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FIJI Import Problem

https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7871

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FIJI Import Problem

PostPosted: Sun Aug 02, 2015 11:34 pm
by Lachie
Hi All,

I'm currently testing a deployment of Omero and one of the major functionalities I require is to be able to batch process a range of Image IDs from FIJI. (Note, eventually I suspect writing scripts within omero will be the optimal way of dealing with this but for now all my analysis is in FIJI).

Using the File>Import>OMERO function I can only seem to import files that are ~1mb. Anything larger and I get the error pasted below.

Any help would be greatly appreciated.
(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 840MB of 38831MB (2%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: Could not open a plane for the given dimensions
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:271)
at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:132)
at ij.Executer.run(Executer.java:65)
at java.lang.Thread.run(Thread.java:662)

Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: Could not open a plane for the given dimensions
at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
at java.util.concurrent.FutureTask.get(FutureTask.java:83)
at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:267)
... 5 more

Caused by: java.lang.IllegalStateException: Could not open a plane for the given dimensions
at io.scif.img.cell.loaders.AbstractArrayLoader.loadArray(AbstractArrayLoader.java:176)
at io.scif.img.cell.SCIFIOCellCache.load(SCIFIOCellCache.java:145)
at io.scif.img.cell.SCIFIOImgCells$CachedCells.get(SCIFIOImgCells.java:122)
at io.scif.img.cell.SCIFIOImgCells$CachedCells.get(SCIFIOImgCells.java:101)
at net.imglib2.img.list.ListRandomAccess.get(ListRandomAccess.java:81)
at net.imglib2.img.cell.CellRandomAccess.getCell(CellRandomAccess.java:130)
at net.imglib2.img.cell.CellRandomAccess.updatePosition(CellRandomAccess.java:470)
at net.imglib2.img.cell.CellRandomAccess.setPosition(CellRandomAccess.java:326)
at net.imglib2.display.projector.composite.CompositeXYProjector.mapSingle(CompositeXYProjector.java:273)
at net.imglib2.display.projector.composite.CompositeXYProjector.map(CompositeXYProjector.java:162)
at net.imagej.display.SourceOptimizedCompositeXYProjector.map(SourceOptimizedCompositeXYProjector.java:100)
at net.imagej.display.DefaultDatasetView.rebuild(DefaultDatasetView.java:401)
at net.imagej.display.DefaultImageDisplay.rebuild(DefaultImageDisplay.java:136)
at net.imagej.display.DefaultImageDisplay.display(DefaultImageDisplay.java:274)
at org.scijava.display.DefaultDisplayService.createDisplay(DefaultDisplayService.java:221)
at org.scijava.display.DefaultDisplayService.createDisplay(DefaultDisplayService.java:207)
at org.scijava.display.DisplayPostprocessor.handleOutput(DisplayPostprocessor.java:116)
at org.scijava.display.DisplayPostprocessor.process(DisplayPostprocessor.java:72)
at org.scijava.module.ModuleRunner.postProcess(ModuleRunner.java:116)
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:176)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)

... 1 more
Caused by: io.scif.FormatException: Error communicating with OMERO
at net.imagej.omero.OMEROFormat.communicationException(OMEROFormat.java:648)
at net.imagej.omero.OMEROFormat.access$400(OMEROFormat.java:77)
at net.imagej.omero.OMEROFormat$Reader.openPlane(OMEROFormat.java:450)
at net.imagej.omero.OMEROFormat$Reader.openPlane(OMEROFormat.java:425)
at io.scif.AbstractReader.openPlane(AbstractReader.java:167)
at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:170)
at io.scif.filters.ChannelFiller.openPlane(ChannelFiller.java:151)
at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:304)
at io.scif.filters.PlaneSeparator.openPlane(PlaneSeparator.java:208)
at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:225)
at io.scif.filters.AbstractReaderFilter.openPlane(AbstractReaderFilter.java:191)
at io.scif.img.cell.loaders.AbstractArrayLoader.read(AbstractArrayLoader.java:223)
at io.scif.img.cell.loaders.AbstractArrayLoader.read(AbstractArrayLoader.java:196)
at io.scif.img.cell.loaders.AbstractArrayLoader.loadArray(AbstractArrayLoader.java:173)
... 27 more

Caused by: omero.InternalException
serverStackTrace = "ome.conditions.InternalException: Wrapped Exception: (java.lang.NegativeArraySizeException):
null
at ome.services.RawPixelsBean.getTile(RawPixelsBean.java:782)
at sun.reflect.GeneratedMethodAccessor2137.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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:218)

at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202)

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$Interceptor.invoke(ProxyCleanupFilter.java:249)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy96.getTile(Unknown Source)
at sun.reflect.GeneratedMethodAccessor2137.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
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 com.sun.proxy.$Proxy96.getTile(Unknown Source)
at sun.reflect.GeneratedMethodAccessor2141.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
at ome.services.throttling.Callback.run(Callback.java:56)
at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:149)
at ome.services.blitz.impl.RawPixelsStoreI.getTile_async(RawPixelsStoreI.java:265)
at sun.reflect.GeneratedMethodAccessor2140.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at omero.cmd.CallContext.invoke(CallContext.java:78)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
at com.sun.proxy.$Proxy97.getTile_async(Unknown Source)
at omero.api._RawPixelsStoreTie.getTile_async(_RawPixelsStoreTie.java:204)
at omero.api._RawPixelsStoreDisp.___getTile(_RawPixelsStoreDisp.java:884)
at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1466)
at IceInternal.Incoming.invoke(Incoming.java:222)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
at Ice.ConnectionI.message(ConnectionI.java:1213)
at IceInternal.ThreadPool.run(ThreadPool.java:321)
at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
at java.lang.Thread.run(Thread.java:745)

"
serverExceptionClass = "ome.conditions.InternalException"
message = " Wrapped Exception: (java.lang.NegativeArraySizeException):
null"
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at java.lang.Class.newInstance0(Class.java:355)
at java.lang.Class.newInstance(Class.java:308)
at IceInternal.BasicStream.createUserException(BasicStream.java:2615)
at IceInternal.BasicStream.access$300(BasicStream.java:12)
at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3099)
at IceInternal.BasicStream.throwException(BasicStream.java:2077)
at IceInternal.Outgoing.throwUserException(Outgoing.java:538)
at omero.api._RawPixelsStoreDelM.getTile(_RawPixelsStoreDelM.java:1186)
at omero.api.RawPixelsStorePrxHelper.getTile(RawPixelsStorePrxHelper.java:5603)
at omero.api.RawPixelsStorePrxHelper.getTile(RawPixelsStorePrxHelper.java:5563)
at net.imagej.omero.OMEROFormat$Reader.openPlane(OMEROFormat.java:446)
... 38 more

Re: FIJI Import Problem

PostPosted: Mon Aug 03, 2015 10:54 am
by bramalingam
Hi,

Thank you for reporting your issue.

Testing locally with the latest versions of Bio-Formats(5.1.3) and Omero-IJ Plugin (5.1.3),we were unable to reproduce the bug. So it could be as simple as upgrading your FIJI installation to incorporate the latest versions of the Plugins.
Help > FIJI update

Aslo,

Going by the error log, it looks like you have the SCIFIO feature(http://fiji.sc/SCIFIO) enabled!

In the extreme case, where the update does not solve your problem (which in this case : should), you could also try disabling the SCIFIO feature by unchecking the SCIFIO option in,
EDIT > Options > ImageJ2

and retrying your import.

Hope that helps.
Please let us know if neither of these suggestions work.

Best,
Balaji

Re: FIJI Import Problem

PostPosted: Tue Aug 04, 2015 12:28 am
by Lachie
Hi Balaji,

Thanks for your response. Unfortunately I'm still having this issue. I'm pretty obsessive about keeping FIJI up to date and seeing the scifio errors concerned me too (I definitely have it disabled).

Just to be a little clearer on my problem, I can open an image through the omero.insight plugin, but when trying to access the same file via: File>Import>Omero I get the error. I've tried it on two different computers now and am seeing the same thing. Perhaps it's something on our omero server side?

Thanks again,
-Lachie

Re: FIJI Import Problem

PostPosted: Wed Aug 05, 2015 10:43 am
by bramalingam
Hi Lachie,

I was initially testing the workflow on Mac-OSX, but retried the same on a windows (VM). In both cases, I couldn't reproduce the exception.

Tried with SCIFIO : "Enabled" and "Disabled"
and here as well, the images opened without any issues (in both cases).

And the set-up at my end is the same as yours:
"(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.6.0_24 [64-bit]; Windows 7 6.1;"

So could you please give us more information on the following,
OMERO Server Version :
OMERO_IJ Plugin Version :
Bio-Formats Version :

Best,
Balaji

Re: FIJI Import Problem

PostPosted: Thu Sep 10, 2015 6:59 pm
by dtrudg
Am seeing the same issue. Anything over approx 1mb will not import.

'An error ocurred while loading the image'

OMERO server is 5.1.3. Current plugins downloaded from OMERO site and added to ImageJ manually (not via ImageJ updater).

Re: FIJI Import Problem

PostPosted: Fri Sep 11, 2015 12:02 pm
by jburel
Thanks for the feedback
We will have to do further tests.
In order to try to narrow down the issue,
did you try/manage to import without using the plugin?

Thanks
Jmarie

Re: FIJI Import Problem

PostPosted: Fri Sep 11, 2015 5:59 pm
by dtrudg
Standalone insight client and the matlab plugin are working nicely, no problems.

I can load the failing images direct from disk into FIJI through the bioformats plugin (latest). The issue is only occuring with the import from OMERO.

Our Ice.MessageSizeMax has been increased to allow large images to work with the matlab plugin. This seems unrelated though, as the ImageJ plugin won't open anything above ~1MB.

Please let me know if I can provide any useful info. I'm not really familiar with what useful logs etc. for debugging are for ImageJ plugins.

Re: FIJI Import Problem

PostPosted: Sun Sep 13, 2015 8:20 pm
by jburel
Thanks for the information, that's useful
I will get back to you asap

Cheers
Jmarie
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