GaussianPlugin.java

package gdsc.utils;

import gdsc.UsageTracker;

/*----------------------------------------------------------------------------- 
 * GDSC Plugins for ImageJ
 * 
 * Copyright (C) 2011 Alex Herbert
 * Genome Damage and Stability Centre
 * University of Sussex, UK
 * 
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *---------------------------------------------------------------------------*/

import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.plugin.PlugIn;
import ij.process.FloatProcessor;

/**
 * Creates a Gaussian image
 */
public class GaussianPlugin implements PlugIn
{
	private static final String TITLE = "Gaussian";
	private static int width = 256;
	private static int height = 256;
	private static float amplitude = 255;
	private static float x = 100;
	private static float y = 130;
	private static float x_sd = 20;
	private static float y_sd = 10;
	private static float angle = 0f;
	private static float noise = 10f;

	/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
	public void run(String arg)
	{
		UsageTracker.recordPlugin(this.getClass(), arg);
		GenericDialog gd = new GenericDialog(TITLE);
		gd.addNumericField("Width", width, 0);
		gd.addNumericField("Height", height, 0);
		gd.addNumericField("Amplitude", amplitude, 0);
		gd.addNumericField("X", x, 1);
		gd.addNumericField("Y", y, 1);
		gd.addNumericField("X_sd", x_sd, 1);
		gd.addNumericField("Y_sd", y_sd, 1);
		gd.addSlider("Angle", 0, 180, angle);
		gd.addNumericField("Noise", noise, 1);

		gd.showDialog();
		if (gd.wasCanceled())
			return;

		width = (int) gd.getNextNumber();
		height = (int) gd.getNextNumber();
		amplitude = (float) gd.getNextNumber();
		x = (float) gd.getNextNumber();
		y = (float) gd.getNextNumber();
		x_sd = (float) gd.getNextNumber();
		y_sd = (float) gd.getNextNumber();
		angle = (float) gd.getNextNumber();
		noise = (float) gd.getNextNumber();

		float[] img = createGaussian(width, height, new float[] { amplitude }, new float[] { x }, new float[] { y },
				new float[] { x_sd }, new float[] { y_sd }, new float[] { (float) (angle * Math.PI / 180.0) });
		FloatProcessor fp = new FloatProcessor(width, height, img, null);
		if (noise > 0)
			fp.noise(noise);
		new ImagePlus("Gaussian", fp).show();
	}

	private float[] createGaussian(int width, int height, float[] amplitude, float[] xpos, float[] ypos, float[] sx,
			float[] sy, float[] angle)
	{
		float[] img = new float[width * height];

		for (int i=0; i<1; i++)
		{
			float sigma_x = sx[i];
			float sigma_y = sy[i];
			float theta = angle[i];
			
			float a = (float) (Math.cos(theta)*Math.cos(theta)/(2*sigma_x*sigma_x) + Math.sin(theta)*Math.sin(theta)/(2*sigma_y*sigma_y));
			float b = (float) (Math.sin(2*theta)/(4*sigma_x*sigma_x) - Math.sin(2*theta)/(4*sigma_y*sigma_y));
			float c = (float) (Math.sin(theta)*Math.sin(theta)/(2*sigma_x*sigma_x) + Math.cos(theta)*Math.cos(theta)/(2*sigma_y*sigma_y));
			
			int index = 0;
			for (int yi=0; yi<height; yi++)
			{
				for (int xi=0; xi<width; xi++) 
				{
					img[index++] += gaussian(xi, yi, amplitude[i], xpos[i], ypos[i], a, b, c);
				}
			}
		}

		return img;
	}

	/**
	 * Generic form of the 2D Gaussian
	 * @param x
	 * @param y
	 * @return
	 */
	private float gaussian(float x, float y, float A, float x0, float y0, float a, float b, float c)
	{
		return (float) (A*Math.exp( -(a*(x-x0)*(x-x0) + 2*b*(x-x0)*(y-y0) + c*(y-y0)*(y-y0)))); 
	}
}