From 300914816e3e5d347efd9eaa5d06c236ad81511e Mon Sep 17 00:00:00 2001 From: cjamin Date: Thu, 5 Oct 2017 08:26:50 +0000 Subject: Move some utils + update doc so that utilities are shown as examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2756 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a707d174a382da7efad3d12a73bb66d2c90da599 --- src/Rips_complex/utilities/CMakeLists.txt | 21 +++ src/Rips_complex/utilities/README | 66 +++++++++ .../utilities/rips_distance_matrix_persistence.cpp | 144 ++++++++++++++++++++ src/Rips_complex/utilities/rips_persistence.cpp | 147 +++++++++++++++++++++ 4 files changed, 378 insertions(+) create mode 100644 src/Rips_complex/utilities/CMakeLists.txt create mode 100644 src/Rips_complex/utilities/README create mode 100644 src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp create mode 100644 src/Rips_complex/utilities/rips_persistence.cpp (limited to 'src/Rips_complex') diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..baa571fa --- /dev/null +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -0,0 +1,21 @@ +cmake_minimum_required(VERSION 2.6) +project(Rips_complex_utilities) + +add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) +target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +add_executable(rips_persistence rips_persistence.cpp) +target_link_libraries(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}) +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") + +install(TARGETS rips_distance_matrix_persistence DESTINATION bin) +install(TARGETS rips_persistence DESTINATION bin) diff --git a/src/Rips_complex/utilities/README b/src/Rips_complex/utilities/README new file mode 100644 index 00000000..ddb7860f --- /dev/null +++ b/src/Rips_complex/utilities/README @@ -0,0 +1,66 @@ +# 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. The output diagram contains one bar per line, written with the convention: + +`p dim b d` + +where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients). + +**Usage** +`rips_persistence [options] ` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. +* `-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 1 with Z/2Z coefficients** +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +outputs: +``` +2 0 0 inf +2 1 0.0983494 inf +2 1 0.104347 inf +2 2 0.138335 inf +``` + +**Example 2 with Z/3Z coefficients** + +rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 + +outputs: +``` +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf +``` + + + + +## `rips_distance_matrix_persistence` ## +Same as `rips_persistence` but taking an distance matrix as input. + +**Example** +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + +outputs: +``` +The complex contains 46 simplices + and has dimension 3 +3 0 0 inf +3 0 0 8.94427 +3 0 0 7.28011 +3 0 0 6.08276 +3 0 0 5.83095 +3 0 0 5.38516 +3 0 0 5 +3 1 11 12.0416 +3 1 6.32456 6.7082 +``` diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp new file mode 100644 index 00000000..d38808c7 --- /dev/null +++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp @@ -0,0 +1,144 @@ +/* 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 // 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 Distance_matrix = std::vector>; + +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); + +int main(int argc, char * argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); + + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file(csv_matrix_file); + Rips_complex rips_complex_from_file(distances, 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); + + 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 & csv_matrix_file + , std::string & filediag + , Filtration_value & threshold + , 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 distance 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") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length 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 set of distance 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/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp new file mode 100644 index 00000000..d504798b --- /dev/null +++ b/src/Rips_complex/utilities/rips_persistence.cpp @@ -0,0 +1,147 @@ +/* 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): Clément Maria + * + * 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 + * 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 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 + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string off_file_points; + std::string filediag; + Filtration_value threshold; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); + + // 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); + + 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 + , Filtration_value & threshold + , 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") + ("max-edge-length,r", + po::value(&threshold)->default_value(std::numeric_limits::infinity()), + "Maximal length 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 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