
> reproduce with the Fiji version as of half an hour ago are now gone.
>
> Ciao,
> Dscho
>
> P.S.: The macro assumes that you have unpacked Fiji into your home
> directory and that you ran File>Open Samples>Cache Sample Images. This is
> so far a Fiji-only function (Wayne, if you read this and re-implement it
> for ImageJ 1.x, please let me know so that I can prevent breakages in
> Fiji).
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Top of Message<https://list.nih.gov/cgi-bin/wa.exe?A2=ind1307&L=IMAGEJ&P=R56424&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4#TOP>|
Previous
Page<https://list.nih.gov/cgi-bin/wa.exe?A1=ind1307&L=IMAGEJ&D=0&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4>|
Permalink <https://list.nih.gov/cgi-bin/wa.exe?A2=IMAGEJ;b6ecca0f.1307>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html