http://imagej.273.s1.nabble.com/Memory-leak-when-using-Macro-to-process-1000-images-tp5009264p5009277.html
buggy behavior if SCIFIO was enabled so I disabled it. and everything went
fine. I think I might have accidentally enabled it from some previous
> Hi all,
>
> >SCIFIO is known to cause memory leaks.
>
> I agree with Wayne's assessment that you should try running with "Use
> SCIFIO when opening files" disabled. Furthermore, in recent versions of
> Fiji all known SCIFIO-related memory leaks have been addressed.
>
> >Can anyone locate in the code below where things are going wrong?
>
> The macro looks correct. I tested with and without SCIFIO enabled and did
> not see a significant memory leak. If you still see crashes with an
> up-to-date Fiji, you should try:
>
> * Running with Java 7
> <
>
http://fiji.sc/Frequently_Asked_Questions#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F> >
> - we've seen this fix hard crashes that were occurring during long image
> processing runs.
> * Launching in debug mode
> <
http://imagej.net/Debugging#Launching_ImageJ_in_debug_mode> from the
> console and recording the exact error on crashing.
> * Trying solutions in the debugging hard JVM crashes
> <
http://imagej.net/Debugging#Debugging_hard_JVM_crashes> guide.
>
> Let us know how things work out.
>
> - Mark
>
> On Tue, Aug 19, 2014 at 11:58 AM, Rasband, Wayne (NIH/NIMH) [E] <
>
[hidden email]> wrote:
>
> > On Aug 19, 2014, at 7:14 AM, George H wrote:
> >
> > > Hi,
> > >
> > > I am using ImageJ v1.49e and I wrote a simple macro that will read in
> > 1000+
> > > images from a directory and perform some processing. Once its all over
> I
> > > save the summaries to a file. I do this all in batchmode so the windows
> > > don't open and close quickly.
> > >
> > > So the issue is that the memory usage keeps rising until the program
> > > crashes. I really do not know why this is happening and I am opening
> and
> > > closing each image.
> >
> > It looks like you are using Fiji so you should verify that "Use SCIFIO
> > when opening files" is disabled in Edit>Options>ImageJ2. SCIFIO is known
> to
> > cause memory leaks. The SCIFIO option is disabled by default in
> > Fiji/ImageJ2 2.0.0-rc14 and later.
> >
> > -wayne
> >
> > > Can anyone locate in the code below where things are going wrong?
> > Thanks.
> > >
> > > -----
> > > Dialog.create("Select Options");
> > > Dialog.addSlider("Subtract Background Rolling:", 0.0, 90.0, 30.0);
> > > Dialog.addSlider("Min Particle Size (px):", 5, 90, 15);
> > > Dialog.addSlider("Min Particle Circularity:", 0.0, 1.0, 0.40);
> > > Dialog.addCheckbox("Save Summaries to file", true);
> > > Dialog.show();
> > >
> > > inputDir = getDirectory("Choose the Input Directory");
> > > inputDir = replace(inputDir, "\\\\", "\\\\\\\\");
> > >
> > > if(inputDir != "") {
> > > inputList = getFileList(inputDir);
> > > rollingValue = Dialog.getNumber();
> > > minParticleSize = Dialog.getNumber();
> > > minParticleCirc = Dialog.getNumber();
> > > saveSummaries = Dialog.getCheckbox();
> > > setBatchMode(true);
> > > for (i=0; i < inputList.length; i++) {
> > > showProgress(i+1, inputList.length);
> > > fileName = inputList[i];
> > > imageAnalysis(inputDir, fileName, rollingValue, minParticleSize,
> > > minParticleCirc);
> > > }
> > > if(saveSummaries) {
> > > selectWindow("Summary");
> > > saveAs("Results", inputDir+"summaries.txt");
> > > }
> > >
> > > call("java.lang.System.gc");
> > > setBatchMode(false);
> > >
> > > if(isOpen("Summary")) {
> > > selectWindow("Summary");
> > > run("Close" );
> > > }
> > > }
> > > else {
> > > exit("Must select an input and output directory");
> > > }
> > >
> > >
> > > function imageAnalysis(inputDir, fileName, rollingValue, circSize,
> > > minCircularity) {
> > > open(inputDir+fileName);
> > > run("Enhance Local Contrast (CLAHE)", "blocksize=127 histogram=256
> > > maximum=3 mask=*None* fast_(less_accurate)");
> > > run("8-bit");
> > > run("Subtract Background...", "rolling="+rollingValue);
> > > setAutoThreshold("Triangle");
> > > setOption("BlackBackground", false);
> > > run("Convert to Mask");
> > > run("Set Measurements...", "area mean min centroid shape feret's
> > > area_fraction redirect=None decimal=3");
> > > run("Analyze Particles...", "size="+circSize+"-Infinity
> > > circularity="+minCircularity+"-1.00 exclude clear summarize");
> > > close();
> > > }
> > >
> > >
> > > --
> > > George
> > >
[hidden email]
> > >
> > > --
> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>