From 0729a55a67503c068e4843c63930d6b29e76f7ac Mon Sep 17 00:00:00 2001 From: pdlotko Date: Fri, 3 Nov 2017 05:10:17 +0000 Subject: a few more changes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2823 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d12b2413620003883e82b3022f8d933aa05e2856 --- .../rips_correlation_matrix_persistence.cpp | 56 +++++++++++++++++++--- 1 file changed, 50 insertions(+), 6 deletions(-) (limited to 'src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp') diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp index 41cf915a..6f12dada 100644 --- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp @@ -24,6 +24,7 @@ #include #include #include +#include #include @@ -38,6 +39,7 @@ using Rips_complex = Gudhi::rips_complex::Rips_complex; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; using Correlation_matrix = std::vector>; +using intervals_common = Gudhi::Persistence_interval_common< double , int >; void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag, Filtration_value& threshold, int& dim_max, int& p, Filtration_value& min_persistence); @@ -66,6 +68,13 @@ int main(int argc, char* argv[]) { } } + //If the treshold, being minimal corelation is in the range [0,1], + //change it to 1-threshold + if ( ( threshold>=0 ) && ( threshold<=1 ) ) + { + threshold = 1-threshold; + } + Rips_complex rips_complex_from_file(correlations, threshold); // Construct the Rips complex in a Simplex Tree @@ -82,15 +91,34 @@ int main(int argc, char* argv[]) { Persistent_cohomology pcoh(simplex_tree); // initializes the coefficient field for homology pcoh.init_coefficients(p); - + //compute persistence pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag + + + //invert the persistence diagram + auto pairs = pcoh.get_persistent_pairs(); + std::vector< intervals_common > processed_persistence_intervals; + processed_persistence_intervals.reserve( pairs.size() ); + for (auto pair :pairs ) + { + double birth = 1-simplex_tree.filtration( get<0>(pair) ); + double death = 1-simplex_tree.filtration( get<1>(pair) ); + unsigned dimension = (unsigned)simplex_tree.dimension( get<0>(pair) ); + int field = get<2>(pair); + processed_persistence_intervals.push_back( + intervals_common(birth, death,dimension,field) + ); + } + + //sort the processed intervals: + std::sort( processed_persistence_intervals.begin() , processed_persistence_intervals.end() ); + + //and write them to a file if (filediag.empty()) { - pcoh.output_diagram(); + write_persistence_intervals_to_stream(processed_persistence_intervals); } else { std::ofstream out(filediag); - pcoh.output_diagram(out); + write_persistence_intervals_to_stream(processed_persistence_intervals,out); out.close(); } return 0; @@ -103,6 +131,9 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std:: hidden.add_options()( "input-file", po::value(&csv_matrix_file), "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); + hidden.add_options() + ("input-file", po::value(&csv_matrix_file), + "Name of file containing a corelation matrix. Can be square or lower triangular matrix. Separator is ';'."); po::options_description visible("Allowed options", 100); visible.add_options()("help,h", "produce help message")( @@ -118,6 +149,19 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std:: "min-persistence,m", po::value(&min_persistence), "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " "intervals"); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("min-edge-corelation,c", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Minimal corelation of an edge for the Rips complex construction.") + ("cpx-dimension,d", po::value(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::value(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals"); po::positional_options_description pos; pos.add("input-file", 1); @@ -132,7 +176,7 @@ void program_options(int argc, char* argv[], std::string& csv_matrix_file, std:: if (vm.count("help") || !vm.count("input-file")) { std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of distance matrix.\n \n"; + std::cout << "of a Rips complex defined on a corelation matrix.\n \n"; std::cout << "The output diagram contains one bar per line, written with the convention: \n"; std::cout << " p dim b d \n"; std::cout << "where dim is the dimension of the homological feature,\n"; -- cgit v1.2.3