private boolean processSlice(
final RandomAccessibleInterval<FloatType> src,
final RandomAccessibleInterval<FloatType> dx,
final RandomAccessibleInterval<FloatType> dy) {
// Gaussian filter.
final ExtendedRandomAccessibleInterval<FloatType, RandomAccessibleInterval<FloatType>>
extended = Views.extendMirrorSingle(src);
try {
Gauss3.gauss(new double[] {sigma, sigma}, extended, src, numThreads);
} catch (final IncompatibleTypeException e) {
errorMessage = BASE_ERROR_MSG + "Incompatible types: " + e.getMessage();
e.printStackTrace();
return false;
}
// Derivatives
PartialDerivative.gradientCentralDifference(extended, dx, 0);
PartialDerivative.gradientCentralDifference(extended, dy, 1);
return true;
}
@Override
public boolean process() {
/* 0. Instantiate tensor holder, and initialize cursors. */
long[] tensorDims = new long[input.numDimensions() + 1];
for (int i = 0; i < input.numDimensions(); i++) {
tensorDims[i] = input.dimension(i);
}
tensorDims[input.numDimensions()] = 3;
try {
D = input.factory().imgFactory(new FloatType()).create(tensorDims, new FloatType());
} catch (IncompatibleTypeException e) {
errorMessage = BASE_ERROR_MESSAGE + "Failed to create tensor holder:\n" + e.getMessage();
return false;
}
/* 1. Create a smoothed version of the input. */
Img<FloatType> smoothed = Gauss.toFloat(new double[] {sigma, sigma}, input);
/* 2. Compute the gradient of the smoothed input, but only algon X & Y */
boolean[] doDimension = new boolean[input.numDimensions()];
doDimension[0] = true;
doDimension[1] = true;
Gradient<FloatType> gradientCalculator = new Gradient<FloatType>(smoothed, doDimension);
gradientCalculator.process();
final Img<FloatType> gradient = gradientCalculator.getResult();
/* 3. Compute the structure tensor. */
final Img<FloatType> J = D.factory().create(D, new FloatType());
final int newDim = input.numDimensions();
final Vector<Chunk> chunks = SimpleMultiThreading.divideIntoChunks(input.size(), numThreads);
Thread[] threads = SimpleMultiThreading.newThreads(numThreads);
for (int i = 0; i < threads.length; i++) {
final Chunk chunk = chunks.get(i);
threads[i] =
new Thread("" + BASE_ERROR_MESSAGE + "thread " + i) {
@Override
public void run() {
float ux, uy;
Cursor<T> cursor = input.localizingCursor();
RandomAccess<FloatType> grad_ra = gradient.randomAccess();
RandomAccess<FloatType> J_ra = J.randomAccess();
cursor.jumpFwd(chunk.getStartPosition());
for (long k = 0; k < chunk.getLoopSize(); k++) {
cursor.fwd();
for (int i = 0; i < input.numDimensions(); i++) {
grad_ra.setPosition(cursor.getLongPosition(i), i);
J_ra.setPosition(cursor.getLongPosition(i), i);
}
grad_ra.setPosition(0, newDim);
ux = grad_ra.get().get();
grad_ra.fwd(newDim);
uy = grad_ra.get().get();
J_ra.setPosition(0, newDim);
J_ra.get().set(ux * ux);
J_ra.fwd(newDim);
J_ra.get().set(ux * uy);
J_ra.fwd(newDim);
J_ra.get().set(uy * uy);
}
}
};
}
SimpleMultiThreading.startAndJoin(threads);
/* 3.5 Smoooth the structure tensor. */
Gauss.inFloat(new double[] {rho, rho, 0}, J);
/* 4. Construct Diffusion tensor. */
for (int i = 0; i < threads.length; i++) {
final Chunk chunk = chunks.get(i);
threads[i] =
new Thread("" + BASE_ERROR_MESSAGE + "thread " + i) {
@Override
public void run() {
Cursor<T> cursor = input.localizingCursor();
RandomAccess<FloatType> J_ra = J.randomAccess();
RandomAccess<FloatType> D_ra = D.randomAccess();
float Jxx, Jxy, Jyy;
double tmp, v1x, v1y, v2x, v2y, mag, mu1, mu2, lambda1, lambda2, di;
double newLambda1, newLambda2, Dxx, Dxy, Dyy;
double scale;
cursor.jumpFwd(chunk.getStartPosition());
for (long k = 0; k < chunk.getLoopSize(); k++) {
cursor.fwd();
for (int j = 0; j < input.numDimensions(); j++) {
D_ra.setPosition(cursor.getLongPosition(j), j);
J_ra.setPosition(cursor.getLongPosition(j), j);
}
// Compute eigenvalues
J_ra.setPosition(0, newDim);
Jxx = J_ra.get().get();
J_ra.fwd(newDim);
Jxy = J_ra.get().get();
J_ra.fwd(newDim);
Jyy = J_ra.get().get();
tmp = Math.sqrt((Jxx - Jyy) * (Jxx - Jyy) + 4 * Jxy * Jxy);
v2x = 2 * Jxy;
v2y = Jyy - Jxx + tmp;
mag = Math.sqrt(v2x * v2x + v2y * v2y);
v2x /= mag;
v2y /= mag;
v1x = -v2y;
v1y = v2x;
mu1 = 0.5 * (Jxx + Jyy + tmp);
mu2 = 0.5 * (Jxx + Jyy - tmp);
// Large one in abs values must be the 2nd
if (Math.abs(mu2) > Math.abs(mu1)) {
lambda1 = mu1;
lambda2 = mu2;
} else {
lambda1 = mu2;
lambda2 = mu1;
}
di = lambda2 - lambda1;
scale = Util.pow(di * di, m);
newLambda1 = alpha + (1 - alpha) * Math.exp(-C / scale);
newLambda2 = alpha;
Dxx = newLambda1 * v1x * v1x + newLambda2 * v2x * v2x;
Dxy = newLambda1 * v1x * v1y + newLambda2 * v2x * v2x;
Dyy = newLambda1 * v1y * v1y + newLambda2 * v2y * v2y;
D_ra.setPosition(0, 2);
D_ra.get().setReal(Dxx);
D_ra.fwd(2);
D_ra.get().setReal(Dxy);
D_ra.fwd(2);
D_ra.get().setReal(Dyy);
}
}
};
}
SimpleMultiThreading.startAndJoin(threads);
return true;
}