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package io.github.mianalysis.mia.process.skeleton;
import java.util.ArrayList;
import org.apache.commons.math3.stat.regression.SimpleRegression;
import ij.ImagePlus;
import ij.plugin.ImageCalculator;
import ij.plugin.filter.Convolver;
import ij.process.ImageProcessor;
import io.github.mianalysis.mia.object.coordinates.Point;
import io.github.mianalysis.mia.process.voxel.BresenhamLine;
public class BreakFixer {
private double angleWeight = 1;
private double distanceWeight = 1;
private double endWeight = 20; // We want to heavily favour linking to another end point
static ArrayList getEndPoints(ImageProcessor iprConn, int x, int y, int nPx) {
// Getting the current point and nPx adjacent points. A line will be fit to these.
ArrayList c = new ArrayList<>();
int[] lc = new int[]{x,y};
iprConn.set(lc[0],lc[1],0);
c.add(lc);
int nAdded = 1;
while (nAdded < nPx) {
nAdded++;
// Check that all points around the current one are accessible
if (lc[0] <= 0 || lc[0] >= iprConn.getWidth()-1 || lc[1] <= 0 || lc[1] >= iprConn.getHeight()-1) break;
// Terminate process if a junction is reached
if (iprConn.get(lc[0]-1,lc[1]+1) > 3 | iprConn.get(lc[0]-1,lc[1]) > 3
| iprConn.get(lc[0]-1,lc[1]-1) > 3 | iprConn.get(lc[0],lc[1]+1) > 3
| iprConn.get(lc[0],lc[1]-1) > 3 | iprConn.get(lc[0]+1,lc[1]+1) > 3
| iprConn.get(lc[0]+1,lc[1]) > 3 | iprConn.get(lc[0]+1,lc[1]-1) > 3) break;
if (iprConn.get(lc[0]-1,lc[1]+1) == 3) {
lc = new int[]{lc[0]-1,lc[1]+1};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0]-1,lc[1]) == 3) {
lc = new int[]{lc[0]-1,lc[1]};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0]-1,lc[1]-1) == 3) {
lc = new int[]{lc[0]-1,lc[1]-1};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0],lc[1]+1) == 3) {
lc = new int[]{lc[0],lc[1]+1};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0],lc[1]-1) == 3) {
lc = new int[]{lc[0],lc[1]-1};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0]+1,lc[1]+1) == 3) {
lc = new int[]{lc[0]+1,lc[1]+1};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0]+1,lc[1]) == 3) {
lc = new int[]{lc[0]+1,lc[1]};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
continue;
}
if (iprConn.get(lc[0]+1,lc[1]-1) == 3) {
lc = new int[]{lc[0]+1,lc[1]-1};
c.add(lc);
iprConn.set(lc[0],lc[1],0);
}
}
return c;
}
public static double getEndAngleRads(ArrayList c) {
double[][] dataX = new double[c.size()][2];
double[][] dataY = new double[c.size()][2];
double cumulative = 0;
dataX[0][0] = cumulative;
dataX[0][1] = c.get(0)[0];
dataY[0][0] = cumulative;
dataY[0][1] = c.get(0)[1];
for (int i=1;i getPotentialLinks(ImageProcessor iprConn, ArrayList c, int x, int y, int distLim, double angleLim, boolean endToEndOnly) {
// Calculating the angle of the line using linear regression
double endAngle = Math.toDegrees(getEndAngleRads(c));
Point p1 = new Point<>(x,y,0);
ArrayList links = new ArrayList<>();
for (int xx = x- distLim; xx= iprConn.getWidth() || yy < 0 || yy >= iprConn.getHeight()) continue;
if (endToEndOnly && iprConn.get(xx, yy) != 2) {
continue;
} else if (iprConn.get(xx,yy) == 0) {
continue;
}
// Checking that the position being tested isn't closer to the next pixel in the tube
// (i.e. a connection would be made in the opposite direction to the tube)
double dist = getDist(x,xx,y,yy);
if (dist > getDist(c.get(1)[0],xx,c.get(1)[1],yy)) continue;
// Checking the position being tested is within an acceptable distance
if (dist > distLim) continue;
Point p2 = new Point<>(xx,yy,0);
double connectionAngle = Math.toDegrees(p1.calculateAngle2D(p2));
double phi = Math.abs(connectionAngle - endAngle) % 360;
double dAngle = phi > 180 ? 360 - phi : phi;
// Checking the position being tested is within an acceptable angle
if (dAngle > angleLim) continue;
links.add(new Link(xx,yy,dAngle,dist,(iprConn.get(xx, yy) == 2)));
}
}
return links;
}
public void process(ImageProcessor iprOrig, int nPx, int distLim, double angleLim, boolean endToEndOnly) {
process(iprOrig,nPx,distLim,angleLim,endToEndOnly,angleWeight,distanceWeight,endWeight);
}
public static void process(ImageProcessor iprOrig, int nPx, int distLim, double angleLim, boolean endToEndOnly, double angleWeight, double distanceWeight, double endWeight) {
// Inverting image, so the the logic is skeleton (255) and background (0)
iprOrig.invert();
// Dividing by 255, so the logic is skeleton (1) and background (0)
iprOrig.multiply(1d/255d);
// Duplicating the image
ImageProcessor iprConn = iprOrig.duplicate();
// Convolving with connectivity kernel
Convolver convolver = new Convolver();
convolver.setNormalize(false);
convolver.convolve(iprConn,new float[]{1,1,1,1,1,1,1,1,1},3,3);
// Multiplying the convolved image with the original image
new ImageCalculator().run("Multiply",new ImagePlus("Conn",iprConn),new ImagePlus("Orig",iprOrig));
// For each pixel with connectivity = 2, any other connectivity = 2 are searched for in the local vicinity. The
// points to be tested are only within an accepted angle from the current end (estimated by the adjacent 5
// pixels).
for (int x=0;x c = getEndPoints(iprConn,x,y,nPx);
// We need more than 1 pixel to determine the orientation
if (c.size() < 2) continue;
// Getting a list of all potential links
ArrayList links = getPotentialLinks(iprConn,c,x,y,distLim,angleLim,endToEndOnly);
// Quit if no links found
if (links.size() == 0) continue;
// Getting the link with the smallest angle
double minScore = Double.MAX_VALUE;
int xx = 0;
int yy = 0;
for (Link link:links) {
if (link.getAngle() < minScore) {
minScore = link.getScore(angleWeight,distanceWeight,endWeight);
xx = link.getX();
yy = link.getY();
}
}
// Doing the linking
int[][] line = BresenhamLine.getLine(x, xx, y, yy);
for (int[] px : line) iprOrig.set(px[0], px[1], 1);
iprOrig.set(x,y,10);
iprOrig.set(xx,yy,10);
// Updating connectivity on the joined ends
iprConn.set(x,y,3);
iprConn.set(xx,yy,3);
}
}
// Returning to standard levels for ImageJ
iprOrig.multiply(255);
iprOrig.invert();
}
public double getAngleWeight() {
return angleWeight;
}
public void setAngleWeight(double angleWeight) {
this.angleWeight = angleWeight;
}
public double getDistanceWeight() {
return distanceWeight;
}
public void setDistanceWeight(double distanceWeight) {
this.distanceWeight = distanceWeight;
}
public double getEndWeight() {
return endWeight;
}
public void setEndWeight(double endWeight) {
this.endWeight = endWeight;
}
}
class Link {
private int x;
private int y;
private double angle;
private double distance;
private boolean isEnd;
public Link(int x, int y, double angle, double distance, boolean isEnd) {
this.x = x;
this.y = y;
this.angle = angle;
this.distance = distance;
this.isEnd = isEnd;
}
public double getScore(double angleWeight, double distanceWeight, double endWeight) {
double endVal = isEnd ? -endWeight : 0;
return Math.abs(angle) * angleWeight + distance * distanceWeight + endVal;
}
public int getX() {
return x;
}
public void setX(int x) {
this.x = x;
}
public int getY() {
return y;
}
public void setY(int y) {
this.y = y;
}
public double getAngle() {
return angle;
}
public void setAngle(double angle) {
this.angle = angle;
}
public double getDistance() {
return distance;
}
public void setDistance(double distance) {
this.distance = distance;
}
}
