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Re: Trainable Weka Segmentation - Result image calibration

Posted by Ignacio Arganda-Carreras-2 on Apr 14, 2015; 10:47am
URL: http://imagej.273.s1.nabble.com/Trainable-Weka-Segmentation-Result-image-calibration-tp5012265p5012467.html

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>

--
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