Re: imagej scripting using kawa - can't use plugins

Posted by ctrueden on Sep 29, 2015; 1:41pm
URL: http://imagej.273.s1.nabble.com/imagej-scripting-using-kawa-can-t-use-plugins-tp5014487p5014489.html

Hi David,

> No matter what higher level programing language I use, I am unable to
> use any plugins, neither using Kawa nor using Clojure.

Some ideas:

1) Try setting the plugins.dir system property to specify your ImageJ
plugins folder [1].

2) Run your Clojure scripts from within ImageJ using the Script Editor [2],
or from the CLI using the ImageJ launcher [3].

3) Try putting all plugin JARs individually on your classpath.

Regards,
Curtis

[1] http://imagej.net/Plugins#Configuring_where_ImageJ_looks_for_plugins
[2] http://imagej.net/Script_Editor
[3] http://imagej.net/Launcher

On Tue, Sep 29, 2015 at 1:37 AM, David Pirotte <[hidden email]> wrote:

> Hello,
>
>         Scripting using higher level languages such as Kawa [an/or
> Clojure], I
>         can't make things happen so that I can use plugins
>
>         I am using Kawa (1) but please note that what is described in this
> report
>         also fails using clojure, since the problem is 'with/within' the
> ImageJ 'eco
>         system' itself (2), not 'with/within' these higher level languages.
>
>
> 1]      Short story:
>
>         No matter what higher level programing language I use, I am unable
> to use any
>         plugins, neither using Kawa nor using Clojure.
>
> I generally can do most, but not everything, of what is defined in the
> imagej core
> jar (3)  - but nothing that is defined in plugins.
>
> A quick look at the imagej launcher code [note that my java knowledge is
> close to
> zero], and it appears that, indeed, an impressive bit of magic occurs at
> launching
> time:
>
>         I wonder if someone else did solve this problem [even if for
> clojure] and
>         would be happy to share the solution with me?
>
>
> 2]      Example - "Non-local Means Denoising" (4)
>
>         Attached:       nlm-small.png           a small image to test
>
>         Code:           ij-core.scm             a kawa scheme very short
> snipset
>         ( here  -> )    http://paste.lisp.org/+3CB7
>
>         [ see at the end of ij-core.scm for a session example if would
> like to try
>         [ it, in which case you need kawa of course, then you would
> compile the
>         [ ij-core.scm file like this:
>
>         [               kawa -C ij-core.scm
>         [               -> ij$Mncore.class
>
> My directory setting is:
>
>         ~/lpdi/projects/kawa
>                 images/
>                         nlm-small.png
>                 jars/
>                         ij-1.49v.jar
>                         ij.jar -> ij-1.49v.jar
>                         NL_Means_1_3.jar
>                         nl-mean.jar -> NL_Means_1_3.jar
>                 ij-core.scm
>                 ij$Mncore.class
>
> Then cd to this location and here a trace of  a simple session:
>
>         export CLASSPATH=.:./jars/ij.jar:./jars/nl-mean.jar
>         kawa
>         (import (ij-core))
>         (define iplus1 (ij-open "nlm-small.png"))
>         (ij-show iplus1)
>         (ij-run iplus1 "Non-local Means Denoising" "sigma=3")
>         ->
>                 Unrecognized command: "Non-local Means Denoising"
>                 #!null
>
> But Kawa sees the classes, here:
>
>         (module-classes "jars/nl-mean.jar")
>         ->
>                 jars/nl-mean.jar:
>                 META-INF/
>                 META-INF/MANIFEST.MF
>                 de/
>                 de/biomedical_imaging/
>                 de/biomedical_imaging/ij/
>                 de/biomedical_imaging/ij/nlMeansPlugin/
>                 de/biomedical_imaging/ij/nlMeansPlugin/FastMathStuff.class
>
> de/biomedical_imaging/ij/nlMeansPlugin/NLMeansDenoising_$WorkerDouble.class
>
> de/biomedical_imaging/ij/nlMeansPlugin/NLMeansDenoising_$WorkerInt.class
>
> de/biomedical_imaging/ij/nlMeansPlugin/NLMeansDenoising_.class
>                 plugins.config
>
>         Plugins.config
>         ...
>         Plugins, "Non-local Means Denoising",
> de.biomedical_imaging.ij.nlMeansPlugin.NLMeansDenoising_
>
> Thanks for some usefull hint(s),
> Cheers,
> David
>
>
> (1)     menu driven, parameterized strings arguments
> (2)     https://www.gnu.org/software/kawa/
> (3)     I'm currently using ij149v.jar
> (4)     https://github.com/thorstenwagner/ij-nl-means
>
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> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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