/**
* Constructs the triangle corresponding to the i-th face in a mesh given the connectivity
* information fcs and the vertices vtc and adds it to the CompoundShape.
*
* @param vtc The vertices of the mesh.
* @param fcs The faces of the mesh, i.e connectivity information.
* @param i The index of the face to be constructed.
*/
private void addTriangleAtIndex(CompoundShape cs, SimpleMatrix vtc, SimpleMatrix fcs, int i) {
SimpleVector face = fcs.getRow(i);
SimpleVector dirU = vtc.getRow((int) face.getElement(1));
dirU.subtract(vtc.getRow((int) face.getElement(0)));
double l2 = dirU.normL2();
SimpleVector dirV = vtc.getRow((int) face.getElement(2));
dirV.subtract(vtc.getRow((int) face.getElement(0)));
if (dirV.normL2() < l2) {
l2 = dirV.normL2();
}
double nN = General.crossProduct(dirU.normalizedL2(), dirV.normalizedL2()).normL2();
if (l2 < Math.sqrt(CONRAD.DOUBLE_EPSILON) || nN < Math.sqrt(CONRAD.DOUBLE_EPSILON)) {
} else {
Triangle t =
new Triangle(
new PointND(vtc.getRow((int) face.getElement(0))),
new PointND(vtc.getRow((int) face.getElement(1))),
new PointND(vtc.getRow((int) face.getElement(2))));
cs.add(t);
}
}
/** @param pathFiberVTK */
public void writeToVectorField(String pathFiberVTK) {
ArrayList<Index3D> indexListe = new ArrayList<Index3D>();
for (int x = 0; x < imgSizeX; x++) {
for (int y = 0; y < imgSizeY; y++) {
for (int z = 0; z < imgSizeZ; z++) {
// Get EigenVec of smallest eigenValue
SimpleVector direction = fieldList.get(2).getSimpleVectorAtIndex(x, y, z);
double length = direction.normL2();
if (length != 0) {
Index3D curIndex = new Index3D(x, y, z);
indexListe.add(curIndex);
}
}
}
}
try {
FileOutputStream foStream = new FileOutputStream(pathFiberVTK);
BufferedWriter bufWriter = new BufferedWriter(new OutputStreamWriter(foStream));
bufWriter.write("# vtk DataFile Version 2.0");
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write("Unstructured Grid Example");
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write("ASCII");
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write("DATASET UNSTRUCTURED_GRID");
bufWriter.write(System.getProperty("line.separator"));
// TODO Not sure why that
bufWriter.write("POINTS " + indexListe.size() + " float");
bufWriter.write(System.getProperty("line.separator"));
// First write positions
for (int poinIdx = 0; poinIdx < indexListe.size(); poinIdx++) {
Index3D index3D = indexListe.get(poinIdx);
bufWriter.write(index3D.x + " " + index3D.y + " " + index3D.z);
bufWriter.write(System.getProperty("line.separator"));
}
bufWriter.write("CELLS " + indexListe.size() + " " + 2 * indexListe.size());
bufWriter.write(System.getProperty("line.separator"));
int indCells = 0;
for (int poinIdx = 0; poinIdx < indexListe.size(); poinIdx++) {
bufWriter.write("1 " + indCells);
bufWriter.write(System.getProperty("line.separator"));
indCells = indCells + 1;
}
bufWriter.write("CELL_TYPES " + indexListe.size());
bufWriter.write(System.getProperty("line.separator"));
for (int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++) {
bufWriter.write("1");
bufWriter.write(System.getProperty("line.separator"));
}
bufWriter.write("POINT_DATA " + indexListe.size());
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write("SCALARS eigenValues float 3");
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write("LOOKUP_TABLE default");
bufWriter.write(System.getProperty("line.separator"));
// Write scalars
for (int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++) {
Index3D coordIdx = indexListe.get(pointIdx);
SimpleVector vec1 =
fieldList.get(0).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
SimpleVector vec2 =
fieldList.get(1).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
SimpleVector vec3 =
fieldList.get(2).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
bufWriter.write(vec1.normL2() + " " + vec2.normL2() + " " + vec3.normL2());
bufWriter.write(System.getProperty("line.separator"));
}
bufWriter.write("SCALARS scalarDirection float 1");
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write("LOOKUP_TABLE default");
bufWriter.write(System.getProperty("line.separator"));
// Write scalars
for (int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++) {
Index3D coordIdx = indexListe.get(pointIdx);
SimpleVector curEigVec =
fieldList.get(2).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
curEigVec = curEigVec.absoluted();
if (curEigVec.max() == curEigVec.getElement(0)) {
bufWriter.write("0");
} else if (curEigVec.max() == curEigVec.getElement(1)) {
bufWriter.write("0.5");
} else {
bufWriter.write("1");
}
bufWriter.write(System.getProperty("line.separator"));
}
for (int eigIdx = 0; eigIdx < 3; eigIdx++) {
bufWriter.write("VECTORS eigenVector" + eigIdx + " float");
// Write scalars
for (int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++) {
Index3D coordIdx = indexListe.get(pointIdx);
SimpleVector curEigVec =
fieldList.get(eigIdx).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
bufWriter.write(System.getProperty("line.separator"));
bufWriter.write(
curEigVec.getElement(0)
+ " "
+ curEigVec.getElement(1)
+ " "
+ ""
+ curEigVec.getElement(2));
}
bufWriter.write(System.getProperty("line.separator"));
}
bufWriter.flush();
foStream.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
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);
}
