Can't open ClearMap plugin from ImageJ

[djarecka]

Hi,

I wanted to try using ClearMap and installed Java-8, ImageJ and installed ClearVolume plugin (ImageJ 2.0.0-rc-43/1.51o; Java 1.8.0_131 [64-bit]; Mac OS X 10.12.1). When I try "Open in ClearVolume" I got an error in "Console":

[ERROR] Module threw error
java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
    at de.mpicbg.jug.plugins.ClearVolumeClientPlugin.run(ClearVolumeClientPlugin.java:37)
    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:748)
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:335)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 10 more

I have also window with "Exception":

ImageJ 2.0.0-rc-43/1.51o; Java 1.8.0_131 [64-bit]; Mac OS X 10.12.1; 81MB of 9209MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
    at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:274)
    at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:161)
    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:270)
    ... 5 more
Caused by: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT
    at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:81)
    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)
    ... 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:335)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
    ... 10 more

Any suggestions what should I install more?

[imagejan]

@djarecka

and installed ClearVolume plugin...

How did you install ClearVolume? Did you follow the instructions on the wiki? If not, you're probably missing a lot of dependencies...

[djarecka]

@imagejan : thanks for your answer! I guess I didn't get the point 4 from the wiki, since I have a new ImageJ and Java-8 I thought it's enough to choose ClearView. I've just installed Java-8 through ImageJ updates and ClearView started working.

Unfortunately I can't open a tif file that contains 2 channels, does it mean that you're not supporting it? or I should install something more (I use Bio-Formats plugin to open the file in ImageJ)

[skalarproduktraum]

Hey @djarecka,

would you be able to share that TIFF so we can have a look? If not, could you let us know what's the size, resolution, and data type (float, int, etc.)?

Thanks!

[djarecka]

@skalarproduktraum : the original file was very big, but created a smaller example that seems to have exactly the same problem: https://www.dropbox.com/s/ast94v7dcdrd8fg/cells_check_imagej.tif?dl=0

Please let me know if you have problem with downloading the file.

[skalarproduktraum]

@djarecka: Thanks for the image! It looks like BioFormats is picking up it's dimensions wrongly, and imports Z slices as timepoints. You can fix this on-the-fly by going to Image > Hyperstacks > Reorder Hyperstack... and setting Slices -> Frames and Frames -> Slices. It then opens fine in ClearVolume:

Please let me know whether this worked for you.

cheers!

ulrik

[djarecka]

@skalarproduktraum : thanks! It works, i.e. I moved to the CL_OUT_OF_RESOURCES error now ;-)

[skalarproduktraum]

Okay, I'll close this issue for now then.