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Task #6500 (closed)

Opened 10 years ago

Closed 9 years ago

Validation of svs file

Reported by: saloynton Owned by:
Priority: minor Milestone: OMERO-4.4
Component: General Version: n.a.
Keywords: n.a. Cc: saloynton, cxallan, jburel, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by saloynton)

I have been given a test svs image from the lecturer to test with OMERO. The image imports but only 6 of the 7 images render. The x y dimensions of the image are 100840 by 70198 so I am assuming that this could be problematic?

I am in need of some advice of what could be done so I can update the lecturer here in Dundee.

The image is available on squig in data repo under Scott User images under the folder Paul felts svs image.


Attachments (1)

log.zip (86.8 KB) - added by wmoore 9 years ago.
Logs during import of svs set, including large image (fails) then deleted.

Download all attachments as: .zip

Change History (30)

comment:1 Changed 10 years ago by mlinkert

  • Sprint set to 2011-08-18 (3)

I suspect this is just the pyramid generation taking a really, really long time. I've got the file imported on gretzky now (as of 16:57 CDT), and am keeping an eye on how long the pyramid generation takes.

comment:2 Changed 10 years ago by saloynton

Thanks for this Melissa, if it helps I have a had the svs file again render the 6 images on gretzky but the seventh image gives the following message: the image could not be be opened the image is not a valid image.

comment:3 Changed 10 years ago by mlinkert

OK, I see the same thing, ~22 hours after initial import.

What I'm trying to do now is see if the tile reading performance can't be improved a bit. I'm seeing ~244 ms/tile (100,000+ tiles) with the largest image in this file, which is beyond terrible (in fairness, this is on my laptop, which is not as fast as gretzky). If speeding things up doesn't solve the problem, it will at least make it easier to find out what's going on without having to wait almost a full day.

comment:4 Changed 10 years ago by jburel

  • Sprint changed from 2011-08-18 (3) to 2011-09-01 (4)

Moved from sprint 2011-08-18 (3)

comment:5 Changed 10 years ago by saloynton

  • Cc jburel added

comment:6 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [0d078fdeb33b74180f3d2621f9823e74c186b6b8/bioformats.git]) Some improvements to tile reading speed.

Notably, the call to 'ifd.printIFD()' now only happens if the log level
is set to TRACE. This saves ~140 ms per tile on my machine!

See #6500.

comment:7 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [0d078fdeb33b74180f3d2621f9823e74c186b6b8/bioformats.git]) Some improvements to tile reading speed.

Notably, the call to 'ifd.printIFD()' now only happens if the log level
is set to TRACE. This saves ~140 ms per tile on my machine!

See #6500.

comment:8 Changed 10 years ago by mlinkert

  • Status changed from new to accepted

comment:9 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [65ec342957922955ba20ab90cda0e1c1bd67adc6/bioformats.git]) Some improvements to tile reading speed.

Notably, the call to 'ifd.printIFD()' now only happens if the log level
is set to TRACE. This saves ~140 ms per tile on my machine!

See #6500.
(cherry picked from commit 0d078fdeb33b74180f3d2621f9823e74c186b6b8)

comment:10 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [65ec342957922955ba20ab90cda0e1c1bd67adc6/bioformats.git]) Some improvements to tile reading speed.

Notably, the call to 'ifd.printIFD()' now only happens if the log level
is set to TRACE. This saves ~140 ms per tile on my machine!

See #6500.
(cherry picked from commit 0d078fdeb33b74180f3d2621f9823e74c186b6b8)

comment:11 Changed 10 years ago by mlinkert

I'm 98% sure I know what the problem is now - the pyramid for the largest image will end up being ~6.7 GB in size, which means that it must be written as a BigTIFF. However, it doesn't look like BfPyramidPixelsBuffer?'s writer has its BigTIFF flag set.

I'm testing now whether forcing the BigTIFF flag to be set solves the problem; should know for sure in another 12-14 hours.

comment:13 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [84cd934e6da7d56e996940db0831f83095cdcea4/bioformats.git]) Fix one more bug in writing BigTIFF files.

I am almost positive that this bug was introduced to mask the bug fixed
in b84d96af39f4576bf02671285213927fd6a586a0.

See #6500.

comment:14 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [84cd934e6da7d56e996940db0831f83095cdcea4/bioformats.git]) Fix one more bug in writing BigTIFF files.

I am almost positive that this bug was introduced to mask the bug fixed
in b84d96af39f4576bf02671285213927fd6a586a0.

See #6500.

comment:15 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [c053689347e8a6bba2b0a05b214cb693da88e4a8/bioformats.git]) Fix one more bug in writing BigTIFF files.

I am almost positive that this bug was introduced to mask the bug fixed
in b84d96af39f4576bf02671285213927fd6a586a0.

See #6500.
(cherry picked from commit 84cd934e6da7d56e996940db0831f83095cdcea4)

comment:16 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [c053689347e8a6bba2b0a05b214cb693da88e4a8/bioformats.git]) Fix one more bug in writing BigTIFF files.

I am almost positive that this bug was introduced to mask the bug fixed
in b84d96af39f4576bf02671285213927fd6a586a0.

See #6500.
(cherry picked from commit 84cd934e6da7d56e996940db0831f83095cdcea4)

comment:17 Changed 10 years ago by jburel

  • Sprint changed from 2011-09-01 (4) to 2011-09-15 (5)

Moved from sprint 2011-09-01 (4)

comment:18 Changed 10 years ago by mlinkert

b36b47680b11d115ebed9e08bb98ccf6a02d2b56 on the '6500-bigtiff-pyramids' branch should partially solve the problem now. It turns on BigTIFF support when generating the pyramids, so that a valid pyramid should be generated for even the largest of the images. Above commits to bioformats.git also fix several problems with writing BigTIFF files.

However, there is one more problem (which I think is outside the scope of what I effectively can debug). When I try to open the largest image in Insight after the pyramid has been generated, I see the following error:

java.lang.Exception: org.openmicroscopy.shoola.env.rnd.RenderingServiceException: RenderImage
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.renderImage(OmeroImageServiceImpl.java:466)
	at org.openmicroscopy.shoola.env.data.views.calls.ImageRenderer$1.doCall(ImageRenderer.java:83)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:662)
Caused by: org.openmicroscopy.shoola.env.rnd.RenderingServiceException: An error occurred while trying to set the cannot render the compressed image.

omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NegativeArraySizeException):
                        null
                        	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:69)
                        	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:188)
                        	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:274)
                        	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
                        	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
                        	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532)
                        	at sun.reflect.GeneratedMethodAccessor705.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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 $Proxy80.renderCompressed(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor705.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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:83)
                        	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 $Proxy80.renderCompressed(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor706.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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:136)
                        	at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344)
                        	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:302)
                        	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:576)
                        	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1688)
                        	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.InternalException"
    message = " Wrapped Exception: (java.lang.NegativeArraySizeException):
               null"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	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._RenderingEngineDelM.renderCompressed(_RenderingEngineDelM.java:1690)
	at omero.api.RenderingEnginePrxHelper.renderCompressed(RenderingEnginePrxHelper.java:2370)
	at omero.api.RenderingEnginePrxHelper.renderCompressed(RenderingEnginePrxHelper.java:2342)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.renderCompressedBI(RenderingControlProxy.java:519)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1546)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1531)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.render(PixelsServicesFactory.java:483)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.renderImage(OmeroImageServiceImpl.java:445)
	at org.openmicroscopy.shoola.env.data.views.calls.ImageRenderer$1.doCall(ImageRenderer.java:83)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:662)

	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.handleException(RenderingControlProxy.java:222)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.renderCompressedBI(RenderingControlProxy.java:523)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1546)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.render(RenderingControlProxy.java:1531)
	at org.openmicroscopy.shoola.env.rnd.PixelsServicesFactory.render(PixelsServicesFactory.java:483)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.renderImage(OmeroImageServiceImpl.java:445)
	... 8 more
Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NegativeArraySizeException):
                        null
                        	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:69)
                        	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:188)
                        	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:274)
                        	at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
                        	at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
                        	at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532)
                        	at sun.reflect.GeneratedMethodAccessor705.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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 $Proxy80.renderCompressed(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor705.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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:83)
                        	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 $Proxy80.renderCompressed(Unknown Source)
                        	at sun.reflect.GeneratedMethodAccessor706.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	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:136)
                        	at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344)
                        	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:302)
                        	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:576)
                        	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1688)
                        	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.InternalException"
    message = " Wrapped Exception: (java.lang.NegativeArraySizeException):
               null"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	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._RenderingEngineDelM.renderCompressed(_RenderingEngineDelM.java:1690)
	at omero.api.RenderingEnginePrxHelper.renderCompressed(RenderingEnginePrxHelper.java:2370)
	at omero.api.RenderingEnginePrxHelper.renderCompressed(RenderingEnginePrxHelper.java:2342)
	at org.openmicroscopy.shoola.env.rnd.RenderingControlProxy.renderCompressedBI(RenderingControlProxy.java:519)
	... 12 more

	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:183)
	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:272)
	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:242)
	at org.openmicroscopy.shoola.agents.imviewer.DataLoader.handleException(DataLoader.java:158)
	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:641)
	at java.awt.EventQueue.access$000(EventQueue.java:84)
	at java.awt.EventQueue$1.run(EventQueue.java:602)
	at java.awt.EventQueue$1.run(EventQueue.java:600)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:611)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:178)
	at java.awt.Dialog$1.run(Dialog.java:1046)
	at java.awt.Dialog$3.run(Dialog.java:1098)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.awt.Dialog.show(Dialog.java:1096)
	at java.awt.Component.show(Component.java:1584)
	at java.awt.Component.setVisible(Component.java:1536)
	at java.awt.Window.setVisible(Window.java:842)
	at java.awt.Dialog.setVisible(Dialog.java:986)
	at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:561)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerControl.stateChanged(ImViewerControl.java:895)
	at org.openmicroscopy.shoola.util.ui.component.AbstractComponent.fireStateChange(AbstractComponent.java:103)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.renderXYPlane(ImViewerComponent.java:1081)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.onRndLoaded(ImViewerComponent.java:2837)
	at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerControl.propertyChange(ImViewerControl.java:968)
	at org.openmicroscopy.shoola.util.ui.component.AbstractComponent.firePropertyChange(AbstractComponent.java:147)
	at org.openmicroscopy.shoola.agents.metadata.view.MetadataViewerComponent.onRndLoaded(MetadataViewerComponent.java:846)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorModel.onRndLoaded(EditorModel.java:2243)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorComponent.setRenderingControl(EditorComponent.java:602)
	at org.openmicroscopy.shoola.agents.metadata.RenderingControlLoader.handleResult(RenderingControlLoader.java:163)
	at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
	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:641)
	at java.awt.EventQueue.access$000(EventQueue.java:84)
	at java.awt.EventQueue$1.run(EventQueue.java:602)
	at java.awt.EventQueue$1.run(EventQueue.java:600)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:611)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

This was also reported in #6621, with Trestle images. In both cases, the SizeX * SizeY exceeds Integer.MAX_VALUE. This looks like a rendering engine limitation to me, but if you (Chris/Jean?-Marie) think it's a Bio-Formats problem then I'll take a closer look.

comment:19 follow-up: Changed 10 years ago by saloynton

I have tested a new svs file made available. I successfully imported the file on the 6th September and left he image to render at over 12 + hours the image has still not rendered. The image is available from /data_repo/Kates Pathology Images/Teaching? svs images

comment:20 in reply to: ↑ 19 Changed 10 years ago by mlinkert

Replying to saloynton:

I have tested a new svs file made available. I successfully imported the file on the 6th September and left he image to render at over 12 + hours the image has still not rendered. The image is available from /data_repo/Kates Pathology Images/Teaching? svs images

That's completely expected at this point. The commit that is supposed to fix this in the server has not been merged into develop, so none of the server builds will work yet. If/when that commit is merged, subsequent server builds should allow the image's pyramid and thumbnail to be generated. As mentioned above, though, there is still a lingering rendering problem.

comment:21 Changed 10 years ago by mlinkert

  • Cc mlinkert-x added
  • Owner mlinkert-x deleted

Removing myself from the owner field, since there isn't much more I can do here at this point.

comment:22 Changed 10 years ago by Melissa Linkert <melissa@…>

(In [b36b47680b11d115ebed9e08bb98ccf6a02d2b56/ome.git]on branches 6500-bigtiff-pyramids, develop) Write pyramids as BigTIFF files.

This prevents pyramid generation from failing if the pyramid file size
ends up being greater than 4 GB.

See #6500.

comment:23 Changed 9 years ago by jburel

  • Sprint changed from 2011-09-15 (5) to 2011-09-29 (6)

Moved from sprint 2011-09-15 (5)

comment:24 Changed 9 years ago by saloynton

  • Status changed from accepted to new

comment:25 Changed 9 years ago by saloynton

  • Milestone changed from OMERO-Beta4.3.2 to OME-5.0
  • Sprint 2011-09-29 (6) deleted

comment:26 Changed 9 years ago by saloynton

  • Description modified (diff)

Changed 9 years ago by wmoore

Logs during import of svs set, including large image (fails) then deleted.

comment:27 Changed 9 years ago by saloynton

Jean-Marie: Is this an issue now that is relevant for the rending engine, if so I can re-name the ticket.

comment:28 Changed 9 years ago by saloynton

ticket closed for 4.4 release, pf svs files tested.

comment:29 Changed 9 years ago by saloynton

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