VertexMeshWriter.cpp

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*/
 
#include "VertexMeshWriter.hpp"
#include "Version.hpp"
#include "Cylindrical2dVertexMesh.hpp"
#include "Toroidal2dVertexMesh.hpp"
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct MeshWriterIterators
{
    typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator* pNodeIter;
    typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator* pElemIter;
};
 
// Implementation
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::VertexMeshWriter(const std::string& rDirectory,
                                                           const std::string& rBaseName,
                                                           const bool clearOutputDir)
    : AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, clearOutputDir),
      mpMesh(nullptr),
      mpIters(new MeshWriterIterators<ELEMENT_DIM, SPACE_DIM>),
      mpNodeMap(nullptr),
      mNodeMapCurrentIndex(0)
{
    mpIters->pNodeIter = nullptr;
    mpIters->pElemIter = nullptr;
 
#ifdef CHASTE_VTK
     // Dubious, since we shouldn't yet know what any details of the mesh are.
     mpVtkUnstructedMesh = vtkUnstructuredGrid::New();
#endif //CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::~VertexMeshWriter()
{
    if (mpIters->pNodeIter)
    {
        delete mpIters->pNodeIter;
        delete mpIters->pElemIter;
    }
 
    delete mpIters;
 
    if (mpNodeMap)
    {
        delete mpNodeMap;
    }
 
#ifdef CHASTE_VTK
     // Dubious, since we shouldn't yet know what any details of the mesh are.
     mpVtkUnstructedMesh->Delete(); // Reference counted
#endif //CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextNode()
{
    if (mpMesh)
    {
        // Sanity check
        assert(this->mNumNodes == mpMesh->GetNumNodes());
 
        std::vector<double> coordinates(SPACE_DIM+1);
 
        // Get the node coordinates using the node iterator (thus skipping deleted nodes)
        for (unsigned j=0; j<SPACE_DIM; j++)
        {
            coordinates[j] = (*(mpIters->pNodeIter))->GetPoint()[j];
        }
        coordinates[SPACE_DIM] = (*(mpIters->pNodeIter))->IsBoundaryNode();
 
        ++(*(mpIters->pNodeIter));
 
        return coordinates;
    }
    else
    {
        return AbstractMeshWriter<ELEMENT_DIM,SPACE_DIM>::GetNextNode();
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexElementData VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextElementWithFaces()
{
    // This method should only be called in 3D
    assert(SPACE_DIM == 3);    // LCOV_EXCL_LINE
    assert(mpMesh);
    assert(this->mNumElements == mpMesh->GetNumElements());
 
    // Create data structure for this element
    VertexElementData elem_data;
 
    // Store node indices owned by this element
    elem_data.NodeIndices.resize((*(mpIters->pElemIter))->GetNumNodes());
    for (unsigned j=0; j<elem_data.NodeIndices.size(); j++)
    {
        unsigned old_index = (*(mpIters->pElemIter))->GetNodeGlobalIndex(j);
        elem_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
    }
 
    // Store faces owned by this element
    elem_data.Faces.resize((*(mpIters->pElemIter))->GetNumFaces());
    for (unsigned i=0; i<elem_data.Faces.size(); i++)
    {
        // Get pointer to this face
        VertexElement<ELEMENT_DIM-1, SPACE_DIM>* p_face = (*(mpIters->pElemIter))->GetFace(i);
 
        // Create data structure for this face
        ElementData face_data;
 
        // Store this face's index
        face_data.AttributeValue = p_face->GetIndex();
 
        // Store node indices owned by this face
        face_data.NodeIndices.resize(p_face->GetNumNodes());
        for (unsigned j=0; j<face_data.NodeIndices.size(); j++)
        {
            unsigned old_index = p_face->GetNodeGlobalIndex(j);
            face_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
        }
 
        // Store this face
        elem_data.Faces[i] = face_data;
 
    }
 
    // Set attribute
    elem_data.AttributeValue = (unsigned)(*(mpIters->pElemIter))->GetAttribute();
    ++(*(mpIters->pElemIter));
 
    return elem_data;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextElement()
{
 
    if (mpMesh)
    {
        assert(this->mNumElements == mpMesh->GetNumElements());
 
        ElementData elem_data;
        elem_data.NodeIndices.resize((*(mpIters->pElemIter))->GetNumNodes());
        for (unsigned j=0; j<elem_data.NodeIndices.size(); j++)
        {
            unsigned old_index = (*(mpIters->pElemIter))->GetNodeGlobalIndex(j);
            elem_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
        }
 
        // Set attribute
        elem_data.AttributeValue = (*(mpIters->pElemIter))->GetAttribute();
        ++(*(mpIters->pElemIter));
 
        return elem_data;
    }
    else
    {
        return AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextElement();
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteVtkUsingMesh(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh, std::string stamp)
{
#ifdef CHASTE_VTK
    assert(SPACE_DIM==3 || SPACE_DIM == 2);    // LCOV_EXCL_LINE
 
    // Create VTK mesh
    MakeVtkMesh(rMesh);
 
    // Now write VTK mesh to file
    assert(mpVtkUnstructedMesh->CheckAttributes() == 0);
    vtkXMLUnstructuredGridWriter* p_writer = vtkXMLUnstructuredGridWriter::New();
#if VTK_MAJOR_VERSION >= 6
    p_writer->SetInputData(mpVtkUnstructedMesh);
#else
    p_writer->SetInput(mpVtkUnstructedMesh);
#endif
    // Uninitialised stuff arises (see #1079), but you can remove valgrind problems by removing compression:
    // **** REMOVE WITH CAUTION *****
    p_writer->SetCompressor(nullptr);
    // **** REMOVE WITH CAUTION *****
 
    std::string vtk_file_name = this->mpOutputFileHandler->GetOutputDirectoryFullPath() + this->mBaseName;
    if (stamp != "")
    {
        vtk_file_name += "_" + stamp;
    }
    vtk_file_name += ".vtu";
 
    p_writer->SetFileName(vtk_file_name.c_str());
    //p_writer->PrintSelf(std::cout, vtkIndent());
    p_writer->Write();
    p_writer->Delete(); // Reference counted
#endif //CHASTE_VTK
}
 
template<>
void VertexMeshWriter<2, 2>::WriteVtkUsingMesh(VertexMesh<2, 2>& rMesh, std::string stamp)
{
#ifdef CHASTE_VTK
    // Create VTK mesh
    VertexMesh<2, 2>* p_mesh_for_vtk = rMesh.GetMeshForVtk();
    MakeVtkMesh(*p_mesh_for_vtk);
 
    // Now write VTK mesh to file
    assert(mpVtkUnstructedMesh->CheckAttributes() == 0);
    vtkXMLUnstructuredGridWriter* p_writer = vtkXMLUnstructuredGridWriter::New();
#if VTK_MAJOR_VERSION >= 6
    p_writer->SetInputData(mpVtkUnstructedMesh);
#else
    p_writer->SetInput(mpVtkUnstructedMesh);
#endif
    // Uninitialised stuff arises (see #1079), but you can remove valgrind problems by removing compression:
    // **** REMOVE WITH CAUTION *****
    p_writer->SetCompressor(nullptr);
    // **** REMOVE WITH CAUTION *****
 
    std::string vtk_file_name = this->mpOutputFileHandler->GetOutputDirectoryFullPath() + this->mBaseName;
    if (stamp != "")
    {
        vtk_file_name += "_" + stamp;
    }
    vtk_file_name += ".vtu";
 
    p_writer->SetFileName(vtk_file_name.c_str());
    //p_writer->PrintSelf(std::cout, vtkIndent());
    p_writer->Write();
    p_writer->Delete(); // Reference counted
#endif //CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::MakeVtkMesh(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh)
{
#ifdef CHASTE_VTK
    // Make the Vtk mesh
    vtkPoints* p_pts = vtkPoints::New(VTK_DOUBLE);
    p_pts->GetData()->SetName("Vertex positions");
    for (unsigned node_num = 0; node_num < rMesh.GetNumNodes(); node_num++)
    {
        c_vector<double, SPACE_DIM> position;
        position = rMesh.GetNode(node_num)->rGetLocation();
        if (SPACE_DIM == 2)
        {
            p_pts->InsertPoint(node_num, position[0], position[1], 0.0);
        }
        else if (SPACE_DIM == 3)
        {
            p_pts->InsertPoint(node_num, position[0], position[1], position[2]);
        }
        else
        {
            NEVER_REACHED;
        }
    }
 
    mpVtkUnstructedMesh->SetPoints(p_pts);
    p_pts->Delete(); // Reference counted
    for (typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator iter = rMesh.GetElementIteratorBegin();
         iter != rMesh.GetElementIteratorEnd();
         ++iter)
    {
        vtkCell* p_cell;
        if (SPACE_DIM == 2)
        {
            p_cell = vtkPolygon::New();
        }
        else
        {
            p_cell = vtkConvexPointSet::New();
        }
        vtkIdList* p_cell_id_list = p_cell->GetPointIds();
        p_cell_id_list->SetNumberOfIds(iter->GetNumNodes());
        for (unsigned j=0; j<iter->GetNumNodes(); ++j)
        {
            p_cell_id_list->SetId(j, iter->GetNodeGlobalIndex(j));
        }
        mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
        p_cell->Delete(); // Reference counted
    }
#endif //CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::AddCellData(std::string dataName, std::vector<double> dataPayload)
{
#ifdef CHASTE_VTK
    vtkDoubleArray* p_scalars = vtkDoubleArray::New();
    p_scalars->SetName(dataName.c_str());
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }
 
    vtkCellData* p_cell_data = mpVtkUnstructedMesh->GetCellData();
    p_cell_data->AddArray(p_scalars);
    p_scalars->Delete(); // Reference counted
#endif //CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::AddPointData(std::string dataName, std::vector<double> dataPayload)
{
#ifdef CHASTE_VTK
    vtkDoubleArray* p_scalars = vtkDoubleArray::New();
    p_scalars->SetName(dataName.c_str());
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }
 
    vtkPointData* p_point_data = mpVtkUnstructedMesh->GetPointData();
    p_point_data->AddArray(p_scalars);
    p_scalars->Delete(); // Reference counted
#endif //CHASTE_VTK
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesUsingMesh(VertexMesh<ELEMENT_DIM,SPACE_DIM>& rMesh)
{
    this->mpMeshReader = nullptr;
    mpMesh = &rMesh;
 
    this->mNumNodes = mpMesh->GetNumNodes();
    this->mNumElements = mpMesh->GetNumElements();
 
    typedef typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator NodeIterType;
    mpIters->pNodeIter = new NodeIterType(mpMesh->GetNodeIteratorBegin());
 
    typedef typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator ElemIterType;
    mpIters->pElemIter = new ElemIterType(mpMesh->GetElementIteratorBegin());
 
    // Set up node map if we might have deleted nodes
    mNodeMapCurrentIndex = 0;
    if (mpMesh->IsMeshChanging())
    {
        mpNodeMap = new NodeMap(mpMesh->GetNumAllNodes());
        for (NodeIterType it = mpMesh->GetNodeIteratorBegin(); it != mpMesh->GetNodeIteratorEnd(); ++it)
        {
            mpNodeMap->SetNewIndex(it->GetIndex(), mNodeMapCurrentIndex++);
        }
    }
    WriteFiles();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFiles()
{
    std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
 
    // Write node file
    std::string node_file_name = this->mBaseName + ".node";
    out_stream p_node_file = this->mpOutputFileHandler->OpenOutputFile(node_file_name);
 
    // Write the node header
    unsigned num_attr = 0;
    unsigned max_bdy_marker = 1; // as we include boundary node information in the node file
    unsigned num_nodes = this->GetNumNodes();
 
    *p_node_file << num_nodes << "\t";
    *p_node_file << SPACE_DIM << "\t";
    *p_node_file << num_attr << "\t";
    *p_node_file << max_bdy_marker << "\n";
    *p_node_file << std::setprecision(6);
 
    // Write each node's data
    for (unsigned item_num=0; item_num<num_nodes; item_num++)
    {
        std::vector<double> current_item = this->GetNextNode();
        *p_node_file << item_num;
        for (unsigned i=0; i<SPACE_DIM+1; i++)
        {
            *p_node_file << "\t" << current_item[i];
        }
        *p_node_file << "\n";
    }
    *p_node_file << comment << "\n";
    p_node_file->close();
 
    // Write element file
    std::string element_file_name = this->mBaseName + ".cell";
    out_stream p_element_file = this->mpOutputFileHandler->OpenOutputFile(element_file_name);
 
    // Write the element header
    num_attr = 1; //Always write element attributes
    unsigned num_elements = this->GetNumElements();
    *p_element_file << num_elements << "\t" << num_attr << "\n";
 
    // Write each element's data
    for (unsigned item_num=0; item_num<num_elements; item_num++)
    {
        if (SPACE_DIM == 2) // In 2D, write the node indices owned by this element
        {
            // Get data for this element
            ElementData elem_data = this->GetNextElement();
 
            // Get the node indices owned by this element
            std::vector<unsigned> node_indices = elem_data.NodeIndices;
 
            // Write this element's index and the number of nodes owned by it to file
            *p_element_file << item_num <<  "\t" << node_indices.size();
 
            // Write the node indices owned by this element to file
            for (unsigned i=0; i<node_indices.size(); i++)
            {
                *p_element_file << "\t" << node_indices[i];
            }
 
            *p_element_file << "\t" << elem_data.AttributeValue;
 
            // New line
            *p_element_file << "\n";
        }
        else // 3D
        {
            assert(SPACE_DIM == 3);    // LCOV_EXCL_LINE
 
            // Get data for this element
            VertexElementData elem_data_with_faces = this->GetNextElementWithFaces();
 
            // Get the node indices owned by this element
            std::vector<unsigned> node_indices = elem_data_with_faces.NodeIndices;
 
            // Write this element's index and the number of nodes owned by it to file
            *p_element_file << item_num <<  "\t" << node_indices.size();
 
            // Write the node indices owned by this element to file
            for (unsigned i=0; i<node_indices.size(); i++)
            {
                *p_element_file << "\t" << node_indices[i];
            }
 
            // Get the faces owned by this element (if any)
            std::vector<ElementData> faces = elem_data_with_faces.Faces;
 
            // Write the number of faces owned by this element to file
            *p_element_file << "\t" << faces.size();
 
            for (unsigned j=0; j<faces.size(); j++)
            {
                // Get the node indices owned by this face
                std::vector<unsigned> face_node_indices = faces[j].NodeIndices;
 
                // Write this face's index and the number of nodes owned by it to file
                *p_element_file << "\t" << faces[j].AttributeValue <<  "\t" << face_node_indices.size();
 
                // Write the node indices owned by this element to file
                for (unsigned i=0; i<face_node_indices.size(); i++)
                {
                    *p_element_file << "\t" << face_node_indices[i];
                }
 
            }
 
            *p_element_file << "\t" << elem_data_with_faces.AttributeValue;
 
            // New line
            *p_element_file << "\n";
        }
    }
 
    *p_element_file << comment << "\n";
    p_element_file->close();
}
 
 
template class VertexMeshWriter<1,1>;
template class VertexMeshWriter<1,2>;
template class VertexMeshWriter<1,3>;
template class VertexMeshWriter<2,2>;
template class VertexMeshWriter<2,3>;
template class VertexMeshWriter<3,3>;