PottsMeshWriter.cpp

/*

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*/

#include "PottsMeshWriter.hpp"
#include "Version.hpp"

template<unsigned SPACE_DIM>
struct MeshPottsWriterIterators
{
    typename AbstractMesh<SPACE_DIM,SPACE_DIM>::NodeIterator* pNodeIter;
    typename PottsMesh<SPACE_DIM>::PottsElementIterator* pElemIter;
};

// Implementation

template<unsigned SPACE_DIM>
PottsMeshWriter<SPACE_DIM>::PottsMeshWriter(const std::string& rDirectory,
                                            const std::string& rBaseName,
                                            const bool clearOutputDir)
    : AbstractMeshWriter<SPACE_DIM, SPACE_DIM>(rDirectory, rBaseName, clearOutputDir),
      mpMesh(nullptr),
      mpIters(new MeshPottsWriterIterators<SPACE_DIM>),
      mpNodeMap(nullptr),
      mNodeMapCurrentIndex(0)
{
    mpIters->pNodeIter = nullptr;
    mpIters->pElemIter = nullptr;
}

template<unsigned SPACE_DIM>
PottsMeshWriter<SPACE_DIM>::~PottsMeshWriter()
{
    if (mpIters->pNodeIter)
    {
        delete mpIters->pNodeIter;
        delete mpIters->pElemIter;
    }

    delete mpIters;

    if (mpNodeMap)
    {
        delete mpNodeMap;
    }
}

template<unsigned SPACE_DIM>
std::vector<double> PottsMeshWriter<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<SPACE_DIM,SPACE_DIM>::GetNextNode();
    }
}

template<unsigned SPACE_DIM>
ElementData PottsMeshWriter<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<SPACE_DIM, SPACE_DIM>::GetNextElement();
    }
}

template<unsigned SPACE_DIM>
void PottsMeshWriter<SPACE_DIM>::WriteFilesUsingMesh(PottsMesh<SPACE_DIM>& rMesh)
{
    this->mpMeshReader = nullptr;
    mpMesh = &rMesh;

    this->mNumNodes = mpMesh->GetNumNodes();
    this->mNumElements = mpMesh->GetNumElements();

    typedef typename AbstractMesh<SPACE_DIM,SPACE_DIM>::NodeIterator NodeIterType;
    mpIters->pNodeIter = new NodeIterType(mpMesh->GetNodeIteratorBegin());

    typedef typename PottsMesh<SPACE_DIM>::PottsElementIterator 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 SPACE_DIM>
void PottsMeshWriter<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
    unsigned num_elements = this->GetNumElements();
    *p_element_file << num_elements << "\t";
    num_attr = 1; // Always write attributes by default
    /*
     * Note that in contrast to other mesh classes, it is perfectly reasonable for
     * a PottsMesh to have no elements, particularly in when it is being used in
     * the context of a CaBasedCellPopulation.
     */
    if (num_elements != 0)
    {
        *p_element_file << num_attr << "\n";
    }
    else
    {
        *p_element_file << 0 << "\n";
    }

    // Write each element's data
    for (unsigned item_num=0; item_num<num_elements; item_num++)
    {
        // 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];
        }

        // Write the element attribute
        *p_element_file << "\t" << elem_data.AttributeValue;

        // New line
        *p_element_file << "\n";
    }

    *p_element_file << comment << "\n";
    p_element_file->close();
}

// Explicit instantiation
template class PottsMeshWriter<1>;
template class PottsMeshWriter<2>;
template class PottsMeshWriter<3>;