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fiji / SPIM_Registration

Deprecated, instead check out: https://github.com/preibischLab/multiview-reconstruction & https://github.com/PreibischLab/BigStitcher
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Merging xml fails #105

Closed schmiedc closed 8 years ago

schmiedc commented 8 years ago

Hi Stephan,

I have a issue with failing of the merging of the xml files for my cluster workflow. Here is the log file of the failed processing. Please find attached also the .xml files in question.

Thanks a lot! Christopher

xml.zip

12 cores available for multi-threading Threads: 1 Load Parameters: directory=/lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/

merged_xml=dataset_merge.xml

Start to merge .xml files Attempting to merge the following XML's in directory '/lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/': /lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/.job_2.xml /lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/dataset.job_01.xml /lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/.job_0.xml /lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/dataset.job_00.xml /lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/dataset.job_02.xml /lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/.job_1.xml Failed to merge XML's: mpicbg.spim.data.SpimDataException: Could not find corresponding ViewSetupId=1 in xml '/lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/dataset.job_01.xml' mpicbg.spim.data.SpimDataException: Could not find corresponding ViewSetupId=1 in xml '/lustre/projects/project-akanksha/Akanksha/16-06-22_LZ2_VW_sqhGFPinj_embryoI_25C_5angles_5min_CHORION!/dataset.job_01.xml' at spim.fiji.plugin.cluster.MergeClusterJobs.merge(MergeClusterJobs.java:66) at spim.fiji.plugin.Merge_Cluster_Jobs.run(Merge_Cluster_Jobs.java:93) at ij.IJ.runUserPlugIn(IJ.java:199) at ij.IJ.runPlugIn(IJ.java:163) at ij.Executer.runCommand(Executer.java:132) at ij.Executer.run(Executer.java:65) at ij.IJ.run(IJ.java:279) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at bsh.Reflect.invokeMethod(Unknown Source) at bsh.Reflect.invokeStaticMethod(Unknown Source) at bsh.Name.invokeMethod(Unknown Source) at bsh.BSHMethodInvocation.eval(Unknown Source) at bsh.BSHPrimaryExpression.eval(Unknown Source) at bsh.BSHPrimaryExpression.eval(Unknown Source) at bsh.BSHBlock.evalBlock(Unknown Source) at bsh.BSHBlock.eval(Unknown Source) at bsh.BSHBlock.eval(Unknown Source) at bsh.BSHTryStatement.eval(Unknown Source) at bsh.Interpreter.eval(Unknown Source) at bsh.Interpreter.source(Unknown Source) at bsh.Interpreter.main(Unknown Source) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258) at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184) at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)

schmiedc commented 8 years ago

Retested. Does not occur anymore. Sorry!