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Task #11349 (closed)

Opened 11 years ago

Closed 10 years ago

Bug: Zeiss CZI files do not import into OMERO

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: Unscheduled
Component: from QA Version: 4.4.8
Keywords: n.a. Cc: ssimard@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

​https://www.openmicroscopy.org/qa2/qa2/qa/feedback/7555/

Comment: Please find a sample CZI file (acquisition in SIM mode) which failed to render on: OMERO version=5.0.0-beta1-DEV-ice34;os.name=Windows+7;os.arch=amd64;os.version=6.1;java.runtime.version=1.6.0_43-b01;java.vm.vendor=Sun+Microsystems+Inc


Stack trace upon importing into OMERO:

Caused by: omero.InternalException
    serverStackTrace = "ome.conditions.InternalException:  Wrapped Exception: (java.lang.NullPointerException):
                        null
                          at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:2355)
                          at loci.formats.in.ZeissCZIReader.openBytes(ZeissCZIReader.java:298)
                          at loci.formats.ImageReader.openBytes(ImageReader.java:416)
                          at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:197)
                          at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:226)
                          at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:320)
                          at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:345)
                          at ome.io.bioformats.BfPixelBuffer.getTileDirect(BfPixelBuffer.java:488)
                          at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:472)
                          at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216)
                          at omeis.providers.re.metadata.StatsFactory$1.run(StatsFactory.java:345)
                          at ome.io.nio.Utils.forEachTile(Utils.java:88)
                          at ome.io.nio.Utils.forEachTile(Utils.java:39)
                          at omeis.providers.re.metadata.StatsFactory.computeLocationStats(StatsFactory.java:330)
                          at ome.logic.RenderingSettingsImpl.computeLocationStats(RenderingSettingsImpl.java:905)
                          at ome.logic.RenderingSettingsImpl.resetChannelBindings(RenderingSettingsImpl.java:834)
                          at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:589)
                          at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:505)
                          at ome.logic.RenderingSettingsImpl.resetDefaults(RenderingSettingsImpl.java:1324)
                          at ome.services.RenderingBean$11.doWork(RenderingBean.java:1848)
                          at sun.reflect.GeneratedMethodAccessor249.invoke(Unknown Source)
                          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                          at java.lang.reflect.Method.invoke(Method.java:597)
                          at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                          at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                          at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                          at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
                          at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)

Other .czi files (including those in test_images_good) have the same problem. Opening any of these files outside of OMERO works as expected.

Attachments (1)

11349.png​ (755.3 KB) - added by jburel 10 years ago.

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Change History (4)

comment:1 Changed 10 years ago by jburel

Tested using Today's build, no problem with any of test_images_good files and the uploaded one (see screenshot)

Last edited 10 years ago by jburel (previous) (diff)

Changed 10 years ago by jburel

comment:2 Changed 10 years ago by jburel

any reason not to close it?

comment:3 Changed 10 years ago by mlinkert

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