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));
// }
}
private void followRay(
SimpleVector pos,
SimpleVector dir,
double energyEV,
FloatProcessor imp,
int scatterCount,
double totalDistance) {
if (energyEV <= 1 || scatterCount > 20000) {
System.out.println("energy low, times scattered: " + scatterCount);
return;
}
// follow ray until next interaction point
SimpleVector oldPos = pos.clone();
double dist = sampler.getDistanceUntilNextInteractionCm(material, energyEV);
pos.add(dir.multipliedBy(dist));
pathlengths.add(dist);
// draw the entire path
// imp.drawLine((int)(scale*oldPos.getElement(0)), (int)(scale*oldPos.getElement(1)),
// (int)(scale*pos.getElement(0)), (int)(scale*pos.getElement(1)));
// draw interaction points only
imp.drawDot((int) (scale * pos.getElement(0)), (int) (scale * pos.getElement(1)));
// choose compton or photoelectric effect
double photo =
material.getAttenuation(energyEV / 1000, AttenuationType.PHOTOELECTRIC_ABSORPTION);
double compton =
material.getAttenuation(energyEV / 1000, AttenuationType.INCOHERENT_ATTENUATION);
if (sampler.random() * (photo + compton) <= photo) {
// photoelectric absorption
energyEV = 0;
// System.out.println("absorbed after " + scatterCount + " collisions");
xs.add(pos.getElement(0));
ys.add(pos.getElement(1));
zs.add(pos.getElement(2));
return;
} else {
// compton scattering
energyEV = sampler.sampleComptonScattering(energyEV, dir);
// send new ray
followRay(pos, dir, energyEV, imp, scatterCount + 1, totalDistance + dist);
}
}
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);
}
