euclidean_kmeans.hpp

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#ifndef GENESIS_UTILS_MATH_EUCLIDEAN_KMEANS_H_
#define GENESIS_UTILS_MATH_EUCLIDEAN_KMEANS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 Lucas Czech and HITS gGmbH
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include "genesis/utils/math/kmeans.hpp"
 
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <functional>
#include <limits>
#include <random>
#include <stdexcept>
#include <string>
#include <unordered_set>
#include <utility>
#include <vector>
 
#ifdef GENESIS_OPENMP
#   include <omp.h>
#endif
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Euclidean K-Means Specialization
// =================================================================================================
 
class EuclideanKmeans
    : public Kmeans< std::vector<double> >
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Constants
    // -------------------------------------------------------------------------
 
    using Point = std::vector<double>;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    EuclideanKmeans( size_t dimensions );
    virtual ~EuclideanKmeans() override = default;
 
    EuclideanKmeans( EuclideanKmeans const& ) = default;
    EuclideanKmeans( EuclideanKmeans&& )      = default;
 
    EuclideanKmeans& operator= ( EuclideanKmeans const& ) = default;
    EuclideanKmeans& operator= ( EuclideanKmeans&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Default K-Means Functions
    // -------------------------------------------------------------------------
 
private:
 
    virtual bool data_validation( std::vector<Point> const& data ) const override;
 
    virtual void update_centroids(
        std::vector<Point>  const& data,
        std::vector<size_t> const& assignments,
        std::vector<Point>&        centroids
    ) override;
 
    virtual double distance( Point const& lhs, Point const& rhs ) const override;
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    size_t dimensions_;
 
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard