Cleaned up some of the code, removed unnecessary parts, enforced naming conventions

I cleaned up some of the code by removing a few of the unused variables/
functions that were floating around.  I also tried to implement a standard
naming convention (pretty much following Google C++ Style Guidelines) for
variables and function names. Also renamed a few functions/variables to be
more explicit about what they are/do.

The main.cpp is still pretty crowded, so I think I need to create a
RingReadWrite class that can be used for all of these algorithms, or
add a few more functions to the GridReadWrite class to make a general Tiff
reader to be used for both reconstruction and ring removal? Also should move
all of the actual ring removal code to it's own class.  That way I can reuse
any functions that may come in handy, while also keeping the main file simple
and clean (beneficial when other ring removal algorithms start to get added).