HDF5 file

[karlglazebrook]

HDF5 files could be made more useful. Right now it is not possible to just take an HDF5 file from someone else, and load it, if things are missing like the templates used, or in the wrong location.

params are stored in the HDF5 file, why not the templates?

Also it is not possible to simply override the templates to workaround this, as the only argument to initialize_from_hdf5() is the filename. It would be better if one could supply a params dict as well whose values would override any values in the file itself.