double alignStep(final RandomAccessibleInterval<T> image) {
// compute error image = warped image - template
computeDifference(Views.extendBorder(image), currentTransform, template, error);
// compute transform parameter update
final double[] gradient = new double[numParameters];
for (int p = 0; p < numParameters; ++p) {
final Cursor<T> err = Views.flatIterable(error).cursor();
for (final T t : Views.flatIterable(Views.hyperSlice(descent, n, p)))
gradient[p] += t.getRealDouble() * err.next().getRealDouble();
}
final double[] dp = new double[numParameters];
LinAlgHelpers.mult(Hinv, gradient, dp);
// udpate transform
currentTransform.preConcatenate(warpFunction.getAffine(dp));
// return norm of parameter update vector
return LinAlgHelpers.length(dp);
}
public Align(final RandomAccessibleInterval<T> template, final ImgFactory<T> factory) {
this.template = template;
final T type = Util.getTypeFromInterval(template);
n = template.numDimensions();
warpFunction = new AffineWarp(n);
numParameters = warpFunction.numParameters();
currentTransform = new AffineTransform(n);
final long[] dim = new long[n + 1];
for (int d = 0; d < n; ++d) dim[d] = template.dimension(d);
dim[n] = n;
final Img<T> gradients = factory.create(dim, type);
gradients(Views.extendBorder(template), gradients);
dim[n] = numParameters;
descent = factory.create(dim, type);
computeSteepestDescents(gradients, warpFunction, descent);
Hinv = computeInverseHessian(descent);
error = factory.create(template, type);
}