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Task #10841 (new)

Opened 11 years ago

Last modified 8 years ago

BUG: Batch image export as jpeg — at Initial Version

Reported by: pwalczysko Owned by:
Priority: critical Milestone: OMERO-5
Component: Export Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: FS demo 4.1

Description

When trying to run Batch image export on big images with "jpeg" option selected, you end up with an error, both in Web and Insight (user-4 on Gretzky, using latest develop branch Inisght build for Insight).

Images tested include e.g. leica-scn/mihaela/...., and .svs images.
Found out during the testing of PR ​https://github.com/ome/scripts/pull/30.
See similar problematics in ticket on this PR, concerning export as one-tiff option.

WARNING:omero.gateway:InternalException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <86:24:41:e3:-51f141ba:13e7811cad3:-7cb2omero.api.Exporter> generateTiff((<ServiceOptsDict: {'omero.session.uuid': '7135aec0-ce92-456e-9be3-3fc047c68241', 'omero.client.uuid': 'bd13d346-5f38-450b-8eb1-4d891dbdf028'}>,), {})
Traceback (most recent call last):
  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 3481, in __call__
    return self.f(*args, **kwargs)
  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero_api_Exporter_ice.py", line 93, in generateTiff
    return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx))
InternalException: exception ::omero::InternalException
{
    serverStackTrace = loci.formats.FormatException: Metadata object has null root; call IMetadata.createRoot() first
    at loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:331)
    at loci.formats.FormatWriter.checkParams(FormatWriter.java:375)
    at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:174)
    at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:201)
    at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:187)
    at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
    at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:413)
    at sun.reflect.GeneratedMethodAccessor254.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:592)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
    at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
    at $Proxy66.doWork(Unknown Source)
    at ome.services.util.Executor$Impl.execute(Executor.java:416)
    at ome.services.util.Executor$Impl.execute(Executor.java:360)
    at ome.services.blitz.impl.ExporterI.do_tiff(ExporterI.java:343)
    at ome.services.blitz.impl.ExporterI.generateTiff_async(ExporterI.java:213)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:592)
    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:59)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
    at $Proxy114.generateTiff_async(Unknown Source)
    at omero.api._ExporterTie.generateTiff_async(_ExporterTie.java:71)
    at omero.api._ExporterDisp.___generateTiff(_ExporterDisp.java:175)
    at omero.api._ExporterDisp.__dispatch(_ExporterDisp.java:248)
    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)

    serverExceptionClass = loci.formats.FormatException
    message = Metadata object has null root; call IMetadata.createRoot() first
}
Traceback (most recent call last):
  File "./script", line 527, in <module>
    runScript()
  File "./script", line 513, in runScript
    fileAnnotation, message = batchImageExport(conn, scriptParams)
  File "./script", line 357, in batchImageExport
    saveAsOmeTiff(conn, img, folder_name)
  File "./script", line 171, in saveAsOmeTiff
    fileSize, block_gen = image.exportOmeTiff(bufsize=65536)
  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 6790, in exportOmeTiff
    size = e.generateTiff(self._conn.SERVICE_OPTS)
  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 3484, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 3481, in __call__
    return self.f(*args, **kwargs)
  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero_api_Exporter_ice.py", line 93, in generateTiff
    return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx))
omero.InternalException: exception ::omero::InternalException
{
    serverStackTrace = loci.formats.FormatException: Metadata object has null root; call IMetadata.createRoot() first
    at loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:331)
    at loci.formats.FormatWriter.checkParams(FormatWriter.java:375)
    at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:174)
    at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:201)
    at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:187)
    at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
    at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:413)
    at sun.reflect.GeneratedMethodAccessor254.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:592)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
    at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
    at $Proxy66.doWork(Unknown Source)
    at ome.services.util.Executor$Impl.execute(Executor.java:416)
    at ome.services.util.Executor$Impl.execute(Executor.java:360)
    at ome.services.blitz.impl.ExporterI.do_tiff(ExporterI.java:343)
    at ome.services.blitz.impl.ExporterI.generateTiff_async(ExporterI.java:213)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:592)
    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:59)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
    at $Proxy114.generateTiff_async(Unknown Source)
    at omero.api._ExporterTie.generateTiff_async(_ExporterTie.java:71)
    at omero.api._ExporterDisp.___generateTiff(_ExporterDisp.java:175)
    at omero.api._ExporterDisp.__dispatch(_ExporterDisp.java:248)
    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)

    serverExceptionClass = loci.formats.FormatException
    message = Metadata object has null root; call IMetadata.createRoot() first
}

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