then. To the point where I don't experience it much any more at all.
you switch windows a lot. This I can't figure out because I turned off
in batch mode. Once you're there, it runs great, and if anything, it likes
> Hi all,
>
> Tim is using MacOS, not Linux.
>
> One issue (of several) with Java on MacOS is the "App Nap" problem. It
> might be on 10.10 that your machine is napping the process, even though it
> is still in the foreground. See this article:
>
>
http://osxdaily.com/2014/05/13/disable-app-nap-mac-os-x/>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect -
http://loci.wisc.edu/software> ImageJ2 lead, Fiji maintainer -
http://imagej.net/User:Rueden> Did you know ImageJ has a forum?
http://forum.imagej.net/>
>
> On Thu, Jan 12, 2017 at 10:02 AM, Michael Schmid <
[hidden email]>
> wrote:
>
> > Hi Timothy, Jim,
> >
> > in my experience, Linux does not have a problem of slowing down
> > processes unless other programs/processes are competing for CPU time.
> > You could run 'top' in a terminal window in parallel to monitor CPU
> usage.
> >
> > Did you check that all windows are properly closed, so memory usage does
> > not go up? You might print nImages() from time to time to make sure.
> >
> > Plugins>Utilites>Montor Memory might be also helpful to see whether
> memory
> > is an issue. Click into the status line of ImageJ from time to time to
> > enforce garbage collection (otherwise memory usage goes up gradually even
> > if everything is properly closed).
> >
> > --
> > Concerning the average between two different frames of a stack: In a
> > macro, it would be enough to duplicate one of the frames, and set the
> stack
> > slice to the other, then calculate the difference. In a java plugin or
> > javascript you could get the two ImageProcessors and run the appropriate
> > process/Blitter class, then get the mean of the pixels.
> >
> > Michael
> > ________________________________________________________________
> >
> > On 12/01/2017 15:50, Ewing James wrote:
> >
> >> Timothy - This sounds like a unix/linux question. See the
> >> documentation on priorities in linux processes.
> >>
> >> As a process ages, its priority for processing may slip downward.
> >> Try using the ‘nice’ command with a negative setting (RTM before you
> >> start fiddling).
> >>
> >> - Jim
> >>
> >> On Jan 12, 2017, at 9:19 AM, Feinstein, Timothy N <
[hidden email]>
> >>> wrote:
> >>>
> >>> I hate to ping the list twice in two days, but this one is a
> >>> puzzle. I wrote a macro that measures the difference between each
> >>> frame of a time series with frame 1, with the ultimate goal of
> >>> measuring the periodicity of the average difference value (with
> >>> Fourier analysis in Excel) to measure ciliary beat frequency. The
> >>> macro uses nested for() loops to open each file in a folder,
> >>> process it framewise and build a results table.
> >>>
> >>> The macro runs pretty fast, but if I walk away from the computer
> >>> for a while at some point it will slow down by almost ten fold,
> >>> making it impractical to run through large data sets overnight.
> >>> Each stack is about 200-500 kb and Fiji has 10 GB of RAM allocated,
> >>> so I doubt that RAM is my problem. I quit all other programs,
> >>> prevented sleep and Fiji remains foregrounded the whole time. I am
> >>> using the latest Fiji update on OSX 10.10.5.
> >>>
> >>> It would be great to know what might cause the slowdown. At the
> >>> same time, odds are my approach could be streamlined quite a bit.
> >>> Right now the macro duplicates out frame 1 and frame n from the
> >>> movie, makes an image of the difference and records the average
> >>> pixel value of the difference image to a results table. Making the
> >>> new images and closing them again seems to take time, even with
> >>> batch mode on. Does anyone know how to measure the average
> >>> difference between frame 1 and frame n of a stack without
> >>> duplicating them out? I pasted the macro below.
> >>>
> >>> Thanks again,
> >>>
> >>>
> >>> T
> >>>
> >>> Timothy Feinstein, Ph.D. Research Scientist University of
> >>> Pittsburgh Department of Developmental Biology
> >>>
> >>> ------------------------------------------------------------
> >>>
> >>>
> >>> //Analyze ciliary beat frequency using cropped movies
> >>
> >> //Requires stable movies. Use the stackreg plugin on
> >> //uncropped originals if you can see sample or camera motion.
> >>
> >> setBatchMode(true);
> >>
> >> if(isOpen("diff_Quant")){
> >> selectWindow("diff_Quant");
> >> run("Close");
> >> }
> >>
> >> if(isOpen("Results")) {
> >> selectWindow("Results");
> >> run("Close");
> >> }
> >>
> >> run("Clear Results");
> >>
> >> run("Set Measurements...", "mean limit display redirect=None
> decimal=5");
> >>
> >> //Find the movies to analyze
> >>
> >> files = getDirectory("Movies");
> >> count = 0;
> >> list = getFileList(files);
> >> n = lengthOf(list);
> >>
> >> //Set up the results table
> >>
> >> for (i=0; i < n; i++) {
> >>
> >> result = 0;
> >> fileName = list[i];
> >> setResult(fileName, result, 1);
> >> updateResults();
> >> }
> >>
> >> IJ.renameResults("diff_Quant");
> >>
> >> //Duplicate out the 1st and nth frame of each movie
> >> //and measure the average difference
> >>
> >> for (i=0; i <= n; i++) {
> >>
> >> open(files+list[count]);
> >> stack = getTitle();
> >> time = 0;
> >> fileName = list[i];
> >> result = 0;
> >> run("Gaussian Blur 3D...", "x=1 y=1 z=1");
> >>
> >> n = nSlices();
> >>
> >> for (slice=1; slice<=(300); slice++){
> >>
> >> selectWindow(stack);
> >> setSlice(1);
> >> run("Duplicate...", "use");
> >> first = getTitle();
> >>
> >> selectWindow(stack);
> >> setSlice(slice + 1);
> >> run("Duplicate...", "use");
> >> test = getTitle();
> >>
> >> imageCalculator("Difference create", first, test);
> >> diff = getTitle();
> >> run("Measure");
> >> mean = getResult("Mean", 0);
> >>
> >> selectWindow("Results");
> >> run("Clear Results");
> >> run("Close");
> >>
> >> selectWindow("diff_Quant");
> >> IJ.renameResults("Results");
> >> result = slice;
> >> setResult(fileName, result, mean);
> >> updateResults();
> >> IJ.renameResults("diff_Quant");
> >>
> >>
> >> selectWindow(first);
> >> run("Close");
> >> selectWindow(test);
> >> run("Close");
> >> selectWindow(diff);
> >> run("Close");
> >> time = time + 0.005;
> >>
> >> }
> >>
> >> selectWindow(stack);
> >> run("Close");
> >> count++;
> >> }
> >>
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>