[ITK] [ITK-users] itk::Fem::Solver update problem
Dženan Zukić
dzenanz at gmail.com
Wed Oct 11 14:06:17 EDT 2017
Hi Yusuf,
as posting attachments on the discourse
<https://discourse.itk.org/t/itk-fem-solver-update-problem/280> forum is
not allowed, here is the updated source code to run on VTK8.
Regards,
Dženan
On Tue, Oct 10, 2017 at 11:36 AM, Yusuf OEZBEK via Insight-users <
insight-users at itk.org> wrote:
> Hello,
>
> Thank you for the answer Francois. Even chaning from raw- to
> smart-pointer for itkMesh did'nt bring any solution. The number of proints,
> cells and cell types are the same for vtkUnstructured grid and itkMesh
> after converting. But I got a new error : "vnl_error_vector_dimension:vnl_matrix::set_row:
> Dimensions [3] and [2] donot match" after the calling m_FemSolver->Update();
> function.
> Do you (or someone else) know, which matrix dimension is meant hier?
>
>
> Same quation is also asked here. But unfortunately without answer:
> https://itk.org/pipermail/insight-users/2009-July/031536.html
>
>
>
> Best regards
>
>
>
> Francois Budin <francois.budin at kitware.com> schrieb am 19:35 Montag,
> 9.Oktober 2017:
>
>
> Hello Yusuf,
>
> I am not sure what the problem is, but here are some ideas you can try to
> understand it or try to solve it:
> 1) Use ITK smart pointers instead of raw pointers. The crash seem to
> indicate that the program was trying to unregister a smart pointer, but
> your mesh is declared as a raw pointer. The issue could come from this.
> 2) Have you tried to look at your data, once converted, to make sure that
> it was converted correctly? Maybe there is a problem during your conversion
> which leads to an empty mesh or something worst.
>
> Hope this helps,
> Francois
>
> PS: As a side note, you may want to join the ITK discourse forum to ask
> your question or help others. The mailing list is still active but more
> people seem to be using the discourse forum now that it is available (
> http://discourse.itk.org/)
>
> On Mon, Oct 9, 2017 at 8:08 AM, Yusuf OEZBEK via Insight-users <
> insight-users at itk.org> wrote:
>
> Dear ITK Users,
>
> According the mail https://public.kitware.com/
> pipermail/insight-users/2007- November/024272.html
> <https://public.kitware.com/pipermail/insight-users/2007-November/024272.html>
> , I have converted my vtkUnstructuredGrid, wich I extracted from a
> vtkPolyData and contains TRIANGLE_CELL's to the itkMesh and than from
> itkMesh to itk::Fem::Object to deform my mesh:
> My problem is: If I call "m_FemSolver->Update();" ,I get a segmentation
> fault, which I really not understand.
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00007fffb1086dd5 in itk::fem::FEMObject<2u>:: DeepCopy (this=0x4cc5ee0,
> Copy=0x4cc1780)
> at /home/toolkits/itk-4.7.2/ Modules/Numerics/FEM/include/
> itkFEMObject.hxx:157
> 157 a->UnRegister();
>
>
> void itkMeshToFemMesh:: updateItkMeshSlot(itk::Mesh< double, 3,
> MeshTraitsType> *itkMesh)
> {
> typedef itk::fem::FEMObject<3> FemObjectType;
> FemObjectType::Pointer m_FemObject= FemObjectType::New();
>
> typedef itk::fem::Solver<3> SolverType;
> typedef SolverType::Pointer SolverPointerType;
> SolverPointerType m_FemSolver= SolverType::New();
>
> // Define the Element Material properties
> typedef itk::fem:: MaterialLinearElasticity MaterialType;
> MaterialType::Pointer material= MaterialType::New();
> material->SetGlobalNumber(0);
> material->SetYoungsModulus( 200E6);
> material-> SetCrossSectionalArea(1.0);
> material->SetThickness(1.0);
> material->SetMomentOfInertia( 1.0);
> material->SetPoissonsRatio(0. 2);
> material-> SetDensityHeatProduct(1.0);
> m_FemObject->AddNextMaterial( material);
>
> // Define the element type
> typedef itk::fem:: Element2DC0LinearTriangularStr ain
> TriangularElementType;
>
> TriangularElementType::Pointer triangularElement=
> TriangularElementType::New();
> triangularElement-> SetMaterial(material. GetPointer());
>
> // Convert mesh points into nodes
> VectorType point(3);
> PointType*ptr;
> PointType pt;
> ptr= &pt;
>
> int numOfPoints= itkMesh->GetNumberOfPoints();
> cout<<"itkMesh numOfPoints: "<<numOfPoints<<endl;
>
> int numberOfCells= itkMesh->GetNumberOfCells();
> cout<<"itkMesh numberOfCells: "<<numberOfCells<<endl;
>
> CellsContainerPointer cellIterator= itkMesh->GetCells();
> CellIterator cells= cellIterator->Begin();
>
> bool flag= true;
>
> for(int k=0; k< numberOfCells; k++)
> {
> CellType *cellPtr= cells.Value();
> cout<<"Cell Value: "<< cells.Value() << " Cell Type= " <<
> cellPtr->GetType()<<endl;
>
> switch(cellPtr->GetType())
> {
> case CellType::TRIANGLE_CELL:
> {
> if(flag== true) // To make sure that the nodes are created just
> once
> {
> for(int j= 0; j< numOfPoints; j++)
> {
> itkMesh->GetPoint(j, ptr);
>
> typedef TriangularElementType::Node TriangularNodeType;
> TriangularNodeType::Pointer triangularNode=
> TriangularNodeType::New();
> point[0]= -1.0;
> point[1]= 2.0;
> point[2]= 3.0;
> triangularNode-> SetCoordinates(point);
> triangularNode-> SetGlobalNumber(j);
> m_FemObject->AddNextNode( triangularNode.GetPointer());
> }
> flag= false;
> }
> PointIdIterator pointIt= cellPtr->PointIdsBegin();
> int i= 0;
>
> while(pointIt!= cellPtr->PointIdsEnd())
> {
> triangularElement->SetNode(i, m_FemObject->GetNode(*pointIt) );
> pointIt++;
> i++;
> }
> cells++;
> triangularElement-> SetGlobalNumber(k);
> m_FemObject->AddNextElement( triangularElement.GetPointer() );
> break;
> }
> }
> }
>
> // Define some Load
> LoadNodePointerType loadNode =LoadNodeType::New();
> loadNode->SetElement( triangularElement);
> loadNode->SetGlobalNumber(3);
> loadNode->SetNode(1);
>
> vnl_vector<double> force(2);
> force[0]= 20.0;
> force[1]= -20.0;
> force[2]= 10.0;
> loadNode->SetForce(force);
> m_FemObject->AddNextLoad( loadNode);
>
> //Solve for displacements.
> m_FemObject->FinalizeMesh();
> m_FemSolver->SetInput(m_ FemObject);
> m_FemSolver->Update(); // SEGMENTATION FAULT
>
> cout<< "Fem Solver Output: "<< m_FemSolver->GetOutput()<< endl;
>
> const unsigned int invalidId= itk::fem::Element::
> InvalidDegreeOfFreedomID;
> int numberOfNodes= m_FemSolver->GetInput()-> GetNumberOfNodes();
>
> for(int i= 0; i< numberOfNodes; i++)
> {
> itk::fem::Element::Node:: Pointer node= m_FemSolver->GetInput()->
> GetNode(i);
> cout<<"Fem Node : "<< node->GetGlobalNumber()<<endl;
>
> for(unsigned int j= 0, dof; (dof= node->GetDegreeOfFreedom(j))!=
> invalidId; j++)
> {
> cout <<"Solver GetSolution: "<< m_FemSolver->GetSolution(dof)< <endl;
> }
> }
>
> // Write the deformed mesh
> typedef itk::FEMObjectSpatialObject<3> FemObjectSpatialObjectType;
> FemObjectSpatialObjectType:: Pointer m_FemSpatialObject=
> FemObjectSpatialObjectType:: New();
> m_FemSpatialObject-> SetFEMObject(m_FemSolver-> GetOutput());
>
> typedef itk::FEMSpatialObjectWriter<3>
> FemSpatialObjectWriterType;
> FemSpatialObjectWriterType:: Pointer femSpatialWriter=
> FemSpatialObjectWriterType:: New();
> femSpatialWriter->SetInput(m_ FemSpatialObject);
> femSpatialWriter->SetFileName( "deformedMesh.meta");
> femSpatialWriter->Update();
> }
>
> Thank you for any help!
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ______________________________ __
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
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> Kitware offers ITK Training Courses, for more information visit:
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>
>
>
>
>
> The ITK community is transitioning from this mailing list to
> discourse.itk.org. Please join us there!
> ________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
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cmake_minimum_required(VERSION 3.8)
PROJECT(vtkUGridToFemMesh)
find_package(VTK REQUIRED)
include(${VTK_USE_FILE})
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
INCLUDE_DIRECTORIES(
${vtkCone_SOURCE_DIR}
${vtkCone_BINARY_DIR}
)
SET(vtkUGridToFemMesh_SRCS
main.cxx
)
add_executable(vtkUGridToFemMesh ${vtkUGridToFemMesh_SRCS})
target_link_libraries(vtkUGridToFemMesh ${VTK_LIBRARIES} ${ITK_LIBRARIES})
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#include <iostream>
#include <vtkSmartPointer.h>
#include <vtkPolyDataReader.h>
#include <vtkUnstructuredGrid.h>
#include <vtkDataSetMapper.h>
#include <vtkActor.h>
#include <vtkRenderer.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkAppendFilter.h>
#include <vtkPoints.h>
#include <vtkHexahedron.h>
#include <vtkTriangle.h>
#include <vtkQuad.h>
#include <vtkTetra.h>
#include <vtkVertex.h>
#include <vtkCellArray.h>
#include <itkDefaultDynamicMeshTraits.h>
#include <itkMesh.h>
#include <itkAutomaticTopologyMeshSource.h>
#include <itkHexahedronCell.h>
#include <itkTriangleCell.h>
#include <itkQuadrilateralCell.h>
#include <itkPolygonCell.h>
#include <itkFEMObject.h>
#include <itkFEMSolver.h>
#include <itkFEMElement3DC0LinearHexahedronStrain.h>
#include <itkFEMElement2DC0LinearTriangularStrain.h>
#include <itkFEMLoadBC.h>
#include <itkFEMObjectSpatialObject.h>
#include <itkFEMSpatialObjectWriter.h>
#include <itkMetaMeshConverter.h>
#include <itkMetaConverterBase.h>
#include <itkMeshSpatialObject.h>
typedef itk::DefaultStaticMeshTraits<double, 3, 3, float, float> MeshTraitsType;
typedef itk::Mesh<double, 3, MeshTraitsType> MeshType;
int main(int, char *[])
{
/////////////////////////// CONVERT VTK POLY DATA TO UNSTRUCTURED GRID ///////////////////////////
cout<<"CONVERT VTK POLY DATA TO UNSTRUCTURED GRID"<<endl;
//Read the content of .ext file
vtkSmartPointer<vtkPolyDataReader> polyReader= vtkSmartPointer<vtkPolyDataReader>::New();
polyReader->SetFileName("extracted.ext");
polyReader->Update();
vtkSmartPointer<vtkAppendFilter> append= vtkSmartPointer<vtkAppendFilter>::New();
append->AddInputConnection(polyReader->GetOutputPort());
append->Update();
vtkSmartPointer<vtkUnstructuredGrid> uGrid= vtkSmartPointer<vtkUnstructuredGrid>::New();
uGrid->ShallowCopy(append->GetOutput());
//Create a mapper and actor
vtkSmartPointer<vtkDataSetMapper> mapper= vtkSmartPointer<vtkDataSetMapper>::New();
mapper->SetInputData(uGrid);
mapper->ScalarVisibilityOff();
vtkSmartPointer<vtkActor> actor= vtkSmartPointer<vtkActor>::New();
actor->SetMapper(mapper);
vtkSmartPointer<vtkRenderer> renderer= vtkSmartPointer<vtkRenderer>::New();
vtkSmartPointer<vtkRenderWindow> renderWindow= vtkSmartPointer<vtkRenderWindow>::New();
renderWindow->AddRenderer(renderer);
vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor= vtkSmartPointer<vtkRenderWindowInteractor>::New();
renderWindowInteractor->SetRenderWindow(renderWindow);
renderer->AddActor(actor);
renderer->SetBackground(0, 0, 0);
renderWindow->Render();
renderWindowInteractor->Start();
/////////////////////////// CONVERT VTK UNSTRUCTURED GRID TO ITK MESH ///////////////////////////
cout<<"CONVERT VTK UNSTRUCTURED GRID TO ITK MESH"<<endl;
MeshType::Pointer itkMesh= MeshType::New();
// Get the points from vtk
vtkPoints* vtkPoints= uGrid->GetPoints();
int numPoints= vtkPoints->GetNumberOfPoints();
// Create a compatible point container for the mesh
// the mesh is created with a null points container
MeshType::PointsContainer::Pointer points= MeshType::PointsContainer::New();
// Resize the point container to be able to fit the vtk points
points->Reserve(numPoints);
// Set the point container on the mesh
itkMesh->SetPoints(points);
for(int i= 0; i< numPoints; i++)
{
double *aPoint= vtkPoints->GetPoint(i);
float itkPoint[3];
itkPoint[0]= static_cast<float>(aPoint[0]);
itkPoint[1]= static_cast<float>(aPoint[1]);
itkPoint[2]= static_cast<float>(aPoint[2]);
itkMesh->SetPoint(i, MeshType::PointType(itkPoint));
}
vtkSmartPointer<vtkCellArray> vtkCells= vtkSmartPointer<vtkCellArray>::New();
vtkCells= uGrid->GetCells();
MeshType::CellsContainerPointer cells= MeshType::CellsContainer::New();
// Extract the cell id's from the vtkUnstructuredGrid
int numCells= vtkCells->GetNumberOfCells();
// Extract cell type for each cell
int *vtkCellTypes= new int[numCells];
int cellId= 0;
for(; cellId< numCells; cellId++)
{
vtkCellTypes[cellId]= uGrid->GetCellType(cellId);
}
// Resize the point container to be able to fit the vtk points
cells->Reserve(numCells);
itkMesh->SetCells(cells);
vtkIdType npts;
vtkIdType *pts;
cellId= 0;
for(vtkCells->InitTraversal(); vtkCells->GetNextCell(npts, pts); cellId++)
{
//cout<<"VTK cell ID= "<<cellId <<" "<<vtkCellTypes[cellId]<<endl;
MeshType::CellAutoPointer c;
switch(vtkCellTypes[cellId])
{
case VTK_HEXAHEDRON:
{
typedef itk::CellInterface<double, MeshType::CellTraits> CellInterfaceType;
typedef itk::HexahedronCell<CellInterfaceType> HexahedronCellType;
HexahedronCellType *t= new HexahedronCellType;
for(int i= 0; i< 8; i++)
{
t->SetPointId(i, static_cast<unsigned long>(pts[i]));
}
//t->SetPointIds((unsigned long*)pts);
c.TakeOwnership(t);
break;
}
case VTK_TRIANGLE:
{
typedef itk::CellInterface<double, MeshType::CellTraits> CellInterfaceType;
typedef itk::TriangleCell<CellInterfaceType> TriangleCellType;
TriangleCellType *t= new TriangleCellType;
for(int i= 0; i< 3; i++)
{
//cout <<"VTK Point ids= "<< pts[i]<<endl;
t->SetPointId(i, static_cast<unsigned long>(pts[i]));
}
c.TakeOwnership(t);
break;
}
case VTK_POLY_VERTEX:
case VTK_LINE:
case VTK_POLY_LINE:
case VTK_TRIANGLE_STRIP:
case VTK_POLYGON:
case VTK_PIXEL:
case VTK_TETRA:
case VTK_VOXEL:
case VTK_WEDGE:
case VTK_PYRAMID:
case VTK_PARAMETRIC_CURVE:
case VTK_PARAMETRIC_SURFACE:
case VTK_EMPTY_CELL:
default:
cout<< "Warning unhandled cell type" << vtkCellTypes[cellId]<<endl;
}
itkMesh->SetCell(cellId, c);
}
/////////////////////////// CONVERT ITK MESH TO FEM MESH ///////////////////////////
cout<<"CONVERT ITK MESH TO FEM MESH"<<endl;
typedef itk::fem::FEMObject<3> FemObjectType;
FemObjectType::Pointer m_FemObject= FemObjectType::New();
typedef itk::fem::Solver<3> SolverType;
SolverType::Pointer m_FemSolver= SolverType::New();
// Define the Element Material properties
typedef itk::fem::MaterialLinearElasticity MaterialType;
MaterialType::Pointer material= MaterialType::New();
material->SetGlobalNumber(0);
material->SetYoungsModulus(200E6);
material->SetCrossSectionalArea(1.0);
material->SetThickness(1.0);
material->SetMomentOfInertia(1.0);
material->SetPoissonsRatio(0.2);
material->SetDensityHeatProduct(1.0);
m_FemObject->AddNextMaterial(material);
// Define the element type
typedef itk::fem::Element2DC0LinearTriangularStrain TriangularElementType;
TriangularElementType::Pointer triangularElement= TriangularElementType::New();
triangularElement->SetMaterial(material.GetPointer());
// Convert mesh points into nodes
typedef itk::fem::Element::VectorType VectorType;
VectorType point(3);
typedef itk::DefaultStaticMeshTraits <double, 3, 3, float, float> MeshTraitsType;
typedef itk::Mesh <double, 3, MeshTraitsType> MeshType;
typedef MeshType::PointType PointType;
PointType*ptr;
PointType pt;
ptr= &pt;
int numOfPoints= itkMesh->GetNumberOfPoints();
cout<<"itkMesh numOfPoints: "<<numOfPoints<<endl;
int numberOfCells= itkMesh->GetNumberOfCells();
cout<<"itkMesh numberOfCells: "<<numberOfCells<<endl;
/*
// Access points
typedef MeshType::PointsContainer::Iterator PointsIterator;
PointsIterator pointIterator= itkMesh->GetPoints()->Begin();
PointsIterator endOfPoints= itkMesh->GetPoints()->End();
MeshType::PointType itkMeshPoints;
while(pointIterator!= endOfPoints)
{
itkMeshPoints= pointIterator.Value();
cout <<"itkMeshPoints: "<< itkMeshPoints <<endl;
++pointIterator;
}
*/
for (int j = 0; j< numOfPoints; j++)
{
point = itkMesh->GetPoint(j, ptr);
typedef TriangularElementType::Node TriangularNodeType;
TriangularNodeType::Pointer triangularNode = TriangularNodeType::New();
point[0] = -4.0;
point[1] = 3.0;
point[2] = 4.0;
triangularNode->SetCoordinates(point);
triangularNode->SetGlobalNumber(j);
m_FemObject->AddNextNode(triangularNode.GetPointer());
//m_FemObject->RenumberNodeContainer();
//cout << "j:" << j << " Mesh points: " << point[0] << "|" << point[1] << "|" << point[2] << endl;
}
typedef MeshType::CellsContainerPointer CellsContainerPointer;
typedef MeshType::CellsContainer::ConstIterator CellIterator;
CellsContainerPointer cellIterator= itkMesh->GetCells();
CellIterator cellsIter= cellIterator->Begin();
typedef MeshType::CellType CellType;
for(int k=0; k< numberOfCells; k++)
{
CellType *cellPtr= cellsIter.Value();
//cout<<"Cell Value: "<< cells.Value() << " Cell Type= " << cellPtr->GetType()<<endl;
switch(cellPtr->GetType())
{
case CellType::TRIANGLE_CELL:
{
typedef itk::TriangleCell <CellType> TriangleType;
typedef TriangleType::PointIdIterator PointIdIterator;
PointIdIterator pointIt= cellPtr->PointIdsBegin();
int i= 0;
while(pointIt!= cellPtr->PointIdsEnd())
{
triangularElement->SetNode(i, m_FemObject->GetNode(*pointIt));
pointIt++;
i++;
}
cellsIter++;
triangularElement->SetGlobalNumber(k);
m_FemObject->AddNextElement(triangularElement.GetPointer());
break;
}
}
}
// Define boundary condiditon load types
typedef itk::fem::LoadBC LoadBCType;
LoadBCType::Pointer loadBc1= LoadBCType::New();
loadBc1->SetElement(m_FemObject->GetElement(0));
loadBc1->SetGlobalNumber(0);
loadBc1->SetDegreeOfFreedom(0);
loadBc1->SetValue(vnl_vector<double>(1, 0.0));
m_FemObject->AddNextLoad(loadBc1);
LoadBCType::Pointer loadBc2= LoadBCType::New();
loadBc2->SetElement(m_FemObject->GetElement(0));
loadBc2->SetGlobalNumber(1);
loadBc2->SetDegreeOfFreedom(1);
loadBc2->SetValue(vnl_vector<double>(1, 0.0));
m_FemObject->AddNextLoad(loadBc2);
LoadBCType::Pointer loadBc3= LoadBCType::New();
loadBc3->SetElement(m_FemObject->GetElement(1));
loadBc3->SetGlobalNumber(2);
loadBc3->SetDegreeOfFreedom(4);
loadBc3->SetValue(vnl_vector<double>(1, 0.0));
m_FemObject->AddNextLoad(loadBc3);
// Define force type
typedef itk::fem::LoadNode LoadNodeType;
LoadNodeType::Pointer loadNode= LoadNodeType::New();
loadNode->SetElement(m_FemObject->GetElement(2));
loadNode->SetGlobalNumber(3);
loadNode->SetNode(1);
vnl_vector<double> force(3);
force[0]= 20.0;
force[1]= -20.0;
force[2]= 10.0;
loadNode->SetForce(force);
m_FemObject->AddNextLoad(loadNode);
//The whole problem is now stored inside the FEM Object class. Now solve for displacements.
m_FemObject->FinalizeMesh();
m_FemSolver->SetInput(m_FemObject);
m_FemSolver->Update();
cout<< "Fem Solver Output: "<< m_FemSolver->GetOutput()<<endl;
const unsigned int invalidId= itk::fem::Element::InvalidDegreeOfFreedomID;
int numberOfNodes= m_FemSolver->GetInput()->GetNumberOfNodes();
for(int i= 0; i< numberOfNodes; i++)
{
itk::fem::Element::Node::Pointer node= m_FemSolver->GetInput()->GetNode(i);
cout<<"Fem Node : "<< node->GetGlobalNumber()<<endl;
for(unsigned int j= 0, dof; (dof= node->GetDegreeOfFreedom(j))!= invalidId; j++)
{
cout <<"Solve Solution: "<< m_FemSolver->GetSolution(dof)<<endl;
}
}
// Write the deformed mesh
typedef itk::FEMObjectSpatialObject<3> FemObjectSpatialObjectType;
FemObjectSpatialObjectType::Pointer m_FemSpatialObject= FemObjectSpatialObjectType::New();
m_FemSpatialObject->SetFEMObject(m_FemSolver->GetOutput());
typedef itk::FEMSpatialObjectWriter<3> FemSpatialObjectWriterType;
FemSpatialObjectWriterType::Pointer femSpatialWriter= FemSpatialObjectWriterType::New();
femSpatialWriter->SetInput(m_FemSpatialObject);
femSpatialWriter->SetFileName("deformedMesh.meta");
femSpatialWriter->Update();
return EXIT_SUCCESS;
}
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