Clear Volume Plugin ERROR

HI,

I’m trying to install this new plugin (Clear Volume) in my computers, both personal and work.
I’ve the Java version 8 installed in both and I´m getting exactly the same error message when I try to run the plugin. I´ve updated Fiji and everything runs perfect, I’m having problems just with this new plugin.

The Error messages appear in two windows.

First “Console” window says:

com.apple.eawt.Application
java.lang.ExceptionInInitializerError
	at clearvolume.renderer.factory.ClearVolumeRendererFactory.internalCreateOpenCLRenderer(ClearVolumeRendererFactory.java:370)
	at clearvolume.renderer.factory.ClearVolumeRendererFactory.newOpenCLRenderer(ClearVolumeRendererFactory.java:324)
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:262)
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:445)
	at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:182)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:303)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:160)
	at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:86)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: com.jogamp.opengl.GLException: Profile GL3 is not available on null, but: [GLProfile[GL2ES1/GL2.sw], GLProfile[GL2ES2/GL2.sw], GLProfile[GL2/GL2.sw], GLProfile[GL2/GL2.sw], GLProfile[GL2GL3/GL2.sw]]
	at com.jogamp.opengl.GLProfile.get(GLProfile.java:991)
	at com.jogamp.opengl.GLProfile.get(GLProfile.java:1004)
	at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.<clinit>(ClearGLVolumeRenderer.java:82)
	... 17 more
[ERROR] Module threw exception
java.lang.NullPointerException
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:273)
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:445)
	at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:182)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:303)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:160)
	at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:86)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

and the second window “Exception” says:

(Fiji Is Just) ImageJ 2.0.0-rc-46/1.50g; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 96MB of 4503MB (2%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:277)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.util.concurrent.FutureTask.get(FutureTask.java:192)
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:273)
	... 5 more
Caused by: java.lang.NullPointerException
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:273)
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:445)
	at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:182)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:303)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:160)
	at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:86)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	... 1 more

Any ideas???

The ClearVolume page shows a similar OpenCL error occurring on Linux but with no solution.

Do you have the Java 8 update site enabled?

The Java 8 update site is required, as mentioned on the ClearVolume page. Previously, the Java 8 update site on Fiji conflicted with ClearVolume. However, that seems not to be the case anymore.

I’m using Mac OS X 10.11.4 with Java 1.8.0_77, Fiji 2.0.0-rc-46/1.50g, and it worked with ImageJ, Fiji, Java8, and ClearVolume update sites turned on.

Hope this helps.

4 Likes

Hmm, I think the exception is about OpenGL (JOGL) libraries not found, not OpenCL (JOCL). Anyway, if the update site doesn’t help, you can try dropping the following jar to your plugins folder:
jogl-all-2.3.2jar

you may also need need the appropriate native implementation, e.g. linux-amd64 for a Linux computer running on an AMD 64-bit processor
jogl-all-2.3.2-natives-linux-amd64.jar
[List of available native implementations (click 2.3.2 and artifact)]
(http://maven.imagej.net/index.html#nexus-search;quick~jogl-all)

In addition you’ll need the gluegen library:
gluegen-rt-main-2.3.2.jar

Regards,
Richard Domander

2 Likes

Yes I´ve the Java 8 update site enabled…

That´s not the problem!

No, it didn´t work. Same errors…
Thanks.

All of that stuff already ships with the Java-8 update site. At least, it’s supposed to… :wink:

Seconded (with 2.0.0-rc-47/1.50i, same OS + Java):

Apple.Iris Pro L64k/G 1536M mem with 40 compute units
Apple.AMD Radeon R9 M370X Compute Engine L32k/G 2048M mem with 10 compute units
AMD Radeon R9 M370X Compute Engine is best in platform Apple
Device name: 	 AMD Radeon R9 M370X Compute Engine (Apple) 

@sdeoliveira What OS and graphics card are you using?