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import ij.IJ;
import ij.ImagePlus;
import ij.gui.GenericDialog;
import ij.plugin.filter.PlugInFilter;
import ij.process.ByteProcessor;
import ij.process.ColorProcessor;
import ij.process.ImageProcessor;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* @author Xavier Philippeau
*
* UnNoise Plugin.
*
* A noise detection and removal filter with edge preservation.
*/
public class UnNoise_ implements PlugInFilter {
private static final int ROAD = 0;
private static final int VARIANCE = 1;
private ImagePlus imgOrig = null;
private int aperture = 0;
private double factor = 0;
private int itermax = 0;
private int estimator;
/**
* This method gets a reference to the image to be locally ranked
* and returns the filter capabilities.
* @param arg calls for the "about" information.
* @param imp This is the image to be processed
*
* @return Returns DOES_8G + DOES_RGB or DONE.
*/
public int setup(String arg, ImagePlus imp) {
// about...
if (arg.equals("about")) {
showAbout();
return DONE;
}
// else...
if (imp==null) return DONE;
//original image
this.imgOrig = imp ;
// Configuration dialog.
GenericDialog gd = new GenericDialog("Parameters");
gd.addChoice("Estimator",new String[] {"ROAD","Variance"}, "ROAD");
gd.addNumericField("Window aperture (size=2*a+1)",2,0);
gd.addNumericField("Variance factor",1.0,1);
gd.addNumericField("Iterations",5,0);
while(true) {
gd.showDialog();
if ( gd.wasCanceled() ) return DONE;
String estimator = gd.getNextChoice();
if (estimator.equalsIgnoreCase("ROAD")) this.estimator=ROAD;
if (estimator.equalsIgnoreCase("Variance")) this.estimator=VARIANCE;
this.aperture = (int) gd.getNextNumber();
this.factor = (double) gd.getNextNumber();
this.itermax = (int) gd.getNextNumber();
if (this.aperture<=0) continue;
if (this.factor<=0) continue;
if (this.itermax<=0) continue;
break;
}
gd.dispose();
return DOES_8G+DOES_RGB;
}
/**
* Filters use this method to process the image. If the
* SUPPORTS_STACKS flag was set, it is called for each slice in
* a stack. ImageJ will lock the image before calling
* this method and unlock it when the filter is finished.
*/
public void run(ImageProcessor ip) {
// project image to HSV color space
ByteProcessor work = null;
if (this.imgOrig.getBitDepth()==24) work=transformRGB(this.imgOrig);
if (this.imgOrig.getBitDepth()==8) work=transformGray(this.imgOrig);
// filter = Noise Estimation (->mask) + Pixel replacement
ByteProcessor mask = null;
for(int i=0;i<this.itermax;i++) {
if (this.estimator==ROAD)
mask = this.ROAD(work,this.aperture,this.factor);
if (this.estimator==VARIANCE)
mask = this.Variance(work,this.aperture,this.factor);
work = this.inpaint(work,mask);
}
// project image to RGB color space
ImageProcessor newIp = null;
if (this.imgOrig.getBitDepth()==24) newIp=invTransformRGB(this.imgOrig,work);
if (this.imgOrig.getBitDepth()==8) newIp=invTransformGray(this.imgOrig,work);
// show new image
ImagePlus newImg = new ImagePlus(this.imgOrig.getTitle()+"_UnNoised", newIp);
newImg.show();
}
// RGB -> HSV
private ByteProcessor transformRGB(ImagePlus img) {
ByteProcessor bp = new ByteProcessor(img.getWidth(),img.getHeight());
for (int y = 0; y < img.getHeight(); y++) {
for (int x = 0; x < img.getWidth(); x++) {
int[] lrgb = img.getPixel(x,y);
float[] hsb = Color.RGBtoHSB(lrgb[0],lrgb[1],lrgb[2],null);
bp.set(x,y,(int)(hsb[2]*255));
}
}
return bp;
}
// GRAY -> HSV
private ByteProcessor transformGray(ImagePlus img) {
ByteProcessor bp = new ByteProcessor(img.getWidth(),img.getHeight());
for (int y = 0; y < img.getHeight(); y++) {
for (int x = 0; x < img.getWidth(); x++) {
int[] lrgb = img.getPixel(x,y);
bp.set(x,y,lrgb[0]);
}
}
return bp;
}
// HSV -> RGB
private ImageProcessor invTransformRGB(ImagePlus img, ByteProcessor bp) {
ImageProcessor out = new ColorProcessor(img.getWidth(),img.getHeight());
for (int y = 0; y < img.getHeight(); y++) {
for (int x = 0; x < img.getWidth(); x++) {
int[] lrgb = img.getPixel(x,y);
float[] hsb = Color.RGBtoHSB(lrgb[0],lrgb[1],lrgb[2],null);
int rgb = Color.HSBtoRGB(hsb[0],hsb[1],bp.get(x,y)/255f);
out.set(x,y,rgb);
}
}
return out;
}
// HSV -> GRAY
private ImageProcessor invTransformGray(ImagePlus img, ByteProcessor bp) {
ImageProcessor out = new ByteProcessor(img.getWidth(),img.getHeight());
for (int y = 0; y < img.getHeight(); y++) {
for (int x = 0; x < img.getWidth(); x++) {
out.set(x,y,bp.get(x,y));
}
}
return out;
}
// About...
private void showAbout() {
IJ.showMessage("UnNoise...","UnNoise Filter by Pseudocode");
}
/**
* Noise estimation using the ROAD Estimator
*
* (ROAD: R. Garnett, T. Huegerich, C. Chui and W.-J. He)
*
* @param c Input data (luminosity/gray-level)
* @param aperture Window aperture
* @param coef variance theshold factor
* @return mask (255="masked" 0="unmasked")
*/
private ByteProcessor ROAD(ByteProcessor c, int aperture, double coef) {
int width = c.getWidth();
int height = c.getHeight();
// value-to-distance table
double[] distance = new double[256];
distance[0]=0;
for(int i=1;i<256;i++) {
double x = (double)i/255;
double log = Math.log(x)/Math.log(2);
distance[i]=1+Math.max(log,-5)/5;
}
ByteProcessor mask = new ByteProcessor(width,height);
for (int y=0; y<height; y++) {
for (int x=0; x<width; x++) {
// compute distances between pixels
int[] dist = new int[(2*aperture+1)*(2*aperture+1)];
int average=0; int count=0;
for(int dy=-aperture;dy<=aperture;dy++) {
for(int dx=-aperture;dx<=aperture;dx++) {
if (c.getPixel(x+dx,y+dy)<0) continue;
int i = Math.abs(c.getPixel(x+dx,y+dy)-c.getPixel(x,y));
dist[count]=(int)(255.0*distance[i]);
count++;
average+=c.getPixel(x+dx,y+dy);
}
}
average/=count;
// Noise estimation (ROAD at rank nmb_pixels/2)
Arrays.sort(dist,0,count);
int road = 0;
int rank=count/2;
for(int i=0;i<rank;i++) road+=dist[i];
// compute threshold (= variance)
int etype=0; count=0;
for(int dy=-aperture;dy<=aperture;dy++) {
for(int dx=-aperture;dx<=aperture;dx++) {
if ((x+dx)<0) continue;
if ((x+dx)>=width) continue;
if ((y+dy)<0) continue;
if ((y+dy)>=height) continue;
double e = c.getPixel(x+dx,y+dy)-average;
etype+=e*e;
count++;
}
}
etype=(int)Math.sqrt(etype/count);
int threshold = (int)(rank*etype);
// pixel exceed threshold -> noise
if ( (road>=(threshold*coef)) && (etype>0) ) {
mask.putPixel(x,y,255);
} else {
mask.putPixel(x,y,0);
}
} }
return mask;
}
/**
* Noise estimation using Variance Estimator
*
* @param c Input data (luminosity/gray-level)
* @param aperture Window aperture
* @param coef variance theshold factor
* @return mask (255="masked" 0="unmasked")
*/
private ByteProcessor Variance(ByteProcessor c, int aperture, double coef) {
int width = c.getWidth();
int height = c.getHeight();
ByteProcessor mask = new ByteProcessor(width,height);
for (int y=0; y<height; y++) {
for (int x=0; x<width; x++) {
// compute average
float average=0; int count=0;
for(int dy=-aperture;dy<=aperture;dy++) {
for(int dx=-aperture;dx<=aperture;dx++) {
if ((x+dx)<0) continue;
if ((x+dx)>=width) continue;
if ((y+dy)<0) continue;
if ((y+dy)>=height) continue;
average += c.get(x+dx,y+dy);
count++;
}
}
average/=count;
// compute variance
float etype=0; count=0;
for(int dy=-aperture;dy<=aperture;dy++) {
for(int dx=-aperture;dx<=aperture;dx++) {
if ((x+dx)<0) continue;
if ((x+dx)>=width) continue;
if ((y+dy)<0) continue;
if ((y+dy)>=height) continue;
float e = Math.abs(c.get(x+dx,y+dy)-average);
etype += e*e;
count++;
}
}
etype=(float)Math.sqrt(etype/count);
// pixel exceed threshold -> noise
if (Math.abs(c.get(x,y)-average)>coef*etype) {
mask.set(x,y,255);
} else {
mask.set(x,y,0);
}
} }
return mask;
}
/**
* Fast (not accurate) Inpainting
*
* @param c Input data (luminosity/gray-level)
* @param mask masked pixel to evaluate
* @return Output data (luminosity/gray-level)
*/
private ByteProcessor inpaint(ByteProcessor c, ByteProcessor mask) {
int width = c.getWidth();
int height = c.getHeight();
ByteProcessor c2 = new ByteProcessor(width,height);
for (int y=0; y<height; y++)
for (int x=0; x<width; x++)
c2.set(x,y,c.get(x,y));
ByteProcessor newmask = new ByteProcessor(width,height);
for (int y=0; y<height; y++)
for (int x=0; x<width; x++)
newmask.set(x,y,mask.get(x,y));
int n = 8;
int[] dx = new int[] {-1,0,1,1,1,0,-1,-1};
int[] dy = new int[] {-1,-1,-1,0,1,1,1,0};
while(true) {
// front-line masked/unmasked
List contourInt = new ArrayList();
for (int y = 0; y < height; y++) {
for (int x = 0; x < width; x++) {
if (mask.get(x,y)==0) continue;
for (int i = 0; i < n; i++) {
int xk = x + dx[i];
int yk = y + dy[i];
if (xk<0 || xk>=width) continue;
if (yk<0 || yk>=height) continue;
if (mask.get(xk,yk)>0) continue;
contourInt.add( new int[] {x,y} );
break;
}
}
}
// exit when no front-line
if (contourInt.isEmpty()) break;
// isophotes continuation
for(int j=0;j<contourInt.size();j++) {
int[] pixel = (int[]) contourInt.get(j);
int x = pixel[0];
int y = pixel[1];
double value=0;
double wsum=0;
for (int i = 0; i < n; i++) {
int xk = x + dx[i];
int yk = y + dy[i];
if (xk<0 || xk>=width) continue;
if (yk<0 || yk>=height) continue;
if (mask.get(xk,yk)>0) continue;
// gradient
double[] grad = gradient(c,xk,yk);
double norme = grad[0];
double angle = grad[1];
// gradient normal = isophote direction
angle+=Math.PI/2;
// Weight of the propagation:
// 1. dotproduct ( gradient normal . propagation vector )
double pscal = Math.cos(angle)*(-dx[i]) + (-Math.sin(angle))*(-dy[i]);
pscal/=Math.sqrt(dx[i]*dx[i]+dy[i]*dy[i]);
// 2. gradient magnitude (O -> omnidirectionnal)
double w = (norme)*Math.abs(pscal)+(1-norme)*1;
value += w*c.get(xk,yk);
wsum+=w;
}
if (wsum<=0) continue;
value/=wsum;
// set new value
c2.set(x,y,(int)value);
// pixel becomes unmasked
newmask.set(x,y,0);
}
mask=newmask;
}
return c2;
}
/**
* Compute the local Gradient of one pixel
*
* @param c Input Data
* @param x X coord
* @param y Y Coord
* @return double[0] = gradient norme (0..1), double[1] = gradient direction (0..2*PI)
*/
private double[] gradient(ByteProcessor c, int x, int y) {
int width = c.getWidth();
int height = c.getHeight();
double cst1 = (0.25*(2-Math.sqrt(2.0)));
double cst2 = (0.5f*(Math.sqrt(2.0)-1));
int px = x-1;
int nx = x+1;
int py = y-1;
int ny = y+1;
if (px<0) px=0;
if (nx>=width) nx=width-1;
if (py<0) py=0;
if (ny>=height) ny=height-1;
int Ipp=c.get(px,py);
int Ipc=c.get(px,y) ;
int Ipn=c.get(px,ny);
int Icp=c.get(x,py);
int Icn=c.get(x,ny);
int Inp=c.get(nx,py);
int Inc=c.get(nx,y) ;
int Inn=c.get(nx,ny);
double IppInn = cst1*(Inn-Ipp);
double IpnInp = cst1*(Ipn-Inp);
int gradx = (int)(IppInn-IpnInp-cst2*Ipc+cst2*Inc);
int grady = (int)(IppInn+IpnInp-cst2*Icp+cst2*Icn);
double norme = Math.sqrt( gradx*gradx + grady*grady );
double angle = 0;
if (norme>0) {
angle = Math.acos(gradx/norme);
if (grady>0) angle = 2*Math.PI - angle;
}
norme/=255;
return new double[] {norme,angle};
}
} |
Filtre UnNoise pour ImageJ
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