Merge branch 'master' into John's-branch
the water top- and side-view are now subplots

made 'toConstantTime' and 'topViewOfWater' more readable
Added 'hold on/off' option to plots.
Plotting is now its own function

Some work on PHI for 2/sigma.
Bathymetry is now stored as a structure.
moved plot utils to folder

added 'plotID' which keeps plot windows from proliferating.
Moved plotting out of the main function
Merge branch 'John's-branch'