Found a bug in the displacement calculation.  The code
had the coordinate transformation from the offline version
(i.e. displacements calculated 'offline' from Matlab).
They are correct now and verified that when only simulating
displacement the same speckle pattern is generated for the first
few steps.  It was only tested with 2 photons, but was shown to
correctly behave in a threaded and non-threaded case (i.e. they
produced the same speckle for both cases).

Debugging of the refractive changes needs to be done next, similar
to what has been done for displacement.