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Diffstat (limited to 'src/Persistent_cohomology/example')
6 files changed, 675 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt new file mode 100644 index 00000000..dca4a04d --- /dev/null +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -0,0 +1,22 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIExPersCohom) + +# NEED TO FIND BOOST NEEDED COMPONENTS TO LINK WITH +find_package(Boost 1.45.0 COMPONENTS system program_options) +message("Boost_lib = ${Boost_LIBRARIES}") + +add_executable ( rips_persistence rips_persistence.cpp ) +target_link_libraries(rips_persistence ${Boost_LIBRARIES}) +add_executable ( rips_persistence_from_alpha_shape_3 rips_persistence_from_alpha_shape_3.cpp ) +target_link_libraries(rips_persistence_from_alpha_shape_3 ${Boost_LIBRARIES}) + +if(GMPXX_FOUND AND GMP_FOUND) + message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") + message("GMP_LIBRARIES = ${GMP_LIBRARIES}") + + add_executable ( rips_multifield_persistence rips_multifield_persistence.cpp ) + target_link_libraries(rips_multifield_persistence ${Boost_LIBRARIES} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + + add_executable ( performance_rips_persistence performance_rips_persistence.cpp ) + target_link_libraries(performance_rips_persistence ${Boost_LIBRARIES} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) +endif() diff --git a/src/Persistent_cohomology/example/README b/src/Persistent_cohomology/example/README new file mode 100644 index 00000000..5dd34b85 --- /dev/null +++ b/src/Persistent_cohomology/example/README @@ -0,0 +1,47 @@ +To build the example, run in a Terminal: + +cd /path-to-example/ +cmake . +make + + +Example of use : + +Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points +sampling a Klein bottle: + +./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -m 100 + +output: +210 0 0 inf +210 1 0.0702103 inf +2 1 0.0702103 inf +2 2 0.159992 inf + +with Z/3Z coefficients: + +./rips_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 3 -m 100 + +output: +3 0 0 inf +3 1 0.0702103 inf + +and the computation with Z/2Z and Z/3Z coefficients simultaneously: + +./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 3 -m 100 + +output: +6 0 0 inf +6 1 0.0702103 inf +2 1 0.0702103 inf +2 2 0.159992 inf + +and finally the computation with all Z/pZ for 2 <= p <= 71 (20 first prime numbers): + + ./rips_multifield_persistence ../../../data/points/Kl.txt -r 0.25 -d 3 -p 2 -q 71 -m 100 + +output: +557940830126698960967415390 0 0 inf +557940830126698960967415390 1 0.0702103 inf +2 1 0.0702103 inf +2 2 0.159992 inf diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp new file mode 100644 index 00000000..37d41ee1 --- /dev/null +++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp @@ -0,0 +1,168 @@ + /* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * + * 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 + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include "gudhi/reader_utils.h" +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/Persistent_cohomology.h" +#include "gudhi/Persistent_cohomology/Multi_field.h" +#include "gudhi/Hasse_complex.h" + +#include <chrono> + +using namespace Gudhi; + +/* Compute the persistent homology of the complex cpx with coefficients in Z/pZ. */ +template< typename FilteredComplex> +void timing_persistence( FilteredComplex & cpx + , int p ); + +/* Compute multi-field persistent homology of the complex cpx with coefficients in + * Z/rZ for all prime number r in [p;q].*/ +template< typename FilteredComplex> +void timing_persistence( FilteredComplex & cpx + , int p + , int q ); + +/* Timings for the computation of persistent homology with different + * representations of a Rips complex and different coefficient fields. The + * Rips complex is built on a set of 10000 points sampling a Klein bottle embedded + * in dimension 5. + * We represent complexes with a simplex tree and + * with a Hasse diagram. The Hasse diagram represents explicitly all + * codimension 1 incidence relations in the complex, and hence leads to + * a faster computation of persistence because boundaries are precomputed. + * Hovewer, the simplex tree may be constructed directly from a point cloud and + * is more compact. + * We compute persistent homology with coefficient fields Z/2Z and Z/1223Z. + * We present also timings for the computation of multi-field persistent + * homology in all fields Z/rZ for r prime between 2 and 1223. + */ +int main (int argc, char * argv[]) +{ + std::chrono::time_point<std::chrono::system_clock> start, end; + int enlapsed_sec; + + std::string filepoints = "../examples/Kl.txt"; + Filtration_value threshold = 0.3; + int dim_max = 3; + int p = 2; + int q = 1223; + +// Extract the points from the file filepoints + typedef std::vector<double> Point_t; + std::vector< Point_t > points; + read_points( filepoints, points ); + +// Compute the proximity graph of the points + start = std::chrono::system_clock::now(); + Graph_t prox_graph = compute_proximity_graph( points, threshold + , euclidean_distance<Point_t> ); + end = std::chrono::system_clock::now(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n"; + +// Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; + start = std::chrono::system_clock::now(); + + st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree + st.expansion( dim_max ); // expand the graph until dimension dim_max + + end = std::chrono::system_clock::now(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n"; + std::cout << " - dimension = " << st.dimension() << std::endl; + std::cout << " - number of simplices = " << st.num_simplices() << std::endl; + +// Sort the simplices in the order of the filtration + start = std::chrono::system_clock::now(); + st.initialize_filtration(); + end = std::chrono::system_clock::now(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n"; + +// Convert the simplex tree into a hasse diagram + start = std::chrono::system_clock::now(); + Hasse_complex<> hcpx(st); + end = std::chrono::system_clock::now(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n"; + + + std::cout << "Timings when using a simplex tree: \n"; + timing_persistence(st,p); + timing_persistence(st,q); + timing_persistence(st,p,q); + + std::cout << "Timings when using a Hasse complex: \n"; + timing_persistence(hcpx,p); + timing_persistence(hcpx,q); + timing_persistence(hcpx,p,q); + + return 0; +} + + +template< typename FilteredComplex> +void +timing_persistence( FilteredComplex & cpx + , int p ) +{ + std::chrono::time_point<std::chrono::system_clock> start, end; + int enlapsed_sec; + + Persistent_cohomology< FilteredComplex, Field_Zp > pcoh (cpx); + pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + + start = std::chrono::system_clock::now(); + + pcoh.compute_persistent_cohomology( INFINITY ); + + end = std::chrono::system_clock::now(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + std::cout << " Compute persistent homology in Z/"<<p<<"Z in " << enlapsed_sec << " sec.\n"; +} + +template< typename FilteredComplex> +void +timing_persistence( FilteredComplex & cpx + , int p + , int q ) +{ + std::chrono::time_point<std::chrono::system_clock> start, end; + int enlapsed_sec; + + Persistent_cohomology< FilteredComplex, Multi_field > pcoh (cpx); + pcoh.init_coefficients( p, q ); //initilizes the coefficient field for homology + // compute persistent homology, disgarding persistent features of life shorter than min_persistence + + start = std::chrono::system_clock::now(); + + pcoh.compute_persistent_cohomology( INFINITY ); + + end = std::chrono::system_clock::now(); + enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end-start).count(); + std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ " + << "with p in ["<<p<<";"<<q<<"] in " << enlapsed_sec << " sec.\n"; +} diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp new file mode 100644 index 00000000..95ef8809 --- /dev/null +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -0,0 +1,152 @@ + /* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * + * 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 + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include "gudhi/reader_utils.h" +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/Persistent_cohomology.h" +#include "gudhi/Persistent_cohomology/Multi_field.h" + +#include <boost/program_options.hpp> + +using namespace Gudhi; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options( int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & min_p + , int & max_p + , Filtration_value & min_persistence ); + +int main (int argc, char * argv[]) +{ + std::string filepoints; + std::string filediag; + Filtration_value threshold; + int dim_max; + int min_p; + int max_p; + Filtration_value min_persistence; + + program_options(argc,argv,filepoints,filediag,threshold,dim_max,min_p,max_p,min_persistence); + +// Extract the points from the file filepoints + typedef std::vector<double> Point_t; + std::vector< Point_t > points; + read_points( filepoints, points ); + +// Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph( points, threshold + , euclidean_distance<Point_t> ); + +// Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; + st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree + st.expansion( dim_max ); // expand the graph until dimension dim_max + +// Sort the simplices in the order of the filtration + st.initialize_filtration(); + +// Compute the persistence diagram of the complex + Persistent_cohomology< Simplex_tree<>, Multi_field > pcoh( st ); + pcoh.init_coefficients( min_p, max_p ); //initilizes the coefficient field for homology + // compute persistent homology, disgarding persistent features of life shorter than min_persistence + pcoh.compute_persistent_cohomology( min_persistence ); + +// Output the diagram in filediag + if(filediag.empty()) { pcoh.output_diagram(); } + else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); } + + return 0; +} + + + +void program_options( int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & min_p + , int & max_p + , Filtration_value & min_persistence ) +{ + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&filepoints), + "Name of file containing a point set. Format is one point per line: X1 ... Xd \n"); + + po::options_description visible("Allowed options"); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("min-field-charac,p", po::value<int>(&min_p)->default_value(2), + "Minimal characteristic p of the coefficient field Z/pZ.") + ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223), + "Minimial characteristic q of the coefficient field Z/pZ.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) + { + std::cout << std::endl; + std::cout << "Compute the persistent homology with various coefficient fields \n"; + std::cout << "of a Rips complex defined on a set of input points. The coefficient \n"; + std::cout << "fields are all the Z/rZ for a prime number r contained in the \n"; + std::cout << "specified range [p,q]\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p1*...*pr dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n"; + std::cout << "feature exists in homology with Z/piZ coefficients."<< std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp new file mode 100644 index 00000000..d7927223 --- /dev/null +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -0,0 +1,146 @@ + /* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Clément Maria + * + * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * + * 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 + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include "gudhi/reader_utils.h" +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/Persistent_cohomology.h" + +#include <boost/program_options.hpp> + +using namespace Gudhi; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options( int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence ); + +int main (int argc, char * argv[]) +{ + std::string filepoints; + std::string filediag ; + Filtration_value threshold ; + int dim_max ; + int p ; + Filtration_value min_persistence; + + program_options(argc,argv,filepoints,filediag,threshold,dim_max,p,min_persistence); + +// Extract the points from the file filepoints + typedef std::vector<double> Point_t; + std::vector< Point_t > points; + read_points( filepoints, points ); + +// Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph( points, threshold + , euclidean_distance<Point_t> ); + +// Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; + st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree + st.expansion( dim_max ); // expand the graph until dimension dim_max + + std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << st.dimension() << " \n"; + +// Sort the simplices in the order of the filtration + st.initialize_filtration(); + +// Compute the persistence diagram of the complex + Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( st ); + pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + + pcoh.compute_persistent_cohomology( min_persistence ); + +// Output the diagram in filediag + if(filediag.empty()) { pcoh.output_diagram(); } + else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); } + + return 0; +} + + + +void program_options( int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence ) +{ + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&filepoints), + "Name of file containing a point set. Format is one point per line: X1 ... Xd "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), + "Maximal length of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) + { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\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"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp b/src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp new file mode 100644 index 00000000..ddaafea2 --- /dev/null +++ b/src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp @@ -0,0 +1,140 @@ + /* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * + * Copyright (C) 2014 INRIA Saclay (France) + * + * 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 + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include "gudhi/reader_utils.h" +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/Persistent_cohomology.h" + +#include <boost/program_options.hpp> + +using namespace Gudhi; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options( int argc, char * argv[] + , std::string & simplex_tree_file + , std::string & output_file + , int & p + , Filtration_value & min_persistence ); + +int main (int argc, char * argv[]) +{ + std::string simplex_tree_file; + std::string output_file ; + int p ; + Filtration_value min_persistence; + + program_options(argc,argv,simplex_tree_file,output_file,p,min_persistence); + + std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() << std::endl; + std::cout << " - p=" << p << " - min_persistence=" << min_persistence << std::endl; + + // Construct the Rips complex in a Simplex Tree + Simplex_tree<> simplex_tree; + + std::ifstream simplex_tree_stream(simplex_tree_file); + simplex_tree_stream >> simplex_tree; + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; + std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << std::endl; + + /* + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + for( auto f_simplex : simplex_tree.filtration_simplex_range() ) + { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) + { std::cout << vertex << " "; } + std::cout << std::endl; + }*/ + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree ); + pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + + pcoh.compute_persistent_cohomology( min_persistence ); + + // Output the diagram in output_file + if(output_file.empty()) { pcoh.output_diagram(); } + else { + std::ofstream out(output_file); + pcoh.output_diagram(out); + out.close(); } + + return 0; +} + + + +void program_options( int argc, char * argv[] + , std::string & simplex_tree_file + , std::string & output_file + , int & p + , Filtration_value & min_persistence ) +{ + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&simplex_tree_file), + "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1 "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; all.add(visible).add(hidden); + + po::variables_map vm; + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + po::notify(vm); + + if (vm.count("help") || !vm.count("input-file")) + { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a Rips complex defined on a set of input points.\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"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} |