DiscreteContinuumMesh.cpp

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#include <boost/lexical_cast.hpp>
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning
#include <vtkIdList.h>
#include <vtkCellArray.h>
#include <vtkLine.h>
#include <vtkPoints.h>
#include <vtkTriangle.h>
#include <vtkPoints.h>
#include <vtkTetra.h>
#include <vtkGenericCell.h>
#include "Exception.hpp"
#include "Warnings.hpp"
#include "Facet.hpp"
#include "Polygon.hpp"
#include "DiscreteContinuumMesh.hpp"
#include "Element.hpp"
#include "UblasVectorInclude.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "VtkMeshWriter.hpp"
#include "BaseUnits.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::DiscreteContinuumMesh() :
    mAttributes(),
    mReferenceLength(BaseUnits::Instance()->GetReferenceLengthScale()),
    mpVtkMesh(),
    mpVtkCellLocator(vtkSmartPointer<vtkCellLocator>::New()),
    mVtkRepresentationUpToDate(false),
    mPointElementMap(),
    mSegmentElementMap(),
    mCellElementMap(),
    mpNetwork(),
    mpCellPopulation(),
    mCellPopulationReferenceLength(BaseUnits::Instance()->GetReferenceLengthScale())
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr<DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM> > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::Create()
{
    MAKE_PTR(DiscreteContinuumMesh<ELEMENT_DIM>, pSelf);
    return pSelf;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::~DiscreteContinuumMesh()
{

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
units::quantity<unit::length> DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetReferenceLengthScale()
{
    return mReferenceLength;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
vtkSmartPointer<vtkUnstructuredGrid> DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetAsVtkUnstructuredGrid()
{
    if(!mVtkRepresentationUpToDate)
    {
        mpVtkMesh = vtkSmartPointer<vtkUnstructuredGrid>::New();
        vtkSmartPointer<vtkPoints> p_vtk_points = vtkSmartPointer<vtkPoints>::New();
        std::vector<c_vector<double, SPACE_DIM> > node_locations = GetNodeLocations();
        p_vtk_points->SetNumberOfPoints(node_locations.size());
        for(unsigned idx=0; idx<node_locations.size(); idx++)
        {
            if(SPACE_DIM==3)
            {
                p_vtk_points->InsertPoint(idx, node_locations[idx][0], node_locations[idx][1], node_locations[idx][2]);
            }
            else
            {
                p_vtk_points->InsertPoint(idx, node_locations[idx][0], node_locations[idx][1], 0.0);
            }
        }
        mpVtkMesh->SetPoints(p_vtk_points);

        // Add vtk tets or triangles
        std::vector<std::vector<unsigned> > element_connectivity =  GetConnectivity();
        unsigned num_elements = element_connectivity.size();
        mpVtkMesh->Allocate(num_elements, num_elements);

        for(unsigned idx=0; idx<num_elements; idx++)
        {
            if(ELEMENT_DIM==3)
            {
                vtkSmartPointer<vtkTetra> p_vtk_element = vtkSmartPointer<vtkTetra>::New();
                unsigned num_nodes = element_connectivity[idx].size();
                for(unsigned jdx=0; jdx<num_nodes; jdx++)
                {
                    p_vtk_element->GetPointIds()->SetId(jdx, element_connectivity[idx][jdx]);
                }
                mpVtkMesh->InsertNextCell(p_vtk_element->GetCellType(), p_vtk_element->GetPointIds());
            }
            else
            {
                vtkSmartPointer<vtkTriangle> p_vtk_element = vtkSmartPointer<vtkTriangle>::New();
                unsigned num_nodes = element_connectivity[idx].size();
                for(unsigned jdx=0; jdx<num_nodes; jdx++)
                {
                    p_vtk_element->GetPointIds()->SetId(jdx, element_connectivity[idx][jdx]);
                }
                mpVtkMesh->InsertNextCell(p_vtk_element->GetCellType(), p_vtk_element->GetPointIds());
            }
        }
        mpVtkCellLocator = vtkSmartPointer<vtkCellLocator>::New();
        mpVtkCellLocator->SetDataSet(mpVtkMesh);
        mpVtkCellLocator->BuildLocator();

        mVtkRepresentationUpToDate = true;
    }
    return mpVtkMesh;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<unsigned> DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetElementRegionMarkers()
{
    return mAttributes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<c_vector<double, SPACE_DIM> > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetElementCentroids()
{
    std::vector<c_vector<double, SPACE_DIM> > centroids(this->GetNumElements());
    for(unsigned idx=0; idx<this->GetNumElements(); idx++)
    {
        centroids[idx] = this->GetElement(idx)->CalculateCentroid();
    }
    return centroids;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<std::vector<unsigned> > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetPointElementMap(std::vector<DimensionalChastePoint<SPACE_DIM> > points)
{
    if(!mVtkRepresentationUpToDate)
    {
        GetAsVtkUnstructuredGrid();
    }

    mPointElementMap.clear();
    mPointElementMap = std::vector<std::vector<unsigned> >(this->GetNumElements());

    std::vector<int> cell_indices(points.size());
    for(unsigned idx=0; idx<points.size(); idx++)
    {
        double x_coords[3];
        x_coords[0] = points[idx].GetLocation(mReferenceLength)[0];
        x_coords[1] = points[idx].GetLocation(mReferenceLength)[1];
        if(SPACE_DIM == 3)
        {
            x_coords[2] = points[idx].GetLocation(mReferenceLength)[2];
        }
        else
        {
            x_coords[2] = 0.0;
        }

        int cell_id=-1;
        cell_id = mpVtkCellLocator->FindCell(x_coords);

        if(cell_id>=0)
        {
            mPointElementMap[cell_id].push_back(idx);
        }
    }
    return mPointElementMap;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
const std::vector<std::vector<CellPtr> >& DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetElementCellMap(bool update)
{
    if (!update)
    {
        return mCellElementMap;
    }

    if(!mVtkRepresentationUpToDate)
    {
        GetAsVtkUnstructuredGrid();
    }

    if (!mpCellPopulation)
    {
        EXCEPTION("A cell population has not been set. Can not create a cell element map.");
    }

    // Loop over all cells and associate cells with the points
    mCellElementMap.clear();
    mCellElementMap = std::vector<std::vector<CellPtr> >(this->GetNumElements());

    double cell_mesh_length_scaling = mCellPopulationReferenceLength/mReferenceLength;
    for (typename AbstractCellPopulation<SPACE_DIM>::Iterator cell_iter = mpCellPopulation->Begin();
            cell_iter != mpCellPopulation->End(); ++cell_iter)
    {
        c_vector<double, SPACE_DIM> location = mpCellPopulation->GetLocationOfCellCentre(*cell_iter);
        double x_coords[3];
        x_coords[0] = location[0]*cell_mesh_length_scaling;
        x_coords[1] = location[1]*cell_mesh_length_scaling;
        if(SPACE_DIM == 3)
        {
            x_coords[2] = location[2]*cell_mesh_length_scaling;
        }
        else
        {
            x_coords[2] = 0.0;
        }
        int cell_id=-1;
        cell_id = mpVtkCellLocator->FindCell(x_coords);

        if(cell_id>=0)
        {
            mCellElementMap[cell_id].push_back(*cell_iter);
        }
    }
    return mCellElementMap;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetElementSegmentMap(bool update,
                                                                                                        bool useVesselSurface)
{
    if (!update)
    {
        return mSegmentElementMap;
    }

    if (!mpNetwork)
    {
        EXCEPTION("A vessel network has not been set. Can not create a vessel element map.");
    }

    mSegmentElementMap.clear();
    unsigned num_elements = this->GetNumElements();
    mSegmentElementMap = std::vector<std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > >(num_elements);

    std::vector<boost::shared_ptr<VesselSegment<SPACE_DIM> > > segments = mpNetwork->GetVesselSegments();

    for (unsigned jdx = 0; jdx < segments.size(); jdx++)
    {
        DimensionalChastePoint<SPACE_DIM> loc1 = segments[jdx]->GetNode(0)->rGetLocation();
        DimensionalChastePoint<SPACE_DIM> loc2 = segments[jdx]->GetNode(1)->rGetLocation();
        double x_coords1[3];
        x_coords1[0] = loc1.GetLocation(mReferenceLength)[0];
        x_coords1[1] = loc1.GetLocation(mReferenceLength)[1];
        if(SPACE_DIM == 3)
        {
            x_coords1[2] = loc1.GetLocation(mReferenceLength)[2];
        }
        else
        {
            x_coords1[2] = 0.0;
        }
        double x_coords2[3];
        x_coords2[0] = loc2.GetLocation(mReferenceLength)[0];
        x_coords2[1] = loc2.GetLocation(mReferenceLength)[1];
        if(SPACE_DIM == 3)
        {
            x_coords2[2] = loc2.GetLocation(mReferenceLength)[2];
        }
        else
        {
            x_coords2[2] = 0.0;
        }

        vtkSmartPointer<vtkIdList> p_id_list = vtkSmartPointer<vtkIdList>::New();
        mpVtkCellLocator->FindCellsAlongLine(x_coords1, x_coords2, 1.e-8, p_id_list);
        unsigned num_intersections = p_id_list->GetNumberOfIds();
        for(unsigned idx=0; idx<num_intersections; idx++)
        {
            mSegmentElementMap[p_id_list->GetId(idx)].push_back(segments[jdx]);
        }
    }

    return mSegmentElementMap;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<std::vector<unsigned> > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetConnectivity()
{
    std::vector<std::vector<unsigned> > connectivity;
    unsigned num_elements = AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumElements();
    for (unsigned idx = 0; idx < num_elements; idx++)
    {
        std::vector<unsigned> node_indexes;
        unsigned num_nodes = AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElement(idx)->GetNumNodes();
        for (unsigned jdx = 0; jdx < num_nodes; jdx++)
        {
            node_indexes.push_back(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetElement(idx)->GetNodeGlobalIndex(jdx));
        }
        connectivity.push_back(node_indexes);
    }
    return connectivity;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<c_vector<double, SPACE_DIM> > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeLocations()
{
    unsigned num_nodes = AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumNodes();
    std::vector<c_vector<double, SPACE_DIM> > locations(num_nodes);
    for (unsigned idx = 0; idx < num_nodes; idx++)
    {
        locations[idx] = AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNode(idx)->rGetLocation();
    }
    return locations;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<DimensionalChastePoint<SPACE_DIM> > DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::GetNodeLocationsAsPoints()
{
    unsigned num_nodes = AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNumNodes();
    std::vector<DimensionalChastePoint<SPACE_DIM> > locations(num_nodes);
    for (unsigned idx = 0; idx < num_nodes; idx++)
    {
        locations[idx] = DimensionalChastePoint<SPACE_DIM>(AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>::GetNode(idx)->rGetLocation(), mReferenceLength);
    }
    return locations;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::ImportDiscreteContinuumMeshFromTetgen(tetgen::tetgenio& mesherOutput, unsigned numberOfElements,
                                                          int *elementList, unsigned numberOfFaces, int *faceList,
                                                          int *edgeMarkerList)
{
    unsigned nodes_per_element = mesherOutput.numberofcorners;

    assert(nodes_per_element == ELEMENT_DIM + 1 || nodes_per_element == (ELEMENT_DIM + 1) * (ELEMENT_DIM + 2) / 2);

    for (unsigned i = 0; i < this->mBoundaryElements.size(); i++)
    {
        delete this->mBoundaryElements[i];
    }
    for (unsigned i = 0; i < this->mElements.size(); i++)
    {
        delete this->mElements[i];
    }
    for (unsigned i = 0; i < this->mNodes.size(); i++)
    {
        delete this->mNodes[i];
    }

    this->mNodes.clear();
    this->mElements.clear();
    this->mBoundaryElements.clear();
    this->mBoundaryNodes.clear();

    // Construct the nodes
    for (unsigned node_index = 0; node_index < (unsigned) mesherOutput.numberofpoints; node_index++)
    {
        this->mNodes.push_back(new Node<SPACE_DIM>(node_index, &mesherOutput.pointlist[node_index * SPACE_DIM], false));
    }

    // Construct the elements
    this->mElements.reserve(numberOfElements);

    unsigned real_element_index = 0;
    for (unsigned element_index = 0; element_index < numberOfElements; element_index++)
    {
        std::vector<Node<SPACE_DIM>*> nodes;
        for (unsigned j = 0; j < ELEMENT_DIM + 1; j++)
        {
            unsigned global_node_index = elementList[element_index * (nodes_per_element) + j];
            assert(global_node_index < this->mNodes.size());
            nodes.push_back(this->mNodes[global_node_index]);

        }

        /*
         * For some reason, tetgen in library mode makes its initial Delaunay mesh
         * with very thin slivers. Hence we expect to ignore some of the elements!
         */
        Element<ELEMENT_DIM, SPACE_DIM>* p_element;
        try
        {
            p_element = new Element<ELEMENT_DIM, SPACE_DIM>(real_element_index, nodes);

            // Shouldn't throw after this point
            this->mElements.push_back(p_element);

            // Add the internals to quadratics
            for (unsigned j = ELEMENT_DIM + 1; j < nodes_per_element; j++)
            {
                unsigned global_node_index = elementList[element_index * nodes_per_element + j];
                assert(global_node_index < this->mNodes.size());
                this->mElements[real_element_index]->AddNode(this->mNodes[global_node_index]);
                this->mNodes[global_node_index]->AddElement(real_element_index);
                this->mNodes[global_node_index]->MarkAsInternal();
            }
            real_element_index++;
        }
        catch (Exception &)
        {
            if (SPACE_DIM == 2)
            {
                WARNING("Triangle has produced a zero area (collinear) element");
            }
            else
            {
                WARNING("Tetgen has produced a zero volume (coplanar) element");
            }
        }
    }

    // Construct the BoundaryElements (and mark boundary nodes)
    unsigned next_boundary_element_index = 0;
    for (unsigned boundary_element_index = 0; boundary_element_index < numberOfFaces; boundary_element_index++)
    {
        /*
         * Tetgen produces only boundary faces (set edgeMarkerList to NULL).
         * Triangle marks which edges are on the boundary.
         */
        if (edgeMarkerList == NULL || edgeMarkerList[boundary_element_index] == 1)
        {
            std::vector<Node<SPACE_DIM>*> nodes;
            for (unsigned j = 0; j < ELEMENT_DIM; j++)
            {
                unsigned global_node_index = faceList[boundary_element_index * ELEMENT_DIM + j];
                assert(global_node_index < this->mNodes.size());
                nodes.push_back(this->mNodes[global_node_index]);
                if (!nodes[j]->IsBoundaryNode())
                {
                    nodes[j]->SetAsBoundaryNode();
                    this->mBoundaryNodes.push_back(nodes[j]);
                }
            }

            /*
             * For some reason, tetgen in library mode makes its initial Delaunay mesh
             * with very thin slivers. Hence we expect to ignore some of the elements!
             */
            BoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>* p_b_element;
            try
            {
                p_b_element = new BoundaryElement<ELEMENT_DIM - 1, SPACE_DIM>(next_boundary_element_index, nodes);
                this->mBoundaryElements.push_back(p_b_element);
                next_boundary_element_index++;
            }
            catch (Exception &)
            {
                // Tetgen is feeding us lies  //Watch this space for coverage
                assert(SPACE_DIM == 3);
            }
        }
    }

    this->RefreshJacobianCachedData();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::SetAttributes(std::vector<unsigned> attributes)
{
    mAttributes = attributes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::SetCellPopulation(AbstractCellPopulation<SPACE_DIM>& rCellPopulation,
                                                                      units::quantity<unit::length> cellLengthScale)
{
    mpCellPopulation = &rCellPopulation;
    mCellPopulationReferenceLength = cellLengthScale;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void DiscreteContinuumMesh<ELEMENT_DIM, SPACE_DIM>::SetVesselNetwork(boost::shared_ptr<VesselNetwork<SPACE_DIM> > pNetwork)
{
    mpNetwork = pNetwork;
}

// Explicit instantiation
template class DiscreteContinuumMesh<2> ;
template class DiscreteContinuumMesh<3> ;