[ome-users] Channel issue with single tif files and OMERO.server

[Simon Li]

Hi Jan

Could you send us the following information please:

Output of `omero admin diagnostics`
Output of `omero config get` (Blank out any usernames/passwords)
Your server logs- zip them up and upload them to https://www.openmicroscopy.org/qa2/qa/upload/
If your server has been running for a while you can just send us the most recent log-files.

Many thanks

Simon


On 22 Apr 2014, at 14:11, Jan Eglinger <jan.eglinger at gmail.com> wrote:

> Dear ome developers and users,
>
> I'm having a problem with single channel tif images uploaded to OMERO.server: while most of them are displayed and downloaded correctly, some of them (only after a while) cannot be displayed nor downloaded any more, while their thumbnails are still displayed.
>
> In the "General" information tab on OMERO.web, it says: "Channels: No channel specified". The full viewer displays "Error instantiating pixel buffer".
> When I run the 'Combine Images...' script, I get the traceback pasted below.
>
> What puzzles me is that the very same images have been accessible already, only now they have become inaccessible. Uploading the same files again (in a different dataset) works as expected.
>
> Any idea what might be wrong?
>
> Thanks,
> Jan
>
>
>
> Traceback (most recent call last):
>  File "./script", line 655, in <module>
>    runAsScript()
>  File "./script", line 641, in runAsScript
>    images, message = combineImages(conn, parameterMap)
>  File "./script", line 483, in combineImages
>    dataset, colourMap)
>  File "./script", line 384, in makeSingleImage
>    plane2D = getPlane(rawPixelStore, pixels, planeZ, 0, 0)
>  File "./script", line 101, in getPlane
>    rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
>  File "/home/eglinger-omero/apps/OMERO/OMERO.server/lib/python/omero_api_RawPixelsStore_ice.py", line 422, in setPixelsId
>    return _M_omero.api.RawPixelsStore._op_setPixelsId.invoke(self, ((pixelsId, bypassOriginalFile), _ctx))
> omero.ResourceError: exception ::omero::ResourceError
> {
>    serverStackTrace = ome.conditions.ResourceError: Error instantiating pixel buffer: /home/eglinger-omero/apps/OMERO/OMERO.data/ManagedRepository/group03_7/2014-04/10/17-19-33.573/2Mutant Insulin und Glucagon (grün) 20x.tif
> at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:787)
> at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:550)
> at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:468)
> at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:272)
> at sun.reflect.GeneratedMethodAccessor626.invoke(Unknown Source)
> 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$Interceptor.invoke(ProxyCleanupFilter.java:241)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
> at com.sun.proxy.$Proxy89.setPixelsId(Unknown Source)
> at sun.reflect.GeneratedMethodAccessor626.invoke(Unknown Source)
> 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.$Proxy89.setPixelsId(Unknown Source)
> at sun.reflect.GeneratedMethodAccessor742.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
> at ome.services.throttling.Callback.run(Callback.java:56)
> at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
> at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
> at ome.services.blitz.impl.RawPixelsStoreI.setPixelsId_async(RawPixelsStoreI.java:194)
> at sun.reflect.GeneratedMethodAccessor741.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
> at omero.cmd.CallContext.invoke(CallContext.java:78)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
> at com.sun.proxy.$Proxy90.setPixelsId_async(Unknown Source)
> at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:258)
> at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:634)
> at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1530)
> at IceInternal.Incoming.invoke(Incoming.java:222)
> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
> at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
> at Ice.ConnectionI.message(ConnectionI.java:1213)
> at IceInternal.ThreadPool.run(ThreadPool.java:321)
> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
> at java.lang.Thread.run(Thread.java:744)
>
>    serverExceptionClass = ome.conditions.ResourceError
>    message = Error instantiating pixel buffer: /home/eglinger-omero/apps/OMERO/OMERO.data/ManagedRepository/group03_7/2014-04/10/17-19-33.573/2Mutant Insulin und Glucagon (grün) 20x.tif
> }
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