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): |
| 25 | null |
| 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) |
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) |
| 97 | AttributeError: 'NoneType' object has no attribute 'save' |