Re: [ome-users] Matlab JPEG2000 comments

Posted by Mario Emmenlauer-3 on Sep 17, 2012; 2:13pm
URL: http://imagej.273.s1.nabble.com/Re-ome-users-Matlab-JPEG2000-comments-tp5000090.html

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: [phone]
>>>>> Biozentrum Basel
>>>>> Klingelbergstrasse 50/70           mailto: mario.emmenlauer * unibas.ch
>>>>> CH-4056 Basel                     http://infectx.org/about_us/emmenlau/
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ome-users mailing list
>>>>> [hidden email]
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> [hidden email]
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html