/**
* 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++;
}
}
/**
* Calculate the current state of the heart at time t using spline evaluation of all vertices in
* all heart components.
*/
@Override
public PrioritizableScene getScene(double time) {
double t = (time * heartBeats) % 1;
System.out.println("Evaluating time step: " + time);
PrioritizableScene scene = new PrioritizableScene();
int componentCount = 0;
for (heartComponents hc : heartComponents.values()) {
String material;
if (hc.getName().contains("myocardium")) {
material = "Heart";
} else if (hc.getName().contains("aorta")) {
material = "Aorta";
} else if (hc.getName().contains("leftVentricle")) {
material = "CoronaryArtery";
} else {
material = "Blood";
}
Mesh m = splines.get(componentCount).evaluateLinearInterpolation(t);
// Mesh m = splines.get(componentCount).evaluateSplines(t);
if (DEBUG) {
String inspectionFolder = heartBase + "meshReference/" + t + "/";
File inspect = new File(inspectionFolder);
if (!inspect.exists()) inspect.mkdirs();
String inspectionFile = inspectionFolder + hc.getName() + ".vtk";
VTKMeshIO wr = new VTKMeshIO(inspectionFile);
wr.setMesh(m);
wr.write();
}
PhysicalObject po = createPhysicalObject(hc.toString(), m, material);
scene.add(po);
componentCount++;
}
scene.setMax(max);
scene.setMin(min);
return scene;
}