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); }