Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #6621 (closed)

Opened 13 years ago

Closed 13 years ago

Last modified 13 years ago

BUG: Trestle Images not displaying fully

Reported by: sylittlewood Owned by: mlinkert
Priority: major Milestone: OMERO-Beta4.3.2
Component: General Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2011-09-15 (5)

Description (last modified by mlinkert)

IN testing Trestle Image import the images are reported as being imported successfully but after processing has occurred on the server the images do not render properly.

This has been verified by running the import test for these images twice.

The images failing are as below with the following error in insight logs.

/Volumes/ome/data_repo/test_images_good/trestle/openslide

CMU-2.tif [Series 1]
CMU-3.tif [Series 1]

Series 2-8 of these images work okay.
Judging by the composition of CMU-1 images after import I believe that these are the highest resolution images of the series.

Change History (5)

comment:1 Changed 13 years ago by sylittlewood

  • Summary changed from BUG: Trestle Images nto displaying fully to BUG: Trestle Images not displaying fully

comment:2 Changed 13 years ago by mlinkert

  • Description modified (diff)

Just moving the stack trace so that the ticket can be viewed in Firefox:

java.lang.Exception: org.openmicroscopy.shoola.env.rnd.RenderingServiceException: RenderImage
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.renderImage(OmeroImageServiceImpl.java:466)
	at org.openmicroscopy.shoola.env.data.views.calls.ImageRenderer$1.doCall(ImageRenderer.java:83)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: org.openmicroscopy.shoola.env.rnd.RenderingServiceException: An error occurred while trying to set the cannot render the plane.

omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NegativeArraySizeException):
                        null
                        	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:69)
                        	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:188)
                        	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:274)
                        	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
                        	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
                        	at sun.reflect.GeneratedMethodAccessor1039.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy86.renderAsPackedInt(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor1039.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy86.renderAsPackedInt(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor1040.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                        	at ome.services.throttling.Callback.run(Callback.java:56)
                        	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                        	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
                        	at ome.services.blitz.impl.RenderingEngineI.renderAsPackedInt_async(RenderingEngineI.java:332)
                        	at omero.api._RenderingEngineTie.renderAsPackedInt_async(_RenderingEngineTie.java:288)
                        	at omero.api._RenderingEngineDisp.___renderAsPackedInt(_RenderingEngineDisp.java:502)
                        	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1680)
                        	at IceInternal.Incoming.invoke(Incoming.java:159)
                        	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                        	at Ice.ConnectionI.message(ConnectionI.java:972)
                        	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                        	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                        	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "
    serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.NegativeArraySizeException):
               null"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._RenderingEngineDelM.renderAsPackedInt(_RenderingEngineDelM.java:1582)
	at omero.api.RenderingEnginePrxHelper.renderAsPackedInt(RenderingEnginePrxHelper.java:2230)
	at omero.api.RenderingEnginePrxHelper.renderAsPackedInt(RenderingEnginePrxHelper.java:2202)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.renderUncompressed(RenderingControlProxy.java:545)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1547)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1531)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.render(PixelsServicesFactory.java:483)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.renderImage(OmeroImageServiceImpl.java:445)
	at org.openmicroscopy.shoola.env.data.views.calls.ImageRenderer$1.doCall(ImageRenderer.java:83)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.handleException(RenderingControlProxy.java:222)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.renderUncompressed(RenderingControlProxy.java:552)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1547)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1531)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.render(PixelsServicesFactory.java:483)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.renderImage(OmeroImageServiceImpl.java:445)
	... 8 more
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NegativeArraySizeException):
                        null
                        	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:69)
                        	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:188)
                        	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:274)
                        	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
                        	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
                        	at sun.reflect.GeneratedMethodAccessor1039.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy86.renderAsPackedInt(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor1039.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:83)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy86.renderAsPackedInt(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor1040.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                        	at ome.services.throttling.Callback.run(Callback.java:56)
                        	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                        	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:136)
                        	at ome.services.blitz.impl.RenderingEngineI.renderAsPackedInt_async(RenderingEngineI.java:332)
                        	at omero.api._RenderingEngineTie.renderAsPackedInt_async(_RenderingEngineTie.java:288)
                        	at omero.api._RenderingEngineDisp.___renderAsPackedInt(_RenderingEngineDisp.java:502)
                        	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1680)
                        	at IceInternal.Incoming.invoke(Incoming.java:159)
                        	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                        	at Ice.ConnectionI.message(ConnectionI.java:972)
                        	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                        	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                        	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "
    serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.NegativeArraySizeException):
               null"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:355)
	at java.lang.Class.newInstance(Class.java:308)
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
	at IceInternal.BasicStream.throwException(BasicStream.java:1632)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
	at omero.api._RenderingEngineDelM.renderAsPackedInt(_RenderingEngineDelM.java:1582)
	at omero.api.RenderingEnginePrxHelper.renderAsPackedInt(RenderingEnginePrxHelper.java:2230)
	at omero.api.RenderingEnginePrxHelper.renderAsPackedInt(RenderingEnginePrxHelper.java:2202)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.renderUncompressed(RenderingControlProxy.java:545)
	... 12 more

	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:183)
	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:272)
	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:242)
	at org.openmicroscopy.shoola.agents.imviewer.DataLoader.handleException(DataLoader.java:158)
	at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
	at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
	at java.awt.EventQueue.access$000(EventQueue.java:85)
	at java.awt.EventQueue$1.run(EventQueue.java:638)
	at java.awt.EventQueue$1.run(EventQueue.java:636)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)
	at java.awt.Dialog$1.run(Dialog.java:1046)
	at java.awt.Dialog$3.run(Dialog.java:1098)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.Dialog.show(Dialog.java:1096)
	at java.awt.Component.show(Component.java:1584)
	at java.awt.Component.setVisible(Component.java:1536)
	at java.awt.Window.setVisible(Window.java:842)
	at java.awt.Dialog.setVisible(Dialog.java:986)
	at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:561)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerControl.stateChanged(ImViewerControl.java:895)
	at org.openmicroscopy.shoola.util.ui.component.AbstractComponent.fireStateChange(AbstractComponent.java:103)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.renderXYPlane(ImViewerComponent.java:1081)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.onRndLoaded(ImViewerComponent.java:2837)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerControl.propertyChange(ImViewerControl.java:968)
	at org.openmicroscopy.shoola.util.ui.component.AbstractComponent.firePropertyChange(AbstractComponent.java:147)
	at org.openmicroscopy.shoola.agents.metadata.view.MetadataViewerComponent.onRndLoaded(MetadataViewerComponent.java:846)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorModel.onRndLoaded(EditorModel.java:2243)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorComponent.setRenderingControl(EditorComponent.java:602)
	at org.openmicroscopy.shoola.agents.metadata.RenderingControlLoader.handleResult(RenderingControlLoader.java:163)
	at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
	at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
	at java.awt.EventQueue.access$000(EventQueue.java:85)
	at java.awt.EventQueue$1.run(EventQueue.java:638)
	at java.awt.EventQueue$1.run(EventQueue.java:636)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

comment:3 Changed 13 years ago by mlinkert

  • Sprint set to 2011-09-15 (5)

comment:4 Changed 13 years ago by mlinkert

  • Resolution set to duplicate
  • Status changed from new to closed

This is the same problem reported in #6500 with SVS files. The pyramids for these very large images end up being > 4 GB, so pyramid generation (and thus rendering) fails because BigTIFF usage is not turned on in the server.

comment:5 Changed 13 years ago by Chris Allan <callan@…>

(In [a0b7ee35ebf0b361fceb264fa8a8be527db9a818/ome.git] on branch develop) Removing Trestle and CellSens? from FS Lite. (See #6621 and #6631)

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.118687 sec.)

We're Hiring!