diff options
Diffstat (limited to 'src/Persistence_representations/utilities/persistence_vectors')
5 files changed, 171 insertions, 217 deletions
diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp index 320d1f63..aa26ce2b 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -20,54 +20,46 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ - #include <gudhi/Persistence_vectors.h> - - using namespace Gudhi; using namespace Gudhi::Persistence_representations; #include <iostream> +int main(int argc, char** argv) { + std::cout << "This program computes average persistence vector of persistence vectors created based on persistence " + "diagrams provided as an input. \n"; + std::cout << "Please call this program with the names of files with persistence diagrams \n"; + std::vector<const char*> filenames; + + if (argc == 1) { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Reading persistence vectors...\n"; + std::vector<Vector_distances_in_diagram<Euclidean_distance>*> lands; + for (size_t i = 0; i != filenames.size(); ++i) { + Vector_distances_in_diagram<Euclidean_distance>* l = new Vector_distances_in_diagram<Euclidean_distance>; + l->load_from_file(filenames[i]); + lands.push_back(l); + } + + Vector_distances_in_diagram<Euclidean_distance> av; + av.compute_average(lands); + + av.print_to_file("average.vect"); + + for (size_t i = 0; i != filenames.size(); ++i) { + delete lands[i]; + } -int main( int argc , char** argv ) -{ - std::cout << "This program computes average persistence vector of persistence vectors created based on persistence diagrams provided as an input. \n"; - std::cout << "Please call this program with the names of files with persistence diagrams \n"; - std::vector< const char* > filenames; - - if ( argc == 1 ) - { - std::cout << "No input files given, the program will now terminate \n"; - return 1; - } - - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - std::cout << "Reading persistence vectors...\n"; - std::vector< Vector_distances_in_diagram< Euclidean_distance >* > lands; - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - Vector_distances_in_diagram< Euclidean_distance >* l = new Vector_distances_in_diagram< Euclidean_distance >; - l->load_from_file( filenames[i] ); - lands.push_back(l ); - } - - Vector_distances_in_diagram< Euclidean_distance > av; - av.compute_average( lands ); - - av.print_to_file( "average.vect" ); - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - delete lands[i]; - } - - std::cout << "Done \n"; + std::cout << "Done \n"; - return 0; + return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp index 5c0d3328..3ab8033c 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -22,89 +22,70 @@ #include <gudhi/Persistence_vectors.h> - - using namespace Gudhi; using namespace Gudhi::Persistence_representations; #include <iostream> #include <sstream> +int main(int argc, char** argv) { + std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created " + "beforehand). \n"; + std::cout << "The first parameter of a program is an integer p. The program compute l^p distance of the vectors. For " + "l^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; -int main( int argc , char** argv ) -{ - std::cout << "This program compute distance of persistence vectors stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The first parameter of a program is an integer p. The program compute l^p distance of the vectors. For l^infty distance choose p = -1. \n"; - std::cout << "The remaining parameters of this programs are names of files with persistence vectors.\n"; - - if ( argc < 3 ) - { - std::cout << "Wrong number of parameters, the program will now terminate \n"; - return 1; - } - - int pp = atoi( argv[1] ); - double p = std::numeric_limits<double>::max(); - if ( pp != -1 ) - { - p = pp; - } - + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } - std::vector< const char* > filenames; - for ( int i = 2 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Vector_distances_in_diagram< Euclidean_distance > > vectors; - vectors.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Vector_distances_in_diagram< Euclidean_distance > l; - l.load_from_file( filenames[file_no] ); - vectors.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > distance( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - distance[i] = v; - } - - //and now we can compute the distances: - for ( size_t i = 0 ; i != vectors.size() ; ++i ) - { - for ( size_t j = i+1 ; j != vectors.size() ; ++j ) - { - distance[i][j] = distance[j][i] = vectors[i].distance( vectors[j] , p ) ; - } - } - - //and now output the result to the screen and a file: - std::ofstream out; - out.open( "distance" ); - for ( size_t i = 0 ; i != distance.size() ; ++i ) - { - for ( size_t j = 0 ; j != distance.size() ; ++j ) - { - std::cout << distance[i][j] << " "; - out << distance[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - - return 0; -} + int pp = atoi(argv[1]); + double p = std::numeric_limits<double>::max(); + if (pp != -1) { + p = pp; + } + std::vector<const char*> filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector<Vector_distances_in_diagram<Euclidean_distance> > vectors; + vectors.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Vector_distances_in_diagram<Euclidean_distance> l; + l.load_from_file(filenames[file_no]); + vectors.push_back(l); + } + // and now we will compute the scalar product of landscapes. + // first we prepare an array: + std::vector<std::vector<double> > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector<double> v(filenames.size(), 0); + distance[i] = v; + } + // and now we can compute the distances: + for (size_t i = 0; i != vectors.size(); ++i) { + for (size_t j = i + 1; j != vectors.size(); ++j) { + distance[i][j] = distance[j][i] = vectors[i].distance(vectors[j], p); + } + } + // and now output the result to the screen and a file: + std::ofstream out; + out.open("distance"); + for (size_t i = 0; i != distance.size(); ++i) { + for (size_t j = 0; j != distance.size(); ++j) { + std::cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); - + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp index 7a1bbaf0..2a79b1ea 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -22,66 +22,56 @@ #include <gudhi/Persistence_vectors.h> - - using namespace Gudhi; using namespace Gudhi::Persistence_representations; #include <iostream> #include <sstream> +int main(int argc, char** argv) { + std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be " + "created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; + + std::vector<const char*> filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector<Vector_distances_in_diagram<Euclidean_distance> > vectors; + vectors.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Vector_distances_in_diagram<Euclidean_distance> l; + l.load_from_file(filenames[file_no]); + vectors.push_back(l); + } + + // and now we will compute the scalar product of landscapes. + + // first we prepare an array: + std::vector<std::vector<double> > scalar_product(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector<double> v(filenames.size(), 0); + scalar_product[i] = v; + } -int main( int argc , char** argv ) -{ - std::cout << "This program compute scalar product of persistence vectors stored in a file (the file needs to be created beforehand). \n"; - std::cout << "The parameters of this programs are names of files with persistence vectors.\n"; + // and now we can compute the scalar product: + for (size_t i = 0; i != vectors.size(); ++i) { + for (size_t j = i; j != vectors.size(); ++j) { + scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product(vectors[j]); + } + } - std::vector< const char* > filenames; - for ( int i = 1 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - std::vector< Vector_distances_in_diagram< Euclidean_distance > > vectors; - vectors.reserve( filenames.size() ); - for ( size_t file_no = 0 ; file_no != filenames.size() ; ++file_no ) - { - Vector_distances_in_diagram< Euclidean_distance > l; - l.load_from_file( filenames[file_no] ); - vectors.push_back( l ); - } - - //and now we will compute the scalar product of landscapes. - - //first we prepare an array: - std::vector< std::vector< double > > scalar_product( filenames.size() ); - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::vector< double > v( filenames.size() , 0 ); - scalar_product[i] = v; - } - - //and now we can compute the scalar product: - for ( size_t i = 0 ; i != vectors.size() ; ++i ) - { - for ( size_t j = i ; j != vectors.size() ; ++j ) - { - scalar_product[i][j] = scalar_product[j][i] = vectors[i].compute_scalar_product( vectors[j] ) ; - } - } - - //and now output the result to the screen and a file: - std::ofstream out; - out.open( "scalar_product" ); - for ( size_t i = 0 ; i != scalar_product.size() ; ++i ) - { - for ( size_t j = 0 ; j != scalar_product.size() ; ++j ) - { - std::cout << scalar_product[i][j] << " "; - out << scalar_product[i][j] << " "; - } - std::cout << std::endl; - out << std::endl; - } - out.close(); - return 0; + // and now output the result to the screen and a file: + std::ofstream out; + out.open("scalar_product"); + for (size_t i = 0; i != scalar_product.size(); ++i) { + for (size_t j = 0; j != scalar_product.size(); ++j) { + std::cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + return 0; } diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp index d7a22e58..3c4c7dad 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -22,43 +22,39 @@ #include <gudhi/Persistence_vectors.h> - - using namespace Gudhi; using namespace Gudhi::Persistence_representations; #include <iostream> #include <sstream> - -int main( int argc , char** argv ) -{ - std::cout << "This program creates persistence vectors of diagrams provided as an input. The first parameter of this program is a dimension of persistence "; - std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence pairs of various dimension, as a second parameter of the "; - std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." << std::endl; - std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; - int dim = atoi( argv[1] ); - unsigned dimension = std::numeric_limits<unsigned>::max(); - if ( dim >= 0 ) - { - dimension = (unsigned)dim; - } - - std::vector< const char* > filenames; - for ( int i = 2 ; i < argc ; ++i ) - { - filenames.push_back( argv[i] ); - } - - for ( size_t i = 0 ; i != filenames.size() ; ++i ) - { - std::cerr << "Creating persistence vectors based on a file : " << filenames[i] << std::endl; - Vector_distances_in_diagram< Euclidean_distance > l( filenames[i] , dimension ); - std::stringstream ss; - ss << filenames[i] << ".vect"; - l.print_to_file( ss.str().c_str() ); - } - std::cout << "Done \n"; - return 0; +int main(int argc, char** argv) { + std::cout << "This program creates persistence vectors of diagrams provided as an input. The first parameter of this " + "program is a dimension of persistence "; + std::cout << " that will be used in creation of the persistence vectors. If our input files contain persistence " + "pairs of various dimension, as a second parameter of the "; + std::cout << " procedure please provide the dimension of persistence you want to use. If in your file there are only " + "birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + int dim = atoi(argv[1]); + unsigned dimension = std::numeric_limits<unsigned>::max(); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cerr << "Creating persistence vectors based on a file : " << filenames[i] << std::endl; + Vector_distances_in_diagram<Euclidean_distance> l(filenames[i], dimension); + std::stringstream ss; + ss << filenames[i] << ".vect"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; } - diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp index c72fc1ee..48e0b258 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -22,27 +22,22 @@ #include <gudhi/Persistence_vectors.h> - - using namespace Gudhi; using namespace Gudhi::Persistence_representations; #include <iostream> #include <sstream> - -int main( int argc , char** argv ) -{ - std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the name of file with persistence vector. \n"; - if ( argc != 2 ) - { - std::cout << "Wrong number of parameters, the program will now terminate. \n"; - return 1; - } - Vector_distances_in_diagram< Euclidean_distance > l; - l.load_from_file( argv[1] ); - l.plot( argv[1] ); - - return 0; +int main(int argc, char** argv) { + std::cout << "This program create a Gnuplot script to plot persistence vector. Please call this program with the " + "name of file with persistence vector. \n"; + if (argc != 2) { + std::cout << "Wrong number of parameters, the program will now terminate. \n"; + return 1; + } + Vector_distances_in_diagram<Euclidean_distance> l; + l.load_from_file(argv[1]); + l.plot(argv[1]); + + return 0; } - |