@Override
public void configure() throws Exception {
// We will now read this from the Configuration. The detector needs to be preconfigured!
// detector = (XRayDetector) UserUtil.queryObject("Select Detector:", "Detector Selection",
// XRayDetector.class);
// detector.configure();
detector = Configuration.getGlobalConfiguration().getDetector();
detector.init();
phantom = UserUtil.queryPhantom("Select Phantom", "Select Phantom");
Material mat = null;
do {
String materialstr = UserUtil.queryString("Enter Background Medium:", "vacuum");
mat = MaterialsDB.getMaterialWithName(materialstr);
} while (mat == null);
phantom.setBackground(mat);
phantom.configure();
rayTracer.setScene((PrioritizableScene) phantom);
environment.setMaterial(phantom.getBackgroundMaterial());
super.configure();
}
@Override
public void configure() throws Exception {
slope = UserUtil.queryDouble("Enter slope of correction transformatoin", slope);
// offset = UserUtil.queryDouble("Enter offset of correction transformation", offset);
measureHard = UserUtil.queryDouble("Measurement of hard material [HU]", measureHard);
measureSoft = UserUtil.queryDouble("Measurement of soft material [HU]", measureSoft);
projectionXShift = UserUtil.queryDouble("Enter projection x shift", projectionXShift);
projectionYShift = UserUtil.queryDouble("Enter projection y shift", projectionYShift);
lambda0 = VolumeAttenuationFactorCorrectionTool.getLambda0(measureHard, measureSoft);
lut = Configuration.getGlobalConfiguration().getBeamHardeningLookupTable();
ImagePlus[] images = ImageUtil.getAvailableImagePlusAsArray();
hardMaterial =
ImageUtil.wrapImagePlus(
(ImagePlus)
JOptionPane.showInputDialog(
null,
"Select projections with hard material: ",
"Select source",
JOptionPane.PLAIN_MESSAGE,
null,
images,
images[0]));
configured = true;
}
/**
* Configures the heart simulation. Currently uses learning shapes as heart description. This will
* be changed later using the HeartParameterLUT class.
*/
public void configure() throws Exception {
// heartBase = UserUtil.queryString("Specify path to model data file.",
// "C:\\Stanford\\CONRAD\\data\\CardiacModel\\");
heartBase = System.getProperty("user.dir") + "\\data\\CardiacModel\\";
heartBeats = UserUtil.queryInt("Number of heart beats in this scene:", 1);
boolean rotTrans = UserUtil.queryBoolean("Apply rotatation and translation?");
if (!rotTrans) {
new SimpleMatrix();
this.rot = SimpleMatrix.I_3;
this.trans = new SimpleVector(3);
} else {
String rtfile =
UserUtil.queryString(
"Specify file containing rotation and translation:", heartBase + "rotTrans.txt");
RotTransIO rtinput = new RotTransIO(rtfile);
this.rot = rtinput.getRotation();
this.trans = rtinput.getTranslation();
}
this.max = new PointND(0, 0, 0);
this.min = new PointND(0, 0, 0);
// read config file for offsets etc
CONRADCardiacModelConfig info = new CONRADCardiacModelConfig(heartBase);
info.read();
// read the PCs of all phases
ActiveShapeModel parameters = new ActiveShapeModel(heartBase + "\\CCmScores.ccm");
double[] scores;
boolean predefined = UserUtil.queryBoolean("Use predefined model?");
if (predefined) {
Object tobj =
UserUtil.chooseObject(
"Choose heart to be simulated:",
"Predefined models:",
PredefinedModels.getList(),
PredefinedModels.getList()[0]);
scores = PredefinedModels.getValue(tobj.toString());
} else {
scores =
UserUtil.queryArray("Specify model parameters: ", new double[parameters.numComponents]);
// the scores are defined with respect to variance but we want to have them with respect to
// standard deviation therefore divide by
// sqrt of variance
for (int i = 0; i < parameters.numComponents; i++) {
scores[i] /= Math.sqrt(parameters.getEigenvalues()[i]);
}
}
SimpleVector paramVec = parameters.getModel(scores).getPoints().getCol(0);
// for all components
// loop through all phases and create splines describing the motion for each vertex
System.out.println("Starting model generation.\n");
System.out.println("__________________________________");
System.out.println("Calculating phantom at each phase.\n");
this.splines = new ArrayList<Mesh4D>();
for (int i = 0; i < numPhases; i++) {
int start = 0;
for (int j = 0; j < i; j++) {
start += (j == 0) ? 0 : info.principalComp[j - 1];
}
double[] param = paramVec.getSubVec(start, info.principalComp[i]).copyAsDoubleArray();
createPhantom(i, param, info, splines);
}
// calculate splines
System.out.println("Fitting temporal splines.\n");
for (int i = 0; i < info.numAnatComp; i++) {
splines.get(i).calculateSplines();
}
System.out.println("__________________________________");
setConfigured(true);
System.out.println("Configuration done.\n");
}