From baa98e772b9d97d8b7c22fc8292f54b5047f0569 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 2 Feb 2018 16:49:52 +0000 Subject: Fix readme and doc issue after merge git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3213 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4fd050a6f686044aa6f6dcc290025e321e0dba1b --- .../doc/Intro_persistent_cohomology.h | 13 ++ .../rips_correlation_matrix_persistence.cpp | 179 --------------------- 2 files changed, 13 insertions(+), 179 deletions(-) delete mode 100644 src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp (limited to 'src/Persistent_cohomology') diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 4dbe82c7..3113a22c 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -162,6 +162,19 @@ persistence diagram with a family of field coefficients. Rips_complex/rips_distance_matrix_persistence.cpp computes the Rips complex of a distance matrix and outputs its persistence diagram. +The file should contain square or lower triangular distance matrix with semicolons as separators. +The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input. +Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file. + +\li +Rips_complex/rips_correlation_matrix_persistence.cpp +computes the Rips complex of a correlation matrix and outputs its persistence diagram. + +Note that no check is performed if the matrix given as the input is a correlation matrix. +It is the user responsibility to ensure that this is the case. The input is to be given either as a square or a lower +triangular matrix. +Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file. + \li Alpha_complex/alpha_complex_3d_persistence.cpp computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. diff --git a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp b/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp deleted file mode 100644 index 676ef793..00000000 --- a/src/Persistent_cohomology/example/rips_correlation_matrix_persistence.cpp +++ /dev/null @@ -1,179 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Pawel Dlotko, Vincent Rouvreau - * - * Copyright (C) 2016 INRIA - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include -#include -#include -#include - -#include - -#include -#include -#include // infinity - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree; -using Filtration_value = Simplex_tree::Filtration_value; -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& correlation_min, int& dim_max, int& p, Filtration_value& min_persistence); - -int main(int argc, char* argv[]) { - std::string csv_matrix_file; - std::string filediag; - Filtration_value correlation_min; - int dim_max; - int p; - Filtration_value min_persistence; - - program_options(argc, argv, csv_matrix_file, filediag, correlation_min, dim_max, p, min_persistence); - - Correlation_matrix correlations = - Gudhi::read_lower_triangular_matrix_from_csv_file(csv_matrix_file); - - // Given a correlation matrix M, we compute component-wise M'[i,j] = 1-M[i,j] to get 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"; - } - } - } - - Filtration_value threshold; - //If the correlation_min, being minimal corelation is in the range [0,1], - //change it to 1-correlation_min - if ( ( correlation_min>=0 ) && ( correlation_min<=1 ) ) - { - threshold = 1-correlation_min; - } - else - { - std::cout << "Wrong value of the treshold corelation (should be between 0 and 1). The program will now terminate.\n"; - return 1; - } - - Rips_complex rips_complex_from_file(correlations, threshold); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree simplex_tree; - - rips_complex_from_file.create_complex(simplex_tree, dim_max); - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - //compute persistence - pcoh.compute_persistent_cohomology(min_persistence); - - - //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()) { - write_persistence_intervals_to_stream(processed_persistence_intervals); - } else { - std::ofstream out(filediag); - write_persistence_intervals_to_stream(processed_persistence_intervals,out); - out.close(); - } - return 0; -} - -void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag, - Filtration_value& correlation_min, int& dim_max, int& p, Filtration_value& min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - 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") - ("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(&correlation_min)->default_value(0), - "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); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - 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 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"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} -- cgit v1.2.3