[ImageJ-bugs] [Bug 857] New: Stack Dump window appears on play image stack

bugzilla at fiji.sc bugzilla at fiji.sc
Thu Jul 17 00:36:19 CDT 2014 

http://fiji.sc/bugzilla/show_bug.cgi?id=857

            Bug ID: 857
           Summary: Stack Dump window appears on play image stack
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: jgburchfield.au at gmail.com
                CC: jgburchfield.au at gmail.com

Stack Dump window appears on play image stack
-After using Image>Stacks>Tools>Animation Options
Every time "\" is pressed to play the stack a Stack Dump window appears (see
below for contents)

"AWT-EventQueue-0" prio=6 id=16 group=main
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at java.awt.EventQueue.getNextEvent(EventQueue.java:479)
    at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:236)
    at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

"AWT-Shutdown" prio=5 id=12 group=main
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:265)
    at java.lang.Thread.run(Thread.java:619)

"AWT-Windows" daemon prio=6 id=13 group=main
   java.lang.Thread.State: RUNNABLE
    at sun.awt.windows.WToolkit.eventLoop(Native Method)
    at sun.awt.windows.WToolkit.run(WToolkit.java:295)
    at java.lang.Thread.run(Thread.java:619)

"Attach Listener" daemon prio=5 id=6 group=system
   java.lang.Thread.State: RUNNABLE

"DestroyJavaVM" prio=5 id=21 group=main
   java.lang.Thread.State: RUNNABLE

"Finalizer" daemon prio=8 id=3 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
    at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:159)

"Java2D Disposer" daemon prio=10 id=11 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:118)
    at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:134)
    at sun.java2d.Disposer.run(Disposer.java:125)
    at java.lang.Thread.run(Thread.java:619)

"Reference Handler" daemon prio=10 id=2 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)

"SciJava-473e8cc3-Thread-47" prio=6 id=127 group=main
   java.lang.Thread.State: RUNNABLE
    at java.lang.Thread.dumpThreads(Native Method)
    at java.lang.Thread.getAllStackTraces(Thread.java:1487)
    at org.scijava.plugins.commands.debug.DumpStack.run(DumpStack.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$2.call(DefaultThreadService.java:164)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:619)

"SciJava-473e8cc3-Thread-48" prio=6 id=129 group=main
   java.lang.Thread.State: TIMED_WAITING
    at sun.misc.Unsafe.park(Native Method)
    at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:198)
    at
java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:424)
    at
java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:323)
    at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:874)
    at
java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:945)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907)
    at java.lang.Thread.run(Thread.java:619)

"Signal Dispatcher" daemon prio=9 id=5 group=system
   java.lang.Thread.State: RUNNABLE

"Start Animation [\]" prio=1 id=128 group=main
   java.lang.Thread.State: TIMED_WAITING
    at java.lang.Thread.sleep(Native Method)
    at ij.IJ.wait(IJ.java:678)
    at ij.plugin.Animator.startAnimation(Animator.java:180)
    at ij.plugin.Animator.run(Animator.java:48)
    at ij.IJ.runPlugIn(IJ.java:172)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Thread.java:619)

"TimerQueue" daemon prio=5 id=24 group=system
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at javax.swing.TimerQueue.run(TimerQueue.java:232)
    at java.lang.Thread.run(Thread.java:619)

"zSelector" prio=6 id=48 group=main
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at ij.gui.StackWindow.run(StackWindow.java:209)
    at java.lang.Thread.run(Thread.java:619)

"zSelector" prio=6 id=123 group=main
   java.lang.Thread.State: WAITING
    at java.lang.Object.wait(Native Method)
    at java.lang.Object.wait(Object.java:485)
    at ij.gui.StackWindow.run(StackWindow.java:209)
    at java.lang.Thread.run(Thread.java:619)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_20
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_20-b02
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 16.3-b01
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~4\Fiji.app/java/win64/jdk1.6.0_20//jre
  imagej.dir => C:\PROGRA~4\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140712080647)
Fiji: http://pacific.mpi-cbg.de/update/ (last check:20140715100940)

Files not up-to-date:
  ff27659f (LOCAL_ONLY) 20110719184843 jars/Fiji.jar
  efd0b4a7 (OBSOLETE_UNINSTALLED) 20100614001000 jars/clibwrapper_jiio.jar
  d760adf7 (OBSOLETE_UNINSTALLED) 20101214182806 jars/commons-math.jar
  85af6645 (OBSOLETE_UNINSTALLED) 20110119134549 jars/imglib-algorithms.jar
  2727a642 (OBSOLETE_UNINSTALLED) 20110119134548 jars/imglib-ij.jar
  3913aead (OBSOLETE_UNINSTALLED) 20110119134549 jars/imglib-io.jar
  4053be28 (OBSOLETE_UNINSTALLED) 20110119134551 jars/imglib-scripting.jar
  785fd9ee (OBSOLETE_UNINSTALLED) 20110119134537 jars/imglib.jar
  b9040757 (OBSOLETE_UNINSTALLED) 20110119134352 jars/jruby.jar
  8e9a4bd8 (OBSOLETE_UNINSTALLED) 20110119134353 jars/junit-4.5.jar
  62509daf (OBSOLETE_UNINSTALLED) 20100614001000 jars/weka.jar
  290be785 (LOCAL_ONLY) 20101217124405 macros/Unwarp_redchannel image.txt
  ec9f9e6e 20100614001000 macros/grey-squares.ijm
  bc1d6c6e 20100614001000 macros/spirals.txt
  c4583991 (LOCAL_ONLY) 20140408102236 macros/testscript_temp_deleteME.ijm
  f7efa1b3 (LOCAL_ONLY) 20110314142721 misc/headless.jar
  5b9f64df (LOCAL_ONLY) 20140214104952 plugins/Convert_LIF_to_TIFF.class
  1a992dbc (OBSOLETE_UNINSTALLED) 20100614001000 plugins/Daltonize_.jar
  3e7c14cf (LOCAL_ONLY) 20140605204040
plugins/Filters/Anisotropic_Diffusion_2D.class
  a8c14ae3 (LOCAL_ONLY) 20140409165641 plugins/HDF5_.jar
  9cdfe434 20101214182818 plugins/Jython_Scripts.jar
  306c9af0 20101214182807 plugins/Macro_Examples.jar
  3589dfdf (LOCAL_ONLY) 20100408181022 plugins/MultiStackReg1_45.jar
  c32c3597 (LOCAL_ONLY) 20080521101406 plugins/MultiStackReg_.jar
  970c7851 (LOCAL_ONLY) 20130815113254
plugins/ROI/BG_Subtraction_from_ROI.class
  6f058434 (LOCAL_ONLY) 20140212100504 plugins/Radial
Profiling/Radial_Profile_Angle_Ext.jar
  0ab9e3b0 (OBSOLETE_UNINSTALLED) 20100614001000 plugins/Record_Screen.jar
  424444d4 (LOCAL_ONLY) 20140428122029 plugins/Region_Growing_Segmentation.jar
  b8e50a7b (OBSOLETE_UNINSTALLED) 20110215125328 plugins/Script_Editor.jar
  4c3e4aee (NOT_INSTALLED) 20110119134407 plugins/Stack_Manipulation.jar
  2f7c1fb1 (LOCAL_ONLY) 20140310193004 plugins/Stack_Sorter.class
  e0122cde (LOCAL_ONLY) 20040909131042 plugins/Stacks - Reducing/Binner_.class
  ab872ecd (LOCAL_ONLY) 20040601145326 plugins/Stacks -
Reducing/Delete_slices_after_here.class
  5e51feb8 (LOCAL_ONLY) 20040601145318 plugins/Stacks -
Reducing/Delete_slices_before_here.class
  794c108d (LOCAL_ONLY) 20010207115620 plugins/Stacks -
Reducing/Slice_Remover.class
  ff504eff (LOCAL_ONLY) 20060627090428 plugins/Stacks -
Reducing/Stack_Splitter.class
  25874f3e (LOCAL_ONLY) 20030627131048 plugins/Stacks -
Reducing/Substack_Maker.class
  b7a74d8a (LOCAL_ONLY) 20080526103622 plugins/Stacks -
Reducing/Substack_Select.jar
  08564324 (LOCAL_ONLY) 20090921122950 plugins/Stacks -
T-functions/Grouped_Stack_Projector.class
  3ae569df (LOCAL_ONLY) 20050202153014 plugins/Stacks -
T-functions/Intensity_v_Time_Monitor.class
  03bba501 (LOCAL_ONLY) 20050202153404 plugins/Stacks -
T-functions/Running_Stack_Projector.class
  1c657c8d (LOCAL_ONLY) 20140305190818 plugins/TIRF_Analysis.class
  5796a251 (LOCAL_ONLY) 20140303144901 plugins/X_Shifter.class
  8c0467d1 (LOCAL_ONLY) 20140120115836 plugins/adaptiveThreshold_win64.jar
  460fd731 (LOCAL_ONLY) 20140303144910 plugins/correctXshift_.jar
  30e408c8 (OBSOLETE_UNINSTALLED) 20110215125326 plugins/loci_tools.jar
  d3260180 (LOCAL_ONLY) 20100614001000 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20100614001000 scripts/Record_Window.py

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