public DefrisePhantom() {
Trajectory trajectory = Configuration.getGlobalConfiguration().getGeometry();
double sourceAxisDistance = trajectory.getSourceToAxisDistance();
double sourceDetectorDistance = trajectory.getSourceToDetectorDistance();
double detectorYAxis = trajectory.getDetectorHeight() * trajectory.getPixelDimensionY();
double detectorXAxis = trajectory.getDetectorWidth() * trajectory.getPixelDimensionX();
double fovRadius = detectorXAxis * sourceAxisDistance / sourceDetectorDistance / 2 * 0.95;
double diskRadius = 4.0 / 5.0 * fovRadius;
double fovHeight = detectorYAxis * sourceAxisDistance / sourceDetectorDistance;
double diskHeight = fovHeight / 15.0;
double diskSpacing = fovHeight / 15.0;
int numDisks = 5;
double diskStart =
-(fovHeight / 2.0)
+ ((fovHeight - (numDisks * diskHeight + diskSpacing * (numDisks - 1))) / 2.0)
+ diskHeight / 2.0;
// Water Body
Cylinder cyl = new Cylinder(fovRadius, fovRadius, fovHeight);
cyl.setName("Water-like body of the phantom");
PhysicalObject po = new PhysicalObject();
po.setMaterial(MaterialsDB.getMaterialWithName("Water")); // D = 1.0
po.setShape(cyl);
add(po);
// Disk Inserts
for (int i = 0; i < numDisks; i++) {
cyl = new Cylinder(diskRadius, diskRadius, diskHeight);
cyl.setName("Disk");
cyl.applyTransform(
new Translation(new SimpleVector(0, 0, diskStart + (diskSpacing + diskHeight) * i)));
po = new PhysicalObject();
po.setMaterial(MaterialsDB.getMaterialWithName("Plexiglass")); // D = 1.95
po.setShape(cyl);
add(po);
}
}
public Grid2D raytraceScene(PrioritizableScene phantomScene, Projection projection) {
Trajectory geom = Configuration.getGlobalConfiguration().getGeometry();
// Grid2D slice = new Grid2D(geom.getDetectorWidth(), geom.getDetectorHeight());
Grid2D slice =
detector.createDetectorGrid(geom.getDetectorWidth(), geom.getDetectorHeight(), projection);
rayTracer.setScene(phantomScene);
// Second rule of optimization is: Optimize later.
PointND raySource = new PointND(0, 0, 0);
raySource.setCoordinates(projection.computeCameraCenter());
StraightLine castLine = new StraightLine(raySource, new SimpleVector(0, 0, 0));
SimpleVector centerPixDir = null;
if (accurate) {
centerPixDir = projection.computePrincipalAxis();
}
// SimpleVector prinpoint = trajectory.getProjectionMatrix(sliceNumber).getPrincipalPoint();
double xcorr = 0; // trajectory.getDetectorWidth()/2 - prinpoint.getElement(0);
double ycorr = 0; // trajectory.getDetectorHeight()/2 - prinpoint.getElement(1);
double length = trajectory.getSourceToDetectorDistance();
Edge environmentEdge = new Edge(new PointND(0), new PointND(length));
ArrayList<PhysicalObject> fallBackBackground = new ArrayList<PhysicalObject>(1);
SimpleVector pixel = new SimpleVector(0, 0);
boolean negate = false;
for (int y = 0; y < trajectory.getDetectorHeight(); y++) {
for (int x = 0; x < trajectory.getDetectorWidth(); x++) {
pixel.setElementValue(0, x - xcorr);
pixel.setElementValue(1, y - ycorr);
SimpleVector dir = projection.computeRayDirection(pixel);
if ((y == 0) && (x == 0)) {
// Check that ray direction is towards origin.
double max = 0;
int index = 0;
for (int i = 0; i < 3; i++) {
if (Math.abs(dir.getElement(i)) > max) {
max = Math.abs(dir.getElement(i));
index = i;
}
}
double t = -raySource.get(index) / dir.getElement(index);
if (t < 0) negate = true;
}
if (negate) dir.negate();
castLine.setDirection(dir);
ArrayList<PhysicalObject> segments = rayTracer.castRay(castLine);
if (accurate) {
double dirCosine = SimpleOperators.multiplyInnerProd(centerPixDir, dir);
length = trajectory.getSourceToDetectorDistance() / dirCosine;
}
if (segments == null) {
fallBackBackground.clear();
segments = fallBackBackground;
} else {
if (accurate) {
environmentEdge =
new Edge(new PointND(0), new PointND(length - getTotalSegmentsLength(segments)));
}
}
environment.setShape(environmentEdge);
segments.add(environment);
/* old code:
double integral = absorptionModel.evaluateLineIntegral(segments);
slice.putPixelValue(x, y, integral);
*/
detector.writeToDetector(slice, x, y, segments);
}
}
return slice;
}