openmicroscopy/bioformats — pull request #820 by joshmoore (2013-12-05 16:25:52+00:00)
Title: 7856 flim ann

This branch propagates the XMLAnnotation created by Bio-Formats on reading the FLIM settings of .sdt file. The block should be equivalent to the xml found by running:
```
bfconvert foo.sdt foo.ome.tiff
tiffcomment foo.ome.tiff > foo-raw.ome.xml
xmllint --format foo-raw.ome.xml > foo.ome.xml
```

The OMERO annotation can typically be found with:
```
omero import foo.sdt
psql omero -c 'select textvalue from annotation order by id desc limit 1'
```

Current issues with this PR:
* It seems to have broken the bfconvert usage which quite critical ("Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 13; The processing instruction target matching "[xX][mM][lL]" is not allowed.")
* Namespace handling in the Annotation blocks is not correct. ("warning : xmlns: URI openmicroscopy.org/.../modulo is not absolute" is printed by xmllint)
* The API changes to `OMEXMLMetadata` are likely not appropriate.

/cc @melissalinkert @jburel