ScanR: fix exposure time units #1187

melissalinkert · 2014-07-01T01:47:50Z

See http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7554.

To test, verify that exposure times are smaller with this change. I was using data/from_skyking/scanr/nadine to test, where the original exposure time was 50.0 and the new time is 0.05. Other datasets should produce similar results.

See http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7554

bramalingam · 2014-07-01T17:59:08Z

Tried uploading the file on Trout, with the following Insight client
http://ci.openmicroscopy.org/view/5.1/job/OMERO-5.1-merge-build/lastSuccessfulBuild/ICE=3.5,label=ome-c6100-3/

The import goes through and thumbnails are generated, but the images are not visible on insight (under the dataset).

And there is an exception in the import log as well,

2014-07-01 18:52:50,986 DEBUG [                    omero.util.IceMapper] (Server-372) Handling:
ome.conditions.InternalException:  Wrapped Exception: (Ice.UnknownException):
null
    at IceInternal.Outgoing.invoke(Outgoing.java:147) ~[ice.jar:na]
    at omero.grid._InteractiveProcessorDelM.execute(_InteractiveProcessorDelM.java:43) ~[blitz.jar:na]
    at omero.grid.InteractiveProcessorPrxHelper.execute(InteractiveProcessorPrxHelper.java:71) ~[blitz.jar:na]
    at omero.grid.InteractiveProcessorPrxHelper.execute(InteractiveProcessorPrxHelper.java:39) ~[blitz.jar:na]
    at ome.services.blitz.impl.MetadataStoreI$6.doWork(MetadataStoreI.java:314) ~[blitz.jar:na]
    at sun.reflect.GeneratedMethodAccessor279.invoke(Unknown Source) ~[na:na]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576) ~[server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.security.basic.EventHandler.invoke(EventHandler.java:154) ~[server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) ~[org.springframework.orm.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) ~[org.springframework.transaction.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) ~[server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) ~[server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at com.sun.proxy.$Proxy68.doWork(Unknown Source) ~[na:na]
    at ome.services.util.Executor$Impl.execute(Executor.java:457) ~[server.jar:na]
    at ome.services.util.Executor$Impl.execute(Executor.java:401) ~[server.jar:na]
    at ome.services.throttling.Adapter.run(Adapter.java:51) ~[blitz.jar:na]
    at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) [blitz.jar:na]
    at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:163) [blitz.jar:na]
    at ome.services.blitz.impl.MetadataStoreI.postProcess_async(MetadataStoreI.java:291) [blitz.jar:na]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at omero.cmd.CallContext.invoke(CallContext.java:78) [blitz.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at com.sun.proxy.$Proxy112.postProcess_async(Unknown Source) [na:na]
    at omero.api._MetadataStoreTie.postProcess_async(_MetadataStoreTie.java:87) [blitz.jar:na]
    at omero.api._MetadataStoreDisp.___postProcess(_MetadataStoreDisp.java:334) [blitz.jar:na]
    at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:415) [blitz.jar:na]
    at IceInternal.Incoming.invoke(Incoming.java:159) [ice.jar:na]
    at Ice.ConnectionI.invokeAll(ConnectionI.java:2357) [ice.jar:na]
    at Ice.ConnectionI.dispatch(ConnectionI.java:1208) [ice.jar:na]
    at Ice.ConnectionI.message(ConnectionI.java:1163) [ice.jar:na]
    at IceInternal.ThreadPool.run(ThreadPool.java:302) [ice.jar:na]
    at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
    at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643) [ice.jar:na]
    at java.lang.Thread.run(Thread.java:744) [na:1.7.0_51]
2014-07-01 18:52:50,987 DEBUG [                    omero.util.IceMapper] (Server-372) Handling:
omero.InternalException: null
    at omero.util.IceMapper.handleException(IceMapper.java:1365) ~[blitz.jar:na]
    at ome.services.throttling.Adapter.run(Adapter.java:53) ~[blitz.jar:na]
    at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) [blitz.jar:na]
    at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:163) [blitz.jar:na]
    at ome.services.blitz.impl.MetadataStoreI.postProcess_async(MetadataStoreI.java:291) [blitz.jar:na]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.7.0_51]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) ~[na:1.7.0_51]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at omero.cmd.CallContext.invoke(CallContext.java:78) [blitz.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at com.sun.proxy.$Proxy112.postProcess_async(Unknown Source) [na:na]
    at omero.api._MetadataStoreTie.postProcess_async(_MetadataStoreTie.java:87) [blitz.jar:na]
    at omero.api._MetadataStoreDisp.___postProcess(_MetadataStoreDisp.java:334) [blitz.jar:na]
    at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:415) [blitz.jar:na]
    at IceInternal.Incoming.invoke(Incoming.java:159) [ice.jar:na]
    at Ice.ConnectionI.invokeAll(ConnectionI.java:2357) [ice.jar:na]
    at Ice.ConnectionI.dispatch(ConnectionI.java:1208) [ice.jar:na]
    at Ice.ConnectionI.message(ConnectionI.java:1163) [ice.jar:na]
    at IceInternal.ThreadPool.run(ThreadPool.java:302) [ice.jar:na]
    at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
    at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643) [ice.jar:na]
    at java.lang.Thread.run(Thread.java:744) [na:1.7.0_51]
2014-07-01 18:52:50,988 WARN  [    ome.formats.OMEROMetadataStoreClient] (2-thread-1) Failed to launch post-processing
omero.InternalException: null
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_51]
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_51]
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_51]
    at java.lang.reflect.Constructor.newInstance(Constructor.java:526) ~[na:1.7.0_51]
    at java.lang.Class.newInstance(Class.java:374) ~[na:1.7.0_51]
    at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142) ~[ice.jar:na]
    at IceInternal.BasicStream.throwException(BasicStream.java:1564) ~[ice.jar:na]
    at IceInternal.Outgoing.throwUserException(Outgoing.java:443) ~[ice.jar:na]
    at omero.api._MetadataStoreDelM.postProcess(_MetadataStoreDelM.java:127) ~[blitz.jar:na]
    at omero.api.MetadataStorePrxHelper.postProcess(MetadataStorePrxHelper.java:364) ~[blitz.jar:na]
    at omero.api.MetadataStorePrxHelper.postProcess(MetadataStorePrxHelper.java:337) ~[blitz.jar:na]
    at ome.formats.OMEROMetadataStoreClient.launchProcessing(OMEROMetadataStoreClient.java:1862) ~[blitz.jar:na]
    at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:296) [blitz.jar:na]
    at omero.cmd.HandleI.steps(HandleI.java:435) [blitz.jar:na]
    at omero.cmd.HandleI$1.doWork(HandleI.java:365) [blitz.jar:na]
    at omero.cmd.HandleI$1.doWork(HandleI.java:361) [blitz.jar:na]
    at sun.reflect.GeneratedMethodAccessor279.invoke(Unknown Source) ~[na:na]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_51]
    at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_51]
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576) [server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.security.basic.EventHandler.invoke(EventHandler.java:154) [server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) [org.springframework.orm.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) [org.springframework.transaction.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) [server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) [server.jar:na]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A]
    at com.sun.proxy.$Proxy68.doWork(Unknown Source) [na:na]
    at ome.services.util.Executor$Impl.execute(Executor.java:457) [server.jar:na]
    at omero.cmd.HandleI.run(HandleI.java:359) [blitz.jar:na]
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) [na:1.7.0_51]
    at ome.services.util.Executor$Impl$1.call(Executor.java:498) [server.jar:na]
    at java.util.concurrent.FutureTask.run(FutureTask.java:262) [na:1.7.0_51]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [na:1.7.0_51]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [na:1.7.0_51]
    at java.lang.Thread.run(Thread.java:744) [na:1.7.0_51]

melissalinkert · 2014-07-01T18:05:22Z

I would be very surprised if that's at all related to this PR. @joshmoore (or anyone else)?

joshmoore · 2014-07-01T18:53:32Z

I'd guess that the processor wasn't running, but I don't know why that would be the case.... Looking at the logs:

2014-07-01 05:52:21,809 INFO  [        ome.services.util.ServiceHandler] (.Server-51)  Excp:    Ice.UnknownException
    unknown = "java.lang.NullPointerException
                at omero.grid.InteractiveProcessorI.execute(InteractiveProcessorI.java:264)
                at sun.reflect.GeneratedMethodAccessor2948.invoke(Unknown Source)

which is something @manics and I have certainly seen before. Definitely not related.

ghost · 2014-07-02T11:08:53Z

The ome-xml data looks fine with the patch applied. Please merge.

ScanR: fix exposure time units

melissalinkert · 2014-07-07T15:18:48Z

--rebased-to #1198

ScanR: fix exposure time units

b99585d

See http://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7554

melissalinkert added the dev_5_0 label Jul 1, 2014

melissalinkert added develop and removed dev_5_0 labels Jul 3, 2014

melissalinkert added a commit that referenced this pull request Jul 4, 2014

Merge pull request #1187 from melissalinkert/scanr-exposure

923651e

ScanR: fix exposure time units

melissalinkert merged commit 923651e into ome:develop Jul 4, 2014

melissalinkert mentioned this pull request Jul 7, 2014

ScanR: fix exposure time units (rebased onto dev_5_0) #1198

Merged

melissalinkert deleted the scanr-exposure branch September 26, 2014 13:29

sbesson added this to the 5.1.0-m1 milestone Oct 14, 2014

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ScanR: fix exposure time units #1187

ScanR: fix exposure time units #1187

melissalinkert commented Jul 1, 2014

bramalingam commented Jul 1, 2014

melissalinkert commented Jul 1, 2014

joshmoore commented Jul 1, 2014

ghost commented Jul 2, 2014

melissalinkert commented Jul 7, 2014

ScanR: fix exposure time units #1187

ScanR: fix exposure time units #1187

Conversation

melissalinkert commented Jul 1, 2014

bramalingam commented Jul 1, 2014

melissalinkert commented Jul 1, 2014

joshmoore commented Jul 1, 2014

ghost commented Jul 2, 2014

melissalinkert commented Jul 7, 2014