private synchronized void initProjectionMatrix(int projectionNumber) {
// load projection Matrix for current Projection.
SimpleMatrix pMat = getGeometry().getProjectionMatrix(projectionNumber).computeP();
float[] pMatFloat = new float[pMat.getCols() * pMat.getRows()];
for (int j = 0; j < pMat.getRows(); j++) {
for (int i = 0; i < pMat.getCols(); i++) {
pMatFloat[(j * pMat.getCols()) + i] = (float) pMat.getElement(j, i);
}
}
JCudaDriver.cuMemcpyHtoD(
projectionMatrix, Pointer.to(pMatFloat), Sizeof.FLOAT * pMatFloat.length);
}
/**
* Creates the meshes of one single phase and adds it to the ArrayList of 4D meshes.
*
* @param phase
* @param parameters
* @param info
* @param splines
*/
private void createPhantom(
int phase, double[] parameters, CONRADCardiacModelConfig info, ArrayList<Mesh4D> splines) {
String pcaFile = heartBase + "\\CardiacModel\\phase_" + phase + ".ccm";
ActiveShapeModel asm = new ActiveShapeModel(pcaFile);
Mesh allComp = asm.getModel(parameters);
if (phase == 0) {
for (int i = 0; i < info.numAnatComp; i++) {
splines.add(new Mesh4D());
}
}
int count = 0;
for (heartComponents hc : heartComponents.values()) {
Mesh comp = new Mesh();
SimpleMatrix pts =
allComp
.getPoints()
.getSubMatrix(info.vertexOffs[count], 0, hc.getNumVertices(), info.vertexDim);
// rotate and translate points
for (int i = 0; i < pts.getRows(); i++) {
SimpleVector row = SimpleOperators.multiply(rot, pts.getRow(i));
row.add(trans);
pts.setRowValue(i, row);
}
comp.setPoints(pts);
comp.setConnectivity(
allComp
.getConnectivity()
.getSubMatrix(info.triangleOffs[count], 0, hc.getNumTriangles(), 3));
splines.get(count).addMesh(comp);
count++;
}
}
private void CreatePhantom() {
// Iterate over all pixels and sum up intensity values of all corresponding ellipses
double sizeX = (double) super.getSize()[0];
double sizeY = (double) super.getSize()[1];
for (int i = 0; i < super.getSize()[0]; ++i) {
double x = ((double) i - (sizeX - 1) / 2.0) / ((sizeX - 1) / 2.0);
for (int j = 0; j < super.getSize()[1]; ++j) {
double y = ((double) j - (sizeY - 1) / 2.0) / ((sizeY - 1) / 2.0);
super.setAtIndex(i, super.getSize()[1] - j - 1, 0.f);
for (int k = 0; k < Ellipses.getRows(); ++k) {
// Extract the ellipse properties here
double xc = x - Ellipses.getElement(k, 3);
double yc = y - Ellipses.getElement(k, 4);
double phi = Ellipses.getElement(k, 5) * Math.PI / 180.0;
double cos = Math.cos(phi);
double sin = Math.sin(phi);
double asq = Ellipses.getElement(k, 1) * Ellipses.getElement(k, 1);
double bsq = Ellipses.getElement(k, 2) * Ellipses.getElement(k, 2);
double Val = Ellipses.getElement(k, 0);
// Check if this pixel is part of the ellipse, if yes, add the given intensity value to it
double help = Math.pow((xc * cos + yc * sin), 2.0);
double help2 = Math.pow((yc * cos - xc * sin), 2.0);
if (help / asq + help2 / bsq <= 1.0)
super.setAtIndex(
i,
super.getSize()[1] - j - 1,
super.getAtIndex(i, super.getSize()[1] - j - 1) + (float) Val);
}
}
}
}
private synchronized void initProjectionMatrix(int projectionNumber) {
// load projection Matrix for current Projection.
SimpleMatrix pMat = getGeometry().getProjectionMatrix(projectionNumber).computeP();
float[] pMatFloat = new float[pMat.getCols() * pMat.getRows()];
for (int j = 0; j < pMat.getRows(); j++) {
for (int i = 0; i < pMat.getCols(); i++) {
pMatFloat[(j * pMat.getCols()) + i] = (float) pMat.getElement(j, i);
}
}
// Obtain the global pointer to the view matrix from
// the module
if (projectionMatrix == null)
projectionMatrix = context.createFloatBuffer(pMatFloat.length, Mem.READ_ONLY);
projectionMatrix.getBuffer().put(pMatFloat);
projectionMatrix.getBuffer().rewind();
commandQueue.putWriteBuffer(projectionMatrix, true).finish();
}
public static void printSimpleMatrix(SimpleMatrix A) {
int n = A.getRows();
int m = A.getCols();
for (int i = 0; i < n; i++) {
for (int j = 0; j < m; j++) {
System.out.print(A.getElement(i, j) + "\t");
}
System.out.print("\n");
}
}
