Re: Pipelining / Multithreading virtual stack processing?

Posted by Rasband, Wayne (NIH/NIMH) [E] on Mar 22, 2011; 6:51pm
URL: http://imagej.273.s1.nabble.com/Pipelining-Multithreading-virtual-stack-processing-tp3684999p3685000.html

On Mar 21, 2011, at 6:27 AM, JesperSP wrote:

> Hi everyone.
>
> I'm doing some analysis on a (virtual) stack of images with a simple ImageJ
> macro script. The analysis is pretty slow, so I was wondering if there is
> some simple way to utilize the dual core/ Hyperthreading of my I5 laptop? I
> have already read a post saying that it's possible to do multithreading in
> javascript
> (http://imagej.588099.n2.nabble.com/a-multithreaded-example-in-javascript-td1478623.html),
> but I was thinking about a different way of speeding up the processing by
> "pipelining" the instructions.

Try using ImageJ 1.45c (or later). Thanks to Stephan Saalfeld and Michael Schmid, all commands in the Process>Filters menu, including Variance, are now multithreaded.

-wayne

> My script does the following:
>
>
> ID=getImageID();
> stackSize=nSlices;
> starttime = getTime();
> run("Clear Results");
> for (i=1;i<stackSize;i++) {
> selectImage(ID);
> setSlice(i);
> run("Duplicate...", "title=mask");
> run("Variance...", "radius=1");
> setThreshold(9,255);
> run("Convert to Mask");
> run("Close-");
> run("Fill Holes");
> run("Erode");
> run("Select All");
> run("Copy");
> close();
> setPasteMode("Transparent-white");
> selectImage(ID);
> run("Paste");
> setThreshold(19,255);
> run("Analyze Particles...", "size=8-Infinity circularity=0.00-1.00
> show=Nothing display exclude include record");
> IJ.log("\\Update:frame:"+i+" fps:"+ 1000*i/(getTime()-starttime));
> }
> close();
>
> The most CPU intensive steps are probably the "Variance" and the "Analyze
> Particles" steps, but in principle these do not need to be run in the same
> CPU core. For example the Variance could be run on image 2 in the stack by
> 2nd CPU core while 1st CPU core is still doing "Analyze Particles". Is there
> any (simple) way to program this in a macro/javascript, or will I have to
> make a real java plugin to do the trick? If anyone knows of another trick
> that might speed up the processing please let me know. My laptop is
> currently processing at a rate of 3.3 fps.
>
> Cheers,
> Jesper
>
> --
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