Exporting images/data to Fiji via the `Export` button hangs on macOS

[elevans]

The user Erosion on the image.sc forum reported that the export function in FLIMJ UI cases the application to hang. See here for the post. So far I have been able to replicate this on an older Intel mac running macOS Sonoma 14.8.3. This issue is not present on Windows or Linux.

This will require some remote debugging.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/the-process-is-unresponsive-when-using-flimj/118363/9

[elevans]

I setup a remote debugging session and traced the bug to here. After obtaining and converting the selected export image/datasets we try to get the current UIService which hangs on macOS.

Edit: Actually it's the show() call after we get the UIService.

[elevans]

A quick progress update. I tracked the bug to some strange JavaFX / SwingUI thread lock bug. It's likely the same issue I ran into earlier when I used JavaFX's openers instead of the swing ones served by the UIService. Unfortunately in this particular case we must interact with UIService to display the images. More debugging is needed...

[elevans]

Here's a thread dump during the thread lock:

Threads class SMR info:
_java_thread_list=0x000060000168c420, length=25, elements={
0x00007f7b78040e00, 0x00007f7b78045000, 0x00007f7b78045800, 0x00007f7b78046000,
0x00007f7b78046800, 0x00007f7b77052a00, 0x00007f7b78814e00, 0x00007f7b78044200,
0x00007f7b77091a00, 0x00007f7b78811600, 0x00007f7b7a893000, 0x00007f7b78653a00,
0x00007f7b7ad08a00, 0x00007f7b7d057800, 0x00007f7b7d08fa00, 0x00007f7b7bb4a200,
0x00007f7b7d07e000, 0x00007f7b7980dc00, 0x00007f7b7c530000, 0x00007f7b7f085600,
0x00007f7b7dcc2200, 0x00007f7b799c1a00, 0x00007f7b7c4a4400, 0x00007f7b7d5c1000,
0x00007f7b7dc81400
}

"Reference Handler" #9 [29955] daemon prio=10 os_prio=31 cpu=5.00ms elapsed=150.12s tid=0x00007f7b78040e00 nid=29955 waiting on condition    [0x0000700001872000]
      java.lang.Thread.State: RUNNABLE
	at java.lang.ref.Reference.waitForReferencePendingList(java.base@21.0.7/Native Method)
	at java.lang.ref.Reference.processPendingReferences(java.base@21.0.7/Reference.java:246)
	at java.lang.ref.Reference$ReferenceHandler.run(java.base@21.0.7/Reference.java:208)

"Finalizer" #10 [29699] daemon prio=8 os_prio=31 cpu=10.50ms elapsed=150.12s tid=0x00007f7b78045000 nid=29699 in Object.wait()    [0x0000700001975000]
      java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at java.lang.Object.wait(java.base@21.0.7/Object.java:339)
	at java.lang.ref.NativeReferenceQueue.await(java.base@21.0.7/NativeReferenceQueue.java:48)
	at java.lang.ref.ReferenceQueue.remove0(java.base@21.0.7/ReferenceQueue.java:158)
	at java.lang.ref.NativeReferenceQueue.remove(java.base@21.0.7/NativeReferenceQueue.java:89)
	- locked <0x0000000680000900> (a java.lang.ref.NativeReferenceQueue$Lock)
	at java.lang.ref.Finalizer$FinalizerThread.run(java.base@21.0.7/Finalizer.java:173)

"Signal Dispatcher" #11 [29443] daemon prio=9 os_prio=31 cpu=0.40ms elapsed=150.12s tid=0x00007f7b78045800 nid=29443 waiting on condition    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"Service Thread" #12 [28931] daemon prio=9 os_prio=31 cpu=38.27ms elapsed=150.12s tid=0x00007f7b78046000 nid=28931 runnable    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"Monitor Deflation Thread" #13 [28419] daemon prio=9 os_prio=31 cpu=22.13ms elapsed=150.12s tid=0x00007f7b78046800 nid=28419 runnable    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"C2 CompilerThread0" #14 [27907] daemon prio=9 os_prio=31 cpu=19755.98ms elapsed=150.12s tid=0x00007f7b77052a00 nid=27907 waiting on condition    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE
      No compile task

"C1 CompilerThread0" #16 [24835] daemon prio=9 os_prio=31 cpu=7213.88ms elapsed=150.12s tid=0x00007f7b78814e00 nid=24835 waiting on condition    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE
      No compile task

"Common-Cleaner" #17 [27395] daemon prio=8 os_prio=31 cpu=4.13ms elapsed=150.06s tid=0x00007f7b78044200 nid=27395 waiting on condition    [0x0000700001f87000]
      java.lang.Thread.State: TIMED_WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000680000a28> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(java.base@21.0.7/LockSupport.java:269)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1852)
	at java.lang.ref.ReferenceQueue.await(java.base@21.0.7/ReferenceQueue.java:71)
	at java.lang.ref.ReferenceQueue.remove0(java.base@21.0.7/ReferenceQueue.java:143)
	at java.lang.ref.ReferenceQueue.remove(java.base@21.0.7/ReferenceQueue.java:218)
	at jdk.internal.ref.CleanerImpl.run(java.base@21.0.7/CleanerImpl.java:140)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)
	at jdk.internal.misc.InnocuousThread.run(java.base@21.0.7/InnocuousThread.java:186)

"Notification Thread" #18 [26883] daemon prio=9 os_prio=31 cpu=0.10ms elapsed=149.94s tid=0x00007f7b77091a00 nid=26883 runnable    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"JavaFX Application Thread" #21 [259] daemon prio=5 os_prio=31 cpu=9562.70ms elapsed=149.29s tid=0x00007f7b78811600 nid=259 in Object.wait()    [0x00007ff7b378c000]
      java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at java.lang.Object.wait(java.base@21.0.7/Object.java:339)
	at java.awt.EventQueue.invokeAndWait(java.desktop@21.0.7/EventQueue.java:1365)
	- locked <0x000000068b01fae0> (a java.awt.EventQueue$1AWTInvocationLock)
	at java.awt.EventQueue.invokeAndWait(java.desktop@21.0.7/EventQueue.java:1346)
	at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:118)
	at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:154)
	at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:72)
	at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:101)
	at org.scijava.display.DefaultDisplayService.createDisplay(DefaultDisplayService.java:213)
	at org.scijava.ui.AbstractUserInterface.show(AbstractUserInterface.java:99)
	at org.scijava.ui.DefaultUIService.show(DefaultUIService.java:263)
	at flimlib.flimj.ui.controller.ExportCtrl.lambda$initialize$1(ExportCtrl.java:100)
	at flimlib.flimj.ui.controller.ExportCtrl$$Lambda/0x00000001319ae468.handle(Unknown Source)
	at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(javafx.base@23.0.2/CompositeEventHandler.java:86)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(javafx.base@23.0.2/EventHandlerManager.java:232)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(javafx.base@23.0.2/EventHandlerManager.java:189)
	at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(javafx.base@23.0.2/CompositeEventDispatcher.java:59)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:58)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.EventUtil.fireEventImpl(javafx.base@23.0.2/EventUtil.java:74)
	at com.sun.javafx.event.EventUtil.fireEvent(javafx.base@23.0.2/EventUtil.java:49)
	at javafx.event.Event.fireEvent(javafx.base@23.0.2/Event.java:199)
	at javafx.scene.Node.fireEvent(javafx.graphics@23.0.2/Node.java:8963)
	at javafx.scene.control.Button.fire(javafx.controls@23.0.2/Button.java:203)
	at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(javafx.controls@23.0.2/ButtonBehavior.java:207)
	at com.sun.javafx.scene.control.behavior.ButtonBehavior$$Lambda/0x0000000131a21370.handle(javafx.controls@23.0.2/Unknown Source)
	at com.sun.javafx.scene.control.inputmap.InputMap.handle(javafx.controls@23.0.2/InputMap.java:274)
	at com.sun.javafx.scene.control.inputmap.InputMap$$Lambda/0x00000001319e8668.handle(javafx.controls@23.0.2/Unknown Source)
	at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(javafx.base@23.0.2/CompositeEventHandler.java:247)
	at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(javafx.base@23.0.2/CompositeEventHandler.java:80)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(javafx.base@23.0.2/EventHandlerManager.java:232)
	at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(javafx.base@23.0.2/EventHandlerManager.java:189)
	at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(javafx.base@23.0.2/CompositeEventDispatcher.java:59)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:58)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(javafx.base@23.0.2/BasicEventDispatcher.java:56)
	at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(javafx.base@23.0.2/EventDispatchChainImpl.java:114)
	at com.sun.javafx.event.EventUtil.fireEventImpl(javafx.base@23.0.2/EventUtil.java:74)
	at com.sun.javafx.event.EventUtil.fireEvent(javafx.base@23.0.2/EventUtil.java:54)
	at javafx.event.Event.fireEvent(javafx.base@23.0.2/Event.java:199)
	at javafx.scene.Scene$MouseHandler.process(javafx.graphics@23.0.2/Scene.java:3987)
	at javafx.scene.Scene.processMouseEvent(javafx.graphics@23.0.2/Scene.java:1893)
	at javafx.scene.Scene$ScenePeerListener.mouseEvent(javafx.graphics@23.0.2/Scene.java:2711)
	at com.sun.javafx.tk.quantum.EmbeddedScene.lambda$mouseEvent$6(javafx.graphics@23.0.2/EmbeddedScene.java:295)
	at com.sun.javafx.tk.quantum.EmbeddedScene$$Lambda/0x0000000131c77268.run(javafx.graphics@23.0.2/Unknown Source)
	at java.security.AccessController.executePrivileged(java.base@21.0.7/AccessController.java:778)
	at java.security.AccessController.doPrivileged(java.base@21.0.7/AccessController.java:400)
	at com.sun.javafx.tk.quantum.EmbeddedScene.lambda$mouseEvent$7(javafx.graphics@23.0.2/EmbeddedScene.java:288)
	at com.sun.javafx.tk.quantum.EmbeddedScene$$Lambda/0x0000000131c76dc0.run(javafx.graphics@23.0.2/Unknown Source)
	at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(javafx.graphics@23.0.2/PlatformImpl.java:456)
	at com.sun.javafx.application.PlatformImpl$$Lambda/0x00000001317d5180.run(javafx.graphics@23.0.2/Unknown Source)
	at java.security.AccessController.executePrivileged(java.base@21.0.7/AccessController.java:778)
	at java.security.AccessController.doPrivileged(java.base@21.0.7/AccessController.java:400)
	at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(javafx.graphics@23.0.2/PlatformImpl.java:455)
	at com.sun.javafx.application.PlatformImpl$$Lambda/0x00000001317d48f0.run(javafx.graphics@23.0.2/Unknown Source)
	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(javafx.graphics@23.0.2/InvokeLaterDispatcher.java:95)

"AWT-Shutdown" #22 [47111] prio=5 os_prio=31 cpu=80.62ms elapsed=149.19s tid=0x00007f7b7a893000 nid=47111 in Object.wait()    [0x000070000259c000]
      java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at java.lang.Object.wait(java.base@21.0.7/Object.java:339)
	at sun.awt.AWTAutoShutdown.run(java.desktop@21.0.7/AWTAutoShutdown.java:291)
	- locked <0x000000068180c7c8> (a java.lang.Object)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"Java2D Queue Flusher" #23 [66831] daemon prio=10 os_prio=31 cpu=450.98ms elapsed=149.06s tid=0x00007f7b78653a00 nid=66831 in Object.wait()    [0x000070000208a000]
      java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at sun.java2d.metal.MTLRenderQueue$QueueFlusher.run(java.desktop@21.0.7/MTLRenderQueue.java:210)
	- locked <0x0000000681806840> (a sun.java2d.metal.MTLRenderQueue$QueueFlusher)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"Java2D Disposer" #24 [71427] daemon prio=10 os_prio=31 cpu=2.16ms elapsed=149.05s tid=0x00007f7b7ad08a00 nid=71427 waiting on condition    [0x00007000027a5000]
      java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000681812b90> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(java.base@21.0.7/LockSupport.java:371)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@21.0.7/AbstractQueuedSynchronizer.java:519)
	at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@21.0.7/ForkJoinPool.java:3780)
	at java.util.concurrent.ForkJoinPool.managedBlock(java.base@21.0.7/ForkJoinPool.java:3725)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1712)
	at java.lang.ref.ReferenceQueue.await(java.base@21.0.7/ReferenceQueue.java:67)
	at java.lang.ref.ReferenceQueue.remove0(java.base@21.0.7/ReferenceQueue.java:158)
	at java.lang.ref.ReferenceQueue.remove(java.base@21.0.7/ReferenceQueue.java:234)
	at sun.java2d.Disposer.run(java.desktop@21.0.7/Disposer.java:145)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"AWT-EventQueue-0" #26 [77575] prio=6 os_prio=31 cpu=2899.22ms elapsed=147.49s tid=0x00007f7b7d057800 nid=77575 runnable    [0x0000700002aad000]
      java.lang.Thread.State: RUNNABLE
	at sun.awt.CGraphicsDevice.nativeGetScreenInsets(java.desktop@21.0.7/Native Method)
	at sun.awt.CGraphicsDevice.getScreenInsets(java.desktop@21.0.7/CGraphicsDevice.java:192)
	at sun.lwawt.macosx.LWCToolkit.getScreenInsets(java.desktop@21.0.7/LWCToolkit.java:506)
	at java.awt.Window.init(java.desktop@21.0.7/Window.java:523)
	at java.awt.Window.<init>(java.desktop@21.0.7/Window.java:554)
	at java.awt.Frame.<init>(java.desktop@21.0.7/Frame.java:428)
	at ij.gui.ImageWindow.<init>(ImageWindow.java:69)
	at ij.gui.ImageWindow.<init>(ImageWindow.java:65)
	at ij.ImagePlus.show(ImagePlus.java:515)
	at ij.ImagePlus.show(ImagePlus.java:487)
	at net.imagej.legacy.display.LegacyImageDisplayViewer.view(LegacyImageDisplayViewer.java:141)
	at net.imagej.legacy.display.LegacyImageDisplayViewer.view(LegacyImageDisplayViewer.java:107)
	at net.imagej.legacy.ui.LegacyUI$1.run(LegacyUI.java:195)
	at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:114)
	at net.imagej.legacy.ui.LegacyUI.show(LegacyUI.java:191)
	at org.scijava.ui.DefaultUIService.onEvent(DefaultUIService.java:394)
	at java.lang.invoke.LambdaForm$DMH/0x0000000131002c00.invokeSpecial(java.base@21.0.7/LambdaForm$DMH)
	at java.lang.invoke.LambdaForm$MH/0x0000000131225800.invoke(java.base@21.0.7/LambdaForm$MH)
	at java.lang.invoke.Invokers$Holder.invokeExact_MT(java.base@21.0.7/Invokers$Holder)
	at jdk.internal.reflect.DirectMethodHandleAccessor.invokeImpl(java.base@21.0.7/DirectMethodHandleAccessor.java:154)
	at jdk.internal.reflect.DirectMethodHandleAccessor.invoke(java.base@21.0.7/DirectMethodHandleAccessor.java:103)
	at java.lang.reflect.Method.invoke(java.base@21.0.7/Method.java:580)
	at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:303)
	at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:277)
	at org.scijava.event.bushe.ThreadSafeEventService.publish(ThreadSafeEventService.java:941)
	at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:53)
	at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:160)
	at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:233)
	at org.scijava.thread.DefaultThreadService$$Lambda/0x000000013122f328.run(Unknown Source)
	at java.awt.event.InvocationEvent.dispatch(java.desktop@21.0.7/InvocationEvent.java:308)
	at java.awt.EventQueue.dispatchEventImpl(java.desktop@21.0.7/EventQueue.java:773)
	at java.awt.EventQueue$4.run(java.desktop@21.0.7/EventQueue.java:720)
	at java.awt.EventQueue$4.run(java.desktop@21.0.7/EventQueue.java:714)
	at java.security.AccessController.executePrivileged(java.base@21.0.7/AccessController.java:778)
	at java.security.AccessController.doPrivileged(java.base@21.0.7/AccessController.java:400)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(java.base@21.0.7/ProtectionDomain.java:87)
	at java.awt.EventQueue.dispatchEvent(java.desktop@21.0.7/EventQueue.java:742)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(java.desktop@21.0.7/EventDispatchThread.java:203)
	at java.awt.EventDispatchThread.pumpEventsForFilter(java.desktop@21.0.7/EventDispatchThread.java:124)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(java.desktop@21.0.7/EventDispatchThread.java:113)
	at java.awt.EventDispatchThread.pumpEvents(java.desktop@21.0.7/EventDispatchThread.java:109)
	at java.awt.EventDispatchThread.pumpEvents(java.desktop@21.0.7/EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.run(java.desktop@21.0.7/EventDispatchThread.java:90)

"Timer-0" #29 [130627] daemon prio=5 os_prio=31 cpu=2.52ms elapsed=146.23s tid=0x00007f7b7d08fa00 nid=130627 in Object.wait()    [0x0000700002bb1000]
      java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at java.lang.Object.wait(java.base@21.0.7/Object.java:339)
	at java.util.TimerThread.mainLoop(java.base@21.0.7/Timer.java:537)
	- locked <0x0000000681812ce8> (a java.util.TaskQueue)
	at java.util.TimerThread.run(java.base@21.0.7/Timer.java:516)

"TimerQueue" #37 [130315] daemon prio=5 os_prio=31 cpu=0.23ms elapsed=141.80s tid=0x00007f7b7bb4a200 nid=130315 waiting on condition    [0x00007000028a8000]
      java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000682800228> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(java.base@21.0.7/LockSupport.java:371)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@21.0.7/AbstractQueuedSynchronizer.java:519)
	at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@21.0.7/ForkJoinPool.java:3780)
	at java.util.concurrent.ForkJoinPool.managedBlock(java.base@21.0.7/ForkJoinPool.java:3725)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1712)
	at java.util.concurrent.DelayQueue.take(java.base@21.0.7/DelayQueue.java:242)
	at javax.swing.TimerQueue.run(java.desktop@21.0.7/TimerQueue.java:165)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"DestroyJavaVM" #38 [6923] prio=5 os_prio=31 cpu=6185.78ms elapsed=139.52s tid=0x00007f7b7d07e000 nid=6923 waiting on condition    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"Thread-3" #39 [31747] daemon prio=5 os_prio=31 cpu=-0.00ms elapsed=139.51s tid=0x00007f7b7980dc00 nid=31747 runnable    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"zSelector" #43 [118559] prio=5 os_prio=31 cpu=0.27ms elapsed=127.66s tid=0x00007f7b7c530000 nid=118559 in Object.wait()    [0x00007000030c3000]
      java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at java.lang.Object.wait(java.base@21.0.7/Object.java:339)
	at ij.gui.StackWindow.run(StackWindow.java:244)
	- locked <0x0000000682800ee8> (a ij.gui.StackWindow)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"QuantumRenderer-0" #1087 [107779] daemon prio=5 os_prio=31 cpu=2558.85ms elapsed=114.49s tid=0x00007f7b7f085600 nid=107779 waiting on condition    [0x00007000032c9000]
      java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000686847ab8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(java.base@21.0.7/LockSupport.java:371)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@21.0.7/AbstractQueuedSynchronizer.java:519)
	at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@21.0.7/ForkJoinPool.java:3780)
	at java.util.concurrent.ForkJoinPool.managedBlock(java.base@21.0.7/ForkJoinPool.java:3725)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1712)
	at java.util.concurrent.LinkedBlockingQueue.take(java.base@21.0.7/LinkedBlockingQueue.java:435)
	at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@21.0.7/ThreadPoolExecutor.java:1070)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@21.0.7/ThreadPoolExecutor.java:1130)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@21.0.7/ThreadPoolExecutor.java:642)
	at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(javafx.graphics@23.0.2/QuantumRenderer.java:126)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"InvokeLaterDispatcher" #1089 [113167] daemon prio=5 os_prio=31 cpu=69.45ms elapsed=114.37s tid=0x00007f7b7dcc2200 nid=113167 in Object.wait()    [0x0000700003eed000]
      java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait0(java.base@21.0.7/Native Method)
	- waiting on <no object reference available>
	at java.lang.Object.wait(java.base@21.0.7/Object.java:366)
	at java.lang.Object.wait(java.base@21.0.7/Object.java:339)
	at com.sun.glass.ui.InvokeLaterDispatcher.run(javafx.graphics@23.0.2/InvokeLaterDispatcher.java:126)
	- locked <0x0000000686824640> (a java.lang.StringBuilder)

"Prism Font Disposer" #1091 [109331] daemon prio=10 os_prio=31 cpu=2.46ms elapsed=113.81s tid=0x00007f7b799c1a00 nid=109331 waiting on condition    [0x0000700003ff0000]
      java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000686824778> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(java.base@21.0.7/LockSupport.java:371)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@21.0.7/AbstractQueuedSynchronizer.java:519)
	at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@21.0.7/ForkJoinPool.java:3780)
	at java.util.concurrent.ForkJoinPool.managedBlock(java.base@21.0.7/ForkJoinPool.java:3725)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1712)
	at java.lang.ref.ReferenceQueue.await(java.base@21.0.7/ReferenceQueue.java:67)
	at java.lang.ref.ReferenceQueue.remove0(java.base@21.0.7/ReferenceQueue.java:158)
	at java.lang.ref.ReferenceQueue.remove(java.base@21.0.7/ReferenceQueue.java:234)
	at com.sun.javafx.font.Disposer.run(javafx.graphics@23.0.2/Disposer.java:96)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"Cleaner-0" #1093 [101387] daemon prio=8 os_prio=31 cpu=0.59ms elapsed=112.40s tid=0x00007f7b7c4a4400 nid=101387 waiting on condition    [0x0000700004705000]
      java.lang.Thread.State: TIMED_WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000686847ca8> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.parkNanos(java.base@21.0.7/LockSupport.java:269)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1852)
	at java.lang.ref.ReferenceQueue.await(java.base@21.0.7/ReferenceQueue.java:71)
	at java.lang.ref.ReferenceQueue.remove0(java.base@21.0.7/ReferenceQueue.java:143)
	at java.lang.ref.ReferenceQueue.remove(java.base@21.0.7/ReferenceQueue.java:218)
	at jdk.internal.ref.CleanerImpl.run(java.base@21.0.7/CleanerImpl.java:140)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)
	at jdk.internal.misc.InnocuousThread.run(java.base@21.0.7/InnocuousThread.java:186)

"pool-2-thread-1" #1100 [123231] prio=5 os_prio=31 cpu=225.66ms elapsed=103.44s tid=0x00007f7b7d5c1000 nid=123231 waiting on condition    [0x00007000041f6000]
      java.lang.Thread.State: WAITING (parking)
	at jdk.internal.misc.Unsafe.park(java.base@21.0.7/Native Method)
	- parking to wait for    <0x0000000684f90ae0> (a java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject)
	at java.util.concurrent.locks.LockSupport.park(java.base@21.0.7/LockSupport.java:371)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionNode.block(java.base@21.0.7/AbstractQueuedSynchronizer.java:519)
	at java.util.concurrent.ForkJoinPool.unmanagedBlock(java.base@21.0.7/ForkJoinPool.java:3780)
	at java.util.concurrent.ForkJoinPool.managedBlock(java.base@21.0.7/ForkJoinPool.java:3725)
	at java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.await(java.base@21.0.7/AbstractQueuedSynchronizer.java:1712)
	at java.util.concurrent.LinkedBlockingQueue.take(java.base@21.0.7/LinkedBlockingQueue.java:435)
	at java.util.concurrent.ThreadPoolExecutor.getTask(java.base@21.0.7/ThreadPoolExecutor.java:1070)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(java.base@21.0.7/ThreadPoolExecutor.java:1130)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(java.base@21.0.7/ThreadPoolExecutor.java:642)
	at java.lang.Thread.runWith(java.base@21.0.7/Thread.java:1596)
	at java.lang.Thread.run(java.base@21.0.7/Thread.java:1583)

"PulseTimer-CVDisplayLink thread" #1101 [172867] daemon prio=5 os_prio=31 cpu=397.79ms elapsed=96.50s tid=0x00007f7b7dc81400 nid=172867 runnable    [0x0000000000000000]
      java.lang.Thread.State: RUNNABLE

"GC Thread#3" os_prio=31 cpu=253.14ms elapsed=147.17s tid=0x00007f7b778b9910 nid=2095 runnable    

"GC Thread#2" os_prio=31 cpu=264.17ms elapsed=149.89s tid=0x00007f7b77811010 nid=26371 runnable    

"GC Thread#1" os_prio=31 cpu=262.74ms elapsed=149.89s tid=0x00007f7b76f115f0 nid=25859 runnable    

"VM Thread" os_prio=31 cpu=44.28ms elapsed=150.14s tid=0x00007f7b76f0a200 nid=17667 runnable    

"VM Periodic Task Thread" os_prio=31 cpu=117.63ms elapsed=150.14s tid=0x00007f7b778087a0 nid=20995 waiting on condition    

"G1 Service" os_prio=31 cpu=9.36ms elapsed=150.16s tid=0x00007f7b76f09170 nid=16387 runnable    

"G1 Refine#0" os_prio=31 cpu=130.00ms elapsed=150.16s tid=0x00007f7b7704ee00 nid=13059 runnable    

"G1 Conc#0" os_prio=31 cpu=644.10ms elapsed=150.16s tid=0x00007f7b77806d20 nid=13571 runnable    

"G1 Main Marker" os_prio=31 cpu=1.75ms elapsed=150.16s tid=0x00007f7b76f07230 nid=14083 runnable    

"GC Thread#0" os_prio=31 cpu=266.66ms elapsed=150.16s tid=0x00007f7b778067b0 nid=14339 runnable    

JNI global refs: 1553, weak refs: 56

Heap
 garbage-first heap      total 262144K, used 201075K [0x0000000680000000, 0x0000000800000000)
    region size 4096K, 25 young (102400K), 5 survivors (20480K)
 Metaspace              used 84393K, committed 85632K, reserved 1179648K
    class space        used 12307K, committed 12864K, reserved 1048576K

The problem seems to be how JavaFX and AWT EDT threads work together when we hit the invoke() function in scijava-common. I'm still testing but it looks like isDispatchThread() fails when we have a JavaFX thread and its causing some thread clashing.

[elevans]

I should have took a closer look at our own history. I believe this bug is a long standing one and the same as #6. Ultimately the bug here is a mismatch in threading models between JavaFX and AWT. I found the same work around that Curtis did (use JavaFX to harvest inputs instead of AWT) when I updated FLIMJ and "fixed" a hanging file opener on macOS.

[elevans]

I've spent most of today on this bug and I think I may have a solution for it :). See this commit in scijava-common. The full explination is there but briefly the problem is that when you click "Export" JavaFX gets a lock on some Apple GUI event loop resources and doesn't let go until its complete. But to complete it, those resources need to be available.