Posted by
Curtis Rueden-2 on
Mar 13, 2020; 7:47pm
URL: http://imagej.273.s1.nabble.com/Error-using-Irregular-Watershed-tp5023028p5023039.html
Hi Pedro,
When asking for help with third party plugins, it is very helpful to
explain:
1. What is this plugin / Where is the website.
2. Where you got the plugin / How you installed it (e.g. downloaded and
copied into ImageJ 1.x manually, or enabled an ImageJ update site in
ImageJ2/Fiji).
3. Steps for reproducing the failure you are seeing.
I assume you are talking about this plugin by Thorsten Wagner and Jan Funke:
https://github.com/thorstenwagner/ij-irregular-watershedWhich I infer was forked from a function of Jan Brocher's BioVoxxel toolbox:
https://github.com/biovoxxel/BioVoxxel-Toolbox/blob/ebb8f9a66e12cab964c2b55e5e0e341174b6cafa/Biovoxxel_Plugins/src/main/java/de/biovoxxel/toolbox/Watershed_Irregular_Features.javaThe ij-irregular-watershed plugin has a dependency on a library called
ij_blob:
https://github.com/thorstenwagner/ij-irregular-watershed/blob/123760d3fd759d52cd9bfabafc6aef3e963dac15/pom.xmlYour error message strongly suggests that the needed ij_blob dependency is
missing from your ImageJ installation.
- Did you build it yourself and install into ImageJ 1.x?
- Or maybe you turned on the ParticleSizer update site, which ships the
ij_irregular_watershed library, but seems to be lacking ij_blob?
You can find the ij_blob source code here:
https://github.com/thorstenwagner/ij-blobAnd the IJ Blob wiki page at:
https://imagej.net/IJ_BlobI have CCed the author Thorsten Wagner.
Thorsten: should ParticleSizer ship ij_blob? What is the recommended
installation route for ij-irregular-watershed? I could not find any
documentation about it, nor any installation instructions on the IJ Blob
wiki page.
Thanks,
Curtis
--
Curtis Rueden
Software architect, LOCI/Eliceiri lab -
https://loci.wisc.edu/softwareImageJ2 lead, Fiji maintainer -
https://imagej.net/User:RuedenHave you tried the Image.sc Forum?
https://forum.image.sc/On Sun, Mar 8, 2020 at 7:05 AM Pedro J Camello <
[hidden email]> wrote:
> Hi all,
>
> I´m getting the following error in the console while trying to apply the
> Irregular Watershed plugin to a binary image. I appreciate any help.
>
> cloooose
> cloooose
> cloooose
> cloooose
> cloooose
> cloooose
> Exception in thread "Irregular Watershed Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
> at
> de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
> at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
> at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.lang.ClassNotFoundException: ij.blob.ManyBlobs
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 5 more
> Exception in thread "Irregular Watershed Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
> at
> de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
> at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
> at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
> at java.lang.Thread.run(Thread.java:748)
> Exception in thread "Watershed Irregular Features Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
> at
> de.biovoxxel.toolbox.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:224)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
> at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
> at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
> at java.lang.Thread.run(Thread.java:748)
> Caused by: java.lang.ClassNotFoundException: ij.blob.ManyBlobs
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ... 5 more
> Exception in thread "Irregular Watershed Preview"
> java.lang.NoClassDefFoundError: ij/blob/ManyBlobs
> at
> de.biomedical_imaging.ij.irregular_watershed.Watershed_Irregular_Features.run(Watershed_Irregular_Features.java:139)
> at
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
> at
> ij.plugin.filter.PlugInFilterRunner.runPreview(PlugInFilterRunner.java:513)
> at
> ij.plugin.filter.PlugInFilterRunner.run(PlugInFilterRunner.java:448)
> at java.lang.Thread.run(Thread.java:748)
>
> --
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http://imagej.nih.gov/ij/list.html>
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