[Insight-users] itk::Mesh and itk::QuadEdgeMesh converter
Alexandre GOUAILLARD
agouaillard at gmail.com
Fri Sep 9 12:12:51 EDT 2011
hi,
Yes, there is that weird type depency at runtime that is not easy as
the poitn type is defined in the trait and you need both the mesh and
the point to share this type. I remember now, sorry i couldn t help
before.
well, those vtk-itk bridges used to go into Insight Applications. I
don t know where it should go now. maybe bill or luis can advise?
alex.
On Fri, Sep 9, 2011 at 11:01 PM, Gao, Yi <gaoyi.cn at gmail.com> wrote:
> Hey Alex,
>
> I think it works now (maybe there is hidden problem in reserve
> function but it seems not emerging in my case).
>
> The previous problem was that in (the mesh var below is a QE mesh)
> mesh->SetPoint( p, QEMeshType::PointType( apoint ));
>
> the "apoint" is double[3]
>
> however, in my typedef of QEmesh, I did used:
> typedef itk::QuadEdgeMesh< double, 3 > QEMeshType;
>
> But when it shows in the compiler error, it's
> itk::QuadEdgeMeshPoint<float, 3u>.
>
> (in fact it's itk::QuadEdgeMeshPoint<float, 3u,
> itk::GeometricalQuadEdge<long unsigned int, long unsigned int,
> bool,bool, true> > )
>
> The solution I had was in the typedef for qemesh, I change it to:
>
> typedef itk::QuadEdgeMeshTraits<double, 3, double, double, double,
> double > qetraits;
> typedef itk::QuadEdgeMesh< vtkFloatingPointType, pointDimension,
> qetraits > QEMeshType;
>
> This time it works!
>
> Do you think cleaning up the code and put it somewhere may help others like me?
>
> Thanks for your help!
>
> Best,
> yi
>
>
>
>
> On Fri, Sep 9, 2011 at 10:52 AM, Alexandre GOUAILLARD
> <agouaillard at gmail.com> wrote:
>> yeah,
>>
>> the reserve function does not work well in QEMesh. It was reported by
>> michel audette a couple of years back, but never addressed.
>>
>> I will give a try at your code over this week end.
>>
>> alex.
>>
>>
>> On Fri, Sep 9, 2011 at 10:41 PM, Gao, Yi <gaoyi.cn at gmail.com> wrote:
>>> Hi Alex and Arnaud,
>>>
>>> Here is the converter I used. It was the convert from vtkpolydata to
>>> itkMesh I got in 2006 (did I get this from you? Or download it
>>> somewhere? Or I wrote it myself? I really forgot... ).
>>>
>>> I just change everything to QEmesh.
>>>
>>> Although I define qemesh <double, 3>, in the compilation error, i get
>>> its type as:
>>> itk::QuadEdgeMeshPoint<float, 3u>. Then I can't use a double[3] to
>>> init the point.
>>>
>>> (in fact it's itk::QuadEdgeMeshPoint<float, 3u,
>>> itk::GeometricalQuadEdge<long unsigned int, long unsigned int, bool,
>>> bool, true> >::QuadEdgeMeshPoint(double [3])’)
>>>
>>> I could change everything I have to float, I will try that also.
>>>
>>>
>>> Here is the converter function:
>>>
>>> typedef itk::QuadEdgeMesh< double, 3 > QEMeshType;
>>>
>>> QEMeshType::Pointer vtkPolyDataToITKQEMesh(
>>> vtkSmartPointer<vtkPolyData> polyData)
>>> {
>>> /// Create a new mesh
>>> QEMeshType::Pointer mesh = QEMeshType::New();
>>>
>>> /// Transfer the points from the vtkPolyData into the itk::Mesh
>>> const unsigned int numberOfPoints = polyData->GetNumberOfPoints();
>>>
>>> vtkSmartPointer<vtkPoints> vtkpoints = polyData->GetPoints();
>>>
>>> mesh->GetPoints()->Reserve( numberOfPoints );
>>>
>>> {
>>> double apoint[3];
>>>
>>> for(unsigned int p =0; p < numberOfPoints; p++)
>>> {
>>> vtkpoints->GetPoint( p, apoint );
>>> mesh->SetPoint( p, QEMeshType::PointType( apoint ));
>>> }
>>> }
>>>
>>> /// Transfer the cells from the vtkPolyData into the itk::Mesh
>>> vtkSmartPointer<vtkCellArray> triangleStrips = polyData->GetStrips();
>>>
>>>
>>> vtkIdType* cellPoints;
>>> vtkIdType numberOfCellPoints;
>>>
>>> /// First count the total number of triangles from all the triangle strips.
>>> unsigned int numberOfTriangles = 0;
>>>
>>> triangleStrips->InitTraversal();
>>>
>>> while( triangleStrips->GetNextCell( numberOfCellPoints, cellPoints ) )
>>> {
>>> numberOfTriangles += numberOfCellPoints-2;
>>> }
>>>
>>> vtkSmartPointer<vtkCellArray> polygons = polyData->GetPolys();
>>>
>>> polygons->InitTraversal();
>>>
>>> while( polygons->GetNextCell( numberOfCellPoints, cellPoints ) )
>>> {
>>> if( numberOfCellPoints == 3 )
>>> {
>>> numberOfTriangles ++;
>>> }
>>> }
>>>
>>>
>>> /// Reserve memory in the itk::Mesh for all those triangles
>>> mesh->GetCells()->Reserve( numberOfTriangles );
>>>
>>>
>>> /// Copy the triangles from vtkPolyData into the itk::Mesh
>>> typedef QEMeshType::CellType CellType;
>>> typedef itk::TriangleCell< CellType > TriangleCellType;
>>>
>>> int cellId = 0;
>>>
>>> /// first copy the triangle strips
>>> triangleStrips->InitTraversal();
>>> while( triangleStrips->GetNextCell( numberOfCellPoints, cellPoints ) )
>>> {
>>>
>>> unsigned int numberOfTrianglesInStrip = numberOfCellPoints - 2;
>>>
>>> unsigned long pointIds[3];
>>> pointIds[0] = cellPoints[0];
>>> pointIds[1] = cellPoints[1];
>>> pointIds[2] = cellPoints[2];
>>>
>>> for( unsigned int t=0; t < numberOfTrianglesInStrip; t++ )
>>> {
>>> QEMeshType::CellAutoPointer c;
>>> TriangleCellType * tcell = new TriangleCellType;
>>> tcell->SetPointIds( pointIds );
>>> c.TakeOwnership( tcell );
>>> mesh->SetCell( cellId, c );
>>> cellId++;
>>> pointIds[0] = pointIds[1];
>>> pointIds[1] = pointIds[2];
>>> pointIds[2] = cellPoints[t+3];
>>> }
>>> }
>>>
>>> /// then copy the normal triangles
>>> polygons->InitTraversal();
>>> while( polygons->GetNextCell( numberOfCellPoints, cellPoints ) )
>>> {
>>> if( numberOfCellPoints !=3 ) // skip any non-triangle.
>>> {
>>> continue;
>>> }
>>> QEMeshType::CellAutoPointer c;
>>> TriangleCellType * t = new TriangleCellType;
>>> //t->SetPointIds( static_cast<unsigned long*>(cellPoints) );
>>> t->SetPointIds( (unsigned long*)cellPoints );
>>> c.TakeOwnership( t );
>>> mesh->SetCell( cellId, c );
>>> cellId++;
>>> }
>>>
>>> return mesh;
>>> }
>>>
>>> Thank you for any hint!
>>>
>>> Best,
>>> yi
>>>
>>> On Fri, Sep 9, 2011 at 9:57 AM, Alexandre GOUAILLARD
>>> <agouaillard at gmail.com> wrote:
>>>> hum,
>>>>
>>>> what is you "converter" between polydata and itk:mesh?
>>>> you shoudl be able to use the old vtkPolydatawriter templated over a QEMesh ...
>>>>
>>>> alex.
>>>>
>>>>
>>>> On Fri, Sep 9, 2011 at 9:32 PM, Gao, Yi <gaoyi.cn at gmail.com> wrote:
>>>>> Dear Alex,
>>>>>
>>>>> Thank you for the reply!
>>>>>
>>>>> I'm trying to use the smoothing filter Arnaud and you contributed. The
>>>>> triangles it gives are much better shaped than the vtk's windowed sinc
>>>>> filter!
>>>>>
>>>>> But my main pipeline is in VTK so in fact I want to convert from
>>>>> vtkPolyData with QE mesh. Since I have converter between vtkPolyData
>>>>> <--> itk::Mesh, then the missing step is itk::Mesh <-->QE mesh. That
>>>>> is where the problem comes from. :)
>>>>>
>>>>> So I'll just get an itk::Mesh and feed it to the smoothing filter for
>>>>> QE mesh, I will try that out!
>>>>>
>>>>> Thanks again! :)
>>>>>
>>>>> Best,
>>>>> yi
>>>>>
>>>>> On Fri, Sep 9, 2011 at 8:47 AM, Alexandre GOUAILLARD
>>>>> <agouaillard at gmail.com> wrote:
>>>>>> dear gao yi,
>>>>>>
>>>>>> an itk:QuadEdgeMesh is an itk:Mesh. You can pass the pointer to the
>>>>>> itk:Pointset directly (sharing memory), then you can just make one
>>>>>> loop on the cell container (and equivalent data) to feed your itk:Mesh
>>>>>> with the cells. There is a little bit of magic to do as the cells
>>>>>> types are a little bit different but nothing fancy. Namely, in a
>>>>>> QEMesh cells are polygons and do not differentiate from triangles,
>>>>>> quads or others. In your case, if you know it s triangular, then it s
>>>>>> easier.
>>>>>>
>>>>>> Any reason you want to change it to itk:Mesh by the way? QEMesh API is
>>>>>> supposedly 100% compatible with Mesh, so if there is a limitation,
>>>>>> please let me know.
>>>>>>
>>>>>> What is your specific problem? If you re at miccai, we can take a look
>>>>>> at it together, otherwise I can give a hand by e-mail.
>>>>>>
>>>>>> alex.
>>>>>>
>>>>>>
>>>>>> On Fri, Sep 9, 2011 at 8:29 PM, Gao, Yi <gaoyi.cn at gmail.com> wrote:
>>>>>>> Dear list,
>>>>>>>
>>>>>>> I'm trying to convert a triangular 2D mesh (all in memory, not in
>>>>>>> file) from itk::QuadEdgeMesh to itk::Mesh (or to VTK polydata).
>>>>>>>
>>>>>>> The itkVTKPolyDataReader and writer can do this... but I will need to
>>>>>>> write to file and then load, which does seem to be the optimal
>>>>>>> solution. :)
>>>>>>>
>>>>>>> I googled but didn't find such a solution, could I get any hint?
>>>>>>>
>>>>>>> Thank you in advance for the help!
>>>>>>>
>>>>>>> Best,
>>>>>>> yi
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>>>>>>
>>>>>
>>>>
>>>
>>
>
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