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

[Jan Eglinger]

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
}