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 <l...@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 <bdezo...@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 >> <l...@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 <bdezo...@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 <l...@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 <bdezo...@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 < >>>>>> l...@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 >>>>>>> <bdezo...@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 >>>>>>>> <bdezo...@gmail.com>wrote: >>>>>>>> >>>>>>>>> Merged >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Sep 30, 2013 at 2:34 PM, Lee Kamentsky < >>>>>>>>> l...@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 < >>>>>>>>>> bdezo...@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 < >>>>>>>>>>> l...@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 < >>>>>>>>>>>> bdezo...@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 < >>>>>>>>>>>>> l...@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@imagej.net >>>>>>>>>>>>>> http://imagej.net/mailman/listinfo/imagej-devel >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
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