imagej scripting using kawa - can't use plugins

Posted by David Pirotte on Sep 29, 2015; 6:37am
URL: http://imagej.273.s1.nabble.com/imagej-scripting-using-kawa-can-t-use-plugins-tp5014487.html

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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