[ome-users] OMERO pyramid creation
Kai Schleicher
kai.schleicher at unibas.ch
Fri Jun 16 13:02:17 BST 2017
Hi,
I have an update to this: while there was no error during upload, I
received an error during processing "failed to read pixels" for one of
the images (example image ID 576
<https://demo.openmicroscopy.org/webclient/?show=image-576> , see
attached error log)
thanks for your help and cheers,
Kai
On 06/16/2017 11:45 AM, Kai Schleicher wrote:
>
> Hi,
>
> first, even though its already a bit in the past: Thanks for the great
> OME meeting! I was happy to meet everyone and see all the new and
> amazing things to come :)
>
> second, thanks for the freshly installed 5.3.2 OMERO demo server! For
> testing I have uploaded some jpegXR compressed multi-sceen BF and FL
> images of our AxioScan slidescanner (*czi), which uploaded with no
> issue (dataset ID 17
> <https://demo.openmicroscopy.org/webclient/?show=dataset-17>, example
> image ID 576
> <https://demo.openmicroscopy.org/webclient/?show=image-576> ).
>
> I noticed however that the OMERO sever spends some time calculating a
> pyramid for my images.
>
> Since these images already contained pyramids that where calculated by
> Zen after acquisition, do you think it would be possible to skip
> pyramid creation on the OMERO server side and use the ones provided in
> the czi instead?
>
> While I could confirm that FIJI/Bio-formats recognises the pyramids in
> those images, I don't really know if they are on the same zoom-level
> that OMERO expects/ likes to use.
>
> Let me know if you wish to have the example images uploaded somewhere
> else other than your demo server :)
>
> Thanks and cheers,
> Kai
>
> --
> >>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
> Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
> Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) |kai.schleicher at unibas.ch |www.biozentrum.unibas.ch |www.microscopynetwork.unibas.ch
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.ArithmeticException: / by zero
at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:811)
at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:774)
at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:650)
at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:503)
at omero.cmd.HandleI.steps(HandleI.java:438)
at omero.cmd.HandleI$1.doWork(HandleI.java:366)
at omero.cmd.HandleI$1.doWork(HandleI.java:362)
at sun.reflect.GeneratedMethodAccessor295.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy72.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at omero.cmd.HandleI.run(HandleI.java:360)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at ome.services.util.Executor$Impl$1.call(Executor.java:484)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
, message=/ by zero}
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665)
at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)
at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:678)
at ome.formats.importer.ImportLibrary.notifyObservers(ImportLibrary.java:246)
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:671)
at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)
at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: import-request-failure
Parameters: {stacktrace=java.lang.ArithmeticException: / by zero
at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:811)
at ome.services.blitz.repo.ManagedImportRequestI.parseData(ManagedImportRequestI.java:774)
at ome.services.blitz.repo.ManagedImportRequestI.pixelData(ManagedImportRequestI.java:650)
at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:503)
at omero.cmd.HandleI.steps(HandleI.java:438)
at omero.cmd.HandleI$1.doWork(HandleI.java:366)
at omero.cmd.HandleI$1.doWork(HandleI.java:362)
at sun.reflect.GeneratedMethodAccessor295.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy72.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:443)
at omero.cmd.HandleI.run(HandleI.java:360)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at ome.services.util.Executor$Impl$1.call(Executor.java:484)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
, message=/ by zero}
at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665)
... 11 more
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