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git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2713 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ecdf0da96de01e37758e157d84aee13c8825dc0e

1 files changed, 77 insertions, 0 deletions

diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
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+++ b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp
@@ -0,0 +1,77 @@
+#include <gudhi/Rips_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/distance_functions.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for std::numeric_limits
+
+int main() {
+  // Type definitions
+  using Simplex_tree = Gudhi::Simplex_tree<>;
+  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 correlation matrix is:
+  // |1	    0.06	0.23	0.01	0.89|
+  // |0.06	1	    0.74	0.01	0.61|
+  // |0.23	0.74	1	    0.72	0.03|
+  // |0.01	0.01	0.72	1	    0.7 |
+  // |0.89	0.61	0.03	0.7	    1   |
+
+
+  Distance_matrix correlations;
+  correlations.push_back({});
+  correlations.push_back({0.06});
+  correlations.push_back({0.23, 0.74});
+  correlations.push_back({0.01, 0.01, 0.72});
+  correlations.push_back({0.89, 0.61, 0.03, 0.7});
+
+  // ----------------------------------------------------------------------------
+  // Convert correlation matrix to a distance matrix:
+  // ----------------------------------------------------------------------------
+  for ( size_t i = 0 ; i != correlations.size() ; ++i )
+  {
+	  for ( size_t j = 0 ; j != correlations[i].size() ; ++j )
+	  {
+		  correlations[i][j] = 1-correlations[i][j];
+		  if ( correlations[i][j] < 0 )
+		  {
+			  std::cerr << "The input matrix is not a correlation matrix. \n";
+			  throw "The input matrix is not a correlation matrix. \n";
+		  }		  
+	  }
+  } 
+  
+  //-----------------------------------------------------------------------------
+  // Now the correlation matrix is really the distance matrix and can be processed further. 
+  //-----------------------------------------------------------------------------
+  Distance_matrix distances = correlations;
+  
+  double threshold = 1.0;
+  Rips_complex rips_complex_from_points(distances, threshold);
+
+  Simplex_tree stree;
+  rips_complex_from_points.create_complex(stree, 1);
+  // ----------------------------------------------------------------------------
+  // Display information about the one skeleton Rips complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Rips complex is of dimension " << stree.dimension() <<
+               " - " << stree.num_simplices() << " simplices - " <<
+               stree.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 : stree.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+
+  return 0;
+}