Improve plotting interface

[kcormi]

A few things to add in:

command line arguments (so no commenting/uncommenting code)
automatically getting the last scan index
adding in the number of the scan to the output plots

[kcormi]

I've started to address this in commits c971cbf, and 3d82684

The plotting now accepts command line arguments and will take the most recent scan (largest index) by default. can also pass a few other arguments. Will continue to develop the interface.