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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 >>> > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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 > >>> > > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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 ... [show rest of quote] 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 > >>>>> > >>> > > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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