http://imagej.273.s1.nabble.com/Trainable-Weka-Segmentation-Result-image-calibration-tp5012265p5012267.html
Thanks for reporting all of this. I will have a look and try to fix it as
> 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)
>