package Skeleton;
import ij.ImagePlus;import ij.ImageStack;import ij.process.ImageProcessor;import java.util.ArrayList;
public class Skeletonize3D { private ImagePlus imRef; private int width = 0; private int height = 0; private int depth = 0; private ImageStack inputImage = null;
public void setup(String arg, ImagePlus imp) { this.imRef = imp; SUM.setImage(this.imRef); }
public ImageProcessor run(ImageProcessor ip) { this.width = this.imRef.getWidth(); this.height = this.imRef.getHeight(); this.depth = this.imRef.getStackSize(); this.inputImage = this.imRef.getStack(); this.prepareData(this.inputImage); this.computeThinImage(this.inputImage);
for(int i = 1; i <= this.inputImage.getSize(); ++i) { this.inputImage.getProcessor(i).multiply(255.0); }
this.inputImage.update(ip); return this.inputImage.getProcessor(1); }
private void prepareData(ImageStack outputImage) { for(int z = 0; z < this.depth; ++z) { for(int x = 0; x < this.width; ++x) { for(int y = 0; y < this.height; ++y) { if (((byte[])((byte[])this.inputImage.getPixels(z + 1)))[x + y * this.width] != 0) { ((byte[])outputImage.getPixels(z + 1))[x + y * this.width] = 1; } } } } }
public void computeThinImage(ImageStack outputImage) { new ImagePlus(); new ArrayList(); int[] eulerLUT = new int[256]; SUM.fillEulerLUT(eulerLUT); int iter = 1;
for(int unchangedBorders = 0; unchangedBorders < 6; ++iter) { unchangedBorders = 0;
for(int currentBorder = 1; currentBorder <= 6; ++currentBorder) { ForkJoinSkeletonize2 fs2 = new ForkJoinSkeletonize2(); ArrayList<int[]> simpleBorderPoints = fs2.thin(outputImage, currentBorder, eulerLUT); boolean noChange = true; int[] index = null;
for(int i = 0; i < simpleBorderPoints.size(); ++i) { index = (int[])simpleBorderPoints.get(i); SUM.setPixel(outputImage, index[0], index[1], index[2], (byte)0); if (!SUM.isSimplePoint(SUM.getNeighborhood(outputImage, index[0], index[1], index[2]))) { SUM.setPixel(outputImage, index[0], index[1], index[2], (byte)1); } else { noChange = false; } }
if (noChange) { ++unchangedBorders; }
simpleBorderPoints.clear(); } } }}
