imagej scripting using kawa - can't use plugins
Locked
imagej scripting using kawa - can't use plugins
 
|
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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
nlm-small.png (99K)
Re: imagej scripting using kawa - can't use plugins
|
Re: imagej scripting using kawa - can't use plugins
|
|
Re: imagej scripting using kawa - can't use plugins
|
|
Hi Kyle,
Curtis, thanks both, sorry for the delay, I had to jump on another project and experiment a bit with the proposed solutions as well... A] NL Mean works! Using the directory setting and ij-core.scm -> ij$Mncore.class mentioned in my previous emal, plus this define in ij-nl-mean.scm [kawa -C ij-nl-mean.scm -> ij$Mnnl$Mnmean.class]: (define (ij-nl-mean iplus1 sigma) (ij-run iplus1 "Non-local Means Denoising" (string-append "sigma=" (number->string sigma)))) then the nl-mean kawa script does work [1] B] "Linear Stack Alignment with SIFT" does not work Note: the images we use are too big to send them here, but who might help probably knows the mpicbg source code and has images to test locally ... ~/lpdi/projects/kawa jars/ ij-1.49v.jar ij.jar -> ij-1.49v.jar mpicbg_-1.0.2.jar mpicbg.jar -> mpicbg_-1.0.2.jar ij-core.scm ij$Mncore.class Session example: david@capac:~/lpdi/projects/kawa 67 $ export CLASSPATH=.:./jars/ij.jar:./jars/mpicbg.jar david@capac:~/lpdi/projects/kawa 68 $ kawa -Dplugins.dir=./jars #|kawa:1|# (import (ij-core)) #|kawa:2|# (define iplus1 (ij-open "/usr/lpdi/projects/tests/mfer/vale/dipe/mosaic1/bf.png")) #|kawa:3|# (define iplus2 (ij-open "/usr/lpdi/projects/tests/mfer/vale/dipe/mosaic1/cpol.png")) #|kawa:4|# (ij-show iplus1) #|kawa:6|# (ij-show iplus2) #|kawa:7|# (ij-run "Images to Stack" "method=[Copy (center)] name=Stack title=[] use") #|kawa:9|# (ij-run "Linear Stack Alignment with SIFT" "initial_gaussian_blur=1.60 steps_per_scale_octave=3 minimum_image_size=64 maximum_image_size=1024 feature_descriptor_size=4 feature_descriptor_orientation_bins=8 closest/next_closest_ratio=0.92 maximal_alignment_error=25 inlier_ratio=0.05 expected_transformation=Translation interpolate") -> Class not found while attempting to run "SIFT_Align" java.lang.NoClassDefFoundError: mpicbg/models/TranslationModel2D Indeed, it is not in mpcibg What other plugin/jar should I add to my CLASSPATH to make this work? Thanks, David [1] nl-mean kawa script #!/bin/sh # -*- mode: scheme; coding: utf-8 -*- export CLASSPATH=\ /usr/lpdi/projects/kawa:\ /usr/lpdi/projects/kawa/jars/ij.jar:\ /usr/lpdi/projects/kawa/jars/nl-mean.jar exec kawa -Dplugins.dir=/usr/lpdi/projects/kawa/jars --script8 "$0" "$@" !# ;;;; ;;;; Copyright (C) 2015 ;;;; David Pirotte <david at altosw dot be> ;;;; This module is part of a set of image processing modules and ;;;; scripts written using Kawa and ImageJ. ;;;; This module is free software: you can redistribute it and/or modify ;;;; it under the terms of the GNU General Public License as published ;;;; by the Free Software Foundation, either version 3 of the License, ;;;; or (at your option) any later version. ;;;; It is distributed in the hope that it will be useful, but WITHOUT ;;;; ANY WARRANTY; without even the implied warranty of ;;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ;;;; General Public License for more details. ;;;; You should have received a copy of the GNU General Public License ;;;; along with this s/w. If not, see <http://www.gnu.org/licenses/>. ;;;; ;;; Commentary: ;;; Code: (import (utils) (ij-core) (ij-nl-mean)) (let* ((cmd (command-line)) (dir (list-ref cmd 1)) (im-name (list-ref cmd 2)) (im-type (list-ref cmd 3)) (im-out (list-ref cmd 4)) (sigma (string->number (list-ref cmd 5))) (im-filename (string-append dir "/" im-name "." im-type)) (iplus (ij-open im-filename))) (ij-nl-mean iplus sigma) (ij-save iplus (string-append dir "/" im-out "." im-type)) (exit)) #| ./nl-mean . images/nlm-small png images/nlm-out 30 |# -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
| Free forum by Nabble | Edit this page |