Started adding code to accept reference images.
Removed the check to see if phys_size is a number.
This was superfluous, since the argument gets converted to a float when it was read in - if it's not a number, an error will already be raised.
Merged with master branch.
Reference images can now be accepted as parameters
These are optional parameters. Information from the headers of these images will be used in several of the processing steps.
Cleaned up the usage message.