Hi Anna, the errors derive from the fact that the writer cannot write the output file.
... Done executing vmtksurfacesmoothing. Writing VTK XML surface file. ERROR: In /usr/css/opt/build/vmtk-1.0.0-git/VTK/IO/vtkXMLWriter.cxx, line 606 vtkXMLPolyDataWriter (0x1010fa0): Error opening output file "var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/P98002893_Post1_residual_blood_MC_clipped_further2_smoothed.vtp" ... A couple of things could be happening here: a. the var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/ does not exist (the writer will not create intermediate directories for you, the target directory where you place your file has to exist) b. the directory exists but you don't have write access to it Try to replace your output path with something like ~/P98002893_Post1_residual_blood_MC_clipped_further2_smoothed.vtp (which means, place it in your home directory, probably /home/alhoppe from what I see) Best, Luca On May 22, 2012, at 7:45 PM, Hoppe, Anna L wrote: > Hi VMTK users, > > I am using the vmtksurfacesmoothing script in vmtk1.0. I have specified in > -ifile & an -ofile, as well as used a passband = 0.1 and iterations = 30 (I > thought I would start with these parameters after reading the "Preparing a > surface for mesh generation" tutorial). However, I get the following output & > errors upon running it: > > Creating vmtkSurfaceSmoothing instance. > Automatic piping vmtksurfacesmoothing > Parsing options vmtksurfacesmoothing > SurfaceInputFileName = > /var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/P98002893_Post1_residual_blood_MC_clipped_further2.vtp > NumberOfIterations = 30 > PassBand = 0.1 > SurfaceOutputFileName = > var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/P98002893_Post1_residual_blood_MC_clipped_further2_smoothed.vtp > Explicit piping vmtksurfacesmoothing > Input vmtksurfacesmoothing members: > Id = 0 > Disabled = 0 > Surface = None > SurfaceInputFileName = > /var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/P98002893_Post1_residual_blood_MC_clipped_further2.vtp > NumberOfIterations = 30 > Method = taubin > PassBand = 0.1 > RelaxationFactor = 0.01 > BoundarySmoothing = 1 > NormalizeCoordinates = 1 > SurfaceOutputFileName = > var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/P98002893_Post1_residual_blood_MC_clipped_further2_smoothed.vtp > Reading VTK XML surface file. > Executing vmtksurfacesmoothing ... > Done executing vmtksurfacesmoothing. > Writing VTK XML surface file. > ERROR: In /usr/css/opt/build/vmtk-1.0.0-git/VTK/IO/vtkXMLWriter.cxx, line 606 > vtkXMLPolyDataWriter (0x1010fa0): Error opening output file > "var/tmp/alhoppe/BIOMOST/Coil_Compaction_Growth_Project/Anna_recon_Hasan_coil_project/98002893/VMTK_reconstructions/Post1L/P98002893_Post1_residual_blood_MC_clipped_further2_smoothed.vtp" > > ERROR: In /usr/css/opt/build/vmtk-1.0.0-git/VTK/IO/vtkXMLWriter.cxx, line 609 > vtkXMLPolyDataWriter (0x1010fa0): Error code "No such file or directory" > > ERROR: In /usr/css/opt/build/vmtk-1.0.0-git/VTK/Filtering/vtkExecutive.cxx, > line 756 > vtkStreamingDemandDrivenPipeline (0x1011a80): Algorithm > vtkXMLPolyDataWriter(0x1010fa0) returned failure for request: vtkInformation > (0xf4d160) > Debug: Off > Modified Time: 3591 > Reference Count: 1 > Registered Events: (none) > Request: REQUEST_DATA > FROM_OUTPUT_PORT: -1 > FORWARD_DIRECTION: 0 > ALGORITHM_AFTER_FORWARD: 1 > > I am not sure how to fix my problem of not being able to open the output > file.... I have looked at > /usr/css/opt/build/vmtk-1.0.0-git/VTK/IO/vtkXMLWriter.cxx, line 606, it just > doesn't make much sense to me. > > Thanks for all the help, > Anna > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > vmtk-users mailing list > vmtk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/vmtk-users ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. 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