density_clustering.hpp

/*
Copyright (c) 2015, Florian Sittel (www.lettis.net)
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

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2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

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SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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*/

#pragma once

#include <vector>
#include <map>
#include <set>
#include <array>
#include <utility>
#include <string>

#include <boost/program_options.hpp>

#include "tools.hpp"

namespace Clustering {
  namespace Density {
    using FreeEnergy = std::pair<std::size_t, float>;
    using Neighbor = Clustering::Tools::Neighbor;
    using Neighborhood = Clustering::Tools::Neighborhood;
    using Box = std::array<int, 2>;
    constexpr int BOX_DIFF[9][2] = {{-1, 1}, { 0, 1}, { 1, 1}
                                  , {-1, 0}, { 0, 0}, { 1, 0}
                                  , {-1,-1}, { 0,-1}, { 1,-1}};
    const int N_NEIGHBOR_BOXES = 9;
//    //! encodes box differences in 3D, i.e. if you are at
//    //! the center box, the 27 different tuples hold the steppings
//    //! to the 27 spacial neighbors (including the center box itself).
//    constexpr int BOX_DIFF[27][3] = {{-1, 1,-1}, { 0, 1,-1}, { 1, 1,-1}
//                                   , {-1, 0,-1}, { 0, 0,-1}, { 1, 0,-1}
//                                   , {-1,-1,-1}, { 0,-1,-1}, { 1,-1,-1}
//                                   , {-1, 1, 0}, { 0, 1, 0}, { 1, 1, 0}
//                                   , {-1, 0, 0}, { 0, 0, 0}, { 1, 0, 0}
//                                   , {-1,-1, 0}, { 0,-1, 0}, { 1,-1, 0}
//                                   , {-1, 1, 1}, { 0, 1, 1}, { 1, 1, 1}
//                                   , {-1, 0, 1}, { 0, 0, 1}, { 1, 0, 1}
//                                   , {-1,-1, 1}, { 0,-1, 1}, { 1,-1, 1}};
//    //! number of neigbor boxes in cubic 3D grid (including center box).
//    const int N_NEIGHBOR_BOXES = 27;
    struct BoxGrid {
      std::vector<int> n_boxes;
      std::vector<Box> assigned_box;
      std::map<Box, std::vector<int>> boxes;
    };
    constexpr Box
    neighbor_box(const Box center, const int i_neighbor);
    BoxGrid
    compute_box_grid(const float* coords,
                     const std::size_t n_rows,
                     const std::size_t n_cols,
                     const float radius);
    bool
    is_valid_box(const Box box,
                 const BoxGrid& grid);
    std::vector<std::size_t>
    calculate_populations(const float* coords,
                          const std::size_t n_rows,
                          const std::size_t n_cols,
                          const float radius);
    std::map<float, std::vector<std::size_t>>
    calculate_populations(const float* coords,
                          const std::size_t n_rows,
                          const std::size_t n_cols,
                          const std::vector<float> radii);
    std::vector<float>
    calculate_free_energies(const std::vector<std::size_t>& pops);
    std::vector<FreeEnergy>
    sorted_free_energies(const std::vector<float>& fe);
    std::tuple<Neighborhood, Neighborhood>
    nearest_neighbors(const float* coords,
                      const std::size_t n_rows,
                      const std::size_t n_cols,
                      const std::vector<float>& free_energy);
    std::set<std::size_t>
    high_density_neighborhood(const float* coords,
                              const std::size_t n_cols,
                              const std::vector<FreeEnergy>& sorted_fe,
                              const std::size_t i_frame,
                              const std::size_t limit,
                              const float max_dist);
    double
    compute_sigma2(const Neighborhood& nh);
    std::vector<std::size_t>
    assign_low_density_frames(const std::vector<std::size_t>& initial_clustering,
                              const Neighborhood& nh_high_dens,
                              const std::vector<float>& free_energy);
    void
    main(boost::program_options::variables_map args);
  } // end namespace Density
} // end namespace Clustering