Re: Particle analyzer and ROI manger

Posted by Susanna Trollvad on
URL: http://imagej.273.s1.nabble.com/Particle-analyzer-and-ROI-manger-tp3684572p3684574.html

2011/5/17 Seitz Arne <[hidden email]>

> Hi Susanna,
>
>
> > I want to create a plugin were I first turn my picture into a HSB
> > stack, choose the brightness slice and delete the other two, then
> > threshold to a preset value, and then do what the "Analyze particles"
> > command from the menu without the user having to give any input. And
> > then I want to rotate the ROIs that get stored in the ROI manager.
> >
> > I have made it work up to the "Analyze particle" step which I'm not
> > quite sure how to do. (But I'm not quite satisfied by the thresholding)
> >
> > Does anyone know how to do the "Analyze particles" step? Or when that's
>
> One way of doing the analysis is by running the command:
> IJ.run(imp,"Analyze Particles...", "size=0.12-Infinity
> circularity=0.00-1.00 show=Nothing exclude clear include add slice");
> With imp being the IaagePlus you wanted to analyse.
>

This also works, but I would like to be able to do it without calling the
"Analyze particles" menu command.

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.

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/
> ---------------------------------------------------------------
>