import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.filter.*;

/*
	Performs the Kuwahara Filter, a noise-reduction filter that preserves edges.

	a  a  ab   b  b
	a  a  ab   b  b
	ac ac abcd bd bd
	c  c  cd   d  d
	c  c  cd   d  d
    
	In the case of a 5x5 sampling window, the mean brightness and the  
	variance of each of the four 3x3 regions (a, b, c, d), are calculated
	and the value of the center pixel (abcd) is set to the mean value 
	of the region that with the smallest variance.
 
	Description based on the one at:
	http://www.incx.nec.co.jp/imap-vision/library/wouter/kuwahara.html
*/
public class Kuwahara_Filter  implements PlugInFilter {
	static int size = 5;
	static boolean filterRGB;
	boolean isRGB;

	public int setup(String arg, ImagePlus imp) {
		if (imp==null)
			return DONE;
		isRGB = imp.getBitDepth()==24;
		if (!showDialog())
			return DONE;
		return IJ.setupDialog(imp, DOES_ALL-DOES_32+SUPPORTS_MASKING);
	}

	public void run(ImageProcessor ip) {
		if (isRGB) {
			if (filterRGB)
				filterRGB(ip);
			else
				filterIntensity(ip);
		} else
			filter(ip);
	}

	public void filter(ImageProcessor ip) {
		Rectangle roi = ip.getRoi();
		int width = roi.width;
		int height = roi.height;
		int size2 = (size+1)/2;
		int offset = (size-1)/2;
		int width2 = ip.getWidth()+offset;
		int height2 = ip.getHeight()+offset;
		float[][] mean = new float[width2][height2];
		float[][] variance = new float[width2][height2];
		int x1start = roi.x;
		int y1start = roi.y;
		double sum, sum2;
		int n, v=0, xbase, ybase;
		for (int y1=y1start-offset; y1<y1start+height; y1++) {
			if ((y1%20)==0) IJ.showProgress(0.7*(y1-y1start)/height);
			for (int x1=x1start-offset; x1<x1start+width; x1++) {
				sum=0; sum2=0; n=0;
				for (int x2=x1; x2<x1+size2; x2++) {
					for (int y2=y1; y2<y1+size2; y2++) {
						v = ip.getPixel(x2, y2);
						sum += v;
						sum2 += v*v;
						n++;
					}
				}
				mean[x1+offset][y1+offset] = (float)(sum/n);
				variance[x1+offset][y1+offset] = (float)(sum2-sum*sum/n);
			}
		}
		//new ImagePlus("Variance", new FloatProcessor(variance)).show(); // ImageJ 1.35b or later
		int xbase2=0, ybase2=0;
		float var, min;
		for (int y1=y1start; y1<y1start+height; y1++) {
			if ((y1%20)==0) IJ.showProgress(0.7+0.3*(y1-y1start)/height);
			for (int x1=x1start; x1<x1start+width; x1++) {
				min = Float.MAX_VALUE;
				xbase = x1; ybase=y1;
				var = variance[xbase][ybase];
				if (var<min) {min= var; xbase2=xbase; ybase2=ybase;}
				xbase = x1+offset;
				var = variance[xbase][ybase];
				if (var<min) {min= var; xbase2=xbase; ybase2=ybase;}
				ybase = y1+offset;
				var = variance[xbase][ybase];
				if (var<min) {min= var; xbase2=xbase; ybase2=ybase;}
				xbase = x1; 
				var = variance[xbase][ybase];
				if (var<min) {min= var; xbase2=xbase; ybase2=ybase;}
				ip.putPixel(x1, y1, (int)(mean[xbase2][ybase2]+0.5));
			}
		}
		IJ.showProgress(1.0);
	}

	void filterRGB(ImageProcessor ip) {
		ColorProcessor cp = (ColorProcessor)ip;
		int width = cp.getWidth();
		int height = cp.getHeight();
		int size = width*height;
		byte[] R = new byte[size];
		byte[] G = new byte[size];
		byte[] B = new byte[size];
		IJ.showStatus("Kuwahara_Filter: red");
		cp.getRGB(R, G, B);
		ImageProcessor red = new ByteProcessor(width, height, R, null);
		filter(red);
		IJ.showStatus("Kuwahara_Filter: green");
		ImageProcessor green = new ByteProcessor(width, height, G, null);
		filter(green);
		IJ.showStatus("Kuwahara_Filter: blue");
		ImageProcessor blue = new ByteProcessor(width, height, B, null);
		filter(blue);
		cp.setRGB((byte[])red.getPixels(), (byte[])green.getPixels(), (byte[])blue.getPixels());
	}

	void filterIntensity(ImageProcessor ip) {
		ColorProcessor cp = (ColorProcessor)ip;
		int width = cp.getWidth();
		int height = cp.getHeight();
		int size = width*height;
		byte[] H = new byte[size];
		byte[] S = new byte[size];
		byte[] B = new byte[size];
		cp.getHSB(H, S, B);
		ImageProcessor ip2 = new ByteProcessor(width, height, B, null);
		filter(ip2);
		cp.setHSB(H, S, (byte[])ip2.getPixels());
	}

	boolean showDialog() {
		GenericDialog gd = new GenericDialog("Kuwahara Filter");
		gd.addNumericField("Sampling window width (must be odd):", size, 0, 3, "");
		if (isRGB)
			gd.addCheckbox("Filter all 3 channels (slower)", filterRGB);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		size = (int) gd.getNextNumber();
		if ((size&1)!=1) size--;
		if (size<3) size = 3;
		if (isRGB)
			filterRGB = gd.getNextBoolean();
		return true;
	}

}