[ome-devel] Olympus SlideScan.ini importer problems with ome.formats.model.ChannelProcessor.process(ChannelProcessor.java:469)
Paul Richards
paulrichards321 at gmail.com
Mon Mar 13 21:11:01 GMT 2017
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/
> test/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(
> OMEROMetadataStoreClient.java:1752)
> at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(
> ManagedImportRequestI.java:623)
> at ome.services.blitz.repo.ManagedImportRequestI.step(
> ManagedImportRequestI.java:501)
> at omero.cmd.HandleI.steps(HandleI.java:438)
> at omero.cmd.HandleI$1.doWork(HandleI.java:366)
> at omero.cmd.HandleI$1.doWork(HandleI.java:362)
> at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection
> (AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.
> invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:150)
> at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(
> HibernateInterceptor.java:111)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at org.springframework.transaction.interceptor.
> TransactionInterceptor.invoke(TransactionInterceptor.java:108)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(
> ProxyCleanupFilter.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$1.call(Executor.java:484)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.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(
> OMEROMetadataStoreClient.java:1752)
> at ome.services.blitz.repo.ManagedImportRequestI.importMetadata(
> ManagedImportRequestI.java:623)
> at ome.services.blitz.repo.ManagedImportRequestI.step(
> ManagedImportRequestI.java:501)
> at omero.cmd.HandleI.steps(HandleI.java:438)
> at omero.cmd.HandleI$1.doWork(HandleI.java:366)
> at omero.cmd.HandleI$1.doWork(HandleI.java:362)
> at sun.reflect.GeneratedMethodAccessor291.invoke(Unknown Source)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
> DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection
> (AopUtils.java:307)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.
> invokeJoinpoint(ReflectiveMethodInvocation.java:183)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:150)
> at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:562)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(
> HibernateInterceptor.java:111)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at org.springframework.transaction.interceptor.
> TransactionInterceptor.invoke(TransactionInterceptor.java:108)
> at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(
> ReflectiveMethodInvocation.java:172)
> at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(
> ProxyCleanupFilter.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$1.call(Executor.java:484)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(
> ThreadPoolExecutor.java:1142)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.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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