////////////////////////////////////////////////////////////////////////////////
//
//  File: ProcessLinear.cpp
//
//  For more information, please see: http://www.nektar.info/
//
//  The MIT License
//
//  Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
//  Department of Aeronautics, Imperial College London (UK), and Scientific
//  Computing and Imaging Institute, University of Utah (USA).
//
//  Permission is hereby granted, free of charge, to any person obtaining a
//  copy of this software and associated documentation files (the "Software"),
//  to deal in the Software without restriction, including without limitation
//  the rights to use, copy, modify, merge, publish, distribute, sublicense,
//  and/or sell copies of the Software, and to permit persons to whom the
//  Software is furnished to do so, subject to the following conditions:
//
//  The above copyright notice and this permission notice shall be included
//  in all copies or substantial portions of the Software.
//
//  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
//  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
//  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
//  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
//  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
//  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
//  DEALINGS IN THE SOFTWARE.
//
//  Description: linearises mesh.
//
////////////////////////////////////////////////////////////////////////////////

#include "ProcessLinear.h"
#include <NekMesh/MeshElements/Element.h>

using namespace std;

namespace Nektar::NekMesh
{

using namespace Nektar::NekMesh;

ModuleKey ProcessLinear::className = GetModuleFactory().RegisterCreatorFunction(
    ModuleKey(eProcessModule, "linearise"), ProcessLinear::create,
    "Linearises mesh.");

ProcessLinear::ProcessLinear(MeshSharedPtr m) : ProcessModule(m)
{
    m_config["all"] =
        ConfigOption(true, "0", "remove curve nodes for all elements.");
    m_config["invalid"] =
        ConfigOption(false, "0", "remove curve nodes if element is invalid.");
    m_config["prismonly"] = ConfigOption(true, "0", "only acts on prims");
    m_config["extract"] =
        ConfigOption(false, "", "dump a mesh of the extracted elements");
}

ProcessLinear::~ProcessLinear()
{
}

void ProcessLinear::Process()
{
    m_log(VERBOSE) << "Linearising mesh." << endl;

    bool all      = m_config["all"].as<bool>();
    bool invalid  = m_config["invalid"].beenSet;
    NekDouble thr = m_config["invalid"].as<NekDouble>();

    if (!all & !invalid)
    {
        m_log(FATAL) << "Must specify an option: 'all' (to remove all "
                     << "curvature) or invalid (to remove curvature that makes "
                     << "elements invalid)." << endl;
    }

    if (all)
    {
        for (auto &edge : m_mesh->m_edgeSet)
        {
            edge->m_edgeNodes.clear();
        }

        for (auto &face : m_mesh->m_faceSet)
        {
            face->m_faceNodes.clear();
        }

        for (int i = 0; i < m_mesh->m_element[m_mesh->m_expDim].size(); i++)
        {
            vector<NodeSharedPtr> empty;
            m_mesh->m_element[m_mesh->m_expDim][i]->SetVolumeNodes(empty);
        }

        m_log(VERBOSE) << "Removed all element curvature." << endl;
    }
    else if (invalid)
    {
        map<int, vector<FaceSharedPtr>> eidToFace;
        map<int, vector<ElementSharedPtr>> eidToElm;

        vector<ElementSharedPtr> els = m_mesh->m_element[m_mesh->m_expDim];
        vector<ElementSharedPtr> el  = els;

        for (int i = 0; i < el.size(); i++)
        {
            vector<EdgeSharedPtr> e = el[i]->GetEdgeList();
            for (int j = 0; j < e.size(); j++)
            {
                eidToElm[e[j]->m_id].push_back(el[i]);
            }
        }

        if (m_mesh->m_expDim > 2)
        {
            for (auto &face : m_mesh->m_faceSet)
            {
                vector<EdgeSharedPtr> es = face->m_edgeList;
                for (int i = 0; i < es.size(); i++)
                {
                    eidToFace[es[i]->m_id].push_back(face);
                }
            }
        }

        set<int> neigh;
        vector<NodeSharedPtr> zeroNodes;
        std::unordered_set<int> clearedEdges, clearedFaces, clearedElmts;

        vector<ElementSharedPtr> dumpEls;

        // Iterate over list of elements of expansion dimension.
        while (el.size() > 0)
        {
            for (int i = 0; i < el.size(); ++i)
            {
                if (m_config["prismonly"].beenSet)
                {
                    if (el[i]->GetConf().m_e != LibUtilities::ePrism)
                    {
                        continue;
                    }
                }

                if (Invalid(el[i], thr)) //(!gfac->IsValid())
                {
                    dumpEls.push_back(el[i]);
                    clearedElmts.insert(el[i]->GetId());
                    ;
                    el[i]->SetVolumeNodes(zeroNodes);

                    vector<FaceSharedPtr> f = el[i]->GetFaceList();
                    for (int j = 0; j < f.size(); j++)
                    {
                        f[j]->m_faceNodes.clear();
                        clearedFaces.insert(f[j]->m_id);
                    }
                    vector<EdgeSharedPtr> e = el[i]->GetEdgeList();
                    for (int j = 0; j < e.size(); j++)
                    {
                        e[j]->m_edgeNodes.clear();
                        clearedEdges.insert(e[j]->m_id);
                    }

                    if (m_mesh->m_expDim > 2)
                    {
                        for (int j = 0; j < e.size(); j++)
                        {
                            auto it = eidToFace.find(e[j]->m_id);
                            for (int k = 0; k < it->second.size(); k++)
                            {
                                clearedEdges.insert(it->second[k]->m_id);
                                it->second[k]->m_faceNodes.clear();
                            }
                        }
                    }

                    for (int j = 0; j < e.size(); j++)
                    {
                        auto it = eidToElm.find(e[j]->m_id);
                        for (int k = 0; k < it->second.size(); k++)
                        {
                            neigh.insert(it->second[k]->GetId());
                        }
                    }
                }
            }

            el.clear();
            for (int i = 0; i < els.size(); i++)
            {
                auto it1 = neigh.find(els[i]->GetId());
                auto it2 = clearedElmts.find(els[i]->GetId());
                if (it1 != neigh.end() && it2 == clearedElmts.end())
                {
                    el.push_back(els[i]);
                }
            }
            neigh.clear();
        }

        m_log(VERBOSE) << "Removed curvature from " << clearedElmts.size()
                       << " elements (" << clearedEdges.size() << " edges, "
                       << clearedFaces.size() << " faces)" << endl;

        if (m_config["extract"].beenSet)
        {
            MeshSharedPtr dmp = std::shared_ptr<Mesh>(new Mesh());
            dmp->m_expDim     = 3;
            dmp->m_spaceDim   = 3;
            dmp->m_nummode    = 2;

            dmp->m_element[3] = dumpEls;

            ModuleSharedPtr mod = GetModuleFactory().CreateInstance(
                ModuleKey(eOutputModule, "xml"), dmp);
            mod->SetLogger(m_log);
            mod->RegisterConfig("outfile",
                                m_config["extract"].as<string>().c_str());
            mod->ProcessVertices();
            mod->ProcessEdges();
            mod->ProcessFaces();
            mod->ProcessElements();
            mod->ProcessComposites();
            mod->Process();
        }
    }
}

bool ProcessLinear::Invalid(ElementSharedPtr el, NekDouble thr)
{
    SpatialDomains::EntityHolder holder;
    // Create elemental geometry.
    SpatialDomains::Geometry *geom = el->GetGeom(m_mesh->m_spaceDim, holder);

    // Generate geometric factors.
    SpatialDomains::GeomFactorsSharedPtr gfac = geom->GetGeomFactors();

    if (!gfac->IsValid())
    {
        return true;
    }

    vector<NodeSharedPtr> ns = el->GetVertexList();
    ElmtConfig c             = el->GetConf();
    c.m_order                = 1;
    c.m_faceNodes            = false;
    c.m_volumeNodes          = false;
    c.m_reorient             = false;

    ElementSharedPtr elL =
        GetElementFactory().CreateInstance(c.m_e, c, ns, el->GetTagList());
    SpatialDomains::Geometry *geomL = elL->GetGeom(m_mesh->m_spaceDim, holder);
    SpatialDomains::GeomFactorsSharedPtr gfacL = geomL->GetGeomFactors();

    LibUtilities::PointsKeyVector p     = geom->GetXmap()->GetPointsKeys();
    SpatialDomains::DerivStorage deriv  = gfac->GetDeriv(p);
    SpatialDomains::DerivStorage derivL = gfacL->GetDeriv(p);
    const int pts                       = deriv[0][0].size();
    Array<OneD, NekDouble> jc(pts);
    Array<OneD, NekDouble> jcL(pts);
    for (int k = 0; k < pts; ++k)
    {
        DNekMat jac(m_mesh->m_expDim, m_mesh->m_expDim, 0.0, eFULL);
        DNekMat jacL(m_mesh->m_expDim, m_mesh->m_expDim, 0.0, eFULL);

        for (int l = 0; l < m_mesh->m_expDim; ++l)
        {
            for (int j = 0; j < m_mesh->m_expDim; ++j)
            {
                jac(j, l)  = deriv[l][j][k];
                jacL(j, l) = derivL[l][j][k];
            }
        }

        if (m_mesh->m_expDim == 2)
        {
            jc[k]  = jac(0, 0) * jac(1, 1) - jac(0, 1) * jac(1, 0);
            jcL[k] = jacL(0, 0) * jacL(1, 1) - jacL(0, 1) * jacL(1, 0);
        }
        else if (m_mesh->m_expDim == 3)
        {
            jc[k] =
                jac(0, 0) * (jac(1, 1) * jac(2, 2) - jac(2, 1) * jac(1, 2)) -
                jac(0, 1) * (jac(1, 0) * jac(2, 2) - jac(2, 0) * jac(1, 2)) +
                jac(0, 2) * (jac(1, 0) * jac(2, 1) - jac(2, 0) * jac(1, 1));
            jcL[k] = jacL(0, 0) *
                         (jacL(1, 1) * jacL(2, 2) - jacL(2, 1) * jacL(1, 2)) -
                     jacL(0, 1) *
                         (jacL(1, 0) * jacL(2, 2) - jacL(2, 0) * jacL(1, 2)) +
                     jacL(0, 2) *
                         (jacL(1, 0) * jacL(2, 1) - jacL(2, 0) * jacL(1, 1));
        }
    }

    Array<OneD, NekDouble> j(pts);
    Vmath::Vdiv(jc.size(), jc, 1, jcL, 1, j, 1);

    NekDouble scaledJac =
        Vmath::Vmin(j.size(), j, 1) / Vmath::Vmax(j.size(), j, 1);

    if (scaledJac < thr)
    {
        return true;
    }

    return false;
}
} // namespace Nektar::NekMesh
