SeH,
Thanks. The equations in the paper don't describe exactly the calculations in the code--they just represent the important computations to illustrate the operation of the algorithms. It might be worthwhile to do a more formal documentation of the math at some point, but right now, it is still changing quite a bit from version to version, so I didn't invest the time. If I were going to invest it though, the first thing I would do is go to the code and put in a bunch of print xxx.shape lines.
Brandon