Adding latest changes.  A lot of work done for notifications about MC-Boost medium
and attributes, as well as added options for selectively choosing which
AO mechanisms to simulate.  There was also an issue with the detector plane
not being set, which is now fixed.

However, there is an issue with detecting photons after initial seed generation.
That is, using seeds during the next run produces 0 detected photons.  Comitting
this for debugging on OSX.
Reloading seed issue was with checks in 'Photon' class for exit
data.  Removed if statement and exit data is always written.
Large changes to logger structure.  Got rid of old write methods that
aren't used anymore.  Also, added ability to write out different OPL's
based on what is simulated.

Currently it blows up when only one flag (sim_displacement) is turned on.
Committing for debugging on OSX.
small changes
It seems that simulating refractive index modulation does not
work correctly.  Also, not sure about displacements.
NEEDS SERIOUS DEBUGGING OVER THESE TWO ASPECTS.
Small changes
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.
Adding changes to MyLAB file to accomodate for PML.
Updating to new RNG behavior when spawning threads.  Code was
slow due to many threads being created.  Now, sticking to
creating only number of hardware threads, which read a vector
containing seeds.  Currently there is an error and committing to
debug on OSX.
More debugging...
Committing a new version that doesn't use seeds of detected photons.
For an unknown reason using a seeded approach has slowed execution
down considerably, which is strange because it should only simulate
photons that exit.  So, this version simulates all photons at each
time step.  Only using this to produce results and test displacement
modulation.

NEEDS DEBUGGING TO FIX SEEDS SLOWDOWN.
Adding changes to take into account the PML from k-Wave.
Needs testing.
small change.
small changes to how seeds are calculated.
Adding matlab script for processing speckle data once it has
been formed from running speckle formation software (i.e. Speckle-boost)
Adding changes to matlab file that generates the .h5 file that the C++ version runs.
Adding beginnings of being able to select MC, kWave, or AO simulations.

To do:
- Implement individual calls for each simulation (reference FIXME's in main.cpp)
Merge branch 'master' of https://github.com/jacobwjs/AO-KWave-MCBoost
blah
Adding latest changes to matlab file.