/**
* 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++;
}
}
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);
}
}
