Inconsistency of coordinates in NIRC2_Preprocessing routines

[henry-ngo]

From comments raised in #15

This is a reminder for me to check the input/output of all coordinates (e.g. cube centers) to ensure they have consistent ordering (y,x) vs. (x,y). I think I will choose (y,x) ordering to keep it consistent with Python 2-d arrays but will decide after more review. Please put any comments on this issue here!

This is also a reminder for everyone to be mindful of the possible inconsistency.