Task #12978 (closed)
Bug: Zeiss PlaneInfo population
Reported by: | mtbcarroll | Owned by: | mlinkert |
---|---|---|---|
Priority: | major | Milestone: | B-F-5.2.0 |
Component: | Bio-Formats | Version: | OMERO-5.1.3 |
Keywords: | ZeissLSMReader, OMETiffReader, our-fault, external | Cc: | audrey.salles@…, bf@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
On importing the LSM file in https://www.openmicroscopy.org/qa2/qa/feedback/11328/ the OMERO server throws,
ome.conditions.ValidationException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC; nested exception is org.hibernate.PropertyValueException: not-null property references a null or transient value: ome.model.core.PlaneInfo.theC at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:648) ~[org.springframework.orm.jar:3.0.1.RELEASE-A] at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412) ~[org.springframework.orm.jar:3.0.1.RELEASE-A] at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117) ~[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$Interceptor.invoke(ProxyCleanupFilter.java:249) ~[server.jar:na] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A] at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) ~[server.jar:na] at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) [org.springframework.aop.jar:3.0.1.RELEASE-A] at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) [org.springframework.aop.jar:3.0.1.RELEASE-A] at com.sun.proxy.$Proxy72.doWork(Unknown Source) ~[na:na] at ome.services.util.Executor$Impl.execute(Executor.java:447) ~[server.jar:na] at ome.services.util.Executor$Impl.execute(Executor.java:391) ~[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.saveToDB_async(MetadataStoreI.java:218) [blitz.jar:na] at sun.reflect.GeneratedMethodAccessor1675.invoke(Unknown Source) ~[na:na] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.7.0_60] at java.lang.reflect.Method.invoke(Method.java:606) ~[na:1.7.0_60] 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.$Proxy106.saveToDB_async(Unknown Source) [na:na] at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:94) [blitz.jar:na] at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:271) [blitz.jar:na] at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:419) [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:745) [na:1.7.0_60]
Change History (12)
comment:1 Changed 9 years ago by mtbcarroll
- Cc audrey.salles@… added
comment:2 Changed 9 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.4
comment:3 Changed 9 years ago by mlinkert
comment:4 Changed 9 years ago by jamoore
- Milestone changed from 5.1.4 to B-F-5.1.4
Splitting 5.1.4 due to milestone decoupling
comment:5 Changed 9 years ago by sbesson
- Milestone changed from B-F-5.1.4 to BF-5.1.5
comment:6 Changed 8 years ago by dlindner
New QA reports/sample files: https://www.openmicroscopy.org/qa2/qa/feedback/16981/ - https://www.openmicroscopy.org/qa2/qa/feedback/16987/
comment:7 Changed 8 years ago by dlindner
Same error (but here not with Zeiss LSM but with an ome.tiff file): https://www.openmicroscopy.org/qa2/qa/feedback/16996/
comment:8 Changed 8 years ago by dlindner
comment:9 Changed 8 years ago by mlinkert
Still planning to work on this before the end of March - some of these are the same issue, some are similar exceptions but slightly different problems. I'll add more details and/or split up into new cards for anything that isn't done before the end of the month. These should all be plain bug fixes though, so if we run out of time for 5.2.0 then they should be safe for 5.2.1.
comment:10 Changed 8 years ago by mlinkert
- Keywords OMETiffReader our-fault external added
- Resolution set to fixed
- Status changed from new to closed
comment:11 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [66079508d3d50f2da3cabea8e97327b2c2a488eb/bioformats.git] on branch develop) Zeiss LSM: read rotation, phase, and illumination counts
See #12978.
comment:12 Changed 8 years ago by Melissa Linkert <melissa@…>
(In [ce5ffc924b0a6a96e8d11226a68f24c39e05d769/bioformats.git] on branch develop) OME-TIFF: make sure Plane attributes are correctly populated
See #12978
The underlying cause here is that the image count is incorrect. There should be 5 phases and 5 rotations in addition to 30 Z - following the convention in the .czi reader, this would mean 5 T (phase in ModuloT) and 150 Z (rotation in ModuloZ). This isn't (yet?) in the "Self-contained bugs" column of https://trello.com/b/Uoadzs9k/formats because I don't know where the phase/rotation counts are coming from.