diff options
Diffstat (limited to 'src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp')
-rw-r--r-- | src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp | 97 |
1 files changed, 55 insertions, 42 deletions
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index c2b49fed..d14ba375 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -38,11 +38,12 @@ using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; -void program_options(int argc, char *argv[], std::string &off_file_points, bool& EXACT, std::string &weight_file, - std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, - int &coeff_field_characteristic, Filtration_value &min_persistence); +void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &safe, + std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence); -bool read_weight_file(const std::string& weight_file, std::vector<double>& weights) { +bool read_weight_file(const std::string &weight_file, std::vector<double> &weights) { // Read weights information from file std::ifstream weights_ifstr(weight_file); if (weights_ifstr.good()) { @@ -57,8 +58,8 @@ bool read_weight_file(const std::string& weight_file, std::vector<double>& weigh return true; } -bool read_cuboid_file(const std::string& cuboid_file, double& x_min, double& y_min, double& z_min, - double& x_max, double& y_max, double& z_max) { +bool read_cuboid_file(const std::string &cuboid_file, double &x_min, double &y_min, double &z_min, double &x_max, + double &y_max, double &z_max) { // Read weights information from file std::ifstream iso_cuboid_str(cuboid_file); if (iso_cuboid_str.is_open()) { @@ -71,8 +72,8 @@ bool read_cuboid_file(const std::string& cuboid_file, double& x_min, double& y_m return true; } -template<typename AlphaComplex3d> -std::vector<typename AlphaComplex3d::Point_3> read_off(const std::string& off_file_points) { +template <typename AlphaComplex3d> +std::vector<typename AlphaComplex3d::Point_3> read_off(const std::string &off_file_points) { // Read the OFF file (input file name given as parameter) and triangulate points Gudhi::Points_3D_off_reader<typename AlphaComplex3d::Point_3> off_reader(off_file_points); // Check the read operation was correct @@ -92,10 +93,11 @@ int main(int argc, char **argv) { int coeff_field_characteristic = 0; Filtration_value min_persistence = 0.; bool exact_version = false; + bool safe_version = false; bool weighted_version = false; bool periodic_version = false; - program_options(argc, argv, off_file_points, exact_version, weight_file, cuboid_file, output_file_diag, + program_options(argc, argv, off_file_points, exact_version, safe_version, weight_file, cuboid_file, output_file_diag, alpha_square_max_value, coeff_field_characteristic, min_persistence); std::vector<double> weights; @@ -107,7 +109,7 @@ int main(int argc, char **argv) { weighted_version = true; } - double x_min=0., y_min=0., z_min=0., x_max=0., y_max=0., z_max=0.; + double x_min = 0., y_min = 0., z_min = 0., x_max = 0., y_max = 0., z_max = 0.; std::ifstream iso_cuboid_str(argv[3]); if (cuboid_file != std::string()) { if (!read_cuboid_file(cuboid_file, x_min, y_min, z_min, x_max, y_max, z_max)) { @@ -119,37 +121,44 @@ int main(int argc, char **argv) { Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::FAST; if (exact_version) { + if (safe_version) { + std::cerr << "You cannot set the exact and the safe version." << std::endl; + exit(-1); + } complexity = Gudhi::alpha_complex::complexity::EXACT; } + if (safe_version) { + complexity = Gudhi::alpha_complex::complexity::SAFE; + } Simplex_tree simplex_tree; - switch(complexity) { + switch (complexity) { case Gudhi::alpha_complex::complexity::FAST: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, - true, true>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, true>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, - true, false>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, false>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, weights); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, - false, true>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, true>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, - false, false>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, false>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); @@ -159,28 +168,28 @@ int main(int argc, char **argv) { case Gudhi::alpha_complex::complexity::EXACT: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, - true, true>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, true>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, - true, false>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, false>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, weights); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, - false, true>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, true>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, - false, false>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, false>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); @@ -190,28 +199,28 @@ int main(int argc, char **argv) { case Gudhi::alpha_complex::complexity::SAFE: if (weighted_version) { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, - true, true>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, true>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, - true, false>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, false>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, weights); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } } else { if (periodic_version) { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, - false, true>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, true>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); } else { - using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, - false, false>; + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, false>; auto points = read_off<Alpha_complex_3d>(off_file_points); Alpha_complex_3d alpha_complex(points); alpha_complex.create_complex(simplex_tree, alpha_square_max_value); @@ -248,9 +257,10 @@ int main(int argc, char **argv) { return 0; } -void program_options(int argc, char *argv[], std::string &off_file_points, bool& EXACT, std::string &weight_file, - std::string &cuboid_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value, - int &coeff_field_characteristic, Filtration_value &min_persistence) { +void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &safe, + std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); hidden.add_options()("input-file", po::value<std::string>(&off_file_points), @@ -258,15 +268,18 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& po::options_description visible("Allowed options", 100); visible.add_options()("help,h", "produce help message")( - "EXACT,e", po::bool_switch(&EXACT), - "To activate EXACT version of Alpha complex 3d (default is false, not available for weighted and/or periodic)")( + "exact,e", po::bool_switch(&exact), + "To activate exact version of Alpha complex 3d (default is false, not available if safe is set)")( + "safe,s", po::bool_switch(&safe), + "To activate safe version of Alpha complex 3d (default is false, not available if exact is set)")( "weight-file,w", po::value<std::string>(&weight_file)->default_value(std::string()), "Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")( "cuboid-file,c", po::value<std::string>(&cuboid_file), "Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")( "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::cout")( - "max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value) + "max-alpha-square-value,r", + po::value<Filtration_value>(&alpha_square_max_value) ->default_value(std::numeric_limits<Filtration_value>::infinity()), "Maximal alpha square value for the Alpha complex construction.")( "field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11), @@ -289,7 +302,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool& std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; std::cout << "of a 3D Alpha complex defined on a set of input points.\n"; - std::cout << "3D Alpha complex can be EXACT or weighted and/or periodic\n\n"; + std::cout << "3D Alpha complex can be exact or safe, weighted and/or periodic\n\n"; std::cout << "The output diagram contains one bar per line, written with the convention: \n"; std::cout << " p dim b d \n"; std::cout << "where dim is the dimension of the homological feature,\n"; |