PVTU2VTU.cpp

Go to the documentation of this file.

 
#include <tclap/CmdLine.h>
 
#include <algorithm>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/xml_parser.hpp>
#include <filesystem>
#include <fstream>
#include <memory>
#include <numeric>
#include <range/v3/algorithm/copy.hpp>
#include <range/v3/algorithm/transform.hpp>
#include <string>
#include <unordered_set>
#include <vector>
 
#include "BaseLib/FileTools.h"
#include "BaseLib/MPI.h"
#include "BaseLib/RunTime.h"
#include "GeoLib/AABB.h"
#include "GeoLib/OctTree.h"
#include "InfoLib/GitInfo.h"
#include "MathLib/Point3d.h"
#include "MeshLib/Elements/Element.h"
#include "MeshLib/IO/VtkIO/VtuInterface.h"
#include "MeshLib/Location.h"
#include "MeshLib/Mesh.h"
#include "MeshLib/Node.h"
#include "MeshLib/Properties.h"
#include "MeshLib/Utils/IntegrationPointWriter.h"
#include "MeshLib/Utils/getOrCreateMeshProperty.h"
#include "MeshToolsLib/IntegrationPointDataTools.h"
 
struct MeshEntityMapInfo
{
    std::size_t partition_id;
    std::size_t original_id;
};
 
template <typename T>
bool createPropertyVector(
    MeshLib::Mesh& merged_mesh,
    std::vector<std::unique_ptr<MeshLib::Mesh>> const& partitioned_meshes,
    MeshLib::PropertyVector<T> const* const pv,
    MeshLib::Properties const& properties,
    std::vector<MeshEntityMapInfo> const& merged_node_map,
    std::vector<MeshEntityMapInfo> const& merged_element_map)
{
    if (pv == nullptr)
    {
        return false;
    }
 
    if (pv->getPropertyName() == "vtkGhostType")
    {
        // Do nothing
        return true;
    }
 
    auto const item_type = pv->getMeshItemType();
 
    auto const pv_name = pv->getPropertyName();
 
    auto const pv_num_components = pv->getNumberOfGlobalComponents();
 
    if (pv_name == "OGS_VERSION" || pv_name == "IntegrationPointMetaData")
    {
        auto new_pv = MeshLib::getOrCreateMeshProperty<T>(
            merged_mesh, pv_name, item_type, pv_num_components);
        new_pv->resize(pv->size());
 
        std::copy(pv->begin(), pv->end(), new_pv->begin());
 
        return true;
    }
 
    std::vector<MeshLib::PropertyVector<T>*> partition_property_vectors;
    partition_property_vectors.reserve(partitioned_meshes.size());
    for (auto const& mesh : partitioned_meshes)
    {
        partition_property_vectors.emplace_back(
            mesh->getProperties().getPropertyVector<T>(pv_name, item_type,
                                                       pv_num_components));
    }
 
    auto createNewCellOrNodePropertyVector =
        [&](std::vector<MeshEntityMapInfo> const& mesh_entity_map)
    {
        auto new_pv = MeshLib::getOrCreateMeshProperty<T>(
            merged_mesh, pv_name, item_type, pv_num_components);
        std::size_t counter = 0;
        for (auto const& entity_info : mesh_entity_map)
        {
            auto const& partition_pv =
                partition_property_vectors[entity_info.partition_id];
            for (int i_com = 0; i_com < pv_num_components; i_com++)
            {
                (*new_pv)[counter * pv_num_components + i_com] =
                    (*partition_pv)[entity_info.original_id *
                                        pv_num_components +
                                    i_com];
            }
            counter++;
        }
    };
 
    if (item_type == MeshLib::MeshItemType::Node)
    {
        createNewCellOrNodePropertyVector(merged_node_map);
        return true;
    }
 
    if (item_type == MeshLib::MeshItemType::Cell)
    {
        createNewCellOrNodePropertyVector(merged_element_map);
        return true;
    }
 
    if (item_type == MeshLib::MeshItemType::IntegrationPoint)
    {
        std::vector<std::vector<std::size_t>> partition_element_offsets;
        partition_element_offsets.reserve(partitioned_meshes.size());
        for (auto const& mesh : partitioned_meshes)
        {
            partition_element_offsets.emplace_back(
                MeshToolsLib::getIntegrationPointDataOffsetsOfMeshElements(
                    mesh->getElements(), *pv, properties));
        }
 
        auto new_pv = MeshLib::getOrCreateMeshProperty<T>(
            merged_mesh, pv_name, item_type, pv_num_components);
 
        // Count the integration points
        std::size_t counter = 0;
        auto const ip_meta_data =
            MeshLib::getIntegrationPointMetaData(properties, pv_name);
 
        for (auto const element : merged_mesh.getElements())
        {
            int const number_of_integration_points =
                MeshToolsLib::getNumberOfElementIntegrationPoints(ip_meta_data,
                                                                  *element);
            counter += number_of_integration_points;
        }
        new_pv->resize(counter * pv_num_components);
 
        auto const global_ip_offsets =
            MeshToolsLib::getIntegrationPointDataOffsetsOfMeshElements(
                merged_mesh.getElements(), *pv, properties);
 
        std::size_t element_counter = 0;
        for (auto const& element_info : merged_element_map)
        {
            MeshLib::PropertyVector<T> const& partition_pv =
                *(partition_property_vectors[element_info.partition_id]);
 
            auto const& offsets =
                partition_element_offsets[element_info.partition_id];
 
            int const begin_pos = offsets[element_info.original_id];
            int const end_pos = offsets[element_info.original_id + 1];
 
            std::copy(partition_pv.begin() + begin_pos,
                      partition_pv.begin() + end_pos,
                      new_pv->begin() + global_ip_offsets[element_counter]);
 
            element_counter++;
        }
    }
 
    return true;
}
 
std::vector<std::string> readVtuFileNames(std::string const& pvtu_file_name)
{
    std::ifstream ins(pvtu_file_name);
 
    if (!ins)
    {
        OGS_FATAL("Could not open pvtu file {:s}.", pvtu_file_name);
    }
 
    using boost::property_tree::ptree;
    ptree pt;
    read_xml(ins, pt);
 
    auto root = pt.get_child("VTKFile");
 
    std::vector<std::string> vtu_file_names;
 
    std::string file_path = BaseLib::extractPath(pvtu_file_name);
 
    for (ptree::value_type const& v : root.get_child("PUnstructuredGrid"))
    {
        if (v.first == "Piece")
        {
            vtu_file_names.push_back(BaseLib::joinPaths(
                file_path,
                // only gets the vtu file name:
                std::filesystem::path(v.second.get("<xmlattr>.Source", ""))
                    .filename()
                    .string()));
        }
    }
 
    if (vtu_file_names.empty())
    {
        OGS_FATAL("PVTU file {:s} does not contain any vtu piece",
                  pvtu_file_name);
    }
 
    return vtu_file_names;
}
 
// all nodes (also 'ghost' nodes) of all meshes sorted by partition
std::tuple<std::vector<MeshLib::Node*>, std::vector<std::size_t>>
getMergedNodesVector(std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes)
{
    std::vector<std::size_t> number_of_nodes_per_partition;
    ranges::transform(meshes, std::back_inserter(number_of_nodes_per_partition),
                      [](auto const& mesh)
                      { return mesh->getNumberOfNodes(); });
    std::vector<std::size_t> const offsets =
        BaseLib::sizesToOffsets(number_of_nodes_per_partition);
 
    std::vector<MeshLib::Node*> all_nodes;
    all_nodes.reserve(offsets.back());
    for (auto const& mesh : meshes)
    {
        ranges::copy(mesh->getNodes(), std::back_inserter(all_nodes));
    }
    return {all_nodes, offsets};
}
 
std::tuple<std::vector<MeshLib::Element*>, std::vector<MeshEntityMapInfo>>
getRegularElements(std::vector<std::unique_ptr<MeshLib::Mesh>> const& meshes)
{
    std::vector<MeshLib::Element*> regular_elements;
 
    std::size_t partition_counter = 0;
    std::vector<MeshEntityMapInfo> merged_element_map;
    for (auto const& mesh : meshes)
    {
        MeshLib::Properties const& properties = mesh->getProperties();
 
        std::vector<unsigned char> const& ghost_id_vector =
            *(properties.getPropertyVector<unsigned char>("vtkGhostType"));
 
        auto const& mesh_elements = mesh->getElements();
 
        auto const last_element_id_of_previous_partition =
            regular_elements.size();
 
        std::copy_if(mesh_elements.begin(), mesh_elements.end(),
                     std::back_inserter(regular_elements),
                     [&ghost_id_vector](auto const element)
                     { return ghost_id_vector[element->getID()] == 0; });
 
        for (auto element_id = last_element_id_of_previous_partition;
             element_id < regular_elements.size();
             element_id++)
        {
            merged_element_map.push_back(
                {partition_counter, regular_elements[element_id]->getID()});
        }
 
        partition_counter++;
    }
 
    return {regular_elements, merged_element_map};
}
 
MeshLib::Node* getExistingNodeFromOctTree(
    GeoLib::OctTree<MeshLib::Node, 16>& oct_tree, Eigen::Vector3d const& extent,
    MeshLib::Node const& node, std::size_t const element_id)
{
    std::vector<MeshLib::Node*> query_nodes;
    auto const eps =
        std::numeric_limits<double>::epsilon() * extent.squaredNorm();
    Eigen::Vector3d const min = node.asEigenVector3d().array() - eps;
    Eigen::Vector3d const max = node.asEigenVector3d().array() + eps;
    oct_tree.getPointsInRange(min, max, query_nodes);
 
    if (query_nodes.empty())
    {
        OGS_FATAL(
            "query_nodes for node [{}], ({}, {}, {}) of element "
            "[{}] are empty, eps is {}",
            node.getID(), node[0], node[1], node[2], element_id, eps);
    }
    auto const it =
        std::find_if(query_nodes.begin(), query_nodes.end(),
                     [&node, eps](auto const* p)
                     {
                         return (p->asEigenVector3d() - node.asEigenVector3d())
                                    .squaredNorm() < eps;
                     });
    if (it == query_nodes.end())
    {
        OGS_FATAL(
            "did not find node: [{}] ({}, {}, {}) of element [{}] in "
            "query_nodes",
            node.getID(), node[0], node[1], node[2], element_id);
    }
    return *it;
}
 
void resetNodesInRegularElements(
    std::vector<MeshLib::Element*> const& regular_elements,
    GeoLib::OctTree<MeshLib::Node, 16>& oct_tree,
    Eigen::Vector3d const& extent)
{
    for (auto& e : regular_elements)
    {
        for (unsigned i = 0; i < e->getNumberOfNodes(); i++)
        {
            auto* const node = e->getNode(i);
            MeshLib::Node* node_ptr = nullptr;
            if (!oct_tree.addPoint(node, node_ptr))
            {
                auto const node_ptr = getExistingNodeFromOctTree(
                    oct_tree, extent, *node, e->getID());
                e->setNode(i, node_ptr);
            }
        }
    }
}
 
std::pair<std::vector<MeshLib::Node*>, std::vector<MeshEntityMapInfo>>
makeNodesUnique(std::vector<MeshLib::Node*> const& all_merged_nodes_tmp,
                std::vector<std::size_t> const& partition_offsets,
                GeoLib::OctTree<MeshLib::Node, 16>& oct_tree)
{
    std::vector<MeshLib::Node*> unique_merged_nodes;
    unique_merged_nodes.reserve(all_merged_nodes_tmp.size());
 
    std::vector<MeshEntityMapInfo> merged_node_map;
    merged_node_map.reserve(all_merged_nodes_tmp.size());
 
    for (std::size_t i = 0; i < partition_offsets.size() - 1; ++i)
    {
        for (std::size_t pos = partition_offsets[i];
             pos < partition_offsets[i + 1];
             ++pos)
        {
            auto* node = all_merged_nodes_tmp[pos];
            MeshLib::Node* node_ptr = nullptr;
            if (oct_tree.addPoint(node, node_ptr))
            {
                unique_merged_nodes.push_back(node);
                merged_node_map.push_back({i, pos - partition_offsets[i]});
            }
        }
    }
    return {unique_merged_nodes, merged_node_map};
}
 
int main(int argc, char* argv[])
{
    TCLAP::CmdLine cmd(
        "This tool merges VTU files of PVTU into one single VTU file. Apart "
        "from the mesh data, all property data are merged as well"
        "\n\nOpenGeoSys-6 software, version " +
            GitInfoLib::GitInfo::ogs_version +
            ".\n"
            "Copyright (c) 2012-2024, OpenGeoSys Community "
            "(http://www.opengeosys.org)",
        ' ', GitInfoLib::GitInfo::ogs_version);
 
    TCLAP::ValueArg<std::string> output_arg(
        "o", "output", "the output mesh (*.vtu)", true, "", "output.vtu");
    cmd.add(output_arg);
 
    TCLAP::ValueArg<std::string> input_arg(
        "i", "input", "the partitioned input mesh (*.pvtu)", true, "",
        "input.pvtu");
    cmd.add(input_arg);
    cmd.parse(argc, argv);
 
    BaseLib::MPI::Setup mpi_setup(argc, argv);
 
    if (BaseLib::getFileExtension(input_arg.getValue()) != ".pvtu")
    {
        OGS_FATAL("The extension of input file name {:s} is not \"pvtu\"",
                  input_arg.getValue());
    }
    if (BaseLib::getFileExtension(output_arg.getValue()) != ".vtu")
    {
        OGS_FATAL("The extension of output file name {:s} is not \"vtu\"",
                  output_arg.getValue());
    }
 
    auto const vtu_file_names = readVtuFileNames(input_arg.getValue());
 
    std::vector<std::unique_ptr<MeshLib::Mesh>> meshes;
    meshes.reserve(vtu_file_names.size());
 
    BaseLib::RunTime io_timer;
    io_timer.start();
    for (auto const& file_name : vtu_file_names)
    {
        auto mesh = std::unique_ptr<MeshLib::Mesh>(
            MeshLib::IO::VtuInterface::readVTUFile(file_name));
 
        MeshLib::Properties const& properties = mesh->getProperties();
 
        if (!properties.existsPropertyVector<unsigned char>("vtkGhostType"))
        {
            OGS_FATAL(
                "Property vector vtkGhostType does not exist in mesh {:s}.",
                file_name);
        }
 
        meshes.emplace_back(std::move(mesh));
    }
    INFO("Reading meshes took {} s", io_timer.elapsed());
 
    BaseLib::RunTime merged_element_timer;
    merged_element_timer.start();
    // If structured binding is used for the returned tuple, Mac compiler gives
    // an error in reference to local binding in calling applyToPropertyVectors.
    auto [regular_elements, merged_element_map] = getRegularElements(meshes);
    INFO(
        "Collection of {} regular elements and computing element map took {} s",
        regular_elements.size(), merged_element_timer.elapsed());
 
    // alternative implementation of getNodesOfRegularElements
    BaseLib::RunTime collect_nodes_timer;
    collect_nodes_timer.start();
    auto [all_merged_nodes_tmp, partition_offsets] =
        getMergedNodesVector(meshes);
    INFO("Collection of {} nodes and computing offsets took {} s",
         all_merged_nodes_tmp.size(), collect_nodes_timer.elapsed());
 
    BaseLib::RunTime merged_nodes_timer;
    merged_nodes_timer.start();
    GeoLib::AABB aabb(all_merged_nodes_tmp.begin(), all_merged_nodes_tmp.end());
    auto oct_tree = std::unique_ptr<GeoLib::OctTree<MeshLib::Node, 16>>(
        GeoLib::OctTree<MeshLib::Node, 16>::createOctTree(
            aabb.getMinPoint(), aabb.getMaxPoint(), 1e-16));
 
    auto [unique_merged_nodes, merged_node_map] =
        makeNodesUnique(all_merged_nodes_tmp, partition_offsets, *oct_tree);
    INFO("Make nodes unique ({} unique nodes) / computing map took {} s",
         unique_merged_nodes.size(), merged_nodes_timer.elapsed());
 
    BaseLib::RunTime reset_nodes_in_elements_timer;
    reset_nodes_in_elements_timer.start();
    auto const extent = aabb.getMaxPoint() - aabb.getMinPoint();
    resetNodesInRegularElements(regular_elements, *oct_tree, extent);
    INFO("Reset nodes in regular elements took {} s",
         reset_nodes_in_elements_timer.elapsed());
 
    BaseLib::RunTime mesh_creation_timer;
    mesh_creation_timer.start();
    // The Node pointers of 'merged_nodes' and Element pointers of
    // 'regular_elements' are shared with 'meshes', the partitioned meshes.
    MeshLib::Mesh merged_mesh =
        MeshLib::Mesh("pvtu_merged_mesh", unique_merged_nodes, regular_elements,
                      false /* compute_element_neighbors */);
    INFO("creation of merged mesh took {} s", mesh_creation_timer.elapsed());
 
    auto const& properties = meshes[0]->getProperties();
 
    BaseLib::RunTime property_timer;
    property_timer.start();
    applyToPropertyVectors(
        properties,
        [&, &merged_node_map = merged_node_map,
         &merged_element_map = merged_element_map](auto type,
                                                   auto const& property)
        {
            return createPropertyVector<decltype(type)>(
                merged_mesh, meshes,
                dynamic_cast<MeshLib::PropertyVector<decltype(type)> const*>(
                    property),
                properties, merged_node_map, merged_element_map);
        });
    INFO("merge properties into merged mesh took {} s",
         property_timer.elapsed());
 
    MeshLib::IO::VtuInterface writer(&merged_mesh);
 
    BaseLib::RunTime writing_timer;
    writing_timer.start();
    auto const result = writer.writeToFile(output_arg.getValue());
    if (!result)
    {
        ERR("Could not write mesh to '{:s}'.", output_arg.getValue());
        return EXIT_FAILURE;
    }
    INFO("writing mesh took {} s", writing_timer.elapsed());
 
    // Since the Node pointers of 'merged_nodes' and Element pointers of
    // 'regular_elements' are held by 'meshes', the partitioned meshes, the
    // memory by these pointers are released by 'meshes' automatically.
    // Therefore, only node vector and element vector of merged_mesh should be
    // cleaned.
    merged_mesh.shallowClean();
 
    return EXIT_SUCCESS;
}