Open Microscopy Environment

Hi,

We upgraded our database to the 4.4.0 and received no errors. However, when I tried to view some of our "Big" images in the database we received a "not a valid image" error and could not see them. These are files uploaded from an apirio scanner and were .svs files. When imported omero made 4 files of differing sizes. The full sized image ~52000X33000 gives us the not a valid image error. This image is tiled in 4.3.4. The second largest image is 13000X8000 pixels and is tiled in 4.4 but all the tiles are black. The smaller images that are not tiled look just fine. I rolled back our database from a backup into 4.3.4 and the images are fine. Is there something special i have to do to upgrade a database with these large images or is this a bug?


ScottG

It sure sounds like a bug. Have you still got your server log files from after you performed the upgrade?

Hi

I hope this is the relevant bit. But it may only pertain to the non loading image and not the all black image. Let me know what to look for if this isn't it.

Scott
from the Blitz log

2012-07-16 11:16:36,883 INFO [ org.perf4j.TimingLogger] (l.Server-2) start[1342451796854] time[29] tag[omero.call.exception]
2012-07-16 11:16:36,883 INFO [ ome.services.util.ServiceHandler] (l.Server-2) Excp: ome.conditions.ResourceError: Error instantiating pixel buffer: /Volumes/dozer/OMERO402/Pixels/Dir-005/5806_pyramid
2012-07-16 11:16:36,887 INFO [ omero.cmd.SessionI] (l.Server-8) Added servant to adapter: 62c5f2e9-61da-473f-8b39-9e8a47aaea02/a:f:9d:8c:28a6c19d:138904db78b:-7fd1omero.api.RawPixelsStore(omero.api._RawPixelsStoreTie@9336bdbd)
2012-07-16 11:16:36,888 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Meth: interface ome.api.RawPixelsStore.setPixelsId
2012-07-16 11:16:36,888 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Args: [5806, true]
2012-07-16 11:16:36,893 INFO [ ome.security.basic.EventHandler] (l.Server-3) Auth: user=2,group=4,event=null(User),sess=62c5f2e9-61da-473f-8b39-9e8a47aaea02
2012-07-16 11:16:36,895 INFO [ ome.io.nio.FilePathResolver] (l.Server-3) Metadata only file, resulting path: /Volumes/dozer/OMERO402/Files/Dir-014/14730
2012-07-16 11:16:36,895 INFO [ ome.io.nio.PixelsService] (l.Server-3) Using Pyramid BfPixelBuffer: /Volumes/dozer/OMERO402/Pixels/Dir-005/5806_pyramid
2012-07-16 11:16:36,912 INFO [ loci.formats.in.MinimalTiffReader] (l.Server-3) Reading IFDs
2012-07-16 11:16:36,930 INFO [ loci.formats.in.MinimalTiffReader] (l.Server-3) Populating metadata
2012-07-16 11:16:36,933 ERROR [ ome.io.bioformats.BfPixelBuffer] (l.Server-3) Failed to instantiate BfPixelsWrapper with /Volumes/dozer/OMERO402/Pixels/Dir-005/5806_pyramid
2012-07-16 11:16:36,933 ERROR [ ome.io.nio.PixelsService] (l.Server-3) Error instantiating pixel buffer: /Volumes/dozer/OMERO402/Pixels/Dir-005/5806_pyramid
java.lang.RuntimeException: java.lang.IllegalArgumentException: Negative position
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:76)
at ome.io.bioformats.BfPixelBuffer.isLittleEndian(BfPixelBuffer.java:92)
at ome.io.bioformats.BfPyramidPixelBuffer.initializeReader(BfPyramidPixelBuffer.java:192)
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:171)
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:141)
at ome.io.nio.PixelsService.createPyramidPixelBuffer(PixelsService.java:636)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:410)
at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:279)
at sun.reflect.GeneratedMethodAccessor640.invoke(Unknown Source)
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: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 $Proxy89.setPixelsId(Unknown Source)
at sun.reflect.GeneratedMethodAccessor640.invoke(Unknown Source)
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: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 $Proxy89.setPixelsId(Unknown Source)
at sun.reflect.GeneratedMethodAccessor840.invoke(Unknown Source)
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:137)
at ome.services.blitz.impl.RawPixelsStoreI.setPixelsId_async(RawPixelsStoreI.java:193)
at sun.reflect.GeneratedMethodAccessor839.invoke(Unknown Source)
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 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 $Proxy90.setPixelsId_async(Unknown Source)
at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:274)
at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:375)
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1297)
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)
Caused by: java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:133)
at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:129)
at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:430)
at ome.io.bioformats.OmeroPixelsPyramidReader.initFile(OmeroPixelsPyramidReader.java:111)
at loci.formats.FormatReader.setId(FormatReader.java:1105)
at ome.io.bioformats.OmeroPixelsPyramidReader.setId(OmeroPixelsPyramidReader.java:92)
at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:60)
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:68)
... 65 more

Hi,

This may also be useful.

Scott

from the blitz log

2012-07-16 11:16:50,668 INFO [ ome.services.util.ServiceHandler] (l.Server-1) Excp: java.lang.IllegalArgumentException: Negative position
2012-07-16 11:16:50,671 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Meth: interface omeis.providers.re.RenderingEngine.renderCompressed
2012-07-16 11:16:50,671 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Args: [Type: XY, z=0, t=0; Region: x=4352 y=768 width=256 height=256]
2012-07-16 11:16:50,673 INFO [ loci.formats.in.MinimalTiffReader] (l.Server-3) Reading IFDs
2012-07-16 11:16:50,681 INFO [ loci.formats.in.MinimalTiffReader] (l.Server-3) Populating metadata
2012-07-16 11:16:50,693 INFO [ omeis.providers.re.Renderer] (l.Server-3) Using: 'omeis.providers.re.HSBStrategy' rendering strategy.
2012-07-16 11:16:50,694 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1342451810671] time[23] tag[omero.call.exception]
2012-07-16 11:16:50,694 WARN [ ome.services.util.ServiceHandler] (l.Server-3) IllegalArgumentException thrown.

java.lang.IllegalArgumentException: Negative position
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:133)
at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:129)
at loci.formats.tiff.TiffParser.getTile(TiffParser.java:645)
at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:839)
at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:696)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:288)
at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:360)
at ome.io.bioformats.BfPixelBuffer.getTileDirect(BfPixelBuffer.java:462)
at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:450)
at ome.io.bioformats.BfPyramidPixelBuffer.getTile(BfPyramidPixelBuffer.java:992)
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216)
at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105)
at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216)
at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311)
at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275)
at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532)
at sun.reflect.GeneratedMethodAccessor628.invoke(Unknown Source)
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.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 $Proxy98.renderCompressed(Unknown Source)
at sun.reflect.GeneratedMethodAccessor628.invoke(Unknown Source)
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: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 $Proxy98.renderCompressed(Unknown Source)
at sun.reflect.GeneratedMethodAccessor895.invoke(Unknown Source)
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:137)
at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344)
at sun.reflect.GeneratedMethodAccessor894.invoke(Unknown Source)
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 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 $Proxy100.renderCompressed_async(Unknown Source)
at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:302)
at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:576)
at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1688)
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)

more errors in the log


2012-07-16 11:20:09,723 INFO [ ome.io.nio.PixelsService] (l.Server-4) Using Pyramid BfPixelBuffer: /Volumes/dozer/OMERO402/Pixels/Dir-005/5084_pyramid
2012-07-16 11:20:09,872 INFO [ loci.formats.in.MinimalTiffReader] (l.Server-4) Reading IFDs
2012-07-16 11:20:10,668 INFO [ loci.formats.in.MinimalTiffReader] (l.Server-4) Populating metadata
2012-07-16 11:20:10,766 ERROR [ ome.io.bioformats.BfPixelBuffer] (l.Server-4) Failed to instantiate BfPixelsWrapper with /Volumes/dozer/OMERO402/Pixels/Dir-005/5084_pyramid
2012-07-16 11:20:10,766 ERROR [ ome.io.nio.PixelsService] (l.Server-4) Error instantiating pixel buffer: /Volumes/dozer/OMERO402/Pixels/Dir-005/5084_pyramid
java.lang.RuntimeException: java.io.EOFException: Attempting to read beyond end of file.
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:76)
at ome.io.bioformats.BfPixelBuffer.isLittleEndian(BfPixelBuffer.java:92)
at ome.io.bioformats.BfPyramidPixelBuffer.initializeReader(BfPyramidPixelBuffer.java:192)
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:171)
at ome.io.bioformats.BfPyramidPixelBuffer.<init>(BfPyramidPixelBuffer.java:141)
at ome.io.nio.PixelsService.createPyramidPixelBuffer(PixelsService.java:636)
at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:410)
at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:279)
at sun.reflect.GeneratedMethodAccessor640.invoke(Unknown Source)
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: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 $Proxy89.setPixelsId(Unknown Source)
at sun.reflect.GeneratedMethodAccessor640.invoke(Unknown Source)
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: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 $Proxy89.setPixelsId(Unknown Source)
at sun.reflect.GeneratedMethodAccessor840.invoke(Unknown Source)
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:137)
at ome.services.blitz.impl.RawPixelsStoreI.setPixelsId_async(RawPixelsStoreI.java:193)
at sun.reflect.GeneratedMethodAccessor839.invoke(Unknown Source)
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 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 $Proxy90.setPixelsId_async(Unknown Source)
at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:274)
at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:375)
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1297)
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)
Caused by: java.io.EOFException: Attempting to read beyond end of file.
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:331)
at loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:362)
at loci.formats.in.JPEG2000MetadataParser.parseBoxes(JPEG2000MetadataParser.java:164)
at loci.formats.in.JPEG2000MetadataParser.<init>(JPEG2000MetadataParser.java:139)
at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:431)
at ome.io.bioformats.OmeroPixelsPyramidReader.initFile(OmeroPixelsPyramidReader.java:111)
at loci.formats.FormatReader.setId(FormatReader.java:1105)
at ome.io.bioformats.OmeroPixelsPyramidReader.setId(OmeroPixelsPyramidReader.java:92)
at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:60)
at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:68)
... 65 more
Caused by: java.nio.BufferUnderflowException
at java.nio.Buffer.nextGetIndex(Buffer.java:478)
at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:336)
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:329)
... 74 more
2012-07-16 11:20:10,768 INFO [ org.perf4j.TimingLogger] (l.Server-4) start[1342452009693] time[1075] tag[omero.call.exception]
2012-07-16 11:20:10,768 INFO [ ome.services.util.ServiceHandler] (l.Server-4) Excp: ome.conditions.ResourceError: Error instantiating pixel buffer: /Volumes/dozer/OMERO402/Pixels/Dir-005/5084_pyramid

While the exceptions are useful I really need to see the whole log to try and find out what's happening. Can you ZIP it up and attach it here or put it up somewhere where the team can grab it?

Hi,

Ok thanks for looking into this. I have attached the Log folder.

Scott

Please note that we now have a ticket and a proposed fix for this problem:

https://trac.openmicroscopy.org.uk/ome/ticket/9372

We're in the process of verifying the fix now, and will post an update once we're sure that it really works.

Thanks everyone,

4.4.1 fixed our issue. We upgraded with no problems today.

Thanks again,
Scott