[Insight-users] [Segfault] itk::NormalQuadEdgeMeshFilter and itk::WarpMeshFilter

[Oscar Esteban]

Dear Alexandre,

Thank you so much.

I didn't realize about the existence of the
itkQuadEdgeMeshToQuadEdgeMeshFilter,
so now I'm trying to use it. Currently, the segfault has moved to a
different place (the faces iterator).

After the itkQuadEdgeMeshToQuadEdgeMeshFilter (I defined a typedef so it
will be ContourCopyType), the QEMesh has uninitialized the members
m_NumberOfFaces and m_NumberOfEdges.

This is my code:

// Read an vtk mesh with VTKPolyDataReader. This is the "prior" I use
inside this method:

template< typename TReferenceImageType, typename TCoordRepType >
> void
> LevelSetsBase<TReferenceImageType, TCoordRepType>
> ::SetShapePrior( typename LevelSetsBase<TReferenceImageType,
> TCoordRepType>::ContourDeformationType* prior ) {
> this->m_ShapePrior = prior;
>         this->m_CurrentContourPosition = ContourDeformationType::New();
> this->m_ContourCopier = ContourCopyType::New();
> m_ContourCopier->SetInput( this->m_ShapePrior );
>  this->m_ContourCopier->Update();
> this->m_CurrentContourPosition = m_ContourCopier->GetOutput();
> }


When I compare m_ShapePrior and m_CurrentContourPosition after the
GetOutput(), I see that m_CurrentContourPosition does not have the
variables mentioned before.

After that, the normals filter comes in, and I get the segfault.

Before, I was manually copying the meshes like this:

 typename ContourDeformationType::PointsContainerConstIterator u_it =
> prior->GetPoints()->Begin();
>     typename ContourDeformationType::PointsContainerConstIterator u_end =
> prior->GetPoints()->End();
>  VectorType zero = itk::NumericTraits<VectorType>::Zero;
> PointType p, newP;
> while( u_it != u_end ) {
>  p = u_it.Value();
> newP.SetPoint( p );
> newP.SetEdge( p.GetEdge() );
>  this->m_CurrentContourPosition->SetPointData(
> this->m_CurrentContourPosition->AddPoint( newP ), zero);
>  ++u_it;
> }
> typename ContourDeformationType::CellsContainerConstIterator c_it  =
> prior->GetCells()->Begin();
>  typename ContourDeformationType::CellsContainerConstIterator c_end =
> prior->GetCells()->End();
> size_t i = 0;
>  while( c_it!=c_end ) {
> typename ContourDeformationType::CellType::CellAutoPointer cellCopy;
>  c_it.Value()->MakeCopy( cellCopy );
> this->m_CurrentContourPosition->SetCell( i++ ,cellCopy );
>  ++c_it;
> }


Thanks in advance

Cheers,
Oscar Esteban

*______________________________________*
*Oscar Esteban*
PhD Student / Researcher

Biomedical Image Technologies (BIT), UPM
ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid
(Spain)
+34 915 495 700 ext.4234

Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5
ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland



On 5 December 2012 21:53, Alexandre GOUAILLARD <agouaillard at gmail.com>wrote:

> dear oscar,
>
> could you share a simple code that reproduce the problem?
>
> There is no unsafe copying of QEMesh, itkQuadEdgeMeshToQuadEdgeMeshFilter
> always hard copy (actually reconstructs the structure) the entire mesh.
> This is because the QuadEdges have no container and other technical
> details. This is one reason why the copying part is relatively slow today.
> Points are safe to shallow copy, cell could be made safe to shallow copy,
> but edge cells need to be added over again. This is what the filter does
> when copying.
>
> regards,
>
> alex.
>
>
>
>
>
> On Thu, Dec 6, 2012 at 9:32 AM, Oscar Esteban <oesteban at die.upm.es> wrote:
>
>> Hi all,
>>
>> I'm trying to compute the Normals of a QuadEdgeMesh after warping it with
>> itk::WarpMeshFilter and a displacement field.
>>
>> I save to vtk files the result and the points seem to be correctly
>> displaced, but when computing the normals, I get a segmentation fault in
>> line 302 of itkQuadEdge.h.
>>
>> I think that the output Mesh after the WarpMeshFilter lacks of some
>> properties needed by the normals filter.
>>
>> In order to solve this, I could copy this properties from the input mesh
>> to the output. This are my questions:
>> - What is missing after the WarpMeshFilter?
>> - How to safely clone (deep-copy) a QuadEdgeMesh? (I have this problem in
>> some other parts of my code).
>>
>> Thank you so much in advance.
>>
>> Best,
>> Oscar Esteban
>>
>> *______________________________________*
>> *Oscar Esteban*
>> PhD Student / Researcher
>>
>> Biomedical Image Technologies (BIT), UPM
>> ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid
>> (Spain)
>> +34 915 495 700 ext.4234
>>
>> Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5
>> ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland
>>
>>
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