Unable to mesh imported vtp surface

[Rodrigo Romarowski]

Hi Everyone,

Thanks for the effort you're putting in this great tool. I am starting to get familiarized with the software in Ubuntu 16.04.

I am having trouble with meshing an imported surface (aorta) from a triangulated vtp file. I can succesfully do a surface remesh in the imported open surface, in the imported closed surface and in the surfaced capped within Simvascular. All the baoundaries in every case seem to be correct.

However, when I try to run the volume meshing with the suggested edgelength, I receive the error "Failed in generating mesh". Meshing with TetGen via VMTK in the same model with the same edgelength does the job. Furthermore, in the terminal log from which I ran Simvascular I get:

Checking surface mesh
Regions: 1
Number of Free Edges on Surface: 0
Number of Non-Manifold Edges on Surface: 0
#67.569# [VtkError] ERROR: ERROR: In /home/hongzhi/ForSV3_201603/Distribution_Use_Server/SimVascular/SV_Source/Code/ThirdParty/vmtk/simvascular_vmtk/vtkvmtkPolyDataSurfaceRemeshing.cxx, line 178
vtkvmtkPolyDataSurfaceRemeshing (0x907a020): CellEntityIdsArray with name specified does not exist
Converting to TetGen...
Converting Points...
Converting Faces...
Array name does not exist in polydata. Regions must be identified and named prior to this function call
Could not add facet markers to mesh
For some reason, mesh is not loaded! TetGen cannot be run.
TetGen Meshing Started...
Error: The point set is trivial.
ERROR: TetGen quit and returned error code 10


Any clues?

Thanks a lot,

Rodrigo

[Adam Updegrove]

Hi Rodrigo,

Thanks for the message. It sounds like you have things set up correctly. Would you mind sharing the project, so I can get a closer look at what is going wrong?

Thanks!

SimVascular Development Team

[Rodrigo Romarowski]

Dear Adam,

Thanks for your quick answer. Actually I managed to solve the problem.

I was trying to mesh before setting up the tags in the Simvascular module, therefore they array with the tag IDs remained with VMTK's default name. It seems that after choosing wall/cap in the corresponging window, the boundary array gets renamed and then the meshing module can recognize them.

Now I'm struggling with building svSolver in our cluster, so I will be back in the forum soon.

Thanks again,

Rodrigo

[Adam Updegrove]

Rodrigo,

Thanks for the update. Glad to hear you got it working.

Start a separate issue if something does come up with building on the cluster.

Thanks!

SimVascular Development Team

[gang fang]

Dear developers,
When I import stl model to SV, it succeed and 50 degree can extract faces.
But when I generate mesh, it failed.
https://drive.google.com/open?id=12RJ5_ ... ExnUidqisi
Could you help to check if model has defects or sv's bug?
Thanks,
Gang

[gang fang]

hi, developers,

here gose more smoothed surface, but also generate mesh failded.
https://drive.google.com/open?id=1ZP61V ... 5FWv3qM3op

The model is generated by mimics, I have add "smooth" steps.
Looking forward to your response. Thank you.

Best,
Gang

[David Parker]

Hi Gang,

I was able to mesh your model no problem. What error message did you see? Meshing errors are displayed at the bottom of the SV window.

What OS are you running and what version of SV are you using?

Cheers,
Dave

[gang fang]

hi, David,
Forgot to say happy new year!
I have put my sv screen shoot on https://drive.google.com/open?id=1EXCn1 ... 5ptHrqT_xi
and log info
Info BlueBerry mbilog backend registered BlueBerry
Info Logfile: C:/Users/lenovo/AppData/Local/SimVascular/SimVascularApplication_2640420696/data/9/mitk-0.log
Info OpenCASCADE module loaded.
Warning QWindowsWindow::setGeometry: Unable to set geometry 1920x22+0+0 on QWidgetWindow/'BlueBerry ApplicationWindow'. Resulting geometry: 1534x16+-1+-7 (frame: 8, 31, 8, 8, custom margin: 0, 0, 0, 0, minimum size: 22x22, maximum size: 16777215x16777215).
Info LOG: Warning: Detected recursive attempt by part org.sv.views.datamanager to create itself (this is probably, but not necessarily, a bug) BlueBerry
Info **** Activating legacy standalone functionality
Info setting active flag
Info BlueBerry Workbench ready BlueBerry
Warning QWindowsWindow::setGeometry: Unable to set geometry 1920x48+0+-1057 on QWidgetWindow/'SimVascular 2019.08.09 (MITK 2018.4.2 VTK 8.1.1 ITK 4.13.2 Qt 5.11.3) - SimVascularWindow'. Resulting geometry: 1920x56+0+-1057 (frame: 8, 31, 8, 8, custom margin: 0, 0, 0, 0, minimum size: 22x48, maximum size: 16777215x16777215).
Warning QWindowsWindow::setGeometry: Unable to set geometry 1920x88+0+-1057 on QWidgetWindow/'SimVascular 2019.08.09 (MITK 2018.4.2 VTK 8.1.1 ITK 4.13.2 Qt 5.11.3) - SimVascularWindow'. Resulting geometry: 1920x96+0+-1057 (frame: 8, 31, 8, 8, custom margin: 0, 0, 0, 0, minimum size: 190x88, maximum size: 16777215x16777215).
Warning QWindowsWindow::setGeometry: Unable to set geometry 1920x121+0+-1057 on QWidgetWindow/'SimVascular 2019.08.09 (MITK 2018.4.2 VTK 8.1.1 ITK 4.13.2 Qt 5.11.3) - SimVascularWindow'. Resulting geometry: 1920x129+0+-1057 (frame: 8, 31, 8, 8, custom margin: 0, 0, 0, 0, minimum size: 322x121, maximum size: 16777215x16777215).
Info **** Activating legacy standalone functionality
Info setting active flag
Info changing layout to big 3D ... widget.stdmulti
Info **** Activating legacy standalone functionality
Info setting active flag
Info **** Activating legacy standalone functionality
Info setting active flag
Info **** Activating legacy standalone functionality
Info setting active flag
Warning Warning: In S:\vtk-8.1.1\Filters\Geometry\vtkDataSetSurfaceFilter.cxx, line 169
vtkDataSetSurfaceFilter (000002641F514A50): Number of cells is zero, no data to process. VtkWarning
Warning Warning: In S:\vtk-8.1.1\Filters\Geometry\vtkDataSetSurfaceFilter.cxx, line 169
vtkDataSetSurfaceFilter (000002641F514A50): Number of cells is zero, no data to process. VtkWarning

Thanks you again!
Gang

[gang fang]

oh, forget to add OS info,

windows 10 and 64bit OS. x64. and i7-8750H CPU 16G RAM.

Best,
Gang

[David Parker]

Hi Gang,

When SV starts it opens a window called mbilog. Messages from the mesher are written to this window. Could you please post the messages written in that window? They should look like

Code: Select all

Remeshing surface with MMG...
  -- MMGS, Release 5.3.8 (Apr. 10, 2017) 
     Copyright (c) IMB-LJLL, 2004-
     Jul 14 2019 19:10:38

  -- MMGS: INPUT DATA
  --  INPUT DATA COMPLETED.     0.000s

  &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
   MODULE MMGS: IMB-LJLL : 5.3.8 (Apr. 10, 2017)
  &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&

  -- PHASE 1 : ANALYSIS

  -- MESH QUALITY   61132
     BEST   1.000000  AVRG.   0.923005  WRST.   0.000155 (14018)

Are you setting the face type (cap or wall) in the SV Modeling tool panel? The mesher needs this information.

Cheers,
Dave