[ImageJ-devel] R scripting integration in ImageJ2

[Curtis Rueden]

Hi Agustin,

Apologies for the long delay in reply.

> I'm contacting you regarding your comment "For what it's worth, we are
> also working on R scripting integration in ImageJ2." in
>
http://stackoverflow.com/questions/18989725/how-can-i-call-execute-an-imagej-macro-with-r
>
> I'm very interested on this issue. What is the stage of this
> integration?

For the past couple of months I have been working on improving the ImageJ
scripting framework in general, paving the way for parameterized scripts.
That branch adding R support has not yet been updated to take advantage of
the improvements, but needs to be.

> Is it something that I could try?

Unless you want to actually help complete the work, I suggest waiting until
it is merged to master and/or split into its own repository (not sure which
route we will go yet). The current status should be considered "alpha" in
that it fundamentally works, but has many remaining loose ends.

> I normally use the raster package in R, but I often find some
> operations to too slow and have done some naive scripting in ImageJ in
> these cases. Being able to call ImageJ commands from within R would be
> very useful for me.

To clarify, the branch in question uses RServe [1] to support running R
scripts from *within ImageJ*. Calling ImageJ from the R environment would
be the other direction; most popular package to do that is called rJava [2]
(by the same developer). See this blog post for examples:

    http://darrenjw.wordpress.com/2011/01/01/calling-java-code-from-r/

Regards,
Curtis

[1] http://rforge.net/Rserve/
[2] http://rforge.net/rJava/


On Wed, Dec 18, 2013 at 4:21 PM, Curtis Rueden <ctrueden at gmail.com> wrote:

> ---------- Forwarded message ----------
> From: Agustin Lobo <Agustin.Lobo at ictja.csic.es>
> Date: Wed, Dec 18, 2013 at 11:40 AM
> Subject: R scripting integration in ImageJ2
> To: ctrueden at gmail.com
>
>
> Dear Curtis Rueden,
>
> I'm contacting you regarding your comment
> "For what it's worth, we are also working on R scripting integration
> in ImageJ2."
> in
>
> http://stackoverflow.com/questions/18989725/how-can-i-call-execute-an-imagej-macro-with-r
>
> I'm very interested on this issue. What is the stage of this integration?
> Is it something that I could try? I normally use the raster package in R,
> but
> I often find some operations to too slow and have done some naive
> scripting in ImageJ in these cases. Being able to call ImageJ commands from
> within R would be very useful for me.
>
> Thanks,
>
> Agus
>
> --
> --
> Dr. Agustin Lobo
> Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
> Lluis Sole Sabaris s/n
> 08028 Barcelona
> Spain
> Tel. 34 934095410
> Fax. 34 934110012
> e-mail Agustin.Lobo at ictja.csic.es
> https://sites.google.com/site/aloboaleu/
>
>
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