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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.ImageProcessor;
/**
* Skeleton Filter
*
* @author Xavier Philippeau (from work of Dr. Chai Quek)
*
*/
public class Skeleton_ implements PlugInFilter {
// neighbours order
private int[] dx = new int[] {-1, 0, 1,1,1,0,-1,-1};
private int[] dy = new int[] {-1,-1,-1,0,1,1, 1, 0};
// Smoothing pattern
private int[] pattern1={-1,1,0,1,0,0,0,0};
private int[] pattern2={0,1,0,1,-1,0,0,0};
private int[] pattern3={0,0,-1,1,0,1,0,0};
private int[] pattern4={0,0,0,1,0,1,-1,0};
private int[] pattern5={0,0,0,0,-1,1,0,1};
private int[] pattern6={-1,0,0,0,0,1,0,1};
private int[] pattern7={0,1,0,0,0,0,-1,1};
private int[] pattern8={0,1,-1,0,0,0,0,1};
// filter configuration
private boolean blackbackground = true;
private int threshold = 0;
// About...
private void showAbout() {
IJ.showMessage("Skeleton...","Skeleton Filter by Pseudocode");
}
public int setup(String arg, ImagePlus imp) {
// about...
if (arg.equals("about")) {
showAbout();
return DONE;
}
// else...
if (imp==null) return DONE;
// Configuration dialog.
GenericDialog gd = new GenericDialog("Parameters");
gd.addChoice("Background color", new String[]{"Black","White"}, "Black");
gd.addNumericField("Black/White threshold",128,0);
while(true) {
gd.showDialog();
if ( gd.wasCanceled() ) return DONE;
this.blackbackground = gd.getNextChoice().equals("Black")?true:false;
this.threshold = (int)gd.getNextNumber();
if (this.threshold<=0) continue;
if (this.threshold>=255) continue;
break;
}
gd.dispose();
return PlugInFilter.DOES_8G;
}
public void run(ImageProcessor ip) {
// ImageProcessor -> ByteProcessor conversion
ByteProcessor bp = new ByteProcessor(ip.getWidth(),ip.getHeight());
for (int y = 0; y < ip.getHeight(); y++) {
for (int x = 0; x < ip.getWidth(); x++) {
bp.set(x,y,ip.getPixel(x,y));
}
}
// filter
ByteProcessor newbp = filter( bp );
// ByteProcessor -> ImageProcessor conversion
ImageProcessor out = new ByteProcessor(ip.getWidth(),ip.getHeight());
for (int y = 0; y < ip.getHeight(); y++) {
for (int x = 0; x < ip.getWidth(); x++) {
out.set(x,y,newbp.get(x,y));
}
}
ImagePlus newImg = new ImagePlus("Skeleton", out);
newImg.show();
}
// -------------------------------------------------------------------------
// Binary value of the gray scale image (0..255) -> (0,1)
private int ChannelValue(ByteProcessor c,int x,int y) {
if (c.getPixel(x,y)<this.threshold) return 0;
return 1;
}
// Neighbourhood
private int neighbourhood(ByteProcessor c,int x,int y) {
int neighbourhood=0;
for(int i=0;i<8;i++)
neighbourhood += ChannelValue(c,x+dx[i],y+dy[i]);
return neighbourhood;
}
// Transitions Count
private int transitions(ByteProcessor c,int x,int y) {
int Trans=0;
for(int i=0;i<8;i++) {
int pc = ChannelValue(c,x+dx[i],y+dy[i]);
int pn = ChannelValue(c,x+dx[(i+1)%8],y+dy[(i+1)%8]);
if ((pc==0) && (pn==1)) Trans++;
}
return Trans;
}
// Match a pattern
private boolean matchPattern(ByteProcessor c,int x,int y,int[] pattern) {
for(int i=0;i<8;i++) {
if (pattern[i]==-1) continue;
int v = ChannelValue(c,x+dx[i],y+dy[i]);
if (pattern[i]!=v) return false;
}
return true;
}
// Match one of the 8 patterns
private boolean matchOneOfPatterns(ByteProcessor c,int x,int y) {
if (matchPattern(c,x,y,pattern1)) return true;
if (matchPattern(c,x,y,pattern2)) return true;
if (matchPattern(c,x,y,pattern3)) return true;
if (matchPattern(c,x,y,pattern4)) return true;
if (matchPattern(c,x,y,pattern5)) return true;
if (matchPattern(c,x,y,pattern6)) return true;
if (matchPattern(c,x,y,pattern7)) return true;
if (matchPattern(c,x,y,pattern8)) return true;
return false;
}
private ByteProcessor thinning(ByteProcessor original) {
int width = original.getWidth();
int height = original.getHeight();
// previous image buffer
ByteProcessor c = new ByteProcessor(width,height);
for(int y=0;y<height;y++)
for(int x=0;x<width;x++)
if (this.blackbackground)
c.set(x,y,255*ChannelValue(original,x,y));
else
c.set(x,y,255-255*ChannelValue(original,x,y));
// new image buffer
ByteProcessor c2 = new ByteProcessor(width,height);
// loop until idempotence
for(int loop=0;;loop++) {
int pixelchangecount=0;
// copy previous image in new image
for(int y=0;y<height;y++)
for(int x=0;x<width;x++)
c2.set(x,y,c.get(x,y));
// for each pixel
for(int y=1;y<height-1;y++) {
for(int x=1;x<width-1;x++) {
// pixel value
int v = ChannelValue(c,x,y);
// pixel not set -> next
if (v==0) continue;
// is a boundary ?
int previousNeighbourhood = neighbourhood(c,x,y);
if (previousNeighbourhood==8) continue;
// is an extremity ?
int currentNeighbourhood = neighbourhood(c2,x,y);
if (currentNeighbourhood<=1) continue;
if (currentNeighbourhood>=6) continue;
// is a connection ?
int transitionsCount = transitions(c2,x,y);
// Addition to the original algorithm:
// Preservation of the "Y curve" near the edges
if (transitionsCount==1 && previousNeighbourhood<=3) continue;
if (transitionsCount==1) {
pixelchangecount++;
c2.set(x,y,0);
continue;
}
// is a deletable pixel ?
boolean matchOne = matchOneOfPatterns(c2,x,y);
if (matchOne) {
pixelchangecount++;
c2.set(x,y,0);
continue;
}
}
}
// no change -> return result
if (pixelchangecount==0) return c;
// swap image buffers, then loop.
ByteProcessor tmp = c;
c=c2;
c2=tmp;
}
}
// Return the skeleton
public ByteProcessor filter(ByteProcessor bp) {
ByteProcessor skel = thinning(bp);
return skel;
}
} |
[image] Filtre Squelette pour ImageJ
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