[ome-users] OMERO 5.0.0-rc1 czi problem
Melissa Linkert
melissa at glencoesoftware.com
Tue Feb 4 09:24:30 GMT 2014
Hi Christophe,
> We tried to upload a 1 GB stack in czi format to the OMERO 5.0.0-rc1 server.
>
> The upload seems to work fine (no errors, metadata seems complete), but then when opening the image in the viewer, nothing happens and we get the following error in Blitz-0.log.
Thank you for the bug report. We are aware of this problem, and are
actively working on a solution as noted here:
http://trac.openmicroscopy.org.uk/ome/ticket/11958
We do anticipate having this fixed in the upcoming 5.0.0 release, but if
you would like to be notified as soon as it is fixed please let me know
and I will CC you on the ticket.
Regards,
-Melissa
On Tue, Feb 04, 2014 at 09:59:53AM +0000, Christophe TREFOIS wrote:
> Dear all,
>
> We tried to upload a 1 GB stack in czi format to the OMERO 5.0.0-rc1 server.
>
> The upload seems to work fine (no errors, metadata seems complete), but then when opening the image in the viewer, nothing happens and we get the following error in Blitz-0.log.
>
> java.lang.NullPointerException: null
> at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2453) ~[bio-formats.jar:na]
> at loci.formats.in.ZeissCZIReader.openBytes(ZeissCZIReader.java:303) ~[bio-formats.jar:na]
> at loci.formats.ImageReader.openBytes(ImageReader.java:435) ~[scifio.jar:na]
> at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197) ~[scifio.jar:na]
> at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226) ~[scifio.jar:na]
> at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:150) ~[scifio.jar:na]
> at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:326) ~[scifio.jar:na]
> at ome.io.bioformats.BfPixelsWrapper.getWholePlane(BfPixelsWrapper.java:361) ~[romio.jar:na]
> at ome.io.bioformats.BfPixelsWrapper.getPlane(BfPixelsWrapper.java:258) ~[romio.jar:na]
> at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:185) ~[romio.jar:na]
> at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:230) ~[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 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.$Proxy114.renderAsPackedInt(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.$Proxy114.renderAsPackedInt(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.renderAsPackedInt_async(RenderingEngineI.java:332) [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.$Proxy116.renderAsPackedInt_async(Unknown Source) [na:na]
> at omero.api._RenderingEngineTie.renderAsPackedInt_async(_RenderingEngineTie.java:264) [blitz.jar:na]
> at omero.api._RenderingEngineDisp.___renderAsPackedInt(_RenderingEngineDisp.java:524) [blitz.jar:na]
> at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1631) [blitz.jar:na]
> at IceInternal.Incoming.invoke(Incoming.java:222) [ice.jar:na]
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482) [ice.jar:na]
> at Ice.ConnectionI.dispatch(ConnectionI.java:1258) [ice.jar:na]
> at Ice.ConnectionI.message(ConnectionI.java:1213) [ice.jar:na]
> at IceInternal.ThreadPool.run(ThreadPool.java:321) [ice.jar:na]
> at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) [ice.jar:na]
> at java.lang.Thread.run(Thread.java:744) [na:1.7.0_51]
> 2014-02-04 04:52:39,328 INFO [ ome.services.util.ServiceHandler] (Server-469) Excp: java.lang.NullPointerException
> 2014-02-04 04:52:39,508 INFO [ ome.services.util.ServiceHandler] (Server-470) Meth: interface ome.api.RawFileStore.write
> 2014-02-04 04:52:39,509 INFO [ ome.services.util.ServiceHandler] (Server-470) Args: [[-104, 1, -39, ... 1 more], 80000000, 5000000]
> 2014-02-04 04:52:39,510 INFO [ ome.security.basic.EventHandler] (Server-470) Auth: user=2,group=4,event=null(User),sess=d9fa5087-9693-49ce-9fcb-5711e72f90de
> 2014-02-04 04:52:39,513 INFO [ org.perf4j.TimingLogger] (Server-470) start[1391507559509] time[4] tag[omero.call.success.ome.services.RawFileBean.write]
> 2014-02-04 04:52:39,513 INFO [ ome.services.util.ServiceHandler] (Server-470) Rslt: null
> 2014-02-04 04:52:39,733 INFO [ ome.services.util.ServiceHandler] (Server-463) Meth: interface ome.api.RawFileStore.write
> 2014-02-04 04:52:39,734 INFO [ ome.services.util.ServiceHandler] (Server-463) Args: [[-45, 1, -14, ... 1 more], 85000000, 5000000]
> 2014-02-04 04:52:39,735 INFO [ ome.security.basic.EventHandler] (Server-463) Auth: user=2,group=4,event=null(User),sess=d9fa5087-9693-49ce-9fcb-5711e72f90de
> 2014-02-04 04:52:39,738 INFO [ org.perf4j.TimingLogger] (Server-463) start[1391507559734] time[4] tag[omero.call.success.ome.services.RawFileBean.write]
>
> And so on...
>
> Thank you for your help in this,
>
> --
> Christophe
>
> ................................................................................
>
> Dipl.-Ing. Christophe TREFOIS
> Ing. Sys. Com. Dipl. EPF
>
> PhD Candidate
>
>
> Université du Luxembourg | University of Luxembourg
>
> Campus Belval | House of Biomedicine
>
> 7, avenue des Hauts-Fourneaux
>
> L-4362 Esch-sur-Alzette
>
> T +352 46 66 44 6124
> F +352 46 66 44 6949
> www.uni.lu/lcsb<http://www.uni.lu/lcsb>
>
>
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