[ome-users] loading data frmo matlab to an Image in OMERO in two phases
Will Moore
will at lifesci.dundee.ac.uk
Thu Aug 4 13:21:32 BST 2011
Hi Alex,
Sorry for the delay - this one kinda slipped through the net...
Once an image is created, with pixel data (either via import, or after
the first use of rawPixelsStore) then you cannot modify the pixel data
again.
A bunch of statistics are calculated, E.g. min & max for each channel,
checksum or hash of the pixels object on disk etc and these cannot
currently be updated.
You will see the same error if you try to modify the pixels of any
existing image in OMERO.
Your options depend on how distinct the sessions are for writing data.
If it's possibly to use the same session (rawPixelsStore) then that
could work.
If you need to write the data in a number of different transactions,
then one option may be to write a separate image each time, then
stitch them together when you're done.
E.g. Combine_Images.py script (although this script doesn't support
combining of multi-T images into a longer movie, but it could be used
to stitch together individual timepoints.
Or you could write your own code to stitch together the images.
Sorry we can't be more helpful just now,
Will.
On 28 Jul 2011, at 12:07, Alexander Tournier wrote:
> Hi All,
>
> I want to write data to OMERO Images, however sometimes I don't have
> all the data at that time.
> So say I load up timeframes 1 to 10 in one go and 11 to 20 later,
> for example.
>
> However, when I try to 'open' the image object a second time I get a
> long error message.
> I've written a short script to show this, attached, error message
> below.
>
> The way I'm doing it now is keeping hold of the rawPixelsStore
> instance, so I can write to the image as long as I have that. Now
> that only works within one matlab session.
>
> Any ideas how to go about this/what I'm doing wrong?
> Thanks,
> Alex
>
>
> ??? Java exception occurred:
> omero.ApiUsageException
> serverStackTrace = "ome.conditions.ApiUsageException: Write-
> method not permitted.
> at
>
> ome.io.nio.RomioPixelBuffer.throwIfReadOnly(RomioPixelBuffer.java:109)
> at
>
> ome.io.nio.RomioPixelBuffer.setPlane(RomioPixelBuffer.java:666)
> at
>
> ome.services.RawPixelsBean.setPlane(RawPixelsBean.java:564)
> at
>
> sun.reflect.GeneratedMethodAccessor1483.invoke(Unknown
> Source)
> 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.EventHandler.invoke(EventHandler.java:150)
> at
>
> org
> .springframework
> .aop
> .framework
> .ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:
> 172)
> at
>
> ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
> at
>
> ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
> 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:231)
> 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
> $Proxy85.setPlane(Unknown Source)
> at
> sun.reflect.GeneratedMethodAccessor1483.invoke(Unknown
> Source)
> 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:
> 83)
> 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
> $Proxy85.setPlane(Unknown Source)
> at
> sun.reflect.GeneratedMethodAccessor1486.invoke(Unknown
> Source)
> 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:136)
> at
>
> ome
> .services
> .blitz.impl.RawPixelsStoreI.setPlane_async(RawPixelsStoreI.java:211)
> at
>
> omero.api._RawPixelsStoreTie.setPlane_async(_RawPixelsStoreTie.java:
> 281)
> at
>
> omero.api._RawPixelsStoreDisp.___setPlane(_RawPixelsStoreDisp.java:
> 943)
> at
>
> omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:
> 1301)
> 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 = "ome.conditions.ApiUsageException"
> message = "Write-method not permitted."
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown
> Source)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown
> Source)
> at java.lang.reflect.Constructor.newInstance(Unknown Source)
> at java.lang.Class.newInstance0(Unknown Source)
> at java.lang.Class.newInstance(Unknown Source)
> at
> IceInternal.BasicStream
> $DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
> at
> IceInternal.BasicStream.throwException(BasicStream.java:1632)
> at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
> at
> omero.api._RawPixelsStoreDelM.setPlane(_RawPixelsStoreDelM.java:1566)
> at
> omero
> .api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:
> 2159)
> at
> omero
> .api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:
> 2131)
>
>
>
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William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee DD1 5EH
United Kingdom
Phone 01382 386364
http://openmicroscopy.org
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