/**
* Apply Gaussian convolution to source and write the result to output. In-place operation
* (source==target) is supported.
*
* <p>If the target type T is {@link DoubleType}, all calculations are done in double precision.
* For all other target {@link RealType RealTypes} float precision is used. General {@link
* NumericType NumericTypes} are computed in their own precision. The source type S and target
* type T are either both {@link RealType RealTypes} or both the same type.
*
* @param sigma standard deviation of isotropic Gaussian.
* @param source source image, must be sufficiently padded (e.g. {@link
* Views#extendMirrorSingle(RandomAccessibleInterval)}) to provide values for the target
* interval plus a border of half the kernel size.
* @param target target image
* @param <S> source type
* @param <T> target type
* @throws IncompatibleTypeException if source and target type are not compatible (they must be
* either both {@link RealType RealTypes} or the same type).
*/
public static <S extends NumericType<S>, T extends NumericType<T>> void gauss(
final double sigma,
final RandomAccessible<S> source,
final RandomAccessibleInterval<T> target)
throws IncompatibleTypeException {
final int n = source.numDimensions();
final double[] s = new double[n];
for (int d = 0; d < n; ++d) s[d] = sigma;
gauss(s, source, target);
}
@Override
public void run() {
double[] sigmas = sigmas();
@SuppressWarnings("unchecked")
Img<T> target = (Img<T>) dataset.getImgPlus();
Img<T> input = target.copy();
ExtendedRandomAccessibleInterval<T, ?> paddedInput = Views.extendMirrorSingle(input);
try {
Gauss3.gauss(sigmas, paddedInput, target);
} catch (Exception e) {
cancel(e.getMessage());
}
}
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;
}