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Task #10188 (closed)

Opened 12 years ago

Closed 12 years ago

BUG: Pyramid generation not occurring

Reported by: rkferguson Owned by: jamoore
Priority: blocker Milestone: OMERO-4.4.7
Component: Insight Version: n.a.
Keywords: FS Cc: fs@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2013-02-12 (5)

Description

PSD and PNG - larger images that require pyramid generation are just giving thumbnails of waiting clock after more than 2 hours.

Images affected: - test_images_good:

/png/4kx4k.png

/png/8kx8k.png

/psd/8kx8k.psd

Change History (13)

comment:1 Changed 12 years ago by bpindelski

Same issue with Canon images. See ​https://trac.openmicroscopy.org.uk/ome/ticket/10131.

Version 0, edited 12 years ago by bpindelski (next)

comment:2 Changed 12 years ago by mtbcarroll

Same issue with DMtest2.dm3 and biosamplefullframe.dm3 and biosamplefullframetif.tif from test_images_good/gatan/

(jmoore checked image IDs to see what was going on)

comment:3 Changed 12 years ago by jburel

Same with bmp/6kx6k* and bmp/8kx8k*

comment:4 Changed 12 years ago by mlinkert

PR opened: ​https://github.com/openmicroscopy/openmicroscopy/pull/615

That seems to solve the problem for me, but I'll wait to close until someone else can confirm.

comment:5 Changed 12 years ago by rkferguson

Retest 13-01-17

Images affected 13-01-16 with note about status on retesting 13-01-17: from - test_images_good

/bmp/6kx6k.bmp - thumbnail not rendering - clock icon - not valid image error message - and DSAccessException - error message below (reproducible).

/bmp/6kx6k-grey.bmp - thumbnail not rendering - clock icon - but image viewable and rendering looks normal

/bmp/8kx8k.bmp - thumbnail not rendering - clock icon - but image viewable and rendering looks normal

/bmp/8kx8k-grey.bmp - thumbnail not rendering - clock icon - but image viewable and rendering looks normal

/canon/2013_03_08_0808.CR2 - thumbnail not rendering - clock icon - not valid image error message

/canon/DNG-CR2.CR2 - thumbnail and rendering has occurred - colours pretty dark/desaturated

/canon/Raw-CR2.CR2 - thumbnail and rendering has occurred- colours washed out and dark

/gatan/DMtest2.dm3 - thumbnail not rendering - clock icon - not valid image error message

/gatan/biosamplefullframe.dm3 - thumbnail not rendering - clock icon - not valid image error message

/gatan/biosamplefullframetif.tif - thumbnail not rendering - clock icon - not valid image error message

/png/4kx4k.png - thumbnail and rendering as expected

/png/8kx8k.png - thumbnail and rendering as expected

/psd/8kx8k.psd - thumbnail not rendering - clock icon - but image viewable and rendering looks normal

java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data. 
Cannot start the Raw pixels store.
 at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:890)
 at org.openmicroscopy.shoola.env.data.OMEROGateway.isLargeImage(OMEROGateway.java:8187)
 at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.isLargeImage(OmeroImageServiceImpl.java:1923)
 at org.openmicroscopy.shoola.env.data.views.calls.PixelsDataLoader$2.doCall(PixelsDataLoader.java:100)
 at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
 at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
 at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
 at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
 at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
 at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
 at java.lang.Thread.run(Thread.java:680)
Caused by: omero.MissingPyramidException
    serverStackTrace = "ome.conditions.MissingPyramidException: Missing pyramid:/OMERO/Pixels/379_pyramid
                         at ome.io.nio.SimpleBackOff.throwMissingPyramidException(SimpleBackOff.java:81)
                         at ome.io.nio.PixelsService.handleMissingPyramid(PixelsService.java:629)
                         at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:440)
                         at ome.services.RawPixelsBean.setPixelsId(RawPixelsBean.java:279)
                         at sun.reflect.GeneratedMethodAccessor1891.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.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 $Proxy87.setPixelsId(Unknown Source)
                         at sun.reflect.GeneratedMethodAccessor1891.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 $Proxy87.setPixelsId(Unknown Source)
                         at sun.reflect.GeneratedMethodAccessor1896.invoke(Unknown Source)
                         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.RawPixelsStoreI.setPixelsId_async(RawPixelsStoreI.java:194)
                         at sun.reflect.GeneratedMethodAccessor1895.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 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 $Proxy88.setPixelsId_async(Unknown Source)
                         at omero.api._RawPixelsStoreTie.setPixelsId_async(_RawPixelsStoreTie.java:281)
                         at omero.api._RawPixelsStoreDisp.___setPixelsId(_RawPixelsStoreDisp.java:382)
                         at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1326)
                         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)
                        "
    serverExceptionClass = "ome.conditions.MissingPyramidException"
    message = "Missing pyramid:/OMERO/Pixels/379_pyramid"
    backOff = 178156
    pixelsID = 379
 at sun.reflect.GeneratedConstructorAccessor155.newInstance(Unknown Source)
 at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
 at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
 at java.lang.Class.newInstance0(Class.java:355)
 at java.lang.Class.newInstance(Class.java:308)
 at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
 at IceInternal.BasicStream.throwException(BasicStream.java:1632)
 at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
 at omero.api._RawPixelsStoreDelM.setPixelsId(_RawPixelsStoreDelM.java:1559)
 at omero.api.RawPixelsStorePrxHelper.setPixelsId(RawPixelsStorePrxHelper.java:2158)
 at omero.api.RawPixelsStorePrxHelper.setPixelsId(RawPixelsStorePrxHelper.java:2130)
 at org.openmicroscopy.shoola.env.data.OMEROGateway.isLargeImage(OMEROGateway.java:8182)
 ... 9 more

 at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)
 at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:287)
 at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)
 at org.openmicroscopy.shoola.agents.metadata.EditorLoader.handleException(EditorLoader.java:159)
 at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
 at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:702)
 at java.awt.EventQueue.access$400(EventQueue.java:82)
 at java.awt.EventQueue$2.run(EventQueue.java:663)
 at java.awt.EventQueue$2.run(EventQueue.java:661)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:672)
 at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)
 at java.awt.Dialog$1.run(Dialog.java:1044)
 at java.awt.Dialog$3.run(Dialog.java:1096)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.awt.Dialog.show(Dialog.java:1094)
 at java.awt.Component.show(Component.java:1591)
 at java.awt.Component.setVisible(Component.java:1543)
 at java.awt.Window.setVisible(Window.java:843)
 at java.awt.Dialog.setVisible(Dialog.java:984)
 at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:557)
 at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showNotificationDialog(UserNotifierImpl.java:145)
 at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyInfo(UserNotifierImpl.java:330)
 at org.openmicroscopy.shoola.agents.metadata.RenderingControlLoader.handleException(RenderingControlLoader.java:151)
 at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
 at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
 at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
 at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:702)
 at java.awt.EventQueue.access$400(EventQueue.java:82)
 at java.awt.EventQueue$2.run(EventQueue.java:663)
 at java.awt.EventQueue$2.run(EventQueue.java:661)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
 at java.awt.EventQueue.dispatchEvent(EventQueue.java:672)
 at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
 at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
 at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
 at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
 at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

comment:6 Changed 12 years ago by mtbcarroll

For me build 119 yields no change to my comment:2 I'm afraid. Image IDs today are 439, 440, 442.

Last edited 12 years ago by mtbcarroll (previous) (diff)

comment:7 Changed 12 years ago by mtbcarroll

Ha, the processing just took a long time, now the thumbnails look fine. I should have had more faithful patience. I have no outstanding problems on this ticket.

comment:8 Changed 12 years ago by bpindelski

Canon images have thumbnails back too.

comment:9 Changed 12 years ago by jmoore

Blazej, user / group / and image number?

comment:10 Changed 12 years ago by rkferguson

User-8

Just rechecked all imports from this morning:

/gatan/biosamplefullframetif.tif - still no thumbnail and not able to view

the rest of /gatan/ are displaying thumbnail and image as expected.

/bmp/

/canon/

/png/

/psd/

are now all displaying thumbnail and image as expected.

Will check final image later in the day.

comment:11 Changed 12 years ago by bpindelski

Josh: user-2/private-1. Images 432, 433 and 434.

comment:12 Changed 12 years ago by rkferguson

Final thumbnail and image rendered.

/gatan/biosamplefullframetif.tif - thumbnail and image rendering as expected.

comment:13 Changed 12 years ago by rkferguson

  • Resolution set to fixed
  • Status changed from new to closed

All issues resolved apart from speed - closing ticket.

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