[ome-users] Matlab JPEG2000 comments

[Melissa Linkert]

Hi Mario,

> Now I see, it works perfectly, thanks! I can see the custom metadata
> in the list, with prefix "custom/", when I access it directly from
> Java code. Works great! :-)

Glad to hear it!

> One off-topic request: The Fiji plugin does not list the metadata
> in the "Original Metadata" page, as I was expecting. Is that by
> design? I think custom Metadata could also be listed in the "Original
> Metadata" page, and it could be helpful to my users... :-)

If the JPEG-2000 comments don't appear when you check the "Display
metadata" box in the "Bio-Formats Import Options" window, then it's
likely that you just have an older version of Bio-Formats installed in
Fiji.  Selecting "Help > Update Fiji" may give you a working version,
otherwise you will likely need to manually download the "trunk build"
files from the "Bio-Formats component builds" section of:

http://loci.wisc.edu/bio-formats/downloads

and copy them to the similarly-named files in Fiji's 'jars' and
'plugins' directories.

Regards,
-Melissa

On Mon, Sep 17, 2012 at 04:13:37PM +0200, Mario Emmenlauer wrote:
> 
> Dear Melissa,
> 
> On 09/16/2012 07:14 PM, Melissa Linkert wrote:
> >Hi Mario,
> >
> >>with the daily builds up until now , I can not read the Matlab JPEG2000
> >>comments (yet). Is the patch already in?
> >
> >Yes, the patch has been in for a few days now, and I can definitely see
> >the comments with the latest daily build.
> >
> >Can you please double-check that the latest daily build is installed
> >(i.e. something did not go wrong when updating)?  If it is, then could
> >you please indicate where you are looking for the comments?  They should
> >be in the original metadata hashtable which can be retrieved by calling
> >'getGlobalMetadata()' on an IFormatReader.
> 
> Now I see, it works perfectly, thanks! I can see the custom metadata
> in the list, with prefix "custom/", when I access it directly from
> Java code. Works great! :-)
> 
> One off-topic request: The Fiji plugin does not list the metadata
> in the "Original Metadata" page, as I was expecting. Is that by
> design? I think custom Metadata could also be listed in the "Original
> Metadata" page, and it could be helpful to my users... :-)
> 
> Cheers,
> 
>    Mario
> 
> 
> >Regards,
> >-Melissa
> >
> >On Thu, Sep 13, 2012 at 08:20:47AM +0200, Mario Emmenlauer wrote:
> >>
> >>Dear Melissa,
> >>
> >>with the daily builds up until now , I can not read the Matlab JPEG2000
> >>comments (yet). Is the patch already in?
> >>
> >>Thanks and all the best,
> >>
> >>     Mario
> >>
> >>
> >>
> >>On 08/28/2012 08:39 AM, Mario Emmenlauer wrote:
> >>>
> >>>Dear Melissa,
> >>>
> >>>thanks a lot for the very very quick and helpful response!
> >>>I'll test the development build ASAP.
> >>>
> >>>Cheers,
> >>>
> >>>     Mario
> >>>
> >>>
> >>>
> >>>On 08/27/2012 04:55 PM, Melissa Linkert wrote:
> >>>>Hi Mario,
> >>>>
> >>>>>I'm trying to read comment fields from a lossless compressed JPEG200
> >>>>>file, created with Matlab (R2011b, in case it matters). Matlab supports
> >>>>>setting a list of arbitrary comments in the file, by specifying a cell
> >>>>>array of strings as a parameter to imwrite().
> >>>>>See http://www.mathworks.ch/help/techdoc/ref/imwrite.html#bsfqp3l-1.
> >>>>>
> >>>>>I'll send a corresponding image in a separate email. Is it possible
> >>>>>to read the comment fields with BioFormats?
> >>>>
> >>>>Thank you for mentioning this, and for sending a file privately.
> >>>>
> >>>>This commit allows the comments to be read and stored in Bio-Formats'
> >>>>original metadata hashtable:
> >>>>
> >>>>https://github.com/melissalinkert/bioformats/commit/eed5a864fb928511a84f9ec48376639b4431b49e
> >>>>
> >>>>
> >>>>A new development build with that fix should be available within a few
> >>>>days, otherwise the upcoming 4.4.3 version of Bio-Formats will include
> >>>>this fix.
> >>>>
> >>>>Regards,
> >>>>-Melissa
> >>>>
> >>>>On Mon, Aug 27, 2012 at 01:54:09PM +0200, Mario Emmenlauer wrote:
> >>>>>
> >>>>>Dear OME Developers,
> >>>>>
> >>>>>I'm trying to read comment fields from a lossless compressed JPEG200
> >>>>>file, created with Matlab (R2011b, in case it matters). Matlab supports
> >>>>>setting a list of arbitrary comments in the file, by specifying a cell
> >>>>>array of strings as a parameter to imwrite().
> >>>>>See http://www.mathworks.ch/help/techdoc/ref/imwrite.html#bsfqp3l-1.
> >>>>>
> >>>>>I'll send a corresponding image in a separate email. Is it possible
> >>>>>to read the comment fields with BioFormats?
> >>>>>
> >>>>>Thanks and all the best,
> >>>>>
> >>>>>    Mario
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>--
> >>>>>Mario Emmenlauer, Dipl.Inf.                  Office: +41-(0)61-26-72200
> >>>>>Biozentrum Basel
> >>>>>Klingelbergstrasse 50/70           mailto: mario.emmenlauer * unibas.ch
> >>>>>CH-4056 Basel                     http://infectx.org/about_us/emmenlau/
> >>>>>
> >>>>>
> >>>>>_______________________________________________
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> >>>>>ome-users at lists.openmicroscopy.org.uk
> >>>>>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>>>
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> >