Hdf5ToVtkConverter.cpp

/*

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*/

#include "UblasCustomFunctions.hpp"
#include "Hdf5ToVtkConverter.hpp"
#include "PetscTools.hpp"
#include "Exception.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "DistributedVectorFactory.hpp"
#include "VtkMeshWriter.hpp"
#include "GenericMeshReader.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "Warnings.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToVtkConverter<ELEMENT_DIM, SPACE_DIM>::Hdf5ToVtkConverter(const FileFinder& rInputDirectory,
                                                               const std::string& rFileBaseName,
                                                               AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh,
                                                               bool parallelVtk,
                                                               bool usingOriginalNodeOrdering)
    : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "vtk_output",0u)
{
#ifdef CHASTE_VTK // Requires "sudo aptitude install libvtk5-dev" or similar

    // Write mesh in a suitable form for VTK
    FileFinder test_output("", RelativeTo::ChasteTestOutput);
    std::string output_directory = rInputDirectory.GetRelativePath(test_output) + "/" + this->mRelativeSubdirectory;

    VtkMeshWriter<ELEMENT_DIM,SPACE_DIM> vtk_writer(output_directory, rFileBaseName, false);

    DistributedVectorFactory* p_factory = pMesh->GetDistributedVectorFactory();

    // Make sure that we are never trying to write from an incomplete data HDF5 file
    assert(this->mpReader->GetNumberOfRows() == pMesh->GetNumNodes());

    DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* p_distributed_mesh = dynamic_cast<DistributedTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>*>(pMesh);

    unsigned num_nodes = pMesh->GetNumNodes();
    if (parallelVtk)
    {
        // If it's not a distributed mesh, then we might want to give a warning and back-off
        if (p_distributed_mesh == nullptr)
        {
            WARNING("Can only write parallel VTK from a DistributedTetrahedralMesh - writing sequential VTK instead");
            parallelVtk = false;
        }

        // If the node ordering flag is set, then we can't do this
        if (usingOriginalNodeOrdering)
        {
            WARNING("Can't write parallel VTK (pvtu) files with original ordering - writing sequential VTK instead");
            parallelVtk = false;
        }

        // Are we now committed to writing .pvtu?
        if (parallelVtk)
        {
           vtk_writer.SetParallelFiles(*pMesh);
           num_nodes = p_distributed_mesh->GetNumLocalNodes();
        }
    }

    Vec data = p_factory->CreateVec();

    do // Loop over datasets via MoveOntoNextDataset method in the abstract class
    {
        // Make sure that we are never trying to write from an incomplete HDF5 dataset.
        assert(this->mpReader->GetNumberOfRows() == pMesh->GetNumNodes());

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

        // Loop over time steps
        for (unsigned time_step=0; time_step<num_timesteps; time_step++)
        {
            // Loop over variables
            for (unsigned variable=0; variable<this->mNumVariables; variable++)
            {
                std::string variable_name = this->mpReader->GetVariableNames()[variable];

                // Gets variable at this time step from HDF5 archive
                this->mpReader->GetVariableOverNodes(data, variable_name, time_step);

                std::vector<double> data_for_vtk;
                data_for_vtk.resize(num_nodes);
                std::ostringstream variable_point_data_name;
                variable_point_data_name << variable_name << "_" << std::setw(6) << std::setfill('0') << time_step;

                if (parallelVtk)
                {
                    // Parallel VTU files
                    double *p_data;
                    VecGetArray(data, &p_data);
                    for (unsigned index=0; index<num_nodes; index++)
                    {
                        data_for_vtk[index]  = p_data[index];
                    }
                    VecRestoreArray(data, &p_data);
                }
                else
                {
                    // One VTU file
                    ReplicatableVector repl_data(data);
                    for (unsigned index=0; index<num_nodes; index++)
                    {
                        data_for_vtk[index] = repl_data[index];
                    }
                }
                // Add this variable into the node "point" data
                vtk_writer.AddPointData(variable_point_data_name.str(), data_for_vtk);
            }
        }
    }
    while ( this->MoveOntoNextDataset() );

    // Tidy up
    PetscTools::Destroy(data);

    // Normally the in-memory mesh is converted
    if (!usingOriginalNodeOrdering)
    {
        vtk_writer.WriteFilesUsingMesh(*(this->mpMesh));
    }
    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::shared_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
            = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file);
        vtk_writer.WriteFilesUsingMeshReader(*p_original_mesh_reader);
    }
#endif //CHASTE_VTK
}

// Explicit instantiation
template class Hdf5ToVtkConverter<1,1>;
template class Hdf5ToVtkConverter<1,2>;
template class Hdf5ToVtkConverter<2,2>;
template class Hdf5ToVtkConverter<1,3>;
template class Hdf5ToVtkConverter<2,3>;
template class Hdf5ToVtkConverter<3,3>;