'Open KLB' triggers exception

erjel commented 5 years ago

Hi,

I currently try to use the TGMM algorithms to my own data set (time series of single fluorescence channel volumes (X, Y, Z) ) following the "Software_Guide_Compact".

In the instructions, there is a part when the TGMM results are exported to xml/ hdf5 by the Fiji bigdataviewer plugin:

Import TGMM objects using MaMuT importer in Fiji. As image data location use
the .xml file generated from the .klb image files, as described in the first section
“Setting up the software environment”

According to the chapter Setting up the software environment I have to use the plugin function Open KLB:

[...] to generate a new .xml file from a .klb image series in Fiji, follow
these steps:
 - Go to “Plugins”, “BigDataViewer”, and select “Open KLB”.

As soon as I press the button a Exception Window appears:

Exception Window Message:

(Fiji Is Just) ImageJ 2.0.0-rc-69/1.52p; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 364MB of 24450MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
    at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:309)
    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: net/preibisch/mvrecon/fiji/spimdata/SpimData2
    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:305)
    ... 5 more
Caused by: java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
    at org.janelia.simview.klb.bdv.ui.KlbIjPlugin.run(KlbIjPlugin.java:25)
    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: net.preibisch.mvrecon.fiji.spimdata.SpimData2
    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

Console Window Message:

[ERROR] Module threw error
java.lang.NoClassDefFoundError: net/preibisch/mvrecon/fiji/spimdata/SpimData2
    at org.janelia.simview.klb.bdv.ui.KlbIjPlugin.run(KlbIjPlugin.java:25)
    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)
Caused by: java.lang.ClassNotFoundException: net.preibisch.mvrecon.fiji.spimdata.SpimData2
    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

tpietzsch commented 4 years ago

@erjel Could you try to activate the BigStitcher update site in your Fiji? This should bring in the net/preibisch/mvrecon/fiji/spimdata/SpimData2 that is not found, and maybe that solves the problem already. (Fiji menu Help -> Update..., then "Manage Update Sites")

tpietzsch commented 4 years ago

Can I close this?

bigdataviewer / bigdataviewer_fiji

'Open KLB' triggers exception #13