From 9899ae167f281d10b1684dfcd02c6838c5bf28df Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 2 Feb 2018 13:51:45 +0100 Subject: GUDHI 2.1.0 as released by upstream in a tarball. --- include/gudhi/PSSK.h | 168 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 168 insertions(+) create mode 100644 include/gudhi/PSSK.h (limited to 'include/gudhi/PSSK.h') diff --git a/include/gudhi/PSSK.h b/include/gudhi/PSSK.h new file mode 100644 index 00000000..630f5623 --- /dev/null +++ b/include/gudhi/PSSK.h @@ -0,0 +1,168 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 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 . + */ + +#ifndef PSSK_H_ +#define PSSK_H_ + +// gudhi include +#include + +#include +#include +#include + +namespace Gudhi { +namespace Persistence_representations { + +/** +* This is a version of a representation presented in https://arxiv.org/abs/1412.6821 +* In that paper the authors are using the representation just to compute kernel. Over here, we extend the usability by +*far. +* Note that the version presented here is not exact, since we are discretizing the kernel. +* The only difference with respect to the original class is the method of creation. We have full (square) image, and for +*every point (p,q), we add a kernel at (p,q) and the negative kernel +* at (q,p) +**/ + +class PSSK : public Persistence_heat_maps { + public: + PSSK() : Persistence_heat_maps() {} + + PSSK(const std::vector >& interval, + std::vector > filter = create_Gaussian_filter(5, 1), size_t number_of_pixels = 1000, + double min_ = -1, double max_ = -1) + : Persistence_heat_maps() { + this->construct(interval, filter, number_of_pixels, min_, max_); + } + + PSSK(const char* filename, std::vector > filter = create_Gaussian_filter(5, 1), + size_t number_of_pixels = 1000, double min_ = -1, double max_ = -1, + unsigned dimension = std::numeric_limits::max()) + : Persistence_heat_maps() { + std::vector > intervals_; + if (dimension == std::numeric_limits::max()) { + intervals_ = read_persistence_intervals_in_one_dimension_from_file(filename); + } else { + intervals_ = read_persistence_intervals_in_one_dimension_from_file(filename, dimension); + } + this->construct(intervals_, filter, number_of_pixels, min_, max_); + } + + protected: + void construct(const std::vector >& intervals_, + std::vector > filter = create_Gaussian_filter(5, 1), + size_t number_of_pixels = 1000, double min_ = -1, double max_ = -1); +}; + +// if min_ == max_, then the program is requested to set up the values itself based on persistence intervals +void PSSK::construct(const std::vector >& intervals_, + std::vector > filter, size_t number_of_pixels, double min_, double max_) { + bool dbg = false; + if (dbg) { + std::cerr << "Entering construct procedure \n"; + getchar(); + } + + if (min_ == max_) { + // in this case, we want the program to set up the min_ and max_ values by itself. + min_ = std::numeric_limits::max(); + max_ = -std::numeric_limits::max(); + + for (size_t i = 0; i != intervals_.size(); ++i) { + if (intervals_[i].first < min_) min_ = intervals_[i].first; + if (intervals_[i].second > max_) max_ = intervals_[i].second; + } + // now we have the structure filled in, and moreover we know min_ and max_ values of the interval, so we know the + // range. + + // add some more space: + min_ -= fabs(max_ - min_) / 100; + max_ += fabs(max_ - min_) / 100; + } + + if (dbg) { + std::cerr << "min_ : " << min_ << std::endl; + std::cerr << "max_ : " << max_ << std::endl; + std::cerr << "number_of_pixels : " << number_of_pixels << std::endl; + getchar(); + } + + this->min_ = min_; + this->max_ = max_; + + // initialization of the structure heat_map + std::vector > heat_map_; + for (size_t i = 0; i != number_of_pixels; ++i) { + std::vector v(number_of_pixels, 0); + heat_map_.push_back(v); + } + this->heat_map = heat_map_; + + if (dbg) std::cerr << "Done creating of the heat map, now we will fill in the structure \n"; + + for (size_t pt_nr = 0; pt_nr != intervals_.size(); ++pt_nr) { + // compute the value of intervals_[pt_nr] in the grid: + int x_grid = + static_cast((intervals_[pt_nr].first - this->min_) / (this->max_ - this->min_) * number_of_pixels); + int y_grid = + static_cast((intervals_[pt_nr].second - this->min_) / (this->max_ - this->min_) * number_of_pixels); + + if (dbg) { + std::cerr << "point : " << intervals_[pt_nr].first << " , " << intervals_[pt_nr].second << std::endl; + std::cerr << "x_grid : " << x_grid << std::endl; + std::cerr << "y_grid : " << y_grid << std::endl; + } + + // x_grid and y_grid gives a center of the kernel. We want to have its lower left corner. To get this, we need to + // shift x_grid and y_grid by a grid diameter. + x_grid -= filter.size() / 2; + y_grid -= filter.size() / 2; + // note that the numbers x_grid and y_grid may be negative. + + if (dbg) { + std::cerr << "After shift : \n"; + std::cerr << "x_grid : " << x_grid << std::endl; + std::cerr << "y_grid : " << y_grid << std::endl; + std::cerr << "filter.size() : " << filter.size() << std::endl; + getchar(); + } + + for (size_t i = 0; i != filter.size(); ++i) { + for (size_t j = 0; j != filter.size(); ++j) { + // if the point (x_grid+i,y_grid+j) is the correct point in the grid. + if (((x_grid + i) >= 0) && (x_grid + i < this->heat_map.size()) && ((y_grid + j) >= 0) && + (y_grid + j < this->heat_map.size())) { + if (dbg) { + std::cerr << y_grid + j << " " << x_grid + i << std::endl; + } + this->heat_map[y_grid + j][x_grid + i] += filter[i][j]; + this->heat_map[x_grid + i][y_grid + j] += -filter[i][j]; + } + } + } + } +} // construct + +} // namespace Persistence_representations +} // namespace Gudhi + +#endif // PSSK_H_ -- cgit v1.2.3