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Re: [ome-users] Matlab JPEG2000 comments

Mario Emmenlauer-3
31 posts
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/
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
>

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Re: [ome-users] Matlab JPEG2000 comments

Melissa Linkert-2
123 posts
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/
> >>>>>
> >>>>>
> >>>>>_______________________________________________
> >>>>>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
> >>>
> >

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Re: [ome-users] Matlab JPEG2000 comments

Melissa Linkert-2
123 posts
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/
> >>>>>>>
> >>>>>>>
> >>>>>>>_______________________________________________
> >>>>>>>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
> >>>>>
> >>>
> >

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