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Task #10354 (closed)

Opened 11 years ago

Closed 11 years ago

BUG: Wrong display of ets and vsi

Reported by: pwalczysko Owned by:
Priority: critical Milestone: 5.0.0-beta1
Component: Import Version: n.a.
Keywords: FS import Cc: fs@…, ux@…,
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: FS Demo 2

Description

During testing of ​https://github.com/openmicroscopy/openmicroscopy/pull/634.

Imported

/Volumes/ome/data_repo/test_images_good/cellsens/brian/Image_28.vsi
and
/Volumes/ome/data_repo/test_images_good/cellsens/brian/SW10082402-02_21.vsi
and
/Volumes/ome/data_repo/test_images_good/cellsens/brian/_Image_28_/stack1/frame_t_0.ets
and
/Volumes/ome/data_repo/test_images_good/cellsens/brian/_SW10082402-02_21_/stack1/frame_t_0.ets

All four images have following problems -

  1. Importer: "Thumbnail cannot be created" message after successfull import
  2. Thumbnails are black in Insight, and grey with placeholder in Web
  3. Full viewer starts opening, but never progresses to the end

Change History (5)

comment:1 Changed 11 years ago by pwalczysko

  • Summary changed from BUG: Wrong display of ets and vdi to BUG: Wrong display of ets and vsi

comment:2 Changed 11 years ago by pwalczysko

Just confirmed that /Volumes/ome/data_repo/test_images_good/cellsens/brian/Image_28.vsi displays correctly on Howe. This suggests that the bug is FS specific

comment:3 Changed 11 years ago by mlinkert

Note that there is no need to import both the .ets files and the .vsi files - choosing just the .vsi file will pick up all of the necessary .ets files.

comment:4 Changed 11 years ago by mlinkert

Stack trace from the Blitz log:

java.lang.IllegalArgumentException: Invalid C index: 1/1
  at loci.formats.FormatTools.getIndex(FormatTools.java:325)
  at loci.formats.FormatTools.getIndex(FormatTools.java:278)
  at loci.formats.ChannelSeparator.getIndex(ChannelSeparator.java:258)
  at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:344)
  at ome.io.bioformats.BfPixelBuffer.getTileDirect(BfPixelBuffer.java:486)
  at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:470)
  at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:216)
  at omeis.providers.re.HSBStrategy.getWavelengthData(HSBStrategy.java:105)
  at omeis.providers.re.HSBStrategy.makeRenderingTasks(HSBStrategy.java:216)
  at omeis.providers.re.HSBStrategy.render(HSBStrategy.java:311)
  at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:275)
  at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511)
  at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478)
  at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532)
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:616)
  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.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 $Proxy102.renderCompressed(Unknown Source)
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:616)
  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:98)
  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 $Proxy102.renderCompressed(Unknown Source)
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:616)
  at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
  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:150)
  at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344)
  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
  at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
  at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
  at java.lang.reflect.Method.invoke(Method.java:616)
  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 $Proxy104.renderCompressed_async(Unknown Source)
  at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:313)
  at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:653)
  at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1766)
  at IceInternal.Incoming.invoke(Incoming.java:159)
  at Ice.ConnectionI.invokeAll(ConnectionI.java:2357)
  at Ice.ConnectionI.dispatch(ConnectionI.java:1208)
  at Ice.ConnectionI.message(ConnectionI.java:1163)
  at IceInternal.ThreadPool.run(ThreadPool.java:302)
  at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
  at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:643)
  at java.lang.Thread.run(Thread.java:679)

comment:5 Changed 11 years ago by mlinkert

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

PR opened: ​https://github.com/openmicroscopy/bioformats/pull/369

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