diff options
Diffstat (limited to 'src/Nerve_GIC/include')
| -rw-r--r-- | src/Nerve_GIC/include/gudhi/GIC.h | 70 |
1 files changed, 51 insertions, 19 deletions
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index c373b25c..e9b7a1f1 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -162,10 +162,21 @@ class Graph_induced_complex { * */ void set_graph_from_file(const std::string& graph_file_name){ - int neighb; int vid; std::ifstream input(graph_file_name); std::string line; std::vector<int> edge(2); + int neighb; int vid; std::ifstream input(graph_file_name); std::string line; std::vector<int> edge(2); int n = 0; while(std::getline(input,line)){ std::stringstream stream(line); stream >> vid; edge[0] = vid; while(stream >> neighb){edge[1] = neighb; st.insert_simplex_and_subfaces(edge);} + n++; + } + + std::vector<int> empty; + for(int i = 0; i < n; i++) adjacency_matrix.insert(std::pair<int,std::vector<int> >(i,empty)); + for (auto simplex : st.complex_simplex_range()) { + if(st.dimension(simplex) == 1){ + std::vector<int> vertices; + for(auto vertex : st.simplex_vertex_range(simplex)) vertices.push_back(vertex); + adjacency_matrix[vertices[0]].push_back(vertices[1]); adjacency_matrix[vertices[1]].push_back(vertices[0]); + } } } @@ -191,6 +202,16 @@ class Graph_induced_complex { } i++; } + + std::vector<int> empty; + for(int i = 0; i < numpts; i++) adjacency_matrix.insert(std::pair<int,std::vector<int> >(i,empty)); + for (auto simplex : st.complex_simplex_range()) { + if(st.dimension(simplex) == 1){ + std::vector<int> vertices; + for(auto vertex : st.simplex_vertex_range(simplex)) vertices.push_back(vertex); + adjacency_matrix[vertices[0]].push_back(vertices[1]); adjacency_matrix[vertices[1]].push_back(vertices[0]); + } + } } public: // Set graph from Rips complex. @@ -204,6 +225,17 @@ class Graph_induced_complex { 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); data_dimension = off_reader.get_point_cloud()[0].size(); + + std::vector<int> empty; int n = off_reader.get_point_cloud().size(); + for(int i = 0; i < n; i++) adjacency_matrix.insert(std::pair<int,std::vector<int> >(i,empty)); + for (auto simplex : st.complex_simplex_range()) { + if(st.dimension(simplex) == 1){ + std::vector<int> vertices; + for(auto vertex : st.simplex_vertex_range(simplex)) vertices.push_back(vertex); + adjacency_matrix[vertices[0]].push_back(vertices[1]); adjacency_matrix[vertices[1]].push_back(vertices[0]); + } + } + } public: // Automatic tuning of Rips complex. @@ -277,6 +309,16 @@ class Graph_induced_complex { Rips_complex rips_complex_from_points(off_reader.get_point_cloud(), delta, Euclidean_distance()); rips_complex_from_points.create_complex(st, 1); + std::vector<int> empty; + for(int i = 0; i < n; i++) adjacency_matrix.insert(std::pair<int,std::vector<int> >(i,empty)); + for (auto simplex : st.complex_simplex_range()) { + if(st.dimension(simplex) == 1){ + std::vector<int> vertices; + for(auto vertex : st.simplex_vertex_range(simplex)) vertices.push_back(vertex); + adjacency_matrix[vertices[0]].push_back(vertices[1]); adjacency_matrix[vertices[1]].push_back(vertices[0]); + } + } + } @@ -337,7 +379,7 @@ class Graph_induced_complex { 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);} + while(stream >> cov){cov_elts.push_back(cov); cov_number.push_back(cov); cover_fct.insert(std::pair<Cover_t,int>(cov,cov));} cover.insert(std::pair<int, std::vector<Cover_t> >(vertex_id, cov_elts)); vertex_id++; } std::vector<Cover_t>::iterator it; @@ -442,17 +484,6 @@ class Graph_induced_complex { std::vector<int> points(num_pts); for(int i = 0; i < num_pts; i++) points[i] = i; std::sort(points.begin(),points.end(),functional_comp); - // Build adjacency matrix - std::vector<int> empty; - for(int i = 0; i < num_pts; i++) adjacency_matrix.insert(std::pair<int,std::vector<int> >(points[i],empty)); - for (auto simplex : st.complex_simplex_range()) { - if(st.dimension(simplex) == 1){ - std::vector<int> vertices; - for(auto vertex : st.simplex_vertex_range(simplex)) vertices.push_back(vertex); - adjacency_matrix[vertices[0]].push_back(vertices[1]); adjacency_matrix[vertices[1]].push_back(vertices[0]); - } - } - int id = 0; int pos = 0; double min_prop_int; double max_prop_int; for(int i = 0; i < res; i++){ @@ -627,7 +658,6 @@ class Graph_induced_complex { public: /** \brief Creates the simplicial complex. * - * \tparam SimplicialComplexForGIC must meet `SimplicialComplexForRips` concept. * @param[in] complex SimplicialComplexForGIC to be created. * */ @@ -685,14 +715,16 @@ class Graph_induced_complex { } // Remove edges - int current_id = 1; - auto simplex = st.complex_simplex_range().begin(); int num_rem = 0; - for(int i = 0; i < simplex_id-1; i++){ + if(simplex_to_remove.size() > 1){ + int current_id = 1; + auto simplex = st.complex_simplex_range().begin(); int num_rem = 0; + for(int i = 0; i < simplex_id-1; 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++; num_rem++;} else simplex++; - } simplex = st.complex_simplex_range().begin(); - for(int i = 0; i < simplex_to_remove[0]; i++) simplex++; st.remove_maximal_simplex(*simplex); + } simplex = st.complex_simplex_range().begin(); + for(int i = 0; i < simplex_to_remove[0]; i++) simplex++; st.remove_maximal_simplex(*simplex); + } // Build the Simplex Tree corresponding to the graph st.expansion(maximal_dim); |