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Task #10841 (new)

Opened 11 years ago

Last modified 8 years ago

BUG: Export as jpeg — at Version 2

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 (last modified by pwalczysko)

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:-7ba4omero.api.RenderingEngine> renderCompressed((object #0 (::omero::romio::PlaneDef)
{
    slice = 0
    x = 0
    y = 0
    z = 0
    t = 0
    region = <nil>
    stride = 0
}, <ServiceOptsDict: {'omero.session.uuid': '9d092919-574d-4f7c-9504-3f661cee3da8', 'omero.client.uuid': 'e6657582-f2cc-4d9e-85f2-b31acf0cfa4b'}>), {})
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_RenderingEngine_ice.py", line 196, in renderCompressed
    return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx))
InternalException: exception ::omero::InternalException
{
    serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (java.lang.NegativeArraySizeException):
null
	at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:69)
	at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:188)
	at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:274)
	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.GeneratedMethodAccessor1366.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.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 $Proxy105.renderCompressed(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor1366.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.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 $Proxy105.renderCompressed(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor1402.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	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.GeneratedMethodAccessor1401.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 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 $Proxy107.renderCompressed_async(Unknown Source)
	at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309)
	at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583)
	at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700)
	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.InternalException
    message =  Wrapped Exception: (java.lang.NegativeArraySizeException):
null
}
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 384, in batchImageExport
    zRange, tRange, greyscale, imgWidth, projectZ=projectZ, format=format, folder_name=folder_name)
  File "./script", line 233, in savePlanesForImage
    savePlane(image, format, cName, (defaultZ,), projectZ, t, c, gScale, imgWidth, folder_name)
  File "./script", line 127, in savePlane
    plane.save(imgName)
AttributeError: 'NoneType' object has no attribute 'save'

Further, when trying to use the download as jpeg option in Web on a big image, a new window in browser is navigated, saying

Page not found. (404)
The requested object or URL was not found on this server. The link you followed is either outdated, inaccurate, or the server has been instructed not to let you have it.

Change History (2)

comment:1 Changed 11 years ago by pwalczysko

  • Description modified (diff)

comment:2 Changed 11 years ago by pwalczysko

  • Description modified (diff)
  • Summary changed from BUG: Batch image export as jpeg to BUG: Export as jpeg
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