GmshMeshReader.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.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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*/
#include <cassert>
#include <sstream>
#include <iostream>

#include "GmshMeshReader.hpp"
#include "Exception.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GmshMeshReader(std::string pathBaseName,
                                                       unsigned orderOfElements,
                                                       unsigned orderOfBoundaryElements) :
       mFileName(pathBaseName),
       mOrderOfElements(orderOfElements),
       mOrderOfBoundaryElements(orderOfBoundaryElements)
{
    assert(SPACE_DIM==ELEMENT_DIM); //There is no fundamental reason for this, but full testing of SPACE_DIM != ELEMENT_DIM would be required.

    // Only linear and quadratic elements
    assert(mOrderOfElements==1 || mOrderOfElements==2);

    if (mOrderOfElements==1)
    {
        mNodesPerElement = ELEMENT_DIM+1;
    }
    else
    {
        mNodesPerElement = (ELEMENT_DIM+1)*(ELEMENT_DIM+2)/2;
    }

    if (mOrderOfBoundaryElements==1)
    {
        mNodesPerBoundaryElement = ELEMENT_DIM;
    }
    else
    {
        mNodesPerBoundaryElement = ELEMENT_DIM*(ELEMENT_DIM+1)/2;
    }

    OpenFiles();
    ReadHeaders();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::~GmshMeshReader()
{
    CloseFiles();
}

template<unsigned  ELEMENT_DIM, unsigned  SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::OpenFiles()
{
    // Open mesh file
    mNodeFile.open(mFileName.c_str());
    mElementFile.open(mFileName.c_str());
    mFaceFile.open(mFileName.c_str());
    if (!mNodeFile.is_open() || !mElementFile.is_open() || !mFaceFile.is_open() )
    {
        EXCEPTION("Could not open data file: " + mFileName);
    }
}

template<unsigned  ELEMENT_DIM, unsigned  SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::CloseFiles()
{
    mNodeFile.close();
    mElementFile.close();
    mFaceFile.close();
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadHeaders()
{
    /*
     * Read mesh format information from the file header
     */
    std::string this_line;
    getline(mNodeFile, this_line);

    assert(this_line == "$MeshFormat");

    //Read the version no.
    getline(mNodeFile, this_line);
    std::stringstream line(this_line);

    line >> mVersionNumber >> mFileType >> mDataSize;

    if(mVersionNumber != 2.2)
    {
        EXCEPTION("Only .msh version 2.2 files are supported.");
    }
    assert(mFileType == 0);

    //Check mesh format close string
    getline(mNodeFile, this_line);
    assert(this_line == "$EndMeshFormat");

    ReadNodeHeader();
    ReadElementHeader();
    ReadFaceHeader();
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadNodeHeader()
{
    //search for the start of the node section
    std::string this_line;
    std::stringstream line(this_line);

    while(this_line != "$Nodes")
    {
        getline(mNodeFile, this_line);
    }
    getline(mNodeFile, this_line);

    line.clear();
    line.str(this_line);
    line >> mNumNodes; //mNodesFile should now be pointing at the start of the node lines in the file.
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadElementHeader()
{
    //Search for the start of the elements section
    std::string this_line;
    std::stringstream line(this_line);

    getline(mElementFile, this_line);
    while(this_line != "$Elements")
    {
        getline(mElementFile, this_line);
    }
    getline(mElementFile, this_line); //Throw away the number of elements specified in the file
    int ele_start = mElementFile.tellg(); //Pointer to the start of the element block.

    mNumElements = 0u;
    getline(mElementFile, this_line);

    while(this_line != "$EndElements")
    {
        line.clear();
        line.str(this_line);

        unsigned ele_index;
        unsigned ele_type;
        line >> ele_index >> ele_type;

        if(ELEMENT_DIM == 2 && (ele_type == GmshTypes::TRIANGLE || ele_type == GmshTypes::QUADRATIC_TRIANGLE))
        {
            mNumElements++;
        }
        else if(ELEMENT_DIM == 3 && (ele_type == GmshTypes::TETRAHEDRON || ele_type == GmshTypes::QUADRATIC_TETRAHEDRON))
        {
            mNumElements++;
        }

        getline(mElementFile, this_line);
    }

    mElementFile.seekg(ele_start); //mElementFile should now be pointing at the start of the node lines in the file.
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::ReadFaceHeader()
{
    //Search for the start of the elements section
    std::string this_line;
    std::stringstream line(this_line);

    getline(mFaceFile, this_line);
    while(this_line != "$Elements")
    {
        getline(mFaceFile, this_line);
    }
    getline(mFaceFile, this_line); //Throw away the number of elements specified in the file
    int face_start = mFaceFile.tellg(); //Pointer to the start of the element block.

    mNumFaces = 0u;
    getline(mFaceFile, this_line);

    while(this_line != "$EndElements")
    {
        line.clear();
        line.str(this_line);

        unsigned ele_index;
        unsigned ele_type;
        line >> ele_index >> ele_type;

        if(ELEMENT_DIM == 2 && (ele_type == GmshTypes::LINE || ele_type == GmshTypes::QUADRATIC_LINE))
        {
            mNumFaces++;
        }
        else if(ELEMENT_DIM == 3 && (ele_type == GmshTypes::TRIANGLE || ele_type == GmshTypes::QUADRATIC_TRIANGLE))
        {
            mNumFaces++;
        }

        getline(mFaceFile, this_line);
    }

    mFaceFile.seekg(face_start); //mFacesFile should now be pointing at the start of the node lines in the file.
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumElements() const
{
    return mNumElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumNodes() const
{
    return mNumNodes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumFaces() const
{
    return mNumFaces;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumCableElements() const
{
    NEVER_REACHED;
    //return mNumCableElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetOrderOfElements()
{
    return mOrderOfElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetOrderOfBoundaryElements()
{
    return mOrderOfBoundaryElements;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumElementAttributes() const
{
    return mNumElementAttributes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumFaceAttributes() const
{
    return mNumFaceAttributes;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNumCableElementAttributes() const
{
    NEVER_REACHED;
    //return mNumCableElementAttributes;
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::Reset()
{
    CloseFiles();

    OpenFiles();
    ReadHeaders();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextNode()
{
    std::vector<double> ret_coords(SPACE_DIM);

    std::string this_line;
    getline(mNodeFile, this_line);

    std::stringstream line(this_line);

    unsigned node_index;
    line >> node_index >> ret_coords[0] >> ret_coords[1];

    if(ELEMENT_DIM == 3)
    {
        line >> ret_coords[2];
    }

    return ret_coords;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNodeAttributes()
{
    return std::vector<double>(0);
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextElementData()
{
    ElementData element_data;
    element_data.NodeIndices.resize(mNodesPerElement);
    element_data.AttributeValue = 0.0; // If an attribute is not read this stays as zero, otherwise overwritten.

    std::string this_line;
    std::stringstream line(this_line);

    unsigned ele_index;
    unsigned ele_type;
    unsigned ele_attributes=0;
    bool volume_element_found = false;

    while(!volume_element_found)
    {
        getline(mElementFile, this_line);
        line.clear();
        line.str(this_line);

        line >> ele_index >> ele_type >> ele_attributes;

        if((ELEMENT_DIM == 2 && (ele_type == GmshTypes::TRIANGLE || ele_type == GmshTypes::QUADRATIC_TRIANGLE) ) ||
           (ELEMENT_DIM == 3 && (ele_type == GmshTypes::TETRAHEDRON || ele_type == GmshTypes::QUADRATIC_TETRAHEDRON)))
        {
            volume_element_found = true;
        }
    }

    //Gmsh can have arbitrary numbers of element attributes, but Chaste only handles one. We pick the first attribute and throw
    //away the remainder.
    if(ele_attributes > 0)
    {
        mNumElementAttributes = 1u;
        line >> element_data.AttributeValue;
    }
    unsigned unused_attr;
    for(unsigned attr_index = 0; attr_index < (ele_attributes-1); ++attr_index)
    {
        line >> unused_attr;
    }

    //Read the node indices
    for(unsigned node_index = 0; node_index < mNodesPerElement; ++node_index)
    {
        line >> element_data.NodeIndices[node_index];

        element_data.NodeIndices[node_index]--; //Gmsh *always* indexes from 1, we index from 0
    }

    return element_data;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextCableElementData()
{
    NEVER_REACHED;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNextFaceData()
{
    ElementData face_data;
    face_data.NodeIndices.resize(mNodesPerBoundaryElement);
    face_data.AttributeValue = 0.0; // If an attribute is not read this stays as zero, otherwise overwritten.

    std::string this_line;
    std::stringstream line(this_line);

    unsigned face_index;
    unsigned face_type;
    unsigned face_attributes=0;
    bool surface_element_found = false;

    while(!surface_element_found)
    {
        getline(mFaceFile, this_line);
        line.clear();
        line.str(this_line);

        line >> face_index >> face_type >> face_attributes;

        if((ELEMENT_DIM == 2 && (face_type == GmshTypes::LINE || face_type == GmshTypes::QUADRATIC_LINE) ) ||
           (ELEMENT_DIM == 3 && (face_type == GmshTypes::TRIANGLE || face_type == GmshTypes::QUADRATIC_TRIANGLE)))
        {
            surface_element_found = true;
        }
    }

    //Gmsh can have arbitrary numbers of element attributes, but Chaste only handles one. We pick the first attribute and throw
    //away the remainder.
    if(face_attributes > 0)
    {
        mNumFaceAttributes = 1u;
        line >> face_data.AttributeValue;
    }
    unsigned unused_attr;
    for(unsigned attr_index = 0; attr_index < (face_attributes-1); ++attr_index)
    {
        line >> unused_attr;
    }

    //Read the node indices
    for(unsigned node_index = 0; node_index < mNodesPerBoundaryElement; ++node_index)
    {
        line >> face_data.NodeIndices[node_index];

        face_data.NodeIndices[node_index]--; //Gmsh *always* indexes from 1, we index from 0
    }

    return face_data;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetNode(unsigned index)
{
    NEVER_REACHED;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetElementData(unsigned index)
{
    NEVER_REACHED;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData GmshMeshReader<ELEMENT_DIM, SPACE_DIM>::GetFaceData(unsigned index)
{
    NEVER_REACHED;
}

// Explicit instantiation

template class GmshMeshReader<0,1>;
template class GmshMeshReader<1,1>;
template class GmshMeshReader<1,2>;
template class GmshMeshReader<1,3>;
template class GmshMeshReader<2,2>;
template class GmshMeshReader<2,3>;
template class GmshMeshReader<3,3>;