Hi,
the likely problem is that your surface is very complex and somehow the
surface remesher incurs in a topological defect somehow.
Try with a smaller edgelength (it's the size of the nominal triangle edge - in
mm if your model is in mm). Also, try inspecting the surface
mesh that the vmtkmeshgenerator produces, maybe you'll notice where it fails.
Feel free to post a screenshot.
Regards
Luca
On Oct 20, 2010, at 2:11 PM, Samuele Zampini wrote:
> Ive followed you advice and I got the following error:
>
>
> sam...@penrose:~/Desktop/naso_ok$ vmtk vmtkmeshgenerator -ifile
> Model_1_tissue.vtp -ofile Model_1_tissue.vtu -edgelength 0.5
> Executing vmtkmeshgenerator -ifile Model_1_tissue.vtp -ofile
> Model_1_tissue.vtu -edgelength 0.5
>
> Creating vmtkMeshGenerator instance.
> Automatic piping vmtkmeshgenerator
> Parsing options vmtkmeshgenerator
> SurfaceInputFileName = Model_1_tissue.vtp
> TargetEdgeLength = 0.5
> MeshOutputFileName = Model_1_tissue.vtu
> Explicit piping vmtkmeshgenerator
> Input vmtkmeshgenerator members:
> Id = 0
> Disabled = 0
> Surface = None
> SurfaceInputFileName = Model_1_tissue.vtp
> TargetEdgeLength = 0.5
> TargetEdgeLengthArrayName =
> TargetEdgeLengthFactor = 1.0
> MaxEdgeLength = 1e+16
> MinEdgeLength = 0.0
> CellEntityIdsArrayName = CellEntityIds
> ElementSizeMode = edgelength
> VolumeElementScaleFactor = 0.8
> BoundaryLayer = 0
> NumberOfSubLayers = 2
> BoundaryLayerThicknessFactor = 0.25
> Tetrahedralize = 0
> MeshOutputFileName = Model_1_tissue.vtu
> Reading VTK XML surface file.
> Executing vmtkmeshgenerator ...
> Capping surface
> Remeshing surface
> Iteration 1/10
> Iteration 2/10
> Iteration 3/10
> Iteration 4/10
> Iteration 5/10
> Iteration 6/10
> Iteration 7/10
> Iteration 8/10
> Iteration 9/10
> Iteration 10/10
> Final mesh improvement
> Computing sizing function
> Converting surface to mesh
> Generating volume mesh
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 315
> vtkvmtkTetGenWrapper (0x5e0dc3a0): Invalid element found.
>
> TetGen command line options: pq1.414000q10.000000q165.000000YsT1.000000e-08zQm
> Warning: Discard an invalid facet.
> #256719 (86237, 35684, 86234) looks like a line.
> Warning: Discard an invalid facet.
> #256720 (86237, 86234, 35684) looks like a line.
> Error: Invalid PLC! Two subfaces intersect.
> 1st (#210616): (82651, 147811, 147810)
> 2nd (#268519): (147810, 170476, 251438)
> ERROR: In /build/buildd/vmtk-0.9.0/vtkVmtk/Misc/vtkvmtkTetGenWrapper.cxx,
> line 429
> vtkvmtkTetGenWrapper (0x5e0dc3a0): TetGen quit with an exception.
>
> An error occurred during tetrahedralization. Will only output surface mesh.
> Done executing vmtkmeshgenerator.
> Writing VTK XML mesh file.
> Output vmtkmeshgenerator members:
> Id = 0
> Mesh = vtkUnstructuredGrid
> CellEntityIdsArrayName = CellEntityIds
> sam...@penrose:~/Desktop/naso_ok$
>
> It seems there are a lot of Invalid Elements.. And, finally, it does not
> generate
> any volume mesh.
>
> Do you think that either tetrahedralizing or linearizing can help?
>
> Thanks,
>
> Samuele
>
>
>
>
> On Wed, Oct 20, 2010 at 12:50 PM, Samuele Zampini <samuele.zamp...@gmail.com>
> wrote:
> Thanks a lot.
>
> Here you can find some examples on how to use vmtkmeshgenerator. All of the
> meshes displayed below have been generated from the surface in Figure 1,
> referred as foo.vtp."
>
> A foo.vtp is very similar to foo.stl (I am not sure for foo.vtk but i think
> it will be similar as well)
>
> I am sorry. I did not know they were similar. Really.
> Thanks again.
>
>
> what you should do is:
>
> vmtksurfacewriter -ifile foo.stl -ofile foo.vtp
>
> and then read the tutorial I gave you.
>
> Joppe
>
> On 20 October 2010 12:43, Samuele Zampini <samuele.zamp...@gmail.com> wrote:
> Dear Joppe, Dear J.J., Dear All,
>
> thanks for answering. Actually, the question is a bit different. In fact I do
> not have a
> .vtu file. But I have .vtk (or .stl) surface mesh file. And, from this file,
> I'd like to generate
> a volume mesh.
>
> I've thought about vmtk, but I am not sure it can do this.
>
> Thanks,
>
> Samuele
>
>
> On Wed, Oct 20, 2010 at 12:38 PM, Joppe Schneiders
> <joppe.schneid...@gmail.com> wrote:
> Follow the tutorial on the vmtk.org website : link
>
> On 20 October 2010 12:35, Samuele Zampini <samuele.zamp...@gmail.com> wrote:
> I am trying to generate a volume mesh, starting from a surface mesh, either in
> .stl or in .vtk format.
>
> Do you think it is possible to do that with vmtk?? Is the answer's yes, how?
>
> Thanks a lot,
>
> --
>
>
>
> --
>
> Samuele Zampini
> ____________________________________________________________________
>
> .~.
> /V\ L I N U X
> // \\ I S T H E
> /( )\ W A Y
> ^^-^^
> cell phone : +393473426510 e.mail: samuele.zamp...@gmail.com
> home : +390331823927 www: samiam1000.spaces.live.com
>
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