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kawa script using mpicbg_-1.0.2.jar -> ERROR

Posted by David Pirotte on Oct 14, 2015; 8:13pm
URL: http://imagej.273.s1.nabble.com/kawa-script-using-mpicbg-1-0-2-jar-ERROR-tp5014635.html

Hello,

        kawa script using mpicbg_-1.0.2.jar
        -> ERROR

"Linear Stack Alignment with SIFT" does not work when scripting using kawa [or
clojure by the way]

                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.jar [see below]

Anyone can give me some hint?

Thanks,
David


david@capac:~/lpdi/projects/kawa/jars 358 $ jar tf mpicbg.jar
META-INF/
META-INF/MANIFEST.MF
mpicbg/
mpicbg/ij/
mpicbg/ij/clahe/
mpicbg/ij/plugin/
Find_PointRoi.class
LICENSE
MOPS_ExtractPointRoi$1.class
MOPS_ExtractPointRoi$Param.class
MOPS_ExtractPointRoi.class
mpicbg/ij/clahe/PlugIn.class
mpicbg/ij/plugin/AbstractBlockFilter.class
mpicbg/ij/plugin/AbstractBlockStatistics.class
mpicbg/ij/plugin/AlignStacksWithLandmarks.class
mpicbg/ij/plugin/DiffusionMask.class
mpicbg/ij/plugin/ElasticAlign$1.class
mpicbg/ij/plugin/ElasticAlign$2.class
mpicbg/ij/plugin/ElasticAlign$Features.class
mpicbg/ij/plugin/ElasticAlign$Param.class
mpicbg/ij/plugin/ElasticAlign$PointMatches.class
mpicbg/ij/plugin/ElasticAlign$Triple.class
mpicbg/ij/plugin/ElasticAlign.class
mpicbg/ij/plugin/ElasticMontage$1.class
mpicbg/ij/plugin/ElasticMontage$2.class
mpicbg/ij/plugin/ElasticMontage$Features.class
mpicbg/ij/plugin/ElasticMontage$Param.class
mpicbg/ij/plugin/ElasticMontage$PointMatches.class
mpicbg/ij/plugin/ElasticMontage$Triple.class
mpicbg/ij/plugin/ElasticMontage.class
mpicbg/ij/plugin/Mean.class
mpicbg/ij/plugin/MSEBlockFlow.class
mpicbg/ij/plugin/MSEGaussianFlow.class
mpicbg/ij/plugin/NormalizeLocalContrast.class
mpicbg/ij/plugin/PMCCBlockFlow.class
mpicbg/ij/plugin/RemoveOutliers.class
mpicbg/ij/plugin/RemoveSaturated.class
mpicbg/ij/plugin/SampleVariance.class
mpicbg/ij/plugin/StandardDeviation.class
plugins.config
SIFT_Align$1.class
SIFT_Align$Param.class
SIFT_Align.class
SIFT_ExtractPointRoi$1.class
SIFT_ExtractPointRoi$Param.class
SIFT_ExtractPointRoi.class
SIFT_Test.class
Stack_Rotate$1.class
Stack_Rotate$GUI.class
Stack_Rotate$MappingThread.class
Stack_Rotate.class
Transform_Affine.class
Transform_MovingLeastSquaresMesh.class
Transform_Perspective.class
Transform_RegularizedAffine.class
Transform_Rigid.class
Transform_Roi.class
Transform_Similarity.class
Transform_SpringMesh$IllustrateThread.class
Transform_SpringMesh$OptimizeThread.class
Transform_SpringMesh.class
META-INF/maven/
META-INF/maven/mpicbg/
META-INF/maven/mpicbg/mpicbg_/
META-INF/maven/mpicbg/mpicbg_/pom.xml
META-INF/maven/mpicbg/mpicbg_/pom.properties

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