/**
* Creates the meshes of one single phase and adds it to the ArrayList of 4D meshes.
*
* @param phase
* @param parameters
* @param info
* @param splines
*/
private void createPhantom(
int phase, double[] parameters, CONRADCardiacModelConfig info, ArrayList<Mesh4D> splines) {
String pcaFile = heartBase + "\\CardiacModel\\phase_" + phase + ".ccm";
ActiveShapeModel asm = new ActiveShapeModel(pcaFile);
Mesh allComp = asm.getModel(parameters);
if (phase == 0) {
for (int i = 0; i < info.numAnatComp; i++) {
splines.add(new Mesh4D());
}
}
int count = 0;
for (heartComponents hc : heartComponents.values()) {
Mesh comp = new Mesh();
SimpleMatrix pts =
allComp
.getPoints()
.getSubMatrix(info.vertexOffs[count], 0, hc.getNumVertices(), info.vertexDim);
// rotate and translate points
for (int i = 0; i < pts.getRows(); i++) {
SimpleVector row = SimpleOperators.multiply(rot, pts.getRow(i));
row.add(trans);
pts.setRowValue(i, row);
}
comp.setPoints(pts);
comp.setConnectivity(
allComp
.getConnectivity()
.getSubMatrix(info.triangleOffs[count], 0, hc.getNumTriangles(), 3));
splines.get(count).addMesh(comp);
count++;
}
}
public void setData(int x, int y, int z, DarkFieldPCA myPCA) {
SimpleMatrix eigenVectors = myPCA.getEigenVectors();
SimpleVector eigenValues = myPCA.getEigenValues();
for (int i = 0; i < fieldList.size(); i++) {
SimpleVector eigenVec = eigenVectors.getCol(i);
double eigenVal = eigenValues.getElement(i);
eigenVec = eigenVec.multipliedBy(eigenVal);
fieldList.get(i).setVector(x, y, z, eigenVec);
}
// /**
// * Threshold that checks, if 3 component of eigenvalues is too small
// * If 3 component is too small, don't consider it as a fiber orientation
// * and ignore it
// */
// double th = 1E-10;
// SimpleVector fiberDir;
// if(myPCA.getEigenValues().getElement(2)<th){
// fiberDir = new SimpleVector(3);
// }else{
// fiberDir = myPCA.getEigenVectors().getCol(2).normalizedL2();
// fiberDir.multiplyBy(myPCA.getEigenValues().getElement(2));
// }
}
public static void printSimpleMatrix(SimpleMatrix A) {
int n = A.getRows();
int m = A.getCols();
for (int i = 0; i < n; i++) {
for (int j = 0; j < m; j++) {
System.out.print(A.getElement(i, j) + "\t");
}
System.out.print("\n");
}
}
/**
* constructor to create a view
*
* @param projection: projection image as Grid2D
* @param radon: radon transformed and derived image as Grid2D
* @param projMatrix: projection matrix as Projection
*/
public View(Grid2D projection, Grid2D radon, Projection projMatrix) {
// Initialize center matrix //
CENTER = new SimpleMatrix(3, 4);
CENTER.setDiagValue(new SimpleVector(1.0, 1.0, 1.0));
// get data out of projection //
this.projectionWidth = projection.getWidth();
this.projectionHeight = projection.getHeight();
// get data out of radon transformed image //
this.radonWidth = radon.getWidth();
this.radonHeight = radon.getHeight();
this.projectionDiag =
Math.sqrt(projectionWidth * projectionWidth + projectionHeight * projectionHeight);
this.lineIncrement = radonWidth / projectionDiag;
this.angleIncrement = radonHeight / Math.PI;
// store radon transformed image //
this.radon = radon;
// get projection matrix P (3x4) //
this.P = SimpleOperators.multiplyMatrixProd(projMatrix.getK(), CENTER);
this.P = SimpleOperators.multiplyMatrixProd(this.P, projMatrix.getRt());
// get source position C (nullspace of the projection) //
DecompositionSVD decoP = new DecompositionSVD(this.P);
this.C = decoP.getV().getCol(3);
// normalize source vectors by last component //
// it is important that the last component is positive to have a positive center
// as it is defined in oriented projective geometry
this.C = this.C.dividedBy(this.C.getElement(3));
}
/**
* method to calculate a mapping K from two source positions C0, C1 to a plane C0 (C1) is the
* source position from the first (second) view
*/
public void createMappingToEpipolarPlane() {
// set up source matrices //
SimpleVector C0 = this.view1.C;
SimpleVector C1 = this.view2.C;
// compute Pluecker coordinates //
double L01 = C0.getElement(0) * C1.getElement(1) - C0.getElement(1) * C1.getElement(0);
double L02 = C0.getElement(0) * C1.getElement(2) - C0.getElement(2) * C1.getElement(0);
double L03 = C0.getElement(0) * C1.getElement(3) - C0.getElement(3) * C1.getElement(0);
double L12 = C0.getElement(1) * C1.getElement(2) - C0.getElement(2) * C1.getElement(1);
double L13 = C0.getElement(1) * C1.getElement(3) - C0.getElement(3) * C1.getElement(1);
double L23 = C0.getElement(2) * C1.getElement(3) - C0.getElement(3) * C1.getElement(2);
// construct B (6x1) //
SimpleVector B = new SimpleVector(L01, L02, L03, L12, L13, L23);
// compute infinity point in direction of B //
SimpleVector N = new SimpleVector(-L03, -L13, -L23, 0);
// compute plane E0 containing B and X0=(0,0,0,1) //
SimpleVector E0 = SimpleOperators.getPlueckerJoin(B, new SimpleVector(0, 0, 0, 1));
// find othonormal basis from plane normals //
// (vectors are of 3x1)
SimpleVector a2 = new SimpleVector(E0.getElement(0), E0.getElement(1), E0.getElement(2));
SimpleVector a3 = new SimpleVector(N.getElement(0), N.getElement(1), N.getElement(2));
// set vectors to unit length
a2.normalizeL2();
a3.normalizeL2();
// calculate cross product to get the last basis vector //
SimpleVector a1 = General.crossProduct(a2, a3).negated();
// (a1 is already of unit length -> no normalization needed)
// set up assembly matrix A (4x3) //
SimpleMatrix A = new SimpleMatrix(4, 3);
A.setSubColValue(0, 0, a1);
A.setSubColValue(0, 1, a2);
A.setSubColValue(0, 2, C0);
// store mapping matrix K (4x3 = 4x4 * 4x3) //
this.K = SimpleOperators.multiplyMatrixProd(SimpleOperators.getPlueckerMatrixDual(B), A);
}
private void CreatePhantom() {
// Iterate over all pixels and sum up intensity values of all corresponding ellipses
double sizeX = (double) super.getSize()[0];
double sizeY = (double) super.getSize()[1];
for (int i = 0; i < super.getSize()[0]; ++i) {
double x = ((double) i - (sizeX - 1) / 2.0) / ((sizeX - 1) / 2.0);
for (int j = 0; j < super.getSize()[1]; ++j) {
double y = ((double) j - (sizeY - 1) / 2.0) / ((sizeY - 1) / 2.0);
super.setAtIndex(i, super.getSize()[1] - j - 1, 0.f);
for (int k = 0; k < Ellipses.getRows(); ++k) {
// Extract the ellipse properties here
double xc = x - Ellipses.getElement(k, 3);
double yc = y - Ellipses.getElement(k, 4);
double phi = Ellipses.getElement(k, 5) * Math.PI / 180.0;
double cos = Math.cos(phi);
double sin = Math.sin(phi);
double asq = Ellipses.getElement(k, 1) * Ellipses.getElement(k, 1);
double bsq = Ellipses.getElement(k, 2) * Ellipses.getElement(k, 2);
double Val = Ellipses.getElement(k, 0);
// Check if this pixel is part of the ellipse, if yes, add the given intensity value to it
double help = Math.pow((xc * cos + yc * sin), 2.0);
double help2 = Math.pow((yc * cos - xc * sin), 2.0);
if (help / asq + help2 / bsq <= 1.0)
super.setAtIndex(
i,
super.getSize()[1] - j - 1,
super.getAtIndex(i, super.getSize()[1] - j - 1) + (float) Val);
}
}
}
}
private SimpleMatrix ShepMod() {
// Modified (better contrast) Shepp-Logan Phantom according
// to P. A. Toft, "The Radon Transform, Theory and Implementation"
// (unpublished dissertation), p. 199.
// One row describes properties for a single ellipse
// Colum Values: A a b x0 y0 phi
SimpleMatrix Shep = new SimpleMatrix(10, 6);
Shep.setRowValue(0, new SimpleVector(new double[] {1.0, 0.69, 0.92, 0, 0, 0}));
Shep.setRowValue(1, new SimpleVector(new double[] {-0.8, 0.6624, 0.8740, 0, -0.0184, 0}));
Shep.setRowValue(2, new SimpleVector(new double[] {-0.2, 0.1100, 0.3100, 0.22, 0.0, -18.0}));
Shep.setRowValue(3, new SimpleVector(new double[] {-0.2, 0.1600, 0.4100, -0.22, 0.0, 18.0}));
Shep.setRowValue(4, new SimpleVector(new double[] {0.1, 0.2100, 0.2500, 0, 0.35, 0}));
Shep.setRowValue(5, new SimpleVector(new double[] {0.1, 0.0460, 0.0460, 0, 0.1, 0}));
Shep.setRowValue(6, new SimpleVector(new double[] {0.1, 0.0460, 0.0460, 0, -0.1, 0}));
Shep.setRowValue(7, new SimpleVector(new double[] {0.1, 0.0460, 0.0230, -0.08, -0.605, 0}));
Shep.setRowValue(8, new SimpleVector(new double[] {0.1, 0.0230, 0.0230, 0, -0.606, 0}));
Shep.setRowValue(9, new SimpleVector(new double[] {0.1, 0.0230, 0.0460, 0.06, -0.605, 0}));
return Shep;
}
private synchronized void initProjectionMatrix(int projectionNumber) {
// load projection Matrix for current Projection.
SimpleMatrix pMat = getGeometry().getProjectionMatrix(projectionNumber).computeP();
float[] pMatFloat = new float[pMat.getCols() * pMat.getRows()];
for (int j = 0; j < pMat.getRows(); j++) {
for (int i = 0; i < pMat.getCols(); i++) {
pMatFloat[(j * pMat.getCols()) + i] = (float) pMat.getElement(j, i);
}
}
JCudaDriver.cuMemcpyHtoD(
projectionMatrix, Pointer.to(pMatFloat), Sizeof.FLOAT * pMatFloat.length);
}
private SimpleMatrix ShepOrig() {
// Original Shepp-Logan Phantom according to:
// Shepp, L. A., & Logan, B. F. (1974).
// The Fourier reconstruction of a head section-LA Shepp.
// IEEE Transactions on Nuclear Science, NS-21, 21�43.
// One row describes properties for a single ellipse
// Colum Values: A a b x0 y0 phi
SimpleMatrix Shep = new SimpleMatrix(10, 6);
Shep.setRowValue(0, new SimpleVector(new double[] {2.0, 0.69, 0.92, 0, 0, 0}));
Shep.setRowValue(1, new SimpleVector(new double[] {-0.98, 0.6624, 0.8740, 0, -0.0184, 0}));
Shep.setRowValue(2, new SimpleVector(new double[] {-0.02, 0.1100, 0.3100, 0.22, 0.0, -18.0}));
Shep.setRowValue(3, new SimpleVector(new double[] {-0.02, 0.1600, 0.4100, -0.22, 0.0, 18.0}));
Shep.setRowValue(4, new SimpleVector(new double[] {0.01, 0.2100, 0.2500, 0, 0.35, 0}));
Shep.setRowValue(5, new SimpleVector(new double[] {0.01, 0.0460, 0.0460, 0, 0.1, 0}));
Shep.setRowValue(6, new SimpleVector(new double[] {0.01, 0.0460, 0.0460, 0, -0.1, 0}));
Shep.setRowValue(7, new SimpleVector(new double[] {0.01, 0.0460, 0.0230, -0.08, -0.605, 0}));
Shep.setRowValue(8, new SimpleVector(new double[] {0.01, 0.0230, 0.0230, 0, -0.606, 0}));
Shep.setRowValue(9, new SimpleVector(new double[] {0.01, 0.0230, 0.0460, 0.06, -0.605, 0}));
return Shep;
}
private synchronized void initProjectionMatrix(int projectionNumber) {
// load projection Matrix for current Projection.
SimpleMatrix pMat = getGeometry().getProjectionMatrix(projectionNumber).computeP();
float[] pMatFloat = new float[pMat.getCols() * pMat.getRows()];
for (int j = 0; j < pMat.getRows(); j++) {
for (int i = 0; i < pMat.getCols(); i++) {
pMatFloat[(j * pMat.getCols()) + i] = (float) pMat.getElement(j, i);
}
}
// Obtain the global pointer to the view matrix from
// the module
if (projectionMatrix == null)
projectionMatrix = context.createFloatBuffer(pMatFloat.length, Mem.READ_ONLY);
projectionMatrix.getBuffer().put(pMatFloat);
projectionMatrix.getBuffer().rewind();
commandQueue.putWriteBuffer(projectionMatrix, true).finish();
}
/**
* Constructs the triangle corresponding to the i-th face in a mesh given the connectivity
* information fcs and the vertices vtc and adds it to the CompoundShape.
*
* @param vtc The vertices of the mesh.
* @param fcs The faces of the mesh, i.e connectivity information.
* @param i The index of the face to be constructed.
*/
private void addTriangleAtIndex(CompoundShape cs, SimpleMatrix vtc, SimpleMatrix fcs, int i) {
SimpleVector face = fcs.getRow(i);
SimpleVector dirU = vtc.getRow((int) face.getElement(1));
dirU.subtract(vtc.getRow((int) face.getElement(0)));
double l2 = dirU.normL2();
SimpleVector dirV = vtc.getRow((int) face.getElement(2));
dirV.subtract(vtc.getRow((int) face.getElement(0)));
if (dirV.normL2() < l2) {
l2 = dirV.normL2();
}
double nN = General.crossProduct(dirU.normalizedL2(), dirV.normalizedL2()).normL2();
if (l2 < Math.sqrt(CONRAD.DOUBLE_EPSILON) || nN < Math.sqrt(CONRAD.DOUBLE_EPSILON)) {
} else {
Triangle t =
new Triangle(
new PointND(vtc.getRow((int) face.getElement(0))),
new PointND(vtc.getRow((int) face.getElement(1))),
new PointND(vtc.getRow((int) face.getElement(2))));
cs.add(t);
}
}
@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;
}
public void setTrajectory(
int numProjectionMatrices,
double sourceToAxisDistance,
double averageAngularIncrement,
double detectorOffsetX,
double detectorOffsetY,
CameraAxisDirection uDirection,
CameraAxisDirection vDirection,
SimpleVector rotationAxis,
PointND rotationCenter,
double angleFirstProjection) {
this.projectionMatrices = new Projection[numProjectionMatrices];
this.primaryAngles = new double[numProjectionMatrices];
this.numProjectionMatrices = numProjectionMatrices;
this.sourceToAxisDistance = sourceToAxisDistance;
this.averageAngularIncrement = averageAngularIncrement;
this.detectorOffsetU = detectorOffsetX;
this.detectorOffsetV = detectorOffsetY;
double cosPhi = Math.cos(General.toRadians(angleFirstProjection));
double sinPhi = Math.sin(General.toRadians(angleFirstProjection));
SimpleMatrix rotMat = new SimpleMatrix(3, 3);
rotMat.setElementValue(0, 0, cosPhi);
rotMat.setElementValue(0, 1, sinPhi);
rotMat.setElementValue(1, 0, -sinPhi);
rotMat.setElementValue(1, 1, cosPhi);
rotMat.setElementValue(2, 2, 1);
SimpleVector centerToCameraIdealAtInitialAngle =
SimpleOperators.multiply(rotMat, new SimpleVector(sourceToAxisDistance, 0, 0));
Plane3D trajPlane =
new Plane3D(
rotationAxis,
SimpleOperators.multiplyInnerProd(rotationAxis, rotationCenter.getAbstractVector()));
double distToPlane = trajPlane.computeDistance(new PointND(centerToCameraIdealAtInitialAngle));
SimpleVector centerToCameraDir =
SimpleOperators.subtract(
SimpleOperators.add(
rotationAxis.multipliedBy(-1 * distToPlane), centerToCameraIdealAtInitialAngle),
rotationCenter.getAbstractVector());
centerToCameraDir.divideBy(centerToCameraDir.normL2());
SimpleVector centerToCameraInitialInPlane =
centerToCameraDir.multipliedBy(sourceToAxisDistance);
for (int i = 0; i < numProjectionMatrices; i++) {
primaryAngles[i] = i * averageAngularIncrement + angleFirstProjection;
// System.out.println(primaryAngles[i] + " " + averageAngularIncrement + " " +
// this.reconDimensions[0] + " " + this.reconDimensions[1]);
projectionMatrices[i] = new Projection();
double rotationAngle = General.toRadians(primaryAngles[i]);
projectionMatrices[i].setRtFromCircularTrajectory(
rotationCenter.getAbstractVector(),
rotationAxis,
sourceToAxisDistance,
centerToCameraInitialInPlane,
uDirection,
vDirection,
rotationAngle);
SimpleVector spacingUV = new SimpleVector(pixelDimensionX, pixelDimensionY);
SimpleVector sizeUV = new SimpleVector(detectorWidth, detectorHeight);
SimpleVector offset = new SimpleVector(detectorOffsetX, detectorOffsetY);
projectionMatrices[i].setKFromDistancesSpacingsSizeOffset(
sourceToDetectorDistance, spacingUV, sizeUV, offset, 1.0, 0);
}
this.projectionStackSize = numProjectionMatrices;
// System.out.println("Defined geometry with SDD " +sourceToDetectorDistance);
}