From c524232f734de875d69e2f190f01a6c976024368 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Thu, 14 Jun 2018 20:39:01 +0200 Subject: GUDHI 2.2.0 as released by upstream in a tarball. --- ...e_one_skeleton_rips_from_correlation_matrix.cpp | 81 ++++++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp (limited to 'example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp') diff --git a/example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp b/example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp new file mode 100644 index 00000000..05bacb9f --- /dev/null +++ b/example/Rips_complex/example_one_skeleton_rips_from_correlation_matrix.cpp @@ -0,0 +1,81 @@ +#include +#include +#include + +#include +#include +#include +#include // 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; + using Distance_matrix = std::vector>; + + // 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: + // ---------------------------------------------------------------------------- + double threshold = 0; + for (size_t i = 0; i != correlations.size(); ++i) { + for (size_t j = 0; j != correlations[i].size(); ++j) { + // Here we check if our data comes from corelation matrix. + if ((correlations[i][j] < -1) || (correlations[i][j] > 1)) { + std::cerr << "The input matrix is not a correlation matrix. The program will now terminate.\n"; + throw "The input matrix is not a correlation matrix. The program will now terminate.\n"; + } + correlations[i][j] = 1 - correlations[i][j]; + // Here we make sure that we will get the treshold value equal to maximal + // distance in the matrix. + if (correlations[i][j] > threshold) threshold = correlations[i][j]; + } + } + + //----------------------------------------------------------------------------- + // Now the correlation matrix is a distance matrix and can be processed further. + //----------------------------------------------------------------------------- + Distance_matrix distances = correlations; + + 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. Note that + // the filtration displayed here comes from the distance matrix computed + // above, which is 1 - initial correlation matrix. Only this way, we obtain + // a complex with filtration. If a correlation matrix is used instead, we would + // have a reverse filtration (i.e. filtration of boundary of each simplex S + // is greater or equal to the filtration of S). + // ---------------------------------------------------------------------------- + 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; +} -- cgit v1.2.3