[ImageJ-devel] Deadlock: DefaultStatusService.showStatus calls EventService.publish / AbstractColorTool.drawIcon gets active dataset view

Barry DeZonia bdezonia at gmail.com
Wed Oct 16 15:25:47 CDT 2013 

Lee,

Using your patch I have an error. Open program and exit and I get this:

java.lang.IllegalStateException: Context already injected:
org.scijava.AbstractContextual#context

at org.scijava.Context.inject(Context.java:281)

at org.scijava.AbstractContextual.setContext(AbstractContextual.java:66)

at org.scijava.event.DefaultEventService.publishLater(
DefaultEventService.java:100)

at org.scijava.app.DefaultStatusService.publish(
DefaultStatusService.java:123)

at org.scijava.app.DefaultStatusService.showStatus(
DefaultStatusService.java:76)

at imagej.module.ModuleRunner.run(ModuleRunner.java:155)

at imagej.module.ModuleRunner.call(ModuleRunner.java:129)

at imagej.module.ModuleRunner.call(ModuleRunner.java:1)

at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)

at java.util.concurrent.FutureTask.run(FutureTask.java:138)

at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(
ThreadPoolExecutor.java:895)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(
ThreadPoolExecutor.java:918)

at java.lang.Thread.run(Thread.java:680)


Plus said patch will not affect the open sample image and then exit
crashes. But that may need to be filed as a separate bug.


On Wed, Oct 16, 2013 at 3:04 PM, Lee Kamentsky <leek at broadinstitute.org>wrote:

> Maybe I wasn't patient enough about refreshing everything.... will submit
> patch momentarily, but have only tested it on a modified version of the
> scijava-common-2.2.0 branch. I'd appreciate you merging and trying it.
>
>
> On Wed, Oct 16, 2013 at 3:54 PM, Barry DeZonia <bdezonia at gmail.com> wrote:
>
>> In imagej/pom.xml I added:
>>
>>  <scijava-common.version>2.2.1-SNAPSHOT</scijava-common.version>
>>
>> in the <properties> section
>>
>>
>> On Wed, Oct 16, 2013 at 2:46 PM, Lee Kamentsky <leek at broadinstitute.org>wrote:
>>
>>> Are you editing one of the POMs to pick up the 2.2.1-SNAPSHOT version of
>>> scijava-common?
>>>
>>>
>>> On Wed, Oct 16, 2013 at 3:45 PM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>
>>>> I'm not having any problems building scijava-common master against IJ2
>>>> master.
>>>>
>>>>
>>>> On Wed, Oct 16, 2013 at 2:25 PM, Lee Kamentsky <leek at broadinstitute.org
>>>> > wrote:
>>>>
>>>>> I have a very simple fix in scijava-common, but it seems that the head
>>>>> of the scijava-common master branch is not going to build with the head of
>>>>> the imagej master branch. How should I proceed? I could branch off off
>>>>> scijava-common-2.2.0 I suppose.
>>>>>
>>>>>
>>>>> On Wed, Oct 16, 2013 at 2:44 PM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>>>
>>>>>> Thanks. I also updated the ticket a bit a few minutes ago. In my
>>>>>> second example problem (closing app with sample image open) it looks like
>>>>>> the original open samples legacy command was not finishing its run. Not
>>>>>> sure if this is related to your event processing changes.
>>>>>>
>>>>>>
>>>>>> On Wed, Oct 16, 2013 at 1:19 PM, Lee Kamentsky <
>>>>>> leek at broadinstitute.org> wrote:
>>>>>>
>>>>>>> Sorry, I missed it. I'll see if I can take a look at it,
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Oct 16, 2013 at 2:15 PM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>>>>>
>>>>>>>> Lee did you see I reopened ticket #1992 (
>>>>>>>> http://trac.imagej.net/ticket/1992) that was related to this code
>>>>>>>> change?
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Oct 7, 2013 at 10:15 AM, Barry DeZonia <bdezonia at gmail.com>wrote:
>>>>>>>>
>>>>>>>>> Merged
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Sep 30, 2013 at 2:34 PM, Lee Kamentsky <
>>>>>>>>> leek at broadinstitute.org> wrote:
>>>>>>>>>
>>>>>>>>>> I submitted a patch to scijava-common with the changes.
>>>>>>>>>>
>>>>>>>>>> https://github.com/scijava/scijava-common/pull/13
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On Mon, Sep 30, 2013 at 3:32 PM, Barry DeZonia <
>>>>>>>>>> bdezonia at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> A proposed fix would be good Lee. I'd like to test the async
>>>>>>>>>>> status update code for responsiveness (i.e. when opening a large image
>>>>>>>>>>> let's say). Let me know when your fix is in place. Thanks.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Sep 27, 2013 at 6:54 AM, Lee Kamentsky <
>>>>>>>>>>> leek at broadinstitute.org> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Thanks Barry, the email was a little rushed - finished it while
>>>>>>>>>>>> going out the door. What do you think about sending the status messages
>>>>>>>>>>>> asynchronously? It looks to me like the AWT event processing will display
>>>>>>>>>>>> them in the order received, so that makes sure that a "Finished" message
>>>>>>>>>>>> will be seen after a "% complete" message. Status reporting is such a
>>>>>>>>>>>> common thing - it'd be a shame for all the worker threads to stall because
>>>>>>>>>>>> a user was using ImageJ to watch a movie of a cat falling off a TV while
>>>>>>>>>>>> their batch job was running.
>>>>>>>>>>>>
>>>>>>>>>>>> I think I'll submit a patch to DefaultStatusService for asynch
>>>>>>>>>>>> reporting and maybe Curtis or you could look it over and accept it. If you
>>>>>>>>>>>> reject, NP.
>>>>>>>>>>>>
>>>>>>>>>>>> --Lee
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Sep 26, 2013 at 7:53 PM, Barry DeZonia <
>>>>>>>>>>>> bdezonia at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Lee,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I added the synchronized keyword yesterday to fix a bug. We
>>>>>>>>>>>>> can undo that change. I can work around the problem in another fashion if
>>>>>>>>>>>>> necessary.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Thu, Sep 26, 2013 at 3:57 PM, Lee Kamentsky <
>>>>>>>>>>>>> leek at broadinstitute.org> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi all, I'm getting a deadly embrace that happens when the
>>>>>>>>>>>>>> AWT event queue thread tries to get a lock within
>>>>>>>>>>>>>> DefaultDatasetView.getColor and when DefaultStatusService.showStatus on a
>>>>>>>>>>>>>> worker thread tries to publish a synchronous request for status display
>>>>>>>>>>>>>> after taking the DefaultDatasetView's lock in DefaultDatasetView.rebuild.
>>>>>>>>>>>>>> It happens periodically, but it's timing-dependent, so not so reproducible.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The bug is somewhat debatable. Possible candidates: It's a
>>>>>>>>>>>>>> little drastic for DefaultDatasetView.getColor to synchronize on the view
>>>>>>>>>>>>>> itself. Maybe some proxy for the color system could have a synchronizing
>>>>>>>>>>>>>> object. The other candidate is DefaultEventService.showStatus which could
>>>>>>>>>>>>>> use EventService.publishLater - I don't think there's much need for status
>>>>>>>>>>>>>> publishers to wait around for the status to show on the screen.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The two stack traces:
>>>>>>>>>>>>>> Thread [AWT-EventQueue-0] (Suspended)
>>>>>>>>>>>>>> DefaultDatasetView.getColor(ChannelCollection) line: 261 Synchronized
>>>>>>>>>>>>>> method on DefaultDatasetView
>>>>>>>>>>>>>>  FgColorTool(AbstractColorTool).drawIcon() line: 175
>>>>>>>>>>>>>> FgColorTool(AbstractColorTool).onEvent(DisplayActivatedEvent)
>>>>>>>>>>>>>> line: 184
>>>>>>>>>>>>>>  NativeMethodAccessorImpl.invoke0(Method, Object, Object[])
>>>>>>>>>>>>>> line: not available [native method]
>>>>>>>>>>>>>> NativeMethodAccessorImpl.invoke(Object, Object[]) line: 39
>>>>>>>>>>>>>>  DelegatingMethodAccessorImpl.invoke(Object, Object[]) line:
>>>>>>>>>>>>>> 25
>>>>>>>>>>>>>> Method.invoke(Object, Object...) line: 597
>>>>>>>>>>>>>>  DefaultEventService$ProxySubscriber<E>.onEvent(E) line: 282
>>>>>>>>>>>>>> DefaultEventService$ProxySubscriber<E>.onEvent(Object) line: 1
>>>>>>>>>>>>>>  DefaultEventBus(ThreadSafeEventService).publish(Object,
>>>>>>>>>>>>>> String, Object, List, List, StackTraceElement[]) line: 971
>>>>>>>>>>>>>>  DefaultEventBus.access$1(DefaultEventBus, Object, String,
>>>>>>>>>>>>>> Object, List, List, StackTraceElement[]) line: 1
>>>>>>>>>>>>>> DefaultEventBus$1.run() line: 201
>>>>>>>>>>>>>>  DefaultThreadService.invoke(Runnable) line: 91
>>>>>>>>>>>>>> DefaultEventBus.publishNow(Object, String, Object, List,
>>>>>>>>>>>>>> List, StackTraceElement[]) line: 195
>>>>>>>>>>>>>>  DefaultEventBus.publishNow(Object) line: 86
>>>>>>>>>>>>>> DefaultEventService.publish(E) line: 95
>>>>>>>>>>>>>>  DefaultDisplayService.setActiveDisplay(Display<?>) line: 129
>>>>>>>>>>>>>> DefaultDisplayService.onEvent(WinActivatedEvent) line: 247
>>>>>>>>>>>>>>  NativeMethodAccessorImpl.invoke0(Method, Object, Object[])
>>>>>>>>>>>>>> line: not available [native method]
>>>>>>>>>>>>>> NativeMethodAccessorImpl.invoke(Object, Object[]) line: 39
>>>>>>>>>>>>>>  DelegatingMethodAccessorImpl.invoke(Object, Object[]) line:
>>>>>>>>>>>>>> 25
>>>>>>>>>>>>>> Method.invoke(Object, Object...) line: 597
>>>>>>>>>>>>>>  DefaultEventService$ProxySubscriber<E>.onEvent(E) line: 282
>>>>>>>>>>>>>> DefaultEventService$ProxySubscriber<E>.onEvent(Object) line: 1
>>>>>>>>>>>>>>  DefaultEventBus(ThreadSafeEventService).publish(Object,
>>>>>>>>>>>>>> String, Object, List, List, StackTraceElement[]) line: 971
>>>>>>>>>>>>>>  DefaultEventBus.access$1(DefaultEventBus, Object, String,
>>>>>>>>>>>>>> Object, List, List, StackTraceElement[]) line: 1
>>>>>>>>>>>>>> DefaultEventBus$1.run() line: 201
>>>>>>>>>>>>>>  DefaultThreadService.invoke(Runnable) line: 91
>>>>>>>>>>>>>> DefaultEventBus.publishNow(Object, String, Object, List,
>>>>>>>>>>>>>> List, StackTraceElement[]) line: 195
>>>>>>>>>>>>>>  DefaultEventBus.publishNow(Object) line: 86
>>>>>>>>>>>>>> DefaultEventService.publish(E) line: 95
>>>>>>>>>>>>>>  AWTWindowEventDispatcher.windowActivated(WindowEvent) line:
>>>>>>>>>>>>>> 94
>>>>>>>>>>>>>> SwingDisplayWindow(Window).processWindowEvent(WindowEvent)
>>>>>>>>>>>>>> line: 1877
>>>>>>>>>>>>>>  SwingDisplayWindow(JFrame).processWindowEvent(WindowEvent)
>>>>>>>>>>>>>> line: 274
>>>>>>>>>>>>>> SwingDisplayWindow(Window).processEvent(AWTEvent) line: 1823
>>>>>>>>>>>>>>  SwingDisplayWindow(Component).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 4630
>>>>>>>>>>>>>> SwingDisplayWindow(Container).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 2099
>>>>>>>>>>>>>>  SwingDisplayWindow(Window).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 2478
>>>>>>>>>>>>>> SwingDisplayWindow(Component).dispatchEvent(AWTEvent) line:
>>>>>>>>>>>>>> 4460
>>>>>>>>>>>>>>  DefaultKeyboardFocusManager(KeyboardFocusManager).redispatchEvent(Component,
>>>>>>>>>>>>>> AWTEvent) line: 1850
>>>>>>>>>>>>>> DefaultKeyboardFocusManager.typeAheadAssertions(Component,
>>>>>>>>>>>>>> AWTEvent) line: 910
>>>>>>>>>>>>>>  DefaultKeyboardFocusManager.dispatchEvent(AWTEvent) line:
>>>>>>>>>>>>>> 409
>>>>>>>>>>>>>> SwingDisplayWindow(Component).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 4502
>>>>>>>>>>>>>>  SwingDisplayWindow(Container).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 2099
>>>>>>>>>>>>>> SwingDisplayWindow(Window).dispatchEventImpl(AWTEvent) line:
>>>>>>>>>>>>>> 2478
>>>>>>>>>>>>>>  SwingDisplayWindow(Component).dispatchEvent(AWTEvent) line:
>>>>>>>>>>>>>> 4460
>>>>>>>>>>>>>> EventQueue.dispatchEvent(AWTEvent) line: 599
>>>>>>>>>>>>>>  DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent(SentEvent).dispatch()
>>>>>>>>>>>>>> line: 55
>>>>>>>>>>>>>> DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch()
>>>>>>>>>>>>>> line: 183
>>>>>>>>>>>>>>  DefaultKeyboardFocusManager.sendMessage(Component,
>>>>>>>>>>>>>> AWTEvent) line: 210
>>>>>>>>>>>>>> DefaultKeyboardFocusManager.dispatchEvent(AWTEvent) line: 286
>>>>>>>>>>>>>>  SwingDisplayWindow(Component).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 4502
>>>>>>>>>>>>>> SwingDisplayWindow(Container).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 2099
>>>>>>>>>>>>>>  SwingDisplayWindow(Window).dispatchEventImpl(AWTEvent)
>>>>>>>>>>>>>> line: 2478
>>>>>>>>>>>>>> SwingDisplayWindow(Component).dispatchEvent(AWTEvent) line:
>>>>>>>>>>>>>> 4460
>>>>>>>>>>>>>>  EventQueue.dispatchEvent(AWTEvent) line: 599
>>>>>>>>>>>>>> SequencedEvent.dispatch() line: 101
>>>>>>>>>>>>>>  EventQueue.dispatchEvent(AWTEvent) line: 597
>>>>>>>>>>>>>> EventDispatchThread.pumpOneEventForFilters(int) line: 269
>>>>>>>>>>>>>>  EventDispatchThread.pumpEventsForFilter(int, Conditional,
>>>>>>>>>>>>>> EventFilter) line: 184
>>>>>>>>>>>>>> EventDispatchThread.pumpEventsForHierarchy(int, Conditional,
>>>>>>>>>>>>>> Component) line: 174
>>>>>>>>>>>>>>  EventDispatchThread.pumpEvents(int, Conditional) line: 169
>>>>>>>>>>>>>> EventDispatchThread.pumpEvents(Conditional) line: 161
>>>>>>>>>>>>>>  EventDispatchThread.run() line: 122
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thread [SciJava-4b2922f6-Thread-27] (Suspended)
>>>>>>>>>>>>>>  Object.wait(long) line: not available [native method]
>>>>>>>>>>>>>> EventQueue$1AWTInvocationLock(Object).wait() line: 485 Waiting
>>>>>>>>>>>>>> for AWT event thread to read invocation request.
>>>>>>>>>>>>>>  EventQueue.invokeAndWait(Runnable) line: 993
>>>>>>>>>>>>>> DefaultThreadService.invoke(Runnable) line: 95
>>>>>>>>>>>>>>  DefaultEventBus.publishNow(Object, String, Object, List,
>>>>>>>>>>>>>> List, StackTraceElement[]) line: 195
>>>>>>>>>>>>>> DefaultEventBus.publishNow(Object) line: 86
>>>>>>>>>>>>>>  DefaultEventService.publish(E) line: 95
>>>>>>>>>>>>>> DefaultStatusService.showStatus(int, int, String) line: 77
>>>>>>>>>>>>>>  DefaultMinMaxMethod<T>.report() line: 296
>>>>>>>>>>>>>> DefaultMinMaxMethod<T>.process() line: 155
>>>>>>>>>>>>>>  DefaultAutoscaleMethod<T>.getRange(IterableInterval<T>)
>>>>>>>>>>>>>> line: 70
>>>>>>>>>>>>>> DefaultAutoscaleService.getDefaultIntervalRange(IterableInterval<RealType<?>>)
>>>>>>>>>>>>>> line: 97
>>>>>>>>>>>>>>  DefaultAutoscaleService.getDefaultRandomAccessRange(RandomAccessibleInterval<RealType<?>>)
>>>>>>>>>>>>>> line: 105
>>>>>>>>>>>>>>  DefaultDatasetView.autoscale(int) line: 176
>>>>>>>>>>>>>> DefaultDatasetView.initializeView(boolean) line: 499
>>>>>>>>>>>>>>  DefaultDatasetView.rebuild() line: 383 Takes the
>>>>>>>>>>>>>> DefaultDatasetView lock.
>>>>>>>>>>>>>> DefaultImageDisplay.rebuild() line: 140
>>>>>>>>>>>>>>  DefaultImageDisplay.display(Object) line: 273
>>>>>>>>>>>>>> DefaultOverlayService.addOverlays(ImageDisplay,
>>>>>>>>>>>>>> List<Overlay>) line: 148
>>>>>>>>>>>>>>  TurboRegRegister.run() line: 144
>>>>>>>>>>>>>> CommandModule.run() line: 196
>>>>>>>>>>>>>>  ModuleRunner.run() line: 168
>>>>>>>>>>>>>> ModuleRunner.call() line: 129
>>>>>>>>>>>>>>  ModuleRunner.call() line: 1
>>>>>>>>>>>>>> FutureTask$Sync.innerRun() line: 303
>>>>>>>>>>>>>>  FutureTask<V>.run() line: 138
>>>>>>>>>>>>>> ThreadPoolExecutor$Worker.runTask(Runnable) line: 886
>>>>>>>>>>>>>>  ThreadPoolExecutor$Worker.run() line: 908
>>>>>>>>>>>>>> Thread.run() line: 662
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> ImageJ-devel mailing list
>>>>>>>>>>>>>> ImageJ-devel at imagej.net
>>>>>>>>>>>>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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