Rcpp::List RadiusSearch(Rcpp::NumericMatrix query_,
Rcpp::NumericMatrix ref_,
double radius,
int max_neighbour,
std::string build,
int cores,
int checks) {
const std::size_t n_dim = query_.ncol();
const std::size_t n_query = query_.nrow();
const std::size_t n_ref = ref_.nrow();
// Column major to row major
arma::mat query(n_dim, n_query);
{
arma::mat temp_q(query_.begin(), n_query, n_dim, false);
query = arma::trans(temp_q);
}
flann::Matrix<double> q_flann(query.memptr(), n_query, n_dim);
arma::mat ref(n_dim, n_ref);
{
arma::mat temp_r(ref_.begin(), n_ref, n_dim, false);
ref = arma::trans(temp_r);
}
flann::Matrix<double> ref_flann(ref.memptr(), n_ref, n_dim);
// Setting the flann index params
flann::IndexParams params;
if (build == "kdtree") {
params = flann::KDTreeSingleIndexParams(1);
} else if (build == "kmeans") {
params = flann::KMeansIndexParams(2, 10, flann::FLANN_CENTERS_RANDOM, 0.2);
} else if (build == "linear") {
params = flann::LinearIndexParams();
}
// Perform the radius search
flann::Index<flann::L2<double> > index(ref_flann, params);
index.buildIndex();
std::vector< std::vector<int> >
indices_flann(n_query, std::vector<int>(max_neighbour));
std::vector< std::vector<double> >
dists_flann(n_query, std::vector<double>(max_neighbour));
flann::SearchParams search_params;
search_params.cores = cores;
search_params.checks = checks;
search_params.max_neighbors = max_neighbour;
index.radiusSearch(q_flann, indices_flann, dists_flann, radius,
search_params);
return Rcpp::List::create(Rcpp::Named("indices") = indices_flann,
Rcpp::Named("distances") = dists_flann);
}
void qr<T>::output(array_2d<T>& q, array_2d<T>& r) const
{
array<T> tau(min_nm);
if(r.rows() != m || r.columns() != n)
r.resize(idx(m, n));
lapack_interface<T>::call_lapack_geqrf(r, tau, a);
//Now construct Q
//Q should be a MxM matrix
if(q.rows() != m || q.columns() != m)
q.resize(idx(m, m));
if(n <= m) {
//Q can hold the MxN values of R needed by lapack's xORGQR routines
for(size_t i = 0; i < m; i++)
for(size_t j = 0; j < n; j++)
q[m*j + i] = r(i,j);
lapack_interface<T>::call_lapack_orgqr(q, tau);
} else {
//create a new array and do a copy since
//Q cannot hold the MxN values of R as needed by lapack's xORGQR routines
array_2d<T> temp_q(r(all(), size_range(0, m - 1)));
lapack_interface<T>::call_lapack_orgqr(temp_q, tau);
//copy the Q values from temp
for(size_t i = 0; i < m; i++)
for(size_t j = 0; j < m; j++)
q[m*j + i] = temp_q[m*j + i];
}
// R is upper triangular
for(size_t i = 0; i < m; i++)
for(size_t j = 0; j < n; j++)
if(i > j)
r(i,j) = 0;
}