ClearVolume + MATLAB

[ctrueden]

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.

[royerloic]

You should be using the main branch (master) instead of a deprecated branch (your link points to very very old code...)

[ctrueden]

(your link points to very very old code...)

Dude, it is the latest tag. And the last commit to touch that source file is the same on master still. I never post links to master because it will change out from under you over time, invalidating the link.

[royerloic]

Oh I see, I saw some cuda flags and assumed it was very old code. I would test in FiJi first and see how it goes, my guess is that there is a GPU, GPU driver problem, or the native libs of JOCL are missing...

[ctrueden]

I am guessing this is a MATLAB-specific issue; from the original thread, it sounds like the plugin works when launched from Fiji normally.

I was thinking it might be some subtle thing with MATLAB's JRE, but upon reflection, perhaps it is as simple as the JARs from the jars/<platform> folder not being added to MATLAB's classpath.

I do not have time to test it, but Andreas, if you are reading this: you could try:

javaaddpath 'C:\Users\andreas\Fiji.app\jars\win64'

Where C:\Uesrs\andreas\Fiji.app is the location of your Fiji installation.

And see if that makes a difference. See the javaaddpath documentation for details.

[mynameisandres]

ctrueden, I attempted your solution.

I did

javaaddpath 'C:\Users\Swag\Documents\4D-SoftwareChet\ae4d-master\Fiji.app\jars\win64'

My MatLab Execution is attached and so is the ImageJ execution error. MATLAB.txt ImageJ.txt

[mynameisandres]

I attempted a clean installation of Fiji, the newest version available. Opened my MatLab version that is running: Java 1.8.0_144-b01 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode

Added to my path

'C:\Users\Swag\Documents\4D-SoftwareChet\ae4d-master\Fiji.app\scripts'

Than by suggestion from ctrueden did

'javaaddpath 'C:\Users\Swag\Documents\4D-SoftwareChet\ae4d-master\Fiji.app\jars\win64'

Getting the same error as mentioned before. It is possible that clearVolume does not work with Imagej-MatLab