diff options
author | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-01-30 16:33:22 +0000 |
---|---|---|
committer | mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-01-30 16:33:22 +0000 |
commit | ab2e89665e16be2dcd36e55df8543d4ff5974675 (patch) | |
tree | a99233d22b7b01f08f714ccaa1e247a860f57e0c /src/Nerve_GIC/include/gudhi | |
parent | 2541dd198e10ffebad5cff7c97b192199db38f88 (diff) |
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2032 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: e8901f1be678dbc71b8e6e7b5666cc475b573b1a
Diffstat (limited to 'src/Nerve_GIC/include/gudhi')
-rw-r--r-- | src/Nerve_GIC/include/gudhi/GIC.h | 127 |
1 files changed, 100 insertions, 27 deletions
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index d8046611..91f0327e 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -27,6 +27,9 @@ #include <gudhi/graph_simplicial_complex.h> #include <gudhi/reader_utils.h> #include <gudhi/Simplex_tree.h> +#include <gudhi/Rips_complex.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/distance_functions.h> #include <boost/graph/adjacency_list.hpp> @@ -36,7 +39,23 @@ #include <string> #include <limits> // for numeric_limits #include <utility> // for pair<> - +#include <functional> // for greater<> +#include <stdexcept> +#include <initializer_list> +#include <algorithm> // for std::max +#include <cstdint> // for std::uint32_t + +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; +using Point = std::vector<float>; + +bool simplex_comp(const std::vector<int>& s1, const std::vector<int>& s2){ + if(s1.size() == s2.size()){ + return s1[0] < s2[0]; + } + else return s1.size() < s2.size(); +} namespace Gudhi { @@ -62,20 +81,59 @@ class Graph_induced_complex { private: std::vector<std::vector<Cover_t> > cliques; + private: + std::map<int, std::vector<Cover_t> > Cov; + + private: + int maximal_dim; + + private: + Simplex_tree<> st; + + public: + void set_cover(const std::string& cover_file_name){ + int vertex_id = 0; Cover_t cov; std::vector<Cover_t> cov_elts, cov_number; + std::ifstream input(cover_file_name); std::string line; + while(std::getline(input,line)){ + cov_elts.clear(); std::stringstream stream(line); + while(stream >> cov){cov_elts.push_back(cov); cov_number.push_back(cov);} + Cov.insert(std::pair<int, std::vector<Cover_t> >(vertex_id, cov_elts)); vertex_id++; + } + std::vector<Cover_t>::iterator it; + std::sort(cov_number.begin(),cov_number.end()); it = std::unique(cov_number.begin(),cov_number.end()); + cov_number.resize(std::distance(cov_number.begin(),it)); maximal_dim = cov_number.size(); + return; + } + + public: + void set_graph_simplex_tree(const double& threshold, const std::string& off_file_name){ + Points_off_reader<Point> off_reader(off_file_name); + Rips_complex rips_complex_from_points(off_reader.get_point_cloud(), threshold, Euclidean_distance()); + rips_complex_from_points.create_complex(st, 1); + return;} + public: template<typename SimplicialComplexForGIC> void create_complex(SimplicialComplexForGIC & complex) { - size_t sz = cliques.size(); - for(int i = 0; i < sz; i++) complex.insert_simplex_and_subfaces(cliques[i]); + size_t sz = cliques.size(); int dimension = 0; + for(int i = 0; i < sz; i++){ + complex.insert_simplex_and_subfaces(cliques[i]); + if(dimension < cliques[i].size()-1) dimension = cliques[i].size()-1; + } + complex.set_dimension(dimension); } public: - void find_all_simplices(std::vector<std::vector<Cover_t> > & cliques, const std::vector<std::vector<Cover_t> > & cover_elts, int & token, std::vector<Cover_t> & simplex_tmp){ + void find_all_simplices(std::vector<std::vector<Cover_t> > & cliques, const std::vector<std::vector<Cover_t> > & cover_elts,\ + int & token, std::vector<Cover_t> & simplex_tmp){ int num_nodes = cover_elts.size(); if(token == num_nodes-1){ int num_clus = cover_elts[token].size(); for(int i = 0; i < num_clus; i++){ std::vector<Cover_t> simplex = simplex_tmp; simplex.push_back(cover_elts[token][i]); + std::vector<Cover_t>::iterator it; + std::sort(simplex.begin(),simplex.end()); it = std::unique(simplex.begin(),simplex.end()); + simplex.resize(std::distance(simplex.begin(),it)); cliques.push_back(simplex); } } @@ -89,34 +147,49 @@ class Graph_induced_complex { } public: - /** \brief Graph_induced_complex constructor from a graph and a cover. - * - * @param[in] graph built on point cloud. - * @param[in] cover of points. - * - * \tparam Cover must be a range for which `std::begin` and `std::end` return input iterators on a - * `Cover_value`. - * - */ - template<typename Cover> - Graph_induced_complex(Simplex_tree & st, const Cover& C, const int& max_dim) { - - // Construct the Simplex Tree corresponding to the graph - st.expansion(max_dim); - - // Find complexes of GIC - cliques.clear(); + void find_simplices() { + + // Find IDs of edges to remove + std::vector<int> simplex_to_remove; int simplex_id = 0; for (auto simplex : st.complex_simplex_range()) { - std::vector<std::vector<Cover_t> > cover_elts; - for (auto vertex : st.simplex_vertex_range(simplex)) { - cover_elts.push_back(C[vertex]); - find_all_simplices(cliques,cover_elts); + if(st.dimension(simplex) == 1){ + std::vector<std::vector<Cover_t> > comp; + for(auto vertex : st.simplex_vertex_range(simplex)) comp.push_back(Cov[vertex]); + if(comp[0].size() == 1 && comp[1].size() == 1 && comp[0][0] == comp[1][0]) simplex_to_remove.push_back(simplex_id); + } + simplex_id++; + } + + // Remove edges + int current_id = 0; auto simplex_tmp = st.complex_simplex_range().begin(); + if(simplex_to_remove[current_id] == 0){st.remove_maximal_simplex(*simplex_tmp); current_id++;} + auto simplex = st.complex_simplex_range().begin(); + for(int i = 1; i < --simplex_id; i++){ + int j = i+1; auto simplex_tmp = simplex; simplex_tmp++; + if(j == simplex_to_remove[current_id]){st.remove_maximal_simplex(*simplex_tmp); current_id++; i++;} + simplex++; + } + + // Build the Simplex Tree corresponding to the graph + st.expansion(maximal_dim); + + // Find simplices of GIC + cliques.clear(); + for (auto simplex : st.complex_simplex_range()) { + std::vector<std::vector<Cover_t> > cover_elts; int token = 0; std::vector<Cover_t> sim; + for (auto vertex : st.simplex_vertex_range(simplex)) cover_elts.push_back(Cov[vertex]); + find_all_simplices(cliques,cover_elts,token,sim); } + std::vector<std::vector<Cover_t> >::iterator it; + std::sort(cliques.begin(),cliques.end()); it = std::unique(cliques.begin(),cliques.end()); + cliques.resize(std::distance(cliques.begin(),it)); } }; -} +} // namespace graph_induced_complex -} +} // namespace Gudhi + +#endif // GIC_H_ |