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diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps_exact.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps_exact.h new file mode 100644 index 00000000..25f8cb47 --- /dev/null +++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps_exact.h @@ -0,0 +1,125 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Mathieu Carriere + * + * Copyright (C) 2018 INRIA (France) + * + * 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/>. + */ + +#ifndef PERSISTENCE_HEAT_MAPS_EXACT_H_ +#define PERSISTENCE_HEAT_MAPS_EXACT_H_ + +// gudhi include +#include <gudhi/read_persistence_from_file.h> +#include <gudhi/common_persistence_representations.h> +#include <gudhi/Weight_functions.h> +#include <gudhi/Debug_utils.h> + +// standard include +#include <cmath> +#include <iostream> +#include <vector> +#include <limits> +#include <fstream> +#include <sstream> +#include <algorithm> +#include <string> +#include <utility> +#include <functional> + +namespace Gudhi { +namespace Persistence_representations { + +/** + * \class Persistence_heat_maps_exact gudhi/Persistence_heat_maps_exact.h + * \brief A class implementing exact persistence heat maps. + * + * \ingroup Persistence_representations + * + * \details + * + * In this class, we propose a way to approximate persistence heat maps, or persistence surfaces, by centering weighted Gaussians on each point of the persistence diagram, and evaluating these (exact) weighted Gaussian functions + * on the pixels of a 2D grid. Note that this scheme is different from the one proposed in Persistence_heat_maps, which first maps the points of the diagram to a 2D grid, and then evaluates the (approximate) weighted Gaussian functions. + * Hence, the difference is that we do not modify the diagram in this implementation, but the code can be slower to run. +**/ + +class Persistence_heat_maps_exact { + + protected: + Persistence_diagram diagram; + int res_x, res_y; + double min_x, max_x, min_y, max_y; + Weight weight; + double sigma; + + public: + + /** \brief Persistence_heat_maps_exact constructor. + * \ingroup Persistence_heat_maps_exact + * + * @param[in] _diagram persistence diagram. + * @param[in] _min_x minimum value of pixel abscissa. + * @param[in] _max_x maximum value of pixel abscissa. + * @param[in] _res_x number of pixels for the x-direction. + * @param[in] _min_y minimum value of pixel ordinate. + * @param[in] _max_y maximum value of pixel ordinate. + * @param[in] _res_y number of pixels for the y-direction. + * @param[in] _weight weight function for the Gaussians. + * @param[in] _sigma bandwidth parameter for the Gaussians. + * + */ + Persistence_heat_maps_exact(const Persistence_diagram & _diagram, double _min_x = 0.0, double _max_x = 1.0, int _res_x = 10, double _min_y = 0.0, double _max_y = 1.0, int _res_y = 10, const Weight & _weight = arctan_weight(1,1), double _sigma = 1.0){ + diagram = _diagram; min_x = _min_x; max_x = _max_x; res_x = _res_x; min_y = _min_y; max_y = _max_y; res_y = _res_y, weight = _weight; sigma = _sigma; + } + + /** \brief Computes the persistence image of a diagram. + * \ingroup Persistence_heat_maps_exact + * + */ + std::vector<std::vector<double> > vectorize() const { + std::vector<std::vector<double> > im; for(int i = 0; i < res_y; i++) im.emplace_back(); + double step_x = (max_x - min_x)/res_x; double step_y = (max_y - min_y)/res_y; + + int num_pts = diagram.size(); + + for(int i = 0; i < res_y; i++){ + double y = min_y + i*step_y; + for(int j = 0; j < res_x; j++){ + double x = min_x + j*step_x; + + double pixel_value = 0; + for(int k = 0; k < num_pts; k++){ + double px = diagram[k].first; double py = diagram[k].second; + pixel_value += weight(std::pair<double,double>(px,py)) * std::exp( -((x-px)*(x-px) + (y-(py-px))*(y-(py-px))) / (2*sigma*sigma) ) / (sigma*std::sqrt(2*pi)); + } + im[i].push_back(pixel_value); + + } + } + + return im; + + } + + + + +}; // class Persistence_heat_maps_exact +} // namespace Persistence_representations +} // namespace Gudhi + +#endif // PERSISTENCE_HEAT_MAPS_EXACT_H_ |