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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) 2016 Inria
+ *
+ * Modification(s):
+ * - YYYY/MM Author: Description of the modification
+ */
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+// to construct a simplex_tree from alpha complex
+#include <gudhi/Simplex_tree.h>
+
+#include <iostream>
+#include <string>
+#include <limits> // for numeric_limits
+
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Filtration_value = Simplex_tree::Filtration_value;
+
+void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag,
+ Filtration_value &alpha_square_max_value, int &coeff_field_characteristic,
+ Filtration_value &min_persistence);
+
+int main(int argc, char **argv) {
+ std::string off_file_points;
+ std::string output_file_diag;
+ Filtration_value alpha_square_max_value;
+ int coeff_field_characteristic;
+ Filtration_value min_persistence;
+
+ program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic,
+ min_persistence);
+
+ // ----------------------------------------------------------------------------
+ // Init of an alpha complex from an OFF file
+ // ----------------------------------------------------------------------------
+ using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
+ Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points);
+
+ Simplex_tree simplex;
+ if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) {
+ // ----------------------------------------------------------------------------
+ // Display information about the alpha complex
+ // ----------------------------------------------------------------------------
+ std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices()
+ << " simplices - " << simplex.num_vertices() << " vertices." << std::endl;
+
+ // Sort the simplices in the order of the filtration
+ simplex.initialize_filtration();
+
+ std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
+ // Compute the persistence diagram of the complex
+ Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(
+ simplex);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(coeff_field_characteristic);
+
+ pcoh.compute_persistent_cohomology(min_persistence);
+
+ // Output the diagram in filediag
+ if (output_file_diag.empty()) {
+ pcoh.output_diagram();
+ } else {
+ std::cout << "Result in file: " << output_file_diag << std::endl;
+ std::ofstream out(output_file_diag);
+ pcoh.output_diagram(out);
+ out.close();
+ }
+ }
+
+ return 0;
+}
+
+void program_options(int argc, char *argv[], std::string &off_file_points, 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),
+ "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>(&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)
+ ->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),
+ "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 an Alpha 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);
+ }
+}