Hdf5ToVtkConverter.cpp

/*
 
Copyright (c) 2005-2024, University of Oxford.
All rights reserved.
 
University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.
 
This file is part of Chaste.
 
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.
 
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
*/
 
#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>;