@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 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); }