[Insight-users] itk::Mesh and itk::QuadEdgeMesh converter

[Alexandre GOUAILLARD]

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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>