Overlays and stack slices

[lechristophe]

Hi,

I'm writing a javascript that uses overlays to draw regions on a stack. What I do is that I set each slice for the ImagePlus, then create a ROI from a coordinates array, then add that roi the overlay. In the end I affect the Overlay to the stack and display the stack with its overlay.

The problem is that it doesn't keep each overlay associated with its slice: I get a single-slice overlay with all ROIs. How can I get overlays to stay associated with the stack slices, like what happens when manually adding ROIs to an overlay in an stack ? Is there a way to use something like over.add(roi) that takes into account which slice this particular overlay element has to be associated with ?

Here is a sample code I use :

importClass(Packages.ij.gui.Overlay);

var imp = IJ.createImage("Stack", "8-bit Black", 200, 200, 2);
var rm = new RoiManager();
var over = new Overlay();

imp.setSlice(1);
xpoints = [26,120,88,161];
ypoints = [38,44,108,158];
var roi1 = new PolygonRoi(convertArrayI(xpoints), convertArrayI(ypoints), xpoints.length, Roi.POLYLINE);
over.add(roi1);

imp.setSlice(2);
xpoints = [116,54,72,152];
ypoints = [38,88,157,123];
var roi2 = new PolygonRoi(convertArrayI(xpoints), convertArrayI(ypoints), xpoints.length, Roi.POLYLINE);
over.add(roi2);

imp.setOverlay(over);
imp.show();

function convertArrayI(arr) {
var jArr = java.lang.reflect.Array.newInstance(java.lang.Integer.TYPE, arr.length);
for (var i = 0; i < arr.length; i++) {
    jArr[i] = arr[i];
  }
  return jArr;
}


 

[Rasband, Wayne (NIH/NIMH) [E]]

On Jan 3, 2012, at 8:07 AM, Christophe Leterrier wrote:

> Hi,
>
> I'm writing a javascript that uses overlays to draw regions on a stack. What I do is that I set each slice for the ImagePlus, then create a ROI from a coordinates array, then add that roi the overlay. In the end I affect the Overlay to the stack and display the stack with its overlay.
>
> The problem is that it doesn't keep each overlay associated with its slice: I get a single-slice overlay with all ROIs. How can I get overlays to stay associated with the stack slices, like what happens when manually adding ROIs to an overlay in an stack ? Is there a way to use something like over.add(roi) that takes into account which slice this particular overlay element has to be associated with ?

Use the setPosition() method to associate an ROI to a particular stack slice. Use the PolygonRoi constructor that accepts a Polygon as the first argument to avoid the convertArrayI() function. Here is an updated version of your example:

  var imp = IJ.createImage("Stack", "8-bit Black", 200, 200, 2);
  var over = new Overlay();
  xpoints = [26,120,88,161];
  ypoints = [38,44,108,158];
  p = new Polygon(xpoints, ypoints, xpoints.length);
  var roi1 = new PolygonRoi(p, Roi.POLYLINE);
  roi1.setPosition(1);
  over.add(roi1);
  xpoints = [116,54,72,152];
  ypoints = [38,88,157,123];
  p = new Polygon(xpoints, ypoints, xpoints.length);
  var roi2 = new PolygonRoi(p, Roi.POLYLINE);
  roi2.setPosition(2);
  over.add(roi2);
  imp.setOverlay(over);
  imp.show();

-wayne

>
> Here is a sample code I use :
>
> importClass(Packages.ij.gui.Overlay);
>
> var imp = IJ.createImage("Stack", "8-bit Black", 200, 200, 2);
> var rm = new RoiManager();
> var over = new Overlay();
>
> imp.setSlice(1);
> xpoints = [26,120,88,161];
> ypoints = [38,44,108,158];
> var roi1 = new PolygonRoi(convertArrayI(xpoints), convertArrayI(ypoints), xpoints.length, Roi.POLYLINE);
> over.add(roi1);
>
> imp.setSlice(2);
> xpoints = [116,54,72,152];
> ypoints = [38,88,157,123];
> var roi2 = new PolygonRoi(convertArrayI(xpoints), convertArrayI(ypoints), xpoints.length, Roi.POLYLINE);
> over.add(roi2);
>
> imp.setOverlay(over);
> imp.show();
>
> function convertArrayI(arr) {
> var jArr = java.lang.reflect.Array.newInstance(java.lang.Integer.TYPE, arr.length);
> for (var i = 0; i < arr.length; i++) {
>    jArr[i] = arr[i];
>  }
>  return jArr;
> }
>
>
>