adds command line functionality to realign.py
adds command line functionality to realign.py

with this commit, realign.py will now work well from the command
line. it could previously be called, but didn't accept any
arguments. this adds the arguments and some basic functionality.

realing.sbatch still needs to be updated for this though

billbrod/spatial-frequency-preferences,billbrod/spatial-frequency-preferences,billbrod/spatial-frequency-preferences