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
>>>> <http://www.vmtk.org/Tutorials/MeshGenerating>
>>>>
>>>> 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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