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Task #12955 (new)

Opened 4 years ago

Last modified 4 years ago

BUG:Measurementtool problems with sdt file

Reported by: omero-qa Owned by: dlindner
Priority: minor Milestone: Unscheduled
Component: from QA Version: 5.1.2
Keywords: n.a. Cc: i.munro@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

https://www.openmicroscopy.org/qa2/qa2/qa/feedback/11159/

Comment: I've been struggling with insight's measurement tool. If I open this file with FLIMfit or Icy then the first time point contains entirely zeroes(as expected). Importing to OMERO & Using insight I seem to see(small) numbers (around 8-ish)
Maybe I'm using the tool incorrectly but would appreciate if somebody could confirm.


    

Attachments (2)

SPWFromJava.ome.tiff (19.7 KB) - added by dlindner 4 years ago.
Screen Shot 2015-07-21 at 16.43.57.png (253.2 KB) - added by dlindner 4 years ago.

Download all attachments as: .zip

Change History (8)

Changed 4 years ago by dlindner

Changed 4 years ago by dlindner

comment:1 Changed 4 years ago by dlindner

When I tried to reproduce this today, I couldn't import the image any more. Upload went fine, it's in the managed repo folder, but it doesn't show up in the project/dataset structure. No error reported, but log file shows:

2015-11-24 10:48:10,730 DEBUG [                    omero.util.IceMapper] (l.Server-0) Handling:
ome.conditions.InternalException: Failed to find script
	at ome.services.scripts.ScriptFinder.getFile(ScriptFinder.java:111) ~[blitz.jar:na]
	at ome.services.scripts.ScriptFinder.createJob(ScriptFinder.java:136) ~[blitz.jar:na]
	at ome.services.blitz.impl.MetadataStoreI$6.doWork(MetadataStoreI.java:298) ~[blitz.jar:na]
	at sun.reflect.GeneratedMethodAccessor301.invoke(Unknown Source) ~[na:na]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_65]
	at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_65]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [spring-aop.jar:3.0.1.RELEASE]
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) ~[spring-orm.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) ~[spring-tx.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) ~[server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [spring-aop.jar:3.0.1.RELEASE]
	at com.sun.proxy.$Proxy72.doWork(Unknown Source) ~[na:na]
	at ome.services.util.Executor$Impl.execute(Executor.java:443) ~[server.jar:na]
	at ome.services.util.Executor$Impl.execute(Executor.java:387) ~[server.jar:na]
	at ome.services.throttling.Adapter.run(Adapter.java:50) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) [blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:154) [blitz.jar:na]
	at ome.services.blitz.impl.MetadataStoreI.postProcess_async(MetadataStoreI.java:281) [blitz.jar:na]
	at sun.reflect.GeneratedMethodAccessor1511.invoke(Unknown Source) ~[na:na]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_65]
	at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_65]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [spring-aop.jar:3.0.1.RELEASE]
	at omero.cmd.CallContext.invoke(CallContext.java:78) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [spring-aop.jar:3.0.1.RELEASE]
	at com.sun.proxy.$Proxy101.postProcess_async(Unknown Source) [na:na]
	at omero.api._MetadataStoreTie.postProcess_async(_MetadataStoreTie.java:78) [blitz.jar:na]
	at omero.api._MetadataStoreDisp.___postProcess(_MetadataStoreDisp.java:304) [blitz.jar:na]
	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:384) [blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:222) [ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2482) [ice.jar:na]
	at Ice.ConnectionI.dispatch(ConnectionI.java:1258) [ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:1213) [ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:321) [ice.jar:na]
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) [ice.jar:na]
	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_65]
2015-11-24 10:48:10,731 DEBUG [                    omero.util.IceMapper] (l.Server-0) Handling:
omero.InternalException: null
	at omero.util.IceMapper.handleException(IceMapper.java:1400) ~[blitz.jar:na]
	at ome.services.throttling.Adapter.run(Adapter.java:52) ~[blitz.jar:na]
	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) [blitz.jar:na]
	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:154) [blitz.jar:na]
	at ome.services.blitz.impl.MetadataStoreI.postProcess_async(MetadataStoreI.java:281) [blitz.jar:na]
	at sun.reflect.GeneratedMethodAccessor1511.invoke(Unknown Source) ~[na:na]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_65]
	at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_65]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [spring-aop.jar:3.0.1.RELEASE]
	at omero.cmd.CallContext.invoke(CallContext.java:78) [blitz.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [spring-aop.jar:3.0.1.RELEASE]
	at com.sun.proxy.$Proxy101.postProcess_async(Unknown Source) [na:na]
	at omero.api._MetadataStoreTie.postProcess_async(_MetadataStoreTie.java:78) [blitz.jar:na]
	at omero.api._MetadataStoreDisp.___postProcess(_MetadataStoreDisp.java:304) [blitz.jar:na]
	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:384) [blitz.jar:na]
	at IceInternal.Incoming.invoke(Incoming.java:222) [ice.jar:na]
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2482) [ice.jar:na]
	at Ice.ConnectionI.dispatch(ConnectionI.java:1258) [ice.jar:na]
	at Ice.ConnectionI.message(ConnectionI.java:1213) [ice.jar:na]
	at IceInternal.ThreadPool.run(ThreadPool.java:321) [ice.jar:na]
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12) [ice.jar:na]
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693) [ice.jar:na]
	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_65]
2015-11-24 10:48:10,732 WARN  [    ome.formats.OMEROMetadataStoreClient] (2-thread-2) Failed to launch post-processing
omero.InternalException: null
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_65]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_65]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_65]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:422) ~[na:1.8.0_65]
	at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_65]
	at IceInternal.BasicStream.createUserException(BasicStream.java:2615) ~[ice.jar:na]
	at IceInternal.BasicStream.access$300(BasicStream.java:12) ~[ice.jar:na]
	at IceInternal.BasicStream$EncapsDecoder11.throwException(BasicStream.java:3406) ~[ice.jar:na]
	at IceInternal.BasicStream.throwException(BasicStream.java:2077) ~[ice.jar:na]
	at IceInternal.Outgoing.throwUserException(Outgoing.java:538) ~[ice.jar:na]
	at omero.api._MetadataStoreDelM.postProcess(_MetadataStoreDelM.java:130) ~[blitz.jar:na]
	at omero.api.MetadataStorePrxHelper.postProcess(MetadataStorePrxHelper.java:401) ~[blitz.jar:na]
	at omero.api.MetadataStorePrxHelper.postProcess(MetadataStorePrxHelper.java:373) ~[blitz.jar:na]
	at ome.formats.OMEROMetadataStoreClient.launchProcessing(OMEROMetadataStoreClient.java:1881) ~[blitz.jar:na]
	at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedImportRequestI.java:411) [blitz.jar:na]
	at omero.cmd.HandleI.steps(HandleI.java:438) [blitz.jar:na]
	at omero.cmd.HandleI$1.doWork(HandleI.java:366) [blitz.jar:na]
	at omero.cmd.HandleI$1.doWork(HandleI.java:362) [blitz.jar:na]
	at sun.reflect.GeneratedMethodAccessor301.invoke(Unknown Source) ~[na:na]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_65]
	at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_65]
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) [spring-aop.jar:3.0.1.RELEASE]
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) [spring-orm.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) [spring-tx.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) [server.jar:na]
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [spring-aop.jar:3.0.1.RELEASE]
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [spring-aop.jar:3.0.1.RELEASE]
	at com.sun.proxy.$Proxy72.doWork(Unknown Source) [na:na]
	at ome.services.util.Executor$Impl.execute(Executor.java:443) [server.jar:na]
	at omero.cmd.HandleI.run(HandleI.java:360) [blitz.jar:na]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_65]
	at ome.services.util.Executor$Impl$1.call(Executor.java:484) [server.jar:na]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_65]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_65]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_65]
	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_65]

comment:2 Changed 4 years ago by jamoore

Dom: where did you try this? That looks like a secondary or unrelated issue.

comment:3 Changed 4 years ago by dlindner

Tried it on eel and then also with a local build of the develop branch, with the attached image SPWFromJava.ome.tiff​. I can't make much sense of the error message yet. Yes, it's actually not related to this ticket except that I used this image. Should I open a new ticket? If so, is it a server issue, ome-tiff issue, ...?

comment:4 Changed 4 years ago by jamoore

If you can reproduce it, might be a new bug ticket. Might be worth retrying with the next daily build.

comment:5 Changed 4 years ago by imunro-x

This si a synthetic file that I generated just to test the issue I was having. In the end that issue turned out to be that the measurement tool keeps reporting on the same T-point even after you change the slider. In order to use the measurement tool with a different T-point you need to completely close the viewer.

comment:6 Changed 4 years ago by dlindner

I created a new ticket for the issue: https://trac.openmicroscopy.org/ome/ticket/13108
It seems to be specific for this image, other images work fine. The error message I quoted above apparently was just a coincidence, not related to the issue.

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