Running Fiji on Windows 10, Java 8 - many many window resizings freezes up screen

Whenever I open an image in FIJ, the image opens repeatedly, freezing my machine.
Here is the bug log (imagine the last 4 lines repeating infinitely and you have the idea). What can I do to stop the windows insanity and get to work?

actionPerformed: time=35945, java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=Open...,when=1469591106222,modifiers=] on menuitem0
runPlugIn: ij.plugin.Commands("open")
openImage: "jpg", C:\Users\DD\Pictures\Camera Roll\WIN_20160522_22_26_23_Pro.jpg
GUI.getMaxWindowBounds: java.awt.Rectangle[x=62,y=0,width=1218,height=720]
Undo.reset
GUI.getMaxWindowBounds: java.awt.Rectangle[x=62,y=0,width=1218,height=720]
windowActivated: WIN_20160522_22_26_23_Pro.jpg
setKeyUp: -1
focusGained: img[WIN_20160522_22_26_23_Pro.jpg (836x720x1x1x1)]
ImageCanvas.paint: img[WIN_20160522_22_26_23_Pro.jpg (836x720x1x1x1)]
windowStateChanged: 0 6
GUI.getMaxWindowBounds: java.awt.Rectangle[x=62,y=0,width=1218,height=720]
maximize: java.awt.Rectangle[x=96,y=0,width=883,height=720]
windowStateChanged: 6 0
windowStateChanged: 0 6

Welcome to the forum @dylevine,

have you downloaded Fiji recently or is it an older version? In any case, have you tried to update your installation?

From your provided information, it is not clear whether you can reproduce the issue with other images. You can try to open one of the sample images (e.g. File > Open Samples > Clown (14K)) and see if the issue remains. If not, there might be a problem with image.

Best,
Stefan

If there are problems with a specific image, it would be helpful to upload it, so that others can try to reproduce.

Regardless, this sounds like a bug in ImageJ (maybe ImageJ 1.x), which should be fixed, if we can successfully reproduce it.

I just downloaded Fiji, the current version. This happens every time I open an image, regardless of whether it is an ImageJ sample or one from my hard drive. They are all small files. This one is just a scan saved as a jpeg, 200dpi.

@dylevine Thanks for the additional information.

I tried reproducing this with the latest Fiji on a Windows 10 VM, and was unable to do so. It is probably something specific to your machine’s hardware—e.g., graphics card or screen resolution.

It would be very helpful if you could acquire a complete stack trace of the running program while the crazy window behavior is taking place. (I hope you are able to follow the directions to acquire the stack trace, but it might be difficult if the constantly-resizing image window repeatedly steals the focus.)

If you are able to take a stack trace and paste it here, perhaps @Wayne can concoct a fix even without being able to reproduce the issue locally.

The other thing you could try is to check whether older versions of ImageJ 1.x also have this problem. You can use the Help :arrow_forward: Update ImageJ… command to switch between versions of ImageJ 1.x. If older versions do not have the problem, but newer ones do, then knowing which version introduced the bug is very helpful for us in understanding the cause and hence crafting a fix.

Another thing you could try is to update to the very latest version of Java 8. If you download and install the latest Java JRE or JDK, and rename the Fiji.app\java to Fiji.app\java.disabled or some such, then ImageJ should detect the newer Java version and use that. Perhaps this issue is a bug in Java itself which has subsequently been fixed.

1 Like

I started by installing ImageJ and it did the same thing. Then I tried FIJI thinking that the old imagej wouldn’t work on my new computer and that FIJI was the new one that would be compatible. I started with FIJI installed in my pictures folder and saw that others thought the destktop was better, so now I’m running it from the destktop, with the same results. I did not try installing a new version of java yet. I tried the NVidia fix plugin but that didn’t help either–the plugin wouldn’t find the location of my .cfg file. Here is the stack dump:

"AWT-EventQueue-0" prio=6 id=25 group=main
   java.lang.Thread.State: RUNNABLE
	at java.awt.event.InvocationEvent.finishedDispatching(InvocationEvent.java:396)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:314)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

"AWT-Shutdown" prio=6 id=24 group=system
   java.lang.Thread.State: WAITING
	at java.lang.Object.wait(Native Method)
	at java.lang.Object.wait(Object.java:502)
	at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
	at java.lang.Thread.run(Thread.java:745)

"AWT-Windows" daemon prio=6 id=13 group=system
   java.lang.Thread.State: RUNNABLE
	at sun.awt.windows.WToolkit.eventLoop(Native Method)
	at sun.awt.windows.WToolkit.run(WToolkit.java:306)
	at java.lang.Thread.run(Thread.java:745)

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

"DestroyJavaVM" prio=5 id=27 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:143)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"GC Daemon" daemon prio=2 id=23 group=system
   java.lang.Thread.State: TIMED_WAITING
	at java.lang.Object.wait(Native Method)
	at sun.misc.GC$Daemon.run(GC.java:117)

"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:143)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at sun.java2d.Disposer.run(Disposer.java:148)
	at java.lang.Thread.run(Thread.java:745)

"RMI Reaper" prio=5 id=22 group=system
   java.lang.Thread.State: WAITING
	at java.lang.Object.wait(Native Method)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
	at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
	at sun.rmi.transport.ObjectTable$Reaper.run(ObjectTable.java:351)
	at java.lang.Thread.run(Thread.java:745)

"RMI TCP Accept-0" daemon prio=5 id=21 group=system
   java.lang.Thread.State: RUNNABLE
	at java.net.DualStackPlainSocketImpl.accept0(Native Method)
	at java.net.DualStackPlainSocketImpl.socketAccept(DualStackPlainSocketImpl.java:131)
	at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
	at java.net.PlainSocketImpl.accept(PlainSocketImpl.java:199)
	at java.net.ServerSocket.implAccept(ServerSocket.java:545)
	at java.net.ServerSocket.accept(ServerSocket.java:513)
	at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.executeAcceptLoop(TCPTransport.java:400)
	at sun.rmi.transport.tcp.TCPTransport$AcceptLoop.run(TCPTransport.java:372)
	at java.lang.Thread.run(Thread.java:745)

"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:502)
	at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)

"SciJava-365a6a43-Thread-0" prio=5 id=17 group=main
   java.lang.Thread.State: TIMED_WAITING
	at sun.misc.Unsafe.park(Native Method)
	at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
	at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
	at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
	at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
	at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

"SciJava-365a6a43-Thread-1" prio=5 id=18 group=main
   java.lang.Thread.State: RUNNABLE
	at java.lang.Thread.dumpThreads(Native Method)
	at java.lang.Thread.getAllStackTraces(Thread.java:1603)
	at org.scijava.plugins.commands.debug.DumpStack.run(DumpStack.java:81)
	at org.scijava.command.CommandModule.run(CommandModule.java:205)
	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:745)

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

@dylevine Thanks for capturing the stack trace. Unfortunately, there is nothing in there regarding window resizing behavior etc. In this case, it might be necessary to capture the stack trace the “hard way” (i.e., from the command line) rather than from the UI.

I could not run the batch file. I gave it a .bat extension and windows 11 blocked it. I tried running it from FIJI but it didn’t work. I don’t have a “break” or a “pause” button. I saw that it might be fn-ctrl-B or Ctrl-fn-f11 or fn-B or Fn-ctrl-b, but since I haven’t gotten to the part where I’ve got the console open in the first place, I thought I’d ask for help first with opening from the console. Thanks and sorry for the inconvenience.

Aha! debug.exe was called debug.exe.exe. I got rid of the extra extension and it worked. Here’s the stack trace before doing any picture opening:

[DEBUG] Found 21 OptionsPlugin plugins.
[DEBUG] Found 54 Converter plugins.
[DEBUG] Found 6 App plugins.
[DEBUG] Found 17 ThresholdMethod plugins.
[DEBUG] Found 16 ConsoleArgument plugins.
[DEBUG] Found 4 IOPlugin plugins.
[DEBUG] Found 5 CodeRunner plugins.
[DEBUG] Found 1 ScriptHeader plugins.
[DEBUG] Found 2 TextFormat plugins.
[DEBUG] Found 26 Tool plugins.
[DEBUG] Found 4 DragAndDropHandler plugins.
[DEBUG] Found 16 Codec plugins.
[DEBUG] Found 3 PlaneConverter plugins.
[DEBUG] Found 30 Translator plugins.
[DEBUG] Found 2 AutoscaleMethod plugins.
[DEBUG] Found 13 CalculatorOp plugins.
[DEBUG] Found 1 LanguageSupportPlugin plugins.
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	ui = legacy,null,null), called from non-EDT Thread:null
file:/C:/Users/DD/Desktop/Fiji.app/java/win64/jdk1.8.0_66/jre/lib/rt.jar
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	progress = -1
	maximum = -1
	status = Running command: Up-to-date check
	warning = false,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates,null,null), called from non-EDT Thread:null
[DEBUG] Executing module: net.imagej.updater.CheckForUpdates@402c8936
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.DebugPreprocessor@79003828,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.legacy.plugin.MacroPreprocessor@1ee34f13,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.legacy.plugin.ActiveImagePlusPreprocessor@3604b1b6,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.ValidityPreprocessor@31722a4e,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActiveChannelCollectionPreprocessor@19804695,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActiveDataViewPreprocessor@26168f24,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActiveDatasetPreprocessor@358c1351,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActiveDatasetViewPreprocessor@150c7ff4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActiveImageDisplayPreprocessor@e23272e,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActiveOverlayPreprocessor@1c5ef661,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.display.process.ActivePositionPreprocessor@499d6820,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.ops.OpEnvironmentPreprocessor@3f184d38,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.display.ActiveDisplayPreprocessor@4313012f,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.DefaultValuePreprocessor@616dad05,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.GatewayPreprocessor@1ce15d9d,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.ServicePreprocessor@1c49f1b4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.ui.UIPreprocessor@4708816b,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.ops.NamespacePreprocessor@4b01190a,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.InitPreprocessor@5d9ab842,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.LoadInputsPreprocessor@e8d2614,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.ui.FilePreprocessor@d0ded77,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.legacy.ui.LegacyInputHarvester@4e076c95,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.ui.awt.widget.AWTInputHarvester@46d785bf,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.ui.swing.widget.SwingInputHarvester@218db6f7,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.ui.swing.widget.SwingMdiInputHarvester@438991e4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.SaveInputsPreprocessor@361f2ec4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.CheckInputsPreprocessor@4c1fafc5,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates,null,null), called from non-EDT Thread:null
[DEBUG] INPUTS:
[DEBUG] OUTPUTS:
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.module.process.DebugPostprocessor@e982bf,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = net.imagej.legacy.plugin.MacroRecorderPostprocessor@f6035f7,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates
	processor = org.scijava.display.DisplayPostprocessor@40c643d1,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	module = net.imagej.updater.CheckForUpdates,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@42210be1
	consumed = false
	progress = -1
	maximum = -1
	status = Command finished: Up-to-date check
	warning = false,null,null), called from non-EDT Thread:null

I copied and pasted the text of the batch file into the FIJI command screen and selected java as the language, and then I got it to work, I think. Here is the console output, I think. Not sure if it is left over from before I opened the picture. Incidentally, the picture I opened was the bitmap of the Fiji icon, very very small. I did every single possible “break” button combo listed in the help, so hopefully one of them worked. Let me know.

Here goes:

    context = org.scijava.Context@42210be1
    consumed = false
    module = net.imagej.ui.swing.script.ScriptEditor
    processor = org.scijava.module.process.InitPreprocessor@432fc3a8,null,null), called from non-EDT Thread:null

[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.module.process.LoadInputsPreprocessor@143f97b2,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.ui.FilePreprocessor@19f5706,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = net.imagej.legacy.ui.LegacyInputHarvester@9fe04ec,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.ui.awt.widget.AWTInputHarvester@34f1a4f8,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.ui.swing.widget.SwingInputHarvester@5c1b37d3,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.ui.swing.widget.SwingMdiInputHarvester@27c76c31,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.module.process.SaveInputsPreprocessor@5e67d541,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.module.process.CheckInputsPreprocessor@67886c11,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor,null,null), called from non-EDT Thread:null
[DEBUG] INPUTS:
[DEBUG] OUTPUTS:
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.module.process.DebugPostprocessor@73e07933,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = net.imagej.legacy.plugin.MacroRecorderPostprocessor@7fbc4f99,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor
        processor = org.scijava.display.DisplayPostprocessor@f43645a,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = net.imagej.ui.swing.script.ScriptEditor,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        progress = -1
        maximum = -1
        status = Command finished: Script...
        warning = false,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        progress = -1
        maximum = -1
        status = Running command: script:New_.js
        warning = false,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a,null,null), called from non-EDT Thread:null
[DEBUG] Executing module: org.scijava.script.ScriptModule@2e58810a
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.DebugPreprocessor@319eb57b,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.legacy.plugin.MacroPreprocessor@1053a73e,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.legacy.plugin.ActiveImagePlusPreprocessor@47963941,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.ValidityPreprocessor@2d2cb068,null,null), called from non-EDT Thread:null
[ERROR] Invalid parameter syntax for script: New_.js
javax.script.ScriptException: Unknown type: echo
        at org.scijava.script.DefaultScriptService.lookupClass(DefaultScriptService.java:266)
        at org.scijava.script.ScriptInfo.parseParam(ScriptInfo.java:374)
        at org.scijava.script.ScriptInfo.parseParam(ScriptInfo.java:346)
        at org.scijava.script.ScriptInfo.parseParameters(ScriptInfo.java:251)
        at org.scijava.module.AbstractModuleInfo.initParameters(AbstractModuleInfo.java:295)
        at org.scijava.module.AbstractModuleInfo.inputList(AbstractModuleInfo.java:257)
        at org.scijava.module.AbstractModuleInfo.inputs(AbstractModuleInfo.java:103)
        at org.scijava.module.DefaultModuleService.getSingleInput(DefaultModuleService.java:270)
        at net.imagej.display.process.SingleInputPreprocessor.getSingleInput(SingleInputPreprocessor.java:99)
        at net.imagej.display.process.SingleInputPreprocessor.process(SingleInputPreprocessor.java:81)
        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$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.IllegalArgumentException: Cannot load class: echo
        at org.scijava.util.ClassUtils.loadClass(ClassUtils.java:217)
        at org.scijava.util.ClassUtils.loadClass(ClassUtils.java:137)
        at org.scijava.script.DefaultScriptService.lookupClass(DefaultScriptService.java:261)
        ... 18 more
Caused by: java.lang.ClassNotFoundException: echo
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at org.scijava.util.ClassUtils.loadClass(ClassUtils.java:209)
        ... 20 more
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActiveChannelCollectionPreprocessor@695dfddb,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActiveDataViewPreprocessor@643add99,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActiveDatasetPreprocessor@1290ac6e,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActiveDatasetViewPreprocessor@5af7f1a4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActiveImageDisplayPreprocessor@5c427c04,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActiveOverlayPreprocessor@6ea6a400,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.display.process.ActivePositionPreprocessor@79c29666,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.ops.OpEnvironmentPreprocessor@1cdd322b,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.display.ActiveDisplayPreprocessor@53b0cfe8,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.DefaultValuePreprocessor@8edf73a,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.GatewayPreprocessor@65f121e7,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.ServicePreprocessor@10480b18,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.ui.UIPreprocessor@45d25976,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.ops.NamespacePreprocessor@22e132d1,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.InitPreprocessor@4ef3c173,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.LoadInputsPreprocessor@1e33137e,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.ui.FilePreprocessor@497df027,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.legacy.ui.LegacyInputHarvester@62a12463,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.ui.awt.widget.AWTInputHarvester@3289891d,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.ui.swing.widget.SwingInputHarvester@3427d4d1,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.ui.swing.widget.SwingMdiInputHarvester@12fdf6ba,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.SaveInputsPreprocessor@79145aba,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.CheckInputsPreprocessor@72be5e4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a,null,null), called from non-EDT Thread:null
[DEBUG] INPUTS:
[DEBUG] OUTPUTS:
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.module.process.DebugPostprocessor@d20388c,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = net.imagej.legacy.plugin.MacroRecorderPostprocessor@701547b4,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a
        processor = org.scijava.display.DisplayPostprocessor@2b8f1286,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        module = org.scijava.script.ScriptModule@2e58810a,null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        progress = -1
        maximum = -1
        status = Command finished: script:New_.js
        warning = false,null,null), called from non-EDT Thread:null

Thank you for your persistence, @dylevine! Unfortunately, there is no full thread dump in any of that output. Was your Command Prompt window active while you pressed Ctrl+Pause? It should look similar to the first one you posted (with "AWT-EventQueue-0" prio=6 id=25 group=main and other threads in double quotes).

Also, it is important that the thread dump be taken during the time that the crazy window resizing stuff is happening. As I said above, this may not end up being feasible in your situation; I am not sure. But unless someone else on another computer can reproduce, it is quite difficult to know what is going wrong on yours.

Probably because the option “Hide file extensions for known file types” was enabled (it is enabled by default, unfortunately). One of the first things you should do on every Windows system is to disable this harmful and confusing option.

1 Like

Hi, I apologize for any repetition here. I cleared the console before opening the image (the flat FIJI ping file), and then I tried new key combos. The only one that did anything was “fn+insert”, and it brought me back to the login screen. from there I got back to the main imageJ window and selected " plugins, debug, dump stack. The very last lines of this look new to me and have to do with window resizing, so maybe that’s it. Let me know if this gives any info at all. Thanks!
DD

   at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
        at sun.java2d.Disposer.run(Disposer.java:148)
        at java.lang.Thread.run(Thread.java:745)

"RMI RenewClean-[192.168.1.70:63208]" daemon prio=5 id=21 group=system
   java.lang.Thread.State: TIMED_WAITING
        at java.lang.Object.wait(Native Method)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
        at sun.rmi.transport.DGCClient$EndpointEntry$RenewCleanThread.run(DGCClient.java:553)
        at java.lang.Thread.run(Thread.java:745)

"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:502)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)

"SciJava-42210be1-Thread-2" prio=4 id=33 group=main
   java.lang.Thread.State: TIMED_WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
        at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
        at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
        at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
        at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

"SciJava-42210be1-Thread-3" prio=4 id=34 group=main
   java.lang.Thread.State: RUNNABLE
        at java.lang.Thread.dumpThreads(Native Method)
        at java.lang.Thread.getAllStackTraces(Thread.java:1603)
        at org.scijava.plugins.commands.debug.DumpStack.run(DumpStack.java:81)
        at org.scijava.command.CommandModule.run(CommandModule.java:205)
        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:745)

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

"TimerQueue" daemon prio=5 id=26 group=system
   java.lang.Thread.State: WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
        at java.util.concurrent.DelayQueue.take(DelayQueue.java:211)
        at javax.swing.TimerQueue.run(TimerQueue.java:171)
        at java.lang.Thread.run(Thread.java:745)

}
        window = org.scijava.ui.swing.viewer.SwingDisplayWindow[frame0,75,-8,1213x736,invalid,layout=java.awt.BorderLayout,title=Stack Dump,resizable,maximized,defaultCloseOperation=DISPOSE_ON_CLOSE,rootPane=javax.swing.JRootPane[,8,31,1197x697,invalid,layout=javax.swing.JRootPane$RootLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=16777673,maximumSize=,minimumSize=,preferredSize=],rootPaneCheckingEnabled=true],null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        display = plugin:class org.scijava.display.DefaultTextDisplay: type=class java.lang.String, name=Stack Dump, objects={"AWT-EventQueue-0" prio=6 id=24 group=main
   java.lang.Thread.State: RUNNABLE
        at java.security.AccessController.getInheritedAccessControlContext(Native Method)
        at java.security.AccessControlContext.optimize(AccessControlContext.java:572)
        at java.security.AccessController.getContext(AccessController.java:826)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:722)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

"AWT-Shutdown" prio=6 id=23 group=system
   java.lang.Thread.State: WAITING
        at java.lang.Object.wait(Native Method)
        at java.lang.Object.wait(Object.java:502)
        at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
        at java.lang.Thread.run(Thread.java:745)

"AWT-Windows" daemon prio=6 id=13 group=system
   java.lang.Thread.State: RUNNABLE
        at sun.awt.windows.WToolkit.eventLoop(Native Method)
        at sun.awt.windows.WToolkit.run(WToolkit.java:306)
        at java.lang.Thread.run(Thread.java:745)

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

"DestroyJavaVM" prio=5 id=27 group=main
   java.lang.Thread.State: RUNNABLE

"Dump Stack" prio=4 id=35 group=main
   java.lang.Thread.State: WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
        at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:429)
        at java.util.concurrent.FutureTask.get(FutureTask.java:191)
        at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:273)
        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:745)

"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:143)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"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:143)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
        at sun.java2d.Disposer.run(Disposer.java:148)
        at java.lang.Thread.run(Thread.java:745)

"RMI RenewClean-[192.168.1.70:63208]" daemon prio=5 id=21 group=system
   java.lang.Thread.State: TIMED_WAITING
        at java.lang.Object.wait(Native Method)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
        at sun.rmi.transport.DGCClient$EndpointEntry$RenewCleanThread.run(DGCClient.java:553)
        at java.lang.Thread.run(Thread.java:745)

"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:502)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)

"SciJava-42210be1-Thread-2" prio=4 id=33 group=main
   java.lang.Thread.State: TIMED_WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
        at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
        at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
        at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
        at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

"SciJava-42210be1-Thread-3" prio=4 id=34 group=main
   java.lang.Thread.State: RUNNABLE
        at java.lang.Thread.dumpThreads(Native Method)
        at java.lang.Thread.getAllStackTraces(Thread.java:1603)
        at org.scijava.plugins.commands.debug.DumpStack.run(DumpStack.java:81)
        at org.scijava.command.CommandModule.run(CommandModule.java:205)
        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:745)

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

"TimerQueue" daemon prio=5 id=26 group=system
   java.lang.Thread.State: WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
        at java.util.concurrent.DelayQueue.take(DelayQueue.java:211)
        at javax.swing.TimerQueue.run(TimerQueue.java:171)
        at java.lang.Thread.run(Thread.java:745)

},null,null), called from non-EDT Thread:null
[DEBUG] publish(
        context = org.scijava.Context@42210be1
        consumed = false
        display = plugin:class org.scijava.display.DefaultTextDisplay: type=class java.lang.String, name=Stack Dump, objects={"AWT-EventQueue-0" prio=6 id=24 group=main
   java.lang.Thread.State: RUNNABLE
        at java.security.AccessController.getInheritedAccessControlContext(Native Method)
        at java.security.AccessControlContext.optimize(AccessControlContext.java:572)
        at java.security.AccessController.getContext(AccessController.java:826)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:722)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

"AWT-Shutdown" prio=6 id=23 group=system
   java.lang.Thread.State: WAITING
        at java.lang.Object.wait(Native Method)
        at java.lang.Object.wait(Object.java:502)
        at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:295)
        at java.lang.Thread.run(Thread.java:745)

"AWT-Windows" daemon prio=6 id=13 group=system
   java.lang.Thread.State: RUNNABLE
        at sun.awt.windows.WToolkit.eventLoop(Native Method)
        at sun.awt.windows.WToolkit.run(WToolkit.java:306)
        at java.lang.Thread.run(Thread.java:745)

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

"DestroyJavaVM" prio=5 id=27 group=main
   java.lang.Thread.State: RUNNABLE

"Dump Stack" prio=4 id=35 group=main
   java.lang.Thread.State: WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
        at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:429)
        at java.util.concurrent.FutureTask.get(FutureTask.java:191)
        at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:273)
        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:745)

"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:143)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
        at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209)

"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:143)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:164)
        at sun.java2d.Disposer.run(Disposer.java:148)
        at java.lang.Thread.run(Thread.java:745)

"RMI RenewClean-[192.168.1.70:63208]" daemon prio=5 id=21 group=system
   java.lang.Thread.State: TIMED_WAITING
        at java.lang.Object.wait(Native Method)
        at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:143)
        at sun.rmi.transport.DGCClient$EndpointEntry$RenewCleanThread.run(DGCClient.java:553)
        at java.lang.Thread.run(Thread.java:745)

"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:502)
        at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157)

"SciJava-42210be1-Thread-2" prio=4 id=33 group=main
   java.lang.Thread.State: TIMED_WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.parkNanos(LockSupport.java:215)
        at java.util.concurrent.SynchronousQueue$TransferStack.awaitFulfill(SynchronousQueue.java:460)
        at java.util.concurrent.SynchronousQueue$TransferStack.transfer(SynchronousQueue.java:362)
        at java.util.concurrent.SynchronousQueue.poll(SynchronousQueue.java:941)
        at java.util.concurrent.ThreadPoolExecutor.getTask(ThreadPoolExecutor.java:1066)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1127)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)

"SciJava-42210be1-Thread-3" prio=4 id=34 group=main
   java.lang.Thread.State: RUNNABLE
        at java.lang.Thread.dumpThreads(Native Method)
        at java.lang.Thread.getAllStackTraces(Thread.java:1603)
        at org.scijava.plugins.commands.debug.DumpStack.run(DumpStack.java:81)
        at org.scijava.command.CommandModule.run(CommandModule.java:205)
        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:745)

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

"TimerQueue" daemon prio=5 id=26 group=system
   java.lang.Thread.State: WAITING
        at sun.misc.Unsafe.park(Native Method)
        at java.util.concurrent.locks.LockSupport.park(LockSupport.java:175)
        at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(AbstractQueuedSynchronizer.java:2039)
        at java.util.concurrent.DelayQueue.take(DelayQueue.java:211)
        at javax.swing.TimerQueue.run(TimerQueue.java:171)
        at java.lang.Thread.run(Thread.java:745)

}
        window = org.scijava.ui.swing.viewer.SwingDisplayWindow[frame0,75,-8,1213x736,invalid,layout=java.awt.BorderLayout,title=Stack Dump,resizable,maximized,defaultCloseOperation=DISPOSE_ON_CLOSE,rootPane=javax.swing.JRootPane[,8,31,1197x697,invalid,layout=javax.swing.JRootPane$RootLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=16777673,maximumSize=,minimumSize=,preferredSize=],rootPaneCheckingEnabled=true],null,null), called from non-EDT Thread:null

Here is the new output, just the very end which I think might actually help–invalid layout? Lots of resizings? The rest of this output is already posted in my last post. Let me know if this helps…
Thank you!
DD

window = org.scijava.ui.swing.viewer.SwingDisplayWindow[frame0,75,-8,1213x736,invalid,layout=java.awt.BorderLayout,title=Stack Dump,resizable,maximized,defaultCloseOperation=DISPOSE_ON_CLOSE,rootPane=javax.swing.JRootPane[,8,31,1197x697,invalid,layout=javax.swing.JRootPane$RootLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=16777673,maximumSize=,minimumSize=,preferredSize=],rootPaneCheckingEnabled=true],null,null), called from non-EDT Thread:null

Here is another attempt at a stack dump with the same issue.

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at ij.gui.ImageWindow.getMaximumBounds(ImageWindow.java:471)
	at ij.gui.ImageWindow.maximize(ImageWindow.java:525)
	at ij.gui.ImageWindow.windowStateChanged(ImageWindow.java:585)
	at java.awt.Window.processWindowStateEvent(Unknown Source)
	at java.awt.Window.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)

@dylevine Interesting; this new stack trace is different from the others, and suggests a bug in one of the ImageJ UI classes. This may, however, be a different bug than the repeated maximization problem.

@Wayne: do you have any ideas about this?

In the latest ImageJ daily build (1.51g6), the ImageWindow.getMaximumBounds() method returns GUI.getMaxWindowBounds() if ‘imp’ is null, which should prevent this particular exception.

Do you see these problems with the legacy version of ImageJ? It is available at

https://imagej.nih.gov/ij/download.html

1 Like

Hi Wayne,
I downloaded the latest version of the java independent zip file about a week ago and now just updated to 1.51f but still have the same problem. I am no longer using FIJI, but am not sure if I got rid of all of the original installation of FIJI. How do I check? PS-the main process that hogs the memory in task manager when the multiple windows happen is java, although imagej32 bit is running as well of course. The only way I can get it to work is when I draw a line on the flashing picture and start analyze–>set measurement, and then hope to minimize the image window before it starts to flash wildly out of control and take over my computer!

Did you download the version of ImageJ bundled with Java 1.8 or with Java 1.6? In either case, try the other version. You should also try upgrading to the latest daily build (1.51g7). It has a fix that should prevent the null pointer exception you got.

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I am running the 32 bit java 1.8 version.I tried running the 64 bit version that came in the zipped file of the java independent imagej download, and my machine won’t run it. In other words, I already had java so I didn’t download one of the’ imagej for windows with java’ packages on the nih website you referred to.

I upgraded to the latest build by using help–>update imagej, and the latest version is still 1.51f. I don’t see any g7 option.

However, when I did update to 1.51f I got an error message that said I had too many builds, so I went in and renamed the 1.51e version “old” and now it seems to have stabilized for the moment. I am doing abunch of percent area calculations while it is stable. The console still gives the same error so perhaps I am still in for the repeating windows later this evening, but for now, I’m happy. Here’s the error I still get with 1.51f:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
	at ij.process.AutoThresholder.getThreshold(AutoThresholder.java:43)
	at ij.process.AutoThresholder.getThreshold(AutoThresholder.java:75)
	at ij.plugin.frame.ColorThresholder.autoSetThreshold(ColorThresholder.java:968)
	at ij.plugin.frame.ColorThresholder.itemStateChanged(ColorThresholder.java:523)
	at java.awt.Choice.processItemEvent(Unknown Source)
	at java.awt.Choice.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)

Why are using a 32-bit version of Java? It is slower and cannot use more than 2 GB of memory.

Is there an error message?

You have to select “daily build” from the drop down menu.

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