Changes between Initial Version and Version 1 of Ticket #10841


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Timestamp:
05/06/13 12:51:24 (7 years ago)
Author:
pwalczysko
Comment:

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  • Ticket #10841 – Description

    initial v1  
    55See similar problematics in ticket on this PR, concerning export as one-tiff option. 
    66{{{ 
    7 WARNING:omero.gateway:InternalException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <86:24:41:e3:-51f141ba:13e7811cad3:-7cb2omero.api.Exporter> generateTiff((<ServiceOptsDict: {'omero.session.uuid': '7135aec0-ce92-456e-9be3-3fc047c68241', 'omero.client.uuid': 'bd13d346-5f38-450b-8eb1-4d891dbdf028'}>,), {}) 
     7WARNING:omero.gateway:InternalException on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <86:24:41:e3:-51f141ba:13e7811cad3:-7ba4omero.api.RenderingEngine> renderCompressed((object #0 (::omero::romio::PlaneDef) 
     8{ 
     9    slice = 0 
     10    x = 0 
     11    y = 0 
     12    z = 0 
     13    t = 0 
     14    region = <nil> 
     15    stride = 0 
     16}, <ServiceOptsDict: {'omero.session.uuid': '9d092919-574d-4f7c-9504-3f661cee3da8', 'omero.client.uuid': 'e6657582-f2cc-4d9e-85f2-b31acf0cfa4b'}>), {}) 
    817Traceback (most recent call last): 
    918  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 3481, in __call__ 
    1019    return self.f(*args, **kwargs) 
    11   File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero_api_Exporter_ice.py", line 93, in generateTiff 
    12     return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx)) 
     20  File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero_api_RenderingEngine_ice.py", line 196, in renderCompressed 
     21    return _M_omero.api.RenderingEngine._op_renderCompressed.invoke(self, ((_def, ), _ctx)) 
    1322InternalException: exception ::omero::InternalException 
    1423{ 
    15     serverStackTrace = loci.formats.FormatException: Metadata object has null root; call IMetadata.createRoot() first 
    16     at loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:331) 
    17     at loci.formats.FormatWriter.checkParams(FormatWriter.java:375) 
    18     at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:174) 
    19     at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:201) 
    20     at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:187) 
    21     at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136) 
    22     at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:413) 
    23     at sun.reflect.GeneratedMethodAccessor254.invoke(Unknown Source) 
    24     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    25     at java.lang.reflect.Method.invoke(Method.java:592) 
    26     at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    27     at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    28     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    29     at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518) 
    30     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    31     at ome.security.basic.EventHandler.invoke(EventHandler.java:154) 
    32     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    33     at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) 
    34     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    35     at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) 
    36     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    37     at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) 
    38     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    39     at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) 
    40     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    41     at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    42     at $Proxy66.doWork(Unknown Source) 
    43     at ome.services.util.Executor$Impl.execute(Executor.java:416) 
    44     at ome.services.util.Executor$Impl.execute(Executor.java:360) 
    45     at ome.services.blitz.impl.ExporterI.do_tiff(ExporterI.java:343) 
    46     at ome.services.blitz.impl.ExporterI.generateTiff_async(ExporterI.java:213) 
    47     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 
    48     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) 
    49     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    50     at java.lang.reflect.Method.invoke(Method.java:592) 
    51     at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    52     at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    53     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    54     at omero.cmd.CallContext.invoke(CallContext.java:59) 
    55     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    56     at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    57     at $Proxy114.generateTiff_async(Unknown Source) 
    58     at omero.api._ExporterTie.generateTiff_async(_ExporterTie.java:71) 
    59     at omero.api._ExporterDisp.___generateTiff(_ExporterDisp.java:175) 
    60     at omero.api._ExporterDisp.__dispatch(_ExporterDisp.java:248) 
    61     at IceInternal.Incoming.invoke(Incoming.java:159) 
    62     at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) 
    63     at Ice.ConnectionI.message(ConnectionI.java:972) 
    64     at IceInternal.ThreadPool.run(ThreadPool.java:577) 
    65     at IceInternal.ThreadPool.access$100(ThreadPool.java:12) 
    66     at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) 
     24    serverStackTrace = ome.conditions.InternalException:  Wrapped Exception: (java.lang.NegativeArraySizeException): 
     25null 
     26        at omeis.providers.re.RGBIntBuffer.<init>(RGBIntBuffer.java:69) 
     27        at omeis.providers.re.RenderingStrategy.getIntBuffer(RenderingStrategy.java:188) 
     28        at omeis.providers.re.HSBStrategy.renderAsPackedInt(HSBStrategy.java:274) 
     29        at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:511) 
     30        at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:478) 
     31        at ome.services.RenderingBean.renderCompressed(RenderingBean.java:532) 
     32        at sun.reflect.GeneratedMethodAccessor1366.invoke(Unknown Source) 
     33        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
     34        at java.lang.reflect.Method.invoke(Method.java:592) 
     35        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
     36        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
     37        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
     38        at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) 
     39        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
     40        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
     41        at $Proxy105.renderCompressed(Unknown Source) 
     42        at sun.reflect.GeneratedMethodAccessor1366.invoke(Unknown Source) 
     43        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
     44        at java.lang.reflect.Method.invoke(Method.java:592) 
     45        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
     46        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
     47        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
     48        at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) 
     49        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
     50        at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) 
     51        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
     52        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
     53        at $Proxy105.renderCompressed(Unknown Source) 
     54        at sun.reflect.GeneratedMethodAccessor1402.invoke(Unknown Source) 
     55        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
     56        at java.lang.reflect.Method.invoke(Method.java:592) 
     57        at ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179) 
     58        at ome.services.throttling.Callback.run(Callback.java:56) 
     59        at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56) 
     60        at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:150) 
     61        at ome.services.blitz.impl.RenderingEngineI.renderCompressed_async(RenderingEngineI.java:344) 
     62        at sun.reflect.GeneratedMethodAccessor1401.invoke(Unknown Source) 
     63        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
     64        at java.lang.reflect.Method.invoke(Method.java:592) 
     65        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
     66        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
     67        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
     68        at omero.cmd.CallContext.invoke(CallContext.java:59) 
     69        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
     70        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
     71        at $Proxy107.renderCompressed_async(Unknown Source) 
     72        at omero.api._RenderingEngineTie.renderCompressed_async(_RenderingEngineTie.java:309) 
     73        at omero.api._RenderingEngineDisp.___renderCompressed(_RenderingEngineDisp.java:583) 
     74        at omero.api._RenderingEngineDisp.__dispatch(_RenderingEngineDisp.java:1700) 
     75        at IceInternal.Incoming.invoke(Incoming.java:159) 
     76        at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) 
     77        at Ice.ConnectionI.message(ConnectionI.java:972) 
     78        at IceInternal.ThreadPool.run(ThreadPool.java:577) 
     79        at IceInternal.ThreadPool.access$100(ThreadPool.java:12) 
     80        at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) 
    6781 
    68     serverExceptionClass = loci.formats.FormatException 
    69     message = Metadata object has null root; call IMetadata.createRoot() first 
     82    serverExceptionClass = ome.conditions.InternalException 
     83    message =  Wrapped Exception: (java.lang.NegativeArraySizeException): 
     84null 
    7085} 
    7186Traceback (most recent call last): 
     
    7489  File "./script", line 513, in runScript 
    7590    fileAnnotation, message = batchImageExport(conn, scriptParams) 
    76   File "./script", line 357, in batchImageExport 
    77     saveAsOmeTiff(conn, img, folder_name) 
    78   File "./script", line 171, in saveAsOmeTiff 
    79     fileSize, block_gen = image.exportOmeTiff(bufsize=65536) 
    80   File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 6790, in exportOmeTiff 
    81     size = e.generateTiff(self._conn.SERVICE_OPTS) 
    82   File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 3484, in __call__ 
    83     return self.handle_exception(e, *args, **kwargs) 
    84   File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero/gateway/__init__.py", line 3481, in __call__ 
    85     return self.f(*args, **kwargs) 
    86   File "/home/omero/slave/workspace/OMERO-merge-develop/src/dist/lib/python/omero_api_Exporter_ice.py", line 93, in generateTiff 
    87     return _M_omero.api.Exporter._op_generateTiff.invoke(self, ((), _ctx)) 
    88 omero.InternalException: exception ::omero::InternalException 
    89 { 
    90     serverStackTrace = loci.formats.FormatException: Metadata object has null root; call IMetadata.createRoot() first 
    91     at loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:331) 
    92     at loci.formats.FormatWriter.checkParams(FormatWriter.java:375) 
    93     at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:174) 
    94     at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:201) 
    95     at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:187) 
    96     at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136) 
    97     at ome.services.blitz.impl.ExporterI$2.doWork(ExporterI.java:413) 
    98     at sun.reflect.GeneratedMethodAccessor254.invoke(Unknown Source) 
    99     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    100     at java.lang.reflect.Method.invoke(Method.java:592) 
    101     at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    102     at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    103     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    104     at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518) 
    105     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    106     at ome.security.basic.EventHandler.invoke(EventHandler.java:154) 
    107     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    108     at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111) 
    109     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    110     at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) 
    111     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    112     at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) 
    113     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    114     at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) 
    115     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    116     at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    117     at $Proxy66.doWork(Unknown Source) 
    118     at ome.services.util.Executor$Impl.execute(Executor.java:416) 
    119     at ome.services.util.Executor$Impl.execute(Executor.java:360) 
    120     at ome.services.blitz.impl.ExporterI.do_tiff(ExporterI.java:343) 
    121     at ome.services.blitz.impl.ExporterI.generateTiff_async(ExporterI.java:213) 
    122     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 
    123     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) 
    124     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    125     at java.lang.reflect.Method.invoke(Method.java:592) 
    126     at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    127     at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    128     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    129     at omero.cmd.CallContext.invoke(CallContext.java:59) 
    130     at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    131     at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    132     at $Proxy114.generateTiff_async(Unknown Source) 
    133     at omero.api._ExporterTie.generateTiff_async(_ExporterTie.java:71) 
    134     at omero.api._ExporterDisp.___generateTiff(_ExporterDisp.java:175) 
    135     at omero.api._ExporterDisp.__dispatch(_ExporterDisp.java:248) 
    136     at IceInternal.Incoming.invoke(Incoming.java:159) 
    137     at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) 
    138     at Ice.ConnectionI.message(ConnectionI.java:972) 
    139     at IceInternal.ThreadPool.run(ThreadPool.java:577) 
    140     at IceInternal.ThreadPool.access$100(ThreadPool.java:12) 
    141     at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) 
    142  
    143     serverExceptionClass = loci.formats.FormatException 
    144     message = Metadata object has null root; call IMetadata.createRoot() first 
    145 } 
     91  File "./script", line 384, in batchImageExport 
     92    zRange, tRange, greyscale, imgWidth, projectZ=projectZ, format=format, folder_name=folder_name) 
     93  File "./script", line 233, in savePlanesForImage 
     94    savePlane(image, format, cName, (defaultZ,), projectZ, t, c, gScale, imgWidth, folder_name) 
     95  File "./script", line 127, in savePlane 
     96    plane.save(imgName) 
     97AttributeError: 'NoneType' object has no attribute 'save' 
    14698}}} 
    147  

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