Task #10841 (new)
Opened 11 years ago
Last modified 8 years ago
BUG: Batch image export as jpeg — at Version 1
Reported by: | pwalczysko | Owned by: | |
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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'