Add distance matrix rips construction (doc, code, test)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1766 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6b9bdecbaf0aca12facb023e66bdea71e8e8cd38

1 files changed, 68 insertions, 0 deletions

diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
new file mode 100644
index 00000000..54fa3aa1
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+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp
@@ -0,0 +1,68 @@
+#include <gudhi/Rips_complex.h>
+// to construct a simplex_tree from rips complex
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <limits>  // for std::numeric_limits
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " threshold\n";
+  std::cerr << "       i.e.: " << progName << " 12.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) usage(argc, argv[0]);
+
+  double threshold = atof(argv[1]);
+
+  // Type definitions
+  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 Distance_matrix = std::vector<std::vector<Filtration_value>>;
+
+  // User defined distance matrix is:
+  // | 0    0.94 0.77 0.99 0.11  |
+  // | 0.94 0    0.26 0.99 0.39  |
+  // | 0.77 0.26 0    0.28 0.97  |
+  // | 0.99 0.99 0.28 0    0.30  |
+  // | 0.11 0.39 0.97 0.30 0     |
+
+  Distance_matrix distances;
+  distances.push_back({});
+  distances.push_back({0.94});
+  distances.push_back({0.77, 0.26});
+  distances.push_back({0.99, 0.99, 0.28});
+  distances.push_back({0.11, 0.39, 0.97, 0.30});
+  
+  // ----------------------------------------------------------------------------
+  // Init of a rips complex from points
+  // ----------------------------------------------------------------------------
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree simplex;
+  if (rips_complex_from_points.create_complex(simplex, 1)) {
+    // ----------------------------------------------------------------------------
+    // Display information about the one skeleton rips complex
+    // ----------------------------------------------------------------------------
+    std::cout << "Rips complex is of dimension " << simplex.dimension() <<
+        " - " << simplex.num_simplices() << " simplices - " <<
+        simplex.num_vertices() << " vertices." << std::endl;
+
+    std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" <<
+        std::endl;
+    for (auto f_simplex : simplex.filtration_simplex_range()) {
+      std::cout << "   ( ";
+      for (auto vertex : simplex.simplex_vertex_range(f_simplex)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << ") -> " << "[" << simplex.filtration(f_simplex) << "] ";
+      std::cout << std::endl;
+    }
+  }
+  return 0;
+}