3D Trainable WEKA Segmentation

[Simon_Carr]

Dear Forum,

I've tried to migrate to the 3D Weka Segmentation Tool for segmenting
volumes of sediments into particles and matrix. This looks like it might
overcome slicing artefacts I have often experienced when using the previous
versions of the Weka segmentation tools.

I'm finding that a number of the training features cause JAVA exceptions and
errors: notably; Hessian, Derivatives, Structure, Laplacian and Edges
(occasionally). These all generate an instant error similar to this:

java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException:
Argument out of range: 1
        java.util.concurrent.FutureTask.report(FutureTask.java:122)
        java.util.concurrent.FutureTask.get(FutureTask.java:192)

trainableSegmentation.FeatureStack3D.updateFeaturesMT(FeatureStack3D.java:1015)

trainableSegmentation.WekaSegmentation.trainClassifier(WekaSegmentation.java:4767)
        trainableSegmentation.Weka_Segmentation$4.run(Weka_Segmentation.java:1459)

        at java.util.concurrent.FutureTask.report(FutureTask.java:122)
        at java.util.concurrent.FutureTask.get(FutureTask.java:192)
        at
trainableSegmentation.FeatureStack3D.updateFeaturesMT(FeatureStack3D.java:1015)
        at
trainableSegmentation.WekaSegmentation.trainClassifier(WekaSegmentation.java:4767)
        at
trainableSegmentation.Weka_Segmentation$4.run(Weka_Segmentation.java:1459)
Caused by: java.lang.IllegalArgumentException: Argument out of range: 1
        at ij.ImageStack.deleteSlice(ImageStack.java:135)
        at trainableSegmentation.FeatureStack3D$5.call(FeatureStack3D.java:464)
        at trainableSegmentation.FeatureStack3D$5.call(FeatureStack3D.java:1)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

I am not sure whether I have failed to add a key update site to FIJI, or
whether there is another issue: I am running FIJI/ImageJ version
2.0.0-rc-65/1.51s on an iMac running Mac OS 10.13.3.

Can anyone help here?

Regards,

Simon



--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Ignacio Arganda-Carreras-2]

Dear Simon,

Have you checked the ImageScience update site in order to use those
features? As stated in the documentation:

*NOTE*: The features named *Derivatives*, *Laplacian* and *Structure* belong
to the ImageScience <https://imagej.net/ImageScience> suite and need to be
activated by enabling the ImageScience update site in the updater
<http://imagej.net/How_to_follow_a_3rd_party_update_site>.

ignacio

On Mon, Feb 5, 2018 at 2:51 PM, Simon_Carr <[hidden email]> wrote:

> Dear Forum,
>
> I've tried to migrate to the 3D Weka Segmentation Tool for segmenting
> volumes of sediments into particles and matrix. This looks like it might
> overcome slicing artefacts I have often experienced when using the previous
> versions of the Weka segmentation tools.
>
> I'm finding that a number of the training features cause JAVA exceptions
> and
> errors: notably; Hessian, Derivatives, Structure, Laplacian and Edges
> (occasionally). These all generate an instant error similar to this:
>
> java.util.concurrent.ExecutionException: java.lang.
> IllegalArgumentException:
> Argument out of range: 1
>         java.util.concurrent.FutureTask.report(FutureTask.java:122)
>         java.util.concurrent.FutureTask.get(FutureTask.java:192)
>
> trainableSegmentation.FeatureStack3D.updateFeaturesMT(
> FeatureStack3D.java:1015)
>
> trainableSegmentation.WekaSegmentation.trainClassifier(
> WekaSegmentation.java:4767)
>         trainableSegmentation.Weka_Segmentation$4.run(Weka_
> Segmentation.java:1459)
>
>         at java.util.concurrent.FutureTask.report(FutureTask.java:122)
>         at java.util.concurrent.FutureTask.get(FutureTask.java:192)
>         at
> trainableSegmentation.FeatureStack3D.updateFeaturesMT(
> FeatureStack3D.java:1015)
>         at
> trainableSegmentation.WekaSegmentation.trainClassifier(
> WekaSegmentation.java:4767)
>         at
> trainableSegmentation.Weka_Segmentation$4.run(Weka_Segmentation.java:1459)
> Caused by: java.lang.IllegalArgumentException: Argument out of range: 1
>         at ij.ImageStack.deleteSlice(ImageStack.java:135)
>         at trainableSegmentation.FeatureStack3D$5.call(
> FeatureStack3D.java:464)
>         at trainableSegmentation.FeatureStack3D$5.call(
> FeatureStack3D.java:1)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>         at
> java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:617)
>         at java.lang.Thread.run(Thread.java:745)
>
> I am not sure whether I have failed to add a key update site to FIJI, or
> whether there is another issue: I am running FIJI/ImageJ version
> 2.0.0-rc-65/1.51s on an iMac running Mac OS 10.13.3.
>
> Can anyone help here?
>
> Regards,
>
> Simon
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--
Ignacio Arganda-Carreras, Ph.D.
Ikerbasque Research Fellow
Departamento de Ciencia de la Computacion e Inteligencia Artificial
Facultad de Informatica, Universidad del Pais Vasco
Paseo de Manuel Lardizabal, 1
20018 Donostia-San Sebastian
Guipuzcoa, Spain

Phone : [phone]
Website: http://sites.google.com/site/iargandacarreras/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html