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author | pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-09-25 20:28:02 +0000 |
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committer | pdlotko <pdlotko@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-09-25 20:28:02 +0000 |
commit | f48ae2be7dcd552f44723b3a6b02cc9aae361aca (patch) | |
tree | cce66d12d54d23e8400908124f9e0064eaeef2f4 /src/Rips_complex | |
parent | 1d611ca664d78d3b0b53264c52b04a8396383140 (diff) |
a missing file...
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
Diffstat (limited to 'src/Rips_complex')
-rw-r--r-- | src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp | 77 |
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 new file mode 100644 index 00000000..0acdfe83 --- /dev/null +++ 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; +} |