MeshalyzerMeshWriter.cpp

/*

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 * Redistributions of source code must retain the above copyright notice,
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 * Redistributions in binary form must reproduce the above copyright notice,
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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*/

#include "MeshalyzerMeshWriter.hpp"
#include "Version.hpp"

// We need these two includes for the node/element/face iterators to compile
#include "AbstractTetrahedralMesh.hpp"
#include "DistributedTetrahedralMesh.hpp"


// Implementation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::MeshalyzerMeshWriter(const std::string& rDirectory,
        const std::string& rBaseName,
        const bool &rCleanDirectory,
        const bool &rSetCoolGraphics)
        : AbstractTetrahedralMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, rCleanDirectory)
{
   /* if (ELEMENT_DIM != SPACE_DIM)
    {
        EXCEPTION("ELEMENT_DIM must be equal to SPACE_DIM");
    }*/

    if (rSetCoolGraphics)
    {
        this->mIndexFromZero = false;
        this->mWriteMetaFile = true;
    }
    else
    {
        this->mIndexFromZero = true;
        this->mWriteMetaFile = false;
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFiles()
{
    std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();

    //Write node file
    out_stream p_node_file = OpenNodeFile();

    //Write the node header
    unsigned num_nodes = this->GetNumNodes();
    *p_node_file << num_nodes << "\n";

    // Write each node's data
    for (unsigned item_num=0; item_num<num_nodes; item_num++)
    {
        std::vector<double> current_item = this->GetNextNode(); //this->mNodeData[item_num];
        for (unsigned i=0; i<SPACE_DIM; i++)
        {
            *p_node_file << current_item[i] << "\t";
        }
        if (SPACE_DIM==2)
        {
            *p_node_file << 0 << "\t";
        }
        if (SPACE_DIM==1)
        {
            *p_node_file << 0 << "\t" << 0 << "\t";
        }
        *p_node_file << "\n";

    }
    *p_node_file << comment;
    p_node_file->close();

    // Write element file
    std::string element_file_name;

    if (ELEMENT_DIM == 3)
    {
        element_file_name = this->mBaseName + ".tetras";
    }
    else if (ELEMENT_DIM == 2)
    {
        element_file_name = this->mBaseName + ".tri";
    }
    else //ELEMENT_DIM == 1
    {
        element_file_name = this->mBaseName + ".cnnx";
    }

    out_stream p_element_file = OpenElementFile();

    // Write the element header
    unsigned num_elements = this->GetNumElements();

    *p_element_file << num_elements << "\n";

    // Write each element's data
    unsigned nodes_per_element = ELEMENT_DIM+1;
    for (unsigned item_num=0; item_num<num_elements; item_num++)
    {
        ElementData element_data = this->GetNextElement();

        std::vector<unsigned> current_item = element_data.NodeIndices;
        for (unsigned i=0; i<nodes_per_element; i++)
        {
            if (this->mIndexFromZero)
            {
                *p_element_file << current_item[i] << "\t";
            }
            else
            {
                *p_element_file << current_item[i]+1 << "\t";
            }
        }

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

    if (ELEMENT_DIM==3)
    {
        // Write boundary face file
        out_stream p_face_file = OpenFaceFile();

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

        *p_face_file << num_faces << "\n";

        // Write each face's data
        double material_property = 0.0;
        for (unsigned item_num=0; item_num<num_faces; item_num++)
        {
            ElementData current_item = this->GetNextBoundaryElement();
            for (unsigned i=0; i<ELEMENT_DIM; i++)
            {
                if (this->mIndexFromZero)
                {
                    *p_face_file << current_item.NodeIndices[i] << "\t";
                }
                else
                {
                    *p_face_file << current_item.NodeIndices[i]+1 <<"\t";
                }
            }
            *p_face_file << material_property << "\n";
        }
        *p_face_file << comment;
        p_face_file->close();

        WriteMetaFile();
    }
}

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteMetaFile()
{
    if (this->mWriteMetaFile)
    {
        std::string meta_file_name = this->mBaseName + ".cg_in";
        out_stream p_meta_file = this->mpOutputFileHandler->OpenOutputFile(meta_file_name);

        *p_meta_file << "1\n" << "0\n";
        std::string face_file_name = this->mBaseName + ".tri";
        *p_meta_file << face_file_name <<"\n";
        std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
        *p_meta_file << comment;
        p_meta_file->close();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::ios_base::openmode MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetOpenMode(bool append)
{
    std::ios_base::openmode mode = std::ios::out;
    if (append)
    {
        mode |= std::ios::app; // Note: bitwise OR operation
    }
    else
    {
        mode |= std::ios::trunc;
    }
    return mode;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
out_stream MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::OpenNodeFile(bool append)
{
    std::string node_file_name = this->mBaseName + ".pts";
    return this->mpOutputFileHandler->OpenOutputFile(node_file_name, GetOpenMode(append));
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
out_stream MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::OpenElementFile(bool append)
{
    std::string element_file_name;

    if (ELEMENT_DIM == 3)
    {
        element_file_name = this->mBaseName + ".tetras";
    }
    else if (ELEMENT_DIM == 2)
    {
        element_file_name = this->mBaseName + ".tri";
    }
    else //ELEMENT_DIM == 1
    {
        element_file_name = this->mBaseName + ".cnnx";
    }

    return this->mpOutputFileHandler->OpenOutputFile(element_file_name, GetOpenMode(append));
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
out_stream MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::OpenFaceFile(bool append)
{
    std::string face_file_name = this->mBaseName + ".tri";
    return this->mpOutputFileHandler->OpenOutputFile(face_file_name, GetOpenMode(append));
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::CreateFilesWithHeaders()
{
    /*
     *  Node file
     */
    out_stream p_node_file = OpenNodeFile();

    //Write the node header
    unsigned num_nodes = this->GetNumNodes();
    *p_node_file << num_nodes << "\n";

    p_node_file->close();

    /*
     *  Element file
     */
    // Write element file
    out_stream p_element_file = OpenElementFile();

    // Write the element header
    unsigned num_elements = this->GetNumElements();
    *p_element_file << num_elements << "\n";

    p_element_file->close();

    /*
     * Face file
     */
    if (ELEMENT_DIM==3)
    {
        // Write boundary face file
        out_stream p_face_file = OpenFaceFile();

        // Write the boundary face header
        unsigned num_faces = this->GetNumBoundaryFaces();
        *p_face_file << num_faces << "\n";

        p_face_file->close();

        WriteMetaFile();
    }

}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::AppendLocalDataToFiles()
{
    out_stream p_node_file = OpenNodeFile(true);

    typedef typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator NodeIterType;

    for (NodeIterType iter = this->mpDistributedMesh->GetNodeIteratorBegin();
         iter != this->mpDistributedMesh->GetNodeIteratorEnd();
         ++iter)
    {
        const c_vector<double, SPACE_DIM>& r_current_item = iter->rGetLocation();
        for (unsigned i=0; i<SPACE_DIM; i++)
        {
            *p_node_file << r_current_item[i] << "\t";
        }
        if (SPACE_DIM==2)
        {
            *p_node_file << 0 << "\t";
        }
        if (SPACE_DIM==1)
        {
            *p_node_file << 0 << "\t" << 0 << "\t";
        }
        *p_node_file << "\n";
    }
    p_node_file->close();

    out_stream p_element_file = OpenElementFile(true);

    typedef typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator ElemIterType;

    for (ElemIterType iter = this->mpDistributedMesh->GetElementIteratorBegin();
         iter != this->mpDistributedMesh->GetElementIteratorEnd();
         ++iter)
    {
        if (this->mpDistributedMesh->CalculateDesignatedOwnershipOfElement(iter->GetIndex()))
        {
            for (unsigned i=0; i<this->mNodesPerElement; i++)
            {
                if (this->mIndexFromZero)
                {
                    *p_element_file << iter->GetNodeGlobalIndex(i) << "\t";
                }
                else
                {
                    *p_element_file << iter->GetNodeGlobalIndex(i)+1 << "\t";
                }
            }

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


    if (ELEMENT_DIM == 3)
    {
        out_stream p_face_file = OpenFaceFile(true);

        typedef typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::BoundaryElementIterator BoundaryElemIterType;

        for (BoundaryElemIterType iter = this->mpDistributedMesh->GetBoundaryElementIteratorBegin();
             iter != this->mpDistributedMesh->GetBoundaryElementIteratorEnd();
             ++iter)
        {
            if (this->mpDistributedMesh->CalculateDesignatedOwnershipOfBoundaryElement((*iter)->GetIndex()))
            {
                for (unsigned i=0; i<ELEMENT_DIM; i++)
                {
                    if (this->mIndexFromZero)
                    {
                        *p_face_file << (*iter)->GetNodeGlobalIndex(i) << "\t";
                    }
                    else
                    {
                        *p_face_file << (*iter)->GetNodeGlobalIndex(i)+1 << "\t";
                    }
                }

                *p_face_file << (*iter)->GetAttribute() << "\n";
            }
        }
        p_face_file->close();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void MeshalyzerMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesFooter()
{
    std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();

    out_stream p_node_file = OpenNodeFile(true);
    *p_node_file << comment;
    p_node_file->close();

    out_stream p_element_file = OpenElementFile(true);
    *p_element_file << comment;
    p_element_file->close();

    if (ELEMENT_DIM == 3)
    {
        out_stream p_face_file = OpenFaceFile(true);
        *p_face_file << comment;
        p_face_file->close();
    }
}


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