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. --- utilities/Rips_complex/CMakeLists.txt | 15 +- .../rips_correlation_matrix_persistence.cpp | 171 +++++++++++++++++++++ .../rips_distance_matrix_persistence.cpp | 2 +- utilities/Rips_complex/rips_persistence.cpp | 2 +- utilities/Rips_complex/ripscomplex.md | 66 +++++++- utilities/Rips_complex/sparse_rips_persistence.cpp | 133 ++++++++++++++++ 6 files changed, 383 insertions(+), 6 deletions(-) create mode 100644 utilities/Rips_complex/rips_correlation_matrix_persistence.cpp create mode 100644 utilities/Rips_complex/sparse_rips_persistence.cpp (limited to 'utilities/Rips_complex') diff --git a/utilities/Rips_complex/CMakeLists.txt b/utilities/Rips_complex/CMakeLists.txt index baa571fa..4b565628 100644 --- a/utilities/Rips_complex/CMakeLists.txt +++ b/utilities/Rips_complex/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_utilities) add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) @@ -7,15 +6,29 @@ 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}) + +add_executable(sparse_rips_persistence sparse_rips_persistence.cpp) +target_link_libraries(sparse_rips_persistence ${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}) + target_link_libraries(sparse_rips_persistence ${TBB_LIBRARIES}) endif() add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $ "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") add_test(NAME Rips_complex_utility_from_rips_on_tore_3D 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") +add_test(NAME Sparse_rips_complex_utility_on_tore_3D COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-e" "0.5" "-m" "0.2" "-d" "3" "-p" "2") install(TARGETS rips_distance_matrix_persistence DESTINATION bin) install(TARGETS rips_persistence DESTINATION bin) +install(TARGETS rips_correlation_matrix_persistence DESTINATION bin) +install(TARGETS sparse_rips_persistence DESTINATION bin) diff --git a/utilities/Rips_complex/rips_correlation_matrix_persistence.cpp b/utilities/Rips_complex/rips_correlation_matrix_persistence.cpp new file mode 100644 index 00000000..c78677d2 --- /dev/null +++ b/utilities/Rips_complex/rips_correlation_matrix_persistence.cpp @@ -0,0 +1,171 @@ +/* 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 +#include // for sort + +// 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; + +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); + + Filtration_value threshold = 0; + + // 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]; + // Here we make sure that the values of corelations lie between -1 and 1. + // If not, we throw an exception. + 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"; + } + if (correlations[i][j] > threshold) threshold = correlations[i][j]; + } + } + + 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. The reason for this procedure is the following: + // The input to the program is a corelation matrix M. When processing it, it is + // turned into 1-M and the obtained persistence intervals are in '1-M' units. + // Below we reverse every (birth,death) pair into (1-birth, 1-death) pair + // so that the input and the output to the program is expressed in the same + // units. + auto pairs = pcoh.get_persistent_pairs(); + std::vector 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); + } + 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/utilities/Rips_complex/rips_distance_matrix_persistence.cpp b/utilities/Rips_complex/rips_distance_matrix_persistence.cpp index ca3c0327..53191ca7 100644 --- a/utilities/Rips_complex/rips_distance_matrix_persistence.cpp +++ b/utilities/Rips_complex/rips_distance_matrix_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/utilities/Rips_complex/rips_persistence.cpp b/utilities/Rips_complex/rips_persistence.cpp index 8405c014..7cee927e 100644 --- a/utilities/Rips_complex/rips_persistence.cpp +++ b/utilities/Rips_complex/rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/utilities/Rips_complex/ripscomplex.md b/utilities/Rips_complex/ripscomplex.md index 4291fae7..6df49310 100644 --- a/utilities/Rips_complex/ripscomplex.md +++ b/utilities/Rips_complex/ripscomplex.md @@ -1,7 +1,15 @@ +--- +layout: page +title: "Rips complex" +meta_title: "Rips complex" +teaser: "" +permalink: /ripscomplex/ +--- +{::comment} +Leave the lines above as it is required by the web site generator 'Jekyll' +{:/comment} -# Rips complex # - ## rips_persistence ## This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention: @@ -39,11 +47,63 @@ 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` + +**Warning** + +As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical tool will not work +properly, this is a known issue. + + +## sparse_rips_persistence ## +This program computes the persistent homology with coefficient field *Z/pZ* +of a sparse (1+epsilon)-approximation of the Rips complex defined on a set of input Euclidean points. The output diagram contains one bar per line, written with the convention: + +`p dim birth death` + +where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). + +**Usage** + +`sparse_rips_persistence [options] ` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +**Example with Z/2Z coefficients** + +`sparse_rips_persistence ../../data/points/tore3D_1307.off -e .5 -m .2 -d 3 -p 2` diff --git a/utilities/Rips_complex/sparse_rips_persistence.cpp b/utilities/Rips_complex/sparse_rips_persistence.cpp new file mode 100644 index 00000000..bcd5c2c5 --- /dev/null +++ b/utilities/Rips_complex/sparse_rips_persistence.cpp @@ -0,0 +1,133 @@ +/* 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): Marc Glisse, Clément Maria + * + * Copyright (C) 2018 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 + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree; +using Filtration_value = Simplex_tree::Filtration_value; +using Sparse_rips = Gudhi::rips_complex::Sparse_rips_complex; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; +using Point = std::vector; +using Points_off_reader = Gudhi::Points_off_reader; + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon, + int& dim_max, int& p, Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string off_file_points; + std::string filediag; + double epsilon; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, epsilon, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Sparse_rips sparse_rips(off_reader.get_point_cloud(), Gudhi::Euclidean_distance(), epsilon); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree simplex_tree; + + sparse_rips.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); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, double& epsilon, + 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(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + 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")( + "approximation,e", po::value(&epsilon)->default_value(.5), + "Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.")( + "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 sparse (1+epsilon)-approximation of the Rips complex \ndefined on a set of input points.\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