Make high level admin & cmd line entry-points

[emlynjdavies]

This kind of use: (pyopia)> pyopia process config.ini --inputfolder='DataFolder' --outputfolder='Ouput'
optional inputs could then overwrite what is defined in the config file
information in the config file can be used to setup the steps and input settings to the functions in the pipeline
process would create a STATS.h5 file from a folder of raw images using default standard steps definitions