3D viewer error message "Java 3D version 1.3 detected, but version >= is required" in OSX

[Kota Miura]

Dear All,

I recently encountered a problem with 3D viewer and found a solution so I
report it here. I am using OSX 10.8.5 and Fiji continuous release version
(and updated to the latest). The error however occurs also with other
variou mac laptops, also with the pure ImageJ1. As I am teaching a course
now with students' own laptops, I think this problem is rather
non-specific.

The problem is that when I invoke 3D viewer, an message appears saying

 "Java 3D version 1.3 detected, but version >= is required. Auto-install
new version?"

 [Plugins > Utilities > Debugging > Test Java3D] does work, by the way.
[Test Marching Cube] does not work.

Clicking OK will be another problem since the neurofly.de (
http://132.187.25.13/) is down at the moment so the automatic download
fails. I then tried swapping the local java3d jars with the ones from
oracle site, but this did not solve the problem (in fact, the jar files
installed under Fiji.app/java/Home/lib/ext/ were indeed version 1.5.2).  I
then realized that the System.getProperty("java.ext.dirs") is set to

Fiji.app/java/macosx-java3d/Home/lib/ext/Library/Java/Extensions

I made such directory under Fiji.app/java/macosx-java3d/Home/lib/ext/ and
moving all java3d jars, jogl jars and libraries there fixed the problem and
now has 3D viewer working.

[Test Marching Cube]  does not work however, returning an error but this
probably is not related to the problem I explained so far (I attach the
error trace below: this problem is also seen with Windows machines as well).

I wonder if I could set the java.ext.dirs to where it should be
(Fiji.app/java/macosx-java3d/Home/lib/ext). If anyone knows a quick
solution for that, it would be very much helpful.

Cheers,
Kota

===
(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_65 [64-bit]; Mac OS X
10.8.5; 29MB of 2881MB (1%)

javax.media.j3d.CapabilityNotSetException: Group: no capability to detach
BranchGroup
at javax.media.j3d.Group.removeChild(Group.java:225)
at MC_Test.displayCase(MC_Test.java:64)
at MC_Test.run(MC_Test.java:42)
at ij.IJ.runUserPlugIn(IJ.java:202)
at ij.IJ.runPlugIn(IJ.java:166)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)
===


--

-------------------------------------------------------------*Dr. Kota Miura*

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging,
European Molecular Biology Laboratory
Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel [phone]

Mobile [phone]

Fax [phone]

http://cmci.embl.de
-------------------------------------------------------------

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

[Dave Martynowicz]

I just ran into this exact same problem today. I just did like you did but now nothing pops up when I hit 3D Viewer.

[ctrueden]

Hi Kota,

> I then realized that the System.getProperty("java.ext.dirs") is set to
> Fiji.app/java/macosx-java3d/Home/lib/ext/Library/Java/Extensions

Thanks for the report! I think this is a problem with the ImageJ launcher.
I filed an issue accordingly:

   https://github.com/imagej/imagej-launcher/issues/21

Regards,
Curtis


On Tue, Jul 29, 2014 at 2:35 AM, Kota Miura <[hidden email]> wrote:

> Dear All,
>
> I recently encountered a problem with 3D viewer and found a solution so I
> report it here. I am using OSX 10.8.5 and Fiji continuous release version
> (and updated to the latest). The error however occurs also with other
> variou mac laptops, also with the pure ImageJ1. As I am teaching a course
> now with students' own laptops, I think this problem is rather
> non-specific.
>
> The problem is that when I invoke 3D viewer, an message appears saying
>
>  "Java 3D version 1.3 detected, but version >= is required. Auto-install
> new version?"
>
>  [Plugins > Utilities > Debugging > Test Java3D] does work, by the way.
> [Test Marching Cube] does not work.
>
> Clicking OK will be another problem since the neurofly.de (
> http://132.187.25.13/) is down at the moment so the automatic download
> fails. I then tried swapping the local java3d jars with the ones from
> oracle site, but this did not solve the problem (in fact, the jar files
> installed under Fiji.app/java/Home/lib/ext/ were indeed version 1.5.2).  I
> then realized that the System.getProperty("java.ext.dirs") is set to
>
> Fiji.app/java/macosx-java3d/Home/lib/ext/Library/Java/Extensions
>
> I made such directory under Fiji.app/java/macosx-java3d/Home/lib/ext/ and
> moving all java3d jars, jogl jars and libraries there fixed the problem and
> now has 3D viewer working.
>
> [Test Marching Cube]  does not work however, returning an error but this
> probably is not related to the problem I explained so far (I attach the
> error trace below: this problem is also seen with Windows machines as
> well).
>
> I wonder if I could set the java.ext.dirs to where it should be
> (Fiji.app/java/macosx-java3d/Home/lib/ext). If anyone knows a quick
> solution for that, it would be very much helpful.
>
> Cheers,
> Kota
>
> ===
> (Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_65 [64-bit]; Mac OS X
> 10.8.5; 29MB of 2881MB (1%)
>
> javax.media.j3d.CapabilityNotSetException: Group: no capability to detach
> BranchGroup
> at javax.media.j3d.Group.removeChild(Group.java:225)
> at MC_Test.displayCase(MC_Test.java:64)
> at MC_Test.run(MC_Test.java:42)
> at ij.IJ.runUserPlugIn(IJ.java:202)
> at ij.IJ.runPlugIn(IJ.java:166)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:695)
> ===
>
>
> --
>
> -------------------------------------------------------------*Dr. Kota
> Miura*
>
> Scientist & IT Engineer
> Centre for Molecular and Cellular Imaging,
> European Molecular Biology Laboratory
> Meyerhofstr. 1
> 69117 Heidelberg
> GERMANY
>
> Tel [phone]
>
> Mobile [phone]
>
> Fax [phone]
>
> http://cmci.embl.de
> -------------------------------------------------------------
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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