open-modify-show-save-alpha-png.bsh

/**
 * Open, modify, show, and save 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.
 * 
 * @author Stephan Saalfeld
 */
import javax.imageio.ImageIO;
import java.awt.image.BufferedImage;

/* name of the png file */
path = "/path/to/example.png";

/* open the file in to a ColorProcessor */
cp = new ColorProcessor(ImageIO.read(new File(path)));
cpPixels = cp.getPixels();
w = cp.getWidth();
h = cp.getHeight();

/* split ARGB channels into individual ByteProcessors */
bpAlpha = new ByteProcessor(w, h);
bpAlphaPixels = bpAlpha.getPixels();
bpRed = new ByteProcessor(w, h);
bpRedPixels = bpRed.getPixels();
bpGreen = new ByteProcessor(w, h);
bpGreenPixels = bpGreen.getPixels();
bpBlue = new ByteProcessor(w, h);
bpBluePixels = bpBlue.getPixels();
for (i = 0; i < cpPixels.length; ++i) {
	bpAlphaPixels[i] = (byte)(cpPixels[i] >> 24);
	bpRedPixels[i] = (byte)(cpPixels[i] >> 16);
	bpGreenPixels[i] = (byte)(cpPixels[i] >> 8);
	bpBluePixels[i] = (byte)cpPixels[i];
}

/* combine individual channels into a composite image and show */
stack = new ImageStack(w, h);
stack.addSlice("red", bpRed);
stack.addSlice("green", bpGreen);
stack.addSlice("blue", bpBlue);
stack.addSlice("alpha", bpAlpha);

imp = new ImagePlus("RGBA-" + path, stack);
imp.setDimensions(4, 1, 1);
imp.setOpenAsHyperStack(true);
cimp = new CompositeImage(imp);
cimp.setMode(CompositeImage.GRAYSCALE);
cimp.show();

/* copy the the alpha channel and punch a hole into the copy */
bpAlphaCopy = bpAlpha.duplicate();
bpAlphaCopyPixels = bpAlphaCopy.getPixels();
r = Math.min(w, h) / 4;
roi = new OvalRoi(w / 2 - r, h / 2 - r, 2 * r, 2 * r);
bpAlphaCopy.setValue(0);
bpAlphaCopy.fill(roi);

/* combine alpha channel copy and color channels into an ARGB raster */
cp2Pixels = new int[w * h];
for (i = 0; i < cp2Pixels.length; ++i) {
	cp2Pixels[i] =
		( ( bpAlphaCopyPixels[i] & 0xff ) << 24 ) |
		( ( bpRedPixels[i] & 0xff ) << 16 ) |
		( ( bpGreenPixels[i] & 0xff ) << 8 ) |
		( bpBluePixels[i] & 0xff );
}
cp2Image = new BufferedImage(w, h, BufferedImage.TYPE_INT_ARGB);
raster = cp2Image.getRaster();
raster.setDataElements(0, 0, w, h, cp2Pixels);

/* show the modified image (alpha is ignored by ImageJ) */
cp2 = new ColorProcessor(cp2Image);
imp2 = new ImagePlus("ARGB-modified-" + path, cp2);
imp2.show();

/* save the modified image (alpha correct) */
ImageIO.write(
	cp2Image,
	"png",
	new File(path + "-modified.png"));