ROI type and ROI Manager

[William O'Connell-3]

Dear listers,

I have a plugin which fits edges to objects in a stack of images. The edge
points  are saved as PolygonRois(type 2) in an RoiManager.  I retrieve the
ROIs in another Plugin with the getRoisAsArray() command. But the ROIs are
now type 4, TRACE_ROIs.  I want to retrieve the coordinate points, but the
getXCoordinates() and getYCoordinates() are not supported.
I welcome any suggestions.
Bill O'Connell

[selwyn]

William O'Connell wrote:
> Dear listers,
>
> I have a plugin which fits edges to objects in a stack of images. The edge
> points  are saved as PolygonRois(type 2) in an RoiManager.  I retrieve the
> ROIs in another Plugin with the getRoisAsArray() command. But the ROIs are
> now type 4, TRACE_ROIs.  I want to retrieve the coordinate points, but the
> getXCoordinates() and getYCoordinates() are not supported.
> I welcome any suggestions.
> Bill O'Connell

You might be able to use the following piece of javascript I adapted
from ListPixelsinROI.js found under the Macros examples at the ImageJ
website.

Selwyn

// List Perimeter Pixels In ROI
//
// Displays the coordinates and values of
// the pixels within a non-rectangular ROI.
//
   var img = IJ.getImage();
   var roi = img.getRoi();
   var mask = roi!=null?roi.getMask():null;
   if (mask==null)
       IJ.error("Non-rectangular ROI required");
   var ip = img.getProcessor();
   var r = roi.getBounds();
   var z = img.getCurrentSlice()-1;
   var toggle = 0;
   for (var y=0; y<r.height; y++) {
      for (var x=0; x<r.width; x++) {
         if (mask.getPixel(x,y)!=toggle) {
             toggle = (toggle == 0) ? 255 : 0;
             IJ.log(x+" \t"+y+" \t"+z+"  \t"+ip.getPixel(r.x+x,r.y+y));
          }
      }
   }

[selwyn]

selwyn wrote:

> William O'Connell wrote:
>> Dear listers,
>>
>> I have a plugin which fits edges to objects in a stack of images. The
>> edge
>> points  are saved as PolygonRois(type 2) in an RoiManager.  I retrieve
>> the
>> ROIs in another Plugin with the getRoisAsArray() command. But the ROIs
>> are
>> now type 4, TRACE_ROIs.  I want to retrieve the coordinate points, but
>> the
>> getXCoordinates() and getYCoordinates() are not supported.
>> I welcome any suggestions.
>> Bill O'Connell
>
> You might be able to use the following piece of javascript I adapted
> from ListPixelsinROI.js found under the Macros examples at the ImageJ
> website.
>
> Selwyn
>
> // List Perimeter Pixels In ROI
> //
> // Displays the coordinates and values of
> // the pixels within a non-rectangular ROI.
> //
>   var img = IJ.getImage();
>   var roi = img.getRoi();
>   var mask = roi!=null?roi.getMask():null;
>   if (mask==null)
>       IJ.error("Non-rectangular ROI required");
>   var ip = img.getProcessor();
>   var r = roi.getBounds();
>   var z = img.getCurrentSlice()-1;
>   var toggle = 0;
>   for (var y=0; y<r.height; y++) {
>      for (var x=0; x<r.width; x++) {
>         if (mask.getPixel(x,y)!=toggle) {
>             toggle = (toggle == 0) ? 255 : 0;
>             IJ.log(x+" \t"+y+" \t"+z+"  \t"+ip.getPixel(r.x+x,r.y+y));
>          }
>      }
>   }

Oops last line should be changed to the following for absolute coordinates:

IJ.log((r.x+x)+" \t"+(r.y+y)+" \t"+z+"  \t"+ip.getPixel(r.x+x,r.y+y));

selwyn

[Wayne Rasband]

> Dear listers,
>
> I have a plugin which fits edges to objects in a stack of images.  
> The edge
> points  are saved as PolygonRois(type 2) in an RoiManager.  I  
> retrieve the
> ROIs in another Plugin with the getRoisAsArray() command. But the  
> ROIs are
> now type 4, TRACE_ROIs.  I want to retrieve the coordinate points,  
> but the
> getXCoordinates() and getYCoordinates() are not supported.
> I welcome any suggestions.
> Bill O'Connell

ROIs returned by getRoisAsArray() have the original types. When I add  
rectangular, oval, polygon and traced ROIs to the ROI Manager and run  
(using the editor's Macros>Evaluate JavaScript command) this  
JavaScript code

     importClass(Packages.ij.plugin.frame.RoiManager);
     manager = RoiManager.getInstance();
     rois = manager.getRoisAsArray();
     for (i=0; i<rois.length; i++)
         print(rois[i].getName()+": "+rois[i].getType());

I get

    0067-0104: 0
    0077-0223: 1
    0251-0159: 2
    0383-0359: 4

In any case, getXCoordinates() and getYCoordinates() work with type 4  
(traced) ROIs.

     importClass(Packages.ij.plugin.frame.RoiManager);
     manager = RoiManager.getInstance();
     rois = manager.getRoisAsArray();
     roi = rois[3];
     print("type: "+roi.getType());
     n= roi.getNCoordinates();
     x = roi.getXCoordinates();
     y = roi.getYCoordinates();
     bounds = roi.getBounds();
     for (i=0; i<n; i++)
         print((bounds.x+x[i])+", "+(bounds.y+y[i]));

It is easier, however, to use the getPolygon() method

     importClass(Packages.ij.plugin.frame.RoiManager);
     manager = RoiManager.getInstance();
     rois = manager.getRoisAsArray();
     roi = rois[3];
     print("type: "+roi.getType());
     p = roi.getPolygon();
     for (i=0; i<p.npoints; i++)
         print(p.xpoints[i]+", "+p.ypoints[i]);

This is what the code looks like in Java

     RoiManager manager = RoiManager.getInstance();
     Roi[] rois = manager.getRoisAsArray();
     Roi roi = rois[3];
     IJ.log("type: "+roi.getType());
     Polygon p = roi.getPolygon();
     for (int i=0; i<p.npoints; i++)
         IJ.log(p.xpoints[i]+", "+p.ypoints[i]);

-wayne

[William O'Connell-3]

Thanks wayne,

I was using the following code rather than  RoiManager.getInstance(), but
they give the same results. Only one instance of RoiManager can be open,
yes?

public class RoiManager_Test implements PlugIn {

     public void run(String arg) {
          RoiManager manager = (RoiManager)findOpenNonImageFrame("ROI");
//          RoiManager manager = RoiManager.getInstance();
          if(manager==null) {
            IJ.error("can't find ROI Manager!");
            return;
          }

        Roi[] rois = manager.getRoisAsArray();
    for(int r=0; r<rois.length; r++) {
    PolygonRoi roi = (PolygonRoi)rois[r];
    IJ.log("Roi " + r + " type is " + roi.getType());
                  IJ.log(roi.toString());
    }

    }


        Frame findOpenNonImageFrame(String sub) {
           Frame fr;
           Frame[] nonIm = WindowManager.getNonImageWindows();
           if(nonIm == null) return null;
           for(int id=0; id<nonIm.length; id++) {
              fr = nonIm[id];
              String s = fr.getTitle();
              IJ.log(s);
              int k = s.indexOf(sub);
              if(k >= 0) return fr;
              }
           return null;
        }


}


On Sun, Aug 3, 2008 at 9:01 AM, Rasband Wayne <[hidden email]> wrote:

> Dear listers,
>>
>> I have a plugin which fits edges to objects in a stack of images. The edge
>> points  are saved as PolygonRois(type 2) in an RoiManager.  I retrieve the
>> ROIs in another Plugin with the getRoisAsArray() command. But the ROIs are
>> now type 4, TRACE_ROIs.  I want to retrieve the coordinate points, but the
>> getXCoordinates() and getYCoordinates() are not supported.
>> I welcome any suggestions.
>> Bill O'Connell
>>
>
>
> ROIs returned by getRoisAsArray() have the original types. When I add
> rectangular, oval, polygon and traced ROIs to the ROI Manager and run (using
> the editor's Macros>Evaluate JavaScript command) this JavaScript code
>
>    importClass(Packages.ij.plugin.frame.RoiManager);
>    manager = RoiManager.getInstance();
>    rois = manager.getRoisAsArray();
>    for (i=0; i<rois.length; i++)
>        print(rois[i].getName()+": "+rois[i].getType());
>
> I get
>
>   0067-0104: 0
>   0077-0223: 1
>   0251-0159: 2
>   0383-0359: 4
>
> In any case, getXCoordinates() and getYCoordinates() work with type 4
> (traced) ROIs.
>
>    importClass(Packages.ij.plugin.frame.RoiManager);
>    manager = RoiManager.getInstance();
>    rois = manager.getRoisAsArray();
>    roi = rois[3];
>    print("type: "+roi.getType());
>    n= roi.getNCoordinates();
>    x = roi.getXCoordinates();
>    y = roi.getYCoordinates();
>    bounds = roi.getBounds();
>    for (i=0; i<n; i++)
>        print((bounds.x+x[i])+", "+(bounds.y+y[i]));
>
> It is easier, however, to use the getPolygon() method
>
>    importClass(Packages.ij.plugin.frame.RoiManager);
>    manager = RoiManager.getInstance();
>    rois = manager.getRoisAsArray();
>    roi = rois[3];
>    print("type: "+roi.getType());
>    p = roi.getPolygon();
>    for (i=0; i<p.npoints; i++)
>        print(p.xpoints[i]+", "+p.ypoints[i]);
>
> This is what the code looks like in Java
>
>    RoiManager manager = RoiManager.getInstance();
>    Roi[] rois = manager.getRoisAsArray();
>    Roi roi = rois[3];
>    IJ.log("type: "+roi.getType());
>    Polygon p = roi.getPolygon();
>    for (int i=0; i<p.npoints; i++)
>        IJ.log(p.xpoints[i]+", "+p.ypoints[i]);
>
> -wayne
>