[ome-users] OMERO 5.0.0-rc1 czi problem

Christophe TREFOIS christophe.trefois at uni.lu
Tue Feb 4 16:52:47 GMT 2014 

I should mention that it opens and displays just fine using Bio-Formats and Fiji.

Thanks,

From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Christophe TREFOIS
Sent: mardi 4 février 2014 11:00
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] OMERO 5.0.0-rc1 czi problem

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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