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Changes between Initial Version and Version 5 of Ticket #9738


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Timestamp:
10/12/12 14:12:29 (12 years ago)
Author:
wmoore
Comment:

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  • Ticket #9738

    • Property Cc cxallan added; jburel removed
    • Property Component changed from Import to Insight
    • Property Summary changed from Bug: Fslite import IMOD to Bug: ROI points display
    • Property Owner changed from mlinkert-x to jburel
    • Property Sprint changed from 2012-10-23 (1) to

  • Ticket #9738 – Description

    initial v5  
    1 Using Insight from webstart on today's build on howe: 
     1This may be a duplicate, but just in case... 
    22 
    3 Importing modelgolgi.mod from test_images_good/imod I get an image where the min and max are 0 (totally black image) but this is the same in ImageJ (BF import) so maybe it's just the image? But if so, we probably shouldn't have this in test_images_good, since it's not very helpful.  
     3Importing modelgolgi.mod from test_images_good/imod I get an image where the min and max are 0 (totally black image - but this is expected), but the ROIs on the image don't show up in Insight (haven't tried web yet). 
    44 
    5 To validate, I tried to import another IMOD image: from_skyking/imod/jcb/Meta4S23.mod and I got 
    6  
    7 {{{ 
    8  
    9 omero.ApiUsageException 
    10     serverStackTrace = "ome.conditions.ApiUsageException: Converting Long 4053969192 to Integer is an overflow. 
    11                                 at ome.io.nio.RomioPixelBuffer.safeLongToInteger(RomioPixelBuffer.java:121) 
    12                                 at ome.io.nio.RomioPixelBuffer.getTimepoint(RomioPixelBuffer.java:598) 
    13                                 at ome.io.nio.RomioPixelBuffer.calculateMessageDigest(RomioPixelBuffer.java:764) 
    14                                 at ome.services.RawPixelsBean.save(RawPixelsBean.java:181) 
    15                                 at ome.services.RawPixelsBean.close(RawPixelsBean.java:209) 
    16                                 at sun.reflect.GeneratedMethodAccessor639.invoke(Unknown Source) 
    17                                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    18                                 at java.lang.reflect.Method.invoke(Method.java:597) 
    19                                 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    20                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    21                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    22                                 at ome.security.basic.EventHandler.invoke(EventHandler.java:154) 
    23                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    24                                 at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182) 
    25                                 at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166) 
    26                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    27                                 at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) 
    28                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    29                                 at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) 
    30                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    31                                 at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) 
    32                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    33                                 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    34                                 at $Proxy94.close(Unknown Source) 
    35                                 at sun.reflect.GeneratedMethodAccessor639.invoke(Unknown Source) 
    36                                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    37                                 at java.lang.reflect.Method.invoke(Method.java:597) 
    38                                 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    39                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    40                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    41                                 at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) 
    42                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    43                                 at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) 
    44                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    45                                 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    46                                 at $Proxy94.close(Unknown Source) 
    47                                 at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:241) 
    48                                 at sun.reflect.GeneratedMethodAccessor721.invoke(Unknown Source) 
    49                                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    50                                 at java.lang.reflect.Method.invoke(Method.java:597) 
    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 $Proxy95.close_async(Unknown Source) 
    58                                 at omero.api._RawPixelsStoreTie.close_async(_RawPixelsStoreTie.java:330) 
    59                                 at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:142) 
    60                                 at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1157) 
    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) 
    67                         " 
    68     serverExceptionClass = "ome.conditions.ApiUsageException" 
    69     message = "Converting Long 4053969192 to Integer is an overflow." 
    70         at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) 
    71         at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) 
    72         at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) 
    73         at java.lang.reflect.Constructor.newInstance(Constructor.java:513) 
    74         at java.lang.Class.newInstance0(Class.java:355) 
    75         at java.lang.Class.newInstance(Class.java:308) 
    76         at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) 
    77         at IceInternal.BasicStream.throwException(BasicStream.java:1632) 
    78         at IceInternal.Outgoing.throwUserException(Outgoing.java:442) 
    79         at omero.api._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:1901) 
    80         at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2642) 
    81         at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2614) 
    82         at ome.formats.OMEROMetadataStoreClient.finalizePixelStore(OMEROMetadataStoreClient.java:2484) 
    83         at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:594) 
    84         at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6410) 
    85         at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250) 
    86         at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85) 
    87         at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54) 
    88         at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110) 
    89         at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) 
    90         at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) 
    91         at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) 
    92         at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) 
    93         at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) 
    94         at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) 
    95         at java.lang.Thread.run(Thread.java:680) 
    96  
    97         at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6459) 
    98         at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1250) 
    99         at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85) 
    100         at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54) 
    101         at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:110) 
    102         at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144) 
    103         at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) 
    104         at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) 
    105         at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) 
    106         at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276) 
    107         at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) 
    108         at java.lang.Thread.run(Thread.java:680) 
    109 Caused by: omero.ApiUsageException 
    110     serverStackTrace = "ome.conditions.ApiUsageException: Converting Long 4053969192 to Integer is an overflow. 
    111                                 at ome.io.nio.RomioPixelBuffer.safeLongToInteger(RomioPixelBuffer.java:121) 
    112                                 at ome.io.nio.RomioPixelBuffer.getTimepoint(RomioPixelBuffer.java:598) 
    113                                 at ome.io.nio.RomioPixelBuffer.calculateMessageDigest(RomioPixelBuffer.java:764) 
    114                                 at ome.services.RawPixelsBean.save(RawPixelsBean.java:181) 
    115                                 at ome.services.RawPixelsBean.close(RawPixelsBean.java:209) 
    116                                 at sun.reflect.GeneratedMethodAccessor639.invoke(Unknown Source) 
    117                                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    118                                 at java.lang.reflect.Method.invoke(Method.java:597) 
    119                                 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    120                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    121                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    122                                 at ome.security.basic.EventHandler.invoke(EventHandler.java:154) 
    123                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    124                                 at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182) 
    125                                 at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166) 
    126                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    127                                 at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108) 
    128                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    129                                 at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241) 
    130                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    131                                 at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116) 
    132                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    133                                 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    134                                 at $Proxy94.close(Unknown Source) 
    135                                 at sun.reflect.GeneratedMethodAccessor639.invoke(Unknown Source) 
    136                                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    137                                 at java.lang.reflect.Method.invoke(Method.java:597) 
    138                                 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    139                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    140                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    141                                 at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98) 
    142                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    143                                 at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43) 
    144                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    145                                 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    146                                 at $Proxy94.close(Unknown Source) 
    147                                 at ome.services.blitz.impl.AbstractAmdServant.close_async(AbstractAmdServant.java:241) 
    148                                 at sun.reflect.GeneratedMethodAccessor721.invoke(Unknown Source) 
    149                                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) 
    150                                 at java.lang.reflect.Method.invoke(Method.java:597) 
    151                                 at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307) 
    152                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183) 
    153                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150) 
    154                                 at omero.cmd.CallContext.invoke(CallContext.java:59) 
    155                                 at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) 
    156                                 at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202) 
    157                                 at $Proxy95.close_async(Unknown Source) 
    158                                 at omero.api._RawPixelsStoreTie.close_async(_RawPixelsStoreTie.java:330) 
    159                                 at omero.api._StatefulServiceInterfaceDisp.___close(_StatefulServiceInterfaceDisp.java:142) 
    160                                 at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1157) 
    161                                 at IceInternal.Incoming.invoke(Incoming.java:159) 
    162                                 at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) 
    163                                 at Ice.ConnectionI.message(ConnectionI.java:972) 
    164                                 at IceInternal.ThreadPool.run(ThreadPool.java:577) 
    165                                 at IceInternal.ThreadPool.access$100(ThreadPool.java:12) 
    166                                 at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) 
    167                         " 
    168     serverExceptionClass = "ome.conditions.ApiUsageException" 
    169     message = "Converting Long 4053969192 to Integer is an overflow." 
    170         at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) 
    171         at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) 
    172         at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) 
    173         at java.lang.reflect.Constructor.newInstance(Constructor.java:513) 
    174         at java.lang.Class.newInstance0(Class.java:355) 
    175         at java.lang.Class.newInstance(Class.java:308) 
    176         at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) 
    177         at IceInternal.BasicStream.throwException(BasicStream.java:1632) 
    178         at IceInternal.Outgoing.throwUserException(Outgoing.java:442) 
    179         at omero.api._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:1901) 
    180         at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2642) 
    181         at omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:2614) 
    182         at ome.formats.OMEROMetadataStoreClient.finalizePixelStore(OMEROMetadataStoreClient.java:2484) 
    183         at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:594) 
    184         at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6410) 
    185         ... 11 more 
    186  
    187 }}} 
     5More details in comments below... 

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