Re: Memory Problems in Fiji using macro setBatchMode(true)

Posted by Cameron Nowell-2 on Aug 12, 2013; 9:39am
URL: http://imagej.273.s1.nabble.com/Memory-Problems-in-Fiji-using-macro-setBatchMode-true-tp5004321p5004391.html

Hi James,

Not sure if it matters but whenever i use the garbage collection option i use

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

i ahve also found that putting a small delay, say 500 - 1000ms (using wait(500);) after the call helps it make sure it works ok

Cheers

Cam

 
Cameron J. Nowell
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________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of James Burchfield [[hidden email]]
Sent: Monday, August 12, 2013 5:17 PM
To: [hidden email]
Subject: Re: Memory Problems in Fiji using macro setBatchMode(true)

I should also mention that the problem is also apparent when not using
batchmode.

*
                       *
*Dr James Burchfield*
The Garvan Institute of Medical Research
384 Victoria Street
Darlinghurst, NSW, 2010
Australia

Email: [hidden email]
Phone:[phone]
Web: *www.garvan.org.au*


On Mon, Aug 12, 2013 at 5:07 PM, James Burchfield <
[hidden email]> wrote:

> Hi all,
>
> I believe I am having a similar issue to this.  I am running a macro
> designed to open an image crop out 2 ROI's resize one of them and save the
> new images.  The process works fine in both ImageJ and Fiji except that it
> rapidly builds up memory usage.
>
> I have tried incorporating the suggested
> run("Collect Garbage"); in Fiji
>
> All this has done is slow down the processing, but the memory issue is
> still there.
>
> I am running the latest nightly build of ImageJ.
>
> Any help would be greatly appreciated.
>
> The macro in question is below.
>
> Cheers,
> James
>
> macro "seperate channels[s]"{
>
>    dir1 = getDirectory("Choose Source Directory ");
>    dest = getDirectory("Choose Destination Directory ");
>    list = getFileList(dir1);
>    greendir = dest + "greenTEMP"+File.separator;
>    reddir = dest + "redTEMP"+File.separator;
>    //print(greendir);
>    File.makeDirectory(greendir);
>    File.makeDirectory(reddir);
>         x=getString("set x offset", 3);
>         y=getString("set y offset", 1);
>    setBatchMode(true);
>    for (i=1; i<list.length; i++) {
>    print (dir1+list[i]);
>       if (endsWith(list[i],".tif")){
>             showProgress(i+1, list.length);
>             open (dir1+list[i]);  //open image i
>             rename ("original" + i);
>         run("Rotate 90 Degrees Right");
>             //define Green Channel
>             w=getWidth()-16;
>             h=getHeight()/2-10;
>             makeRectangle(x, y, w, h);
>             run("Duplicate...", "title=Green");
>             saveAs("Tiff", greendir+"green_"+i+".tif");
>         close("Green");
>
>
>         //define red channel
>         selectWindow("original"+i);
>             w_red=w/1.975*2;
>             h_red=h/1.985*2;
>             makeRectangle(3, 10+h_red, w_red, h_red);
>             run("Duplicate...", "title=Red_Original");
>         run("Scale...", "x=1.975 y=1.985 interpolation=Bicubic create
> title=Red_Engorged");
>         close("Red_Original");
>         run("Scale...", "x=0.5 y=0.5 interpolation=Bilinear average create
> title=Red");
>         close("Red_Engorged");
>         selectWindow("Red");
>         run("Rotate... ", "angle=0.25 grid=2 interpolation=Bilinear
> stack");
>         saveAs("Tiff", reddir +"red_"+i+".tif");
>         close("Red");
>         close("original" + i);
>         run("Collect Garbage");
>         }
>         }
>
>

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