1 files changed, 152 insertions, 0 deletions
diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp
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+++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_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):       Siddharth Pritam, Vincent Rouvreau
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#include <gudhi/Flag_complex_edge_collapser.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/reader_utils.h>
+#include <gudhi/graph_simplicial_complex.h>
+
+#include <boost/program_options.hpp>
+#include <boost/range/adaptor/transformed.hpp>
+
+using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
+using Filtration_value = Simplex_tree::Filtration_value;
+using Vertex_handle = Simplex_tree::Vertex_handle;
+
+using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>;
+using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>;
+
+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, int& edge_collapse_iter_nb,
+                     Filtration_value& min_persistence);
+
+int main(int argc, char* argv[]) {
+  std::string csv_matrix_file;
+  std::string filediag;
+  Filtration_value threshold;
+  int dim_max = 2;
+  int p;
+  int edge_collapse_iter_nb;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, edge_collapse_iter_nb,
+                  min_persistence);
+
+  Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file);
+  std::cout << "Read the distance matrix succesfully, of size: " << distances.size() << std::endl;
+
+  Proximity_graph proximity_graph = Gudhi::compute_proximity_graph<Simplex_tree>(boost::irange((size_t)0,
+                                                                                               distances.size()),
+                                                                                 threshold,
+                                                                                 [&distances](size_t i, size_t j) {
+                                                                                   return distances[j][i];
+                                                                                 });
+
+  auto edges_from_graph = boost::adaptors::transform(edges(proximity_graph), [&](auto&&edge){
+        return std::make_tuple(source(edge, proximity_graph),
+                               target(edge, proximity_graph),
+                               get(Gudhi::edge_filtration_t(), proximity_graph, edge));
+      });
+  std::vector<Filtered_edge> edges_list(edges_from_graph.begin(), edges_from_graph.end());
+  std::vector<Filtered_edge> remaining_edges;
+  for (int iter = 0; iter < edge_collapse_iter_nb; iter++) {
+    auto remaining_edges = Gudhi::collapse::flag_complex_collapse_edges(edges_list);
+    edges_list = std::move(remaining_edges);
+    remaining_edges.clear();
+  }
+
+  Simplex_tree stree;
+  for (Vertex_handle vertex = 0; static_cast<std::size_t>(vertex) < distances.size(); vertex++) {
+    // insert the vertex with a 0. filtration value just like a Rips
+    stree.insert_simplex({vertex}, 0.);
+  }
+  for (auto filtered_edge : edges_list) {
+    stree.insert_simplex({std::get<0>(filtered_edge), std::get<1>(filtered_edge)}, std::get<2>(filtered_edge));
+  }
+
+  stree.expansion(dim_max);
+
+  std::cout << "The complex contains " << stree.num_simplices() << " simplices  after collapse. \n";
+  std::cout << "   and has dimension " << stree.dimension() << " \n";
+
+  // Sort the simplices in the order of the filtration
+  stree.initialize_filtration();
+  // Compute the persistence diagram of the complex
+  Persistent_cohomology pcoh(stree);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(3);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+  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, int& edge_collapse_iter_nb,
+                     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.")(
+      "edge-collapse-iterations,i", po::value<int>(&edge_collapse_iter_nb)->default_value(1),
+      "Number of iterations edge collapse is performed.")(
+      "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 after edge collapse 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);
+  }
+}