Hi Christophe,
> In his message, Johannes hinted at a coming evolution of common maths,
> in order to get a version number in the jar name, and maybe to
> update it to a newer version? If this is still planned, would it be
> possible to update the stock common math in Fiji, in order to run
> the SMLM GCSD plugins natively?
Indeed, there is now a separate commons-math3 artifact for version 3.x. The
new version should (hopefully) be backwards compatible with the GCSD
plugins.
I updated the version in Fiji to commons-math3-3.2.jar [1], and uploaded
affected plugins [2] to the Fiji update site.
The nice thing about the 3.x version is that it now uses a different
package prefix than 2.x did. So if ever an ImageJ plugin still wants to
depend on commons-math 2.x, it will not conflict with plugins depending on
the 3.x version.
Regards,
Curtis
[1]
https://github.com/fiji/fiji/commit/a1b4545d8f8f705943b531b1b6566fd8b5763b14[2] The following 3 plugins were affected:
* Script Editor
* Simple Neurite Tracer
* Trainable Weka Segmentation
In my tests all still seems to be working, but if anyone encounters any
trouble, please let us know! In particular, I did not really test the
Simple Neurite Tracer since the 3D Viewer is not working right now on my
machine.
On Wed, Nov 20, 2013 at 3:47 PM, Christophe Leterrier <
[hidden email]> wrote:
> They are so much not mine that I keep spelling them wrong! GCSD plugins,
> sorry.
>
> Cheers,
>
> C.
>
>
> On Wed, Nov 20, 2013 at 10:46 PM, Christophe Leterrier <
>
[hidden email]> wrote:
>
> > Hi Johannes,
> >
> > I am aware that you are at a Hackaton from your Twitter feed and previous
> > emails to the list. I took care of not suggesting any urgency in my
> email,
> > I was just asking if it could be beneficial to update the currently used
> > common maths in Fiji for the GSDC plugins (which are not mine) and
> > potentially others at some point in the future.
> >
> > Thanks for the help,
> >
> > Christophe
> >
> >
> > On Wed, Nov 20, 2013 at 7:13 PM, Johannes Schindelin <
> >
[hidden email]> wrote:
> >
> >> Hi,
> >>
> >> On Tue, 19 Nov 2013, Christophe Leterrier wrote:
> >>
> >> > I was able to install the SMLM part of the GFSC plugins, the part that
> >> > interests me and that depends only on 3 jars:
> >> >
> >> > commons-math3-3.1.1.jar
> >> > ejml-0.23.jar
> >> > xstream-1.4.4.jar
> >> >
> >> > I added the xstream and ejml jars in the Fiji jars folder, but the
> >> plugins
> >> > didn't run with the stock Fiji common-math.jar (no version number).
> >> > Replacing the common-math.jar by the GCSD commons-math3-3.1.1.jar in
> >> Fiji,
> >> > I got the plugins to run.
> >>
> >> You should be able to "shadow" commons-math on your plugin site, then.
> >> Just rename it so the name is commons-math-3.1.1.jar and remove
> >> commons-math-3.0-SNAPSHOT.jar. The updater should then offer you the
> >> option to shadow that file via your update site.
> >>
> >> Please note that I am not really available for assistance this week, as
> I
> >> have some "real" work to do for a change ;-)
> >>
> >> Ciao,
> >> Johannes
> >>
> >
> >
>
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