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

Wed Mar 8 22:10:05 GMT 2017

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/formats-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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