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Task #9624 (closed)

Opened 12 years ago

Closed 9 years ago

Bug: UBM Index out of bounds during import

Reported by: rleigh Owned by: jburel
Priority: critical Milestone: 5.x
Component: Insight Version: 4.4.8
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

While the import succeeds, the following error is logged:

org.openmicroscopy.shoola.env.data.DSOutOfServiceException: Thumbnail service null for pixelsID: 3424
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getThumbnailByLongestSide(OMEROGateway.java:3282)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.createImportedImage(OmeroImageServiceImpl.java:283)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:207)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1398)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:679)
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.ArrayIndexOutOfBoundsException):
                        null
                        "
    serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.ArrayIndexOutOfBoundsException):
               null"
	at sun.reflect.GeneratedConstructorAccessor17.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
	at java.lang.Class.newInstance0(Class.java:372)
	at java.lang.Class.newInstance(Class.java:325)
	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._ThumbnailStoreDelM.getThumbnailByLongestSide(_ThumbnailStoreDelM.java:441)
	at omero.api.ThumbnailStorePrxHelper.getThumbnailByLongestSide(ThumbnailStorePrxHelper.java:666)
	at omero.api.ThumbnailStorePrxHelper.getThumbnailByLongestSide(ThumbnailStorePrxHelper.java:638)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getThumbnailByLongestSide(OMEROGateway.java:3276)
	... 13 more

After import, no thumbnail is shown, and the image can't be viewed (invalid image error).

Change History (10)

comment:1 Changed 12 years ago by rleigh

  • Milestone changed from OMERO-4.4.4 to OMERO-4.5

comment:2 Changed 12 years ago by jmoore

  • Summary changed from UBM: Index out of bounds during import to Bug: Index out of bounds during import

I don't know what "UBM" means, so I'm switching this to BUG.

comment:3 Changed 12 years ago by jburel

  • Summary changed from Bug: Index out of bounds during import to Bug: UBM Index out of bounds during import

comment:4 Changed 11 years ago by rleigh

  • Keywords FS added

Still present on current develop for 4.5. Given that the image is uint32, and won't view in Insight, does this also affect thumbnail generation?

comment:5 Changed 11 years ago by rleigh

Does it want to do something a bit more intelligent with the LUT for such a wide colourspace? Like quantise the values to fit in 16 bits and/or autoscale the range?

Current stacktrace:

java.lang.ArrayIndexOutOfBoundsException: 65536
        at omeis.providers.re.quantum.Quantization_8_16_bit.buildLUT(Quantization_8_16_bit.java:272)
        at omeis.providers.re.quantum.Quantization_8_16_bit.onWindowChange(Quantization_8_16_bit.java:283)
        at omeis.providers.re.quantum.QuantumStrategy.setWindow(QuantumStrategy.java:323)
        at omeis.providers.re.QuantumManager.initStrategies(QuantumManager.java:118)
        at omeis.providers.re.Renderer.<init>(Renderer.java:352)
        at ome.services.ThumbnailBean.load(ThumbnailBean.java:344)
        at ome.services.ThumbnailBean.errorIfInvalidState(ThumbnailBean.java:695)
        at ome.services.ThumbnailBean.createScaledImage(ThumbnailBean.java:565)
        at ome.services.ThumbnailBean._createThumbnail(ThumbnailBean.java:814)
        at ome.services.ThumbnailBean.retrieveThumbnail(ThumbnailBean.java:1051)
        at ome.services.ThumbnailBean.retrieveThumbnailAndUpdateMetadata(ThumbnailBean.java:1006)
        at ome.services.ThumbnailBean.getThumbnailByLongestSide(ThumbnailBean.java:1086)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:592)
        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.EventHandler.invoke(EventHandler.java:154)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
        at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        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 $Proxy85.getThumbnailByLongestSide(Unknown Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:592)
        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:98)
        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 $Proxy85.getThumbnailByLongestSide(Unknown Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:592)
        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:150)
        at ome.services.blitz.impl.ThumbnailStoreI.getThumbnailByLongestSide_async(ThumbnailStoreI.java:94)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:592)
        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 omero.cmd.CallContext.invoke(CallContext.java:59)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
        at $Proxy86.getThumbnailByLongestSide_async(Unknown Source)
        at omero.api._ThumbnailStoreTie.getThumbnailByLongestSide_async(_ThumbnailStoreTie.java:127)
        at omero.api._ThumbnailStoreDisp.___getThumbnailByLongestSide(_ThumbnailStoreDisp.java:383)
        at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:672)
        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)

comment:6 Changed 11 years ago by sylittlewood

This is still occurring in b117 from 2013-01-16. No thumbnails and no image viewer. Web shows index out of bound exception. Insight log below

2013-01-16 17:11:58,570 ERROR [py.shoola.env.data.OmeroImageServiceImpl] ( Thread-59) Thumbnail service null for pixelsID: [1347]
2013-01-16 17:12:00,703 ERROR [a.agents.metadata.RenderingControlLoader] (entQueue-0) Data Retrieval Failure: java.lang.NullPointerException: No rendering engine.
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.<init>(RenderingControlProxy.java:783)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.makeNew(PixelsServicesFactory.java:656)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.createRenderingControl(PixelsServicesFactory.java:252)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.loadRenderingControl(OmeroImageServiceImpl.java:592)
	at org.openmicroscopy.shoola.env.data.views.calls.RenderingControlLoader$1.doCall(RenderingControlLoader.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Data Retrieval Failure: java.lang.NullPointerException: No rendering engine.
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.<init>(RenderingControlProxy.java:783)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.makeNew(PixelsServicesFactory.java:656)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.createRenderingControl(PixelsServicesFactory.java:252)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.loadRenderingControl(OmeroImageServiceImpl.java:592)
	at org.openmicroscopy.shoola.env.data.views.calls.RenderingControlLoader$1.doCall(RenderingControlLoader.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Exception in thread "AWT-EventQueue-0"

2013-01-16 17:12:04,598 ERROR [a.agents.metadata.RenderingControlLoader] (entQueue-0) Data Retrieval Failure: java.lang.NullPointerException: No rendering engine.
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.<init>(RenderingControlProxy.java:783)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.makeNew(PixelsServicesFactory.java:656)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.createRenderingControl(PixelsServicesFactory.java:252)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.loadRenderingControl(OmeroImageServiceImpl.java:592)
	at org.openmicroscopy.shoola.env.data.views.calls.RenderingControlLoader$1.doCall(RenderingControlLoader.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Data Retrieval Failure: java.lang.NullPointerException: No rendering engine.
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.<init>(RenderingControlProxy.java:783)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.makeNew(PixelsServicesFactory.java:656)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.createRenderingControl(PixelsServicesFactory.java:252)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.loadRenderingControl(OmeroImageServiceImpl.java:592)
	at org.openmicroscopy.shoola.env.data.views.calls.RenderingControlLoader$1.doCall(RenderingControlLoader.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Exception in thread "AWT-EventQueue-0"

comment:7 Changed 11 years ago by rleigh

Import no longer leads to exceptions being thrown, and succeeds. However, the thumbnail is black and the image is not viewable (it's uint32).

comment:8 Changed 11 years ago by mlinkert

  • Keywords FS removed

This is a 32-bit rendering issue, not an FS problem.

comment:9 Changed 11 years ago by jburel

  • Milestone changed from OMERO-4.4.9 to OMERO-4.4.x
  • Version set to 4.4.8

adding support for 32bit images and for float images is outside the scope of 4.4.9. Pushing to 4.4.x

Last edited 11 years ago by jburel (previous) (diff)

comment:10 Changed 9 years ago by mlinkert

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

The file (sxm/steve/UBM*/SG2.PR3) imports, creates thumbnails and displays correctly in the full viewer without throwing an exception now that 32-bit rendering is supported.

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