Hi,
I would like to extract centrelines from imported STL models. I get the following message: "No valid data!". I have also tried to import the model as .vtp (VTK polydata), and it hasn't worked either. I suppose, I get that message because the segmentation wasn't done on the same project. Is that right? Is there any other way of doing that?
Best regards
Rudolf
Extract paths from imported STL
-
Gabriel Maher
- Posts: 32
- Joined: Tue Feb 09, 2016 9:17 am
Re: Extract paths from imported STL
Hi Rudolf,
The error message "no valid data" indicates the centerline extraction process is failing.
For centerline extraction to work your model needs to have the proper cap/wall information set up. After importing your model double click on it in the data manager to open the model window which shows a list of faces of your model. For each face set whether that face is a wall or a cap and then try rerunning the centerline extraction process.
It may also be that when importing your model the faces are not properly identified. You can try experimenting with the separation angle to get SimVascular to properly load your model.
Best,
Gabriel
The error message "no valid data" indicates the centerline extraction process is failing.
For centerline extraction to work your model needs to have the proper cap/wall information set up. After importing your model double click on it in the data manager to open the model window which shows a list of faces of your model. For each face set whether that face is a wall or a cap and then try rerunning the centerline extraction process.
It may also be that when importing your model the faces are not properly identified. You can try experimenting with the separation angle to get SimVascular to properly load your model.
Best,
Gabriel
-
Octavia Larentis
- Posts: 1
- Joined: Tue Oct 17, 2017 10:01 am
Re: Extract paths from imported STL
I am having a similar issue. What does the separation angle represent ?
-
Nathan Wilson
- Posts: 46
- Joined: Tue Jun 20, 2006 9:19 am
Re: Extract paths from imported STL
Hello,
The separation angle reflects the difference between outward surface normals of adjacent triangles and is used to create logical surface patches of triangles. Holes, duplicate points, and very rough surfaces cause problems.
You surface has to have a certain amount of smoothness to be able to select surfaces. Can you post a few images of your segmentation?
Nathan
SimVascular Development Team
The separation angle reflects the difference between outward surface normals of adjacent triangles and is used to create logical surface patches of triangles. Holes, duplicate points, and very rough surfaces cause problems.
You surface has to have a certain amount of smoothness to be able to select surfaces. Can you post a few images of your segmentation?
Nathan
SimVascular Development Team
-
Rudolf Hellmuth
- Posts: 19
- Joined: Mon Jul 25, 2016 7:32 am
Re: Extract paths from imported STL
I was able to overcome the 'no valid data' error by extracting surfaces and giving them walls or caps status. However, there was an internal error, which caused SimVascular to close.
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 240
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Degenerate descent detected. Target not reached.
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 213
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Can't find a steepest descent edge. Target not reached.
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 213
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Can't find a steepest descent edge. Target not reached.
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 213
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Can't find a steepest descent edge. Target not reached.
Grouping Sections...
Merging Sections...
./simvascular: line 68: 2768 Aborted (core dumped) $SV_HOME/Bin/simvascular -qt$*
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!37.962! [VtkGenericWarning] WARNING: Generic Warning: In /home/hongzhi/ForSV3_201603/SourceCode/VTK/Common/Core/vtkMath.cxx, line 520
Unable to factor linear system
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 240
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Degenerate descent detected. Target not reached.
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 213
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Can't find a steepest descent edge. Target not reached.
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 213
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Can't find a steepest descent edge. Target not reached.
!38.232! [VtkWarning] WARNING: Warning: In /home/hongzhi/ForSV3_201603/SourceCode/SimVascular/Code/ThirdParty/vmtk/vtkvmtkSteepestDescentLineTracer.cxx, line 213
vtkvmtkSteepestDescentLineTracer (0x7f664047f2d0): Can't find a steepest descent edge. Target not reached.
Grouping Sections...
Merging Sections...
./simvascular: line 68: 2768 Aborted (core dumped) $SV_HOME/Bin/simvascular -qt$*
-
Adam Updegrove
- Posts: 236
- Joined: Fri Aug 30, 2013 4:11 pm
Re: Extract paths from imported STL
Hi Rudolf,
You may have poor quality elements on your surface causing problems for the centerline calculation. This shouldn't crash the program, and I will look to reproduce this, but I typically perform a global surface remesh before trying to extract centerline paths. Global surface remesh can be found in the sv modeling module. Let me know if this doesn't help. I can also take a look at your project if you'd like.
Thanks!
SimVascular Development Team
You may have poor quality elements on your surface causing problems for the centerline calculation. This shouldn't crash the program, and I will look to reproduce this, but I typically perform a global surface remesh before trying to extract centerline paths. Global surface remesh can be found in the sv modeling module. Let me know if this doesn't help. I can also take a look at your project if you'd like.
Thanks!
SimVascular Development Team