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Task #6604 (closed)

Opened 13 years ago

Closed 13 years ago

Bug: li-flim import via Insight and Importer

Reported by: cblackburn Owned by:
Priority: minor Milestone: Unscheduled
Component: Import Version: n.a.
Keywords: n.a. Cc: jburel, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by cblackburn)

Both imports, lifetime-simple.fli and lifetime-extended.fli succeeded but the latter image shows a black thumbnail and gives and "Image is not a valid image" error on trying to view.

I have attached a screenshot for someone to check that lifetime-simple.fli is what's expected as it a small image or apparently random pixels.

(Same outcome in both Insight and Importer)

Attachments (1)

li-flim-import.jpg​ (22.5 KB) - added by cblackburn 13 years ago.

Download all attachments as: .zip

Change History (4)

Changed 13 years ago by cblackburn

comment:1 Changed 13 years ago by cblackburn

Importing to a local Ubuntu server (same build as gretzky) produced an error for lifetime-extended.fli.

org.openmicroscopy.shoola.env.data.DSOutOfServiceException: Thumbnail service null for pixelsID: 971
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getThumbnailByLongestSide(OMEROGateway.java:3183)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.createImportedImage(OmeroImageServiceImpl.java:254)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:181)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1326)
	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$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.ArrayIndexOutOfBoundsException):
                        65536
                        	at omeis.providers.re.quantum.Quantization_8_16_bit.buildLUT(Quantization_8_16_bit.java:255)
                        	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:116)
                        	at omeis.providers.re.Renderer.<init>(Renderer.java:352)
                        	at ome.services.ThumbnailBean.load(ThumbnailBean.java:333)
                        	at ome.services.ThumbnailBean.errorIfInvalidState(ThumbnailBean.java:699)
                        	at ome.services.ThumbnailBean.createScaledImage(ThumbnailBean.java:569)
                        	at ome.services.ThumbnailBean._createThumbnail(ThumbnailBean.java:818)
                        	at ome.services.ThumbnailBean.retrieveThumbnail(ThumbnailBean.java:1055)
                        	at ome.services.ThumbnailBean.retrieveThumbnailAndUpdateMetadata(ThumbnailBean.java:1010)
                        	at ome.services.ThumbnailBean.getThumbnailByLongestSide(ThumbnailBean.java:1090)
                        	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: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.EventHandler.invoke(EventHandler.java:150)
                        	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:231)
                        	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 $Proxy78.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: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 $Proxy78.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: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.ThumbnailStoreI.getThumbnailByLongestSide_async(ThumbnailStoreI.java:93)
                        	at omero.api._ThumbnailStoreTie.getThumbnailByLongestSide_async(_ThumbnailStoreTie.java:127)
                        	at omero.api._ThumbnailStoreDisp.___getThumbnailByLongestSide(_ThumbnailStoreDisp.java:359)
                        	at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:647)
                        	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.ArrayIndexOutOfBoundsException):
               65536"
	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._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:3171)
	... 13 more

comment:2 Changed 13 years ago by cblackburn

  • Description modified (diff)
  • Summary changed from Bug: li-flim import via Insight to Bug: li-flim import via Insight and Importer

comment:3 Changed 13 years ago by jburel

  • Milestone changed from OMERO-Beta4.3.2 to Unscheduled
  • Resolution set to duplicate
  • Sprint 2011-09-01 (4) deleted
  • Status changed from new to closed

This is a rendering engine limitation. see ​http://trac.openmicroscopy.org.uk/ome/ticket/3187

Last edited 13 years ago by jburel (previous) (diff)
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