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Task #9624 (closed)

Opened 7 years ago

Closed 4 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 7 years ago by rleigh

  • Milestone changed from OMERO-4.4.4 to OMERO-4.5

comment:2 Changed 7 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 7 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 7 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 7 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 7 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 7 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 7 years ago by mlinkert

  • Keywords FS removed

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

comment:9 Changed 6 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 6 years ago by jburel (previous) (diff)

comment:10 Changed 4 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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