Re: Access 3D positions from ROI Manager

Posted by Michael Doube on Aug 29, 2008; 5:12pm
URL: http://imagej.273.s1.nabble.com/Access-3D-positions-from-ROI-Manager-tp3695210p3695211.html

I found a solution, which is in a sphere-fitting plugin just ported
(from C++) and published here:

http://doube.org/plugins.html#fitsphere

Mike

Michael Doube wrote:

> Hello
>
> I'm writing a plugin that would benefit from having access to 3D
> coordinate data from point selections listed in the ROI manager,  but
> I'm having trouble getting access to them - in particular the Z
> coordinates.
>
> getSliceNumber() looks like a useful method but it expects a String
> index, which I don't know how to retrieve.  This is what I have so far:
>
> Mike
>
> public class Fit_Sphere implements PlugInFilter {
>     ImagePlus imp;
>     RoiManager roiMan = RoiManager.getInstance();
>        
>     public int setup(String arg, ImagePlus imp) {
>         this.imp = imp;
>         return DOES_ALL + STACK_REQUIRED;
>     }
>    
>     public void run(ImageProcessor ip) {
>         if (roiMan.getCount() < 5) IJ.error("ROI Manager contains < 5
> ROIs");
>         double xSum = 0, ySum = 0, zSum = 0;
>         Roi[] roiArray = roiMan.getRoisAsArray();
>         Hashtable roiHash = roiMan.getROIs();
>         List listRoi = roiMan.getList();
>         for (int i = 0; i<roiMan.getCount(); i++){
>             Roi roi = roiArray[i];
>             IJ.log("Roi "+i+" contains: "+roiArray[i]+" which has
> integer typecode "+roi.getType());
>             if (roi.getType() == 10){
>                  Rectangle xy = roi.getBoundingRect();
>                  xSum += xy.getX();
>                  ySum += xy.getY();
>                  zSum +=  //???
>             }
>         }
>
>
>

--
Dr Michael Doube  BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London  SW7 2AZ
United Kingdom