[ome-users] Matlab JPEG2000 comments

Melissa Linkert melissa at glencoesoftware.com
Mon Sep 17 16:39:59 BST 2012 

Hi Mario,

> >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
> 
> I don't know why this is not working for me. I replaced the following
> jars with "daily build" and "trunk build" from your page, but the
> Metadata does not show. Did I miss something?
>   Fiji.app/jars/loci-common-4.4.2.jar
>   Fiji.app/jars/bio-formats-4.4-SNAPSHOT.jar
>   Fiji.app/jars/ome-xml-4.4.2.jar
>   Fiji.app/jars/poi-loci-4.4-SNAPSHOT.jar
>   Fiji.app/plugins/loci_plugins-4.4-SNAPSHOT.jar

You will need to update Fiji.app/jars/scifio-4.4-SNAPSHOT.jar as well.

Regards,
-Melissa

On Mon, Sep 17, 2012 at 05:36:54PM +0200, Mario Emmenlauer wrote:
> 
> Hi again,
> 
> On 09/17/2012 04:35 PM, Melissa Linkert wrote:
> >>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
> 
> I don't know why this is not working for me. I replaced the following
> jars with "daily build" and "trunk build" from your page, but the
> Metadata does not show. Did I miss something?
>   Fiji.app/jars/loci-common-4.4.2.jar
>   Fiji.app/jars/bio-formats-4.4-SNAPSHOT.jar
>   Fiji.app/jars/ome-xml-4.4.2.jar
>   Fiji.app/jars/poi-loci-4.4-SNAPSHOT.jar
>   Fiji.app/plugins/loci_plugins-4.4-SNAPSHOT.jar
> 
> Cheers,
> 
>     Mario
> 
> 
> >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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> >>>>>
> >>>
> >

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