@Override
public void workOnSlice(int sliceNumber) {
PrioritizableScene phantomScene = phantom;
if (phantom instanceof AnalyticPhantom4D) {
AnalyticPhantom4D scene4D = (AnalyticPhantom4D) phantom;
phantomScene = scene4D.getScene(((double) sliceNumber) / trajectory.getProjectionStackSize());
String disableAutoCenterBoolean =
Configuration.getGlobalConfiguration()
.getRegistryEntry(RegKeys.DISABLE_CENTERING_4DPHANTOM_PROJECTION_RENDERING);
boolean disableAutoCenter = false;
if (disableAutoCenterBoolean != null) {
disableAutoCenter = Boolean.parseBoolean(disableAutoCenterBoolean);
}
Translation centerTranslation = new Translation(new SimpleVector(0, 0, 0));
if (!disableAutoCenter) {
SimpleVector center =
SimpleOperators.add(
phantom.getMax().getAbstractVector(), phantom.getMin().getAbstractVector())
.dividedBy(2);
centerTranslation = new Translation(center.negated());
}
for (PhysicalObject o : phantomScene) {
o.getShape().applyTransform(centerTranslation);
// System.out.println(o.getShape().getMax() + " " + o.getShape().getMin());
// Translate a part of XCAT to the center of source & detector for 2D projection (e.g. knee
// at the center of the 2d projection)
String translationString =
Configuration.getGlobalConfiguration()
.getRegistryEntry(RegKeys.GLOBAL_TRANSLATION_4DPHANTOM_PROJECTION_RENDERING);
if (translationString != null) {
// Center b/w RKJC & LKJC: -292.6426 211.7856 440.7783 (subj 5, static60),-401.1700
// 165.9885 478.5600 (subj 2, static60)
// XCAT Center by min & max: -177.73999504606988, 179.8512744259873, 312.19713254613583
// translationVector = (XCAT Center by min & max) - (Center b/w RKJC & LKJC)=>
// 114.9026, -31.9343, -128.5811 (subj5), 120, 3, -110(subj2) Try 114.0568 2.4778
// -106.2550
String[] values = translationString.split(", ");
SimpleVector translationVector =
new SimpleVector(
Double.parseDouble(values[0]),
Double.parseDouble(values[1]),
Double.parseDouble(values[2]));
Translation translationToRotationCenter = new Translation(translationVector);
o.getShape().applyTransform(translationToRotationCenter);
}
}
// System.out.println(phantomScene.getMax() + " " + phantomScene.getMin());
}
Grid2D slice = raytraceScene(phantomScene, trajectory.getProjectionMatrix(sliceNumber));
this.imageBuffer.add(slice, sliceNumber);
}
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;
}
