Task #9726 (closed)
Opened 7 years ago
Closed 6 years ago
Bug: No thumbnails for JPEG with FS
| Reported by: | rleigh | Owned by: | jburel |
|---|---|---|---|
| Priority: | critical | Milestone: | 5.0.0-beta1 |
| Component: | Insight | Version: | n.a. |
| Keywords: | FS | Cc: | fs@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | FS demo 4.4 |
Description
See attached image.
No thumbnails for big images, small image, or clocks for big images needing pyramids generating. Images are viewable however.
Attachments (3)
Change History (11)
Changed 7 years ago by rleigh
comment:1 Changed 7 years ago by rleigh
comment:2 Changed 7 years ago by bpindelski
Tested on gretzky. 8k x 8k JPEG still causes the mentioned exception. Thumbnails are still not generated in the Data Manager - images are viewable though.
comment:3 Changed 7 years ago by rleigh
- Keywords FS added
comment:4 Changed 7 years ago by rleigh
Thumbnails still fail to be created on import. I can't see the above exceptions in any of the logs though, so the cause of the present failure is not obvious. Attached screenshot and logfile.
Note that it looks like every other image fails, and the exception is due to a hibernate failure. Looks exactly like the black/duplicate thumbnail issue. Maybe we're reusing the id from the previous import and this leads to the database error.
2013-01-28 09:56:48,471 WARN [ ome.services.util.ServiceHandler] (l.Server-0) Unknown exception thrown. org.hibernate.NonUniqueObjectException: a different object with the same identifier value was already associated with the session: [ome.model.meta.Experimenter#4] at org.hibernate.engine.StatefulPersistenceContext.checkUniqueness(StatefulPersistenceContext.java:637) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performUpdate(DefaultSaveOrUpdateEventListener.java:305) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsDetached(DefaultSaveOrUpdateEventListener.java:246) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:112) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93) at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:679) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:671) at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:252) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.engine.Cascade.cascade(Cascade.java:127) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.cascadeOnUpdate(DefaultSaveOrUpdateEventListener.java:376) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performUpdate(DefaultSaveOrUpdateEventListener.java:350) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.entityIsDetached(DefaultSaveOrUpdateEventListener.java:246) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:112) at org.hibernate.event.def.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:93) at org.hibernate.impl.SessionImpl.fireSaveOrUpdate(SessionImpl.java:679) at org.hibernate.impl.SessionImpl.saveOrUpdate(SessionImpl.java:671) at org.hibernate.engine.CascadingAction$5.cascade(CascadingAction.java:252) at org.hibernate.engine.Cascade.cascadeToOne(Cascade.java:392) at org.hibernate.engine.Cascade.cascadeAssociation(Cascade.java:335) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:204) at org.hibernate.engine.Cascade.cascadeComponent(Cascade.java:313) at org.hibernate.engine.Cascade.cascadeProperty(Cascade.java:215) at org.hibernate.engine.Cascade.cascade(Cascade.java:161) at org.hibernate.event.def.AbstractFlushingEventListener.cascadeOnFlush(AbstractFlushingEventListener.java:154) at org.hibernate.event.def.AbstractFlushingEventListener.prepareEntityFlushes(AbstractFlushingEventListener.java:145) at org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:88) at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50) at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1208) at ome.logic.UpdateImpl.afterUpdate(UpdateImpl.java:294) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:312) at ome.logic.UpdateImpl.doAction(UpdateImpl.java:302) at ome.logic.UpdateImpl.saveAndReturnObject(UpdateImpl.java:118) at ome.security.basic.BasicSecuritySystem.loadEventContext(BasicSecuritySystem.java:430) at ome.security.basic.EventHandler.doLogin(EventHandler.java:210) at ome.security.basic.EventHandler.invoke(EventHandler.java:146) 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 $Proxy89.setPixelsId(Unknown Source) at sun.reflect.GeneratedMethodAccessor1697.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy89.setPixelsId(Unknown Source) at sun.reflect.GeneratedMethodAccessor1729.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) 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:150) at ome.services.blitz.impl.ThumbnailStoreI.setPixelsId_async(ThumbnailStoreI.java:142) at sun.reflect.GeneratedMethodAccessor1728.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:592) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) at omero.cmd.CallContext.invoke(CallContext.java:59) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) at $Proxy90.setPixelsId_async(Unknown Source) at omero.api._ThumbnailStoreTie.setPixelsId_async(_ThumbnailStoreTie.java:190) at omero.api._ThumbnailStoreDisp.___setPixelsId(_ThumbnailStoreDisp.java:232) at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:728) 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) 2013-01-28 09:56:48,471 INFO [ ome.services.util.ServiceHandler] (l.Server-0) Excp: org.hibernate.NonUniqueObjectException: a different object with the same identifier value was already associated with the session: [ome.model.meta.Experimenter#4] 2013-01-28 09:56:48,473 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Meth: interface ome.api.StatefulServiceInterface.close 2013-01-28 09:56:48,473 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Args: () 2013-01-28 09:56:48,474 INFO [ ome.security.basic.EventHandler] (l.Server-3) Auth: user=4,group=7,event=null(User),sess=1b787284-8a02-4d91-98e3-816f3b01ed5a 2013-01-28 09:56:48,475 INFO [ loci.formats.FormatHandler] (l.Server-3) Populating metadata 2013-01-28 09:56:48,717 INFO [ org.perf4j.TimingLogger] (l.Server-3) start[1359367008473] time[244] tag[omero.call.success.ome.services.ThumbnailBean.close] 2013-01-28 09:56:48,717 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Rslt: null 2013-01-28 09:56:48,717 INFO [ ome.services.util.ServiceHandler] (l.Server-3) Cleanup: ome.services.ThumbnailBean@2021eda4 2013-01-28 09:56:48,717 INFO [ omero.cmd.SessionI] (l.Server-3) Unregistered servant:1b787284-8a02-4d91-98e3-816f3b01ed5a/86:24:41:e3:-637f1f0a:13c7f988fd1:-7eafomero.api.ThumbnailStore(omero.api._ThumbnailStoreTie@7d2884d2)
comment:5 Changed 7 years ago by mlinkert
The OOM from comment 1 is definitely not an FS issue - it has to do with the fact that the current JPEG reader has no way to retrieve individual tiles. Leaving the keyword for now, though, since the last exception may be FS-related.
comment:6 Changed 6 years ago by jburel
- Cc fs@… added
- Milestone changed from OMERO-4.4.9 to OMERO-5
- Sprint set to FS Demo 4.3
Moving back 4.3 to assess the status of this ticket. Only for the last part of the ticket. The out of memory is not FS related.
comment:7 Changed 6 years ago by jburel
- Sprint changed from FS Demo 4.3 to FS demo 4.4
Moved from sprint FS Demo 4.3
comment:8 Changed 6 years ago by jburel
- Resolution set to fixed
- Status changed from new to closed
Problem in thumbnail bean
see https://github.com/openmicroscopy/openmicroscopy/pull/1257
Closing.
Note: See
TracTickets for help on using
tickets.
You may also have a look at Agilo extensions to the ticket.
Importing jpeg/8kx8k.jpg:
omero.InternalException serverStackTrace = "java.lang.RuntimeException: omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:58) at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397) at java.awt.image.Raster.createWritableRaster(Raster.java:938) at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056) at javax.imageio.ImageReader.getDestination(ImageReader.java:2879) at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:925) at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:897) at javax.imageio.ImageIO.read(ImageIO.java:1422) at javax.imageio.ImageIO.read(ImageIO.java:1326) at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118) at loci.formats.FormatReader.setId(FormatReader.java:1228) at loci.formats.DelegateReader.setId(DelegateReader.java:266) at loci.formats.in.JPEGReader.setId(JPEGReader.java:85) at loci.formats.ImageReader.setId(ImageReader.java:742) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:55) at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:69) at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:104) at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:683) at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:433) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:629) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:1383) at sun.reflect.GeneratedMethodAccessor1818.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) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space" at ome.formats.OMEROMetadataStoreClient.resetDefaultsAndGenerateThumbnails(OMEROMetadataStoreClient.java:2573) at ome.formats.importer.ImportLibrary.importImageInternal(ImportLibrary.java:757) at ome.services.blitz.repo.ManagedRepositoryI.importMetadata(ManagedRepositoryI.java:136) at omero.grid._ManagedRepositoryTie.importMetadata(_ManagedRepositoryTie.java:71) at omero.grid._ManagedRepositoryDisp.___importMetadata(_ManagedRepositoryDisp.java:257) at omero.grid._ManagedRepositoryDisp.__dispatch(_ManagedRepositoryDisp.java:374) 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: omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:58) at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397) at java.awt.image.Raster.createWritableRaster(Raster.java:938) at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056) at javax.imageio.ImageReader.getDestination(ImageReader.java:2879) at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:925) at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:897) at javax.imageio.ImageIO.read(ImageIO.java:1422) at javax.imageio.ImageIO.read(ImageIO.java:1326) at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118) at loci.formats.FormatReader.setId(FormatReader.java:1228) at loci.formats.DelegateReader.setId(DelegateReader.java:266) at loci.formats.in.JPEGReader.setId(JPEGReader.java:85) at loci.formats.ImageReader.setId(ImageReader.java:742) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:55) at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:69) at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:104) at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:683) at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:433) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:629) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:1383) at sun.reflect.GeneratedMethodAccessor1818.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) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space" at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at java.lang.Class.newInstance0(Class.java:355) at java.lang.Class.newInstance(Class.java:308) at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) at IceInternal.BasicStream.throwException(BasicStream.java:1632) at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.api._IRenderingSettingsDelM.resetDefaultsInSet(_IRenderingSettingsDelM.java:728) at omero.api.IRenderingSettingsPrxHelper.resetDefaultsInSet(IRenderingSettingsPrxHelper.java:935) at omero.api.IRenderingSettingsPrxHelper.resetDefaultsInSet(IRenderingSettingsPrxHelper.java:907) at ome.formats.OMEROMetadataStoreClient.resetDefaultsAndGenerateThumbnails(OMEROMetadataStoreClient.java:2566) ... 11 more " serverExceptionClass = "" message = "omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:58) at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397) at java.awt.image.Raster.createWritableRaster(Raster.java:938) at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056) at javax.imageio.ImageReader.getDestination(ImageReader.java:2879) at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:925) at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:897) at javax.imageio.ImageIO.read(ImageIO.java:1422) at javax.imageio.ImageIO.read(ImageIO.java:1326) at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118) at loci.formats.FormatReader.setId(FormatReader.java:1228) at loci.formats.DelegateReader.setId(DelegateReader.java:266) at loci.formats.in.JPEGReader.setId(JPEGReader.java:85) at loci.formats.ImageReader.setId(ImageReader.java:742) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:55) at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:69) at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:104) at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:683) at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:433) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:629) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:1383) at sun.reflect.GeneratedMethodAccessor1818.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) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space"" at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at java.lang.Class.newInstance0(Class.java:355) at java.lang.Class.newInstance(Class.java:308) at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) at IceInternal.BasicStream.throwException(BasicStream.java:1632) at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.grid._ManagedRepositoryDelM.importMetadata(_ManagedRepositoryDelM.java:91) at omero.grid.ManagedRepositoryPrxHelper.importMetadata(ManagedRepositoryPrxHelper.java:117) at omero.grid.ManagedRepositoryPrxHelper.importMetadata(ManagedRepositoryPrxHelper.java:89) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:560) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6414) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:200) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1399) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6463) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:200) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1399) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54) at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110) at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) Caused by: omero.InternalException serverStackTrace = "java.lang.RuntimeException: omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:58) at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397) at java.awt.image.Raster.createWritableRaster(Raster.java:938) at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056) at javax.imageio.ImageReader.getDestination(ImageReader.java:2879) at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:925) at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:897) at javax.imageio.ImageIO.read(ImageIO.java:1422) at javax.imageio.ImageIO.read(ImageIO.java:1326) at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118) at loci.formats.FormatReader.setId(FormatReader.java:1228) at loci.formats.DelegateReader.setId(DelegateReader.java:266) at loci.formats.in.JPEGReader.setId(JPEGReader.java:85) at loci.formats.ImageReader.setId(ImageReader.java:742) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:55) at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:69) at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:104) at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:683) at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:433) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:629) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:1383) at sun.reflect.GeneratedMethodAccessor1818.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) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space" at ome.formats.OMEROMetadataStoreClient.resetDefaultsAndGenerateThumbnails(OMEROMetadataStoreClient.java:2573) at ome.formats.importer.ImportLibrary.importImageInternal(ImportLibrary.java:757) at ome.services.blitz.repo.ManagedRepositoryI.importMetadata(ManagedRepositoryI.java:136) at omero.grid._ManagedRepositoryTie.importMetadata(_ManagedRepositoryTie.java:71) at omero.grid._ManagedRepositoryDisp.___importMetadata(_ManagedRepositoryDisp.java:257) at omero.grid._ManagedRepositoryDisp.__dispatch(_ManagedRepositoryDisp.java:374) 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: omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:58) at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397) at java.awt.image.Raster.createWritableRaster(Raster.java:938) at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056) at javax.imageio.ImageReader.getDestination(ImageReader.java:2879) at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:925) at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:897) at javax.imageio.ImageIO.read(ImageIO.java:1422) at javax.imageio.ImageIO.read(ImageIO.java:1326) at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118) at loci.formats.FormatReader.setId(FormatReader.java:1228) at loci.formats.DelegateReader.setId(DelegateReader.java:266) at loci.formats.in.JPEGReader.setId(JPEGReader.java:85) at loci.formats.ImageReader.setId(ImageReader.java:742) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:55) at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:69) at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:104) at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:683) at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:433) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:629) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:1383) at sun.reflect.GeneratedMethodAccessor1818.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) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space" at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at java.lang.Class.newInstance0(Class.java:355) at java.lang.Class.newInstance(Class.java:308) at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) at IceInternal.BasicStream.throwException(BasicStream.java:1632) at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.api._IRenderingSettingsDelM.resetDefaultsInSet(_IRenderingSettingsDelM.java:728) at omero.api.IRenderingSettingsPrxHelper.resetDefaultsInSet(IRenderingSettingsPrxHelper.java:935) at omero.api.IRenderingSettingsPrxHelper.resetDefaultsInSet(IRenderingSettingsPrxHelper.java:907) at ome.formats.OMEROMetadataStoreClient.resetDefaultsAndGenerateThumbnails(OMEROMetadataStoreClient.java:2566) ... 11 more " serverExceptionClass = "" message = "omero.InternalException serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space at java.awt.image.DataBufferByte.<init>(DataBufferByte.java:58) at java.awt.image.ComponentSampleModel.createDataBuffer(ComponentSampleModel.java:397) at java.awt.image.Raster.createWritableRaster(Raster.java:938) at javax.imageio.ImageTypeSpecifier.createBufferedImage(ImageTypeSpecifier.java:1056) at javax.imageio.ImageReader.getDestination(ImageReader.java:2879) at com.sun.imageio.plugins.jpeg.JPEGImageReader.readInternal(JPEGImageReader.java:925) at com.sun.imageio.plugins.jpeg.JPEGImageReader.read(JPEGImageReader.java:897) at javax.imageio.ImageIO.read(ImageIO.java:1422) at javax.imageio.ImageIO.read(ImageIO.java:1326) at loci.formats.in.ImageIOReader.initFile(ImageIOReader.java:118) at loci.formats.FormatReader.setId(FormatReader.java:1228) at loci.formats.DelegateReader.setId(DelegateReader.java:266) at loci.formats.in.JPEGReader.setId(JPEGReader.java:85) at loci.formats.ImageReader.setId(ImageReader.java:742) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelFiller.setId(ChannelFiller.java:263) at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:542) at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274) at ome.io.bioformats.BfPixelsWrapper.<init>(BfPixelsWrapper.java:55) at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:69) at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:104) at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:683) at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:433) at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:500) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:629) at ome.logic.RenderingSettingsImpl.resetDefaultsInSet(RenderingSettingsImpl.java:1383) at sun.reflect.GeneratedMethodAccessor1818.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) " serverExceptionClass = "ome.conditions.InternalException" message = " Wrapped Exception: (java.lang.OutOfMemoryError): Java heap space"" at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at java.lang.Class.newInstance0(Class.java:355) at java.lang.Class.newInstance(Class.java:308) at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) at IceInternal.BasicStream.throwException(BasicStream.java:1632) at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.grid._ManagedRepositoryDelM.importMetadata(_ManagedRepositoryDelM.java:91) at omero.grid.ManagedRepositoryPrxHelper.importMetadata(ManagedRepositoryPrxHelper.java:117) at omero.grid.ManagedRepositoryPrxHelper.importMetadata(ManagedRepositoryPrxHelper.java:89) at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:560) at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6414) ... 12 more