save state; test clustering not OK, all others OK

[epclust.git] / epclust / src / computeMedoidsIndices.cpp

#include <Rcpp.h>

// [[Rcpp::depends(BH, bigmemory)]]
#include <bigmemory/MatrixAccessor.hpp>

#include <numeric>
#include <cfloat>

using namespace Rcpp;

//' computeMedoidsIndices
//'
//' Compute medoids indices
//'
//' @param pMedoids External pointer
//' @param ref_series reference series
//'
//' @return A map serie number -> medoid index
// [[Rcpp::export]]
IntegerVector computeMedoidsIndices(SEXP pMedoids, NumericMatrix ref_series)
{
	XPtr<BigMatrix> pMed(pMedoids);
	MatrixAccessor<double> medoids = MatrixAccessor<double>(*pMed);
	int nb_series = ref_series.ncol(),
		K = pMed->ncol(),
		L = pMed->nrow();
	IntegerVector mi(nb_series);

	for (int i=0; i<nb_series ; i++)
	{
		// mi[i] <- which.min( rowSums( sweep(medoids, 2, ref_series[i,], '-')^2 ) )
		mi[i] = 0;
		double best_dist = DBL_MAX;
		for (int j=0; j<K; j++)
		{
			double dist_ij = 0.;
			for (int k=0; k<L; k++)
			{
				double delta = ref_series(k,i) - *(medoids[j]+k);
				dist_ij += delta * delta;
			}
			if (dist_ij < best_dist)
			{
				mi[i] = j+1; //R indices start at 1
				best_dist = dist_ij;
			}
		}
	}

	return mi;
}