BioFormatsFormat: update Metadata API usage

As the convenience methods shadowing ImageMetadata API were removed from
Metadata, all invocations have been converted to get(index).<method>
BioFormatsFormat: Preserve Calibration values

When parsing, the BioFormatsFormat will now attach an OMEXMLMetadataImpl
object to its loci.formats Reader. This allows the subsequent extraction
of OMEXML values (in this case, physicalpixelsizes) which can now be
directly populated during populateImageMetadata calls.