TrianglesMeshWriter.cpp

/*

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*/

#include "TrianglesMeshWriter.hpp"

#include "AbstractTetrahedralMesh.hpp"
#include "Version.hpp"

#include <cassert>

// Implementation
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::TrianglesMeshWriter(
    const std::string& rDirectory,
    const std::string& rBaseName,
    const bool clearOutputDir)
        : AbstractTetrahedralMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, clearOutputDir)
{
}

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::SetWriteFilesAsBinary()
{
    this->mFilesAreBinary=true;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFiles()
{
    std::string comment = "#\n# " + ChasteBuildInfo::GetProvenanceString();
//    PetscTools::Barrier("DodgyBarrierBeforeNODE");
    MeshEventHandler::BeginEvent(MeshEventHandler::NODE);
    // Write node file
    std::string node_file_name = this->mBaseName + ".node";
    out_stream p_node_file = this->mpOutputFileHandler->OpenOutputFile(node_file_name, std::ios::binary | std::ios::trunc);

    // Write the node header
    unsigned num_attr = 0;

    if (this->mpMesh && !this->mFilesAreBinary) 
    {
        // Assumes that all nodes have the same number of attributes as the first node in the mesh.
        num_attr = this->mpMesh->GetNumNodeAttributes();
    }
    unsigned max_bdy_marker = 0;
    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;
    if (this->mFilesAreBinary)
    {
        *p_node_file << "\tBIN\n";
    }
    else
    {
        *p_node_file << "\n";
    }

    *p_node_file << std::setprecision(20);

    // Write each node's data
    for (unsigned item_num=0; item_num<num_nodes; item_num++)
    {
        if (this->mpMesh && !this->mFilesAreBinary && num_attr!=0) 
        {

            WriteItem(p_node_file, item_num, this->GetNextNode(), this->mpMesh->GetNode(item_num)->rGetNodeAttributes());
        }
        else
        {
            WriteItem(p_node_file, item_num, this->GetNextNode());
        }
    }
    *p_node_file << comment << "\n";
    p_node_file->close();
//    PetscTools::Barrier("DodgyBarrierAfterNODE");
    MeshEventHandler::EndEvent(MeshEventHandler::NODE);
    MeshEventHandler::BeginEvent(MeshEventHandler::ELE);
    if (ELEMENT_DIM < SPACE_DIM)
    {
        WriteElementsAsFaces();
        WriteFacesAsEdges();
        return;
    }

    // Write element file
    std::string element_file_name = this->mBaseName + ".ele";
    out_stream p_element_file = this->mpOutputFileHandler->OpenOutputFile(element_file_name, std::ios::binary | std::ios::trunc);

    // Write the element header
    unsigned num_elements = this->GetNumElements();
    num_attr = 1u; // We have a single region code

    // The condition below allows the writer to cope with a NodesOnlyMesh
    if (num_elements == 0)
    {
        *p_element_file << 0 << "\t";
        *p_element_file << 0 << "\t";
        *p_element_file << 0;
        if (this->mFilesAreBinary)
        {
            *p_element_file << "\tBIN\n";
        }
        else
        {
            *p_element_file << "\n";
        }
        p_element_file->close();
    }
    else
    {
        ElementData element_data = this->GetNextElement();

        unsigned nodes_per_element = element_data.NodeIndices.size();
        if (nodes_per_element != ELEMENT_DIM+1)
        {
            // Check that this is a quadratic mesh
            assert(ELEMENT_DIM == SPACE_DIM);
            assert(nodes_per_element == (ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2);
         }

        *p_element_file << num_elements << "\t";
        *p_element_file << nodes_per_element << "\t";
        *p_element_file << num_attr;
        if (this->mFilesAreBinary)
        {
            *p_element_file << "\tBIN\n";
        }
        else
        {
            *p_element_file << "\n";
        }

        // Write each element's data
        std::vector<double> attribute_values(1);
        for (unsigned item_num=0; item_num<num_elements; item_num++)
        {
            /*
             * If item_num==0 we will already have got the element above (in order to
             * get the number of nodes per element).
             */
            if (item_num > 0)
            {
                element_data = this->GetNextElement();
            }
            attribute_values[0] =  element_data.AttributeValue;
            WriteItem(p_element_file, item_num, element_data.NodeIndices, attribute_values);
        }
        *p_element_file << comment << "\n";
        p_element_file->close();
    }
//    PetscTools::Barrier("DodgyBarrierAfterELE");
    MeshEventHandler::EndEvent(MeshEventHandler::ELE);
    MeshEventHandler::BeginEvent(MeshEventHandler::FACE);
    // Write boundary face file
    std::string face_file_name = this->mBaseName;

    if (ELEMENT_DIM == 1)
    {
        // In 1-D there is no boundary file: it's trivial to calculate
        return;
    }
    else if (ELEMENT_DIM == 2)
    {
        face_file_name = face_file_name + ".edge";
    }
    else
    {
        face_file_name = face_file_name + ".face";
    }
    out_stream p_face_file = this->mpOutputFileHandler->OpenOutputFile(face_file_name, std::ios::binary | std::ios::trunc);

    // Write the boundary face header
    if (num_elements != 0)
    {
        unsigned num_faces = this->GetNumBoundaryFaces();

        *p_face_file << num_faces << "\t";
        *p_face_file << max_bdy_marker;
        if (this->mFilesAreBinary)
        {
            *p_face_file << "\tBIN\n";
        }
        else
        {
            *p_face_file << "\n";
        }

        // Write each face's data
        std::vector<double> default_marker(0);
        for (unsigned item_num=0; item_num<num_faces; item_num++)
        {
            ElementData face_data = this->GetNextBoundaryElement();
            WriteItem(p_face_file, item_num, face_data.NodeIndices, default_marker);
        }
        *p_face_file << comment << "\n";
        p_face_file->close();

        if (this->GetNumCableElements() > 0)
        {
            // Write cable element file
            std::string cable_element_file_name = this->mBaseName + ".cable";
            out_stream p_cable_element_file = this->mpOutputFileHandler->OpenOutputFile(cable_element_file_name, std::ios::binary | std::ios::trunc);

            // Write the cable element header
            unsigned num_cable_elements = this->GetNumCableElements();
            num_attr = 1u; // We have a single region code - which is actually a radius

            *p_cable_element_file << num_cable_elements << "\t";
            *p_cable_element_file << 2 << "\t";
            *p_cable_element_file << num_attr;
            if (this->mFilesAreBinary)
            {
                *p_cable_element_file << "\tBIN\n";
            }
            else
            {
                *p_cable_element_file << "\n";
            }

            // Write each element's data
            std::vector<double> attribute_values(1);
            for (unsigned item_num=0; item_num<num_cable_elements; item_num++)
            {
                ElementData cable_element_data = this->GetNextCableElement();
                attribute_values[0] = cable_element_data.AttributeValue;
                WriteItem(p_cable_element_file, item_num, cable_element_data.NodeIndices, attribute_values);
            }
            *p_cable_element_file << comment;
            p_cable_element_file->close();
        }
    }
//    PetscTools::Barrier("DodgyBarrierAfterFACE");
    MeshEventHandler::EndEvent(MeshEventHandler::FACE);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteElementsAsFaces()
{
    std::string comment = "#\n# " + ChasteBuildInfo::GetProvenanceString();

    std::string element_file_name = this->mBaseName;
    if (ELEMENT_DIM == 1 && (SPACE_DIM == 2 || SPACE_DIM == 3))
    {
        element_file_name = element_file_name + ".edge";
    }
    else if (ELEMENT_DIM == 2 && SPACE_DIM == 3)
    {
        element_file_name = element_file_name + ".face";
    }

    out_stream p_element_file = this->mpOutputFileHandler->OpenOutputFile(element_file_name, std::ios::binary | std::ios::trunc);

    // Write the element header
    unsigned num_elements = this->GetNumElements();
    assert(SPACE_DIM != ELEMENT_DIM);    // LCOV_EXCL_LINE
    unsigned num_attr = 1;

    *p_element_file << num_elements << "\t";
    //*p_element_file << nodes_per_element << "\t";
    *p_element_file << num_attr;
    if (this->mFilesAreBinary)
    {
        *p_element_file << "\tBIN\n";
    }
    else
    {
        *p_element_file << "\n";
    }

    // Write each element's data
    std::vector<double> attribute_values(1);
    for (unsigned item_num=0; item_num<num_elements; item_num++)
    {
        ElementData element_data = this->GetNextElement();
        attribute_values[0] =  element_data.AttributeValue;
        WriteItem(p_element_file, item_num, element_data.NodeIndices, attribute_values);
    }

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFacesAsEdges()
{
    std::string comment = "#\n# " + ChasteBuildInfo::GetProvenanceString();

    if (ELEMENT_DIM == 1 && (SPACE_DIM == 2 || SPACE_DIM == 3))
    {
        return;
    }

    assert(SPACE_DIM == 3 && ELEMENT_DIM == 2);    // LCOV_EXCL_LINE

    std::string face_file_name = this->mBaseName;
    face_file_name = face_file_name + ".edge";

    out_stream p_face_file = this->mpOutputFileHandler->OpenOutputFile(face_file_name, std::ios::binary | std::ios::trunc);

    // Write the boundary face header
    unsigned num_faces = this->GetNumBoundaryFaces();

    unsigned max_bdy_marker = 0;
    std::vector<double> default_marker(0);

    *p_face_file << num_faces << "\t";
    *p_face_file << max_bdy_marker;
    if (this->mFilesAreBinary)
    {
        *p_face_file << "\tBIN\n";
    }
    else
    {
        *p_face_file << "\n";
    }

    // Write each face's data
    for (unsigned item_num=0; item_num<num_faces; item_num++)
    {
        ElementData face_data = this->GetNextBoundaryElement();
        WriteItem(p_face_file, item_num, face_data.NodeIndices, default_marker);
    }
    *p_face_file << comment << "\n";
    p_face_file->close();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<class T_DATA>
void TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteItem(out_stream &pFile, unsigned itemNumber,
                                                            const std::vector<T_DATA> &dataPacket)
{
    //Writing with no attribute
    //Instantiates the attribute variety with the attributes empty
    WriteItem(pFile, itemNumber, dataPacket, std::vector<double>());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<class T_DATA>
void TrianglesMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteItem(out_stream &pFile, unsigned itemNumber,
                                                            const std::vector<T_DATA> &dataPacket,
                                                            const std::vector<double> &rAttributes)
{
    if (this->mFilesAreBinary)
    {
        // No item numbers
        // Write raw data out of std::vector into the file
        pFile->write((char*)&dataPacket[0], dataPacket.size()*sizeof(T_DATA));

        // Write raw attribute(s)
        // MSVC 10 will trip an assertion on accessing the 0th element if the vector is empty.
        // Note that C++11 gives vectors a .data() method which would be a better way of doing this!
        if (!rAttributes.empty())
        {
            pFile->write((char*)&rAttributes[0], rAttributes.size()*sizeof(double));
        }
    }
    else
    {
        *pFile << itemNumber;
        for (unsigned i=0; i<dataPacket.size(); i++)
        {
            *pFile << "\t" << dataPacket[i];
        }
        for (unsigned i=0; i<rAttributes.size(); i++)
        {
            *pFile << "\t" << rAttributes[i];
        }
        *pFile << "\n";
    }
}

// Explicit instantiation
template class TrianglesMeshWriter<1,1>;
template class TrianglesMeshWriter<1,2>;
template class TrianglesMeshWriter<1,3>;
template class TrianglesMeshWriter<2,2>;
template class TrianglesMeshWriter<2,3>;
template class TrianglesMeshWriter<3,3>;

template void TrianglesMeshWriter<1, 1>::WriteItem(out_stream &, unsigned, const std::vector<unsigned> &, const std::vector<double>   & );
template void TrianglesMeshWriter<1, 1>::WriteItem(out_stream &, unsigned, const std::vector<double>   &, const std::vector<double>   & );
template void TrianglesMeshWriter<1, 2>::WriteItem(out_stream &, unsigned, const std::vector<unsigned> &, const std::vector<double>   & );
template void TrianglesMeshWriter<1, 2>::WriteItem(out_stream &, unsigned, const std::vector<double>   &, const std::vector<double>   & );
template void TrianglesMeshWriter<1, 3>::WriteItem(out_stream &, unsigned, const std::vector<unsigned> &, const std::vector<double>   & );
template void TrianglesMeshWriter<1, 3>::WriteItem(out_stream &, unsigned, const std::vector<double>   &, const std::vector<double>   & );
template void TrianglesMeshWriter<2, 2>::WriteItem(out_stream &, unsigned, const std::vector<unsigned> &, const std::vector<double>   & );
template void TrianglesMeshWriter<2, 2>::WriteItem(out_stream &, unsigned, const std::vector<double>   &, const std::vector<double>   & );
template void TrianglesMeshWriter<2, 3>::WriteItem(out_stream &, unsigned, const std::vector<unsigned> &, const std::vector<double>   & );
template void TrianglesMeshWriter<2, 3>::WriteItem(out_stream &, unsigned, const std::vector<double>   &, const std::vector<double>   & );
template void TrianglesMeshWriter<3, 3>::WriteItem(out_stream &, unsigned, const std::vector<unsigned> &, const std::vector<double>   & );
template void TrianglesMeshWriter<3, 3>::WriteItem(out_stream &, unsigned, const std::vector<double>   &, const std::vector<double>   & );