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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