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diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp
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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): Pawel Dlotko, Vincent Rouvreau
+ *
+ * Copyright (C) 2016 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/reader_utils.h>
+
+#include <boost/program_options.hpp>
+
+#include <string>
+#include <vector>
+#include <limits> // infinity
+
+// Types definition
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
+using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
+using Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag,
+ Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence);
+
+int main(int argc, char* argv[]) {
+ std::string csv_matrix_file;
+ std::string filediag;
+ Filtration_value threshold;
+ int dim_max;
+ int p;
+ Filtration_value min_persistence;
+
+ program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence);
+
+ Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+ Rips_complex rips_complex_from_file(distances, threshold);
+
+ // Construct the Rips complex in a Simplex Tree
+ Simplex_tree simplex_tree;
+
+ rips_complex_from_file.create_complex(simplex_tree, dim_max);
+ std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+ std::cout << " and has dimension " << simplex_tree.dimension() << " \n";
+
+ // Sort the simplices in the order of the filtration
+ simplex_tree.initialize_filtration();
+
+ // Compute the persistence diagram of the complex
+ Persistent_cohomology pcoh(simplex_tree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p);
+
+ 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& csv_matrix_file, 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>(&csv_matrix_file),
+ "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.");
+
+ 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(std::numeric_limits<Filtration_value>::infinity()),
+ "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. Enter a negative value to see zero length "
+ "intervals");
+
+ 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 distance matrix.\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);
+ }
+}