1. A method of computing a transformation between a discrete reference signal with a suspect signal, the method comprising: providing a set of feature locations representing the discrete reference signal, and providing a seed set of initial transform parameters, wherein the feature locations and transform parameters are represented as digital, electronic signals in an electronic memory; using the seed set, computing a least squares minimization that finds linear transform candidates that minimize error when the linear transforms are used to align the feature locations of the discrete reference signal and corresponding feature locations in the suspect signal, including computing a measure of correlation corresponding to the linear transform candidates; and evaluating the linear transform candidates for each of the seeds to identify a subset of the candidates representing refined estimates of linear transform candidates.