The implementation in the frequency domain is more or less the same as in the space domain. We only use FFT's to compute the products for the correlation (see equation D.24) in an efficient way, due to the fact that a convolution in the space domain corresponds to a multiplication in the frequency domain. Input are the zero mean magnitude images.
The cross products are obtained by computing the pointwize product of the zeropadded master x conj(slave). A block function is used to compute the norms. Note that the correlation window (the overlap) does not have a constant size with this method, but varies between winsizeL/P and .5winsizeL/P.