Hdf5ToXdmfConverter.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
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*/

#include "Hdf5ToXdmfConverter.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToXdmfConverter<ELEMENT_DIM, SPACE_DIM>::Hdf5ToXdmfConverter(const FileFinder& rInputDirectory,
                                                                 const std::string& rFileBaseName,
                                                                 AbstractTetrahedralMesh<ELEMENT_DIM, SPACE_DIM>* pMesh)
    : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "xdmf_output", 0u),
      XdmfMeshWriter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory.GetRelativePath(FileFinder("", RelativeTo::ChasteTestOutput)) + "/xdmf_output",
                                            rFileBaseName, false /* Not cleaning directory*/)
{
    // Set number of time steps
    std::vector<double> time_values = this->mpReader->GetUnlimitedDimensionValues();
    unsigned num_timesteps = time_values.size();
    this->mNumberOfTimePoints = num_timesteps;
    // Set time step size
    if (num_timesteps > 1)
    {
        this->mTimeStep = time_values[1] - time_values[0];
    }
    // Write
    this->WriteFilesUsingMesh(*pMesh);
}

#ifndef _MSC_VER

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void Hdf5ToXdmfConverter<ELEMENT_DIM, SPACE_DIM>::AddDataOnNodes(XERCES_CPP_NAMESPACE_QUALIFIER DOMElement* pGridElement,
                                                                 XERCES_CPP_NAMESPACE_QUALIFIER DOMDocument* pDomDocument,
                                                                 unsigned timeStep)
{
    // Use xerces namespace for convenience
    XERCES_CPP_NAMESPACE_USE

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

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

        /*
         * e.g. <Attribute Center="Node" Name="V">
         */
        DOMElement* p_attr_element =  pDomDocument->createElement(X("Attribute"));
        p_attr_element->setAttribute(X("Name"), X(variable_name));
        p_attr_element->setAttribute(X("Center"), X("Node"));
        pGridElement->appendChild(p_attr_element);

        /*
         * e.g. <DataItem Dimensions="1 12 1" ItemType="HyperSlab">
         */
        DOMElement* p_hype_element =  pDomDocument->createElement(X("DataItem"));
        p_hype_element->setAttribute(X("ItemType"), X("HyperSlab"));
        std::stringstream dim_stream;

        // First index is time value, second is number of nodes, third is variable index
        /* DistributedVectorFactory* p_factory = AbstractHdf5Converter<ELEMENT_DIM, SPACE_DIM>::mpMesh->GetDistributedVectorFactory();
        dim_stream << "1 " << p_factory->GetHigh()-p_factory->GetLow() << " 1"; */
        unsigned num_nodes = AbstractHdf5Converter<ELEMENT_DIM, SPACE_DIM>::mpMesh->GetNumNodes();
        dim_stream << "1 " << num_nodes << " 1";
        p_hype_element->setAttribute(X("Dimensions"), X(dim_stream.str()));
        p_attr_element->appendChild(p_hype_element);

        /*
         * e.g. <DataItem Dimensions="3 3" Format="XML">
         */
        DOMElement* p_xml_element =  pDomDocument->createElement(X("DataItem"));
        p_xml_element->setAttribute(X("Format"), X("XML"));
        p_xml_element->setAttribute(X("Dimensions"), X("3 3"));
        p_hype_element->appendChild(p_xml_element);

        /*
         * e.g. 0 0 0 1 1 1 1 12 1
         */
        std::stringstream XMLStream;
        XMLStream << timeStep << " 0 " << var_index << " ";
        XMLStream << "1 1 1 ";
        /* XMLStream << "1 " << p_factory->GetHigh()-p_factory->GetLow() << " 1"; */
        XMLStream << "1 " << num_nodes << " 1";
        DOMText* p_xml_text = pDomDocument->createTextNode(X(XMLStream.str()));
        p_xml_element->appendChild(p_xml_text);

        /*
         * e.g. <DataItem Dimensions="2 12 2" Format="HDF" NumberType="Float" Precision="8">
         */
        DOMElement* p_hdf_element =  pDomDocument->createElement(X("DataItem"));
        p_hdf_element->setAttribute(X("Format"), X("HDF"));
        p_hdf_element->setAttribute(X("NumberType"), X("Float"));
        p_hdf_element->setAttribute(X("Precision"), X("8"));
        std::stringstream hdf_dims_stream;
        /* hdf_dims_stream << num_timesteps << " " << p_factory->GetHigh()-p_factory->GetLow() << " " << this->mNumVariables; */
        hdf_dims_stream << num_timesteps << " " << num_nodes << " " << this->mNumVariables;
        p_hdf_element->setAttribute(X("Dimensions"), X(hdf_dims_stream.str()));
        p_hype_element->appendChild(p_hdf_element);

        /*
         * e.g. ../cube_2mm_12_elements.h5:/Data
         */
        std::stringstream HDFStream;
        HDFStream << "../" << AbstractHdf5Converter<ELEMENT_DIM, SPACE_DIM>::mFileBaseName << ".h5:/Data";
        DOMText* p_hdf_text = pDomDocument->createTextNode(X(HDFStream.str()));
        p_hdf_element->appendChild(p_hdf_text);
    }
}

#endif

// Explicit instantiation
template class Hdf5ToXdmfConverter<1,1>;
template class Hdf5ToXdmfConverter<1,2>;
template class Hdf5ToXdmfConverter<2,2>;
template class Hdf5ToXdmfConverter<1,3>;
template class Hdf5ToXdmfConverter<2,3>;
template class Hdf5ToXdmfConverter<3,3>;