/** * Creates a new FloatProcessor using the specified FloatProcessor. Set 'cm' to null to use the * default grayscale LUT. */ public SerializableFloatProcessor(FloatProcessor floatProcessor) { floatProcessor = (FloatProcessor) floatProcessor.duplicate(); this.width = floatProcessor.getWidth(); this.height = floatProcessor.getHeight(); this.pixels = (float[]) floatProcessor.getPixels(); this.cm = floatProcessor.getColorModel(); resetRoi(); if (pixels != null) findMinAndMax(); }
@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; }