Bug: Cellr images very slow rendering

[bpindelski]

Imported all images from the cellr/colin folder. Thumbnails generated ok, but browsing time points when there is more than 10 seems to be too much for gretzky. Clicking on the time point slider in the Image Viewer doesn't change the rendered image.

Image name: cellr/colin/07-06-21/07-06-21_d.mtb [FITC]
Server: gretzky
Build: OMERO.insight-4.4.4-766-7e18246-dirty-ice33-b111-mac

[jmoore]

Blazej, could you re-try today and see if it's equally slow. My thinking is that there are fewer people working today. If it still is slow, perhaps check the server log for OOMs. Thanks.

Note: please CC minimally fs@.. for any fs-related tickets.

[bpindelski]

Josh, I seem to have found the culprit. Today it's still the same (i.e. I can't view any time point greater than 4), but managed to tail -f Blitz-0.log on gretzky. When browsing an image with T > 4, the following errors appear in the server log:

java.lang.RuntimeException: ome.io.nio.DimensionsOutOfBoundsException: T '4' greater than sizeT '4'.
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:248)
	at omeis.providers.re.GreyScaleStrategy.renderAsPackedInt(GreyScaleStrategy.java:153)
	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
	at sun.reflect.GeneratedMethodAccessor1439.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.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 $Proxy108.renderAsPackedInt(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor1439.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 $Proxy108.renderAsPackedInt(Unknown Source)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	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.RenderingEngineI.renderAsPackedInt_async(RenderingEngineI.java:332)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	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 $Proxy110.renderAsPackedInt_async(Unknown Source)
	at omero.api._RenderingEngineTie.renderAsPackedInt_async(_RenderingEngineTie.java:288)
	at omero.api._RenderingEngineDisp.___renderAsPackedInt(_RenderingEngineDisp.java:502)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1680)
	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: ome.io.nio.DimensionsOutOfBoundsException: T '4' greater than sizeT '4'.
	at ome.io.bioformats.BfPixelsWrapper.checkBounds(BfPixelsWrapper.java:111)
	at ome.io.bioformats.BfPixelsWrapper.getPlane(BfPixelsWrapper.java:265)
	at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:179)
	at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:230)

[jburel]

it looks like an index problem during the import. Then it is impossible to generate the image.

[bpindelski]

Closing. This has been an issue pointed out by Melissa and has now been fixed.