diff options
author | Gard Spreemann <gspr@nonempty.org> | 2019-09-25 14:29:41 +0200 |
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committer | Gard Spreemann <gspr@nonempty.org> | 2019-09-25 14:29:41 +0200 |
commit | 599d68cd916f533bdb66dd9e684dd5703233b6bb (patch) | |
tree | 4b825dc642cb6eb9a060e54bf8d69288fbee4904 /example/Cech_complex | |
parent | a2e642954ae39025e041471d486ecbac25dff440 (diff) |
Delete all files in order to incorporate upstream's move to git.
Diffstat (limited to 'example/Cech_complex')
-rw-r--r-- | example/Cech_complex/CMakeLists.txt | 16 | ||||
-rw-r--r-- | example/Cech_complex/cech_complex_example_from_points.cpp | 54 | ||||
-rw-r--r-- | example/Cech_complex/cech_complex_example_from_points_for_doc.txt | 31 | ||||
-rw-r--r-- | example/Cech_complex/cech_complex_step_by_step.cpp | 166 |
4 files changed, 0 insertions, 267 deletions
diff --git a/example/Cech_complex/CMakeLists.txt b/example/Cech_complex/CMakeLists.txt deleted file mode 100644 index ab391215..00000000 --- a/example/Cech_complex/CMakeLists.txt +++ /dev/null @@ -1,16 +0,0 @@ -cmake_minimum_required(VERSION 2.6) -project(Cech_complex_examples) - -add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) -target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY}) -if (TBB_FOUND) - target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) -endif() -add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:Cech_complex_example_step_by_step> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3") - -add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp) -if (TBB_FOUND) - target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES}) -endif() -add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>) diff --git a/example/Cech_complex/cech_complex_example_from_points.cpp b/example/Cech_complex/cech_complex_example_from_points.cpp deleted file mode 100644 index 3cc5a4df..00000000 --- a/example/Cech_complex/cech_complex_example_from_points.cpp +++ /dev/null @@ -1,54 +0,0 @@ -#include <gudhi/Cech_complex.h> -#include <gudhi/Simplex_tree.h> - -#include <iostream> -#include <string> -#include <vector> -#include <array> - -int main() { - // Type definitions - using Point_cloud = std::vector<std::array<double, 2>>; - using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; - using Filtration_value = Simplex_tree::Filtration_value; - using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; - - Point_cloud points; - points.push_back({1., 0.}); // 0 - points.push_back({0., 1.}); // 1 - points.push_back({2., 1.}); // 2 - points.push_back({3., 2.}); // 3 - points.push_back({0., 3.}); // 4 - points.push_back({3. + std::sqrt(3.), 3.}); // 5 - points.push_back({1., 4.}); // 6 - points.push_back({3., 4.}); // 7 - points.push_back({2., 4. + std::sqrt(3.)}); // 8 - points.push_back({0., 4.}); // 9 - points.push_back({-0.5, 2.}); // 10 - - // ---------------------------------------------------------------------------- - // Init of a Cech complex from points - // ---------------------------------------------------------------------------- - Filtration_value max_radius = 1.; - Cech_complex cech_complex_from_points(points, max_radius); - - Simplex_tree stree; - cech_complex_from_points.create_complex(stree, 2); - // ---------------------------------------------------------------------------- - // Display information about the one skeleton Cech complex - // ---------------------------------------------------------------------------- - std::cout << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - " - << stree.num_vertices() << " vertices." << std::endl; - - std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl; - for (auto f_simplex : stree.filtration_simplex_range()) { - std::cout << " ( "; - for (auto vertex : stree.simplex_vertex_range(f_simplex)) { - std::cout << vertex << " "; - } - std::cout << ") -> " - << "[" << stree.filtration(f_simplex) << "] "; - std::cout << std::endl; - } - return 0; -} diff --git a/example/Cech_complex/cech_complex_example_from_points_for_doc.txt b/example/Cech_complex/cech_complex_example_from_points_for_doc.txt deleted file mode 100644 index be0afc76..00000000 --- a/example/Cech_complex/cech_complex_example_from_points_for_doc.txt +++ /dev/null @@ -1,31 +0,0 @@ -Iterator on Cech complex simplices in the filtration order, with [filtration value]: - ( 0 ) -> [0] - ( 1 ) -> [0] - ( 2 ) -> [0] - ( 3 ) -> [0] - ( 4 ) -> [0] - ( 5 ) -> [0] - ( 6 ) -> [0] - ( 7 ) -> [0] - ( 8 ) -> [0] - ( 9 ) -> [0] - ( 10 ) -> [0] - ( 9 4 ) -> [0.5] - ( 9 6 ) -> [0.5] - ( 10 1 ) -> [0.559017] - ( 10 4 ) -> [0.559017] - ( 1 0 ) -> [0.707107] - ( 2 0 ) -> [0.707107] - ( 3 2 ) -> [0.707107] - ( 6 4 ) -> [0.707107] - ( 9 6 4 ) -> [0.707107] - ( 2 1 ) -> [1] - ( 2 1 0 ) -> [1] - ( 4 1 ) -> [1] - ( 5 3 ) -> [1] - ( 7 3 ) -> [1] - ( 7 5 ) -> [1] - ( 7 6 ) -> [1] - ( 8 6 ) -> [1] - ( 8 7 ) -> [1] - ( 10 4 1 ) -> [1] diff --git a/example/Cech_complex/cech_complex_step_by_step.cpp b/example/Cech_complex/cech_complex_step_by_step.cpp deleted file mode 100644 index 6fbbde5b..00000000 --- a/example/Cech_complex/cech_complex_step_by_step.cpp +++ /dev/null @@ -1,166 +0,0 @@ -/* 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): Vincent Rouvreau - * - * Copyright (C) 2018 Inria - * - * 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/graph_simplicial_complex.h> -#include <gudhi/distance_functions.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Points_off_io.h> - -#include <gudhi/Miniball.hpp> - -#include <boost/program_options.hpp> - -#include <string> -#include <vector> -#include <limits> // infinity -#include <utility> // for pair -#include <map> - -// ---------------------------------------------------------------------------- -// rips_persistence_step_by_step is an example of each step that is required to -// build a Rips over a Simplex_tree. Please refer to rips_persistence to see -// how to do the same thing with the Rips_complex wrapper for less detailed -// steps. -// ---------------------------------------------------------------------------- - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree<>; -using Simplex_handle = Simplex_tree::Simplex_handle; -using Filtration_value = Simplex_tree::Filtration_value; -using Point = std::vector<double>; -using Points_off_reader = Gudhi::Points_off_reader<Point>; -using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; - -class Cech_blocker { - private: - using Point_cloud = std::vector<Point>; - using Point_iterator = Point_cloud::const_iterator; - using Coordinate_iterator = Point::const_iterator; - using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; - - public: - bool operator()(Simplex_handle sh) { - std::vector<Point> points; - for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) { - points.push_back(point_cloud_[vertex]); -#ifdef DEBUG_TRACES - std::cout << "#(" << vertex << ")#"; -#endif // DEBUG_TRACES - } - Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points); -#ifdef DEBUG_TRACES - std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl; -#endif // DEBUG_TRACES - simplex_tree_.assign_filtration(sh, radius); - return (radius > max_radius_); - } - Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud) - : simplex_tree_(simplex_tree), max_radius_(max_radius), point_cloud_(point_cloud) { - dimension_ = point_cloud_[0].size(); - } - - private: - Simplex_tree simplex_tree_; - Filtration_value max_radius_; - std::vector<Point> point_cloud_; - int dimension_; -}; - -void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max); - -int main(int argc, char* argv[]) { - std::string off_file_points; - Filtration_value max_radius; - int dim_max; - - program_options(argc, argv, off_file_points, max_radius, dim_max); - - // Extract the points from the file filepoints - Points_off_reader off_reader(off_file_points); - - // Compute the proximity graph of the points - Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(), max_radius, - Gudhi::Minimal_enclosing_ball_radius()); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree st; - // insert the proximity graph in the simplex tree - st.insert_graph(prox_graph); - // expand the graph until dimension dim_max - st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud())); - - std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << st.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - -#if DEBUG_TRACES - std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n"; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : st.filtration_simplex_range()) { - std::cout << " " - << "[" << st.filtration(f_simplex) << "] "; - for (auto vertex : st.simplex_vertex_range(f_simplex)) { - std::cout << static_cast<int>(vertex) << " "; - } - std::cout << std::endl; - } -#endif // DEBUG_TRACES - - return 0; -} - -void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value<std::string>(&off_file_points), - "Name of an OFF file containing a point set.\n"); - - po::options_description visible("Allowed options", 100); - visible.add_options()("help,h", "produce help message")( - "max-radius,r", - po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), - "Maximal length of an edge for the Rips complex construction.")( - "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute."); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Construct a Cech complex defined on a set of input points.\n \n"; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - exit(-1); - } -} |