The first time you have to return into python all the gains evaporate. As I said, we improved python code a few times and it never even got near. What it did was a bunch of convolutions, dot products, multiplications, fft, gamma probability equations. Even vector comparisons used numpy. Used direct hdf5 interface numpy has and fast view interface for overlaps.

Numba choked on the code by the way and crashed unless views were removed. And then it produced much worse performance.