[ImageJ-bugs] [Bug 1076] New: ClearVolume crashes

bugzilla at fiji.sc bugzilla at fiji.sc
Thu May 28 12:42:03 CDT 2015 

http://fiji.sc/bugzilla/show_bug.cgi?id=1076

            Bug ID: 1076
           Summary: ClearVolume crashes
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Linux
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: sapristi at gmail.com
                CC: sapristi at gmail.com

When opening the ClearVolume Network Client the whole JVM segfaults:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x00007f28a2d62d80, pid=27327, tid=139811869296384
#
# JRE version: Java(TM) SE Runtime Environment (7.0_67-b01) (build
1.7.0_67-b01)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.65-b04 mixed mode linux-amd64
compressed oops)
# Problematic frame:
# C  [ld-linux-x86-64.so.2+0x9d80]  _dl_rtld_di_serinfo+0x670
#
# Failed to write core dump. Core dumps have been disabled. To enable core
dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /home/albert/Programming/fiji-linux64-20091014/Fiji.app/hs_err_pid27327.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
#
Aborted


Additionally, when using the "Open in ClearVolume", it fails with an exception
if no images are open, and it throws an exception if an RGB stack is open,
leaving the splash screen looping forever. Eventually the whole of Fiji
freezes. The exception in the case of no images:

(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_67 [64-bit]; Linux
3.13.11-031311ckt16-generic; 59MB of 4096MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
    at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
    at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    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:188)
    at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
    ... 5 more
Caused by: java.lang.NullPointerException
    at
net.imagej.legacy.translate.ImagePlusDatasetConverter.populateInputCandidates(ImagePlusDatasetConverter.java:126)
    at
org.scijava.convert.DefaultConvertService.getCompatibleInputs(DefaultConvertService.java:111)
    at
org.scijava.widget.AbstractInputHarvester.getObjects(AbstractInputHarvester.java:153)
    at
org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:128)
    at
org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:94)
    at
org.scijava.widget.AbstractInputHarvester.harvest(AbstractInputHarvester.java:75)
    at
org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:76)
    at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:104)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:156)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
    at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    ... 1 more


And the exception in the case of an RGB image stack being open:

(Fiji Is Just) ImageJ 2.0.0-rc-30/1.49s; Java 1.7.0_67 [64-bit]; Linux
3.13.11-031311ckt16-generic; 75MB of 4096MB (1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException:
java.lang.NullPointerException
    at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
    at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:162)
    at ij.IJ.runPlugIn(IJ.java)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    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:188)
    at
net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
    ... 5 more
Caused by: java.lang.NullPointerException
    at
de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initClearVolumeUnsignedShortArrayImg(ImgLib2ClearVolume.java:264)
    at
de.mpicbg.jug.clearvolume.ImgLib2ClearVolume.initRealImgs(ImgLib2ClearVolume.java:418)
    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$2.call(DefaultThreadService.java:181)
    at java.util.concurrent.FutureTask.run(FutureTask.java:262)
    at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.13.11-031311ckt16-generic
  java.version => 1.7.0_67
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.7.0_67-b01
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 24.65-b04
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to:
/home/albert/Programming/fiji-linux64-20091014/Fiji.app/java/linux-amd64/jdk1.7.0_67//jre
  imagej.dir => /home/albert/Programming/fiji-linux64-20091014/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150522062918)
Fiji: http://fiji.sc/update/ (last check:20150528120151)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20150527195605)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606112449)
MOSAIC ToolSuite:
http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last
check:20150227140151)

Files not up-to-date:
  1581bc4d (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-macosx
  75db148f (MODIFIED) 20120131124042 Contents/MacOS/ImageJ-tiger
  1ad3be0d (LOCAL_ONLY) 20090930112722 jars/jpedalSTD.jar
  32a5cb57 (LOCAL_ONLY) 20090910082726 macros/StartupMacros.txt
  dc7fce6b (LOCAL_ONLY) 20111014094119 plugins/Motion_Deblur.jar
  32738eb1 (LOCAL_ONLY) 20120511160900
plugins/SAT-lib-Drosophila-3rd-instar.clj
  3335decb (LOCAL_ONLY) 20101016092738 plugins/T2-NIT.jar
  063de9b3 (LOCAL_ONLY) 20150526100515 plugins/dynamic_vision_sensor-like.py
  7c95e931 (LOCAL_ONLY) 20140420121925 plugins/test_haskell_splitAt.py
  7f241f66 (LOCAL_ONLY) 20100603001850 plugins/tests/Example_Cursors.class
  a47f6af3 (LOCAL_ONLY) 20130425143259 plugins/tests/crop-file.py
  d3260180 (LOCAL_ONLY) 20090910082729 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20090910082729 scripts/Record_Window.py

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