diff options
author | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-04-20 15:56:06 +0000 |
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committer | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-04-20 15:56:06 +0000 |
commit | 7f9e8f11f70e8387ef29c3fa13016121dca79cbe (patch) | |
tree | abd50b927970f7de1cb07f2041e093a22a446753 /src/Persistence_representations | |
parent | 905be209a0e62121c125c37e01f4d2eae5aa606d (diff) |
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3385 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 2a83e62e132ce406986efa1456b5f1bca6b93691
Diffstat (limited to 'src/Persistence_representations')
7 files changed, 344 insertions, 13 deletions
diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index 79d39c4d..89284e38 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -37,3 +37,12 @@ add_test(NAME Persistence_weighted_gaussian COMMAND $<TARGET_FILE:Persistence_weighted_gaussian>) install(TARGETS Persistence_weighted_gaussian DESTINATION bin) +add_executable ( Persistence_image persistence_image.cpp ) +add_test(NAME Persistence_image + COMMAND $<TARGET_FILE:Persistence_image>) +install(TARGETS Persistence_image DESTINATION bin) + +add_executable ( Landscape landscape.cpp ) +add_test(NAME Landscape + COMMAND $<TARGET_FILE:Landscape>) +install(TARGETS Landscape DESTINATION bin) diff --git a/src/Persistence_representations/example/landscape.cpp b/src/Persistence_representations/example/landscape.cpp new file mode 100644 index 00000000..5fa84a7c --- /dev/null +++ b/src/Persistence_representations/example/landscape.cpp @@ -0,0 +1,51 @@ +/* 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/>. + */ + +#include <gudhi/Landscape.h> + +#include <iostream> +#include <vector> +#include <utility> + +using LS = Gudhi::Persistence_representations::Landscape; + +int main(int argc, char** argv) { + + std::vector<std::pair<double, double> > persistence; + + persistence.push_back(std::make_pair(1, 2)); + persistence.push_back(std::make_pair(6, 8)); + persistence.push_back(std::make_pair(0, 4)); + persistence.push_back(std::make_pair(3, 8)); + + int nb_ls = 3; double min_x = 0.0; double max_x = 10.0; int res_x = 100; + + LS ls(persistence, nb_ls, min_x, max_x, res_x); + std::vector<std::vector<double> > L = ls.vectorize(); + + for(int i = 0; i < nb_ls; i++){ + for(int j = 0; j < res_x; j++) std::cout << L[i][j] << " "; + std::cout << std::endl; + } + + return 0; +} diff --git a/src/Persistence_representations/example/persistence_image.cpp b/src/Persistence_representations/example/persistence_image.cpp new file mode 100644 index 00000000..dfa469d4 --- /dev/null +++ b/src/Persistence_representations/example/persistence_image.cpp @@ -0,0 +1,54 @@ +/* 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/>. + */ + +#include <gudhi/Persistence_image.h> +#include <gudhi/Persistence_weighted_gaussian.h> + +#include <iostream> +#include <vector> +#include <utility> +#include <string> + +using PI = Gudhi::Persistence_representations::Persistence_image; +using Weight = std::function<double (std::pair<double,double>) >; + +int main(int argc, char** argv) { + + std::vector<std::pair<double, double> > persistence; + + persistence.push_back(std::make_pair(1, 2)); + persistence.push_back(std::make_pair(6, 8)); + persistence.push_back(std::make_pair(0, 4)); + persistence.push_back(std::make_pair(3, 8)); + + double min_x = 0.0; double max_x = 10.0; int res_x = 100; double min_y = 0.0; double max_y = 10.0; int res_y = 100; double sigma = 1.0; Weight weight = Gudhi::Persistence_representations::Persistence_weighted_gaussian::linear_weight; + + PI pim(persistence, min_x, max_x, res_x, min_y, max_y, res_y, weight, sigma); + std::vector<std::vector<double> > P = pim.vectorize(); + + for(int i = 0; i < res_y; i++){ + for(int j = 0; j < res_x; j++) std::cout << P[i][j] << " "; + std::cout << std::endl; + } + + return 0; +} diff --git a/src/Persistence_representations/example/persistence_weighted_gaussian.cpp b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp index dea5dab6..234f6323 100644 --- a/src/Persistence_representations/example/persistence_weighted_gaussian.cpp +++ b/src/Persistence_representations/example/persistence_weighted_gaussian.cpp @@ -48,11 +48,11 @@ int main(int argc, char** argv) { double tau = 1; int m = 10000; - PWG PWG1(persistence1, sigma, m, PWG::arctan_weight); - PWG PWG2(persistence2, sigma, m, PWG::arctan_weight); + PWG PWG1(persistence1, sigma, m, PWG::arctan_weight(1,1)); + PWG PWG2(persistence2, sigma, m, PWG::arctan_weight(1,1)); - PWG PWGex1(persistence1, sigma, -1, PWG::arctan_weight); - PWG PWGex2(persistence2, sigma, -1, PWG::arctan_weight); + PWG PWGex1(persistence1, sigma, -1, PWG::arctan_weight(1,1)); + PWG PWGex2(persistence2, sigma, -1, PWG::arctan_weight(1,1)); // Linear PWG diff --git a/src/Persistence_representations/include/gudhi/Landscape.h b/src/Persistence_representations/include/gudhi/Landscape.h new file mode 100644 index 00000000..d6608a57 --- /dev/null +++ b/src/Persistence_representations/include/gudhi/Landscape.h @@ -0,0 +1,103 @@ +/* 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 LANDSCAPE_H_ +#define LANDSCAPE_H_ + +// gudhi include +#include <gudhi/read_persistence_from_file.h> +#include <gudhi/common_persistence_representations.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> + +using PD = std::vector<std::pair<double,double> >; + +namespace Gudhi { +namespace Persistence_representations { + +/** + * \class Landscape gudhi/Landscape.h + * \brief A class implementing the Landscapes. + * + * \ingroup Persistence_representations + * + * \details + * +**/ + +class Landscape { + + protected: + PD diagram; + int res_x, nb_ls; + double min_x, max_x; + + public: + + /** \brief Landscape constructor. + * \ingroup Landscape + * + */ + Landscape(PD _diagram, int _nb_ls = 5, double _min_x = 0.0, double _max_x = 1.0, int _res_x = 10){diagram = _diagram; nb_ls = _nb_ls; min_x = _min_x; max_x = _max_x; res_x = _res_x;} + + /** \brief Computes the landscape of a diagram. + * \ingroup Landscape + * + */ + std::vector<std::vector<double> > vectorize() { + std::vector<std::vector<double> > ls; for(int i = 0; i < nb_ls; i++) ls.emplace_back(); + int num_pts = diagram.size(); double step = (max_x - min_x)/res_x; + + for(int i = 0; i < res_x; i++){ + double x = min_x + i*step; double t = x / std::sqrt(2); std::vector<double> events; + for(int j = 0; j < num_pts; j++){ + double px = diagram[j].first; double py = diagram[j].second; + if(t >= px && t <= py){ if(t >= (px+py)/2) events.push_back(std::sqrt(2)*(py-t)); else events.push_back(std::sqrt(2)*(t-px)); } + } + + std::sort(events.begin(), events.end(), [](const double & a, const double & b){return a > b;}); int nb_events = events.size(); + for (int j = 0; j < nb_ls; j++){ if(j < nb_events) ls[j].push_back(events[j]); else ls[j].push_back(0); } + } + + return ls; + } + + + + +}; + +} // namespace Landscape +} // namespace Gudhi + +#endif // LANDSCAPE_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_image.h b/src/Persistence_representations/include/gudhi/Persistence_image.h new file mode 100644 index 00000000..6c9f75b7 --- /dev/null +++ b/src/Persistence_representations/include/gudhi/Persistence_image.h @@ -0,0 +1,117 @@ +/* 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_IMAGE_H_ +#define PERSISTENCE_IMAGE_H_ + +// gudhi include +#include <gudhi/read_persistence_from_file.h> +#include <gudhi/common_persistence_representations.h> +#include <gudhi/Debug_utils.h> +#include <gudhi/Persistence_weighted_gaussian.h> + +// standard include +#include <cmath> +#include <iostream> +#include <vector> +#include <limits> +#include <fstream> +#include <sstream> +#include <algorithm> +#include <string> +#include <utility> +#include <functional> + +using PD = std::vector<std::pair<double,double> >; +using Weight = std::function<double (std::pair<double,double>) >; + +namespace Gudhi { +namespace Persistence_representations { + +/** + * \class Persistence_image gudhi/Persistence_image.h + * \brief A class implementing the Persistence Images. + * + * \ingroup Persistence_representations + * + * \details + * +**/ + +class Persistence_image { + + protected: + PD diagram; + int res_x, res_y; + double min_x, max_x, min_y, max_y; + Weight weight; + double sigma; + + public: + + /** \brief Persistence Image constructor. + * \ingroup Persistence_image + * + */ + Persistence_image(PD _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, + Weight _weight = Gudhi::Persistence_representations::Persistence_weighted_gaussian::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_image + * + */ + std::vector<std::vector<double> > vectorize() { + 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; + + } + + + + +}; + +} // namespace Persistence_image +} // namespace Gudhi + +#endif // PERSISTENCE_IMAGE_H_ diff --git a/src/Persistence_representations/include/gudhi/Persistence_weighted_gaussian.h b/src/Persistence_representations/include/gudhi/Persistence_weighted_gaussian.h index b30e0273..9a63fccd 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_weighted_gaussian.h +++ b/src/Persistence_representations/include/gudhi/Persistence_weighted_gaussian.h @@ -97,7 +97,7 @@ class Persistence_weighted_gaussian{ * @param[in] _weight weight function for the points in the diagrams. * */ - Persistence_weighted_gaussian(PD _diagram, double _sigma = 1.0, int _approx = 1000, Weight _weight = arctan_weight){diagram = _diagram; sigma = _sigma; approx = _approx; weight = _weight;} + Persistence_weighted_gaussian(PD _diagram, double _sigma = 1.0, int _approx = 1000, Weight _weight = arctan_weight(1,1)){diagram = _diagram; sigma = _sigma; approx = _approx; weight = _weight;} PD get_diagram() const {return this->diagram;} double get_sigma() const {return this->sigma;} @@ -115,16 +115,13 @@ class Persistence_weighted_gaussian{ * @param[in] p point in 2D. * */ - static double pss_weight(std::pair<double,double> p){ - if(p.second > p.first) return 1; - else return -1; - } + static double pss_weight(std::pair<double,double> p) {if(p.second > p.first) return 1; else return -1;} + static double linear_weight(std::pair<double,double> p) {return std::abs(p.second - p.first);} + static double const_weight(std::pair<double,double> p) {return 1;} + static std::function<double (std::pair<double,double>) > arctan_weight(double C, double power) {return [=](std::pair<double,double> p){return C * atan(std::pow(std::abs(p.second - p.first), power));};} - static double arctan_weight(std::pair<double,double> p){ - return atan(p.second - p.first); - } - std::vector<std::pair<double,double> > Fourier_feat(PD diag, std::vector<std::pair<double,double> > z, Weight weight = arctan_weight){ + std::vector<std::pair<double,double> > Fourier_feat(PD diag, std::vector<std::pair<double,double> > z, Weight weight = arctan_weight(1,1)){ int md = diag.size(); std::vector<std::pair<double,double> > b; int mz = z.size(); for(int i = 0; i < mz; i++){ double d1 = 0; double d2 = 0; double zx = z[i].first; double zy = z[i].second; |