Re: Particle analyzer and ROI manger

Posted by Arne Seitz on May 17, 2011; 2:30pm
URL: http://imagej.273.s1.nabble.com/Particle-analyzer-and-ROI-manger-tp3684572p3684576.html

> I am a bit confused about how the code below works. How can you call
> the
> getInstance method to the RoiManger if you havent first created a
> RoiManger
> object? Is that something that is done but not shown in the code below?
> But
> then what is the point of the getInstance() function because then you
> already have the RoiManager object.
 
I'm sorry because I forgot to mention that the code was assuming that there is an existing RoiManager (which might have been created with the "Analyze Particles" command).
To get a reference to this RoiManager you can use
        RoiManager.getInstance();

With
        RoiManager.getInstance().getROIs()
you can get the ROIs as Hashtable

Alternatively you can also use:
        RoiManager.getInstance().getRoisAsArray()
In order to get the array of ROIs.

> When you use the "Analyze Particles" command it seems as though a
> RoiManager
> is created and a bunch of ROIs are stored in an array, and there is a
> method
> in RoiManager called getRoiAsArray(), which I think I would like to
> use. How
> would I do that?
>
> >
> > > done how to access the ROIs in the ROI manager?
> >
> > This is how I managed to get access to the ROIs of the ROi Manager.
> >
> > private void growROI(double grow){
> >
> >                Hashtable RoiTab=RoiManager.getInstance().getROIs();
> >
> >                Enumeration e = RoiTab.keys();
> >                 while (e.hasMoreElements()) {
> >                  Object key = e.nextElement();
> >                  Roi roi = (Roi) RoiTab.get(key);
> >                  Rectangle rect=roi.getBoundingRect();
> >                  int h=(int)grow*rect.height;
> >                  int w=(int)grow*rect.width;
> >                  rect.grow(h, w);
> >                  Roi nroi=new Roi(rect);
> >                  RoiTab.put(key, nroi);
> >                  }
> >
> >        }
> >
> >
> >
> > >
> > > Here is what I have written so far:
> > >
> > > import ij.*;
> > > import ij.plugin.filter.PlugInFilter;
> > > import ij.process.*;
> > > import java.awt.*;
> > > import ij.plugin.filter.*;
> > > import ij.gui.*;
> > > import ij.measure.*;
> > > import ij.text.*;
> > > import java.util.*;
> > > import ij.plugin.Thresholder;
> > > import ij.plugin.filter.ParticleAnalyzer;
> > >
> > >
> > > public class Roi_test implements PlugInFilter, Measurements {
> > >     ImagePlus imp;
> > >     ImageConverter convert;
> > >     ImageStack stacky;
> > >     Thresholder treshy;
> > >     ParticleAnalyzer party;
> > >
> > >     public int setup(String arg, ImagePlus imp) {
> > >
> > >         if (arg.equals("about")) {
> > >             showAbout(); return DONE;
> > >         }
> > >
> > >         this.imp = imp;
> > >         return DOES_RGB;
> > >     }
> > >
> > >     public void run(ImageProcessor ip) {
> > >
> > >     int ht = imp.getHeight();
> > >         int wd = imp.getWidth();
> > >
> > >         ImagePlus dst = NewImage.createRGBImage("HSB", wd, ht, 1,
> > > NewImage.FILL_BLACK);
> > >
> > >         ImageProcessor srcp = imp.getProcessor();
> > >         ImageProcessor dstp = dst.getProcessor();
> > >         int[] srcpix = (int[])srcp.getPixels();
> > >         int[] dstpix = (int[])dstp.getPixels();
> > >
> > >            Rectangle r = srcp.getRoi();
> > >            //debug("roi bounds: "+r);
> > >
> > >            for (int y=r.y; y<(r.y+r.height); y++) {
> > >                for (int x=r.x; x<(r.x+r.width); x++) {
> > >                    int i = x + y*wd;
> > >                    dstpix[i] = srcpix[i];
> > >                }
> > >            }
> > >         dst.show();
> > >
> > >     //Convert to HSB and delete H and S slice
> > >     convert = new ImageConverter(dst);
> > >     convert.convertToHSB();
> > >     stacky = dst.getImageStack();
> > >     dst.setSlice(3);
> > >     stacky.deleteSlice(1);
> > >     stacky.deleteSlice(2);
> > >
> > >     //Threshold
> > >     //Use ThresholdtoSelection?
> > >     dstp.setThreshold(10, 255, dstp.getLutUpdateMode());
> > >     treshy = new Thresholder();
> > >     treshy.run("Convert to Mask");
> > >
> > >     //Analyze particles
> > >     party = new ParticleAnalyzer();
> > >     party.analyze(dst);
> > >     }
> > >
> > >     void showAbout() {
> > >               IJ.showMessage("AHHH!!");
> > >       }
> > >
> > > }
> > >
> > >
> > >
> > > //Susanna
> >
> > Cheers Arne
> >
> >
> > ---------------------------------------------------------------
> > Dr. Arne Seitz
> > Head of Bioimaging and Optics Platform (PT-BIOP)
> > Ecole Polytechnique Fédérale de Lausanne (EPFL)
> > Faculty of Life Sciences
> > Station 15, AI 0241
> > CH-1015 Lausanne
> >
> > Phone: [phone]
> > Fax:      [phone]
> > http://biop.epfl.ch/
> > ---------------------------------------------------------------
> >