[ome-users] Matlab JPEG2000 comments

[Mario Emmenlauer]

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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>>>>>>
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>