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 --- src/Rips_complex/utilities/CMakeLists.txt | 8 + .../rips_correlation_matrix_persistence.cpp | 179 +++++++++++++++++++++ src/Rips_complex/utilities/ripscomplex.md | 23 ++- 3 files changed, 209 insertions(+), 1 deletion(-) create mode 100644 src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp (limited to 'src/Rips_complex') diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index baa571fa..b99fc808 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -7,9 +7,13 @@ target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_L add_executable(rips_persistence rips_persistence.cpp) target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) +add_executable(rips_correlation_matrix_persistence rips_correlation_matrix_persistence.cpp) +target_link_libraries(rips_correlation_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + if (TBB_FOUND) target_link_libraries(rips_distance_matrix_persistence ${TBB_LIBRARIES}) target_link_libraries(rips_persistence ${TBB_LIBRARIES}) + target_link_libraries(rips_correlation_matrix_persistence ${TBB_LIBRARIES}) endif() add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $ @@ -17,5 +21,9 @@ add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") +add_test(NAME Rips_complex_utility_from_rips_correlation_matrix COMMAND $ + "${CMAKE_SOURCE_DIR}/data/correlation_matrix/lower_triangular_correlation_matrix.csv" "-c" "0.3" "-d" "3" "-p" "3" "-m" "0") + install(TARGETS rips_distance_matrix_persistence DESTINATION bin) install(TARGETS rips_persistence DESTINATION bin) +install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp new file mode 100644 index 00000000..676ef793 --- /dev/null +++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp @@ -0,0 +1,179 @@ +/* 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(); + } +} diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md index 4291fae7..3f064e67 100644 --- a/src/Rips_complex/utilities/ripscomplex.md +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -39,11 +39,32 @@ Same as `rips_persistence` but taking a distance matrix as input. **Usage** -`rips_persistence [options] ` +`rips_distance_matrix_persistence [options] ` where `` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'. +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. **Example** `rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + + +## rips_correlation_matrix_persistence ## + +Same as `rips_distance_matrix_persistence` but taking a correlation matrix as input. + +**Usage** + +`rips_correlation_matrix_persistence [options] ` + +where +`` is the path to the file containing a correlation matrix. Can be square or lower triangular matrix. Separator is ';'. +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. +Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file. + +**Example** + +`rips_correlation_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` -- cgit v1.2.3