/**
 * Open, modify, save and show a PNG image with an alpha
 * channel.  This script's purpose is to demontrate how this
 * can be done and where ImageJ needs to be bypassed.  For
 * real data processing, I suggest to transfer it into a
 * Java plugin as single pixel processing is prohibitively
 * slow from Beanshell.
 * 
 * Requires ImageJ 1.47o or later.
 * 
 * @author Stephan Saalfeld
 */
import javax.imageio.ImageIO;
import java.awt.image.BufferedImage;

/* open a PNG with alpha into a ColorProcessor */
path = IJ.getFilePath("Open PNG with alpha");
cp = new ColorProcessor(ImageIO.read(new File(path)));
w = cp.getWidth();
h = cp.getHeight();

/* get the alpha channel and punch a hole into it */
bpAlpha = cp.getChannel(4, null);
r = Math.min(w, h)/4;
roi = new OvalRoi(w/2-r, h/2-r, 2*r, 2*r);
bpAlpha.setValue(0);
bpAlpha.fill(roi);

/* restore the modified alpha channel and create a BufferedImage */
cp.setChannel(4, bpAlpha);
cp2Image = new BufferedImage(w, h, BufferedImage.TYPE_INT_ARGB);
raster = cp2Image.getRaster();
raster.setDataElements(0, 0, w, h, cp.getPixels());

/* save and show the modified image */
path2 = path + "-modified.png";
ImageIO.write(
	cp2Image,
	"png",
	new File(path2));
IJ.open(path2);