1 files changed, 125 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
new file mode 100644
index 00000000..be74cf50
--- /dev/null
+++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp
@@ -0,0 +1,125 @@
+/*    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 <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+#include <CGAL/algorithm.h>
+#include <CGAL/assertions.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 <iterator>
+#include <vector>
+#include <fstream>  // for std::ofstream
+#include <algorithm>  // for std::sort
+
+
+using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<3> >;
+using Point = Kernel::Point_d;
+using Alpha_complex = Gudhi::alpha_complex::Alpha_complex<Kernel>;
+using Simplex_tree = Gudhi::Simplex_tree<>;
+using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< Simplex_tree,
+      Gudhi::persistent_cohomology::Field_Zp >;
+
+std::vector<Point> random_points() {
+  // Instanciate a random point generator
+  CGAL::Random rng(0);
+
+  // Generate "points_number" random points in a vector
+  std::vector<Point> points;
+
+  // Generates 1000 random 3D points on a sphere of radius 4.0
+  CGAL::Random_points_on_sphere_d<Point> rand_outside(3, 4.0, rng);
+  CGAL::cpp11::copy_n(rand_outside, 1000, std::back_inserter(points));
+  // Generates 2000 random 3D points in a sphere of radius 3.0
+  CGAL::Random_points_in_ball_d<Point> rand_inside(3, 3.0, rng);
+  CGAL::cpp11::copy_n(rand_inside, 2000, std::back_inserter(points));
+
+  return points;
+}
+
+/*
+ * Compare two intervals by dimension, then by length.
+ */
+struct cmp_intervals_by_dim_then_length {
+  explicit cmp_intervals_by_dim_then_length(Simplex_tree * sc)
+      : sc_(sc) { }
+
+  template<typename Persistent_interval>
+  bool operator()(const Persistent_interval & p1, const Persistent_interval & p2) {
+    if (sc_->dimension(get < 0 > (p1)) == sc_->dimension(get < 0 > (p2)))
+      return (sc_->filtration(get < 1 > (p1)) - sc_->filtration(get < 0 > (p1))
+              > sc_->filtration(get < 1 > (p2)) - sc_->filtration(get < 0 > (p2)));
+    else
+      return (sc_->dimension(get < 0 > (p1)) > sc_->dimension(get < 0 > (p2)));
+  }
+  Simplex_tree* sc_;
+};
+
+int main(int argc, char **argv) {
+  std::vector<Point> points = random_points();
+
+  std::cout << "Points size=" << points.size() << std::endl;
+  // Alpha complex persistence computation from generated points
+  Alpha_complex alpha_complex_from_points(points);
+  std::cout << "alpha_complex_from_points" << std::endl;
+
+  Simplex_tree simplex;
+  std::cout << "simplex" << std::endl;
+  if (alpha_complex_from_points.create_complex(simplex, 0.6)) {
+    std::cout << "simplex" << std::endl;
+    // ----------------------------------------------------------------------------
+    // 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;
+
+    Persistent_cohomology pcoh(simplex);
+
+    // initializes the coefficient field for homology - Z/3Z
+    pcoh.init_coefficients(3);
+    pcoh.compute_persistent_cohomology(0.2);
+
+    // Custom sort and output persistence
+    cmp_intervals_by_dim_then_length cmp(&simplex);
+    auto persistent_pairs = pcoh.get_persistent_pairs();
+    std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp);
+    for (auto pair : persistent_pairs) {
+      std::cout << simplex.dimension(get<0>(pair)) << " "
+            << simplex.filtration(get<0>(pair)) << " "
+            << simplex.filtration(get<1>(pair)) << std::endl;
+    }
+
+    // Persistent Betti numbers
+    std::cout << "The persistent Betti numbers in interval [0.40, 0.41] are : ";
+    for (int dim = 0; dim < simplex.dimension(); dim++)
+      std::cout << "b" << dim << " = " << pcoh.persistent_betti_number(dim, 0.40, 0.41) << " ; ";
+    std::cout << std::endl;
+
+    // Betti numbers
+    std::vector<int> betti_numbers = pcoh.betti_numbers();
+    std::cout << "The Betti numbers are : ";
+    for (std::size_t i = 0; i < betti_numbers.size(); i++)
+      std::cout << "b" << i << " = " << betti_numbers[i] << " ; ";
+    std::cout << std::endl;
+  }
+  return 0;
+}
+