Put OME-TIFF CustomAttributes/StructuredAnnotations in the original metadata hashtable

[mlinkert]

See the files in ome-tiff/ian/. All of the useful information is stored in ca:CustomAttributes, but that is not propagated to original metadata which means that it is not accessible from OMERO.

[jmoore]

Are those blocks also converted to XmlAnnotations? Is there anything more we can do with them?

[mlinkert]

They aren't converted to XmlAnnotations? at the moment. We may be able to do that too, but I haven't looked carefully enough at this point - there are a lot of moving parts here, especially since the files use the 2008-02 schema and so have to go through half a dozen stylesheets before Bio-Formats can even think about doing anything with the XML.

[mlinkert]

There are two parts to this. The first issue is that the 2008-09-to-2009-09.xsl stylesheet drops all CustomAttributes?, when it should convert to StructuredAnnotations. That's unfortunately a little tricky - do we always create an XMLAnnotation? Or try to guess the type?

Once the stylesheet does CustomAttributes? -> StructuredAnnotations, the second part is to update OMEXMLServiceImpl.getOriginalMetadata(...) so that it fetchs all top-level StructuredAnnotations and puts them in the hashtable in some sort of sensible way.

[jmoore]

I would think we would start by converting all custom attributes to a single xml annotation. We may from there add specific handling for well-known ones, but most likely storing the whole block as XML will be a) more useful/informative and b)less likely to lose any information. The flip side is that it will require more post-processing.

[mlinkert]

PR filed: ​https://github.com/openmicroscopy/bioformats/pull/272