FibreReader.cpp

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*/

#include "FibreReader.hpp"

#include <sstream>
#include "Exception.hpp"

template<unsigned DIM>
FibreReader<DIM>::FibreReader(const FileFinder& rFileFinder, FibreFileType fibreFileType)
   : mFileIsBinary(false), // overwritten by ReadNumLinesOfDataFromFile() if applicable.
     mNextIndex(0u)
{
    if (fibreFileType == AXISYM)
    {
        mNumItemsPerLine = DIM;
    }
    else //(fibreFileType == ORTHO)
    {
        mNumItemsPerLine = DIM*DIM;
    }
    mTokens.resize(mNumItemsPerLine);

    mFilePath = rFileFinder.GetAbsolutePath();
    mDataFile.open(mFilePath.c_str());
    if (!mDataFile.is_open())
    {
        EXCEPTION("Failed to open fibre file " + rFileFinder.GetAbsolutePath());
    }

    // Note: this method will close the file on error
    ReadNumLinesOfDataFromFile();
}

template<unsigned DIM>
FibreReader<DIM>::~FibreReader()
{
    mDataFile.close();
}

template<unsigned DIM>
void FibreReader<DIM>::GetAllAxi(std::vector< c_vector<double, DIM> >& direction)
{
    assert(direction.empty());
    if (mNumItemsPerLine != DIM)
    {
        EXCEPTION("Use GetAllOrtho when reading orthotropic fibres");
    }
    direction.reserve(mNumLinesOfData);
    for (unsigned i=0; i<mNumLinesOfData; i++)
    {
        c_vector<double, DIM> temp_vector;
        GetFibreVector(i, temp_vector, false);
        direction.push_back(temp_vector);
    }
}

template<unsigned DIM>
void FibreReader<DIM>::GetAllOrtho(std::vector< c_vector<double, DIM> >& first_direction,
                                   std::vector< c_vector<double, DIM> >& second_direction,
                                   std::vector< c_vector<double, DIM> >& third_direction)
{
    assert(first_direction.empty());
    assert(second_direction.empty());
    assert(third_direction.empty());
    if (mNumItemsPerLine != DIM*DIM)
    {
        EXCEPTION("Use GetAllAxi when reading axisymmetric fibres");
    }
    for (unsigned i=0; i<mNumLinesOfData; i++)
    {
        c_matrix<double, DIM, DIM> temp_matrix;
        GetFibreSheetAndNormalMatrix(i, temp_matrix, true);

        //Note that although the matrix appears row-wise in the ascii .ortho file,
        //for convenience it is stored column-wise.
        matrix_column<c_matrix<double, DIM, DIM> > col0(temp_matrix, 0);
        first_direction.push_back(col0);
        if (DIM>=2)
        {
            matrix_column<c_matrix<double, DIM, DIM> > col1(temp_matrix, 1);
            second_direction.push_back(col1);
        }
        if (DIM==3)
        {
            matrix_column<c_matrix<double, DIM, DIM> > col2(temp_matrix, 2);
            third_direction.push_back(col2);
        }
    }
}

template<unsigned DIM>
void FibreReader<DIM>::GetFibreSheetAndNormalMatrix(unsigned fibreIndex,
                                                    c_matrix<double,DIM,DIM>& rFibreMatrix,
                                                    bool checkOrthogonality)
{
    if (mNumItemsPerLine != DIM*DIM)
    {
        EXCEPTION("Use GetFibreVector when reading axisymmetric fibres");
    }
    if (fibreIndex < mNextIndex)
    {
        EXCEPTION("Fibre reads must be monotonically increasing; " << fibreIndex
                << " is before expected next index " << mNextIndex);
    }
    if (mFileIsBinary)
    {

        // Skip to the desired index
        mDataFile.seekg((fibreIndex-mNextIndex)*mNumItemsPerLine*sizeof(double), std::ios::cur);
        // Take mNumItemsPerLine from the ifstream
        mDataFile.read((char*)&(rFibreMatrix(0,0)), mNumItemsPerLine*sizeof(double));
        mNextIndex = fibreIndex+1;
    }
    else
    {
        unsigned num_entries = 0u;
        while (fibreIndex >= mNextIndex)
        {
             num_entries = GetTokensAtNextLine();
             mNextIndex++;
        }
        if (num_entries < mNumItemsPerLine)
        {
            EXCEPTION("A line is incomplete in " << mFilePath
                          << " - each line should contain " << DIM*DIM << " entries");
        }
        for (unsigned i=0; i<DIM; i++)
        {
            for (unsigned j=0; j<DIM; j++)
            {
                rFibreMatrix(i,j) = mTokens[DIM*i + j];
            }
        }
    }

    // The binary file and ascii file are row-major. However, we store column major matrices.
    rFibreMatrix = trans(rFibreMatrix);

    if (checkOrthogonality)
    {
        // Note that we define this matrix before setting it as otherwise the profiling build will break (see #2367)
        c_matrix<double,DIM,DIM> temp;
        temp = prod(trans(rFibreMatrix), rFibreMatrix);

        // Check temp is equal to the identity
        for (unsigned i=0; i<DIM; i++)
        {
            for (unsigned j=0; j<DIM; j++)
            {
                double val = (i==j ? 1.0 : 0.0);

                if (fabs(temp(i,j)-val) > 1e-4)
                {
                    EXCEPTION("Read fibre-sheet matrix, " << rFibreMatrix << " from file "
                                  << " which is not orthogonal (tolerance 1e-4)");
                }
            }
        }
    }
}

template<unsigned DIM>
void FibreReader<DIM>::GetFibreVector(unsigned fibreIndex,
                                      c_vector<double,DIM>& rFibreVector,
                                      bool checkNormalised)
{
    if (mNumItemsPerLine != DIM)
    {
        EXCEPTION("Use GetFibreSheetAndNormalMatrix when reading orthotropic fibres");
    }
    if (fibreIndex < mNextIndex)
    {
        EXCEPTION("Fibre reads must be monotonically increasing; " << fibreIndex
                  << " is before expected next index " << mNextIndex);
    }

    if (mFileIsBinary)
    {
        // Skip to the desired index
        mDataFile.seekg((fibreIndex-mNextIndex)*mNumItemsPerLine*sizeof(double), std::ios::cur);
        // Take mNumItemsPerLine from the ifstream
        mDataFile.read((char*)&rFibreVector[0], mNumItemsPerLine*sizeof(double));
        mNextIndex = fibreIndex+1;
    }
    else
    {
        unsigned num_entries = 0u;
        while (fibreIndex >= mNextIndex)
        {
            num_entries = GetTokensAtNextLine();
            mNextIndex++;
        }
        if (num_entries < mNumItemsPerLine)
        {
            EXCEPTION("A line is incomplete in " << mFilePath
                          << " - each line should contain " << DIM << " entries");
        }
        for (unsigned i=0; i<DIM; i++)
        {
            rFibreVector(i) = mTokens[i];
        }
    }


    if (checkNormalised && fabs(norm_2(rFibreVector)-1)>1e-4)
    {
        EXCEPTION("Read vector " << rFibreVector << " from file "
                      << mFilePath << " which is not normalised (tolerance 1e-4)");
    }
}

template<unsigned DIM>
unsigned FibreReader<DIM>::GetTokensAtNextLine()
{
    assert(mTokens.size() == mNumItemsPerLine);

    std::string line;
    bool blank_line;

    do
    {
        getline(mDataFile, line);

        if (line.empty() && mDataFile.eof())
        {
            mDataFile.close();
            std::string error =   "End of file " + mFilePath + " reached. Either file contains fewer "
                                + "definitions than defined in header, or one of the GetNext[..] methods "
                                + "has been called too often";
            EXCEPTION(error);
        }

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

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

    // Get rid of any trailing whitespace
    std::string::iterator iter = line.end();
    iter--;
    unsigned nchars2delete = 0;
    while (*iter == ' ' || *iter == '\t')
    {
        nchars2delete++;
        iter--;
    }
    line.erase(line.length()-nchars2delete);

    std::stringstream line_stream(line);

    unsigned index = 0;
    while (!line_stream.eof())
    {
        double item;
        line_stream >> item;
        if (index >= mNumItemsPerLine)
        {
            EXCEPTION("Too many entries in a line in " + mFilePath);
        }
        mTokens[index++] = item;
    }

    return index; // the number of entries put into mTokens
}

template<unsigned DIM>
void FibreReader<DIM>::ReadNumLinesOfDataFromFile()
{
    std::string raw_line;
    bool blank_line = false;
    do
    {
        getline(mDataFile, raw_line);
        //Strip comments following a hash
        raw_line = raw_line.substr(0, raw_line.find('#'));
        //Check for blank line
        blank_line = (raw_line.find_first_not_of(" \t",0) == std::string::npos);
    }
    while (blank_line);

    std::stringstream header_line(raw_line);

    header_line >> mNumLinesOfData;

    std::string extras;
    header_line >> extras;

    if (extras == "BIN")
    {
        mFileIsBinary = true;
    }
    else if (extras!="")
    {
        mDataFile.close();
        EXCEPTION("First (non comment) line of the fibre orientation file should contain the number of lines of data in the file (and possibly a BIN tag) at most");
    }
}

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