#include "topologyenumerator.hpp"
#include <algorithm>
#include <boost/graph/biconnected_components.hpp>
#include <iostream>
#include <math.h>
#include <numeric>
#include <unordered_set>

const bool debugIsOn{false};
const bool savePlyFiles{true};

// size_t binomialCoefficient(size_t n, size_t m) {
//  assert(n > m);
//  return tgamma(n + 1) / (tgamma(m + 1) * tgamma(n - m + 1));
//}

// void TopologyEnumerator::createLabelMesh(
//    const std::vector<vcg::Point3d> vertices,
//    const std::filesystem::path &savePath) const {
//  const std::string allOnes(patternTopology.getNumberOfPossibleEdges(), '1');
//  const std::vector<vcg::Point2i> allEdges =
//      TrianglePatternTopology::convertToEdges(allOnes, vertices.size());
//  TrianglePatternGeometry labelMesh;
//  std::vector<vcg::Point3d> labelVertices(allEdges.size());
//  for (size_t edgeIndex = 0; edgeIndex < allEdges.size(); edgeIndex++) {
//    const vcg::Point3d edgeMidpoint =
//        (vertices[allEdges[edgeIndex][0]] + vertices[allEdges[edgeIndex][1]])
//        / 2;
//    labelVertices[edgeIndex] = edgeMidpoint;
//  }
//  labelMesh.set(labelVertices);
//  labelMesh.savePly(std::filesystem::path(savePath)
//                        .append(std::string("labelMesh.ply"))
//                        .string());
//}

size_t TopologyEnumerator::getEdgeIndex(size_t ni0, size_t ni1) const
{
    if (ni1 <= ni0) {
        std::swap(ni0, ni1);
    }
    assert(ni1 > ni0);
    const size_t &n = numberOfNodes;
    return (n * (n - 1) / 2) - (n - ni0) * ((n - ni0) - 1) / 2 + ni1 - ni0 - 1;
}

TopologyEnumerator::TopologyEnumerator() {}

void TopologyEnumerator::computeValidPatterns(const std::vector<size_t> &reducedNumberOfNodesPerSlot,
                                              const std::string &desiredResultsPath,
                                              const int &numberOfDesiredEdges)
{
    assert(reducedNumberOfNodesPerSlot.size() == 5);
    assert(reducedNumberOfNodesPerSlot[0] == 0 || reducedNumberOfNodesPerSlot[0] == 1);
    assert(reducedNumberOfNodesPerSlot[1] == 0 || reducedNumberOfNodesPerSlot[1] == 1);
    std::vector<size_t> numberOfNodesPerSlot{reducedNumberOfNodesPerSlot[0],
                                             reducedNumberOfNodesPerSlot[1],
                                             reducedNumberOfNodesPerSlot[1],
                                             reducedNumberOfNodesPerSlot[2],
                                             reducedNumberOfNodesPerSlot[3],
                                             reducedNumberOfNodesPerSlot[2],
                                             reducedNumberOfNodesPerSlot[4]};
    // Generate an edge mesh wih all possible edges
    numberOfNodes = std::accumulate(numberOfNodesPerSlot.begin(), numberOfNodesPerSlot.end(), 0);
    const size_t numberOfAllPossibleEdges = numberOfNodes * (numberOfNodes - 1) / 2;

    std::vector<vcg::Point2i> allPossibleEdges(numberOfAllPossibleEdges);
    const int &n = numberOfNodes;
    for (size_t edgeIndex = 0; edgeIndex < numberOfAllPossibleEdges; edgeIndex++) {
        const int ni0 = n - 2
                        - std::floor(std::sqrt(-8 * edgeIndex + 4 * n * (n - 1) - 7) / 2.0 - 0.5);
        const int ni1 = edgeIndex + ni0 + 1 - n * (n - 1) / 2 + (n - ni0) * ((n - ni0) - 1) / 2;
        allPossibleEdges[edgeIndex] = vcg::Point2i(ni0, ni1);
    }
    PatternGeometry patternGeometryAllEdges;
    patternGeometryAllEdges.add(numberOfNodesPerSlot, allPossibleEdges);
    // Create Results path
    auto resultPath = std::filesystem::path(desiredResultsPath);
    assert(std::filesystem::exists(resultPath));

    auto allResultsPath = resultPath.append("Results");
    std::filesystem::create_directory(allResultsPath);
    std::string setupString;
    //  for (size_t numberOfNodes : reducedNumberOfNodesPerSlot) {
    for (size_t numberOfNodesPerSlotIndex = 0;
         numberOfNodesPerSlotIndex < reducedNumberOfNodesPerSlot.size();
         numberOfNodesPerSlotIndex++) {
        std::string elemID;
        if (numberOfNodesPerSlotIndex == 0 || numberOfNodesPerSlotIndex == 1) {
            elemID = "v";
        } else if (numberOfNodesPerSlotIndex == 2 || numberOfNodesPerSlotIndex == 3) {
            elemID = "e";
        } else {
            elemID = "c";
        }
        setupString += std::to_string(reducedNumberOfNodesPerSlot[numberOfNodesPerSlotIndex])
                       + elemID + "_";
    }
    setupString += std::to_string(PatternGeometry().getFanSize()) + "fan";
    if (debugIsOn) {
        setupString += "_debug";
    }
    auto resultsPath = std::filesystem::path(allResultsPath).append(setupString);
    //    std::filesystem::remove_all(resultsPath); // delete previous results
    std::filesystem::create_directory(resultsPath);

    if (debugIsOn) {
        patternGeometryAllEdges.save(
            std::filesystem::path(resultsPath).append("allPossibleEdges.ply").string());
    }
    //  statistics.numberOfPossibleEdges = numberOfAllPossibleEdges;

    std::vector<vcg::Point2i> validEdges = getValidEdges(numberOfNodesPerSlot,
                                                         resultsPath,
                                                         patternGeometryAllEdges,
                                                         allPossibleEdges);
    PatternGeometry patternAllValidEdges;
    patternAllValidEdges.add(patternGeometryAllEdges.getVertices(), validEdges);
    if (debugIsOn) {
        // Export all valid edges in a ply
        patternAllValidEdges.save(
            std::filesystem::path(resultsPath).append("allValidEdges.ply").string());
    }
    //  statistics.numberOfValidEdges = validEdges.size();

    // Find pairs of intersecting edges
    const std::unordered_map<size_t, std::unordered_set<size_t>> intersectingEdges
        = patternAllValidEdges.getIntersectingEdges(statistics.numberOfIntersectingEdgePairs);
    if (debugIsOn) {
        auto intersectingEdgesPath = std::filesystem::path(resultsPath)
                                         .append("All_intersecting_edge_pairs");
        std::filesystem::create_directory(intersectingEdgesPath);
        // Export intersecting pairs in ply files
        for (auto mapIt = intersectingEdges.begin(); mapIt != intersectingEdges.end(); mapIt++) {
            for (auto setIt = mapIt->second.begin(); setIt != mapIt->second.end(); setIt++) {
                PatternGeometry intersectingEdgePair;
                const size_t ei0 = mapIt->first;
                const size_t ei1 = *setIt;
                vcg::tri::Allocator<PatternGeometry>::AddEdge(
                    intersectingEdgePair,
                    patternGeometryAllEdges.getVertices()[validEdges[ei0][0]],
                    patternGeometryAllEdges.getVertices()[validEdges[ei0][1]]);
                vcg::tri::Allocator<PatternGeometry>::AddEdge(
                    intersectingEdgePair,
                    patternGeometryAllEdges.getVertices()[validEdges[ei1][0]],
                    patternGeometryAllEdges.getVertices()[validEdges[ei1][1]]);
                intersectingEdgePair.save(std::filesystem::path(intersectingEdgesPath)
                                              .append(std::to_string(mapIt->first) + "_"
                                                      + std::to_string(*setIt) + ".ply")
                                              .string());
            }
        }
    }

    //  assert(validEdges.size() == allPossibleEdges.size() -
    //  coincideEdges.size() -
    //                                   duplicateEdges.size());

    //  PatternSet patternSet;
    //  const std::vector<vcg::Point3d> nodes =
    //  patternGeometryAllEdges.getVertices(); const size_t numberOfNodes =
    //  nodes.size(); patternSet.nodes.resize(numberOfNodes); for (size_t
    //  nodeIndex = 0; nodeIndex < numberOfNodes; nodeIndex++) {
    //    patternSet.nodes[nodeIndex] =
    //        vcg::Point3d(nodes[nodeIndex][0], nodes[nodeIndex][1],0);
    //  }
    //  if (std::filesystem::exists(std::filesystem::path(resultsPath)
    //                                  .append("patterns.patt")
    //                                  .string())) {
    //    std::filesystem::remove(
    //        std::filesystem::path(resultsPath).append("patterns.patt"));
    //  }
    if (numberOfDesiredEdges == -1) {
        for (size_t numberOfEdges = 2; numberOfEdges <= validEdges.size(); numberOfEdges++) {
            std::cout << "Computing " + setupString << " with " << numberOfEdges << " edges."
                      << std::endl;

            auto perEdgeResultPath = std::filesystem::path(resultsPath)
                                         .append(std::to_string(numberOfEdges));
            if (std::filesystem::exists(perEdgeResultPath)) {
                //                if (debugIsOn) {
                std::filesystem::remove_all(perEdgeResultPath);

                //                } else {
                //                    continue;
                //                }
            }
            std::filesystem::create_directory(perEdgeResultPath);
            computeValidPatterns(numberOfNodesPerSlot,
                                 numberOfEdges,
                                 perEdgeResultPath,
                                 patternGeometryAllEdges.getVertices(),
                                 intersectingEdges,
                                 validEdges);
            statistics.print(setupString, perEdgeResultPath);
            statistics.reset();
        }
    } else {
        std::cout << "Computing " + setupString << " with " << numberOfDesiredEdges << " edges."
                  << std::endl;

        auto perEdgeResultPath = std::filesystem::path(resultsPath)
                                     .append(std::to_string(numberOfDesiredEdges));
        if (std::filesystem::exists(perEdgeResultPath)) {
            //            return;
            std::filesystem::remove_all(perEdgeResultPath);
        }
        std::filesystem::create_directory(perEdgeResultPath);
        computeValidPatterns(numberOfNodesPerSlot,
                             numberOfDesiredEdges,
                             perEdgeResultPath,
                             patternGeometryAllEdges.getVertices(),
                             intersectingEdges,
                             validEdges);
        statistics.print(setupString, perEdgeResultPath);
    }
}

void TopologyEnumerator::computeEdgeNodes(const std::vector<size_t> &numberOfNodesPerSlot,
                                          std::vector<size_t> &nodesEdge0,
                                          std::vector<size_t> &nodesEdge1,
                                          std::vector<size_t> &nodesEdge2)
{
    // Create vectors holding the node indices of each pattern node of each
    // triangle edge
    size_t nodeIndex = 0;
    if (numberOfNodesPerSlot[0] != 0) {
        nodesEdge0.push_back(nodeIndex++);
    }
    if (numberOfNodesPerSlot[1] != 0)
        nodesEdge1.push_back(nodeIndex++);
    if (numberOfNodesPerSlot[2] != 0)
        nodesEdge2.push_back(nodeIndex++);

    if (numberOfNodesPerSlot[3] != 0) {
        for (size_t edgeNodeIndex = 0; edgeNodeIndex < numberOfNodesPerSlot[3]; edgeNodeIndex++) {
            nodesEdge0.push_back(nodeIndex++);
        }
    }
    if (numberOfNodesPerSlot[4] != 0) {
        for (size_t edgeNodeIndex = 0; edgeNodeIndex < numberOfNodesPerSlot[4]; edgeNodeIndex++) {
            nodesEdge1.push_back(nodeIndex++);
        }
    }

    if (numberOfNodesPerSlot[5] != 0) {
        for (size_t edgeNodeIndex = 0; edgeNodeIndex < numberOfNodesPerSlot[5]; edgeNodeIndex++) {
            nodesEdge2.push_back(nodeIndex++);
        }
    }
    if (numberOfNodesPerSlot[1] != 0) {
        assert(numberOfNodesPerSlot[2]);
        nodesEdge0.push_back(1);
        nodesEdge1.push_back(2);
    }

    if (numberOfNodesPerSlot[0] != 0) {
        nodesEdge2.push_back(0);
    }
}

std::unordered_set<size_t> TopologyEnumerator::computeCoincideEdges(
    const std::vector<size_t> &numberOfNodesPerSlot)
{
    /*
   * A coincide edge is defined as an edge connection between two nodes that lay
   * on a triangle edge and which have another node in between
   * */
    std::vector<size_t> nodesEdge0; // left edge
    std::vector<size_t> nodesEdge1; // bottom edge
    std::vector<size_t> nodesEdge2; // right edge
    computeEdgeNodes(numberOfNodesPerSlot, nodesEdge0, nodesEdge1, nodesEdge2);

    std::vector<size_t> coincideEdges0 = getCoincideEdges(nodesEdge0);
    std::vector<size_t> coincideEdges1 = getCoincideEdges(nodesEdge1);
    std::vector<size_t> coincideEdges2 = getCoincideEdges(nodesEdge2);
    std::unordered_set<size_t> coincideEdges{coincideEdges0.begin(), coincideEdges0.end()};
    std::copy(coincideEdges1.begin(),
              coincideEdges1.end(),
              std::inserter(coincideEdges, coincideEdges.end()));
    std::copy(coincideEdges2.begin(),
              coincideEdges2.end(),
              std::inserter(coincideEdges, coincideEdges.end()));

    if (numberOfNodesPerSlot[0] && numberOfNodesPerSlot[1]) {
        coincideEdges.insert(getEdgeIndex(0, 2));
    }

    if (numberOfNodesPerSlot[0] && numberOfNodesPerSlot[2]) {
        assert(numberOfNodesPerSlot[1]);
        coincideEdges.insert(getEdgeIndex(0, 3));
    }

    return coincideEdges;
}

std::unordered_set<size_t> TopologyEnumerator::computeDuplicateEdges(
    const std::vector<size_t> &numberOfNodesPerSlot)
{
    /*
   * A duplicate edges are all edges the "right" edge since due to rotational
   * symmetry "left" edge=="right" edge
   * */
    std::unordered_set<size_t> duplicateEdges;
    std::vector<size_t> nodesEdge0; // left edge
    std::vector<size_t> nodesEdge1; // bottom edge
    std::vector<size_t> nodesEdge2; // right edge
    computeEdgeNodes(numberOfNodesPerSlot, nodesEdge0, nodesEdge1, nodesEdge2);
    if (numberOfNodesPerSlot[5]) {
        for (size_t edge2NodeIndex = 0; edge2NodeIndex < nodesEdge2.size() - 1; edge2NodeIndex++) {
            const size_t nodeIndex = nodesEdge2[edge2NodeIndex];
            const size_t nextNodeIndex = nodesEdge2[edge2NodeIndex + 1];
            duplicateEdges.insert(getEdgeIndex(nodeIndex, nextNodeIndex));
        }
    }

    return duplicateEdges;
}

std::vector<vcg::Point2i> TopologyEnumerator::getValidEdges(
    const std::vector<size_t> &numberOfNodesPerSlot,
    const std::filesystem::path &resultsPath,
    const PatternGeometry &patternGeometryAllEdges,
    const std::vector<vcg::Point2i> &allPossibleEdges)
{
    std::unordered_set<size_t> coincideEdges = computeCoincideEdges(numberOfNodesPerSlot);
    // Export each coincide edge into a ply file
    if (!coincideEdges.empty() && debugIsOn) {
        auto coincideEdgesPath = std::filesystem::path(resultsPath).append("Coincide_edges");
        std::filesystem::create_directories(coincideEdgesPath);
        for (auto coincideEdgeIndex : coincideEdges) {
            PatternGeometry::EdgeType e = patternGeometryAllEdges.edge[coincideEdgeIndex];
            PatternGeometry singleEdgeMesh;
            vcg::Point3d p0 = e.cP(0);
            vcg::Point3d p1 = e.cP(1);
            std::vector<vcg::Point3d> edgeVertices;
            edgeVertices.push_back(p0);
            edgeVertices.push_back(p1);
            singleEdgeMesh.add(edgeVertices);
            singleEdgeMesh.add(std::vector<vcg::Point2i>{vcg::Point2i{0, 1}});
            singleEdgeMesh.save(std::filesystem::path(coincideEdgesPath)
                                    .append(std::to_string(coincideEdgeIndex))
                                    .string()
                                + ".ply");
        }
    }
    statistics.numberOfCoincideEdges = coincideEdges.size();

    // Compute duplicate edges
    std::unordered_set<size_t> duplicateEdges = computeDuplicateEdges(numberOfNodesPerSlot);
    if (!duplicateEdges.empty() && debugIsOn) {
        // Export duplicate edges in a single ply file
        auto duplicateEdgesPath = std::filesystem::path(resultsPath).append("duplicate");
        std::filesystem::create_directory(duplicateEdgesPath);
        PatternGeometry patternDuplicateEdges;
        for (auto duplicateEdgeIndex : duplicateEdges) {
            PatternGeometry::EdgeType e = patternGeometryAllEdges.edge[duplicateEdgeIndex];
            vcg::Point3d p0 = e.cP(0);
            vcg::Point3d p1 = e.cP(1);
            vcg::tri::Allocator<PatternGeometry>::AddEdge(patternDuplicateEdges, p0, p1);
        }
        patternDuplicateEdges.save(
            std::filesystem::path(duplicateEdgesPath).append("duplicateEdges.ply").string());
    }
    statistics.numberOfDuplicateEdges = duplicateEdges.size();

    // Create the set of all possible edges without coincide and duplicate edges
    std::vector<vcg::Point2i> validEdges;
    for (size_t edgeIndex = 0; edgeIndex < allPossibleEdges.size(); edgeIndex++) {
        if (coincideEdges.count(edgeIndex) == 0 && duplicateEdges.count(edgeIndex) == 0) {
            validEdges.push_back(allPossibleEdges[edgeIndex]);
        }
    }

    return validEdges;
}

void TopologyEnumerator::exportPattern(const std::filesystem::path &saveToPath,
                                       PatternGeometry &patternGeometry,
                                       const bool saveTilledPattern) const
{
    const std::string patternName = patternGeometry.getLabel();
    std::filesystem::create_directory(saveToPath);
    patternGeometry.save(std::filesystem::path(saveToPath).append(patternName).string() + ".ply");
    if (saveTilledPattern) {
        PatternGeometry tiledPatternGeometry = PatternGeometry::createTile(patternGeometry);
        tiledPatternGeometry.save(
            std::filesystem::path(saveToPath).append(patternName + "_tiled").string() + ".ply");
    }
}

void TopologyEnumerator::computeValidPatterns(
    const std::vector<size_t> &numberOfNodesPerSlot,
    const size_t &numberOfDesiredEdges,
    const std::filesystem::path &resultsPath,
    const std::vector<vcg::Point3d> &allVertices,
    const std::unordered_map<size_t, std::unordered_set<size_t>> &intersectingEdges,
    const std::vector<vcg::Point2i> &validEdges)
{
    assert(numberOfNodesPerSlot.size() == 7);
    // Iterate over all patterns which have numberOfDesiredEdges edges from
    // from the validEdges Identify patterns that contain dangling edges
    const bool enoughValidEdgesExist = validEdges.size() >= numberOfDesiredEdges;
    if (!enoughValidEdgesExist) {
        std::filesystem::remove_all(resultsPath); // delete previous results folder
        return;
    }
    assert(enoughValidEdgesExist);

    // Create pattern result paths
    const auto validPatternsPath = std::filesystem::path(resultsPath).append("Valid");
    const bool validPathCreatedSuccesfully = std::filesystem::create_directories(validPatternsPath);
    assert(validPathCreatedSuccesfully && std::filesystem::exists(validPatternsPath));
    //  std::ofstream validPatternsFileStream;
    //  validPatternsFileStream.open(
    //      validPatternsPath.append("patterns.patt").string());
    const std::string compressedPatternsFilePath
        = std::filesystem::path(validPatternsPath).append("patterns.patt").string();
    PatternIO::PatternSet patternSet;
    patternSet.nodes = allVertices;
    const int patternSetBufferSize = 10000;

    const size_t numberOfPatterns = PatternGeometry::binomialCoefficient(validEdges.size(),
                                                                         numberOfDesiredEdges);
    statistics.numberOfPatterns = numberOfPatterns;

    // Initialize pattern binary representation
    std::string patternBinaryRepresentation;
    patternBinaryRepresentation = std::string(numberOfDesiredEdges, '1');
    patternBinaryRepresentation += std::string(validEdges.size() - numberOfDesiredEdges, '0');
    std::sort(patternBinaryRepresentation.begin(), patternBinaryRepresentation.end());
    /*TODO: Performance could be improved by changing the patternGeometry with
   * respect to the previous one. Maybe I could xor the binaryRepresentation
   * to the previous one.*/
    //  std::string previousPatternBinaryRepresentation(validEdges.size(),'0');
    size_t patternIndex = 0;
    bool validPatternsExist = false;
    const bool exportTilledPattern = debugIsOn;
    const bool saveCompressedFormat = false;
    do {
        patternIndex++;
        const std::string patternName = std::to_string(patternIndex);
        //    std::cout << "Pattern name:" + patternBinaryRepresentation <<
        //    std::endl; isValidPattern(patternBinaryRepresentation, validEdges,
        //                   numberOfDesiredEdges);
        // Create the geometry of the pattern
        // Compute the pattern edges from the binary representation
        std::vector<vcg::Point2i> patternEdges(numberOfDesiredEdges);
        size_t patternEdgeIndex = 0;
        for (size_t validEdgeIndex = 0; validEdgeIndex < patternBinaryRepresentation.size();
             validEdgeIndex++) {
            if (patternBinaryRepresentation[validEdgeIndex] == '1') {
                assert(patternEdgeIndex < numberOfDesiredEdges);
                patternEdges[patternEdgeIndex++] = validEdges[validEdgeIndex];
            }
        }

        PatternGeometry patternGeometry;
        patternGeometry.add(allVertices, patternEdges);
        patternGeometry.setLabel(patternName);

        // Check if pattern contains intersecting edges
        const bool patternContainsIntersectingEdges
            = patternGeometry.hasIntersectingEdges(patternBinaryRepresentation, intersectingEdges);
        // Export the tiled ply file if it contains intersecting edges
        if (patternContainsIntersectingEdges) {
            // create the tiled geometry of the pattern
            statistics.numberOfPatternsWithIntersectingEdges++;
            if (debugIsOn) {
                if (savePlyFiles) {
                    exportPattern(std::filesystem::path(resultsPath).append("Intersecting"),
                                  patternGeometry,
                                  exportTilledPattern);
                }
            } else {
                continue; // should be uncommented in order to improve performance
            }
        }

        const bool tiledPatternHasEdgesWithAngleSmallerThanThreshold
            = patternGeometry.hasAngleSmallerThanThreshold(numberOfNodesPerSlot, 15);
        if (tiledPatternHasEdgesWithAngleSmallerThanThreshold) {
            statistics.numberOfPatternsViolatingAngleThreshold++;
            if (debugIsOn /*|| savePlyFiles*/) {
                if (savePlyFiles) {
                    exportPattern(std::filesystem::path(resultsPath)
                                      .append("ExceedingAngleThreshold"),
                                  patternGeometry,
                                  exportTilledPattern);
                }
            } else {
                continue;
            }
        }

        const bool tiledPatternHasNodeWithValenceGreaterThanDesired
            = patternGeometry.hasValenceGreaterThan(numberOfNodesPerSlot, 6);
        if (tiledPatternHasNodeWithValenceGreaterThanDesired) {
            statistics.numberOfPatternsViolatingValenceThreshold++;
            if (debugIsOn) {
                if (savePlyFiles) {
                    auto highValencePath = std::filesystem::path(resultsPath)
                                               .append("HighValencePatterns");
                    exportPattern(highValencePath, patternGeometry, exportTilledPattern);
                }
            } else {
                continue;
            }
        }

        // Compute the tiled valence
        const bool tiledPatternHasDanglingEdges = patternGeometry.hasDanglingEdges(
            numberOfNodesPerSlot); // marks the nodes with valence>=1
                                   // Create the tiled geometry of the pattern
        const bool hasFloatingComponents = !patternGeometry.isFullyConnectedWhenTiled();

        PatternGeometry fanPatternGeometry = PatternGeometry::createFan(patternGeometry);
        const int interfaceNodeVi = 3;
        std::vector<PatternGeometry::EdgeType *> connectedEdges;
        vcg::edge::VEStarVE(&fanPatternGeometry.vert[interfaceNodeVi], connectedEdges);
        if (!connectedEdges.empty()) {
            for (int i = 1; i < 6; i++) {
                vcg::tri::Allocator<PatternGeometry>::AddEdge(fanPatternGeometry,
                                                              interfaceNodeVi
                                                                  + (i - 1) * patternGeometry.VN(),
                                                              interfaceNodeVi
                                                                  + i * patternGeometry.VN());
            }
        }
        vcg::tri::Clean<PatternGeometry>::MergeCloseVertex(fanPatternGeometry, 0.0000005);
        vcg::tri::Allocator<PatternGeometry>::CompactEveryVector(fanPatternGeometry);
        vcg::tri::UpdateTopology<PatternGeometry>::VertexEdge(fanPatternGeometry);
        vcg::tri::UpdateTopology<PatternGeometry>::EdgeEdge(fanPatternGeometry);
        //        for (PatternGeometry::VertexType &v : tilledPatternGeometry.vert) {
        //            std::vector<PatternGeometry::EdgeType *> connectedEdges;
        //            vcg::edge::VEStarVE(&v, connectedEdges);
        //            if (connectedEdges.size() == 1) {
        //                vcg::tri::Allocator<PatternGeometry>::DeleteVertex(tilledPatternGeometry, v);
        //                vcg::tri::Allocator<PatternGeometry>::DeleteEdge(tilledPatternGeometry,
        //                                                                 *connectedEdges[0]);
        //            }
        //        }
        //        //        vcg::tri::Allocator<PatternGeometry>::CompactEveryVector(tilledPatternGeometry);
        //        fanPatternGeometry.updateEigenEdgeAndVertices();

        BoostGraph fanPatternGraph(fanPatternGeometry.VN());
        //        std::cout << "Edges:";
        for (const PatternGeometry::EdgeType &e : fanPatternGeometry.edge) {
            if (e.IsD() || e.cV(0)->IsD() || e.cV(1)->IsD()) {
                continue;
            }
            const int vi0 = fanPatternGeometry.getIndex(e.cV(0));
            const int vi1 = fanPatternGeometry.getIndex(e.cV(1));
            boost::add_edge(vi0, vi1, fanPatternGraph);
            //            std::cout << vi0 << "," << vi1 << " ";
        }
        //        std::cout << std::endl;

        std::vector<vertex_t> articulationPoints;
        boost::articulation_points(fanPatternGraph, std::back_inserter(articulationPoints));
        const bool hasArticulationPoints = !articulationPoints.empty();
        //        if (hasArticulationPoints /*&& !patternContainsIntersectingEdges
        //            && !tiledPatternHasDanglingEdges && !hasFloatingComponents
        //            && !tiledPatternHasNodeWithValenceGreaterThanDesired
        //            && !tiledPatternHasEdgesWithAngleSmallerThanThreshold*/) {
        //            for (PatternGeometry::VertexType &v : patternGeometry.vert) {
        //                v.C() = vcg::Color4b::Yellow;
        //            }
        //            //            std::cout << "AP:";
        //            for (const int articulationPointVi : articulationPoints) {
        //                if (articulationPointVi >= patternGeometry.VN()) {
        //                    continue;
        //                }
        //                //                std::cout << articulationPointVi << " ";
        //                patternGeometry.vert[articulationPointVi].C() = vcg::Color4b::Red;
        //            }
        //            PatternGeometry tilledPatternGeometry = PatternGeometry::createTile(patternGeometry);
        //            //            std::cout << std::endl;
        //            std::vector<glm::vec3> fanVertexColors(tilledPatternGeometry.VN(), glm::vec3(0, 0, 1));
        //            for (const PatternGeometry::VertexType &v : tilledPatternGeometry.vert) {
        //                const auto vColor = glm::vec3(v.cC()[0] / 255, v.cC()[1] / 255, v.cC()[2] / 255);
        //                const auto vi = tilledPatternGeometry.getIndex(v);
        //                fanVertexColors[vi] = vColor;
        //            }
        //            //            tilledPatternGeometry.updateEigenEdgeAndVertices();
        //            //            tilledPatternGeometry.registerForDrawing()
        //            //                ->addNodeColorQuantity("ap_tilled", fanVertexColors)
        //            //                ->setEnabled(true);
        //            //            polyscope::show();
        //            //            tilledPatternGeometry.unregister();
        //        }
        // duplicated here
        // Check dangling edges with vcg method
        //    const bool vcg_tiledPatternHasDangling =
        //        tiledPatternGeometry.hasUntiledDanglingEdges();
        if (tiledPatternHasDanglingEdges /*&& !hasFloatingComponents && !hasArticulationPoints*/) {
            statistics.numberOfPatternsWithADanglingEdgeOrNode++;
            if (debugIsOn) {
                if (savePlyFiles) {
                    auto danglingEdgesPath = std::filesystem::path(resultsPath).append("Dangling");
                    exportPattern(danglingEdgesPath, patternGeometry, exportTilledPattern);
                }
            } else {
                continue;
            }
        }

        if (hasFloatingComponents /*&& !hasArticulationPoints && !tiledPatternHasDanglingEdges */) {
            statistics.numberOfPatternsWithMoreThanASingleCC++;
            if (debugIsOn) {
                if (savePlyFiles) {
                    auto moreThanOneCCPath = std::filesystem::path(resultsPath)
                                                 .append("MoreThanOneCC");
                    std::filesystem::create_directory(moreThanOneCCPath);
                    patternGeometry.save(
                        std::filesystem::path(moreThanOneCCPath).append(patternName).string()
                        + ".ply");
                    PatternGeometry tiledPatternGeometry = PatternGeometry::createTile(
                        patternGeometry); // the marked nodes of hasDanglingEdges are

                    std::vector<std::pair<int, PatternGeometry::EdgePointer>> eCC;
                    vcg::tri::Clean<PatternGeometry>::edgeMeshConnectedComponents(tiledPatternGeometry,
                                                                                  eCC);
                    vcg::tri::UpdateFlags<PatternGeometry>::EdgeClear(tiledPatternGeometry);
                    const size_t numberOfCC_edgeBased = eCC.size();
                    std::sort(eCC.begin(),
                              eCC.end(),
                              [](const std::pair<int, PatternGeometry::EdgePointer> &a,
                                 const std::pair<int, PatternGeometry::EdgePointer> &b) {
                                  return a.first > b.first;
                              });

                    PatternGeometry::EdgePointer &ep = eCC[0].second;
                    size_t colorsRegistered = 0;
                    std::stack<EdgePointer> stack;
                    stack.push(ep);
                    while (!stack.empty()) {
                        EdgePointer ep = stack.top();
                        stack.pop();

                        for (int i = 0; i < 2; ++i) {
                            vcg::edge::VEIterator<PatternGeometry::EdgeType> vei(ep->V(i));
                            while (!vei.End()) {
                                if (!vei.E()->IsV()) {
                                    vei.E()->SetV();
                                    stack.push(vei.E());
                                    tiledPatternGeometry
                                        .vert[tiledPatternGeometry.getIndex(vei.V1())]
                                        .C()
                                        = vcg::Color4b::Blue;
                                    tiledPatternGeometry
                                        .vert[tiledPatternGeometry.getIndex(vei.V0())]
                                        .C()
                                        = vcg::Color4b::Blue;
                                    colorsRegistered++;
                                }
                                ++vei;
                            }
                        }
                    }

                    assert(colorsRegistered == eCC[0].first);

                    if (exportTilledPattern) {
                        tiledPatternGeometry.save(std::filesystem::path(moreThanOneCCPath)
                                                      .append(patternName + "_tiled")
                                                      .string()
                                                  + ".ply");
                    }
                }
            } else {
                continue;
            }
        }

        if (hasArticulationPoints /*&& !hasFloatingComponents && !tiledPatternHasDanglingEdges */) {
            statistics.numberOfPatternsWithArticulationPoints++;
            if (debugIsOn) {
                if (savePlyFiles) {
                    auto articulationPointsPath = std::filesystem::path(resultsPath)
                                                      .append("ArticulationPoints");
                    exportPattern(articulationPointsPath, patternGeometry, exportTilledPattern);
                }
            } else {
                continue;
            }
        }

        const bool isValidPattern = !patternContainsIntersectingEdges
                                    && !tiledPatternHasDanglingEdges && !hasFloatingComponents
                                    && !hasArticulationPoints
                                    && !tiledPatternHasNodeWithValenceGreaterThanDesired
                                    && !tiledPatternHasEdgesWithAngleSmallerThanThreshold;
        if (isValidPattern) {
            //        if(patternName=='2055'){
            //            PatternGeometry tiledPatternGeometry = PatternGeometry::createTile(
            //                patternGeometry); // the marked nodes of hasDanglingEdges are
            //            tiledPatternGeometry.registerForDrawing(std::array<double, 3>{0, 0, 1});
            //            polyscope::show();
            //            tiledPatternGeometry.unregister();
            //            }
            statistics.numberOfValidPatterns++;
            validPatternsExist = true;
            if (savePlyFiles) {
                exportPattern(validPatternsPath, patternGeometry, exportTilledPattern);
            }
            if (saveCompressedFormat) {
                PatternIO::Pattern pattern;
                pattern.edges = patternEdges;
                pattern.name = patternIndex;
                patternSet.patterns.emplace_back(pattern);
                // Save valid patterns
                //            if (patternIndex% patternSetBufferSize == 0) {
                if (statistics.numberOfValidPatterns % patternSetBufferSize == 0) {
                    PatternIO::save(compressedPatternsFilePath, patternSet);
                    patternSet.patterns.clear();
                    patternSet.patterns.reserve(patternSetBufferSize);
                }
            }
        }

        //    assert(vcg_tiledPatternHasDangling == tiledPatternHasDanglingEdges);
    } while (std::next_permutation(patternBinaryRepresentation.begin(),
                                   patternBinaryRepresentation.end()));
    if (!patternSet.patterns.empty() && saveCompressedFormat) {
        PatternIO::save(compressedPatternsFilePath, patternSet);
    }

    if (!validPatternsExist) {
        std::filesystem::remove_all(validPatternsPath);
        if (!debugIsOn) {
            std::filesystem::remove_all(resultsPath);
        }
    }
}

std::vector<size_t> TopologyEnumerator::getCoincideEdges(
    const std::vector<size_t> &edgeNodeIndices) const
{
    std::vector<size_t> coincideEdges;
    if (edgeNodeIndices.size() < 3)
        return coincideEdges;
    for (size_t edgeNodeIndex = 0; edgeNodeIndex < edgeNodeIndices.size() - 2; edgeNodeIndex++) {
        const size_t &firstNodeIndex = edgeNodeIndices[edgeNodeIndex];
        for (size_t secondEdgeNodeIndex = edgeNodeIndex + 2;
             secondEdgeNodeIndex < edgeNodeIndices.size();
             secondEdgeNodeIndex++) {
            const size_t &secondNodeIndex = edgeNodeIndices[secondEdgeNodeIndex];
            coincideEdges.push_back(getEdgeIndex(firstNodeIndex, secondNodeIndex));
        }
    }
    return coincideEdges;
}

bool TopologyEnumerator::isValidPattern(const std::string &patternBinaryRepresentation,
                                        const std::vector<vcg::Point2i> &validEdges,
                                        const size_t &numberOfDesiredEdges) const
{
    return true;
}