FibreWriter.cpp

/*

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 * Redistributions in binary form must reproduce the above copyright notice,
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   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 "FibreWriter.hpp"
#include "Version.hpp"

template<unsigned DIM>
FibreWriter<DIM>::FibreWriter(const std::string& rDirectory,
                              const std::string& rBaseName,
                              const bool clearOutputDir)
    : mBaseName(rBaseName),
      mFileIsBinary(false)
{
    mpOutputFileHandler = new OutputFileHandler(rDirectory, clearOutputDir);
}

template<unsigned DIM>
FibreWriter<DIM>::~FibreWriter()
{
    delete mpOutputFileHandler;
}

template<unsigned DIM>
void FibreWriter<DIM>::WriteAllAxi(const std::vector< c_vector<double, DIM> >& fibres)
{
    // Write axi file
    out_stream p_axi_file = OpenFileAndWriteHeader(this->mBaseName + ".axi", fibres.size());

    //Now give the fibre directions
    for (unsigned i=0; i<fibres.size();i++ )
    {
        if (this->mFileIsBinary)
        {
            p_axi_file->write((char*)&fibres[i][0], DIM*sizeof(double));
        }
        else
        {
            for(unsigned j=0; j<DIM; j++)
            {
                *p_axi_file << fibres[i][j] << "\t";
            }
            *p_axi_file <<"\n";
        }
    }
    *p_axi_file << "#\n# " <<  ChasteBuildInfo::GetProvenanceString();
    p_axi_file->close();
}

template<unsigned DIM>
void FibreWriter<DIM>::WriteAllOrtho(const std::vector< c_vector<double, DIM> >& fibres,
                                     const std::vector< c_vector<double, DIM> >& second,
                                     const std::vector< c_vector<double, DIM> >& third)
{
    assert(fibres.size() == second.size());
    assert(second.size() == third.size());
    // Write ortho file
    out_stream p_file = OpenFileAndWriteHeader(this->mBaseName + ".ortho", fibres.size());

    //Now give the fibre directions
    for (unsigned i=0; i<fibres.size();i++ )
    {
        if (this->mFileIsBinary)
        {
            //The binary file is row-major
            p_file->write((char*)&fibres[i][0], DIM*sizeof(double));
            p_file->write((char*)&second[i][0], DIM*sizeof(double));
            p_file->write((char*)&third[i][0], DIM*sizeof(double));
        }
        else
        {
            //The ascii file is row-major
            for(unsigned j=0; j<DIM; j++)
            {
                *p_file << fibres[i][j] << "\t";
            }
            for(unsigned j=0; j<DIM; j++)
            {
                *p_file << second[i][j] << "\t";
            }
            for(unsigned j=0; j<DIM; j++)
            {
                *p_file << third[i][j] << "\t";
            }
            *p_file <<"\n";
        }
    }
    *p_file << "#\n# " <<  ChasteBuildInfo::GetProvenanceString();
    p_file->close();
}

template<unsigned DIM>
out_stream FibreWriter<DIM>::OpenFileAndWriteHeader(const std::string& rFileName, unsigned numItems)
{
    out_stream p_fibre_file = this->mpOutputFileHandler->OpenOutputFile(rFileName);

    //Header line says how many fibres are coming...
    *p_fibre_file << numItems;
    //... and whether the fibres are binary
    if (this->mFileIsBinary)
    {
        *p_fibre_file << "\tBIN\n";
    }
    else
    {
        *p_fibre_file << "\n";
    }
    return p_fibre_file;
}


template<unsigned DIM>
void FibreWriter<DIM>::SetWriteFileAsBinary()
{
    mFileIsBinary = true;
}

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