Re: Classifying ROIs in the RoiManager

Posted by Olivier Burri on
URL: http://imagej.273.s1.nabble.com/Classifying-ROIs-in-the-RoiManager-tp5012523p5012527.html

Hello,

We had a similar need a while back, use this function

/*
 * Returns an array of indexes of ROIs that match
 * the given regular expression
 */
function findRoisWithName(roiName) {
        nR = roiManager("Count");
        roiIdx = newArray(nR);
        k=0;
        clippedIdx = newArray(0);
       
        for (i=0; i<nR; i++) {
                roiManager("Select", i);
                rName = Roi.getName();
                if (matches(rName, roiName)) {
                        roiIdx[k] = i;
                        k++;
                }
        }
        if (k>0) {
                clippedIdx = Array.trim(roiIdx,k);
        }
       
        return clippedIdx;
}


In your case, it would look something like this
Idx = findRoisWithName("triangle.*");

For (i=0; i< Idx.length; i++) {
        roiManager("Select", Idx[i]);
        // TO THINGS HERE
}

In case you want your ROIs sorted, then use roiManager("Sort"); before, as suggested by Romain

Best

Oli

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Romain Guiet
> Sent: Monday, April 20, 2015 8:04
> To: [hidden email]
> Subject: Re: Classifying ROIs in the RoiManager
>
> Hi Avital,
>
> maybe you could use the macro functions :
> Roi.getType : Returns, as a string, the type of the current selection.
> Roi.setName(name)
> roiManager(cmd), with cmd = "Sort", to sort your ROIs
>
> more on : http://imagej.nih.gov/ij/developer/macro/functions.html#Top
>
> I hope it will help you,
>
> Cheers,
>
> Romain
>
>
> ---------------------------------------------------------------
> Dr. Romain Guiet
> Bioimaging and Optics Platform (PT-BIOP) Ecole Polytechnique Fédérale de
> Lausanne (EPFL) Faculty of Life Sciences Station 19, AI 0140
> CH-1015 Lausanne
>
> Phone: [+4121 69] 39629
> http://biop.epfl.ch/
> ---------------------------------------------------------------
>
> ________________________________________
> De : ImageJ Interest Group [[hidden email]] de la part de Avital
> Steinberg [[hidden email]] Envoyé : dimanche 19 avril 2015
> 21:09 À : [hidden email] Objet : Classifying ROIs in the RoiManager
>
> Hi,
> I would like to be able to choose ROIs belonging to a certain class from the
> ROI manager in a macro. For example, I renamed the ROIs as triangle1,
> triangle2, triangle3, circle1, circle2, rectangle1, rectangle2.
>
> I would like to be able to add triangles and iterate over all the triangles. I can
> sort the ROIs in the RoiManager, so that the ROIs of a certain class will be in
> consecutive order.
>
> However, in order to be able to choose only triangles, I would have to keep
> track of how many triangles there are.
>
> Is there an easier way to select (and iterate over) only ROIs of a certain class
> (such as triangles or circles), without having to keep track of the number of
> objects in each class and their order?
>
> Thanks,
> Avital
>
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