clearvolume / imglib2-clearvolume Goto Github PK

Java 98.93% HTML 1.07%

imglib2-clearvolume's Introduction

Welcome to 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. The biologists can immediately decide whether a sample is worth imaging.

ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. Moreover, it has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. In addition, it offers the possibility of remote viewing of volume data

Building from source

In order to only build the Java parts of the project, simply run ./gradlew build. Should you also want to build the native/C++ parts (e.g., for LabVIEW integration), run build.bat or build.sh.

Wiki and Website

For up to date information about the project, please go to the website or have a look at the wiki

imglib2-clearvolume's People

Contributors

Stargazers

Watchers

Forkers

habi lostintoky0 wisamreid

imglib2-clearvolume's Issues

Images > 2GiB are not supported

Even if the present graphics card has enough memory, the plugin bails out with

java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 5086604250 > 2147483647
at net.imglib2.img.array.ArrayImgFactory.numEntitiesRangeCheck(ArrayImgFactory.java:71)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:79)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:58)
at de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.createSuitableNativeImg(ClearVolumeUnsignedShortType.java:320)
at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:63)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:355)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:328)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:419)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
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)
[ERROR] Module threw exception
java.lang.RuntimeException: Number of elements in Container too big, use for example CellContainer instead: 5086604250 > 2147483647
at net.imglib2.img.array.ArrayImgFactory.numEntitiesRangeCheck(ArrayImgFactory.java:71)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:79)
at net.imglib2.img.array.ArrayImgFactory.createByteInstance(ArrayImgFactory.java:58)
at de.mpicbg.jug.clearvolume.ClearVolumeUnsignedShortType.createSuitableNativeImg(ClearVolumeUnsignedShortType.java:320)
at net.imglib2.img.array.ArrayImgFactory.create(ArrayImgFactory.java:63)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopy(ImgLib2ClearVolume.java:355)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.makeClearVolumeUnsignedShortTypeCopies(ImgLib2ClearVolume.java:328)
at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:419)
at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:156)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:208)
at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:135)
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:80)
at org.scijava.command.CommandModule.run(CommandModule.java:201)
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)

@fjug suggested to use cell images. Maybe @tpietzsch also has some suggestions? :)

The bug was originally reported by @yafshar.

pom.xml unresolved dependencies

When compiling, I am getting an error while retrieving net.clearvolume:clearvolume:jar:1.0-SNAPSHOT.

Here is the full error message:

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 11.237 s
[INFO] Finished at: 2016-03-01T14:24:45-05:00
[INFO] Final Memory: 19M/233M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project imglib-clearvolume: Could not resolve dependencies for project sc.fiji:imglib-
clearvolume:jar:1.1.0: The following artifacts could not be resolved: net.clearvolume:clearvolume:jar:1.0-SNAPSHOT, net.
clearvolume:cleargl:jar:1.0-SNAPSHOT, net.clearvolume:clearcuda:jar:0.9-SNAPSHOT: Could not find artifact net.clearvolum
e:clearvolume:jar:1.0-SNAPSHOT in imagej.public (http://maven.imagej.net/content/groups/public) -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException

The repository seems to have been moved http://maven.imagej.net/content/groups/public/net/

Update 1:

It seems to be available here: http://dl.bintray.com/clearvolume/ClearVolume/net/clearvolume/

I found that url in the pom.xml, so maybe it is just a configuration error. I will keep looking into this

Update 2:

Turns out this is only a problem with compiling in development mode: mvn or mvn -P development. Running mvn -P production compiles nicely

ClearVolume Fiji plugin broken on Windows 10 and Fedora Linux

Dear all,

I just tested ClearVolume on a recent Windows 10 x64. It's a fresh and up-to-date Fiji installation, with only the ClearVolume update site activated. I opened t1-head.tif and hit the menu "Open in ClearVolume". The window opens but stays white. An exception is thrown as shown below.

I'm just wondering about the right strategy to approach this: Shall we update ClearVolume and all its dependencies? ClearVolume.jar for example is from 2016... Or might it make sense to just fix the bug here in the one particular affected version?

null
ClearGLWindow: GLProfile[GL4bc/GL4bc.hw]
1.0
1.0
1.0
WindowsJan 15, 2019 9:53:55 PM org.bridj.BridJ log
INFO: Library not found : atiocl64
Jan 15, 2019 9:53:55 PM org.bridj.BridJ log
INFO: Library not found : amdocl64
Jan 15, 2019 9:53:55 PM org.bridj.BridJ log
INFO: Library not found : atiocl32
Jan 15, 2019 9:53:55 PM org.bridj.BridJ log
INFO: Library not found : atiocl
Jan 15, 2019 9:53:55 PM org.bridj.BridJ log
INFO: Library not found : amdocl32
Jan 15, 2019 9:53:55 PM org.bridj.BridJ log
INFO: Library not found : amdocl
clearcl.exceptions.ClearCLException
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:161)
at clearcl.backend.jocl.ClearCLBackendJOCL.releaseImage(ClearCLBackendJOCL.java:1153)
at clearcl.ClearCLImage.close(ClearCLImage.java:628)
at clearcl.benchmark.Benchmark.executeBenchmarkOnDevice(Benchmark.java:248)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:115)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:54)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:46)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
Caused by: java.lang.NullPointerException
at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$releaseImage$40(ClearCLBackendJOCL.java:1154)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:154)
... 22 more
java.lang.NullPointerException
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:60)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:46)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
clearcl.exceptions.ClearCLException
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:161)
at clearcl.backend.jocl.ClearCLBackendJOCL.setKernelArgument(ClearCLBackendJOCL.java:626)
at clearcl.ClearCLKernel.setArgumentsInternal(ClearCLKernel.java:259)
at clearcl.ClearCLKernel.lambda$run$0(ClearCLKernel.java:306)
at clearcl.util.ElapsedTime.measure(ElapsedTime.java:39)
at clearcl.ClearCLKernel.run(ClearCLKernel.java:302)
at clearcl.ClearCLKernel.run(ClearCLKernel.java:285)
at clearcl.benchmark.Benchmark.executeBenchmarkOnDevice(Benchmark.java:234)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:115)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:54)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:49)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
Caused by: java.lang.NullPointerException
at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$setKernelArgument$20(ClearCLBackendJOCL.java:726)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:154)
... 26 more
java.lang.NullPointerException
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:60)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:49)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
clearcl.exceptions.ClearCLException: Pointer instance cannot have NULL peer ! (use null Pointer instead)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:146)
at clearcl.backend.javacl.ClearCLBackendJavaCL.getContextPeerPointer(ClearCLBackendJavaCL.java:268)
at clearcl.ClearCLDevice.createContext(ClearCLDevice.java:160)
at clearcl.benchmark.Benchmark.executeBenchmarkOnDevice(Benchmark.java:162)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:115)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:54)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:46)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
Caused by: java.lang.IllegalArgumentException: Pointer instance cannot have NULL peer ! (use null Pointer instead)
at org.bridj.Pointer.(Pointer.java:248)
at org.bridj.Pointer$OrderedPointer.(Pointer.java:260)
at org.bridj.TypedPointer.(TypedPointer.java:47)
at org.bridj.TypedPointer.(TypedPointer.java:51)
at com.nativelibs4java.opencl.library.IOpenCLLibrary$cl_context.(IOpenCLLibrary.java:799)
at com.nativelibs4java.opencl.library.OpenCLLibrary.clCreateContext(OpenCLLibrary.java:77)
at clearcl.backend.javacl.ClearCLBackendJavaCL.lambda$getContextPeerPointer$12(ClearCLBackendJavaCL.java:291)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:139)
... 22 more
java.lang.NullPointerException
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:60)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:46)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
clearcl.exceptions.ClearCLException: Pointer instance cannot have NULL peer ! (use null Pointer instead)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:146)
at clearcl.backend.javacl.ClearCLBackendJavaCL.getContextPeerPointer(ClearCLBackendJavaCL.java:268)
at clearcl.ClearCLDevice.createContext(ClearCLDevice.java:160)
at clearcl.benchmark.Benchmark.executeBenchmarkOnDevice(Benchmark.java:162)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:115)
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:54)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:49)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
Caused by: java.lang.IllegalArgumentException: Pointer instance cannot have NULL peer ! (use null Pointer instead)
at org.bridj.Pointer.(Pointer.java:248)
at org.bridj.Pointer$OrderedPointer.(Pointer.java:260)
at org.bridj.TypedPointer.(TypedPointer.java:47)
at org.bridj.TypedPointer.(TypedPointer.java:51)
at com.nativelibs4java.opencl.library.IOpenCLLibrary$cl_context.(IOpenCLLibrary.java:799)
at com.nativelibs4java.opencl.library.OpenCLLibrary.clCreateContext(OpenCLLibrary.java:77)
at clearcl.backend.javacl.ClearCLBackendJavaCL.lambda$getContextPeerPointer$12(ClearCLBackendJavaCL.java:291)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:139)
... 22 more
java.lang.NullPointerException
at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:60)
at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:49)
at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:69)
at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:99)
at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:48)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:130)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
--> Using backend: ClearCLBackendJOCL

2 available OpenCL devices:

Device name: Intel(R) UHD Graphics 620, type: GPU, OpenCL version: 2.00000
max global memory: 6804168704
max local memory: 65536
clock freq: 1150Mhz
nb compute units: 24
extensions: cl_khr_3d_image_writes cl_khr_byte_addressable_store cl_khr_fp16 cl_khr_depth_images cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_icd cl_khr_image2d_from_buffer cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_intel_subgroups cl_intel_required_subgroup_size cl_intel_subgroups_short cl_khr_spir cl_intel_accelerator cl_intel_media_block_io cl_intel_driver_diagnostics cl_intel_device_side_avc_motion_estimation cl_khr_priority_hints cl_khr_throttle_hints cl_khr_create_command_queue cl_khr_fp64 cl_khr_subgroups cl_khr_il_program cl_khr_mipmap_image cl_khr_mipmap_image_writes cl_intel_planar_yuv cl_intel_packed_yuv cl_intel_motion_estimation cl_intel_advanced_motion_estimation cl_khr_gl_sharing cl_khr_gl_depth_images cl_khr_gl_event cl_khr_gl_msaa_sharing cl_intel_dx9_media_sharing cl_khr_dx9_media_sharing cl_khr_d3d10_sharing cl_khr_d3d11_sharing cl_intel_d3d11_nv12_media_sharing cl_intel_simultaneous_sharing

Device name: Intel(R) Core(TM) i7-8650U CPU @ 1.90GHz, type: CPU, OpenCL version: 2.00000
max global memory: 17010429952
max local memory: 32768
clock freq: 1900Mhz
nb compute units: 8
extensions: cl_khr_icd cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_byte_addressable_store cl_khr_depth_images cl_khr_3d_image_writes cl_intel_exec_by_local_thread cl_khr_spir cl_khr_fp64 cl_khr_image2d_from_buffer cl_intel_vec_len_hint cl_khr_dx9_media_sharing cl_intel_dx9_media_sharing cl_khr_d3d11_sharing cl_khr_gl_sharing

Selected device:
Device name: Intel(R) UHD Graphics 620, type: GPU, OpenCL version: 2.00000
max global memory: 6804168704
max local memory: 65536
clock freq: 1150Mhz
nb compute units: 24
extensions: cl_khr_3d_image_writes cl_khr_byte_addressable_store cl_khr_fp16 cl_khr_depth_images cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_icd cl_khr_image2d_from_buffer cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_intel_subgroups cl_intel_required_subgroup_size cl_intel_subgroups_short cl_khr_spir cl_intel_accelerator cl_intel_media_block_io cl_intel_driver_diagnostics cl_intel_device_side_avc_motion_estimation cl_khr_priority_hints cl_khr_throttle_hints cl_khr_create_command_queue cl_khr_fp64 cl_khr_subgroups cl_khr_il_program cl_khr_mipmap_image cl_khr_mipmap_image_writes cl_intel_planar_yuv cl_intel_packed_yuv cl_intel_motion_estimation cl_intel_advanced_motion_estimation cl_khr_gl_sharing cl_khr_gl_depth_images cl_khr_gl_event cl_khr_gl_msaa_sharing cl_intel_dx9_media_sharing cl_khr_dx9_media_sharing cl_khr_d3d10_sharing cl_khr_d3d11_sharing cl_intel_d3d11_nv12_media_sharing cl_intel_simultaneous_sharing

Device name: ClearCLDevice [mClearCLPlatform=ClearCLPlatform [name=Intel(R) OpenCL], name=Intel(R) UHD Graphics 620]
javax.mail.AuthenticationFailedException: 534-5.7.14 <https://accounts.google.com/signin/continue?sarp=1&scc=1&plt=AKgnsbvc
534-5.7.14 C7yuTIXKexjoAyKPweFmApW-yKXLwdYSt-RI-BjK2kpL9ltE0T13qcs7VkrkpSRHeGpjNr
534-5.7.14 HgC8Oeb6hcaZIKp1SSuGKBF2HAQ04ZKHxMCPuuPAdcbcEE8W1agoKSsxtB7NLdoZgLfNTM
534-5.7.14 5MhoSTqvD14NbEUx7bBph34RZfBDKZRsznSbs48f2k1-djlPnh4dxWChtbx0RuQLiEaxZ8
534-5.7.14 8LdY3uba3uhbD3ZHUpxuYRO8PNIgnIF1yaTcj7oLCK5h4uLSVD> Please log in via
534-5.7.14 your web browser and then try again.
534-5.7.14 Learn more at
534 5.7.14 https://support.google.com/mail/answer/78754 b18sm72218439wrw.83 - gsmtp

at com.sun.mail.smtp.SMTPTransport$Authenticator.authenticate(SMTPTransport.java:826)
at com.sun.mail.smtp.SMTPTransport.authenticate(SMTPTransport.java:761)
at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:685)
at javax.mail.Service.connect(Service.java:317)
at javax.mail.Service.connect(Service.java:176)
at javax.mail.Service.connect(Service.java:125)
at javax.mail.Transport.send0(Transport.java:253)
at javax.mail.Transport.send(Transport.java:124)
at badtrack.email.GmailClient.sendMessage(GmailClient.java:83)
at badtrack.email.GmailBadTrackNotifier.notify(GmailBadTrackNotifier.java:65)
at badtrack.BadTrack$1.uncaughtException(BadTrack.java:198)
at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1057)
at java.lang.ThreadGroup.uncaughtException(ThreadGroup.java:1052)
at java.lang.Thread.dispatchUncaughtException(Thread.java:1959)

com.jogamp.opengl.util.AnimatorBase$UncaughtAnimatorException: com.jogamp.opengl.GLException: Caught ClearCLException: null on thread SciJava-2ca15c06-Thread-1-FPSAWTAnimator#00-Timer0
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:92)
at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
at java.util.TimerThread.mainLoop(Timer.java:555)
at java.util.TimerThread.run(Timer.java:505)
Caused by: com.jogamp.opengl.GLException: Caught ClearCLException: null on thread SciJava-2ca15c06-Thread-1-FPSAWTAnimator#00-Timer0
at com.jogamp.opengl.GLException.newGLException(GLException.java:76)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1327)
at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
... 4 more
Caused by: clearcl.exceptions.ClearCLException
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:161)
at clearcl.backend.jocl.ClearCLBackendJOCL.enqueueWriteToImage(ClearCLBackendJOCL.java:1003)
at clearcl.ClearCLImage.readFrom(ClearCLImage.java:375)
at clearcl.ClearCLImage.readFrom(ClearCLImage.java:396)
at clearvolume.renderer.opencl.OpenCLDevice.writeImage(OpenCLDevice.java:365)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.fillWithByteBuffer(OpenCLVolumeRenderer.java:406)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.prepareVolumeDataArray(OpenCLVolumeRenderer.java:230)
at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:153)
at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:818)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
... 7 more
Caused by: java.lang.NullPointerException
at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$enqueueWriteToImage$31(ClearCLBackendJOCL.java:1005)
at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:154)
... 19 more

not starting ununtu 20

(base) amsalem@amsalem-Kubuntu-home:~$ uname -a
Linux amsalem-Kubuntu-home 5.8.0-43-generic #49-Ubuntu SMP Fri Feb 5 03:01:28 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
(base) amsalem@amsalem-Kubuntu-home:~$ clinfo 
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [2]
param: 4, val: 0
Number of platforms                               2
  Platform Name                                   Intel Gen OCL Driver
  Platform Vendor                                 Intel
  Platform Version                                OpenCL 2.0 beignet 1.3
  Platform Profile                                FULL_PROFILE
  Platform Extensions                             cl_khr_global_int32_base_atomics cl_khr_global_int32_extended_atomics cl_khr_local_int32_base_atomics cl_khr_local_int32_extended_atomics cl_khr_byte_addressable_store cl_khr_3d_image_writes cl_khr_image2d_from_buffer cl_khr_depth_images cl_khr_spir cl_khr_icd cl_intel_accelerator cl_intel_subgroups cl_intel_subgroups_short
  Platform Extensions function suffix             Intel
DRM_IOCTL_I915_GEM_APERTURE failed: Invalid argument
Assuming 131072kB available aperture size.
May lead to reduced performance or incorrect rendering.
get chip id failed: -1 [2]
param: 4, val: 0
beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware
(If you have multiple ICDs installed and OpenCL works, you can ignore this message)

  Platform Name                                   AMD Accelerated Parallel Processing
  Platform Vendor                                 Advanced Micro Devices, Inc.
  Platform Version                                OpenCL 2.1 AMD-APP (3052.0)
  Platform Profile                                FULL_PROFILE
  Platform Extensions                             cl_khr_icd cl_amd_event_callback cl_amd_offline_devices 
  Platform Host timer resolution                  1ns
  Platform Extensions function suffix             AMD

  Platform Name                                   Intel Gen OCL Driver
Number of devices                                 0

  Platform Name                                   AMD Accelerated Parallel Processing
Number of devices                                 0

error in console

null
ClearGLWindow: GLProfile[GL4/GL4.hw]
1.0
1.0
1.0
LinuxFeb 17, 2021 5:39:10 PM org.bridj.BridJ log
INFO: Library not found : atiocl64
Feb 17, 2021 5:39:10 PM org.bridj.BridJ log
INFO: Library not found : amdocl64
Feb 17, 2021 5:39:10 PM org.bridj.BridJ log
INFO: Library not found : atiocl32
Feb 17, 2021 5:39:10 PM org.bridj.BridJ log
INFO: Library not found : atiocl
Feb 17, 2021 5:39:10 PM org.bridj.BridJ log
INFO: Library not found : amdocl32
Feb 17, 2021 5:39:10 PM org.bridj.BridJ log
INFO: Library not found : amdocl
clearcl.exceptions.OpenCLException: OpenCL error: -1 -> CL_DEVICE_NOT_FOUND
	at clearcl.backend.BackendUtils.checkOpenCLError(BackendUtils.java:346)
	at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$getNumberOfDevicesForPlatform$4(ClearCLBackendJOCL.java:135)
	at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:156)
	at clearcl.backend.jocl.ClearCLBackendJOCL.getNumberOfDevicesForPlatform(ClearCLBackendJOCL.java:133)
	at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$getNumberOfDevicesForPlatform$3(ClearCLBackendJOCL.java:125)
	at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:156)
	at clearcl.backend.jocl.ClearCLBackendJOCL.getNumberOfDevicesForPlatform(ClearCLBackendJOCL.java:124)
	at clearcl.ClearCLPlatform.getNumberOfDevices(ClearCLPlatform.java:59)
	at clearcl.ClearCL.getAllDevices(ClearCL.java:236)
	at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:60)
	at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:63)
	at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:83)
	at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:105)
	at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:50)
	at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:132)
	at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:824)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
	at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
	at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
	at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
	at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
	at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
	at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
	at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
	at java.util.TimerThread.mainLoop(Timer.java:555)
	at java.util.TimerThread.run(Timer.java:505)
clearcl.exceptions.OpenCLException: OpenCL error: -1 -> CL_DEVICE_NOT_FOUND
	at clearcl.backend.BackendUtils.checkOpenCLError(BackendUtils.java:346)
	at clearcl.backend.javacl.ClearCLBackendJavaCL.lambda$getNumberOfDevicesForPlatform$4(ClearCLBackendJavaCL.java:138)
	at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:156)
	at clearcl.backend.javacl.ClearCLBackendJavaCL.getNumberOfDevicesForPlatform(ClearCLBackendJavaCL.java:136)
	at clearcl.backend.javacl.ClearCLBackendJavaCL.lambda$getNumberOfDevicesForPlatform$3(ClearCLBackendJavaCL.java:128)
	at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:156)
	at clearcl.backend.javacl.ClearCLBackendJavaCL.getNumberOfDevicesForPlatform(ClearCLBackendJavaCL.java:127)
	at clearcl.ClearCLPlatform.getNumberOfDevices(ClearCLPlatform.java:59)
	at clearcl.ClearCL.getAllDevices(ClearCL.java:236)
	at clearcl.benchmark.Benchmark.getFastestDevice(Benchmark.java:60)
	at clearcl.backend.ClearCLBackends.isFunctionalBackend(ClearCLBackends.java:63)
	at clearcl.backend.ClearCLBackends.getFunctionalBackend(ClearCLBackends.java:83)
	at clearcl.backend.ClearCLBackends.getBestBackend(ClearCLBackends.java:105)
	at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:50)
	at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:132)
	at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:824)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
	at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
	at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
	at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
	at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
	at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
	at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
	at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
	at java.util.TimerThread.mainLoop(Timer.java:555)
	at java.util.TimerThread.run(Timer.java:505)
 --> Using backend: ClearCLBackendJOCL
clearcl.backend.jocl.ClearCLBackendJOCL@7796998
clearcl.exceptions.OpenCLException: OpenCL error: -1 -> CL_DEVICE_NOT_FOUND
	at clearcl.backend.BackendUtils.checkOpenCLError(BackendUtils.java:346)
	at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$getNumberOfDevicesForPlatform$4(ClearCLBackendJOCL.java:135)
	at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:156)
	at clearcl.backend.jocl.ClearCLBackendJOCL.getNumberOfDevicesForPlatform(ClearCLBackendJOCL.java:133)
	at clearcl.backend.jocl.ClearCLBackendJOCL.lambda$getNumberOfDevicesForPlatform$3(ClearCLBackendJOCL.java:125)
	at clearcl.backend.BackendUtils.checkExceptions(BackendUtils.java:156)
	at clearcl.backend.jocl.ClearCLBackendJOCL.getNumberOfDevicesForPlatform(ClearCLBackendJOCL.java:124)
	at clearcl.ClearCLPlatform.getNumberOfDevices(ClearCLPlatform.java:59)
	at clearcl.ClearCL.getAllDevices(ClearCL.java:236)
	at clearvolume.renderer.opencl.OpenCLDevice.initCL(OpenCLDevice.java:57)
	at clearvolume.renderer.opencl.OpenCLVolumeRenderer.initVolumeRenderer(OpenCLVolumeRenderer.java:132)
	at clearvolume.renderer.cleargl.ClearGLVolumeRenderer.init(ClearGLVolumeRenderer.java:824)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:644)
	at jogamp.opengl.GLDrawableHelper.init(GLDrawableHelper.java:667)
	at jogamp.opengl.GLAutoDrawableBase$1.run(GLAutoDrawableBase.java:431)
	at jogamp.opengl.GLDrawableHelper.invokeGLImpl(GLDrawableHelper.java:1291)
	at jogamp.opengl.GLDrawableHelper.invokeGL(GLDrawableHelper.java:1147)
	at com.jogamp.newt.opengl.GLWindow.display(GLWindow.java:759)
	at com.jogamp.opengl.util.AWTAnimatorImpl.display(AWTAnimatorImpl.java:81)
	at com.jogamp.opengl.util.AnimatorBase.display(AnimatorBase.java:452)
	at com.jogamp.opengl.util.FPSAnimator$MainTask.run(FPSAnimator.java:178)
	at java.util.TimerThread.mainLoop(Timer.java:555)
	at java.util.TimerThread.run(Timer.java:505)

Thanks

Automatic deployment to update site

@kephale has a very nice script for SciView, that automatically deploys the latest build to a Fiji update site, if it succeeded: https://github.com/scenerygraphics/SciView/blob/master/sciview_deploy.sh

We should add something like that!

java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT

Hey guys,

I just wanted to check if the current build works inside Fiji, before we update the update site. However, when trying to open T1-head.tif in ClearVolume, this error message comes up. I just downloaded the recent master branch (2019-03-25), and used mvn install to install it to my Fiji.

Do I have to install some additional Jogamp dependency manually?

Cheers,
Robert

(Fiji Is Just) ImageJ 2.0.0-rc-71/1.52i; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 61MB of 12101MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)
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:748)
Caused by: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
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:299)
... 5 more
Caused by: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:90)
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)
... 1 more
Caused by: java.lang.ClassNotFoundException: com.jogamp.newt.awt.NewtCanvasAWT
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 10 more

Add build instructions

Unfortunately, there are no build instructions so far and just doing a normal maven build does not work.

Apparent bug in Fiji+ClearVolume

From Aryeh Weiss via the ImageJ mailing list:

After running ClearVolume, subsequent menu panels (eg, reslice, adjust contrast/brightness), open with transparent backgrounds. Here is a screenshot showing what I mean:

This happens on a Windows 7-64bit system, running Java 1.8.0_102 (latest java), It also happens with the java 8 that comes with Fiji (1.8.0_66). It does not happen on my macbook (OSX10.11) system.

Aside, I also found both WIndows and OSX that I could not export ClearVolume rendered volumes to Fiji, I could not get a console or control panel with "C", and could not get a display of the values selected by the sliders (like gamma, min, max, etc). Has anyone succeeded in getting these functionalities to work?

ClearVolume + MATLAB

From Andres Barragan via the ImageJ mailing list:

ClearVolume appears now in the plugins but I am getting an exception. Any ideas? For some reason I do not get this exception when simply running the executable of ImageJ.

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52e; Java 1.8.0_144 [64-bit]; Windows 10 10.0; 320MB of 1910MB (16%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303)
	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:748)
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:299)
	... 5 more
Caused by: java.lang.NullPointerException
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:284)
	at de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:511)
	at de.mpicbg.jug.clearvolume.gui.ClearVolumeManager.run(ClearVolumeManager.java:182)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.launchClearVolumeManager(GenericClearVolumeGui.java:306)
	at de.mpicbg.jug.clearvolume.gui.GenericClearVolumeGui.<init>(GenericClearVolumeGui.java:163)
	at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:90)
	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)
	... 1 more

I investigated a little, and based on the relevant code, I guess that ClearVolumeRendererFactory.newBestRenderer and/or ClearVolumeRendererFactory.newOpenCLRenderer must be returning null. But more investigation required to discern why that would be the case from a MATLAB environment.

Bug in ClearVolume Fiji plugin on MacOS - missing dependencies?

Hi guys,

I just downloaded a fresh copy of Fiji from the website and activated the ClearVolume update site. I opened the sample image "flybrain.tif" and clicked the menu Plugins > ClearVolume > Open in ClearVolume. Clear Volume it self does not open (just the teaser). After some seconds, I get this message in the Console window:


Nov 30, 2016 5:12:54 PM org.bridj.BridJ log
INFO: Library not found : atiocl64
Nov 30, 2016 5:12:54 PM org.bridj.BridJ log
INFO: Library not found : amdocl64
Nov 30, 2016 5:12:54 PM org.bridj.BridJ log
INFO: Library not found : atiocl32
Nov 30, 2016 5:12:54 PM org.bridj.BridJ log
INFO: Library not found : atiocl
Nov 30, 2016 5:12:54 PM org.bridj.BridJ log
INFO: Library not found : amdocl32
Nov 30, 2016 5:12:54 PM org.bridj.BridJ log
INFO: Library not found : amdocl
java.lang.UnsatisfiedLinkError: com.nativelibs4java.opencl.JavaCL$OpenCLProbeLibrary.clGetPlatformIDs(ILorg/bridj/Pointer;Lorg/bridj/Pointer;)I
	at com.nativelibs4java.opencl.JavaCL$OpenCLProbeLibrary.clGetPlatformIDs(Native Method)
	at com.nativelibs4java.opencl.JavaCL$OpenCLProbeLibrary.getPlatformIDs(JavaCL.java:150)
	at com.nativelibs4java.opencl.JavaCL$OpenCLProbeLibrary.getPlatformIDs(JavaCL.java:155)
	at com.nativelibs4java.opencl.JavaCL$OpenCLProbeLibrary.hasOpenCL1_0(JavaCL.java:166)
	at com.nativelibs4java.opencl.JavaCL.<clinit>(JavaCL.java:225)
	at clearvolume.renderer.opencl.OpenCLAvailability.isOpenCLAvailable(OpenCLAvailability.java:9)
	at clearvolume.renderer.factory.ClearVolumeRendererFactory.newOpenCLRenderer(ClearVolumeRendererFactory.java:314)
	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)
[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 this in the log window:



(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Mac OS X 10.12; 110MB of 7802MB (1%)
 
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NullPointerException
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:288)
	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:284)
	... 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

Does anyone know how to fix this?

Thanks!
Robert