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Task #12001 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

BUG: svs files do not display right (memoizer broken)

Reported by:	pwalczysko	Owned by:	mlinkert
Priority:	blocker	Milestone:	5.0.0
Component:	Bio-Formats	Version:	5.0.0-rc3
Keywords:	n.a.	Cc:	ux@…, fs@…, jrswedlow
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description (last modified by pwalczysko)

Import test_images_good/svs/alexandra

the thumbs are black
when full viewer is opened, the display is distorted, some tiles are grey, some black (see screenshot)

All the imports were done to Gretzky port 4064 except the one mentioned in the comment (svs), which was done locally.

References

Attachments (6)

Screen Shot 2014-02-18 at 18.13.09.png (474.9 KB) - added by pwalczysko 10 years ago.
Screen Shot 2014-02-18 at 18.24.23.png (183.8 KB) - added by pwalczysko 10 years ago.
Screen Shot 2014-02-18 at 18.28.05.png (275.4 KB) - added by pwalczysko 10 years ago.
Screen Shot 2014-02-18 at 18.34.08.png (68.3 KB) - added by pwalczysko 10 years ago.
Blitz-0.log (3.0 MB) - added by pwalczysko 10 years ago.
Blitz-0-repeat.log (3.0 MB) - added by pwalczysko 10 years ago.

Change History (21)

Changed 10 years ago by pwalczysko

Attachment Screen Shot 2014-02-18 at 18.13.09.png added

comment:1 Changed 10 years ago by pwalczysko

The same is valid for Trestle CMU-1.

Changed 10 years ago by pwalczysko

Attachment Screen Shot 2014-02-18 at 18.24.23.png added

comment:2 Changed 10 years ago by pwalczysko

The same for hamamatsu

Changed 10 years ago by pwalczysko

Attachment Screen Shot 2014-02-18 at 18.28.05.png added

comment:3 Changed 10 years ago by pwalczysko

Gatan also has problems.

Changed 10 years ago by pwalczysko

Attachment Screen Shot 2014-02-18 at 18.34.08.png added

comment:4 Changed 10 years ago by pwalczysko

Repeated on a local server (also RC3).
Additionally to a distorted display of svs files which do import, I have import Failures on svs as well.

omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.RuntimeException):
                        java.io.IOException: Bad file descriptor
                        	at ome.util.checksum.AbstractChecksumProvider.putFile(AbstractChecksumProvider.java:103)
                        	at ome.services.RawFileBean.save(RawFileBean.java:212)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	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.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:218)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202)
                        	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$Interceptor.invoke(ProxyCleanupFilter.java:241)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at com.sun.proxy.$Proxy100.save(Unknown Source)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	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.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 com.sun.proxy.$Proxy100.save(Unknown Source)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:606)
                        	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:149)
                        	at ome.services.blitz.impl.RawFileStoreI.save_async(RawFileStoreI.java:130)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	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 omero.cmd.CallContext.invoke(CallContext.java:78)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at com.sun.proxy.$Proxy101.save_async(Unknown Source)
                        	at omero.api._RawFileStoreTie.save_async(_RawFileStoreTie.java:85)
                        	at omero.api._RawFileStoreDisp.___save(_RawFileStoreDisp.java:306)
                        	at omero.api._RawFileStoreDisp.__dispatch(_RawFileStoreDisp.java:392)
                        	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)
                        "
    serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.RuntimeException):
               java.io.IOException: Bad file descriptor"
	at sun.reflect.GeneratedConstructorAccessor29.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at IceInternal.BasicStream.createUserException(BasicStream.java:2615)
	at IceInternal.BasicStream.access$300(BasicStream.java:12)
	at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099)
	at IceInternal.BasicStream.throwException(BasicStream.java:2077)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
	at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:184)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:581)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:553)
	at ome.formats.importer.transfers.TransferState.save(TransferState.java:113)
	at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:105)
	at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:406)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6325)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:236)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1352)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:695)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6351)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:236)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1352)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:695)
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.RuntimeException):
                        java.io.IOException: Bad file descriptor
                        	at ome.util.checksum.AbstractChecksumProvider.putFile(AbstractChecksumProvider.java:103)
                        	at ome.services.RawFileBean.save(RawFileBean.java:212)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	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.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:218)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202)
                        	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$Interceptor.invoke(ProxyCleanupFilter.java:241)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at com.sun.proxy.$Proxy100.save(Unknown Source)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	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.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 com.sun.proxy.$Proxy100.save(Unknown Source)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                        	at java.lang.reflect.Method.invoke(Method.java:606)
                        	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:149)
                        	at ome.services.blitz.impl.RawFileStoreI.save_async(RawFileStoreI.java:130)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                        	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
                        	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 omero.cmd.CallContext.invoke(CallContext.java:78)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at com.sun.proxy.$Proxy101.save_async(Unknown Source)
                        	at omero.api._RawFileStoreTie.save_async(_RawFileStoreTie.java:85)
                        	at omero.api._RawFileStoreDisp.___save(_RawFileStoreDisp.java:306)
                        	at omero.api._RawFileStoreDisp.__dispatch(_RawFileStoreDisp.java:392)
                        	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)
                        "
    serverExceptionClass = "ome.conditions.InternalException"
    message = " Wrapped Exception: (java.lang.RuntimeException):
               java.io.IOException: Bad file descriptor"
	at sun.reflect.GeneratedConstructorAccessor29.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at IceInternal.BasicStream.createUserException(BasicStream.java:2615)
	at IceInternal.BasicStream.access$300(BasicStream.java:12)
	at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099)
	at IceInternal.BasicStream.throwException(BasicStream.java:2077)
	at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
	at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:184)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:581)
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:553)
	at ome.formats.importer.transfers.TransferState.save(TransferState.java:113)
	at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:105)
	at ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85)
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:406)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImageFile(OMEROGateway.java:6325)
	... 12 more

comment:5 Changed 10 years ago by pwalczysko

Priority changed from critical to blocker

comment:6 Changed 10 years ago by pwalczysko

Tried to import in-place the INCELL2000 plate in public folder. This import went to Gretzky. The import proceeded, but I got an error prior to the import output (see below).

Created session 6b99835d-5582-4949-9e19-4b093b5f3952 (petr@localhost:4064). Idle timeout: 10.0 min. Current group: Super In-place Lab
2014-02-18 19:07:37,991 205        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.0-rc2-229-0b8ea4b-ice33-b587
2014-02-18 19:07:38,005 219        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.0-rc2-229-0b8ea4b-ice33-b587 revision: 8e03f2e date: 18 February 2014
2014-02-18 19:07:38,012 226        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2014-02-18 19:07:38,014 228        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-02-18 19:07:38,312 526        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-02-18 19:10:24,006 166220     [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /home/omero/petr-data/INCELL2000/INMAC384-DAPI-CM-eGFP_59223_1.zip
java.io.EOFException: null
	at java.util.zip.ZipInputStream.readFully(ZipInputStream.java:409) ~[na:1.6.0_20]
	at java.util.zip.ZipInputStream.readEnd(ZipInputStream.java:371) ~[na:1.6.0_20]
	at java.util.zip.ZipInputStream.read(ZipInputStream.java:156) ~[na:1.6.0_20]
	at java.util.zip.ZipInputStream.closeEntry(ZipInputStream.java:100) ~[na:1.6.0_20]
	at java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:78) ~[na:1.6.0_20]
	at loci.common.ZipHandle.<init>(ZipHandle.java:88) ~[formats-common.jar:na]
	at loci.common.Location.getHandle(Location.java:305) ~[formats-common.jar:na]
	at loci.common.Location.getHandle(Location.java:285) ~[formats-common.jar:na]
	at loci.common.Location.getHandle(Location.java:275) ~[formats-common.jar:na]
	at loci.common.Location.checkValidId(Location.java:338) ~[formats-common.jar:na]
	at loci.formats.ImageReader.getReader(ImageReader.java:181) ~[formats-api.jar:na]
	at loci.formats.ImageReader.setId(ImageReader.java:754) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573) ~[formats-api.jar:na]
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573) ~[formats-api.jar:na]
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573) ~[formats-api.jar:na]
	at loci.formats.Memoizer.setId(Memoizer.java:471) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:573) ~[formats-api.jar:na]
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414) [blitz.jar:na]
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:595) [blitz.jar:na]
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:367) [commons-io.jar:1.4]
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:335) [commons-io.jar:1.4]
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:368) [blitz.jar:na]
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229) [blitz.jar:na]
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180) [blitz.jar:na]
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:111) [blitz.jar:na]
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:683) [blitz.jar:na]

Last edited 10 years ago by pwalczysko (previous) (diff)

comment:7 Changed 10 years ago by pwalczysko

Gretzky:

Last login: Tue Feb 18 18:56:01 2014 from ls25165.dyn.lifesci.dundee.ac.uk
omero@gretzky:~$ java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01, mixed mode)
omero@gretzky:~$

comment:8 Changed 10 years ago by pwalczysko

My localhost:

Last login: Tue Feb 18 09:28:04 on ttys003
[petr@ls25165 ~]$ java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
[petr@ls25165 ~]$

comment:9 Changed 10 years ago by pwalczysko

Description modified (diff)

comment:10 Changed 10 years ago by pwalczysko

From my Blitzlog on localhost (svs import, see above):

(l.Server-8) start[1392749279227] time[3] tag[omero.call.exception]
2014-02-18 18:47:59,231 INFO  [                 org.perf4j.TimingLogger] (l.Server-9) start[1392749279227] time[3] tag[omero.call.exception]
2014-02-18 18:47:59,236 ERROR [          omeis.providers.re.HSBStrategy] (l.Server-4) Pixels could not be closed successfully.
java.io.IOException: Bad file descriptor
	at java.io.RandomAccessFile.close0(Native Method) ~[na:1.7.0_51]
	at java.io.RandomAccessFile.close(RandomAccessFile.java:645) ~[na:1.7.0_51]
	at loci.common.NIOFileHandle.close(NIOFileHandle.java:203) ~[formats-common.jar:na]
	at loci.common.RandomAccessInputStream.close(RandomAccessInputStream.java:182) ~[formats-common.jar:na]
	at loci.formats.FormatReader.close(FormatReader.java:908) ~[formats-api.jar:na]
	at loci.formats.in.MinimalTiffReader.close(MinimalTiffReader.java:347) ~[formats-bsd.jar:na]
	at loci.formats.in.SVSReader.close(SVSReader.java:193) ~[formats-gpl.jar:na]
	at loci.formats.ImageReader.close(ImageReader.java:540) ~[formats-api.jar:na]
	at loci.formats.ImageReader.close(ImageReader.java:761) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:577) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:577) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:577) ~[formats-api.jar:na]
	at loci.formats.Memoizer.close(Memoizer.java:446) ~[formats-bsd.jar:na]
	at ome.io.bioformats.BfPixelsWrapper.close(BfPixelsWrapper.java:125) ~[romio.jar:na]
	at ome.io.bioformats.BfPixelBuffer.close(BfPixelBuffer.java:135) ~[romio.jar:na]
	at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:126) [rendering.jar:na]
	at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) [rendering.jar:na]
	at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) [rendering.jar:na]
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) [rendering.jar:na]
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) [rendering.jar:na]
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) [server.jar:na]
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) [server.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 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.$Proxy93.renderCompressed(Unknown Source) [na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy93.renderCompressed(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.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) [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.$Proxy95.renderCompressed_async(Unknown Source) [na:na]
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) [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]
2014-02-18 18:47:59,236 WARN  [        ome.services.util.ServiceHandler] (l.Server-8) Unknown exception thrown.

java.lang.RuntimeException: java.io.IOException: Bad file descriptor
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:246) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) ~[rendering.jar:na]
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) ~[rendering.jar:na]
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) ~[server.jar:na]
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) ~[server.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 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.$Proxy93.renderCompressed(Unknown Source) [na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy93.renderCompressed(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.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) [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.$Proxy95.renderCompressed_async(Unknown Source) [na:na]
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) [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]
Caused by: java.io.IOException: Bad file descriptor
	at java.io.RandomAccessFile.length(Native Method) ~[na:1.7.0_51]
	at loci.common.NIOFileHandle.length(NIOFileHandle.java:213) ~[formats-common.jar:na]
	at loci.common.RandomAccessInputStream.length(RandomAccessInputStream.java:154) ~[formats-common.jar:na]
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:685) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:923) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:745) ~[formats-bsd.jar:na]
	at loci.formats.in.SVSReader.openBytes(SVSReader.java:165) ~[formats-gpl.jar:na]
	at loci.formats.ImageReader.openBytes(ImageReader.java:435) ~[formats-api.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189) ~[formats-bsd.jar:na]
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:329) ~[formats-api.jar:na]
	at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:345) ~[romio.jar:na]
	at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:475) ~[romio.jar:na]
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216) ~[rendering.jar:na]
	... 60 common frames omitted
2014-02-18 18:47:59,236 WARN  [        ome.services.util.ServiceHandler] (l.Server-9) Unknown exception thrown.

java.lang.RuntimeException: java.io.IOException: Bad file descriptor
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:246) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) ~[rendering.jar:na]
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) ~[rendering.jar:na]
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) ~[server.jar:na]
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) ~[server.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 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.$Proxy93.renderCompressed(Unknown Source) [na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy93.renderCompressed(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.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) [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.$Proxy95.renderCompressed_async(Unknown Source) [na:na]
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) [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]
Caused by: java.io.IOException: Bad file descriptor
	at java.io.RandomAccessFile.length(Native Method) ~[na:1.7.0_51]
	at loci.common.NIOFileHandle.length(NIOFileHandle.java:213) ~[formats-common.jar:na]
	at loci.common.RandomAccessInputStream.length(RandomAccessInputStream.java:154) ~[formats-common.jar:na]
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:685) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:923) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:745) ~[formats-bsd.jar:na]
	at loci.formats.in.SVSReader.openBytes(SVSReader.java:165) ~[formats-gpl.jar:na]
	at loci.formats.ImageReader.openBytes(ImageReader.java:435) ~[formats-api.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189) ~[formats-bsd.jar:na]
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:329) ~[formats-api.jar:na]
	at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:345) ~[romio.jar:na]
	at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:475) ~[romio.jar:na]
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216) ~[rendering.jar:na]
	... 60 common frames omitted
2014-02-18 18:47:59,236 ERROR [          omeis.providers.re.HSBStrategy] (l.Server-1) Pixels could not be closed successfully.
java.io.IOException: Bad file descriptor
	at java.io.RandomAccessFile.close0(Native Method) ~[na:1.7.0_51]
	at java.io.RandomAccessFile.close(RandomAccessFile.java:645) ~[na:1.7.0_51]
	at loci.common.NIOFileHandle.close(NIOFileHandle.java:203) ~[formats-common.jar:na]
	at loci.common.RandomAccessInputStream.close(RandomAccessInputStream.java:182) ~[formats-common.jar:na]
	at loci.formats.FormatReader.close(FormatReader.java:908) ~[formats-api.jar:na]
	at loci.formats.in.MinimalTiffReader.close(MinimalTiffReader.java:347) ~[formats-bsd.jar:na]
	at loci.formats.in.SVSReader.close(SVSReader.java:193) ~[formats-gpl.jar:na]
	at loci.formats.ImageReader.close(ImageReader.java:540) ~[formats-api.jar:na]
	at loci.formats.ImageReader.close(ImageReader.java:761) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:577) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:577) ~[formats-api.jar:na]
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:577) ~[formats-api.jar:na]
	at loci.formats.Memoizer.close(Memoizer.java:446) ~[formats-bsd.jar:na]
	at ome.io.bioformats.BfPixelsWrapper.close(BfPixelsWrapper.java:125) ~[romio.jar:na]
	at ome.io.bioformats.BfPixelBuffer.close(BfPixelBuffer.java:135) ~[romio.jar:na]
	at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:126) [rendering.jar:na]
	at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) [rendering.jar:na]
	at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) [rendering.jar:na]
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) [rendering.jar:na]
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) [rendering.jar:na]
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) [server.jar:na]
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) [server.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 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.$Proxy93.renderCompressed(Unknown Source) [na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy93.renderCompressed(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.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) [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.$Proxy95.renderCompressed_async(Unknown Source) [na:na]
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) [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]
2014-02-18 18:47:59,236 INFO  [        ome.services.util.ServiceHandler] (l.Server-9)  Excp:	java.lang.RuntimeException: java.io.IOException: Bad file descriptor
2014-02-18 18:47:59,236 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Excp:	java.lang.RuntimeException: java.io.IOException: Bad file descriptor
2014-02-18 18:47:59,236 INFO  [                 org.perf4j.TimingLogger] (l.Server-4) start[1392749279227] time[8] tag[omero.call.exception]
2014-02-18 18:47:59,237 INFO  [                 org.perf4j.TimingLogger] (l.Server-1) start[1392749279227] time[9] tag[omero.call.exception]
2014-02-18 18:47:59,237 INFO  [        ome.services.util.ServiceHandler] (l.Server-4)  Excp:	ome.conditions.ResourceError: Bad file descriptor Please check server log.
2014-02-18 18:47:59,237 INFO  [        ome.services.util.ServiceHandler] (l.Server-1)  Excp:	ome.conditions.ResourceError: Bad file descriptor Please check server log.
2014-02-18 18:47:59,255 INFO  [        ome.services.util.ServiceHandler] (l.Server-6)  Meth:	interface omeis.providers.re.RenderingEngine.renderCompressed
2014-02-18 18:47:59,255 INFO  [        ome.services.util.ServiceHandler] (l.Server-4)  Meth:	interface omeis.providers.re.RenderingEngine.renderCompressed
2014-02-18 18:47:59,255 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Meth:	interface omeis.providers.re.RenderingEngine.renderCompressed
2014-02-18 18:47:59,255 INFO  [        ome.services.util.ServiceHandler] (l.Server-6)  Args:	[Type: XY, z=0, t=0; Region: x=0 y=336 width=1024 height=16]
2014-02-18 18:47:59,255 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Meth:	interface omeis.providers.re.RenderingEngine.renderCompressed
2014-02-18 18:47:59,256 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Args:	[Type: XY, z=0, t=0; Region: x=0 y=16 width=1024 height=16]
2014-02-18 18:47:59,256 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Args:	[Type: XY, z=0, t=0; Region: x=0 y=496 width=1024 height=16]
2014-02-18 18:47:59,256 INFO  [        ome.services.util.ServiceHandler] (l.Server-4)  Args:	[Type: XY, z=0, t=0; Region: x=0 y=176 width=1024 height=16]
2014-02-18 18:47:59,256 INFO  [             omeis.providers.re.Renderer] (l.Server-8) Using: 'omeis.providers.re.HSBStrategy' rendering strategy.
2014-02-18 18:47:59,256 INFO  [             omeis.providers.re.Renderer] (l.Server-4) Using: 'omeis.providers.re.HSBStrategy' rendering strategy.
2014-02-18 18:47:59,258 INFO  [                 org.perf4j.TimingLogger] (l.Server-8) start[1392749279256] time[2] tag[omero.call.exception]
2014-02-18 18:47:59,258 INFO  [                 org.perf4j.TimingLogger] (l.Server-4) start[1392749279256] time[2] tag[omero.call.exception]
2014-02-18 18:47:59,260 WARN  [        ome.services.util.ServiceHandler] (l.Server-4) Unknown exception thrown.

java.lang.RuntimeException: java.io.IOException: Stream Closed
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:246) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) ~[rendering.jar:na]
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) ~[rendering.jar:na]
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) ~[server.jar:na]
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) ~[server.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 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.$Proxy93.renderCompressed(Unknown Source) [na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy93.renderCompressed(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.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) [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.$Proxy95.renderCompressed_async(Unknown Source) [na:na]
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) [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]
Caused by: java.io.IOException: Stream Closed
	at java.io.RandomAccessFile.length(Native Method) ~[na:1.7.0_51]
	at loci.common.NIOFileHandle.length(NIOFileHandle.java:213) ~[formats-common.jar:na]
	at loci.common.RandomAccessInputStream.length(RandomAccessInputStream.java:154) ~[formats-common.jar:na]
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:685) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:923) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:745) ~[formats-bsd.jar:na]
	at loci.formats.in.SVSReader.openBytes(SVSReader.java:165) ~[formats-gpl.jar:na]
	at loci.formats.ImageReader.openBytes(ImageReader.java:435) ~[formats-api.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189) ~[formats-bsd.jar:na]
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:329) ~[formats-api.jar:na]
	at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:345) ~[romio.jar:na]
	at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:475) ~[romio.jar:na]
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216) ~[rendering.jar:na]
	... 60 common frames omitted
2014-02-18 18:47:59,260 WARN  [        ome.services.util.ServiceHandler] (l.Server-8) Unknown exception thrown.

java.lang.RuntimeException: java.io.IOException: Stream Closed
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:246) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311) ~[rendering.jar:na]
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275) ~[rendering.jar:na]
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) ~[rendering.jar:na]
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) ~[server.jar:na]
	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) ~[server.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 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.$Proxy93.renderCompressed(Unknown Source) [na:na]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
	at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
	at com.sun.proxy.$Proxy93.renderCompressed(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.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) [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.$Proxy95.renderCompressed_async(Unknown Source) [na:na]
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) [blitz.jar:na]
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) [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]
Caused by: java.io.IOException: Stream Closed
	at java.io.RandomAccessFile.length(Native Method) ~[na:1.7.0_51]
	at loci.common.NIOFileHandle.length(NIOFileHandle.java:213) ~[formats-common.jar:na]
	at loci.common.RandomAccessInputStream.length(RandomAccessInputStream.java:154) ~[formats-common.jar:na]
	at loci.formats.tiff.TiffParser.getTile(TiffParser.java:685) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:923) ~[formats-bsd.jar:na]
	at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:745) ~[formats-bsd.jar:na]
	at loci.formats.in.SVSReader.openBytes(SVSReader.java:165) ~[formats-gpl.jar:na]
	at loci.formats.ImageReader.openBytes(ImageReader.java:435) ~[formats-api.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:189) ~[formats-bsd.jar:na]
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:197) ~[formats-bsd.jar:na]
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:329) ~[formats-api.jar:na]
	at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:345) ~[romio.jar:na]
	at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:475) ~[romio.jar:na]
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216) ~[rendering.jar:na]
	... 60 common frames omitted
2014-02-18 18:47:59,260 INFO  [        ome.services.util.ServiceHandler] (l.Server-4)  Excp:	java.lang.RuntimeException: java.io.IOException: Stream Closed
2014-02-18 18:47:59,261 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Excp:	java.lang.RuntimeException: java.io.IOException: Stream Closed
2014-02-18 18:47:59,265 INFO  [        ome.services.util.ServiceHandler] (l.Server-3)  Meth:	interface omeis.providers.re.RenderingEngine.renderCompressed
2014-02-18 18:47:59,265 INFO  [        ome.services.util.ServiceHandler] (l.Server-3)  Args:	[Type: XY, z=0, t=0; Region: x=0 y=32 width=1024 height=16]
2014-02-18 18:47:59,265 INFO  [        ome.services.util.ServiceHandler] (l.Server-2)  Meth:	interface omeis.providers.re.RenderingEngine.renderCompressed
2014-02-18 18:47:59,265 INFO  [        ome.services.util.ServiceHandler] (l.Server-2)  Args:	[Type: XY, z=0, t=0; Region: x=0 y=192 width=1024 height=16]
2014-02-18 18:47:59,296 DEBUG [                   loci.formats.Memoizer] (l.Server-6) loaded memo file: /OMERO/BioFormatsCache/Users/petr/var/omero/ManagedRepository/user-4_5/2013-11/28/13-36-23.236/.UMD001_ORO.svs.bfmemo (143065 bytes)
2014-02-18 18:47:59,296 DEBUG [                   loci.formats.Memoizer] (l.Server-6) start[1392749279256] time[40] tag[loci.formats.Memoizer.loadMemo]
2014-02-18 18:47:59,296 DEBUG [                   loci.formats.Memoizer] (l.Server-6) start[1392749279256] t

comment:11 Changed 10 years ago by pwalczysko

Uploading my Blitzlog from localhost (see the excerpt of it in previous comment).

Changed 10 years ago by pwalczysko

Attachment Blitz-0.log added

comment:12 Changed 10 years ago by pwalczysko

Repeated the import of the alexandra folder locally. The impot was again "successful", but there are "Bad descriptors" remarks in Blitz (see attached, the Blitz was started from scratch just for this import).
3 out of 3 svs files in the alexandra folder have wrong display in full viewer.
2 out of 3 have black thumbs, the one which imported 1st and the one which imported 2nd.

Changed 10 years ago by pwalczysko

Attachment Blitz-0-repeat.log added

comment:13 Changed 10 years ago by mlinkert

PR opened that seems to fix this locally: https://github.com/openmicroscopy/bioformats/pull/924

comment:14 Changed 10 years ago by jamoore

Resolution set to fixed
Status changed from new to closed
Summary changed from BUG: svs files do not display right to BUG: svs files do not display right (memoizer broken)

This was an issue with the memoizer: due to the migration of packages from ome.scifio the stored memo had corrupted file handles leading to the "screwy" (Petr's word) representation. This should become a well-defined term, and if this happens again, we should look into the memoizer *first*.

comment:15 Changed 10 years ago by jamoore

Petr clarified for me that the use of the word "screwy" actually came from me during the beta1 demo back in 2013. His use of it for the same bug must have triggered my memory. Thanks either way!

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