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Task #2358 (closed)

Opened 9 years ago

Closed 9 years ago

BUG: Importing lsm

Reported by: jburel Owned by: cxallan
Priority: critical Milestone: OMERO-Beta4.2
Component: Import Version: n.a.
Keywords: n.a. Cc: cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2010-05-13 (9)

Description (last modified by jburel)

Using r6984
Follow the exception when trying to import 2chZT.lsm

2010-05-14 22:24:14,091 57590      [2-thread-1] DEBUG      ome.formats.importer.gui.GuiImporter  - java.lang.NullPointerException
	at ome.formats.OMEROMetadataStoreClient.handleAbstractLightSource(OMEROMetadataStoreClient.java:1079)
	at ome.formats.OMEROMetadataStoreClient.getIObjectContainer(OMEROMetadataStoreClient.java:2322)
	at ome.formats.OMEROMetadataStoreClient.getSourceObject(OMEROMetadataStoreClient.java:1022)
	at ome.formats.OMEROMetadataStoreClient.getLaser(OMEROMetadataStoreClient.java:4388)
	at ome.formats.OMEROMetadataStoreClient.setLaserLaserMedium(OMEROMetadataStoreClient.java:4424)
	at loci.formats.meta.FilterMetadata.setLaserLaserMedium(FilterMetadata.java:978)
	at loci.formats.in.ZeissLSMReader.populateMetadataStore(ZeissLSMReader.java:941)
	at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:850)
	at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:400)
	at loci.formats.FormatReader.setId(FormatReader.java:1011)
	at loci.formats.ImageReader.setId(ImageReader.java:644)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:59)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
	at java.util.concurrent.FutureTask.run(FutureTask.java:123)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)
	at java.lang.Thread.run(Thread.java:613)

Change History (19)

comment:1 Changed 9 years ago by jburel

  • Description modified (diff)

comment:2 Changed 9 years ago by cxallan

  • Status changed from new to assigned

comment:3 Changed 9 years ago by cxallan

As of r7034 fails with:

2010-05-18 13:43:25,822 594798     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Volumes/ome/data_repo/test_images_good/lsm/C1.lsm
java.lang.RuntimeException: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.ArrayIndexOutOfBoundsException):
                        4
                        	at ome.formats.OMEROMetadataStore.getFilter(OMEROMetadataStore.java:1239)
                        	at ome.formats.OMEROMetadataStore.handle(OMEROMetadataStore.java:708)
                        	at ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:213)
                        	at ome.services.blitz.impl.MetadataStoreI$4.doWork(MetadataStoreI.java:198)
                        	at sun.reflect.GeneratedMethodAccessor307.invoke(Unknown Source)
                        	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                        	at java.lang.reflect.Method.invoke(Method.java:597)
                        	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:409)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:144)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy54.doWork(Unknown Source)
                        	at ome.services.util.Executor$Impl.execute(Executor.java:339)
                        	at ome.services.throttling.Adapter.run(Adapter.java:51)
                        	at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                        	at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:146)
                        	at ome.services.blitz.impl.MetadataStoreI.updateObjects_async(MetadataStoreI.java:183)
                        	at omero.api._MetadataStoreTie.updateObjects_async(_MetadataStoreTie.java:92)
                        	at omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:173)
                        	at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:337)
                        	at IceInternal.Incoming.invoke(Incoming.java:159)
                        	at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                        	at Ice.ConnectionI.message(ConnectionI.java:972)
                        	at IceInternal.ThreadPool.run(ThreadPool.java:577)
                        	at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                        	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "

comment:4 Changed 9 years ago by cxallan

  • Owner changed from bwzloranger to cxallan
  • Status changed from assigned to new

As of bio-formtas:r6301 these files fail with:

2010-05-18 15:50:09,673 1644082    [2-thread-1] DEBUG      ome.formats.importer.gui.GuiImporter  - Error processing references.
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:150)
	at ome.formats.OMEROMetadataStoreClient.postProcess(OMEROMetadataStoreClient.java:1659)
	at ome.formats.importer.ImportLibrary.importMetadata(ImportLibrary.java:251)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:437)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
	at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
	at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149)
	at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:637)
Caused by: java.lang.RuntimeException: Unable to synchronize reference Dichroic:0:1 --> omero.model.LightPath:0:0
	at ome.formats.model.ReferenceProcessor.process(ReferenceProcessor.java:121)
	... 15 more

comment:5 Changed 9 years ago by cxallan

  • Status changed from new to assigned

comment:6 Changed 9 years ago by cxallan

(In [7038]) Correct LightPath? support. (See #2388, #2358)

comment:7 Changed 9 years ago by cxallan

Back to the ArrayOutOfBoundsException as of r7038. It appears that the channel indexes are being incremented where they don't necessarily need to be.

    public void setLightPathDichroicRef(String dichroic, int imageIndex, int channelIndex)

Examples of the containers:

2010-05-18 16:31:09,655 385981     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Channel:0:0 == omero.model.ChannelI@49940c14,Channel:0:0
2010-05-18 16:31:09,657 385983     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.Channel:0:1 == omero.model.ChannelI@31818dbc,omero.model.Channel:0:1

2010-05-18 16:31:10,160 386486     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:0 == omero.model.LightPathI@277b8705,omero.model.LightPath:0:0
2010-05-18 16:31:10,160 386486     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:1 == omero.model.LightPathI@5b40c349,omero.model.LightPath:0:1
2010-05-18 16:31:10,160 386486     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:2 == omero.model.LightPathI@6f3d346d,omero.model.LightPath:0:2
2010-05-18 16:31:10,166 386492     [2-thread-1] DEBUG      ome.formats.OMEROMetadataStoreClient  - omero.model.LightPath:0:3 == omero.model.LightPathI@1307e9af,omero.model.LightPath:0:3

comment:8 Changed 9 years ago by cxallan

  • Owner changed from cxallan to mlinkert-x
  • Status changed from assigned to new

comment:9 Changed 9 years ago by cxallan

(In [7039]) Further LightPath? emission and excitation filter reference fixes. (See #2388, #2358)

comment:10 Changed 9 years ago by mlinkert

Should be fixed in ​bio-formats:r6337.

comment:11 Changed 9 years ago by cxallan

  • Owner changed from mlinkert-x to cxallan
  • Status changed from new to assigned

comment:12 Changed 9 years ago by cxallan

  • Remaining Time set to 0
  • Resolution set to fixed
  • Status changed from assigned to closed

(In [7043]) Upgrading to ​bio-formats:r6340. (Fixes #2358, #2377, #2380, #2381, #2390)

comment:13 Changed 9 years ago by cxallan

New exception on different LSM data:

2010-05-19 14:52:09,335 596312     [2-thread-1] ERROR  importer.gui.ErrorHandler$MyErrorHandler  - INTERNAL_EXCEPTION: /Users/callan/testimages/lsm_martin/01-01.lsm
java.lang.IllegalArgumentException: 0 must not be null and positive.
        at ome.xml.r201004.primitives.PositiveInteger.<init>(PositiveInteger.java:41)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:112)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:91)
        at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:643)
        at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:400)
        at loci.formats.FormatReader.setId(FormatReader.java:1012)
        at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:324)
        at loci.formats.FormatReader.setId(FormatReader.java:1012)
        at loci.formats.ImageReader.setId(ImageReader.java:644)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:177)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:485)
        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:213)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:399)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:340)
        at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:215)
        at ome.formats.importer.gui.ImportHandler.access$1(ImportHandler.java:149)
        at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:134)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:98)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:207)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:637)

comment:14 Changed 9 years ago by cxallan

  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:15 Changed 9 years ago by cxallan

  • Owner changed from cxallan to mlinkert-x
  • Status changed from reopened to new

comment:16 Changed 9 years ago by mlinkert

Fixed in ​bio-formats:r6353.

comment:17 Changed 9 years ago by cxallan

  • Status changed from new to assigned

comment:18 Changed 9 years ago by cxallan

  • Owner changed from mlinkert-x to cxallan

comment:19 Changed 9 years ago by cxallan

  • Resolution set to fixed
  • Status changed from assigned to closed

(In [7066]) Updating to ​bio-formats:r6355. (Fixes #2358, #2367, #2368, #2406)

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