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Task #12583 (new)

Opened 10 years ago

Last modified 10 years ago

Bug: TIFF StripByteCounts value parsed incorrectly — at Version 1

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: Unscheduled
Component: Bio-Formats Version: 5.0.5
Keywords: TiffReader Cc: yohan.jarosz@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by jamoore)

https://www.openmicroscopy.org/qa2/qa/feedback/9563/

Exception occurs while importing this file due to the StripByteCounts? tag being parsed incorrectly. The byte count for a strip should be 32640 (see output of tiffdump), but it's currently reported as -312550. Likely the tag type is not being respected.


java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {message=, stacktrace=java.lang.NegativeArraySizeException
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:688)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:923)
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:745)
	at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:288)
	at loci.formats.DelegateReader.openBytes(DelegateReader.java:205)
	at loci.formats.ImageReader.openBytes(ImageReader.java:431)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:193)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:185)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:193)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:325)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:325)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
	at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:730)
	at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:661)
	at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:531)
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:381)
	at omero.cmd.HandleI.steps(HandleI.java:436)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:361)
	at sun.reflect.GeneratedMethodAccessor277.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$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 com.sun.proxy.$Proxy69.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:457)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at ome.services.util.Executor$Impl$1.call(Executor.java:498)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
}

	at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:627)
	at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:301)
	at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
	at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
	at IceInternal.Incoming.invoke(Incoming.java:222)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
	at Ice.ConnectionI.message(ConnectionI.java:1213)
	at IceInternal.ThreadPool.run(ThreadPool.java:321)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:695)

Change History (1)

comment:1 Changed 10 years ago by jamoore

  • Component changed from from QA to Bio-Formats
  • Description modified (diff)
  • Keywords TiffReader added
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