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+/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ * Author(s): Vincent Rouvreau
+ *
+ * Copyright (C) 2014 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#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>
+
+#include <string>
+
+using namespace Gudhi;
+using namespace Gudhi::persistent_cohomology;
+
+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;
+
+ // Read the list of simplices from a file.
+ 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() << 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);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p);
+
+ 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;
+ exit(-1);
+ }
+}