Extended the Python utilities 3D numpy arrays

This adds two new functions to get and set 3D numpy arrays, note
that we want Fortran ordered 3D arrays to avoid expensive deep
copies, but could add code to convert (warn right now if C order).
Hack to ensure the extents are properly updated

There is a bug in the VTK/ParaView pipeline that we need to work
around in order to get the full extents if they are chanegd in the
Python operator.