http://imagej.273.s1.nabble.com/Trainable-Weka-Segmentation-Result-image-calibration-tp5012265p5012492.html
> reading Fiji jars without manifest. Therefore it's not related to the
> plugin. I hope this will be fixed with the updates of those external
> Hello Jan,
>
> Regarding the exceptions you mentioned, I had a look and it seems they are
> originated in the weka library reading Fiji jars without manifest.
> Therefore it's not related to the plugin. I hope this will be fixed with
> the updates of those external jars. I cannot even reproduce the error with
> the debugger in Eclipse...
>
> Cheers!
>
> ignacio
>
> On Tue, Mar 31, 2015 at 12:53 PM, Ignacio Arganda-Carreras <
>
[hidden email]> wrote:
>
> > Hello Jan,
> >
> > Thanks for reporting all of this. I will have a look and try to fix it as
> > soon as i can!
> >
> > Best,
> >
> > ignacio
> >
> > On Tue, Mar 31, 2015 at 12:15 PM, Jan Eglinger <
[hidden email]>
> > wrote:
> >
> >> Hi Ignacio,
> >>
> >> I have a question/feature request for your Trainable Weka Segmentation
> >> plugin again :)
> >> Currently, the probability map you get upon clicking the "Get
> >> probability" button is not calibrated/scaled. I think adding a simple
> >>
> >> result.setCalibration(trainingImage.getCalibration())
> >>
> >> to WekaSegmentation.java in line #4489 [1] would do the trick.
> >> I would have filed a pull request, but couldn't test it quickly because
> >> of maven-javadoc-plugin failing when trying to run maven (I have to sort
> >> that out later).
> >>
> >> In addition, I noticed that a NullPointerException is thrown (now
> >> displayed in the new ImageJ Console [2]) upon starting Trainable Weka
> >> Segmentation, related to the GenericObjectEditor class of weka when you
> try
> >> to insert classifiers [3]. I pasted the stack trace below [4]. Don't
> know
> >> if that's something important to fix, but it might annoy users now that
> the
> >> Console is there.
> >>
> >> Best regards,
> >> Jan
> >>
> >>
> >> [1]:
https://github.com/fiji/Trainable_Segmentation/blob/> >> master/src/main/java/trainableSegmentation/WekaSegmentation.java#L4489
> >>
> >> [2]:
http://imagej.net/2015-03-26_-_ImageJ_2.0.0-rc-28_released> >>
> >> [3]:
https://github.com/fiji/Trainable_Segmentation/blob/> >> master/src/main/java/trainableSegmentation/Weka_
> >> Segmentation.java#L2350-2371
> >>
> >> [4]: Console output:
> >>
> >> Refreshing GOE props...
> >> java.lang.NullPointerException
> >> at weka.core.ClassCache.initFromManifest(ClassCache.java:248)
> >> at weka.core.ClassCache.initFromJar(ClassCache.java:293)
> >> at weka.core.ClassCache.initFromClasspathPart(
> >> ClassCache.java:351)
> >> at weka.core.ClassCache.initialize(ClassCache.java:373)
> >> at weka.core.ClassCache.<init>(ClassCache.java:111)
> >> at weka.core.ClassDiscovery.initCache(ClassDiscovery.java:447)
> >> at weka.core.ClassDiscovery.clearCache(ClassDiscovery.java:481)
> >> at weka.core.ClassDiscovery.clearClassCache(
> >> ClassDiscovery.java:490)
> >> at weka.core.WekaPackageManager.refreshGOEProperties(
> >> WekaPackageManager.java:1143)
> >> at weka.core.WekaPackageManager.loadPackages(
> >> WekaPackageManager.java:1134)
> >> at weka.core.WekaPackageManager.loadPackages(
> >> WekaPackageManager.java:1047)
> >> at weka.gui.GenericObjectEditor.determineClasses(
> >> GenericObjectEditor.java:177)
> >> at weka.gui.GenericObjectEditor.<clinit>(GenericObjectEditor.
> >> java:247)
> >> at sun.misc.Unsafe.ensureClassInitialized(Native Method)
> >> at sun.reflect.UnsafeFieldAccessorFactory.newFieldAccessor(
> >> UnsafeFieldAccessorFactory.java:25)
> >> at sun.reflect.ReflectionFactory.newFieldAccessor(
> >> ReflectionFactory.java:122)
> >> at java.lang.reflect.Field.acquireFieldAccessor(Field.java:918)
> >> at java.lang.reflect.Field.getFieldAccessor(Field.java:899)
> >> at java.lang.reflect.Field.get(Field.java:358)
> >> at trainableSegmentation.Weka_Segmentation.<clinit>(Weka_
> >> Segmentation.java:2358)
> >> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> >> Method)
> >> at sun.reflect.NativeConstructorAccessorImpl.newInstance(
> >> NativeConstructorAccessorImpl.java:39)
> >> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
> >> DelegatingConstructorAccessorImpl.java:27)
> >> at java.lang.reflect.Constructor.newInstance(Constructor.java:
> >> 513)
> >> at java.lang.Class.newInstance0(Class.java:355)
> >> at java.lang.Class.newInstance(Class.java:308)
> >> at ij.IJ.runUserPlugIn(IJ.java:197)
> >> at ij.IJ.runPlugIn(IJ.java:163)
> >> at ij.Executer.runCommand(Executer.java:131)
> >> at ij.Executer.run(Executer.java:64)
> >> at java.lang.Thread.run(Thread.java:619)
> >>
> >
> >
> >
> > --
> > Ignacio Arganda-Carreras, Ph.D.
> > Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> > Bâtiment 2
> > INRA Centre de Versailles-Grignon
> > Route de St-Cyr (RD10)
> > 78026 Versailles Cedex France
> >
> > Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> > Website:
http://sites.google.com/site/iargandacarreras/> > <
http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> Bâtiment 2
> INRA Centre de Versailles-Grignon
> Route de St-Cyr (RD10)
> 78026 Versailles Cedex France
>
> Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> Website:
http://sites.google.com/site/iargandacarreras/> <
http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>