Using Fiji with Java 1.7 on OSX

[Nissan Pow]

Hi,

I'm trying to use Fiji with Java 1.7 on OSX in order to use the
Trainable Weka Segmentation plugin (it requires 1.7). So I tried
starting Fiji using the --system flag, and I got an error about "no
J3D in java.library.path". I was able to get past this error by
creating a directory Library/Java/Extensions under
Fiji.app/java/macosx-java3d/Home/lib/ext and copying all the
jars/jnilib files from Fiji.app/java/macosx-java3d/Home/lib/ext into
Library/Java/Extensions. But now I'm getting an error about "no jogl
in java.library.path" and I can't figure out how to fix it. Is anyone
using the Trainable Weka Segmentation plugin on OSX?

Exception in thread "J3D-Renderer-1" java.lang.UnsatisfiedLinkError:
no jogl in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1886)
at java.lang.Runtime.loadLibrary0(Runtime.java:849)
at java.lang.System.loadLibrary(System.java:1088)
at com.sun.opengl.impl.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:189)
at com.sun.opengl.impl.NativeLibLoader.access$000(NativeLibLoader.java:49)
at com.sun.opengl.impl.NativeLibLoader$DefaultAction.loadLibrary(NativeLibLoader.java:80)
at com.sun.opengl.impl.NativeLibLoader.loadLibrary(NativeLibLoader.java:103)
at com.sun.opengl.impl.NativeLibLoader.access$200(NativeLibLoader.java:49)
at com.sun.opengl.impl.NativeLibLoader$1.run(NativeLibLoader.java:111)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.opengl.impl.NativeLibLoader.loadCore(NativeLibLoader.java:109)
at com.sun.opengl.impl.macosx.MacOSXGLDrawableFactory.<clinit>(MacOSXGLDrawableFactory.java:53)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:190)
at javax.media.opengl.GLDrawableFactory.getFactory(GLDrawableFactory.java:108)
at javax.media.j3d.JoglPipeline$QueryCanvas.<init>(JoglPipeline.java:9010)
at javax.media.j3d.JoglPipeline.getBestConfiguration(JoglPipeline.java:8774)
at javax.media.j3d.Renderer.doWork(Renderer.java:495)
at javax.media.j3d.J3dThread.run(J3dThread.java:256)

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[dscho]

Hi,

On Sat, 18 Oct 2014, Nissan Pow wrote:

> I'm trying to use Fiji with Java 1.7 on OSX in order to use the
> Trainable Weka Segmentation plugin (it requires 1.7).

It should not require Java 1.7. Please download the plugin from

http://jenkins.imagej.net/view/Fiji/job/Trainable_Segmentation/29/

and replace the local version in Fiji.app/plugins/ with it. On MacOSX you
will have to Ctrl+click the Fiji icon in the Finder and select Open
Package Contents to get into the Fiji.app/ directory.

Ciao,
Johannes

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[Nissan Pow]

Hi Johannes,

just tried using the plugin from that link, and it's still complaining
about 1.7:

(Fiji Is Just) ImageJ 2.0.0-rc-15/1.49i; Java 1.6.0_65 [64-bit]; Mac
OS X 10.9.4; 39MB of 1875MB (2%)

java.lang.UnsupportedClassVersionError:
weka/filters/unsupervised/attribute/IndependentComponents :
Unsupported major.minor version 51.0

This plugin requires Java 1.7 or later.



2014-10-18 23:13 GMT-04:00 Johannes Schindelin <[hidden email]>:

> Hi,
>
> On Sat, 18 Oct 2014, Nissan Pow wrote:
>
>> I'm trying to use Fiji with Java 1.7 on OSX in order to use the
>> Trainable Weka Segmentation plugin (it requires 1.7).
>
> It should not require Java 1.7. Please download the plugin from
>
> http://jenkins.imagej.net/view/Fiji/job/Trainable_Segmentation/29/
>
> and replace the local version in Fiji.app/plugins/ with it. On MacOSX you
> will have to Ctrl+click the Fiji icon in the Finder and select Open
> Package Contents to get into the Fiji.app/ directory.
>
> Ciao,
> Johannes

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