Method flattenImage

ij/src/main/java/ij/ImagePlus.java:3408–3423

Flattens Overlay 'overlay' on slice 'slice' of ImageStack 'stack'. Copied from OverlayCommands by Marcel Boeglin 2014.01.08.

(ImageStack stack, int slice, Overlay overlay, boolean showAll)

	 * Copied from OverlayCommands by Marcel Boeglin 2014.01.08.
	*/
	private void flattenImage(ImageStack stack, int slice, Overlay overlay, boolean showAll) {
		ImageProcessor ips = stack.getProcessor(slice);
		ImagePlus imp1 = new ImagePlus("temp", ips);
		int w = imp1.getWidth();
		int h = imp1.getHeight();
		for (int i=0; i<overlay.size(); i++) {
			Roi r = overlay.get(i);
			int roiPosition = r.getPosition();
			//IJ.log(slice+" "+i+" "+roiPosition+" "+showAll+" "+overlay.size());
			if (!(roiPosition==0 || roiPosition==slice || showAll))
				r.setLocation(w, h);
		}
		imp1.setOverlay(overlay);
		ImagePlus imp2 = imp1.flatten();
		stack.setPixels(imp2.getProcessor().getPixels(), slice);
	}

	/** Flattens Overlay 'overlay' on slice 'slice' corresponding to
	 * coordinates 'z' and 't' in RGB-HyperStack 'stack'.