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Task #10188 (closed)

Opened 11 years ago

Closed 11 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 11 years ago by bpindelski

Same issue with Canon images. See ​https://trac.openmicroscopy.org.uk/ome/ticket/10131. All the Canon images are big (at least one dimension higher than 3000 pixels), showinf doesn't render them correctly either (black screen in image preview).

Last edited 11 years ago by bpindelski (previous) (diff)

comment:2 Changed 11 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 11 years ago by jburel

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

comment:4 Changed 11 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 11 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 11 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 11 years ago by mtbcarroll (previous) (diff)

comment:7 Changed 11 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 11 years ago by bpindelski

Canon images have thumbnails back too.

comment:9 Changed 11 years ago by jmoore

Blazej, user / group / and image number?

comment:10 Changed 11 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 11 years ago by bpindelski

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

comment:12 Changed 11 years ago by rkferguson

Final thumbnail and image rendered.

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

comment:13 Changed 11 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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