Add support for JPEG XR data

[mlinkert]

See files in data/jpegxr/ and:

​http://en.wikipedia.org/wiki/JPEG_XR
​http://www.microsoft.com/download/en/details.aspx?displaylang=en&id=1915

Design requirements from Melissa:

I'd expect that anything using this library would be able to input just
a file or stream of compressed bytes, and get at least the following in return:

• whether or not the file/stream is actually JPEG XR data
• the stream of decompressed bytes representing the image
• the number of bytes per pixel
• the number of bits per pixel (e.g. if 2 bytes are stored, but only 12 bits are valid)
• the number of channels
• any text metadata stored in the stream (e.g. creating software, creation date)

[mlinkert]

Also see zeiss-czi/zeiss/zen-2012/{*.czi, AxioScan?.Z1, Lightsheet}

[bpindelski]

Work in progress: ​https://github.com/bpindelski/bioformats/tree/jpegxr

[jamoore]

In discussion with Blazej and Jean-marie, pushing to beta3. A PR should be opened before the end of the year for review.

[jamoore]

Thanks for the breakdown, Blazej! Is it fair to assume that the remaining work needs to happen in roughly the order of the ticket numbers? If not, do you have a guess at the order?

[bpindelski]

It has to happen in the order of the created tickets (order is also defined in par. 7.1 of Rec. ITU-T T.832 (01/2012)). I left #12102 open, as there will certainly be work to do there as the code drills down deeper into the spec. #12109 might be too broadly defined and it depends how well the library will handle preparation of information required in the codestream decoders.

[mlinkert]

See also QA 8006.

[bpindelski]

Tasks outstanding, but initial PR open ​https://github.com/openmicroscopy/bioformats/pull/1014.

[mlinkert]

See also the file in zeiss-czi/jianguo.

[sbesson]

More information about the cost of trying to implement JPEG-XR can be read at ​http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-September/005616.html and ​http://blog.openmicroscopy.org/file-formats/community/2016/01/06/format-support/ .

[mtbcarroll]

See ​http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/ -

the user community has raised their concerns to ZEISS and a partnership has been established with Glencoe Software to add a Java-based JPEG-XR decoder to Bio-Formats

[sbesson]

With ​https://github.com/openmicroscopy/bioformats/pull/2648, this can now be marked as fixed