[ome-users] Error instantiating pixel buffer
Mark Woodbridge
m.woodbridge at imperial.ac.uk
Fri Mar 14 12:20:11 GMT 2014
Hi,
We've uploaded a ~30GB czi file to OMERO 5, which seemed to complete
successfully (file sizes match), but it can't be viewed in Insight.
There is a corresponding exception in the server logs which I've
attached. The 63624_pyramid file referenced is empty.
Does anyone have any suggestions regarding the cause? We'd be really
grateful for any help.
Thanks,
Mark.
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2014-03-13 14:17:07,636 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1394720227631] time[4] tag[omero.bulkLoadMetadata]
2014-03-13 14:17:07,636 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1394720227631] time[5] tag[omero.loadMetadataByDimensionPool]
2014-03-13 14:17:07,636 INFO [ ome.services.ThumbnailCtx] (l.Server-7) New thumbnail object set size: 0
2014-03-13 14:17:07,636 INFO [ ome.services.ThumbnailCtx] (l.Server-7) Dimension pool size: 0
2014-03-13 14:17:07,636 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1394720227636] time[0] tag[omero.createMissingThumbnailMetadata]
2014-03-13 14:17:07,640 INFO [ ome.io.nio.FilePathResolver] (l.Server-1) Metadata only file, resulting path: /data/omero/ManagedRepository/mspitale_3/2014-03/04/17-22-32.236/130510 HCF1 Image6.czi
2014-03-13 14:17:07,642 INFO [ ome.security.basic.EventHandler] (l.Server-3) Auth: user=3,group=104,event=5623581(User),sess=9881be1c-9044-4aa7-97f6-3e50ee6fb829
2014-03-13 14:17:07,708 INFO [ org.perf4j.TimingLogger] (l.Server-7) start[1394720227607] time[101] tag[omero.call.success.ome.services.ThumbnailBean.getThumbnail]
2014-03-13 14:17:07,708 INFO [ ome.services.util.ServiceHandler] (l.Server-7) Rslt: [-1, -40, -1, ... 1 more]
2014-03-13 14:17:07,709 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1394720227643] time[66] tag[omero.bulkLoadMetadata]
2014-03-13 14:17:07,709 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1394720227643] time[66] tag[omero.loadMetadataByDimensionPool]
2014-03-13 14:17:07,710 INFO [ ome.services.ThumbnailCtx] (l.Server-3) New thumbnail object set size: 0
2014-03-13 14:17:07,710 INFO [ ome.services.ThumbnailCtx] (l.Server-3) Dimension pool size: 0
2014-03-13 14:17:07,710 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1394720227710] time[0] tag[omero.createMissingThumbnailMetadata]
2014-03-13 14:17:07,719 INFO [ ome.io.nio.PixelsService] (l.Server-1) Using Pyramid BfPixelBuffer: /data/omero/Pixels/Dir-063/63624_pyramid
2014-03-13 14:17:07,725 ERROR [ ome.io.nio.PixelsService] (l.Server-1) Error instantiating pixel buffer: /data/omero/Pixels/Dir-063/63624_pyramid
ome.conditions.ResourceError: FormatException: /data/omero/Pixels/Dir-063/63624_pyramid
Invalid TIFF file
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:78) ~[romio.jar:na]
at ome.io.bioformats.BfPixelBuffer.isLittleEndian(BfPixelBuffer.java:98) ~[romio.jar:na]
at ome.io.bioformats.BfPyramidPixelBuffer.initializeReader(BfPyramidPixelBuffer.java:212) ~[romio.jar:na]
at ome.io.bioformats.BfPyramidPixelBuffer.init(BfPyramidPixelBuffer.java:187) ~[romio.jar:na]
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:171) ~[romio.jar:na]
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:160) ~[romio.jar:na]
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:143) ~[romio.jar:na]
at ome.io.nio.PixelsService.createPyramidPixelBuffer(PixelsService.java:806) [romio.jar:na]
at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:527) [romio.jar:na]
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:468) [romio.jar:na]
at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) [server.jar:na]
at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:1324) [server.jar:na]
at ome.services.ThumbnailBean._resetDefaults(ThumbnailBean.java:1288) [server.jar:na]
at ome.services.ThumbnailBean.resetDefaults(ThumbnailBean.java:1258) [server.jar:na]
at sun.reflect.GeneratedMethodAccessor1066.invoke(Unknown Source) ~[na:na]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.security.basic.EventHandler.invoke(EventHandler.java:154) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:218) [server.jar:na]
at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) [org.springframework.transaction.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at com.sun.proxy.$Proxy97.resetDefaults(Unknown Source) [na:na]
at sun.reflect.GeneratedMethodAccessor1066.invoke(Unknown Source) ~[na:na]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at com.sun.proxy.$Proxy97.resetDefaults(Unknown Source) [na:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) [blitz.jar:na]
at ome.services.throttling.Callback.run(Callback.java:56) [blitz.jar:na]
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) [blitz.jar:na]
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149) [blitz.jar:na]
at ome.services.blitz.impl.ThumbnailStoreI.resetDefaults_async(ThumbnailStoreI.java:136) [blitz.jar:na]
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at omero.cmd.CallContext.invoke(CallContext.java:78) [blitz.jar:na]
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
at com.sun.proxy.$Proxy98.resetDefaults_async(Unknown Source) [na:na]
at omero.api._ThumbnailStoreTie.resetDefaults_async(_ThumbnailStoreTie.java:183) [blitz.jar:na]
at omero.api._ThumbnailStoreDisp.___resetDefaults(_ThumbnailStoreDisp.java:589) [blitz.jar:na]
at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:724) [blitz.jar:na]
at IceInternal.Incoming.invoke(Incoming.java:159) [ice.jar:na]
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) [ice.jar:na]
at Ice.ConnectionI.message(ConnectionI.java:972) [ice.jar:na]
at IceInternal.ThreadPool.run(ThreadPool.java:577) [ice.jar:na]
at IceInternal.ThreadPool.access$100(ThreadPool.java:12) [ice.jar:na]
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) [ice.jar:na]
2014-03-13 14:17:07,729 INFO [ org.perf4j.TimingLogger] (l.Server-1) start[1394720227595] time[134] tag[omero.call.exception]
2014-03-13 14:17:07,729 INFO [ ome.services.util.ServiceHandler] (l.Server-1) Excp: ome.conditions.ResourceError: Error instantiating pixel buffer: /data/omero/Pixels/Dir-063/63624_pyramid
2014-03-13 14:17:07,736 INFO [ org.perf4j.TimingLogger] (l.Server-9) start[1394720227553] time[182] tag[omero.call.success.ome.services.ThumbnailBean.getThumbnail]
2014-03-13 14:17:07,736 INFO [ ome.services.util.ServiceHandler] (l.Server-9) Rslt: [-1, -40, -1, ... 1 more]
2014-03-13 14:17:07,805 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1394720227612] time[192] tag[omero.call.success.ome.services.ThumbnailBean.getThumbnail]
2014-03-13 14:17:07,805 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Rslt: [-1, -40, -1, ... 1 more]
2014-03-13 14:17:07,826 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Meth: interface ome.api.StatefulServiceInterface.close
2014-03-13 14:17:07,826 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Args: ()
2014-03-13 14:17:07,829 INFO [ ome.security.basic.EventHandler] (l.Server-2) Auth: user=3,group=104,event=null(User),sess=9881be1c-9044-4aa7-97f6-3e50ee6fb829
2014-03-13 14:17:07,830 INFO [ org.perf4j.TimingLogger] (l.Server-2) start[1394720227826] time[4] tag[omero.call.success.ome.services.ThumbnailBean.close]
2014-03-13 14:17:07,830 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Rslt: null
2014-03-13 14:17:07,831 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Cleanup: ome.services.ThumbnailBean at 2c217f8c
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