[ome-devel] Olympus SlideScan.ini importer problems with ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469)

Mon Mar 13 21:33:08 GMT 2017

Not ready yet: looking for feedback on the NPEs especially
ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469) but
I'm also continuing to debug it as well. Not giving up yet!!! Thanks for
any of your help!

On Mon, Mar 13, 2017 at 5:26 PM, Sebastien Besson (Staff) <
s.besson at dundee.ac.uk> wrote:

> Hi Paul,
>
> many thanks for this, we’ll take a look at your Pull Request at the
> earliest.
>
> To be sure we agree on the expectations, we understand the current state
> of the
> pull request matches the state of this thread i.e. you are looking for
> feedback especially
> regarding NPEs thrown at OMERO import time. Is that correct or is the pull
> request
> opened for potential inclusion into the mainline?
>
> Best,
> Sebastien
>
> On 13 Mar 2017, at 21:11, Paul Richards <paulrichards321 at gmail.com> wrote:
>
> I have sent pull requests #2786 #2787.
>
> On Fri, Mar 10, 2017 at 10:22 AM, David Gault (Staff) <
> d.gault at dundee.ac.uk> wrote:
>
>> Hi Paul,
>>
>> The work on the reader looks like it is coming along nicely. I was able
>> to carry out some debugging of the exceptions you have been seeing. The
>> first exception is due to a missing ExperimenterID which can be set as
>> below at the same point which you are setting instrument and objective ID’s.
>>
>> store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
>>
>> Once that NullPointerException is resolved you will see a number of other
>> exceptions relating to null values on the Pixels object for sizeC, sizeT,
>> sizeZ etc. These largely relate to the handling of resolutions depending on
>> if the flattenedResolutions is set to true or not. In this regard we had a
>> numerous bits of feedback on various sections of code, would it be possible
>> to upload the reader to GitHub? It might make it easier to provide comments
>> on the individual sections or lines of code.
>>
>> With Thanks,
>> David Gault
>>
>> On 8 Mar 2017, at 22:10, Paul Richards <paulrichards321 at gmail.com> wrote:
>>
>> You can grab a small test slide here: http://medtech.med.wayne.edu/t
>> est/SG09-599.zip
>>
>> You would then change into that directory and import SlideScan.ini or any
>> of the other .ini files.
>>
>> Here is the crucial part of the import log after all the jpg files are
>> uploaded:
>>
>> 2017-03-08 16:32:28,615 19727      [      main] INFO
>> ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
>> 2017-03-08 16:32:28,753 19865      [      main] INFO
>> ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 4000
>> 2017-03-08 16:32:28,980 20092      [l.Client-1] ERROR
>> ome.formats.importer.cli.ErrorHandler - INTERNAL_EXCEPTION:
>> /home/omero/SG09-599/SlideScan.ini
>> java.lang.RuntimeException: Failure response on import!
>> Category: ::omero::grid::ImportRequest
>> Name: import-request-failure
>> Parameters: {stacktrace=java.lang.NullPointerException
>> at ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469)
>> at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetada
>> taStoreClient.java:1752)
>> at ome.services.blitz.repo.ManagedImportRequestI.importMetadata
>> (ManagedImportRequestI.java:623)
>> at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedIm
>> portRequestI.java:501)
>> at omero.cmd.HandleI.steps(HandleI.java:438)
>> at omero.cmd.HandleI$1.doWork(HandleI.java:366)
>> at omero.cmd.HandleI$1.doWork(HandleI.java:362)
>> at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>> thodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:498)
>> at org.springframework.aop.support.AopUtils.invokeJoinpointUsin
>> gReflection(AopUtils.java:307)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:150)
>> at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at org.springframework.orm.hibernate3.HibernateInterceptor.
>> invoke(HibernateInterceptor.java:111)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at org.springframework.transaction.interceptor.TransactionInter
>> ceptor.invoke(TransactionInterceptor.java:108)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(Pr
>> oxyCleanupFilter.java:249)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(
>> JdkDynamicAopProxy.java:202)
>> at com.sun.proxy.$Proxy72.doWork(Unknown Source)
>> at ome.services.util.Executor$Impl.execute(Executor.java:443)
>> at omero.cmd.HandleI.run(HandleI.java:360)
>> at java.util.concurrent.Executors$RunnableAdapter.call(
>> Executors.java:511)
>> at ome.services.util.Executor$Impl$1.call(Executor.java:484)
>> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
>> Executor.java:1142)
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
>> lExecutor.java:617)
>> at java.lang.Thread.run(Thread.java:745)
>> , message=}
>>
>> at ome.formats.importer.ImportLibrary$ImportCallback.onFinished
>> (ImportLibrary.java:665)
>> at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334)
>> at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
>> at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
>> at IceInternal.Incoming.invoke(Incoming.java:222)
>> at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
>> at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
>> at Ice.ConnectionI.message(ConnectionI.java:1213)
>> at IceInternal.ThreadPool.run(ThreadPool.java:321)
>> at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
>> at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> java.lang.RuntimeException: Failure response on import!
>> Category: ::omero::grid::ImportRequest
>> Name: import-request-failure
>> Parameters: {stacktrace=java.lang.NullPointerException
>> at ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469)
>> at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetada
>> taStoreClient.java:1752)
>> at ome.services.blitz.repo.ManagedImportRequestI.importMetadata
>> (ManagedImportRequestI.java:623)
>> at ome.services.blitz.repo.ManagedImportRequestI.step(ManagedIm
>> portRequestI.java:501)
>> at omero.cmd.HandleI.steps(HandleI.java:438)
>> at omero.cmd.HandleI$1.doWork(HandleI.java:366)
>> at omero.cmd.HandleI$1.doWork(HandleI.java:362)
>> at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>> thodAccessorImpl.java:43)
>> at java.lang.reflect.Method.invoke(Method.java:498)
>> at org.springframework.aop.support.AopUtils.invokeJoinpointUsin
>> gReflection(AopUtils.java:307)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .invokeJoinpoint(ReflectiveMethodInvocation.java:183)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:150)
>> at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at org.springframework.orm.hibernate3.HibernateInterceptor.
>> invoke(HibernateInterceptor.java:111)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at org.springframework.transaction.interceptor.TransactionInter
>> ceptor.invoke(TransactionInterceptor.java:108)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(Pr
>> oxyCleanupFilter.java:249)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
>> at org.springframework.aop.framework.ReflectiveMethodInvocation
>> .proceed(ReflectiveMethodInvocation.java:172)
>> at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(
>> JdkDynamicAopProxy.java:202)
>> at com.sun.proxy.$Proxy72.doWork(Unknown Source)
>> at ome.services.util.Executor$Impl.execute(Executor.java:443)
>> at omero.cmd.HandleI.run(HandleI.java:360)
>> at java.util.concurrent.Executors$RunnableAdapter.call(
>> Executors.java:511)
>> at ome.services.util.Executor$Impl$1.call(Executor.java:484)
>> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
>> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool
>> Executor.java:1142)
>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo
>> lExecutor.java:617)
>> at java.lang.Thread.run(Thread.java:745)
>> , message=}
>>
>> at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:665)
>> ~[blitz.jar:na]
>> at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:334) [blitz.jar:na]
>> at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
>> [blitz.jar:na]
>> at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
>> [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_121]
>> 2017-03-08 16:32:28,985 20097      [      main] ERROR
>>  ome.formats.importer.ImportLibrary - Error on import
>> java.lang.Exception: Import failure
>> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:560)
>> ~[blitz.jar:na]
>> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289)
>> ~[blitz.jar:na]
>> at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:293)
>> [blitz.jar:na]
>> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:950)
>> [blitz.jar:na]
>> 2017-03-08 16:32:28,985 20097      [      main] INFO
>> ome.formats.importer.ImportLibrary - Exiting on error
>>
>> ==> Summary
>> 494 files uploaded, 0 filesets created, 0 images imported, 1 error in
>> 0:00:17.810
>>
>>
>>
>>
>>
>> On Wed, Mar 8, 2017 at 4:55 PM, Paul Richards <paulrichards321 at gmail.com>
>> wrote:
>>
>>> Hello,
>>>
>>> I have successfully developed a separate open source C++ program to
>>> convert Olympus SlideScan.ini pyramid images into big tiff format. I have
>>> since been working on a open microscopy version of this importer, but keep
>>> running into a java NullPointer exception on import. I have been debugging
>>> this for about a week with no luck. I can import the images fine if I do
>>> not assign resolutionCount > 1, but then I do not see the pyramid view.
>>> Attached is the log with the java runtime error. I have tried different
>>> version of bioformats, and grabbed yesterday's git version of the open
>>> microscopy source code and also tried 5.2.7 with no luck. I keep getting
>>> the same NullPointer error. I know I must be doing something wrong!
>>>
>>> Here is the source code of the import module:
>>>
>>> http://medtech.med.wayne.edu/test/OlympusINIReader.java
>>>
>>> (just plop this file into bioformats-5.3.4/components/formats-gpl/src/loci/in
>>> and run ant in the formats-gpl directory)
>>>
>>> http://medtech.med.wayne.edu/test/readers.txt
>>>
>>> (this file goes into bioformats-5.3.4/components/fo
>>> rmats-api/src/loci/formatsats-api/src/)
>>>
>>> Please let me know if you would like me to use the git tree for these, I
>>> didn't include them since they are not working properly.
>>>
>>> Any help is greatly appreciated!
>>>
>>> Best Regards,
>>>
>>> Paul Richards
>>> Web Developer
>>> Wayne State University School of Medicine
>>>
>>
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>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>
>>
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>>
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>>
>>
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