#include <mlpack/core.hpp>
#include <mlpack/methods/neighbor_search/neighbor_search.hpp>
#include <mlpack/methods/hdbscan/hdbscan.hpp>
#include <mlpack/core/tree/cover_tree.hpp>
#include <iostream>
#include <math.h>

using namespace mlpack;
using namespace mlpack::neighbor; // NeighborSearch and NearestNeighborSort
using namespace mlpack::metric;
using namespace mlpack::hdbscan;
using namespace std;

// HDBSCAN metric is defined as :
template<>
template<typename VecTypeA, typename VecTypeB>
double HdbscanDistance::Evaluate(
    const VecTypeA& a,
    const VecTypeB& b)
{
  double dcoreA = a(a.n_rows-1);
  double dcoreB = b(b.n_rows-1);
  typename VecTypeB::elem_type dist = sqrt(arma::accu(arma::square(a - b) - (dcoreA - dcoreB)*(dcoreA - dcoreB)));

  double temp = std::max(std::max(dcoreA, dcoreB), dist);
  return temp;
}

int main()
{
	arma::mat dataSynthetic1;

    data::Load("manyPatches.csv", dataSynthetic1, true);
    dataSynthetic1.resize(dataSynthetic1.n_rows-1, dataSynthetic1.n_cols);
    neighbor::NeighborSearch<neighbor::NearestNeighborSort , metric::EuclideanDistance> neighborSearch;
    arma::Mat<size_t> neighbors;
    arma::mat distances;
    neighborSearch.Train(dataSynthetic1);
    neighborSearch.Search(5, neighbors, distances);
    arma::mat dataWithDcore = arma::conv_to<arma::mat>::from(dataSynthetic1);
    dataWithDcore.resize(dataWithDcore.n_rows+1, dataWithDcore.n_cols);
    dataWithDcore.row(dataWithDcore.n_rows-1) = distances.row(distances.n_rows-1);

    std::cout<<"\nPoint 1741 is : \n";
    dataWithDcore.col(1741).print();
    std::cout<<"\nPoint 1734 is : \n";
    dataWithDcore.col(1734).print();
    std::cout<<"\nPoint 1729 is : \n";
    dataWithDcore.col(1729).print();
    std::cout<<"\nPoint 1731 is : \n";
    dataWithDcore.col(1731).print();
    std::cout<<"\nPoint 1744 is : \n";
    dataWithDcore.col(1744).print();
    std::cout<<"\nPoint 1727 is : \n";
    dataWithDcore.col(1727).print();
    std::cout<<"\nResultant mst is : \n";

    metric::HdbscanDistance h;
    emst::DualTreeBoruvka<metric::HdbscanDistance, arma::mat, tree::KDTree> dtb(dataWithDcore, false, h);
    arma::mat resultsMST;
    dtb.ComputeMST(resultsMST);
    resultsMST = trans(resultsMST);
    resultsMST.print();
}

First few lines of output are:
Point 1741 is :
   3.0503e+02
   4.0717e+02
   2.5126e+00

Point 1734 is :
   3.0529e+02
   4.0621e+02
   2.4534e+00

Point 1729 is :
   3.0286e+02
   4.0592e+02
   2.5126e+00

Point 1731 is :
   3.0332e+02
   4.0598e+02
   2.5770e+00

Point 1744 is :
   3.0471e+02
   4.0751e+02
   2.6024e+00

Point 1727 is :
   3.0600e+02
   4.0525e+02
   3.2150e+00

Distance between 1729 and 1734 : 2.51258

Distance between 1729 and 1731 : 2.577

Resultant mst is :
   1.7340e+03   1.7410e+03   2.5126e+00
   1.7290e+03   1.7310e+03   2.5770e+00 	//Shouldn't this be 1729 and 1734 ??
   1.7310e+03   1.7340e+03   2.5770e+00
   1.7340e+03   1.7440e+03   2.6024e+00
   1.7270e+03   1.7340e+03   3.2150e+00
   2.5920e+03   2.6040e+03   3.3885e+00
   2.6030e+03   2.6040e+03   3.3885e+00