diff options
7 files changed, 32 insertions, 295 deletions
diff --git a/data/points/grid_10_10_10_in_0_2.off b/data/points/grid_10_10_10_in_0_2.off deleted file mode 100644 index 7618e065..00000000 --- a/data/points/grid_10_10_10_in_0_2.off +++ /dev/null @@ -1,127 +0,0 @@ -OFF -125 0 0 -0 0 0 -0 0 0.2 -0 0 0.4 -0 0 0.6 -0 0 0.8 -0 0.2 0 -0 0.2 0.2 -0 0.2 0.4 -0 0.2 0.6 -0 0.2 0.8 -0 0.4 0 -0 0.4 0.2 -0 0.4 0.4 -0 0.4 0.6 -0 0.4 0.8 -0 0.6 0 -0 0.6 0.2 -0 0.6 0.4 -0 0.6 0.6 -0 0.6 0.8 -0 0.8 0 -0 0.8 0.2 -0 0.8 0.4 -0 0.8 0.6 -0 0.8 0.8 -0.2 0 0 -0.2 0 0.2 -0.2 0 0.4 -0.2 0 0.6 -0.2 0 0.8 -0.2 0.2 0 -0.2 0.2 0.2 -0.2 0.2 0.4 -0.2 0.2 0.6 -0.2 0.2 0.8 -0.2 0.4 0 -0.2 0.4 0.2 -0.2 0.4 0.4 -0.2 0.4 0.6 -0.2 0.4 0.8 -0.2 0.6 0 -0.2 0.6 0.2 -0.2 0.6 0.4 -0.2 0.6 0.6 -0.2 0.6 0.8 -0.2 0.8 0 -0.2 0.8 0.2 -0.2 0.8 0.4 -0.2 0.8 0.6 -0.2 0.8 0.8 -0.4 0 0 -0.4 0 0.2 -0.4 0 0.4 -0.4 0 0.6 -0.4 0 0.8 -0.4 0.2 0 -0.4 0.2 0.2 -0.4 0.2 0.4 -0.4 0.2 0.6 -0.4 0.2 0.8 -0.4 0.4 0 -0.4 0.4 0.2 -0.4 0.4 0.4 -0.4 0.4 0.6 -0.4 0.4 0.8 -0.4 0.6 0 -0.4 0.6 0.2 -0.4 0.6 0.4 -0.4 0.6 0.6 -0.4 0.6 0.8 -0.4 0.8 0 -0.4 0.8 0.2 -0.4 0.8 0.4 -0.4 0.8 0.6 -0.4 0.8 0.8 -0.6 0 0 -0.6 0 0.2 -0.6 0 0.4 -0.6 0 0.6 -0.6 0 0.8 -0.6 0.2 0 -0.6 0.2 0.2 -0.6 0.2 0.4 -0.6 0.2 0.6 -0.6 0.2 0.8 -0.6 0.4 0 -0.6 0.4 0.2 -0.6 0.4 0.4 -0.6 0.4 0.6 -0.6 0.4 0.8 -0.6 0.6 0 -0.6 0.6 0.2 -0.6 0.6 0.4 -0.6 0.6 0.6 -0.6 0.6 0.8 -0.6 0.8 0 -0.6 0.8 0.2 -0.6 0.8 0.4 -0.6 0.8 0.6 -0.6 0.8 0.8 -0.8 0 0 -0.8 0 0.2 -0.8 0 0.4 -0.8 0 0.6 -0.8 0 0.8 -0.8 0.2 0 -0.8 0.2 0.2 -0.8 0.2 0.4 -0.8 0.2 0.6 -0.8 0.2 0.8 -0.8 0.4 0 -0.8 0.4 0.2 -0.8 0.4 0.4 -0.8 0.4 0.6 -0.8 0.4 0.8 -0.8 0.6 0 -0.8 0.6 0.2 -0.8 0.6 0.4 -0.8 0.6 0.6 -0.8 0.6 0.8 -0.8 0.8 0 -0.8 0.8 0.2 -0.8 0.8 0.4 -0.8 0.8 0.6 -0.8 0.8 0.8 diff --git a/data/points/grid_10_10_10_in_0_2.weights b/data/points/grid_10_10_10_in_0_2.weights deleted file mode 100644 index fea8f879..00000000 --- a/data/points/grid_10_10_10_in_0_2.weights +++ /dev/null @@ -1,125 +0,0 @@ -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 -1e-6 diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index a0db9b42..df96fcfd 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -39,6 +39,7 @@ #include <utility> #include <list> #include <vector> +#include <cstdlib> #include "alpha_complex_3d_helper.h" @@ -78,7 +79,7 @@ using Persistent_cohomology = void usage(const std::string& progName) { std::cerr << "Usage: " << progName - << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + << " path_to_the_OFF_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); } @@ -90,13 +91,7 @@ int main(int argc, char* const argv[]) { } int coeff_field_characteristic = atoi(argv[2]); - - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } + Filtration_value min_persistence = strtof(argv[3], nullptr); // Read points from file std::string offInputFile(argv[1]); diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp index 8a335075..b189e980 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 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 @@ -39,6 +39,7 @@ #include <utility> #include <list> #include <vector> +#include <cstdlib> #include "alpha_complex_3d_helper.h" @@ -57,32 +58,33 @@ using Point_3 = Kernel::Point_3; // filtration with alpha values needed type definition using Alpha_value_type = Alpha_shape_3::FT; using Object = CGAL::Object; -using Dispatch = CGAL::Dispatch_output_iterator< - CGAL::cpp11::tuple<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, - std::back_insert_iterator< std::vector<Alpha_value_type> > > >; +using Dispatch = + CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>, + CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >, + std::back_insert_iterator<std::vector<Alpha_value_type> > > >; using Cell_handle = Alpha_shape_3::Cell_handle; using Facet = Alpha_shape_3::Facet; using Edge_3 = Alpha_shape_3::Edge; using Vertex_handle = Alpha_shape_3::Vertex_handle; -using Vertex_list = std::list<Vertex_handle>; +using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; // gudhi type definition using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; using Filtration_value = ST::Filtration_value; using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >; +using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; +using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; +using Persistent_cohomology = + Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; -void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; +void usage(const std::string& progName) { + std::cerr << "Usage: " << progName + << " path_to_the_OFF_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); } -int main(int argc, char * const argv[]) { +int main(int argc, char* const argv[]) { // program args management if (argc != 4) { std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; @@ -90,13 +92,7 @@ int main(int argc, char * const argv[]) { } int coeff_field_characteristic = atoi(argv[2]); - - Filtration_value min_persistence = 0.0; - int returnedScanValue = sscanf(argv[3], "%f", &min_persistence); - if ((returnedScanValue == EOF) || (min_persistence < -1.0)) { - std::cerr << "Error: " << argv[3] << " is not correct\n"; - usage(argv[0]); - } + Filtration_value min_persistence = strtof(argv[3], nullptr); // Read points from file std::string offInputFile(argv[1]); @@ -143,28 +139,28 @@ int main(int argc, char * const argv[]) { Filtration_value filtration_max = 0.0; for (auto object_iterator : the_objects) { // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { + if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); count_cells++; if (dim_max < 3) { // Cell is of dim 3 dim_max = 3; } - } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { + } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) { vertex_list = from_facet<Vertex_list, Facet>(*facet); count_facets++; if (dim_max < 2) { // Facet is of dim 2 dim_max = 2; } - } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { + } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) { vertex_list = from_edge<Vertex_list, Edge_3>(*edge); count_edges++; if (dim_max < 1) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Vertex_handle * vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { + } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { count_vertices++; vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); } @@ -213,7 +209,6 @@ int main(int argc, char * const argv[]) { std::cout << "facets \t\t" << count_facets << std::endl; std::cout << "cells \t\t" << count_cells << std::endl; - std::cout << "Information of the Simplex Tree: " << std::endl; std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; @@ -233,7 +228,7 @@ int main(int argc, char * const argv[]) { std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; // Compute the persistence diagram of the complex - PCOH pcoh(simplex_tree); + Persistent_cohomology pcoh(simplex_tree, true); // initializes the coefficient field for homology pcoh.init_coefficients(coeff_field_characteristic); diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp index 33efbdc7..63731a4a 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -83,8 +83,8 @@ using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; -void usage(char* const progName) { - std::cerr << "Usage: " << progName << " path_to_file_graph path_to_iso_cuboid_3_file " +void usage(const std::string& progName) { + std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_iso_cuboid_3_file " "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); } diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 85b0ab34..96cc57e9 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -49,6 +49,7 @@ #include "alpha_complex_3d_helper.h" +// Alpha_shape_3 templates type definitions using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; // For CGAL < 4.11 @@ -102,8 +103,8 @@ using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; -void usage(char* const progName) { - std::cerr << "Usage: " << progName << " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > " +void usage(const std::string& progName) { + std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file coeff_field_characteristic[integer > " "0] min_persistence[float >= -1.0]\n"; exit(-1); } diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp index ab2e29b4..a4a2a9f8 100644 --- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -86,8 +86,8 @@ using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; -void usage(char* const progName) { - std::cerr << "Usage: " << progName << " path_to_the_OFF_File path_to_weight_file path_to_the_cuboid_file " +void usage(const std::string& progName) { + std::cerr << "Usage: " << progName << " path_to_the_OFF_file path_to_weight_file path_to_the_cuboid_file " "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); } @@ -96,7 +96,6 @@ int main(int argc, char* const argv[]) { // program args management if (argc != 6) { std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - // file with points, file with weights, cuboid file, field characteristics, minimum persistence. usage(argv[0]); } @@ -206,8 +205,7 @@ int main(int argc, char* const argv[]) { // Edge_3 is of dim 1 dim_max = 1; } - } else if (const Alpha_shape_3::Vertex_handle* vertex = - CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) { + } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { count_vertices++; vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); } |