weka segmentation does not load.

[Aryeh Weiss]

When I run advanced weka segmentation, I get the  exception which
appears at the end of this email.

Some relevant info:

Operating System: Mac OSX 10.6.8
Fiji implementation of ImageJ
ij.jar version 1.47d27
Java 1.6.0_35 (64 bit)

Fiji is fully updated, and I uninstalled and then reinstalled weka.jar.

I do not have this problem when running on a 32-bit winxp which runs as
a VM under virtualbox on my mac,

Here is the exception:

java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at ij.Command.runPlugIn(Command.java:146)
        at ij.Command.runCommand(Command.java:95)
        at ij.Executer.run(Executer.java:64)
        at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.IncompatibleClassChangeError: class
hr.irb.fastRandomForest.FastRandomForest has interface
weka.classifiers.Classifier as super class
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
        at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:225)
        at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:217)
        at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:212)
        at
trainableSegmentation.Weka_Segmentation.<init>(Weka_Segmentation.java:249)
        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:183)
        at ij.IJ.runPlugIn(IJ.java:152)
        ... 8 more


Thanks in advance for any ideas or fixes.
--aryeh
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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

[Ignacio Arganda-Carreras]

Hello Aryeh,

I can't reproduce the error, but that does not say much because i'm also
unable to update Fiji :P

Did you use a fresh installation of Fiji?

ignacio

On Tue, Oct 2, 2012 at 10:41 AM, Aryeh Weiss <[hidden email]> wrote:

> When I run advanced weka segmentation, I get the  exception which appears
> at the end of this email.
>
> Some relevant info:
>
> Operating System: Mac OSX 10.6.8
> Fiji implementation of ImageJ
> ij.jar version 1.47d27
> Java 1.6.0_35 (64 bit)
>
> Fiji is fully updated, and I uninstalled and then reinstalled weka.jar.
>
> I do not have this problem when running on a 32-bit winxp which runs as a
> VM under virtualbox on my mac,
>
> Here is the exception:
>
> java.lang.reflect.**InvocationTargetException
>         at sun.reflect.**NativeMethodAccessorImpl.**invoke0(Native Method)
>         at sun.reflect.**NativeMethodAccessorImpl.**invoke(**
> NativeMethodAccessorImpl.java:**39)
>         at sun.reflect.**DelegatingMethodAccessorImpl.**invoke(**
> DelegatingMethodAccessorImpl.**java:25)
>         at java.lang.reflect.Method.**invoke(Method.java:597)
>         at ij.Command.runPlugIn(Command.**java:146)
>         at ij.Command.runCommand(Command.**java:95)
>         at ij.Executer.run(Executer.java:**64)
>         at java.lang.Thread.run(Thread.**java:680)
> Caused by: java.lang.**IncompatibleClassChangeError: class
> hr.irb.fastRandomForest.**FastRandomForest has interface
> weka.classifiers.Classifier as super class
>         at java.lang.ClassLoader.**defineClass1(Native Method)
>         at java.lang.ClassLoader.**defineClassCond(ClassLoader.**java:631)
>         at java.lang.ClassLoader.**defineClass(ClassLoader.java:**615)
>         at java.security.**SecureClassLoader.defineClass(**
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.**defineClass(URLClassLoader.**
> java:283)
>         at java.net.URLClassLoader.**access$000(URLClassLoader.**java:58)
>         at java.net.URLClassLoader$1.run(**URLClassLoader.java:197)
>         at java.security.**AccessController.doPrivileged(**Native Method)
>         at java.net.URLClassLoader.**findClass(URLClassLoader.java:**190)
>         at java.lang.ClassLoader.**loadClass(ClassLoader.java:**306)
>         at fiji.FijiClassLoader.**loadClass(FijiClassLoader.**java:225)
>         at fiji.FijiClassLoader.**loadClass(FijiClassLoader.**java:217)
>         at fiji.FijiClassLoader.**loadClass(FijiClassLoader.**java:212)
>         at trainableSegmentation.Weka_**Segmentation.<init>(Weka_**
> Segmentation.java:249)
>         at sun.reflect.**NativeConstructorAccessorImpl.**newInstance0(Native
> Method)
>         at sun.reflect.**NativeConstructorAccessorImpl.**newInstance(**
> NativeConstructorAccessorImpl.**java:39)
>         at sun.reflect.**DelegatingConstructorAccessorI**mpl.newInstance(*
> *DelegatingConstructorAccessorI**mpl.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:**183)
>         at ij.IJ.runPlugIn(IJ.java:152)
>         ... 8 more
>
>
> Thanks in advance for any ideas or fixes.
> --aryeh
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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

[Rasband, Wayne (NIH/NIMH) [E]]

On Oct 2, 2012, at 10:41 AM, Aryeh Weiss wrote:

> When I run advanced weka segmentation, I get the  exception which
> appears at the end of this email.
>
> Some relevant info:
>
> Operating System: Mac OSX 10.6.8
> Fiji implementation of ImageJ
> ij.jar version 1.47d27
> Java 1.6.0_35 (64 bit)
>
> Fiji is fully updated, and I uninstalled and then reinstalled weka.jar.

A better way to report Fiji-specific bugs is to use Fiji's Help>Report a Bug command.

-wayne

> I do not have this problem when running on a 32-bit winxp which runs as
> a VM under virtualbox on my mac,
>
> Here is the exception:
>
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at ij.Command.runPlugIn(Command.java:146)
> at ij.Command.runCommand(Command.java:95)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:680)
> Caused by: java.lang.IncompatibleClassChangeError: class
> hr.irb.fastRandomForest.FastRandomForest has interface
> weka.classifiers.Classifier as super class
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
> at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
> at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:225)
> at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:217)
> at fiji.FijiClassLoader.loadClass(FijiClassLoader.java:212)
> at
> trainableSegmentation.Weka_Segmentation.<init>(Weka_Segmentation.java:249)
> 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:183)
> at ij.IJ.runPlugIn(IJ.java:152)
> ... 8 more
>
>
> Thanks in advance for any ideas or fixes.
> --aryeh
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Aryeh Weiss]

On 10/2/12 5:57 PM, Ignacio Arganda-Carreras wrote:
> Hello Aryeh,
>
> I can't reproduce the error, but that does not say much because i'm also
> unable to update Fiji :P
>
> Did you use a fresh installation of Fiji?
>

Reinstallation of Fiji solved the problem. It is strange, since I moved
my plugin and macro directories to teh new installation, and also
updated to the latest daily build of imagej.

The one difference I noted is that the "old" installation displayed a
microscope for its logo, while the "new" installation displays the Fiji
logo. I do not know what this indicates, but maybe someone else does.

Sorry about reporting to the list instead of reporting it as a Fiji bug.
I did not realize that this plugin only runs in Fiji.

Best regards,
--aryeh
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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

[Ignacio Arganda-Carreras]

I'm glad it fixed it. Maybe Johannes can tell us more about the logo
behavior :)

ignacio

On Tue, Oct 2, 2012 at 4:07 PM, Aryeh Weiss <[hidden email]> wrote:

> On 10/2/12 5:57 PM, Ignacio Arganda-Carreras wrote:
>
>> Hello Aryeh,
>>
>> I can't reproduce the error, but that does not say much because i'm also
>> unable to update Fiji :P
>>
>> Did you use a fresh installation of Fiji?
>>
>>
> Reinstallation of Fiji solved the problem. It is strange, since I moved my
> plugin and macro directories to teh new installation, and also updated to
> the latest daily build of imagej.
>
> The one difference I noted is that the "old" installation displayed a
> microscope for its logo, while the "new" installation displays the Fiji
> logo. I do not know what this indicates, but maybe someone else does.
>
> Sorry about reporting to the list instead of reporting it as a Fiji bug. I
> did not realize that this plugin only runs in Fiji.
>
> Best regards,
>
> --aryeh
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>

--
Ignacio Arganda-Carreras, Ph.D.
Seung's lab, 46-5065
Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St.
Cambridge, MA 02139
USA

Phone: [phone]
Website: http://bioweb.cnb.csic.es/~iarganda/index_EN.html

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