PottsMeshReader.cpp

/*

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*/

#include "PottsMeshReader.hpp"
#include "Exception.hpp"

#include <sstream>

template<unsigned SPACE_DIM>
PottsMeshReader<SPACE_DIM>::PottsMeshReader(std::string pathBaseName)
    : mFilesBaseName(pathBaseName),
      mIndexFromZero(false), // initially assume that nodes are not numbered from zero
      mNumNodes(0),
      mNumElements(0),
      mNodesRead(0),
      mElementsRead(0),
      mNumElementAttributes(0)
{
    OpenFiles();
    ReadHeaders();
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumElements() const
{
    return mNumElements;
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumNodes() const
{
    return mNumNodes;
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumElementAttributes() const
{
    return mNumElementAttributes;
}

template<unsigned SPACE_DIM>
ElementData PottsMeshReader<SPACE_DIM>::GetNextFaceData()
{
    ElementData ret;
    ret.NodeIndices = std::vector<unsigned>();
    ret.AttributeValue = 0;
    return ret;
}

template<unsigned SPACE_DIM>
unsigned PottsMeshReader<SPACE_DIM>::GetNumFaces() const
{
    return 0;
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::Reset()
{
    CloseFiles();
    OpenFiles();
    ReadHeaders();

    mNodesRead = 0;
    mElementsRead = 0;
}

template<unsigned SPACE_DIM>
std::vector<double> PottsMeshReader<SPACE_DIM>::GetNextNode()
{
    std::vector<double> node_data;

    std::string buffer;
    GetNextLineFromStream(mNodesFile, buffer);

    std::stringstream buffer_stream(buffer);

    unsigned index;
    buffer_stream >> index;

    unsigned offset = mIndexFromZero ? 0 : 1;
    if (index != mNodesRead + offset)
    {
        EXCEPTION("Data for node " << mNodesRead << " missing");
    }

    double node_value;
    for (unsigned i=0; i<SPACE_DIM+1; i++)
    {
        buffer_stream >> node_value;
        node_data.push_back(node_value);
    }

    mNodesRead++;
    return node_data;
}

template<unsigned SPACE_DIM>
ElementData PottsMeshReader<SPACE_DIM>::GetNextElementData()
{
    // Create data structure for this element
    ElementData element_data;

    std::string buffer;
    GetNextLineFromStream(mElementsFile, buffer);

    std::stringstream buffer_stream(buffer);

    unsigned element_index;
    buffer_stream >> element_index;

    unsigned offset = mIndexFromZero ? 0 : 1;
    if (element_index != mElementsRead + offset)
    {
        EXCEPTION("Data for element " << mElementsRead << " missing");
    }

    unsigned num_nodes_in_element;
    buffer_stream >> num_nodes_in_element;

    // Store node indices owned by this element
    unsigned node_index;
    for (unsigned i=0; i<num_nodes_in_element; i++)
    {
        buffer_stream >> node_index;
        element_data.NodeIndices.push_back(node_index - offset);
    }

    if (mNumElementAttributes > 0)
    {
        assert(mNumElementAttributes==1);

        unsigned attribute_value;
        buffer_stream >> attribute_value;
        element_data.AttributeValue = attribute_value;
    }
    else
    {
        element_data.AttributeValue = 0;
    }

    mElementsRead++;
    return element_data;
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::OpenFiles()
{
    OpenNodeFile();
    OpenElementsFile();
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::OpenNodeFile()
{
    // Nodes definition
    std::string file_name = mFilesBaseName + ".node";
    mNodesFile.open(file_name.c_str());
    if (!mNodesFile.is_open())
    {
        EXCEPTION("Could not open data file: " + file_name);
    }
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::OpenElementsFile()
{
    // Elements definition
    std::string file_name;
    file_name = mFilesBaseName + ".cell";

    mElementsFile.open(file_name.c_str());
    if (!mElementsFile.is_open())
    {
        EXCEPTION("Could not open data file: " + file_name);
    }
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::ReadHeaders()
{
    std::string buffer;

    GetNextLineFromStream(mNodesFile, buffer);
    std::stringstream buffer_stream(buffer);
    buffer_stream >> mNumNodes >> mNumNodeAttributes;

    // Get the next line to see if nodes are indexed from zero or not
    GetNextLineFromStream(mNodesFile, buffer);
    std::stringstream node_buffer_stream(buffer);

    unsigned first_index;
    node_buffer_stream >> first_index;
    assert(first_index == 0 || first_index == 1);
    mIndexFromZero = (first_index == 0);

    // Close, reopen, skip header
    mNodesFile.close();
    OpenNodeFile();
    GetNextLineFromStream(mNodesFile, buffer);

    GetNextLineFromStream(mElementsFile, buffer);
    std::stringstream element_buffer_stream(buffer);

    element_buffer_stream >> mNumElements >> mNumElementAttributes;
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::CloseFiles()
{
    mNodesFile.close();
    mElementsFile.close();
}

template<unsigned SPACE_DIM>
void PottsMeshReader<SPACE_DIM>::GetNextLineFromStream(std::ifstream& fileStream, std::string& rawLine)
{
    bool line_is_blank;

    do
    {
        getline(fileStream, rawLine);

        if (fileStream.eof())
        {
            EXCEPTION("Cannot get the next line from node or element file due to incomplete data");
        }

        // Get rid of any comment
        rawLine = rawLine.substr(0,rawLine.find('#', 0));

        line_is_blank = (rawLine.find_first_not_of(" \t", 0) == std::string::npos);
    }
    while (line_is_blank);
}

// Explicit instantiation

template class PottsMeshReader<1>;
template class PottsMeshReader<2>;
template class PottsMeshReader<3>;