[ImageJ-devel] TANGO

[Jean Ollion]

Hello Curtis,
Thank you for your detailed answer.
Another developer took care of the distribution on the fiji update site so
i'm not aware of these problems i will look at it. Though I think the
system specific files are only installation scripts for the mongodb
database, and do not need to be included in the java.library.path

About the confusion Ij1/Ij2 yes it has been cleared up, thank you. i wasn't
aware that fiji was already ij2 so when i said "use imagej1" it actually
meant "stay in legacy mode", but anyway it wasn'f the problem.

About mcib, it is an independent update site, and used as a dependency of
tango (this is documented on tango's website but still not on the readme
file of the update site, wich is bad!). We already tested this installation
on fresh linux, windows and macosx systems, including Alexandra's system.
The problem Alexandra is experimenting is recent, i am trying to solve it
with her, if we don't manage, i will ask you for advice.
Best,
Jean
Le 31 mai 2015 10:06, "Curtis Rueden" <ctrueden at wisc.edu> a écrit :

> Hi Jean,
>
> > @Curtis, in your answer to Alexandra, what do you mean by "It would be
> > best for TANGO to be distributed via an ImageJ update site, which are
> > only supported in ImageJ2" ?
>
> I was responding to Alexandra's statement at the beginning of the thread:
>
> > One of the developers of TANGO told me to use ImageJ1 because he
> > wasn't sure how the switch between libraries is managed.
>
> I understand that Tango has an official update site, which is great! What
> I meant is that I think update sites are the best way to distribute complex
> plugins like Tango—and update sites only work with ImageJ2, not ImageJ1.
>
> Hence, the advice to "use ImageJ1" struck me as odd. Based on my
> conversation with Alex in another thread, I think there was some confusion
> about what constitutes "ImageJ1" vs. "ImageJ2", which has hopefully been
> cleared up.
>
> > for some reason in her system (macosx64) only tango is updated and not
> > mcib (but it works properly in my system, linux64). Any clue about
> > what the problem might be?
>
> I took a look at the Tango update site, and noticed a couple of problems:
>
> 1) TANGO's platform-specific libraries are not in the correct locations. TANGO
> ships its libraries in lib/Linux64, lib/Win64 and lib/Mac64, which will not
> be added to the java.library.path properly.
>
> - 64-bit Linux libraries should go in lib/linux64
> - 64-bit Windows libraries should go in lib/win64
> - OS X libraries should go in lib/macosx
>
> You can verify this for yourself on each platform by running "ImageJ-xyz
> --dry-run" and noting the value of the "-Djava.library.path" argument.
> E.g., on my OS X system, it is:
>
>
>   -Djava.library.path=/Applications/Fiji.app/lib/macosx:/Applications/Fiji.app/mm/macosx
>
> 2) TANGO's lib/Mac64 directory does not have any OS X native libraries in
> it. I'm not sure whether this is intentional, though.
>
> 3) The TANGO update site does not ship any mcib libraries. You can verify
> this by running Help > Update..., changing the View Options to "View files
> of the 'Tango' update site" and typing "mcib" into the Search box.
>
> I downloaded http://sites.imagej.net/Tango/db.xml.gz and searched it for
> "mcib" and the string does not appear. This means that in fact, no files
> with "mcib" in the name have ever been uploaded to the Tango update site.
>
> Perhaps the reason TANGO works on your Linux system is that you have the
> mcib library present in a different directory of the java.library.path?
> Perhaps a system-wide installation? You may want to test on another fresh
> Linux system, rather than only your developer system.
>
> HTH,
> Curtis
>
>
> On Sat, May 30, 2015 at 11:35 AM, Jean Ollion <ollion at mnhn.fr> wrote:
>
>> Hello To everyone,
>>
>> There is no roadblock to tango working in ij2, the problem of Alexandra
>> is only due to a problem with the fiji updater, for some reason in her
>> system (macosx64) only tango is updated and not mcib (but it works properly
>> in my system, linux64). Any clue about what the problem might be?
>>
>> @Curtis, in your answer to Alexandra, what do you mean by "It would be
>> best for TANGO to be distributed via an ImageJ update site, which are only
>> supported in ImageJ2" ?
>> For the moment our pugin Tango is distributed under FIJI via an official
>> update site, and works in legacy mode (uses the "old" plugin system, and
>> doesn't use libraries of ImageJ2). Do you mean this type of distribution
>> won't be supported anymore?
>>
>> Best,
>> Jean
>>  Dear Alex and IJ2 developers,
>>
>> TANGO uses its own library for image processing and object analysis. We
>> use ImageJ and IJ1 mainly for opening images and drawing Rois of our 3D
>> objects as a overlay of the image. We would be happy to discuss more about
>> integration of TANGO into IJ2 . For completeness if you want to add plugins
>> into TANGO (filtering, segmentation, or measurements),you can use our own
>> MCIB library. We however already provide basic functions to exchange image
>> data between TANGO and IJ1, maybe we should write, using some help, basic
>> data exchange between TANGO and IJ2.
>>
>> Best,
>>
>> Thomas
>>
>> PS : in copy the main developer of TANGO, Jean
>>
>> On 29/05/15 05:25, Curtis Rueden wrote:
>>
>> Hi Alex,
>>
>>  > One of the developers of TANGO told me to use ImageJ1 because he
>> > wasn't sure how the switch between libraries is managed. Do I need to
>> > reinstall in this case?
>>
>>  When he says "use ImageJ1" he means:
>>   http://imagej.net/download.html
>>
>>  But please, encourage the TANGO developer to contact the imagej-devel
>> mailing list to discuss any roadblocks to TANGO working properly in
>> ImageJ2. It would be best for TANGO to be distributed via an ImageJ update
>> site, which are only supported in ImageJ2.
>>
>>  Regards,
>> Curtis
>>
>> On Thu, May 28, 2015 at 3:48 PM, Alexandra Bortnick <
>> alexandra.bortnick at gmail.com> wrote:
>>
>>> Hi Curtis,
>>>
>>>  One of the developers of TANGO told me to use ImageJ1 because he
>>> wasn't sure how the switch between libraries is managed. Do I need to
>>> reinstall in this case?
>>>
>>>  -Alex
>>>
>>>
>>
>>
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>>
>>
>>
>
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