AbstractHdf5Converter.cpp

/*

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*/

#include "AbstractHdf5Converter.hpp"
#include "Version.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractHdf5Converter<ELEMENT_DIM, SPACE_DIM>::AbstractHdf5Converter(std::string inputDirectory,
                                                                     std::string fileBaseName,
                                                                     AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh,
                                                                     std::string subdirectoryName)
    : mFileBaseName(fileBaseName),
      mpMesh(pMesh),
      mRelativeSubdirectory(subdirectoryName)
{
    // Store directory, mesh and filenames and create the reader
    mpReader = new Hdf5DataReader(inputDirectory, mFileBaseName);

    // Create new directory in which to store everything
    mpOutputFileHandler = new OutputFileHandler(inputDirectory + "/" + mRelativeSubdirectory, false);

    // Check the data file for basic validity
    std::vector<std::string> variable_names = mpReader->GetVariableNames();
    mNumVariables = variable_names.size();

    if (mpReader->GetNumberOfRows() != mpMesh->GetNumNodes())
    {
        delete mpReader;
        delete mpOutputFileHandler;
        EXCEPTION("Mesh and HDF5 file have a different number of nodes");
    }

    // Write an info file
    if (PetscTools::AmMaster())
    {
        // Note that we don't want the child processes to write info files
        out_stream p_file = mpOutputFileHandler->OpenOutputFile(mFileBaseName + "_times.info");

        std::vector<double> time_values = mpReader->GetUnlimitedDimensionValues();
        unsigned num_timesteps = time_values.size();
        double first_timestep = time_values.front();
        double last_timestep = time_values.back();

        double timestep = num_timesteps > 1 ? time_values[1] - time_values[0] : DOUBLE_UNSET;

        *p_file << "Number of timesteps " << num_timesteps << std::endl;
        *p_file << "timestep " << timestep << std::endl;
        *p_file << "First timestep " << first_timestep << std::endl;
        *p_file << "Last timestep " << last_timestep << std::endl;
        *p_file << ChasteBuildInfo::GetProvenanceString();

        p_file->close();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>::~AbstractHdf5Converter()
{
    delete mpReader;
    delete mpOutputFileHandler;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>::GetSubdirectory()
{
    return mRelativeSubdirectory;
}

// Explicit instantiation

template class AbstractHdf5Converter<1,1>;
template class AbstractHdf5Converter<1,2>;
template class AbstractHdf5Converter<2,2>;
template class AbstractHdf5Converter<1,3>;
template class AbstractHdf5Converter<2,3>;
template class AbstractHdf5Converter<3,3>;