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author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-03-19 10:20:16 +0100 |
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committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-03-19 10:20:16 +0100 |
commit | d9bbfcaf73da6071ee52d05a04b152667027e976 (patch) | |
tree | b2a3ef920a31e80da5845962679da0a40b5df307 /src | |
parent | 0dbb5fd9a2096ba830c77954429ab49202228728 (diff) |
Remove examples
Diffstat (limited to 'src')
-rw-r--r-- | src/Collapse/example/CMakeLists.txt | 9 | ||||
-rw-r--r-- | src/Collapse/example/rips_persistence_with_sc.cpp | 179 |
2 files changed, 0 insertions, 188 deletions
diff --git a/src/Collapse/example/CMakeLists.txt b/src/Collapse/example/CMakeLists.txt deleted file mode 100644 index c9cba3fa..00000000 --- a/src/Collapse/example/CMakeLists.txt +++ /dev/null @@ -1,9 +0,0 @@ -project(Collapse_examples) - -add_executable ( Collapse_example_rips_persistence_with_collapse rips_persistence_with_sc.cpp ) -target_link_libraries(Collapse_example_rips_persistence_with_collapse Boost::program_options) - -if (TBB_FOUND) - target_link_libraries(Collapse_example_rips_persistence_with_collapse ${TBB_LIBRARIES}) -endif() -add_test(NAME Collapse_example_rips_persistence_with_collapse COMMAND $<TARGET_FILE:Collapse_example_rips_persistence_with_collapse>) diff --git a/src/Collapse/example/rips_persistence_with_sc.cpp b/src/Collapse/example/rips_persistence_with_sc.cpp deleted file mode 100644 index 46ec8eca..00000000 --- a/src/Collapse/example/rips_persistence_with_sc.cpp +++ /dev/null @@ -1,179 +0,0 @@ -#include <gudhi/FlagComplexSpMatrix.h> -#include <gudhi/Rips_complex.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Rips_edge_list.h> -#include <gudhi/distance_functions.h> -#include <gudhi/reader_utils.h> -#include <gudhi/PointSetGen.h> - -// Types definition -using Vector_of_points = std::vector<Point>; - -using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = double; -using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; -using Rips_edge_list = Gudhi::rips_edge_list::Rips_edge_list<Filtration_value>; -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; -using Distance_matrix = std::vector<std::vector<Filtration_value>>; - - -class filt_edge_to_dist_matrix -{ -public: - template<class Distance_matrix, class Filtered_sorted_edge_list> - filt_edge_to_dist_matrix(Distance_matrix & distance_mat, Filtered_sorted_edge_list & edge_filt, std::size_t number_of_points) - { - double inf = std::numeric_limits<double>::max(); - doubleVector distances ; - std::pair<std::size_t, std::size_t> e; - for(std::size_t indx = 0; indx < number_of_points; indx++) { - for (std::size_t j = 0; j <= indx; j++) { - if( j == indx) - distances.push_back(0); - - else - distances.push_back(inf); - } - distance_mat.push_back(distances); - distances.clear(); - } - - for(auto edIt = edge_filt.begin(); edIt != edge_filt.end(); edIt++) { - e=std::minmax(std::get<1>(*edIt),std::get<2>(*edIt)); - distance_mat.at(std::get<1>(e)).at(std::get<0>(e)) = std::get<0>(*edIt); - } - } -}; - - -int main(int argc, char * const argv[]) { - - auto the_begin = std::chrono::high_resolution_clock::now(); - PointSetGen point_generator; - std::string out_file_name = "default"; - std::string in_file_name = "default"; - std::size_t number_of_points; - - typedef size_t Vertex_handle; - typedef std::vector< std::tuple<Filtration_value, Vertex_handle, Vertex_handle > > Filtered_sorted_edge_list; - - int dimension; - double end_threshold; - double steps; - char manifold; - - Vector_of_points * point_vector; - - int dim_max = 2; - - point_generator.program_options(argc, argv, steps, end_threshold, manifold, dimension, dim_max, in_file_name, out_file_name); - - std::cout << "The current input values to run the program is: "<< std::endl; - std::cout << "steps, end_threshold, manifold, dimension, max_complex_dimension, in_file_name, out_file_name" << std::endl; - std::cout << steps << ", " << end_threshold << ", " << manifold << ", " << dimension << ", " << dim_max << ", " << in_file_name << ", " << out_file_name << std::endl; - - Map map_empty; - - std::string filediag_aft ("./PersistenceOutput/collapsed_persistence_diags") ; - - filediag_aft = filediag_aft+"_"+ out_file_name+ ".txt"; - - Distance_matrix distances; - Distance_matrix *sparse_distances = new Distance_matrix(); - - - if(manifold == 'f') { - Gudhi::Points_off_reader<Point> off_reader(in_file_name); - if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << in_file_name << "\n"; - exit(-1); // ----- >> - } - - point_vector = new Vector_of_points(off_reader.get_point_cloud().begin(), off_reader.get_point_cloud().end()); - dimension = point_vector->at(0).dimension() ; - number_of_points = point_vector->size(); - std::cout << "Successfully read " << number_of_points << " point_vector.\n"; - std::cout << "Ambient dimension is " << dimension << ".\n"; - } - else if (manifold == 'm'){ - std::string csv_file_name(in_file_name); - distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name); - number_of_points = distances.size(); - std::cout << "Read the distance matrix succesfully, of size: " << number_of_points << std::endl; - } - else { - std::cerr << "Wrong parameters for input manifold..." <<std::endl; - exit(-1); - } - - std::cout << "Point Set Generated." <<std::endl; - - Filtered_sorted_edge_list * edge_t = new Filtered_sorted_edge_list(); - std::cout << "Computing the one-skeleton for threshold: " << end_threshold << std::endl; - - if(manifold == 'm') { //Input is a distance 'm'atrix //Creating the edge list - Rips_edge_list Rips_edge_list_from_file(distances, end_threshold); - Rips_edge_list_from_file.create_edges(*edge_t); - std::cout<< "Sorted edge list computed" << std::endl; - } - else{ //Point cloud input //Creating the edge list - Rips_edge_list Rips_edge_list_from_points(*point_vector, end_threshold, Gudhi::Euclidean_distance()); - Rips_edge_list_from_points.create_edges(*edge_t); - std::cout<< "Sorted edge list computed" << std::endl; - std::cout << "Total number of edges before collapse are: " << edge_t->size() << std::endl; - } - - //Now we will perform filtered edge collapse to sparsify the edge list edge_t. - std::cout<< "Filtered edge collapse begins" << std::endl; - FlagComplexSpMatrix * mat_filt_edge_coll = new FlagComplexSpMatrix(number_of_points,*edge_t); - std::cout<< "Matrix instansiated" << std::endl; - if(edge_t->size() >0){ - delete edge_t; - edge_t = new Filtered_sorted_edge_list(); - *edge_t = mat_filt_edge_coll->filtered_edge_collapse(); - filt_edge_to_dist_matrix(*sparse_distances, *edge_t, number_of_points); - std::cout << "Total number of vertices after collapse in the sparse matrix are: " << mat_filt_edge_coll->num_vertices() << std::endl; - } - else - { - std::cerr << "Total number of egdes are zero." <<std::endl; - exit(-1) ; - } - - // Rips_complex rips_complex_before_collapse(distances, end_threshold); - Rips_complex rips_complex_after_collapse(*sparse_distances, end_threshold); - - Simplex_tree simplex_tree_aft; - rips_complex_after_collapse.create_complex(simplex_tree_aft, dim_max); - - std::cout << "The complex contains " << simplex_tree_aft.num_simplices() << " simplices after collapse. \n"; - std::cout << " and has dimension " << simplex_tree_aft.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree_aft.initialize_filtration(); - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh_aft(simplex_tree_aft); - // initializes the coefficient field for homology - pcoh_aft.init_coefficients(2); - - // pcoh_bfr.compute_persistent_cohomology(steps); - pcoh_aft.compute_persistent_cohomology(steps); - if (filediag_aft.empty()) { - pcoh_aft.output_diagram(); - } - else { - std::ofstream out(filediag_aft); - pcoh_aft.output_diagram(out); - out.close(); - } - - auto the_end = std::chrono::high_resolution_clock::now(); - - std::cout << "Total computation time : " << std::chrono::duration<double, std::milli>(the_end- the_begin).count() - << " ms\n" << std::endl; - return 0; - -} - |