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ClearVolume / clearvolume

ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data.
http://clearvolume.github.io
GNU Lesser General Public License v3.0
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Clear Volume Plugin crash on the last Fiji version (imglib2 error) #70

Closed bpavie closed 6 years ago

bpavie commented 6 years ago

I have just donwloaded the last version of FIJI and then installed the ClearVolume Plugin

Opening the sample dataset Fly Brain, I used the Open in ClearVolume and got the following error message:

null [ERROR] Module threw error java.lang.AbstractMethodError: de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.getNativeTypeFactory()Lnet/imglib2/type/NativeTypeFactory; at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:140) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:380) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:354) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:446) 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:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [ERROR] Module threw error java.lang.AbstractMethodError: de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.getNativeTypeFactory()Lnet/imglib2/type/NativeTypeFactory; at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:140) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:380) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:354) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:446) 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:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

royerloic commented 6 years ago

Thanks for the report... Seems that something new in FiJi is breaking CV. Investigating...

Sent from my iPhone

On May 30, 2018, at 05:11, Benjamin Pavie notifications@github.com wrote:

I have just donwloaded the last version of FIJI and then installed the ClearVolume Plugin

Opening the sample dataset Fly Brain, I used the Open in ClearVolume and got the following error message:

null [ERROR] Module threw error java.lang.AbstractMethodError: de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.getNativeTypeFactory()Lnet/imglib2/type/NativeTypeFactory; at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:140) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:380) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:354) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:446) 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.(GenericClearVolumeGui.java:160) at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:86) at org.scijava.command.CommandModule.run(CommandModule.java:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) [ERROR] Module threw error java.lang.AbstractMethodError: de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.getNativeTypeFactory()Lnet/imglib2/type/NativeTypeFactory; at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:140) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:380) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:354) at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:446) 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.(GenericClearVolumeGui.java:160) at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:86) at org.scijava.command.CommandModule.run(CommandModule.java:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

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fjug commented 6 years ago

I am on it with Tobias. Changes in ImgLib Type System are the cause, but we are already pushing the fix. @royerloic , could you build and test? (We have interviews all day)

fjug commented 6 years ago

Fixed... in a few minutes I am sure I recovered the upload password and all should work perfectly fine again in Fiji! Sorry for the wait...

royerloic commented 6 years ago

Thank Guys!

I just tested it and it works. Also just informed a user about the fix…

Cheers,

Loic

On 3. Jun 2018, at 09:51, Florian Jug notifications@github.com wrote:

Closed #70 https://github.com/ClearVolume/ClearVolume/issues/70.

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