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scifio / scifio-ome-xml

SCIFIO plug-in providing support for the OME data model, including readers, writers and translators for OME-XML and OME-TIFF formats.
http://scif.io/
BSD 2-Clause "Simplified" License
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How to get the complete OME-XML-String? #7

Closed hornm closed 10 years ago

hornm commented 10 years ago

Hi Mark, what is the right way to get the OME-XML metadata as a XML-String from arbitrary image formats? So far we are only able to retrieve the default image metadata without the additional information (as, for instance, available in this image file). This is the code how we currently get the xml-string.

Thanks for your help! Martin

hinerm commented 10 years ago

@hornm your code looks correct to me. What are you expecting to see in the output xml? When I run Fiji, for example, and use the Bio-Formats importer to view the XML, it's pretty sparse.. just the standard metadata stuff. So there is probably a different reason that the information you're looking for isn't in your xml..

Anyway if you can tell me what the output should be I will try to figure out why it's not there :)

hornm commented 10 years ago

You are right, the xml in this case is pretty sparse, but there is still a difference and fiji (first image) returns a bit more information (the 'TiffData' section)

xml_fiji xml_knime

Thanks a lot!

hinerm commented 10 years ago

Thanks @hornm! This looks like something's being lost in the translation process. I'll look into it shortly.

hinerm commented 10 years ago

OK so there were 2 bugs. First, OME-formats needed to be updated for the latest XML schemas, which it now is.

Second, there is a bug in how Translators are discovered that is currently preventing proper translation to OME-XML. @ctrueden and I had a long talk today about how to resolve that, and it will take another SCIFIO release to sort out. But it's in the works now!

Will close this ticket once we update to a new SCIFIO..

ctrueden commented 10 years ago

@hinerm: Can you remind me why we forked the ome.xml package into io.scif.ome.xml? It was some dependency issue IIRC, but the ome-formats project currently does still depend on loci:ome-xml:4.4.10 and loci:scifio:4.4.10, so we haven't avoided the dependencies...

hornm commented 10 years ago

Great! Thanks for your help!

hinerm commented 10 years ago

@ctrueden I'm not sure. It looks like we started off trying to make ome-formats stand on its own, and then were like "this is silly let's use ome-xml." I couldn't find any significant changes, so I started a branch to remove some of the duplicated classes.

I am keeping the OMEXMLService duplication for now, since I think it makes sense to convert it to a SJC service. But open to thoughts on that.

ctrueden commented 10 years ago

@hinerm Thanks, I'll comment further on the branch.

hinerm commented 10 years ago

@hornm with the scifio-ome-xml 0.7.0 release, translation is now fixed and you should be able to actually see the full ome-xml.

Let us know if you have any more problems! Thanks!