Task #9372 (closed)
Bug: big image fails with 'Negative size'
| Reported by: | jamoore | Owned by: | rleigh |
|---|---|---|---|
| Priority: | blocker | Milestone: | OMERO-4.4.1 |
| Component: | Bio-Formats | Version: | n.a. |
| Keywords: | n.a. | Cc: | mlinkert, cxallan, cneves, rleigh |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
or "read beyond end of file". One simple example is:
Caused by: java.io.EOFException: Attempting to read beyond end of file. at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:331) ... 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
from forum thread: https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=1256
Change History (11)
comment:1 Changed 7 years ago by jmoore
comment:2 Changed 7 years ago by cneves
This issue is easily reproduced by merging https://github.com/cneves/openmicroscopy/tree/postdecorators/7202_unittest_review on top of develop and running the omeropy unittest:
python setup.py test -s test.gatewaytest.image.ImageTest.testThumbnail
comment:3 Changed 7 years ago by rleigh
Definitely occuring during pyramid generation in the minimal tiff reader (for me):
2012-07-18 11:53:06,211 INFO [ loci.formats.in.MinimalTiffReader] (2-thread-1) Reading IFDs 2012-07-18 11:53:06,216 INFO [ loci.formats.in.MinimalTiffReader] (2-thread-1) Populating metadata 2012-07-18 11:53:06,219 ERROR [ ome.io.nio.PixelsService] (2-thread-1) Error closing pixel pyramid. 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 loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:518) at loci.formats.FormatReader.setId(FormatReader.java:1105) at ome.io.bioformats.OmeroPixelsPyramidWriter.postProcess(OmeroPixelsPyramidWriter.java:85) at ome.io.bioformats.OmeroPixelsPyramidWriter.close(OmeroPixelsPyramidWriter.java:52) at ome.io.bioformats.BfPyramidPixelBuffer.closeWriter(BfPyramidPixelBuffer.java:415) at ome.io.bioformats.BfPyramidPixelBuffer.close(BfPyramidPixelBuffer.java:650) at ome.io.nio.PixelsService.makePyramid(PixelsService.java:210) at ome.services.pixeldata.PixelDataHandler.process(PixelDataHandler.java:137) at ome.services.pixeldata.PixelDataHandler.doWork(PixelDataHandler.java:88) at sun.reflect.GeneratedMethodAccessor100.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.Executor$Impl$Interceptor.invoke(Executor.java:508) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.security.basic.NullEventHandler.invoke(NullEventHandler.java:39) 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 $Proxy66.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:406) at ome.services.util.Executor$Impl.execute(Executor.java:350) at ome.services.pixeldata.PixelDataThread$1.call(PixelDataThread.java:146) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) Caused by: java.nio.BufferUnderflowException at java.nio.Buffer.nextGetIndex(Buffer.java:480) at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:336) at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:329) ... 44 more 2012-07-18 11:53:06,222 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Added StatsInfo:9550 for ome.model.core.Channel:Id_9579 - C:0 Max:255.0 Min:0.0 2012-07-18 11:53:06,222 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Added StatsInfo:9551 for ome.model.core.Channel:Id_9580 - C:1 Max:255.0 Min:0.0 2012-07-18 11:53:06,223 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Added StatsInfo:9552 for ome.model.core.Channel:Id_9581 - C:2 Max:255.0 Min:0.0 2012-07-18 11:53:06,223 INFO [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) HANDLED EventLog:482795(entityId=6633) [342205 ms.] 2012-07-18 11:53:06,244 ERROR [ ome.services.util.ServiceHandler] (2-thread-1) Method interface ome.services.util.Executor$Work.doWork invocation took 342230
comment:4 Changed 7 years ago by rleigh
2012-07-18 11:07:53,161 ERROR [ ome.services.pixeldata.PixelDataHandler] (2-thread-1) Failed to handle pixels 6645 java.lang.IllegalArgumentException: Negative position at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:610) at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:133) at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118) at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532) at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254) at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:129) at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:430) at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:518) at loci.formats.FormatReader.setId(FormatReader.java:1105) at ome.io.bioformats.OmeroPixelsPyramidWriter.postProcess(OmeroPixelsPyramidWriter.java:85) at ome.io.bioformats.OmeroPixelsPyramidWriter.close(OmeroPixelsPyramidWriter.java:52) at ome.io.bioformats.BfPyramidPixelBuffer.closeWriter(BfPyramidPixelBuffer.java:415) at ome.io.bioformats.BfPyramidPixelBuffer.close(BfPyramidPixelBuffer.java:650) at ome.io.nio.PixelsService.makePyramid(PixelsService.java:210) at ome.services.pixeldata.PixelDataHandler.process(PixelDataHandler.java:137) at ome.services.pixeldata.PixelDataHandler.doWork(PixelDataHandler.java:88) at sun.reflect.GeneratedMethodAccessor100.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:508) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.security.basic.NullEventHandler.invoke(NullEventHandler.java:39) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.tools.hibernate.ProxyCleanupFilter$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 $Proxy66.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:406) at ome.services.util.Executor$Impl.execute(Executor.java:350) at ome.services.pixeldata.PixelDataThread$1.call(PixelDataThread.java:146) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) at java.util.concurrent.FutureTask.run(FutureTask.java:138) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:619) 2012-07-18 11:07:53,172 ERROR [ ome.services.util.ServiceHandler] (2-thread-1) Method interface ome.services.util.Executor$Work.doWork invocation took 1590321
comment:5 Changed 7 years ago by jmoore
My best guess is that this is a result of the int_vs_long_srv branch:
commit 99864f17cc312c59cbd35f3e62105198078711bb
Merge: 53a32a5 379605e
Author: Chris Allan <callan@blackcat.ca>
Date: Fri Jun 22 13:23:00 2012
Merge remote-tracking branch 'origin/develop' into int_vs_long_srv
Conflicts:
components/insight/LIB/ome-io.jar
components/romio/ivy.xml
components/server/src/ome/services/RawPixelsBean.java
etc/omero.properties
lib/repository/ome-io-17db504.jar
lib/repository/ome-io-362b9a2.jar
lib/repository/poi-loci-362b9a2.jar
comment:6 Changed 7 years ago by rleigh
Reverting 99864f17cc312c59cbd35f3e62105198078711bb (git revert -m 2), imports still fail as above.
comment:7 Changed 7 years ago by mlinkert
comment:8 Changed 7 years ago by rleigh
All imports and pyramid generation using test_images_good/svs appear to work just fine. All the big images are viewable at all zoom levels. There's a single exception in test_images_good/svs/alexandra/UMD001_ORO.svs. One of the series imports as:
UMD001_ORO.svs [UMD001_ORO.svs]
Rather than [Series n]. The PixelData?-0 log shows:
2012-07-19 13:04:04,051 INFO [ ome.io.nio.FilePathResolver] (2-thread-1) Metadata only file, resulting path: /OMERO/Files/Dir-005/5465
which I think corresponds to this image. I'm not sure if it's a related issue, or a bug in the SVS reader. In insight, it claims to be 577x368 pixels, 4 timepoints, 3 channels. This looks a bit suspect though (particularly the timepoints), and having the filename as the series name is not common to any of the other SVS files.
Perhaps not related directly, but
% ls ~/images/test_images_good/svs/*.svs /Users/rleigh/images/test_images_good/svs/5794_001.svs /Users/rleigh/images/test_images_good/svs/UMD001_ORO.svs
These two files don't show up in the Insight importer file browser. But these do:
% ls ~/images/test_images_good/svs/alexandra/*.svs /Users/rleigh/images/test_images_good/svs/alexandra/UMD001_ORO.svs /Users/rleigh/images/test_images_good/svs/alexandra/UMD009_HE.svs /Users/rleigh/images/test_images_good/svs/alexandra/UMD019_Tri.svs
comment:9 Changed 7 years ago by mlinkert
Extra SVS series issue confirmed and PR opened: https://github.com/openmicroscopy/bioformats/pull/107
comment:10 Changed 7 years ago by mlinkert
- Remaining Time changed from 2.0 to 0
- Resolution set to fixed
- Status changed from new to closed
PRs merged and 4.4.1 released as a result.
comment:11 Changed 7 years ago by jmoore
- Milestone changed from OMERO-4.4.3 to OMERO-4.4.1
- Sprint 2012-07-31 (1) deleted
This was released as 4.4.1. Moving back.
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Error from Carlos:
012-07-17 23:02:10,985 INFO [ loci.formats.in.MinimalTiffReader] (Server-110) Reading IFDs2012-07-17 23:02:10,985 INFO [ loci.formats.in.MinimalTiffReader] (Server-110) Populating metadata 2012-07-17 23:02:10,986 ERROR [ ome.io.bioformats.BfPixelBuffer] (Server-110) Failed to instantiate BfPixelsWrapper with /home/weblitz/JCB_DV4/OMERO/Pixels/Dir-137/137354_pyramid 2012-07-17 23:02:10,986 ERROR [ ome.io.nio.PixelsService] (Server-110) Error instantiating pixel buffer: /home/ weblitz/JCB_DV4/OMERO/Pixels/Dir-137/137354_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.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:487) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:1313) at ome.services.ThumbnailBean._resetDefaults(ThumbnailBean.java:1266) at ome.services.ThumbnailBean.resetDefaults(ThumbnailBean.java:1236) 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: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 $Proxy96.resetDefaults(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: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 $Proxy96.resetDefaults(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:137) at ome.services.blitz.impl.ThumbnailStoreI.resetDefaults_async(ThumbnailStoreI.java:136) 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 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 $Proxy97.resetDefaults_async(Unknown Source) at omero.api._ThumbnailStoreTie.resetDefaults_async(_ThumbnailStoreTie.java:183) at omero.api._ThumbnailStoreDisp.___resetDefaults(_ThumbnailStoreDisp.java:589) at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:724) 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) ... 72 more 2012-07-17 23:02:10,988 INFO [ org.perf4j.TimingLogger] (Server-110) start[1342580530970] time[18] tag[omero.call.exception] 2012-07-17 23:02:10,988 INFO [ ome.services.util.ServiceHandler] (Server-110) Excp: ome.conditions.ResourceError: Error instantiating pixel buffer: /home/weblitz/JCB_DV4/OMERO/Pixels/Dir-137/137354_pyramid2012-07-17 23:03:00,014 INFO [ ome.services.blitz.fire.SessionManagerI] (2-thread-4) Performing requestHeartbeats 2012-07-17 23:03:42,613 INFO [ome.services.sessions.state.SessionCache] (2-thread-2) Synchronizing session cache. Count = 62012-07-17 23:03:42,614 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Executor.doWork -- ome.services.session s.SessionManagerImpl.reload(6d557b41-0270-49f2-bbc0-316e1b4c011d)2012-07-17 23:03:42,614 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Args: [null, InternalSF@1968164628] 2012-07-17 23:03:42,616 INFO [ ome.security.basic.EventHandler] (2-thread-2) Auth: user=0,group=0,event=null(Sessions),sess=a8b30e48-ef37-4c6d-8b5f-0252fc1b6751 2012-07-17 23:03:42,622 INFO [ org.perf4j.TimingLogger] (2-thread-2) start[1342580622614] time[8] tag[omero.c all.success.ome.services.sessions.SessionManagerImpl$6.doWork]2012-07-17 23:03:42,622 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Rslt: (ome.model.meta.Experimenter:I d_0, ome.model.meta.ExperimenterGroup:Id_0, (1, 0), ... 4 more)2012-07-17 23:03:42,622 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Executor.doWork -- ome.services.session s.SessionManagerImpl.reload(58d8c6dc-7d96-4e71-85d7-253dc9a04e6c)2012-07-17 23:03:42,622 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Args: [null, InternalSF@1968164628] 2012-07-17 23:03:42,624 INFO [ ome.security.basic.EventHandler] (2-thread-2) Auth: user=0,group=0,event=null(Sessions),sess=a8b30e48-ef37-4c6d-8b5f-0252fc1b6751 2012-07-17 23:03:42,629 INFO [ org.perf4j.TimingLogger] (2-thread-2) start[1342580622622] time[7] tag[omero.c all.success.ome.services.sessions.SessionManagerImpl$6.doWork]2012-07-17 23:03:42,629 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Rslt: (ome.model.meta.Experimenter:I d_100, ome.model.meta.ExperimenterGroup:Id_0, (0, 200, 1, ... 1 more), ... 4 more)2012-07-17 23:03:42,629 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Executor.doWork -- ome.services.session s.SessionManagerImpl.reload(af301aea-88d1-464e-970d-c0a62c69a6f8)2012-07-17 23:03:42,629 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Args: [null, InternalSF@1968164628] 2012-07-17 23:03:42,631 INFO [ ome.security.basic.EventHandler] (2-thread-2) Auth: user=0,group=0,event=null(Sessions),sess=a8b30e48-ef37-4c6d-8b5f-0252fc1b6751 2012-07-17 23:03:42,635 INFO [ org.perf4j.TimingLogger] (2-thread-2) start[1342580622629] time[6] tag[omero.c all.success.ome.services.sessions.SessionManagerImpl$6.doWork]2012-07-17 23:03:42,636 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Rslt: (ome.model.meta.Experimenter:I d_5603, ome.model.meta.ExperimenterGroup:Id_5703, (5752, 5757, 5758, ... 5 more), ... 4 more)2012-07-17 23:03:42,636 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Executor.doWork -- ome.services.session s.SessionManagerImpl.reload(b5f94a53-f735-4589-b2f6-016a829f0dcf)2012-07-17 23:03:42,636 INFO [ ome.services.util.ServiceHandler] (2-thread-2) Args: [null, InternalSF@1968164628]