Some refactoring/tidying

Make the GeoTools methods static, so don't need to make a pointless
GeoTools instance before using them.

Remove the old extract_region method, as we are using the new one that
regrids at the same time

Tidy the file readers a bit by adding inner functions to do the data
extraction/gridding, so we can call several times for different variables
(eg when we add the angles)

Fix some whitespace issues for PEP8 compliance