Z_Code_Stack.java

package sc.fiji.cookbook;

import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.gui.ImageWindow;
import ij.measure.Calibration;
import ij.plugin.PlugIn;
import ij.process.ColorProcessor;
import ij.process.ImageProcessor;

public class Z_Code_Stack implements PlugIn {

	ImageStack depthCoded;
	ImageProcessor ipc3;

	@Override
	public void run(final String arg) {
		final ImagePlus imp1 = WindowManager.getCurrentImage();
		if (imp1 == null) {
			IJ.noImage();
			return;
		}
		final int stackSize = imp1.getStackSize();
		if (stackSize < 2) {
			IJ.error("Reslicer", "Stack required");
			return;
		}
		final Calibration cal = imp1.getCalibration();
		final int width = imp1.getWidth();
		final int height = imp1.getHeight();
		IJ.newImage("New", "8-bit Black", 1, 1, stackSize);
		IJ.run("Spectrum");
		final ImagePlus imp2 = WindowManager.getCurrentImage();
		final ImageWindow winimp2 = imp2.getWindow();
		final ImageStack img1 = imp1.getStack();
		final ImageStack dcStack = new ImageStack(width, height);
		double val = 0;

		for (int i = 1; i <= stackSize; i++) {
			imp2.setSlice(i);
			val = (255) * ((double) i / (double) stackSize);
			IJ.run("Add...", "slice value=" + val);
		}

		IJ.run("RGB Color");
		ImageProcessor ip1 = imp1.getProcessor();
		final int[] rgb = new int[3];
		for (int n = 1; n <= stackSize; n++) {
			ipc3 = new ColorProcessor(width, height);
			ip1 = img1.getProcessor(n);
			imp2.setSlice(n);
			final ColorProcessor ipc2 = (ColorProcessor) imp2.getProcessor();

			for (int x = 0; x < width; x++) {
				for (int y = 0; y < height; y++) {
					ipc2.getPixel(0, 0, rgb);

					rgb[0] =
						(int) (((double) ip1.getPixel(x, y) / (double) 255) * rgb[0]);
					rgb[1] =
						(int) (((double) ip1.getPixel(x, y) / (double) 255) * rgb[1]);
					rgb[2] =
						(int) (((double) ip1.getPixel(x, y) / (double) 255) * rgb[2]);
					ipc3.putPixel(x, y, rgb);

				}
			}
			dcStack.addSlice("depth coded", ipc3);
		}
		new ImagePlus("Depth Coded Stack", dcStack).show();
		final ImagePlus impD = WindowManager.getCurrentImage();
		final ImageWindow winD = impD.getWindow();

		impD.setCalibration(cal);
		imp2.changes = false;
		winimp2.close();
		System.gc();
		WindowManager.setCurrentWindow(winD);

	}

}