/**
* Computes and plots correlation functions
*
* @param tauMax is the maximum time for correlation functions
*/
public void computeCorrelation(int tauMax) {
plotFrame.clearData();
double energyAccumulator = 0, magnetizationAccumulator = 0;
double energySquaredAccumulator = 0, magnetizationSquaredAccumulator = 0;
for (int t = 0; t < numberOfPoints; t++) {
energyAccumulator += energy[t];
magnetizationAccumulator += magnetization[t];
energySquaredAccumulator += energy[t] * energy[t];
magnetizationSquaredAccumulator += magnetization[t] * magnetization[t];
}
double averageEnergySquared = Math.pow(energyAccumulator / numberOfPoints, 2);
double averageMagnetizationSquared = Math.pow(magnetizationAccumulator / numberOfPoints, 2);
// compute normalization factors
double normE = (energySquaredAccumulator / numberOfPoints) - averageEnergySquared;
double normM = (magnetizationSquaredAccumulator / numberOfPoints) - averageMagnetizationSquared;
for (int tau = 1; tau <= tauMax; tau++) {
double c_MAccumulator = 0;
double c_EAccumulator = 0;
int counter = 0;
for (int t = 0; t < numberOfPoints - tau; t++) {
c_MAccumulator += magnetization[t] * magnetization[t + tau];
c_EAccumulator += energy[t] * energy[t + tau];
counter++;
}
// correlation function defined so that c(0) = 1 and c(infinity) -> 0
plotFrame.append(0, tau, ((c_MAccumulator / counter) - averageMagnetizationSquared) / normM);
plotFrame.append(1, tau, ((c_EAccumulator / counter) - averageEnergySquared) / normE);
}
plotFrame.setVisible(true);
}
/** Creates a particles at random locations. */
public void calculate() {
frame.clearDrawables(); // remove old cirlces
int n = control.getInt("number of particles");
double r = control.getDouble("radius");
for (int i = 0; i < n; i++) {
double x = -10 + 20 * Math.random();
double y = -10 + 20 * Math.random();
frame.addDrawable(InteractiveShape.createCircle(x, y, r));
}
}
/**
* Sets the start frame for this model. Also sets the initial time to the video clip time at the
* start frame.
*
* @param n the desired start frame
*/
public void setStartFrame(int n) {
VideoClip clip = trackerPanel.getPlayer().getVideoClip();
n = Math.max(n, clip.getFirstFrameNumber()); // not less than first frame
int end = clip.getLastFrameNumber();
n = Math.min(n, end); // not greater than last frame
n = Math.min(n, getEndFrame()); // not greater than endFrame
if (n == startFrame) return;
startFrame = n;
refreshInitialTime();
lastValidFrame = -1;
refreshSteps();
trackerPanel.repaint();
firePropertyChange("model_start", null, getStartFrame()); // $NON-NLS-1$
}
/**
* Sets the end frame for this model.
*
* @param n the desired end frame
*/
public void setEndFrame(int n) {
VideoClip clip = trackerPanel.getPlayer().getVideoClip();
int end = clip.getLastFrameNumber();
n = Math.max(n, 0); // not less than zero
n = Math.max(n, getStartFrame()); // not less than startFrame
if (n == getEndFrame()) return;
endFrame = n < end ? n : Integer.MAX_VALUE;
if (n < lastValidFrame) {
trimSteps();
} else {
refreshSteps();
}
trackerPanel.repaint();
firePropertyChange("model_end", null, getEndFrame()); // $NON-NLS-1$
}
private void positionInspector() {
if (inspectorX != Integer.MIN_VALUE) {
// trackerPanel will select this track when getInspector() is called
// only if loader has set the showInspector flag (so refreshing is false)
refreshing = !showInspector;
loading = true; // prevents setting trackerPanel changed flag
getInspector();
refreshing = loading = false;
TFrame frame = trackerPanel.getTFrame();
Dimension dim = Toolkit.getDefaultToolkit().getScreenSize();
if (inspectorH != Integer.MIN_VALUE)
inspector.setSize(inspector.getWidth(), Math.min(inspectorH, dim.height));
int x = Math.max(frame.getLocation().x + inspectorX, 0);
x = Math.min(x, dim.width - inspector.getWidth());
int y = Math.max(frame.getLocation().y + inspectorY, 0);
y = Math.min(y, dim.height - inspector.getHeight());
inspector.setLocation(x, y);
inspectorX = Integer.MIN_VALUE;
}
}
/** Refreshes step positions. */
protected void refreshSteps() {
locked = true;
if (refreshStepsLater) return;
// return if this is an empty dynamic system
if (this instanceof DynamicSystem) {
DynamicSystem system = (DynamicSystem) this;
if (system.particles.length == 0) return;
}
if (trackerPanel != null) {
refreshDerivsLater = trackerPanel.getPlayer().getClipControl().isPlaying();
int n = trackerPanel.getFrameNumber();
VideoClip clip = trackerPanel.getPlayer().getVideoClip();
// determine last frame to be marked (must satisfy both model and clip)
int end = Math.min(getEndFrame(), n);
while (end > getStartFrame() && !clip.includesFrame(end)) {
end--;
}
if (end <= lastValidFrame) return;
if (lastValidFrame == -1) {
reset(); // initializes model, sets lastValidFrame to marked frame, if any
if (lastValidFrame == -1 || end <= lastValidFrame) return;
}
int start = lastValidFrame;
Tracker.logTime(
this.getClass().getSimpleName()
+ this.hashCode()
+ " refreshing steps "
+ start
+ " to "
+ end); //$NON-NLS-1$ //$NON-NLS-2$
boolean singleStep = (end - start == 1);
// step forward to end
ImageCoordSystem coords = trackerPanel.getCoords();
// get underlying coords if appropriate
boolean useDefault = isUseDefaultReferenceFrame();
while (useDefault && coords instanceof ReferenceFrame) {
coords = ((ReferenceFrame) coords).getCoords();
}
double startTime = t0 + dt * tracePtsPerStep * (start - getStartFrame()) / clip.getStepSize();
double stepSize = 1.0 * clip.getStepSize() / tracePtsPerStep;
int stepCount = (tracePtsPerStep * (end - start)) / clip.getStepSize();
ParticleModel[] models = getModels();
// prepare larger trace arrays and copy existing points into them
for (ParticleModel next : models) {
next.locked = false;
int traceLength = next.traceX.length + stepCount;
next.prevX = next.traceX;
next.prevY = next.traceY;
next.traceX = new double[traceLength];
next.traceY = new double[traceLength];
System.arraycopy(next.prevX, 0, next.traceX, 0, next.prevX.length);
System.arraycopy(next.prevY, 0, next.traceY, 0, next.prevY.length);
}
for (int i = 0; i < stepCount; i++) {
int stepNumber = i + 1;
int frameNumber = start + (int) (stepNumber * stepSize);
time = startTime + stepNumber * dt;
Point2D[] points = getNextTracePositions();
if (points == null) continue;
AffineTransform transform = coords.getToImageTransform(frameNumber);
for (int j = 0; j < models.length; j++) {
transform.transform(points[j], points[j]);
// determine if point is invalid due to out of bounds
boolean valid =
Math.abs(points[j].getX()) < xLimit && Math.abs(points[j].getY()) < yLimit;
if (!valid && !invalidWarningShown) {
invalidWarningShown = true;
Runnable runner = new Runnable() { // avoids deadlock?
public void run() {
// if (invalidWarningShown) return;
JOptionPane.showMessageDialog(
trackerPanel,
TrackerRes.getString("ParticleModel.Dialog.Offscreen.Message1")
+ XML.NEW_LINE //$NON-NLS-1$
+ TrackerRes.getString(
"ParticleModel.Dialog.Offscreen.Message2"), //$NON-NLS-1$
TrackerRes.getString("ParticleModel.Dialog.Offscreen.Title"), // $NON-NLS-1$
JOptionPane.WARNING_MESSAGE);
}
};
SwingUtilities.invokeLater(runner);
}
models[j].traceX[models[j].prevX.length + i] = valid ? points[j].getX() : Double.NaN;
models[j].traceY[models[j].prevY.length + i] = valid ? points[j].getY() : Double.NaN;
if (stepNumber % tracePtsPerStep == 0) { // refresh position step
saveState(frameNumber);
PositionStep step = (PositionStep) models[j].getStep(frameNumber);
if (step == null) {
step = createPositionStep(models[j], frameNumber, 0, 0);
step.setFootprint(models[j].getFootprint());
models[j].steps.setStep(frameNumber, step);
}
step.getPosition().setPosition(valid ? points[j] : nan); // this method is fast
}
}
}
int count = 4 + (end - start);
int startUpdate = start;
// step back twice to pick up possible valid derivatives
if (startUpdate > clip.getStepSize()) startUpdate -= clip.getStepSize();
if (startUpdate > clip.getStepSize()) startUpdate -= clip.getStepSize();
lastValidFrame = end;
for (ParticleModel next : models) {
next.steps.setLength(end + 1);
coords = trackerPanel.getCoords(); // get active coords
// special treatment if this is the origin of current reference frame
if (coords instanceof ReferenceFrame
&& ((ReferenceFrame) coords).getOriginTrack() == next) {
// set origins of reference frame
boolean prev = next.refreshing; // save refreshing value
next.refreshing = true;
((ReferenceFrame) coords).setOrigins();
// then set positions to zero wrt origins
for (int i = 0; i < clip.getStepCount(); i++) {
int frameNumber = clip.stepToFrame(i);
PositionStep step = (PositionStep) next.getStep(frameNumber);
if (step == null) continue;
AffineTransform transform = coords.getToImageTransform(frameNumber);
next.point.setLocation(0, 0);
transform.transform(next.point, next.point);
step.getPosition().setPosition(next.point); // this method is fast
}
next.refreshing = prev; // restore refreshing value
if (!refreshDerivsLater) {
next.updateDerivatives(startUpdate, count);
}
} else if (!refreshDerivsLater) {
next.updateDerivatives(startUpdate, count);
}
if (next.vAtOrigin) next.vTailsToOriginItem.doClick();
if (next.aAtOrigin) next.aTailsToOriginItem.doClick();
if (!refreshDerivsLater) {
if (singleStep)
next.support.firePropertyChange("step", null, new Integer(n)); // $NON-NLS-1$
else next.support.firePropertyChange("steps", null, null); // $NON-NLS-1$
}
// erase refreshed steps
for (int i = start + 1; i <= end; i++) {
Step step = next.getStep(i);
if (step != null) step.erase();
}
next.locked = true;
}
trackerPanel.repaint();
}
}
public double cosh(double x) {
double ex, mex;
ex = Math.exp(x);
mex = 1 / ex;
return (ex + mex) / 2;
}
public double tanh(double x) {
double ex, mex;
ex = Math.exp(x);
mex = 1 / ex;
return (ex - mex) / (ex + mex);
}
public double freeenergy(double x) {
return 0.5 * Jq * x * x - 1.0 / beta * Math.log(2 * cosh(beta * (Jq * x + b)));
}
public double evaluate(double x) {
return Math.sqrt(1 - x * x);
}