AFI: populate magnification and physical pixel size metadata (rebased from develop)

Fixes http://trac.openmicroscopy.org.uk/ome/ticket/12360. `test_images_good/afi/5400.afi` should now show `NominalMagnification`, `PhysicalSizeX`, and `PhysicalSizeY` values after import.

/cc @aleksandra-tarkowska
--rebased-from #1162 from @melissalinkert