Program: 11405
Project: 11405
Buggy source:
@Override public void run(){
  op.checkIfCancelled();
  final int x0=rectangle.x;
  final int y0=rectangle.y;
  final int w=rectangle.width;
  final int h=rectangle.height;
  final int xMax=x0 + w;
  final int yMax=y0 + h;
  final Rectangle sourceRectangle=getSourceRectangle(x0,y0,w,h);
  for (int i=0; i < sourceTiles.length; ++i) {
    sourceTiles[i]=op.getSourceTile(srcBandList.srcBands[i],sourceRectangle);
    dataBuffers[i]=sourceTiles[i].getDataBuffer();
  }
  final TileIndex srcIndex=new TileIndex(sourceTiles[0]);
  for (int y=y0; y < yMax; ++y) {
    for (int x=x0; x < xMax; ++x) {
      PolOpUtils.getMeanCoherencyMatrix(x,y,halfWindowSizeX,halfWindowSizeY,srcWidth,srcHeight,sourceProductType,srcIndex,dataBuffers,Tr,Ti);
      int clusterIdx;
synchronized (clusterCounter) {
        if (mask[y][x] < -64) {
          clusterIdx=findClosestCluster(Tr,Ti,pvCenterList);
          computeSummationOfT3(clusterIdx + 1,Tr,Ti,pvSumRe,pvSumIm);
          clusterCounter[0][clusterIdx]+=1;
          mask[y][x]=(byte)(-128 + clusterIdx);
        }
 else         if (mask[y][x] < 0) {
          clusterIdx=findClosestCluster(Tr,Ti,pdCenterList);
          computeSummationOfT3(clusterIdx + 1,Tr,Ti,pdSumRe,pdSumIm);
          clusterCounter[1][clusterIdx]+=1;
          mask[y][x]=(byte)(-64 + clusterIdx);
        }
 else         if (mask[y][x] < 64) {
          clusterIdx=findClosestCluster(Tr,Ti,psCenterList);
          computeSummationOfT3(clusterIdx + 1,Tr,Ti,psSumRe,psSumIm);
          clusterCounter[2][clusterIdx]+=1;
          mask[y][x]=(byte)clusterIdx;
        }
 else {
          java.util.List<ClusterInfo> allCenterList=new ArrayList<>();
          allCenterList.addAll(pvCenterList);
          allCenterList.addAll(pdCenterList);
          allCenterList.addAll(psCenterList);
          clusterIdx=findClosestCluster(Tr,Ti,allCenterList);
          if (clusterIdx >= pvNumClusters + pdNumClusters) {
            clusterIdx-=pvNumClusters + pdNumClusters;
            computeSummationOfT3(clusterIdx + 1,Tr,Ti,psSumRe,psSumIm);
            clusterCounter[2][clusterIdx]+=1;
            mask[y][x]=(byte)clusterIdx;
          }
 else           if (clusterIdx >= pvNumClusters) {
            clusterIdx-=pvNumClusters;
            computeSummationOfT3(clusterIdx + 1,Tr,Ti,pdSumRe,pdSumIm);
            clusterCounter[1][clusterIdx]+=1;
            mask[y][x]=(byte)(-64 + clusterIdx);
          }
 else {
            computeSummationOfT3(clusterIdx + 1,Tr,Ti,pvSumRe,pvSumIm);
            clusterCounter[0][clusterIdx]+=1;
            mask[y][x]=(byte)(-128 + clusterIdx);
          }
        }
      }
    }
  }
}

Fixed version (ground truth):
@Override public void run(){
  op.checkIfCancelled();
  final int x0=rectangle.x;
  final int y0=rectangle.y;
  final int w=rectangle.width;
  final int h=rectangle.height;
  final int xMax=x0 + w;
  final int yMax=y0 + h;
  final Rectangle sourceRectangle=getSourceRectangle(x0,y0,w,h);
  for (int i=0; i < sourceTiles.length; ++i) {
    sourceTiles[i]=op.getSourceTile(srcBandList.srcBands[i],sourceRectangle);
    dataBuffers[i]=sourceTiles[i].getDataBuffer();
  }
  final TileIndex srcIndex=new TileIndex(sourceTiles[0]);
  for (int y=y0; y < yMax; ++y) {
    for (int x=x0; x < xMax; ++x) {
      PolOpUtils.getMeanCoherencyMatrix(x,y,halfWindowSizeX,halfWindowSizeY,srcWidth,srcHeight,sourceProductType,srcIndex,dataBuffers,Tr,Ti);
synchronized (clusterCounter) {
        if (category[y][x] == Categories.vol) {
          cluster[y][x]=findClosestCluster(Tr,Ti,pvCenterList);
          computeSummationOfT3(cluster[y][x] + 1,Tr,Ti,pvSumRe,pvSumIm);
          clusterCounter[0][cluster[y][x]]+=1;
        }
 else         if (category[y][x] == Categories.dbl) {
          cluster[y][x]=findClosestCluster(Tr,Ti,pdCenterList);
          computeSummationOfT3(cluster[y][x] + 1,Tr,Ti,pdSumRe,pdSumIm);
          clusterCounter[1][cluster[y][x]]+=1;
        }
 else         if (category[y][x] == Categories.suf) {
          cluster[y][x]=findClosestCluster(Tr,Ti,psCenterList);
          computeSummationOfT3(cluster[y][x] + 1,Tr,Ti,psSumRe,psSumIm);
          clusterCounter[2][cluster[y][x]]+=1;
        }
 else {
          final int nearestPvCluster=findClosestCluster(Tr,Ti,pvCenterList);
          final int nearestPdCluster=findClosestCluster(Tr,Ti,pdCenterList);
          final int nearestPsCluster=findClosestCluster(Tr,Ti,psCenterList);
          final double dPv=HAlphaWishart.computeWishartDistance(Tr,Ti,pvCenterList.get(nearestPvCluster));
          final double dPd=HAlphaWishart.computeWishartDistance(Tr,Ti,pdCenterList.get(nearestPdCluster));
          final double dPs=HAlphaWishart.computeWishartDistance(Tr,Ti,psCenterList.get(nearestPsCluster));
          if (dPv <= dPd && dPv <= dPs) {
            cluster[y][x]=nearestPvCluster;
            computeSummationOfT3(cluster[y][x] + 1,Tr,Ti,pvSumRe,pvSumIm);
            clusterCounter[0][cluster[y][x]]+=1;
            category[y][x]=Categories.vol;
          }
 else           if (dPd <= dPv && dPd <= dPs) {
            cluster[y][x]=nearestPdCluster;
            computeSummationOfT3(cluster[y][x] + 1,Tr,Ti,pdSumRe,pdSumIm);
            clusterCounter[1][cluster[y][x]]+=1;
            category[y][x]=Categories.dbl;
          }
 else {
            cluster[y][x]=nearestPsCluster;
            computeSummationOfT3(cluster[y][x] + 1,Tr,Ti,psSumRe,psSumIm);
            clusterCounter[2][cluster[y][x]]+=1;
            category[y][x]=Categories.suf;
          }
        }
      }
    }
  }
}