macro loop Analyze Particles

Posted by lechristophe on May 07, 2008; 8:38am
URL: http://imagej.273.s1.nabble.com/macro-loop-Analyze-Particles-tp3696311.html

Dear ImageJers,

I'm totally confused about a piece of macro code I'm trying to debug
with no success. I want to analyze particles for each slice of a
stack, but I want to have an automatic threshold detection for each
slice separately (as the intensity levels of the objects can be very
different from one slice to another), so I cannot just launch the
Analyze Particle command for the whole stack. I've tested that if you
trigger an AutoThreshold for each slice and then do an Analyze
Particle with the "slice" argument, it will do what I want.

So I just want to loop that for each slice, and I've written this piece of code:


//code starts

macro "multi_detector" {
    run("Set Scale...", "distance=0 known=1 pixel=1 unit=pixel");
    run("Set Measurements...", "area mean circularity feret's
integrated slice redirect=None decimal=3");
    StackID=getImageID();
    print("\\Clear");
    print("start");
    print("source ID "+StackID);
    print(nSlices+" slices");

    for (k=0; k<nSlices; k++) {
        print("begin loop slice "+(k+1));
        selectImage(StackID);
        setSlice(k+1);
        setAutoThreshold();
        run("Analyze Particles...", "size=50-Infinity
circularity=0.00-1.00 show=Masks display record slice");
        print("AP slice "+(k+1)+" done");
        MASK1ID=getImageID();
        print("mask ID for slice"+(k+1)+":"+MASK1ID);
    }
print("finished");
}


// code ends

But the "for" loop doesn't work ! It does the first slice and then
finishes. What is the problem here ? I'm sure it is something evident
but I can't find what... I've added a lot of prints for debugging but
the macro is just a couple of instructions, and I can't manage to find
what's wrong. By the way, this is IJ 1.41a with Java 1.6 dp under OSX
10.4.

On a related note, having an option in the Analyze Particles command
to batch the Analyze Particle on a stack with a different automatic
threshold for each slice would be great, so my macro would shrink to
one line, and I would'nt have to reconstruct the mask stack
afterwars...

Thank you for your help,

Christophe