/**
* 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 SimpleMatrix ShepMod() {
// Modified (better contrast) Shepp-Logan Phantom according
// to P. A. Toft, "The Radon Transform, Theory and Implementation"
// (unpublished dissertation), p. 199.
// One row describes properties for a single ellipse
// Colum Values: A a b x0 y0 phi
SimpleMatrix Shep = new SimpleMatrix(10, 6);
Shep.setRowValue(0, new SimpleVector(new double[] {1.0, 0.69, 0.92, 0, 0, 0}));
Shep.setRowValue(1, new SimpleVector(new double[] {-0.8, 0.6624, 0.8740, 0, -0.0184, 0}));
Shep.setRowValue(2, new SimpleVector(new double[] {-0.2, 0.1100, 0.3100, 0.22, 0.0, -18.0}));
Shep.setRowValue(3, new SimpleVector(new double[] {-0.2, 0.1600, 0.4100, -0.22, 0.0, 18.0}));
Shep.setRowValue(4, new SimpleVector(new double[] {0.1, 0.2100, 0.2500, 0, 0.35, 0}));
Shep.setRowValue(5, new SimpleVector(new double[] {0.1, 0.0460, 0.0460, 0, 0.1, 0}));
Shep.setRowValue(6, new SimpleVector(new double[] {0.1, 0.0460, 0.0460, 0, -0.1, 0}));
Shep.setRowValue(7, new SimpleVector(new double[] {0.1, 0.0460, 0.0230, -0.08, -0.605, 0}));
Shep.setRowValue(8, new SimpleVector(new double[] {0.1, 0.0230, 0.0230, 0, -0.606, 0}));
Shep.setRowValue(9, new SimpleVector(new double[] {0.1, 0.0230, 0.0460, 0.06, -0.605, 0}));
return Shep;
}
private SimpleMatrix ShepOrig() {
// Original Shepp-Logan Phantom according to:
// Shepp, L. A., & Logan, B. F. (1974).
// The Fourier reconstruction of a head section-LA Shepp.
// IEEE Transactions on Nuclear Science, NS-21, 21�43.
// One row describes properties for a single ellipse
// Colum Values: A a b x0 y0 phi
SimpleMatrix Shep = new SimpleMatrix(10, 6);
Shep.setRowValue(0, new SimpleVector(new double[] {2.0, 0.69, 0.92, 0, 0, 0}));
Shep.setRowValue(1, new SimpleVector(new double[] {-0.98, 0.6624, 0.8740, 0, -0.0184, 0}));
Shep.setRowValue(2, new SimpleVector(new double[] {-0.02, 0.1100, 0.3100, 0.22, 0.0, -18.0}));
Shep.setRowValue(3, new SimpleVector(new double[] {-0.02, 0.1600, 0.4100, -0.22, 0.0, 18.0}));
Shep.setRowValue(4, new SimpleVector(new double[] {0.01, 0.2100, 0.2500, 0, 0.35, 0}));
Shep.setRowValue(5, new SimpleVector(new double[] {0.01, 0.0460, 0.0460, 0, 0.1, 0}));
Shep.setRowValue(6, new SimpleVector(new double[] {0.01, 0.0460, 0.0460, 0, -0.1, 0}));
Shep.setRowValue(7, new SimpleVector(new double[] {0.01, 0.0460, 0.0230, -0.08, -0.605, 0}));
Shep.setRowValue(8, new SimpleVector(new double[] {0.01, 0.0230, 0.0230, 0, -0.606, 0}));
Shep.setRowValue(9, new SimpleVector(new double[] {0.01, 0.0230, 0.0460, 0.06, -0.605, 0}));
return Shep;
}