Hdf5ToMeshalyzerConverter.cpp

/*

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#include "Hdf5ToMeshalyzerConverter.hpp"
#include "MeshalyzerMeshWriter.hpp"
#include "GenericMeshReader.hpp"
#include "UblasCustomFunctions.hpp"
#include "HeartConfig.hpp"
#include "PetscTools.hpp"
#include "Exception.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "DistributedVectorFactory.hpp"
#include "Version.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void Hdf5ToMeshalyzerConverter<ELEMENT_DIM,SPACE_DIM>::Write(std::string type)
{
    out_stream p_file = out_stream(NULL);
    if (PetscTools::AmMaster())
    {
        p_file = this->mpOutputFileHandler->OpenOutputFile(this->mFileBaseName + "_" + type + ".dat");

        // Check how many digits are to be output in the solution (0 goes to default value of digits)
        unsigned num_digits = HeartConfig::Instance()->GetVisualizerOutputPrecision();
        if (num_digits != 0)
        {
           p_file->precision(num_digits);
        }
    }

    unsigned num_nodes = this->mpReader->GetNumberOfRows();
    unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();

    DistributedVectorFactory factory(num_nodes);

    Vec data = factory.CreateVec();
    ReplicatableVector repl_data(num_nodes);
    for (unsigned time_step=0; time_step<num_timesteps; time_step++)
    {
        this->mpReader->GetVariableOverNodes(data, type, time_step);
        repl_data.ReplicatePetscVector(data);

        assert(repl_data.GetSize() == num_nodes);

        if (PetscTools::AmMaster())
        {
            for (unsigned i=0; i<num_nodes; i++)
            {
                *p_file << repl_data[i] << "\n";
            }
        }
    }
    PetscTools::Destroy(data);
    if (PetscTools::AmMaster())
    {
        std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
        *p_file << comment;
        p_file->close();
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToMeshalyzerConverter<ELEMENT_DIM,SPACE_DIM>::Hdf5ToMeshalyzerConverter(std::string inputDirectory,
                                                                            std::string fileBaseName,
                                                                            AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                                                            bool usingOriginalNodeOrdering)
    : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(inputDirectory, fileBaseName, pMesh, "output")
{
    std::vector<std::string> variable_names = this->mpReader->GetVariableNames();
    for (unsigned i=0; i<variable_names.size(); i++)
    {
        Write(variable_names[i]);
    }

    // Write mesh in a suitable form for meshalyzer
    std::string output_directory = inputDirectory + "/" + this->mRelativeSubdirectory;
    MeshalyzerMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer(output_directory, fileBaseName+"_mesh", false);

    // Normal case is that the in-memory mesh is converted
    if (!usingOriginalNodeOrdering)
    {
        // The second argument tells the writer to not follow original element ordering for performance reasons.
        mesh_writer.WriteFilesUsingMesh(*(this->mpMesh), false);
    }
    else
    {
        // In this case we expect the mesh to have been read in from file
        // Note that the next line will throw if the mesh has not been read from file
        std::string original_file = this->mpMesh->GetMeshFileBaseName();
        std::auto_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
            = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file);
        mesh_writer.WriteFilesUsingMeshReader(*p_original_mesh_reader);
    }
    PetscTools::Barrier("Hdf5ToMeshalyzerConverter");
}

// Explicit instantiation

template class Hdf5ToMeshalyzerConverter<1,1>;
template class Hdf5ToMeshalyzerConverter<1,2>;
template class Hdf5ToMeshalyzerConverter<2,2>;
template class Hdf5ToMeshalyzerConverter<1,3>;
template class Hdf5ToMeshalyzerConverter<2,3>;
template class Hdf5ToMeshalyzerConverter<3,3>;