[ome-devel] File import help
Brian Bodensteiner
brian at intelligent-imaging.com
Sat Jun 1 01:03:19 BST 2019
Hi,
We’re working with some of our users to improve SlideBook file import for OMERO but could use some help. First, we tested using stock OMERO.insight 5.4.10. Importing the .SLD files results in the following error (as the default importer does not handle new data):
2019-05-31 16:53:17,563 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) processor is INTEL_64 os.arch is amd64
2019-05-31 16:53:17,563 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) architecture is WINDOWS_64 os.name <http://os.name/> is windows 10
2019-05-31 16:53:17,566 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) architecture is WINDOWS_64 os.name <http://os.name/> is windows 10
2019-05-31 16:53:17,566 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) platform specific path is META-INF/lib/windows_64/
2019-05-31 16:53:17,566 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) mappedLib is turbojpeg.dll
2019-05-31 16:53:17,566 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) URL is jar:file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/turbojpeg.jar!/META-INF/lib/windows_64/turbojpeg.dll
2019-05-31 16:53:17,566 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) URL path is file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/turbojpeg.jar!/META-INF/lib/windows_64/turbojpeg.dll
2019-05-31 16:53:17,570 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) Extracting 'jar:file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/turbojpeg.jar!/META-INF/lib/windows_64/turbojpeg.dll' to 'C:\Users\bode\AppData\Local\Temp\turbojpeg716059823595712527.dll'
2019-05-31 16:53:24,193 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) OMERO Version: 5.4.10-ice36-b105
2019-05-31 16:53:24,195 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) Bioformats version: 5.9.2 revision: 9fc607f85b8900be786813296f1eee75cc1ed883 date: 31 August 2018
2019-05-31 16:53:24,211 INFO [ ome.formats.importer.ImportCandidates] ( Thread-14) Depth: 4 Metadata Level: MINIMUM
2019-05-31 16:53:24,252 INFO [ loci.formats.ImageReader] ( Thread-14) SlidebookReader initializing C:\Users\bode\Desktop\Streaming Phasor Test.sld
2019-05-31 16:53:24,256 INFO [ loci.formats.FormatHandler] ( Thread-14) Finding offsets to pixel data
2019-05-31 16:53:24,598 INFO [ loci.formats.FormatHandler] ( Thread-14) Determining dimensions
2019-05-31 16:53:24,604 INFO [ ome.formats.importer.ImportCandidates] ( Thread-14) 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 387ms. (393ms total) [0 unknowns]
Next, we copied the SlideBook6Reader.jar into the lib folder. This is picked up and executed, and the metadata is read correctly. However, no pixel data is read, and I get the following exception:
2019-05-31 16:55:13,347 WARN [ o.o.s.a.m.editor.AnnotationTaskPane] (nitializer) UI for displaying ROIS annotations not implemented yet!
2019-05-31 16:55:13,737 DEBUG [ omero.gateway.facility.Facility$1] ( Thread-10) Created new BrowseFacility
2019-05-31 16:55:21,534 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) processor is INTEL_64 os.arch is amd64
2019-05-31 16:55:21,535 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) architecture is WINDOWS_64 os.name <http://os.name/> is windows 10
2019-05-31 16:55:21,537 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) architecture is WINDOWS_64 os.name <http://os.name/> is windows 10
2019-05-31 16:55:21,537 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] (entQueue-0) platform specific path is META-INF/lib/windows_64/
2019-05-31 16:55:21,537 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) mappedLib is turbojpeg.dll
2019-05-31 16:55:21,537 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) URL is jar:file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/turbojpeg.jar!/META-INF/lib/windows_64/turbojpeg.dll
2019-05-31 16:55:21,537 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) URL path is file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/turbojpeg.jar!/META-INF/lib/windows_64/turbojpeg.dll
2019-05-31 16:55:21,541 DEBUG [ org.scijava.nativelib.BaseJniExtractor] (entQueue-0) Extracting 'jar:file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/turbojpeg.jar!/META-INF/lib/windows_64/turbojpeg.dll' to 'C:\Users\bode\AppData\Local\Temp\turbojpeg2282115949619483911.dll'
2019-05-31 16:55:30,033 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) OMERO Version: 5.4.10-ice36-b105
2019-05-31 16:55:30,034 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) Bioformats version: 5.9.2 revision: 9fc607f85b8900be786813296f1eee75cc1ed883 date: 31 August 2018
2019-05-31 16:55:30,053 INFO [ ome.formats.importer.ImportCandidates] ( Thread-14) Depth: 4 Metadata Level: MINIMUM
2019-05-31 16:55:30,067 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] ( Thread-14) architecture is WINDOWS_64 os.name <http://os.name/> is windows 10
2019-05-31 16:55:30,068 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] ( Thread-14) architecture is WINDOWS_64 os.name <http://os.name/> is windows 10
2019-05-31 16:55:30,068 DEBUG [ org.scijava.nativelib.NativeLibraryUtil] ( Thread-14) platform specific path is META-INF/lib/windows_64/
2019-05-31 16:55:30,068 DEBUG [ org.scijava.nativelib.BaseJniExtractor] ( Thread-14) mappedLib is SlideBook6Reader.dll
2019-05-31 16:55:30,069 DEBUG [ org.scijava.nativelib.BaseJniExtractor] ( Thread-14) URL is jar:file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/SlideBook6Reader.jar!/META-INF/lib/windows_64/SlideBook6Reader.dll
2019-05-31 16:55:30,069 DEBUG [ org.scijava.nativelib.BaseJniExtractor] ( Thread-14) URL path is file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/SlideBook6Reader.jar!/META-INF/lib/windows_64/SlideBook6Reader.dll
2019-05-31 16:55:30,072 DEBUG [ org.scijava.nativelib.BaseJniExtractor] ( Thread-14) Extracting 'jar:file:/C:/Users/bode/Downloads/OMERO.insight-5.4.10-ice36-b105-win(1)/OMERO.insight-5.4.10-ice36-b105-win/libs/SlideBook6Reader.jar!/META-INF/lib/windows_64/SlideBook6Reader.dll' to 'C:\Users\bode\AppData\Local\Temp\SlideBook6Reader2121001236271405033.dll'
2019-05-31 16:55:30,111 INFO [ loci.formats.ImageReader] ( Thread-14) SlideBook6Reader initializing C:\Users\bode\Desktop\Streaming Phasor Test.sld
2019-05-31 16:55:30,218 INFO [ ome.formats.importer.ImportCandidates] ( Thread-14) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 159ms. (165ms total) [0 unknowns]
2019-05-31 16:55:31,552 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) OMERO Version: 5.4.10-ice36-b105
2019-05-31 16:55:31,552 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) Bioformats version: 5.9.2 revision: 9fc607f85b8900be786813296f1eee75cc1ed883 date: 31 August 2018
2019-05-31 16:55:31,554 INFO [ ome.formats.importer.ImportCandidates] ( Thread-14) Depth: 4 Metadata Level: MINIMUM
2019-05-31 16:55:31,574 INFO [ loci.formats.ImageReader] ( Thread-14) SlideBook6Reader initializing C:\Users\bode\Desktop\Streaming Phasor Test.sld
2019-05-31 16:55:31,630 INFO [ ome.formats.importer.ImportCandidates] ( Thread-14) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 73ms. (76ms total) [0 unknowns]
2019-05-31 16:55:31,631 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) OMERO Version: 5.4.10-ice36-b105
2019-05-31 16:55:31,631 INFO [ ome.formats.importer.ImportConfig] ( Thread-14) Bioformats version: 5.9.2 revision: 9fc607f85b8900be786813296f1eee75cc1ed883 date: 31 August 2018
2019-05-31 16:55:32,980 DEBUG [ ome.services.blitz.util.CurrentPlatform] ( Thread-14) recognized current operating system as being Microsoft Windows
2019-05-31 16:55:33,877 INFO [ o.f.i.transfers.UploadFileTransfer] ( Thread-14) Transferring C:\Users\bode\Desktop\Streaming Phasor Test.sld...
2019-05-31 16:55:42,722 ERROR [o.o.s.e.data.views.calls.ThumbnailLoader] ( Thread-17) API erroromero.InternalException
serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.AssertionError):
File not open.
at loci.formats.in.SlideBook6Reader.readImagePlaneBuf(Native Method)
at loci.formats.in.SlideBook6Reader.openBytes(SlideBook6Reader.java:153)
at loci.formats.ImageReader.openBytes(ImageReader.java:460)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:227)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:149)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:341)
at ome.io.bioformats.BfPixelsWrapper.getWholePlane(BfPixelsWrapper.java:366)
at ome.io.bioformats.BfPixelsWrapper.getPlane(BfPixelsWrapper.java:263)
at ome.io.bioformats.BfPixelBuffer.getPlane(BfPixelBuffer.java:209)
at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:208)
at omeis.providers.re.GreyScaleStrategy.renderAsPackedInt(GreyScaleStrategy.java:153)
at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558)
at ome.services.ThumbnailBean.createScaledImage(ThumbnailBean.java:648)
at ome.services.ThumbnailBean.retrieveThumbnail(ThumbnailBean.java:1255)
at ome.services.ThumbnailBean.getThumbnailWithoutDefault(ThumbnailBean.java:1127)
at sun.reflect.GeneratedMethodAccessor943.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.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:216)
at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:200)
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.$Proxy102.getThumbnailWithoutDefault(Unknown Source)
at sun.reflect.GeneratedMethodAccessor943.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:93)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy102.getThumbnailWithoutDefault(Unknown Source)
at sun.reflect.GeneratedMethodAccessor1291.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:172)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:140)
at ome.services.blitz.impl.ThumbnailStoreI.getThumbnailWithoutDefault_async(ThumbnailStoreI.java:132)
at sun.reflect.GeneratedMethodAccessor1290.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 omero.cmd.CallContext.invoke(CallContext.java:85)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy103.getThumbnailWithoutDefault_async(Unknown Source)
at omero.api._ThumbnailStoreTie.getThumbnailWithoutDefault_async(_ThumbnailStoreTie.java:162)
at omero.api._ThumbnailStoreDisp.___getThumbnailWithoutDefault(_ThumbnailStoreDisp.java:607)
at omero.api._ThumbnailStoreDisp.__dispatch(_ThumbnailStoreDisp.java:1026)
at IceInternal.Incoming.invoke(Incoming.java:221)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2536)
at Ice.ConnectionI.dispatch(ConnectionI.java:1145)
at Ice.ConnectionI.message(ConnectionI.java:1056)
at IceInternal.ThreadPool.run(ThreadPool.java:395)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832)
at java.lang.Thread.run(Thread.java:748)
"
serverExceptionClass = "ome.conditions.InternalException"
message = " Wrapped Exception: (java.lang.AssertionError):
File not open."
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at java.lang.Class.newInstance(Unknown Source)
at IceInternal.BasicStream.createUserException(BasicStream.java:2779)
at IceInternal.BasicStream.access$300(BasicStream.java:14)
at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298)
at IceInternal.BasicStream.throwException(BasicStream.java:2291)
at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399)
at omero.api.ThumbnailStorePrxHelper.end_getThumbnailWithoutDefault(ThumbnailStorePrxHelper.java:3248)
at omero.api.ThumbnailStorePrxHelper.getThumbnailWithoutDefault(ThumbnailStorePrxHelper.java:3119)
at omero.api.ThumbnailStorePrxHelper.getThumbnailWithoutDefault(ThumbnailStorePrxHelper.java:3106)
at org.openmicroscopy.shoola.env.data.views.calls.ThumbnailLoader.loadThumbnail(ThumbnailLoader.java:342)
at org.openmicroscopy.shoola.env.data.views.calls.ThumbnailLoader.handleBatchCall(ThumbnailLoader.java:245)
at org.openmicroscopy.shoola.env.data.views.calls.ThumbnailLoader.access$100(ThumbnailLoader.java:73)
at org.openmicroscopy.shoola.env.data.views.calls.ThumbnailLoader$1.doCall(ThumbnailLoader.java:218)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Unknown Source)
I’ve tested the same jars in Fiji and they are working fine, so I am guessing there is something different going on in terms of file open/close flow. I can’t find the source of the "File not open.” error message - it is the case that in order to read pixel data the file must be parsed and read, but I’d also presume this happens when the metadata is read. We have some specific exceptions thrown when a file is closed and then attempted to be read, so it would help to understand where that message is coming from. We also updated the jar on the server as well, though it’s unclear if that’s required or not (is pixel data stored directly or accessed on the server).
Anyway any direction you could provide would be much appreciated. This feels like the right direction - similar to Fiji dropping the library into the Bio-Formats installation immediately moves things to the SlideBook6Reader.jar.
Thanks again for your help,
Brian
Brian Bodensteiner
Vice President Engineering
Intelligent Imaging Innovations (3i)
3509 Ringsby Court
Denver, CO 80216 USA
1-424-744-5941
www.intelligent-imaging.com <http://www.intelligent-imaging.com/>
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