Fix setting of log levels

Move instantiation of log out of parse_args() to make it global. Also add
messages demonstrating loggin level.
Move generation of 6-well origins into function

It becomes member function of six_well_scan and the six_well_just_corners_scan
becomes child of six_well_scan.

Also beginning transition of language to "origins" for the corner of the well
because the "top-left corner of the top-left well" is unweildly and particularly
because it was confusing whether we were talking about a single corner or the
scan that includes the four corners of each well.
move scan starting point for each well to bot-left

Update language to specify the "origin" of each well as the bottom left corner
Also build well sub-scans from the origin up.