@Override
  public void configure() throws Exception {
    Configuration config = Configuration.getGlobalConfiguration();
    setConfiguration(config);
    //		double [] minmax = null;
    checkDelta();
    setNumberOfProjections(config.getGeometry().getPrimaryAngles().length);
    double maxRange = (Math.PI + (2 * delta));
    if (getPrimaryAngles() != null) {
      // minmax = DoubleArrayUtil.minAndMaxOfArray(primaryAngles);
      double factor = 15 - (deltaX / Math.PI * 180);
      if (factor < 1) factor = 1;
      double range =
          (computeScanRange() + (factor * config.getGeometry().getAverageAngularIncrement()))
              * Math.PI
              / 180.0;
      offset = ((maxRange - range) / 2);
      offset = factor * config.getGeometry().getAverageAngularIncrement() / 180.0 * Math.PI / 2;
      deltaX = range - Math.PI;
      if (debug) System.out.println("delta: " + delta * 180 / Math.PI);
      if (debug) System.out.println("Angular Offset: " + offset + " " + maxRange + " " + range);
      if (debug) System.out.println("deltaX: " + deltaX);
    }

    if (this.numberOfProjections == 0) {
      throw new Exception("Number of projections not known");
    }
    setConfigured(true);
  }
 public static void main(String[] args) {
   CONRAD.setup();
   Configuration config = Configuration.getGlobalConfiguration();
   CircularTrajectory traj = new CircularTrajectory(config.getGeometry());
   double[] startAngles = new double[] {0, 20, 40};
   for (int j = 0; j < startAngles.length; j++) {
     traj.setTrajectory(
         2,
         600,
         90,
         0,
         0,
         CameraAxisDirection.ROTATIONAXIS_PLUS,
         CameraAxisDirection.DETECTORMOTION_PLUS,
         new SimpleVector(0, 0, 1),
         new PointND(0, 0, 0),
         startAngles[j]);
     for (int i = 0; i < traj.getNumProjectionMatrices(); i++) {
       System.out.println("Matrix: " + traj.getProjectionMatrix(i).toString());
     }
     System.out.println(" ");
   }
 }
  @Override
  public Grid2D applyToolToImage(Grid2D imageProcessor) {
    FloatProcessor imp = new FloatProcessor(imageProcessor.getWidth(), imageProcessor.getHeight());
    imp.setPixels(imageProcessor.getBuffer());

    if (!initBead) initializeBead();
    ImageProcessor imp1 = imp.duplicate(); // original

    double[][] beadMean3D = config.getBeadMeanPosition3D(); // [beadNo][x,y,z]
    double[] uv = new double[1];

    SimpleMatrix pMatrix = config.getGeometry().getProjectionMatrix(imageIndex).computeP();
    // [projection #][bead #][u, v, state[0: initial, 1: registered, 2: updated by hough searching]]
    double[][][] beadPosition2D = config.getBeadPosition2D();

    int noBeadRegistered = 0;

    double[][] xy1 = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
    double[][] xy2 =
        new double[WeightBearingBeadPositionBuilder.beadNo]
            [2]; // warped	(mapped to the mean), control points, reference

    double[][] xy1_hat = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original
    double[][] xy2_hat = new double[WeightBearingBeadPositionBuilder.beadNo][2]; // original

    // double distanceReferenceToCurrentBead = 0;

    for (int i = WeightBearingBeadPositionBuilder.currentBeadNo; i >= 0; i--) {

      if (beadMean3D[i][0] != 0
          || beadMean3D[i][1] != 0
          || beadMean3D[i][2] != 0) { // assume bead 3d is registered.

        uv = compute2DCoordinates(beadMean3D[i], pMatrix);

        // find bead location if registered by txt: state 1
        if (beadPosition2D[imageIndex][i][2] == 1) {

          noBeadRegistered++;

          if (isDisplay) {
            imp1.setValue(2);
            imp1.drawLine(
                (int) Math.round(beadPosition2D[imageIndex][i][0] - 10),
                (int) Math.round(beadPosition2D[imageIndex][i][1] - 10),
                (int) Math.round(beadPosition2D[imageIndex][i][0] + 10),
                (int) Math.round(beadPosition2D[imageIndex][i][1] + 10));
            imp1.drawLine(
                (int) Math.round(beadPosition2D[imageIndex][i][0] - 10),
                (int) Math.round(beadPosition2D[imageIndex][i][1] + 10),
                (int) Math.round(beadPosition2D[imageIndex][i][0] + 10),
                (int) Math.round(beadPosition2D[imageIndex][i][1] - 10));
            imp1.drawString(
                "Bead " + i + " (state:" + (int) beadPosition2D[imageIndex][i][2] + ")",
                (int) beadPosition2D[imageIndex][i][0],
                (int) beadPosition2D[imageIndex][i][1] - 10);
          }

          xy1[noBeadRegistered - 1][0] = beadPosition2D[imageIndex][i][0];
          xy1[noBeadRegistered - 1][1] = beadPosition2D[imageIndex][i][1];

          xy2[noBeadRegistered - 1][0] = uv[0];
          xy2[noBeadRegistered - 1][1] = uv[1];

        } else if (imageIndex != 0
            && imageIndex != config.getGeometry().getNumProjectionMatrices() - 1) {

          if (beadPosition2D[imageIndex - 1][i][2] == 1
              && beadPosition2D[imageIndex + 1][i][2] == 1) {

            noBeadRegistered++;

            double xMean =
                (beadPosition2D[imageIndex - 1][i][0] + beadPosition2D[imageIndex - 1][i][0]) / 2;
            double yMean =
                (beadPosition2D[imageIndex + 1][i][1] + beadPosition2D[imageIndex + 1][i][1]) / 2;

            if (isDisplay) {
              imp1.setValue(2);
              imp1.drawLine(
                  (int) Math.round(xMean - 10),
                  (int) Math.round(yMean - 10),
                  (int) Math.round(xMean + 10),
                  (int) Math.round(yMean + 10));
              imp1.drawLine(
                  (int) Math.round(xMean - 10),
                  (int) Math.round(yMean + 10),
                  (int) Math.round(xMean + 10),
                  (int) Math.round(yMean - 10));
              imp1.drawString("Bead " + i + " (state:" + "M)", (int) xMean, (int) yMean - 10);
            }

            xy1[noBeadRegistered - 1][0] = xMean;
            xy1[noBeadRegistered - 1][1] = yMean;

            xy2[noBeadRegistered - 1][0] = uv[0];
            xy2[noBeadRegistered - 1][1] = uv[1];
          }
        }

        // mean projected bead
        //				imp1.drawLine((int) Math.round(uv[0]-10), (int) Math.round(uv[1]), (int)
        // Math.round(uv[0]+10), (int) Math.round(uv[1]));
        //				imp1.drawLine((int) Math.round(uv[0]), (int) Math.round(uv[1]-10), (int)
        // Math.round(uv[0]), (int) Math.round(uv[1]+10));
      }
    }

    if (isDisplay) {
      for (int x = 0; x < config.getGeometry().getDetectorWidth(); x += 50)
        imp1.drawLine(x, 0, x, config.getGeometry().getDetectorHeight());
      for (int y = 0; y < config.getGeometry().getDetectorHeight(); y += 50)
        imp1.drawLine(0, y, config.getGeometry().getDetectorWidth(), y);
    }

    if (isCornerIncluded) {
      xy1[noBeadRegistered + 0][0] = 0;
      xy1[noBeadRegistered + 0][1] = 0;
      xy2[noBeadRegistered + 0][0] = 0;
      xy2[noBeadRegistered + 0][1] = 0;

      xy1[noBeadRegistered + 1][0] = 0;
      xy1[noBeadRegistered + 1][1] = config.getGeometry().getDetectorHeight();
      xy2[noBeadRegistered + 1][0] = 0;
      xy2[noBeadRegistered + 1][1] = config.getGeometry().getDetectorHeight();

      xy1[noBeadRegistered + 2][0] = config.getGeometry().getDetectorWidth();
      xy1[noBeadRegistered + 2][1] = 0;
      xy2[noBeadRegistered + 2][0] = config.getGeometry().getDetectorWidth();
      xy2[noBeadRegistered + 2][1] = 0;

      xy1[noBeadRegistered + 3][0] = config.getGeometry().getDetectorWidth();
      xy1[noBeadRegistered + 3][1] = config.getGeometry().getDetectorHeight();
      xy2[noBeadRegistered + 3][0] = config.getGeometry().getDetectorWidth();
      xy2[noBeadRegistered + 3][1] = config.getGeometry().getDetectorHeight();

      noBeadRegistered = noBeadRegistered + 4;
    }

    boolean fScaling = true;

    double minX = Double.MAX_VALUE;
    double maxX = 0;
    double minY = Double.MAX_VALUE;
    double maxY = 0;
    double c = 0;
    if (fScaling) { // ----- scaling to reduce condition # of A matrix
      for (int i = 0; i < noBeadRegistered; i++) {
        minX = Math.min(minX, xy1[i][0]);
        maxX = Math.max(maxX, xy1[i][0]);
        minY = Math.min(minY, xy1[i][1]);
        maxY = Math.max(maxY, xy1[i][1]);
      }
      c = Math.max(maxX - minX, maxY - minY);

      for (int i = 0; i < noBeadRegistered; i++) {
        xy1_hat[i][0] = (xy1[i][0] - minX) / c;
        xy1_hat[i][1] = (xy1[i][1] - minY) / c;

        xy2_hat[i][0] = (xy2[i][0] - minX) / c;
        xy2_hat[i][1] = (xy2[i][1] - minY) / c;
      }
    } else {
      xy1_hat = xy1;
      xy2_hat = xy2;
    }

    ImageProcessor imp2 = imp1.duplicate(); // warped

    /*
     * A*x = b
     * Matrix A = (n + 3) * (n + 3);
     * n (noBeadRegistered + 4): # of control points + 4 corner points (assume corner points are static)
     */

    int n = noBeadRegistered + 3;

    SimpleMatrix A = new SimpleMatrix(n, n);
    SimpleVector x_x = new SimpleVector(n);
    SimpleVector x_y = new SimpleVector(n);
    SimpleVector b_x = new SimpleVector(n);
    SimpleVector b_y = new SimpleVector(n);

    double rij = 0;
    double valA = 0;
    double valb_x = 0;
    double valb_y = 0;

    // Matrix L formation
    // alpha: mean of distances between control points' xy-projections) is a constant only present
    // on the diagonal of K
    // lambda: TPS smoothing regularization coefficient

    double alpha = 0.0;
    double lambda = 1.6; // 1.6
    for (int i = 0; i < noBeadRegistered; i++) { // i= # of row
      for (int j = i; j < noBeadRegistered; j++) { // j= # of column
        alpha +=
            Math.sqrt(
                Math.pow(xy2_hat[i][0] - xy2_hat[j][0], 2)
                    + Math.pow(xy2_hat[i][1] - xy2_hat[j][1], 2));
      }
    }
    alpha = alpha / Math.pow(noBeadRegistered, 2);

    for (int i = 0; i < n; i++) { // i= # of row
      for (int j = i; j < n; j++) { // j= # of column
        if (i < 3 && j < 3) valA = 0;
        else if (i >= 3 && j >= 3 && i == j) {
          valA = Math.pow(alpha, 2) * lambda;
          // valA = lambda;
          if (imageIndex < 10)
            System.out.println("Regularization = " + valA + ", lambda= " + lambda);
        } else if (i == 0 && j >= 0) valA = 1;
        else if (i == 1 && j >= 3) valA = xy1_hat[j - 3][0];
        else if (i == 2 && j >= 3) valA = xy1_hat[j - 3][1];
        else {
          rij =
              Math.pow(xy1_hat[j - 3][0] - xy1_hat[i - 3][0], 2)
                  + Math.pow(xy1_hat[j - 3][1] - xy1_hat[i - 3][1], 2);
          if (rij == 0) valA = 0;
          else valA = rij * Math.log(rij);
        }

        A.setElementValue(i, j, valA);
        A.setElementValue(j, i, valA);
      }

      if (i < 3) {
        valb_x = 0;
        valb_y = 0;
      } else {
        //				valb_x = xy2_hat[i-3][0]-xy1_hat[i-3][0];
        //				valb_y = xy2_hat[i-3][1]-xy1_hat[i-3][1];
        valb_x = xy2[i - 3][0] - xy1[i - 3][0];
        valb_y = xy2[i - 3][1] - xy1[i - 3][1];
        //				if (imageIndex > 150 && imageIndex < 170)
        //					System.out.println("Idx" + imageIndex + ",Elevation" + (i-3) + ": " + valb_x + "---"
        // + valb_y);
      }

      b_x.setElementValue(i, valb_x);
      b_y.setElementValue(i, valb_y);
    }

    // System.out.println("A condition number=" + A.conditionNumber(MatrixNormType.MAT_NORM_L1));
    // System.out.println("A condition number=" + A.conditionNumber(MatrixNormType.MAT_NORM_LINF));

    x_x = Solvers.solveLinearSysytemOfEquations(A, b_x);
    x_y = Solvers.solveLinearSysytemOfEquations(A, b_y);

    if (fScaling) {
      // ----- pixel space coefficients a, b scaling back
      double tmpA0 =
          x_x.getElement(0) - x_x.getElement(1) * (minX / c) - x_x.getElement(2) * (minY / c);
      for (int j = 0; j < noBeadRegistered; j++) {
        tmpA0 -=
            Math.log(c)
                * 2
                * x_x.getElement(j + 3)
                * (Math.pow(xy1_hat[j][0], 2) + Math.pow(xy1_hat[j][1], 2));
      }
      x_x.setElementValue(0, tmpA0);
      tmpA0 = x_y.getElement(0) - x_y.getElement(1) * (minX / c) - x_y.getElement(2) * (minY / c);
      for (int j = 0; j < noBeadRegistered; j++) {
        tmpA0 -=
            Math.log(c)
                * 2
                * x_y.getElement(j + 3)
                * (Math.pow(xy1_hat[j][0], 2) + Math.pow(xy1_hat[j][1], 2));
      }
      x_y.setElementValue(0, tmpA0);

      x_x.setElementValue(1, x_x.getElement(1) / c);
      x_y.setElementValue(1, x_y.getElement(1) / c);
      x_x.setElementValue(2, x_x.getElement(2) / c);
      x_y.setElementValue(2, x_y.getElement(2) / c);

      for (int i = 3; i < n; i++) {
        x_x.setElementValue(i, x_x.getElement(i) / Math.pow(c, 2));
        x_y.setElementValue(i, x_y.getElement(i) / Math.pow(c, 2));
      }
      // ----- pixel space coefficients a, b scaling back end
    }

    double devU = 0;
    double devV = 0;
    // Do warping
    // if (imageIndex == 0) {
    for (int y = 0; y < config.getGeometry().getDetectorHeight(); y++) {
      // for (int y=252; y<253; y++) {
      for (int x = 0; x < config.getGeometry().getDetectorWidth(); x++) {
        // for (int x=606; x<607; x++) {
        devU = x_x.getElement(0) + x_x.getElement(1) * x + x_x.getElement(2) * y;
        devV = x_y.getElement(0) + x_y.getElement(1) * x + x_y.getElement(2) * y;
        for (int i = 0; i < noBeadRegistered; i++) {
          rij = Math.pow(xy1[i][0] - x, 2) + Math.pow(xy1[i][1] - y, 2);
          if (rij > 0) {
            devU += x_x.getElement(i + 3) * rij * Math.log(rij);
            devV += x_y.getElement(i + 3) * rij * Math.log(rij);
          }
        }

        //					devU = 0;
        //					devV = 0;

        imp2.setf(x, y, (float) imp1.getInterpolatedValue(x - devU, y - devV));

        // System.out.println("x, y=" + x + ", " + y + "\t" + devU + ", " + devV);
        // maxDevU = Math.max(maxDevU, devU);
        // maxDevV = Math.max(maxDevV, devV);
      }
    }

    // Error estimate after transformation
    //			for (int i=0; i<= WeightBearingBeadPositionBuilder.currentBeadNo; i++){
    //
    //				if (beadMean3D[i][0] != 0 || beadMean3D[i][1] != 0 || beadMean3D[i][2] != 0){ // assume
    // bead 3d is registered.
    //
    //					// find bead location if registered by txt: state 1
    //					if (beadPosition2D[imageIndex][i][2] == 1){
    //
    //						// Projected Reference
    //						uv = compute2DCoordinates(beadMean3D[i], pMatrix);
    //						double x = uv[0];
    //						double y = uv[1];
    //						// bead detected position in 2d
    //						// Transform to 2D coordinates, time variant position
    //						//beadPosition2D[imageIndex][i][0];
    //						//beadPosition2D[imageIndex][i][1];
    //
    //						devU = x_x.getElement(0) + x_x.getElement(1)*x + x_x.getElement(2)*y;
    //						devV = x_y.getElement(0) + x_y.getElement(1)*x + x_y.getElement(2)*y;
    //						for (int j=0; j<noBeadRegistered; j++){
    //							rij = Math.pow(xy1[j][0]-x, 2) + Math.pow(xy1[j][1]-y, 2);
    //							if (rij > 0) {
    //								devU += x_x.getElement(j+3)*rij*Math.log(rij);
    //								devV += x_y.getElement(j+3)*rij*Math.log(rij);
    //							}
    //						}
    //
    //						distanceReferenceToCurrentBead +=
    // Math.sqrt(Math.pow(uv[0]-(beadPosition2D[imageIndex][i][0]+devU),
    // 2)+Math.pow(uv[1]-(beadPosition2D[imageIndex][i][1]+devV), 2));
    //
    //					}
    //				}
    //			}
    //			System.out.println("Euclidean distance\t" + imageIndex + "\t" +
    // distanceReferenceToCurrentBead/noBeadRegistered);

    // }

    if (isDisplay) {
      for (int i = WeightBearingBeadPositionBuilder.currentBeadNo; i >= 0; i--) {

        if (beadMean3D[i][0] != 0
            || beadMean3D[i][1] != 0
            || beadMean3D[i][2] != 0) { // assume bead 3d is registered.

          uv = compute2DCoordinates(beadMean3D[i], pMatrix);

          imp2.setValue(2);
          // mean projected bead
          imp2.drawLine(
              (int) Math.round(uv[0] - 10),
              (int) Math.round(uv[1]),
              (int) Math.round(uv[0] + 10),
              (int) Math.round(uv[1]));
          imp2.drawLine(
              (int) Math.round(uv[0]),
              (int) Math.round(uv[1] - 10),
              (int) Math.round(uv[0]),
              (int) Math.round(uv[1] + 10));
        }
      }
    }
    Grid2D result = new Grid2D((float[]) imp2.getPixels(), imp2.getWidth(), imp2.getHeight());
    return result;
  }