Error while exporting ROI

[Mohammedhusen]

Dear Team,

Hope you are doing well.

while exporting ROI we are getting below error in the version "OMERO.web 5.16.0." , could you please help us to resolve this error?

This method cannot handle tiled images yet. roi_export_error.txt

Regards, Mohammedhusen Khatib

[will-moore]

Hi, I'm just going to put the stack trace here in a details block to make it easier for others to read:

ome.conditions.ApiUsageException

``` WARNING:omero.gateway:ApiUsageException on to <5cb3e25b-9cb3-4b2d-8cbd-b49f484a158bomero.api.IRoi> getShapeStatsRestricted(([8], 0, 0, [0, 1, 2]), {}) Traceback (most recent call last): File "/opt/omero/server/venv3/lib/python3.8/site-packages/omero/gateway/__init__.py", line 4856, in __call__ return self.f(*args, **kwargs) File "/opt/omero/server/venv3/lib/python3.8/site-packages/omero_api_IRoi_ice.py", line 826, in getShapeStatsRestricted return _M_omero.api.IRoi._op_getShapeStatsRestricted.invoke(self, ((shapeIdList, zForUnattached, tForUnattached, channels), _ctx)) omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: This method cannot handle tiled images yet. at ome.services.roi.GeomTool.getStatsRestricted(GeomTool.java:415) at ome.services.blitz.impl.RoiI$8.doWork(RoiI.java:260) at jdk.internal.reflect.GeneratedMethodAccessor292.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy81.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.util.Executor$Impl.execute(Executor.java:392) at ome.services.throttling.Adapter.run(Adapter.java:50) at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:154) at ome.services.blitz.impl.RoiI.getShapeStatsRestricted_async(RoiI.java:252) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy111.getShapeStatsRestricted_async(Unknown Source) at omero.api._IRoiTie.getShapeStatsRestricted_async(_IRoiTie.java:148) at omero.api._IRoiDisp.___getShapeStatsRestricted(_IRoiDisp.java:436) at omero.api._IRoiDisp.__dispatch(_IRoiDisp.java:657) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = This method cannot handle tiled images yet. } Traceback (most recent call last): File "./script", line 419, in run_script() File "./script", line 402, in run_script result = batch_roi_export(conn, script_params) File "./script", line 332, in batch_roi_export for row in get_export_data(conn, script_params, image, units): File "./script", line 114, in get_export_data stats = roi_service.getShapeStatsRestricted( File "/opt/omero/server/venv3/lib/python3.8/site-packages/omero/gateway/__init__.py", line 4859, in __call__ return self.handle_exception(e, *args, **kwargs) File "/opt/omero/server/venv3/lib/python3.8/site-packages/omero/gateway/__init__.py", line 4856, in __call__ return self.f(*args, **kwargs) File "/opt/omero/server/venv3/lib/python3.8/site-packages/omero_api_IRoi_ice.py", line 826, in getShapeStatsRestricted return _M_omero.api.IRoi._op_getShapeStatsRestricted.invoke(self, ((shapeIdList, zForUnattached, tForUnattached, channels), _ctx)) omero.ApiUsageException: exception ::omero::ApiUsageException { serverStackTrace = ome.conditions.ApiUsageException: This method cannot handle tiled images yet. at ome.services.roi.GeomTool.getStatsRestricted(GeomTool.java:415) at ome.services.blitz.impl.RoiI$8.doWork(RoiI.java:260) at jdk.internal.reflect.GeneratedMethodAccessor292.invoke(Unknown Source) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:568) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.security.basic.EventHandler.invoke(EventHandler.java:154) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:119) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:249) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy81.doWork(Unknown Source) at ome.services.util.Executor$Impl.execute(Executor.java:447) at ome.services.util.Executor$Impl.execute(Executor.java:392) at ome.services.throttling.Adapter.run(Adapter.java:50) at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89) at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:154) at ome.services.blitz.impl.RoiI.getShapeStatsRestricted_async(RoiI.java:252) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at omero.cmd.CallContext.invoke(CallContext.java:85) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213) at com.sun.proxy.$Proxy111.getShapeStatsRestricted_async(Unknown Source) at omero.api._IRoiTie.getShapeStatsRestricted_async(_IRoiTie.java:148) at omero.api._IRoiDisp.___getShapeStatsRestricted(_IRoiDisp.java:436) at omero.api._IRoiDisp.__dispatch(_IRoiDisp.java:657) at IceInternal.Incoming.invoke(Incoming.java:221) at Ice.ConnectionI.invokeAll(ConnectionI.java:2536) at Ice.ConnectionI.dispatch(ConnectionI.java:1145) at Ice.ConnectionI.message(ConnectionI.java:1056) at IceInternal.ThreadPool.run(ThreadPool.java:395) at IceInternal.ThreadPool.access$300(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:832) at java.base/java.lang.Thread.run(Thread.java:829) serverExceptionClass = ome.conditions.ApiUsageException message = This method cannot handle tiled images yet. } ```

The main issue here is that a "tiled" image could be very large, and the server wants to avoid having to calculate pixel stats on a massive area. Are your ROIs themselves very big? E.g. 1k x 1k or smaller? What kind of shapes are they? Ellipse, Rectangle etc?

Possible options:

• Server-side fix: the getShapeStatsRestricted() method could check the bounds of an ROI and only reject the request if the ROI/Shape itself is too big, instead of checking the size of the Image
• Client-side (script) fix: We could fetch the raw pixels for a Shape and calculate the stats client-side. This is only feasible if the Shapes are not too big and the Shape is simple, e.g. Circle (maybe Ellipse) or Rectangle. E.g. see the "simple FRAP" script before it got updated to use getShapeStatsRestricted