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Diffstat (limited to 'src/Collapse/utilities')
4 files changed, 429 insertions, 0 deletions
diff --git a/src/Collapse/utilities/CMakeLists.txt b/src/Collapse/utilities/CMakeLists.txt new file mode 100644 index 00000000..c742144b --- /dev/null +++ b/src/Collapse/utilities/CMakeLists.txt @@ -0,0 +1,33 @@ +project(Collapse_utilities) + +# From a point cloud +add_executable ( point_cloud_edge_collapse_rips_persistence point_cloud_edge_collapse_rips_persistence.cpp ) +target_link_libraries(point_cloud_edge_collapse_rips_persistence Boost::program_options) + +if (TBB_FOUND) + target_link_libraries(point_cloud_edge_collapse_rips_persistence ${TBB_LIBRARIES}) +endif() +add_test(NAME Edge_collapse_utilities_point_cloud_rips_persistence COMMAND $<TARGET_FILE:point_cloud_edge_collapse_rips_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "off_results.pers") + +install(TARGETS point_cloud_edge_collapse_rips_persistence DESTINATION bin) + +# From a distance matrix +add_executable ( distance_matrix_edge_collapse_rips_persistence distance_matrix_edge_collapse_rips_persistence.cpp ) +target_link_libraries(distance_matrix_edge_collapse_rips_persistence Boost::program_options) + +if (TBB_FOUND) + target_link_libraries(distance_matrix_edge_collapse_rips_persistence ${TBB_LIBRARIES}) +endif() +add_test(NAME Edge_collapse_utilities_distance_matrix_rips_persistence COMMAND $<TARGET_FILE:distance_matrix_edge_collapse_rips_persistence> + "${CMAKE_SOURCE_DIR}/data/distance_matrix/tore3D_1307_distance_matrix.csv" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "csv_results.pers") + +install(TARGETS distance_matrix_edge_collapse_rips_persistence DESTINATION bin) + +if (DIFF_PATH) + add_test(Edge_collapse_utilities_diff_persistence ${DIFF_PATH} + "off_results.pers" "csv_results.pers") + set_tests_properties(Edge_collapse_utilities_diff_persistence PROPERTIES DEPENDS + "Edge_collapse_utilities_point_cloud_rips_persistence;Edge_collapse_utilities_distance_matrix_rips_persistence") + +endif() diff --git a/src/Collapse/utilities/collapse.md b/src/Collapse/utilities/collapse.md new file mode 100644 index 00000000..1f41bb1f --- /dev/null +++ b/src/Collapse/utilities/collapse.md @@ -0,0 +1,63 @@ +--- +layout: page +title: "Collapse" +meta_title: "Edge collapse" +teaser: "" +permalink: /collapse/ +--- +{::comment} +Leave the lines above as it is required by the web site generator 'Jekyll' +{:/comment} + + +## point_cloud_edge_collapse_rips_persistence ## +This program computes the Rips graph defined on a set of input points, using Euclidean distance, and collapses edges. +This program finally computes persistent homology with coefficient field *Z/pZ* of the Rips complex built on top of these collapse edges. +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** + +`point_cloud_edge_collapse_rips_persistence [options] <OFF input file>` + +**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. +* `-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. +* `-i [ --edge-collapse-iterations ]` (default = 1) Number of iterations edge collapse is performed. + +Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. + +**Example 1 with Z/2Z coefficients** + +`point_cloud_edge_collapse_rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +**Example 2 with Z/3Z coefficients** + +`point_cloud_edge_collapse_rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3` + + +## distance_matrix_edge_collapse_rips_persistence ## + +Same as `point_cloud_edge_collapse_rips_persistence` but taking a distance matrix as input. + +**Usage** + +`distance_matrix_edge_collapse_rips_persistence [options] <CSV input file>` + +where +`<CSV input file>` 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** + +`distance_matrix_edge_collapse_rips_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` + diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp new file mode 100644 index 00000000..11ee5871 --- /dev/null +++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp @@ -0,0 +1,152 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Siddharth Pritam, Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#include <gudhi/Flag_complex_edge_collapser.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> + +#include <boost/program_options.hpp> +#include <boost/range/adaptor/transformed.hpp> + +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Vertex_handle = Simplex_tree::Vertex_handle; + +using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; +using Distance_matrix = std::vector<std::vector<Filtration_value>>; + +void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag, + Filtration_value& threshold, int& dim_max, int& p, int& edge_collapse_iter_nb, + Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value threshold; + int dim_max = 2; + int p; + int edge_collapse_iter_nb; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, edge_collapse_iter_nb, + min_persistence); + + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); + std::cout << "Read the distance matrix succesfully, of size: " << distances.size() << std::endl; + + Proximity_graph proximity_graph = Gudhi::compute_proximity_graph<Simplex_tree>(boost::irange((size_t)0, + distances.size()), + threshold, + [&distances](size_t i, size_t j) { + return distances[j][i]; + }); + + auto edges_from_graph = boost::adaptors::transform(edges(proximity_graph), [&](auto&&edge){ + return std::make_tuple(source(edge, proximity_graph), + target(edge, proximity_graph), + get(Gudhi::edge_filtration_t(), proximity_graph, edge)); + }); + std::vector<Filtered_edge> edges_list(edges_from_graph.begin(), edges_from_graph.end()); + std::vector<Filtered_edge> remaining_edges; + for (int iter = 0; iter < edge_collapse_iter_nb; iter++) { + auto remaining_edges = Gudhi::collapse::flag_complex_collapse_edges(edges_list); + edges_list = std::move(remaining_edges); + remaining_edges.clear(); + } + + Simplex_tree stree; + for (Vertex_handle vertex = 0; static_cast<std::size_t>(vertex) < distances.size(); vertex++) { + // insert the vertex with a 0. filtration value just like a Rips + stree.insert_simplex({vertex}, 0.); + } + for (auto filtered_edge : edges_list) { + stree.insert_simplex({std::get<0>(filtered_edge), std::get<1>(filtered_edge)}, std::get<2>(filtered_edge)); + } + + stree.expansion(dim_max); + + std::cout << "The complex contains " << stree.num_simplices() << " simplices after collapse. \n"; + std::cout << " and has dimension " << stree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + stree.initialize_filtration(); + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(stree); + // initializes the coefficient field for homology + pcoh.init_coefficients(3); + + pcoh.compute_persistent_cohomology(min_persistence); + 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, int& edge_collapse_iter_nb, + Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()( + "input-file", po::value<std::string>(&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<std::string>(&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<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "edge-collapse-iterations,i", po::value<int>(&edge_collapse_iter_nb)->default_value(1), + "Number of iterations edge collapse is performed.")( + "min-persistence,m", po::value<Filtration_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 after edge collapse 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; + exit(-1); + } +} diff --git a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp new file mode 100644 index 00000000..0eea742c --- /dev/null +++ b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp @@ -0,0 +1,181 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Siddharth Pritam, Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#include <gudhi/Flag_complex_edge_collapser.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/graph_simplicial_complex.h> + +#include <boost/program_options.hpp> +#include <boost/range/adaptor/transformed.hpp> + +#include<utility> // for std::pair +#include<vector> +#include<tuple> + +// Types definition + +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Vertex_handle = Simplex_tree::Vertex_handle; +using Point = std::vector<Filtration_value>; +using Vector_of_points = std::vector<Point>; + +using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& threshold, int& dim_max, int& p, int& edge_collapse_iter_nb, + Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string off_file_points; + std::string filediag; + double threshold; + int dim_max; + int p; + int edge_collapse_iter_nb; + double min_persistence; + + program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, edge_collapse_iter_nb, min_persistence); + + std::cout << "The current input values to run the program is: " << std::endl; + std::cout << "min_persistence, threshold, max_complex_dimension, off_file_points, filediag" + << std::endl; + std::cout << min_persistence << ", " << threshold << ", " << dim_max + << ", " << off_file_points << ", " << filediag << std::endl; + + Gudhi::Points_off_reader<Point> off_reader(off_file_points); + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << off_file_points << "\n"; + exit(-1); // ----- >> + } + + Vector_of_points point_vector = off_reader.get_point_cloud(); + if (point_vector.size() <= 0) { + std::cerr << "Empty point cloud." << std::endl; + exit(-1); // ----- >> + } + + std::cout << "Successfully read " << point_vector.size() << " point_vector.\n"; + std::cout << "Ambient dimension is " << point_vector[0].size() << ".\n"; + + Proximity_graph proximity_graph = Gudhi::compute_proximity_graph<Simplex_tree>(point_vector, + threshold, + Gudhi::Euclidean_distance()); + + if (num_edges(proximity_graph) <= 0) { + std::cerr << "Total number of egdes are zero." << std::endl; + exit(-1); + } + + auto edges_from_graph = boost::adaptors::transform(edges(proximity_graph), [&](auto&&edge){ + return std::make_tuple(source(edge, proximity_graph), + target(edge, proximity_graph), + get(Gudhi::edge_filtration_t(), proximity_graph, edge)); + }); + std::vector<Filtered_edge> edges_list(edges_from_graph.begin(), edges_from_graph.end()); + + std::vector<Filtered_edge> remaining_edges; + for (int iter = 0; iter < edge_collapse_iter_nb; iter++) { + auto remaining_edges = Gudhi::collapse::flag_complex_collapse_edges(edges_list); + edges_list = std::move(remaining_edges); + remaining_edges.clear(); + } + + Simplex_tree stree; + for (Vertex_handle vertex = 0; static_cast<std::size_t>(vertex) < point_vector.size(); vertex++) { + // insert the vertex with a 0. filtration value just like a Rips + stree.insert_simplex({vertex}, 0.); + } + + for (auto filtered_edge : edges_list) { + stree.insert_simplex({std::get<0>(filtered_edge), std::get<1>(filtered_edge)}, std::get<2>(filtered_edge)); + } + + stree.expansion(dim_max); + + std::cout << "The complex contains " << stree.num_simplices() << " simplices after collapse. \n"; + std::cout << " and has dimension " << stree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + stree.initialize_filtration(); + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(stree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + 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, int& edge_collapse_iter_nb, + Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value<std::string>(&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<std::string>(&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<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "edge-collapse-iterations,i", po::value<int>(&edge_collapse_iter_nb)->default_value(1), + "Number of iterations edge collapse is performed.")( + "min-persistence,m", po::value<Filtration_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, after edge collapse, 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; + exit(-1); + } +} |