autopew CLI

[morganjwilliams]

At the moment the interface to autopew is largely via scripts/notebooks, but in some cases it might make sense to instead use a command line interface with a common specification for input files etc (e.g. using click). This could look something like:

autopew calibrate src.csv dest.csv -n 'BSE_2_stage' # create a calibration - BSE image to stage coordinates
autopew transform sample_points.csv stage_coords.csv -n 'BSE_2_stage' # transform sample points

This would generally be more interoperable with other automation tools, and might make autopew a bit more versatile.