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diff --git a/src/Rips_complex/concept/Simplicial_complex_for_rips.h b/src/Rips_complex/concept/Simplicial_complex_for_rips.h new file mode 100644 index 00000000..dc871177 --- /dev/null +++ b/src/Rips_complex/concept/Simplicial_complex_for_rips.h @@ -0,0 +1,55 @@ +/* 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): 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_ +#define CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_ + +namespace Gudhi { + +namespace rips_complex { + +/** \brief The concept SimplicialComplexForRips describes the requirements for a type to implement a simplicial + * complex, that can be created from a `Rips_complex`. The only available model for the moment is the `Simplex_tree`. + */ +struct SimplicialComplexForRips { + /** \brief Handle to specify the simplex filtration value. */ + typedef unspecified Filtration_value; + + /** \brief Inserts a given range `Gudhi::rips_complex::Rips_complex::OneSkeletonGraph` in the simplicial + * complex. */ + template<class OneSkeletonGraph> + void insert_graph(const OneSkeletonGraph& skel_graph); + + /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension as + * explained in \ref ripsdefinition. */ + void expansion(int max_dim); + + /** \brief Returns the number of vertices in the simplicial complex. */ + std::size_t num_vertices(); + +}; + +} // namespace rips_complex + +} // namespace Gudhi + +#endif // CONCEPT_RIPS_COMPLEX_SIMPLICIAL_COMPLEX_FOR_RIPS_H_ diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h new file mode 100644 index 00000000..64fd34bc --- /dev/null +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -0,0 +1,152 @@ +/* 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, 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_ +#define DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_ + +namespace Gudhi { + +namespace rips_complex { + +/** \defgroup rips_complex Rips complex + * + * \author Clément Maria, Pawel Dlotko, Vincent Rouvreau + * + * @{ + * + * \section ripsdefinition Rips complex definition + * + * Rips_complex + * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a> is a + * one skeleton graph that allows to construct a + * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> + * from it. + * The input can be a point cloud with a given distance function, or a distance matrix. + * + * The filtration value of each edge is computed from a user-given distance function, or directly from the distance + * matrix. + * + * All edges that have a filtration value strictly greater than a given threshold value are not inserted into + * the complex. + * + * When creating a simplicial complex from this one skeleton graph, rips inserts the one skeleton graph into the data + * structure, and then expands the simplicial when required. + * + * \image html "rips_complex_representation.png" "Rips-complex one skeleton graph representation" + * + * On this example, as edges (4,5), (4,6) and (5,6) are in the complex, simplex (4,5,6) is added with the filtration + * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$. + * And so on for simplex (0,1,2,3). + * + * \section ripspointsdistance Point cloud and distance function + * + * \subsection ripspointscloudexample Example from a point cloud and a distance function + * + * This example builds the one skeleton graph from the given points, threshold value, and distance function. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Rips_complex/example_one_skeleton_rips_from_points.cpp + * + * When launching (rips maximal distance between 2 points is 12.0, is expanded until dimension 1 - one skeleton graph + * in other words): + * + * \code $> ./oneskeletonripspoints + * \endcode + * + * the program output is: + * + * \include Rips_complex/one_skeleton_rips_for_doc.txt + * + * \subsection ripsoffexample Example from OFF file + * + * This example builds the Rips_complex from the given points in an OFF file, threshold value, and distance + * function. + * Then it creates a `Simplex_tree` with it. + * + * + * Then, it is asked to display information about the rips complex. + * + * \include Rips_complex/example_rips_complex_from_off_file.cpp + * + * When launching: + * + * \code $> ./ripsoffreader ../../data/points/alphacomplexdoc.off 12.0 3 + * \endcode + * + * the program output is: + * + * \include Rips_complex/full_skeleton_rips_for_doc.txt + * + * + * + * \section ripsdistancematrix Distance matrix + * + * \subsection ripsdistancematrixexample Example from a distance matrix + * + * This example builds the one skeleton graph from the given distance matrix and threshold value. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp + * + * When launching (rips maximal distance between 2 points is 1.0, is expanded until dimension 1 - one skeleton graph + * with other words): + * + * \code $> ./oneskeletonripsdistance + * \endcode + * + * the program output is: + * + * \include Rips_complex/one_skeleton_rips_for_doc.txt + * + * \subsection ripscsvdistanceexample Example from a distance matrix read in a csv file + * + * This example builds the one skeleton graph from the given distance matrix read in a csv file and threshold value. + * Then it creates a `Simplex_tree` with it. + * + * + * Then, it is asked to display information about the rips complex. + * + * \include Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp + * + * When launching: + * + * \code $> ./ripscsvdistancereader ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3 + * \endcode + * + * the program output is: + * + * \include Rips_complex/full_skeleton_rips_for_doc.txt + * + * \copyright GNU General Public License v3. + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + */ +/** @} */ // end defgroup rips_complex + +} // namespace rips_complex + +} // namespace Gudhi + +#endif // DOC_RIPS_COMPLEX_INTRO_RIPS_COMPLEX_H_ diff --git a/src/Rips_complex/doc/rips_complex_representation.ipe b/src/Rips_complex/doc/rips_complex_representation.ipe new file mode 100644 index 00000000..7f6028f4 --- /dev/null +++ b/src/Rips_complex/doc/rips_complex_representation.ipe @@ -0,0 +1,326 @@ +<?xml version="1.0"?> +<!DOCTYPE ipe SYSTEM "ipe.dtd"> +<ipe version="70107" creator="Ipe 7.1.10"> +<info created="D:20150603143945" 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ripsoffreader example_rips_complex_from_off_file.cpp ) +target_link_libraries(ripsoffreader ${Boost_SYSTEM_LIBRARY}) + +add_executable ( oneskeletonripspoints example_one_skeleton_rips_from_points.cpp ) +target_link_libraries(oneskeletonripspoints ${Boost_SYSTEM_LIBRARY}) + +# Distance matrix +add_executable ( oneskeletonripsdistance example_one_skeleton_rips_from_distance_matrix.cpp ) +target_link_libraries(oneskeletonripsdistance ${Boost_SYSTEM_LIBRARY}) + +add_executable ( ripscsvdistancereader example_rips_complex_from_csv_distance_matrix_file.cpp ) +target_link_libraries(ripscsvdistancereader ${Boost_SYSTEM_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(ripsoffreader ${TBB_LIBRARIES}) + target_link_libraries(oneskeletonripspoints ${TBB_LIBRARIES}) + target_link_libraries(oneskeletonripsdistance ${TBB_LIBRARIES}) + target_link_libraries(ripscsvdistancereader ${TBB_LIBRARIES}) +endif() + +add_test(oneskeletonripspoints ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripspoints) +add_test(oneskeletonripsdistance ${CMAKE_CURRENT_BINARY_DIR}/oneskeletonripsdistance) + +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(ripsoffreader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt) +add_test(ripsoffreader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader alphacomplexdoc.off 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt) + +file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(ripscsvdistancereader_doc_12_1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 1 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt) +add_test(ripscsvdistancereader_doc_12_3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvdistancereader full_square_distance_matrix.csv 12.0 3 ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt) + + +if (DIFF_PATH) + # Do not forget to copy test results files in current binary dir + file(COPY "one_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "full_skeleton_rips_for_doc.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(ripsoffreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt) + add_test(ripsoffreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt) + add_test(ripscsvreader_doc_12_1_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt) + add_test(ripscsvreader_doc_12_3_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt) +endif() diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp new file mode 100644 index 00000000..90bd8e38 --- /dev/null +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_distance_matrix.cpp @@ -0,0 +1,58 @@ +#include <gudhi/Rips_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> +#include <vector> +#include <limits> // for std::numeric_limits + +int main() { + // Type definitions + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + using Distance_matrix = std::vector<std::vector<Filtration_value>>; + + // User defined distance matrix is: + // | 0 0.94 0.77 0.99 0.11 | + // | 0.94 0 0.26 0.99 0.39 | + // | 0.77 0.26 0 0.28 0.97 | + // | 0.99 0.99 0.28 0 0.30 | + // | 0.11 0.39 0.97 0.30 0 | + + Distance_matrix distances; + distances.push_back({}); + distances.push_back({0.94}); + distances.push_back({0.77, 0.26}); + distances.push_back({0.99, 0.99, 0.28}); + distances.push_back({0.11, 0.39, 0.97, 0.30}); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from points + // ---------------------------------------------------------------------------- + double threshold = 1.0; + Rips_complex rips_complex_from_points(distances, threshold); + + Simplex_tree stree; + rips_complex_from_points.create_complex(stree, 1); + // ---------------------------------------------------------------------------- + // Display information about the one skeleton rips complex + // ---------------------------------------------------------------------------- + std::cout << "Rips complex is of dimension " << stree.dimension() << + " - " << stree.num_simplices() << " simplices - " << + stree.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << stree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + + return 0; +} diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp new file mode 100644 index 00000000..5d1216a0 --- /dev/null +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_points.cpp @@ -0,0 +1,52 @@ +#include <gudhi/Rips_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> +#include <vector> +#include <limits> // for std::numeric_limits + +int main() { + // Type definitions + using Point = std::vector<double>; + using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + + std::vector<Point> points; + points.push_back({1.0, 1.0}); + points.push_back({7.0, 0.0}); + points.push_back({4.0, 6.0}); + points.push_back({9.0, 6.0}); + points.push_back({0.0, 14.0}); + points.push_back({2.0, 19.0}); + points.push_back({9.0, 17.0}); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from points + // ---------------------------------------------------------------------------- + double threshold = 12.0; + Rips_complex rips_complex_from_points(points, threshold, Euclidean_distance()); + + Simplex_tree stree; + rips_complex_from_points.create_complex(stree, 1); + // ---------------------------------------------------------------------------- + // Display information about the one skeleton rips complex + // ---------------------------------------------------------------------------- + std::cout << "Rips complex is of dimension " << stree.dimension() << + " - " << stree.num_simplices() << " simplices - " << + stree.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << stree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + return 0; +} diff --git a/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp new file mode 100644 index 00000000..cc6c3a33 --- /dev/null +++ b/src/Rips_complex/example/example_rips_complex_from_csv_distance_matrix_file.cpp @@ -0,0 +1,72 @@ +#include <gudhi/Rips_complex.h> +// to construct Rips_complex from a OFF file of points +#include <gudhi/reader_utils.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> +#include <vector> + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " filename.csv threshold dim_max [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1)); + + std::string csv_file_name(argv[1]); + double threshold = atof(argv[2]); + int dim_max = atoi(argv[3]); + + // Type definitions + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + using Distance_matrix = std::vector<std::vector<Filtration_value>>; + + // ---------------------------------------------------------------------------- + // Init of a rips complex from a distance matrix in a csv file + // Default separator is ';' + // ---------------------------------------------------------------------------- + Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name); + Rips_complex rips_complex_from_file(distances, threshold); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 5) { + ouput_file_stream.open(std::string(argv[4])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + Simplex_tree stree; + rips_complex_from_file.create_complex(stree, dim_max); + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the rips complex + // ---------------------------------------------------------------------------- + output_stream << "Rips complex is of dimension " << stree.dimension() << + " - " << stree.num_simplices() << " simplices - " << + stree.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << stree.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + + ouput_file_stream.close(); + return 0; +} diff --git a/src/Rips_complex/example/example_rips_complex_from_off_file.cpp b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp new file mode 100644 index 00000000..b6c961d0 --- /dev/null +++ b/src/Rips_complex/example/example_rips_complex_from_off_file.cpp @@ -0,0 +1,71 @@ +#include <gudhi/Rips_complex.h> +// to construct Rips_complex from a OFF file of points +#include <gudhi/Points_off_io.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> + +#include <iostream> +#include <string> +#include <vector> + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " filename.off threshold dim_max [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1)); + + std::string off_file_name(argv[1]); + double threshold = atof(argv[2]); + int dim_max = atoi(argv[3]); + + // Type definitions + using Point = std::vector<float>; + using Simplex_tree = Gudhi::Simplex_tree<>; + using Filtration_value = Simplex_tree::Filtration_value; + using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; + + // ---------------------------------------------------------------------------- + // Init of a rips complex from an OFF file + // ---------------------------------------------------------------------------- + Gudhi::Points_off_reader<Point> off_reader(off_file_name); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Euclidean_distance()); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 5) { + ouput_file_stream.open(std::string(argv[4])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + Simplex_tree stree; + rips_complex_from_file.create_complex(stree, dim_max); + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the rips complex + // ---------------------------------------------------------------------------- + output_stream << "Rips complex is of dimension " << stree.dimension() << + " - " << stree.num_simplices() << " simplices - " << + stree.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << + std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << stree.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + + ouput_file_stream.close(); + return 0; +} diff --git a/src/Rips_complex/example/full_skeleton_rips_for_doc.txt b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt new file mode 100644 index 00000000..319931e0 --- /dev/null +++ b/src/Rips_complex/example/full_skeleton_rips_for_doc.txt @@ -0,0 +1,26 @@ +Rips complex is of dimension 3 - 24 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 2 1 0 ) -> [6.7082] + ( 3 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 3 1 0 ) -> [9.43398] + ( 3 2 0 ) -> [9.43398] + ( 3 2 1 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 5 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/example/one_skeleton_rips_for_doc.txt b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt new file mode 100644 index 00000000..b0e25cc5 --- /dev/null +++ b/src/Rips_complex/example/one_skeleton_rips_for_doc.txt @@ -0,0 +1,20 @@ +Rips complex is of dimension 1 - 18 simplices - 7 vertices. +Iterator on rips complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [5] + ( 5 4 ) -> [5.38516] + ( 2 0 ) -> [5.83095] + ( 1 0 ) -> [6.08276] + ( 3 1 ) -> [6.32456] + ( 2 1 ) -> [6.7082] + ( 6 5 ) -> [7.28011] + ( 4 2 ) -> [8.94427] + ( 3 0 ) -> [9.43398] + ( 6 4 ) -> [9.48683] + ( 6 3 ) -> [11] diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h new file mode 100644 index 00000000..f0f39db8 --- /dev/null +++ b/src/Rips_complex/include/gudhi/Rips_complex.h @@ -0,0 +1,186 @@ +/* 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, 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 <http://www.gnu.org/licenses/>. + */ + +#ifndef RIPS_COMPLEX_H_ +#define RIPS_COMPLEX_H_ + +#include <gudhi/Debug_utils.h> +#include <gudhi/graph_simplicial_complex.h> + +#include <boost/graph/adjacency_list.hpp> + +#include <iostream> +#include <vector> +#include <map> +#include <string> +#include <limits> // for numeric_limits +#include <utility> // for pair<> + + +namespace Gudhi { + +namespace rips_complex { + +/** + * \class Rips_complex + * \brief Rips complex data structure. + * + * \ingroup rips_complex + * + * \details + * The data structure is a one skeleton graph, or Rips graph, containing edges when the edge length is less or equal + * to a given threshold. Edge length is computed from a user given point cloud with a given distance function, or a + * distance matrix. + * + * \tparam Filtration_value must meet `SimplicialComplexForRips` concept. + */ +template<typename Filtration_value> +class Rips_complex { + public: + /** + * \brief Type of the one skeleton graph stored inside the Rips complex structure. + */ + typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS + , boost::property < vertex_filtration_t, Filtration_value > + , boost::property < edge_filtration_t, Filtration_value >> OneSkeletonGraph; + + private: + typedef int Vertex_handle; + + public: + /** \brief Rips_complex constructor from a list of points. + * + * @param[in] points Range of points. + * @param[in] threshold rips value. + * @param[in] distance distance function that returns a `Filtration_value` from 2 given points. + * + * \tparam InputPointRange must be a range for which `std::begin` and `std::end` return input iterators on a + * point. + * + * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where + * `Point` is a point from the `InputPointRange`, and that returns a `Filtration_value`. + */ + template<typename InputPointRange, typename Distance > + Rips_complex(const InputPointRange& points, Filtration_value threshold, Distance distance) { + compute_proximity_graph<InputPointRange, Distance >(points, threshold, distance); + } + + /** \brief Rips_complex constructor from a distance matrix. + * + * @param[in] distance_matrix Range of distances. + * @param[in] threshold rips value. + * + * \tparam InputDistanceRange must have a `size()` method and on which `distance_matrix[i][j]` returns + * the distance between points \f$i\f$ and \f$j\f$ as long as \f$ 0 \leqslant i \leqslant j \leqslant + * distance\_matrix.size().\f$ + */ + template<typename InputDistanceRange> + Rips_complex(const InputDistanceRange& distance_matrix, Filtration_value threshold) { + compute_proximity_graph(boost::irange((size_t)0, distance_matrix.size()), threshold, + [&](size_t i, size_t j){return distance_matrix[j][i];}); + } + + /** \brief Initializes the simplicial complex from the Rips graph and expands it until a given maximal + * dimension. + * + * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept. + * + * @param[in] complex SimplicialComplexForRips to be created. + * @param[in] dim_max graph expansion for rips until this given maximal dimension. + * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0. + * + */ + template <typename SimplicialComplexForRips> + void create_complex(SimplicialComplexForRips& complex, int dim_max) { + GUDHI_CHECK(complex.num_vertices() == 0, + std::invalid_argument("Rips_complex::create_complex - simplicial complex is not empty")); + + // insert the proximity graph in the simplicial complex + complex.insert_graph(rips_skeleton_graph_); + // expand the graph until dimension dim_max + complex.expansion(dim_max); + } + + private: + /** \brief Computes the proximity graph of the points. + * + * If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the + * distance function between points u and v is smaller than threshold. + * + * \tparam InputPointRange furnishes `.begin()` and `.end()` + * methods. + * + * \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where + * `Point` is a point from the `InputPointRange`, and that returns a `Filtration_value`. + */ + template< typename InputPointRange, typename Distance > + void compute_proximity_graph(const InputPointRange& points, Filtration_value threshold, + Distance distance) { + std::vector< std::pair< Vertex_handle, Vertex_handle > > edges; + std::vector< Filtration_value > edges_fil; + + // Compute the proximity graph of the points. + // If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the + // distance function between points u and v is smaller than threshold. + // -------------------------------------------------------------------------------------------- + // Creates the vector of edges and its filtration values (returned by distance function) + Vertex_handle idx_u = 0; + for (auto it_u = std::begin(points); it_u != std::end(points); ++it_u) { + Vertex_handle idx_v = idx_u + 1; + for (auto it_v = it_u + 1; it_v != std::end(points); ++it_v, ++idx_v) { + Filtration_value fil = distance(*it_u, *it_v); + if (fil <= threshold) { + edges.emplace_back(idx_u, idx_v); + edges_fil.push_back(fil); + } + } + ++idx_u; + } + + // -------------------------------------------------------------------------------------------- + // Creates the proximity graph from edges and sets the property with the filtration value. + // Number of points is labeled from 0 to idx_u-1 + // -------------------------------------------------------------------------------------------- + // Do not use : rips_skeleton_graph_ = OneSkeletonGraph(...) -> deep copy of the graph (boost graph is not + // move-enabled) + rips_skeleton_graph_.~OneSkeletonGraph(); + new(&rips_skeleton_graph_)OneSkeletonGraph(edges.begin(), edges.end(), edges_fil.begin(), idx_u); + + auto vertex_prop = boost::get(vertex_filtration_t(), rips_skeleton_graph_); + + using vertex_iterator = typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator; + vertex_iterator vi, vi_end; + for (std::tie(vi, vi_end) = boost::vertices(rips_skeleton_graph_); + vi != vi_end; ++vi) { + boost::put(vertex_prop, *vi, 0.); + } + } + + private: + OneSkeletonGraph rips_skeleton_graph_; +}; + +} // namespace rips_complex + +} // namespace Gudhi + +#endif // RIPS_COMPLEX_H_ diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt new file mode 100644 index 00000000..87bad2ed --- /dev/null +++ b/src/Rips_complex/test/CMakeLists.txt @@ -0,0 +1,25 @@ +cmake_minimum_required(VERSION 2.6) +project(Rips_complex_tests) + +if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") +endif() + +add_executable ( rips_complex_UT test_rips_complex.cpp ) +target_link_libraries(rips_complex_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(rips_complex_UT ${TBB_LIBRARIES}) +endif() + +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + +add_test(rips_complex_UT ${CMAKE_CURRENT_BINARY_DIR}/rips_complex_UT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/rips_complex_UT.xml --log_level=test_suite --report_level=no) diff --git a/src/Rips_complex/test/README b/src/Rips_complex/test/README new file mode 100644 index 00000000..28236b52 --- /dev/null +++ b/src/Rips_complex/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./rips_complex_UT --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp new file mode 100644 index 00000000..1bdd0512 --- /dev/null +++ b/src/Rips_complex/test/test_rips_complex.cpp @@ -0,0 +1,353 @@ +/* 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): Vincent Rouvreau + * + * Copyright (C) 2016 INRIA Saclay (France) + * + * 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 <http://www.gnu.org/licenses/>. + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "rips_complex" +#include <boost/test/unit_test.hpp> + +#include <cmath> // float comparison +#include <limits> +#include <string> +#include <vector> +#include <algorithm> // std::max + +#include <gudhi/Rips_complex.h> +// to construct Rips_complex from a OFF file of points +#include <gudhi/Points_off_io.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> +#include <gudhi/reader_utils.h> + +// Type definitions +using Point = std::vector<double>; +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Simplex_tree::Filtration_value>; +using Distance_matrix = std::vector<std::vector<Filtration_value>>; + +bool are_almost_the_same(float a, float b) { + return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); +} + +BOOST_AUTO_TEST_CASE(RIPS_DOC_OFF_file) { + // ---------------------------------------------------------------------------- + // + // Init of a rips complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double rips_threshold = 12.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - rips threshold=" << + rips_threshold << "==========" << std::endl; + + Gudhi::Points_off_reader<Point> off_reader(off_file_name); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Euclidean_distance()); + + const int DIMENSION_1 = 1; + Simplex_tree st; + rips_complex_from_file.create_complex(st, DIMENSION_1); + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION_1); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 18); + + // Check filtration values of vertices is 0.0 + for (auto f_simplex : st.skeleton_simplex_range(0)) { + BOOST_CHECK(st.filtration(f_simplex) == 0.0); + } + + // Check filtration values of edges + for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) { + if (DIMENSION_1 == st.dimension(f_simplex)) { + std::vector<Point> vp; + std::cout << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << ","; + vp.push_back(off_reader.get_point_cloud().at(vertex)); + } + std::cout << ") - distance =" << Euclidean_distance()(vp.at(0), vp.at(1)) << + " - filtration =" << st.filtration(f_simplex) << std::endl; + BOOST_CHECK(vp.size() == 2); + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), Euclidean_distance()(vp.at(0), vp.at(1)))); + } + } + + const int DIMENSION_2 = 2; + Simplex_tree st2; + rips_complex_from_file.create_complex(st2, DIMENSION_2); + std::cout << "st2.dimension()=" << st2.dimension() << std::endl; + BOOST_CHECK(st2.dimension() == DIMENSION_2); + + std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl; + BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl; + BOOST_CHECK(st2.num_simplices() == 23); + + Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1})); + Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2})); + Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2})); + Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); + std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl; + BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12)))); + + Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5})); + Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6})); + Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6})); + Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6})); + std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl; + BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46)))); + + const int DIMENSION_3 = 3; + Simplex_tree st3; + rips_complex_from_file.create_complex(st3, DIMENSION_3); + std::cout << "st3.dimension()=" << st3.dimension() << std::endl; + BOOST_CHECK(st3.dimension() == DIMENSION_3); + + std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl; + BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl; + BOOST_CHECK(st3.num_simplices() == 24); + + Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3})); + Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3})); + Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3})); + Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3})); + std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 << + " - f023= " << f023 << std::endl; + BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023))))); + +} + +using Vector_of_points = std::vector<Point>; + +bool is_point_in_list(Vector_of_points points_list, Point point) { + for (auto& point_in_list : points_list) { + if (point_in_list == point) { + return true; // point found + } + } + return false; // point not found +} + +class Custom_square_euclidean_distance { + public: + template< typename Point > + auto operator()(const Point& p1, const Point& p2) -> typename Point::value_type { + auto it1 = p1.begin(); + auto it2 = p2.begin(); + typename Point::value_type dist = 0.; + for (; it1 != p1.end(); ++it1, ++it2) { + typename Point::value_type tmp = (*it1) - (*it2); + dist += tmp*tmp; + } + return dist; + } +}; + +BOOST_AUTO_TEST_CASE(Rips_complex_from_points) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 0.0, 0.0, 1.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 0.0, 1.0, 0.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 1.0, 0.0, 0.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + + // ---------------------------------------------------------------------------- + // Init of a rips complex from the list of points + // ---------------------------------------------------------------------------- + Rips_complex rips_complex_from_points(points, 2.0, Custom_square_euclidean_distance()); + + std::cout << "========== Rips_complex_from_points ==========" << std::endl; + Simplex_tree st; + const int DIMENSION = 3; + rips_complex_from_points.create_complex(st, DIMENSION); + + // Another way to check num_simplices + std::cout << "Iterator on rips complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : st.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << st.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 15); + + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION); + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == 4); + + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl; + switch (st.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 0.0)); + break; + case 1: + case 2: + case 3: + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), 2.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } +} + +BOOST_AUTO_TEST_CASE(Rips_doc_csv_file) { + // ---------------------------------------------------------------------------- + // + // Init of a rips complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string csv_file_name("full_square_distance_matrix.csv"); + double rips_threshold = 12.0; + std::cout << "========== CSV FILE NAME = " << csv_file_name << " - rips threshold=" << + rips_threshold << "==========" << std::endl; + + Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name); + Rips_complex rips_complex_from_file(distances, rips_threshold); + + const int DIMENSION_1 = 1; + Simplex_tree st; + rips_complex_from_file.create_complex(st, DIMENSION_1); + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION_1); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 18); + + // Check filtration values of vertices is 0.0 + for (auto f_simplex : st.skeleton_simplex_range(0)) { + BOOST_CHECK(st.filtration(f_simplex) == 0.0); + } + + // Check filtration values of edges + for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) { + if (DIMENSION_1 == st.dimension(f_simplex)) { + std::vector<Simplex_tree::Vertex_handle> vvh; + std::cout << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << ","; + vvh.push_back(vertex); + } + std::cout << ") - filtration =" << st.filtration(f_simplex) << std::endl; + BOOST_CHECK(vvh.size() == 2); + BOOST_CHECK(are_almost_the_same(st.filtration(f_simplex), distances[vvh.at(0)][vvh.at(1)])); + } + } + + const int DIMENSION_2 = 2; + Simplex_tree st2; + rips_complex_from_file.create_complex(st2, DIMENSION_2); + std::cout << "st2.dimension()=" << st2.dimension() << std::endl; + BOOST_CHECK(st2.dimension() == DIMENSION_2); + + std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl; + BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl; + BOOST_CHECK(st2.num_simplices() == 23); + + Simplex_tree::Filtration_value f01 = st2.filtration(st2.find({0, 1})); + Simplex_tree::Filtration_value f02 = st2.filtration(st2.find({0, 2})); + Simplex_tree::Filtration_value f12 = st2.filtration(st2.find({1, 2})); + Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); + std::cout << "f012= " << f012 << " | f01= " << f01 << " - f02= " << f02 << " - f12= " << f12 << std::endl; + BOOST_CHECK(are_almost_the_same(f012, std::max(f01, std::max(f02,f12)))); + + Simplex_tree::Filtration_value f45 = st2.filtration(st2.find({4, 5})); + Simplex_tree::Filtration_value f56 = st2.filtration(st2.find({5, 6})); + Simplex_tree::Filtration_value f46 = st2.filtration(st2.find({4, 6})); + Simplex_tree::Filtration_value f456 = st2.filtration(st2.find({4, 5, 6})); + std::cout << "f456= " << f456 << " | f45= " << f45 << " - f56= " << f56 << " - f46= " << f46 << std::endl; + BOOST_CHECK(are_almost_the_same(f456, std::max(f45, std::max(f56,f46)))); + + const int DIMENSION_3 = 3; + Simplex_tree st3; + rips_complex_from_file.create_complex(st3, DIMENSION_3); + std::cout << "st3.dimension()=" << st3.dimension() << std::endl; + BOOST_CHECK(st3.dimension() == DIMENSION_3); + + std::cout << "st3.num_vertices()=" << st3.num_vertices() << std::endl; + BOOST_CHECK(st3.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st3.num_simplices()=" << st3.num_simplices() << std::endl; + BOOST_CHECK(st3.num_simplices() == 24); + + Simplex_tree::Filtration_value f123 = st3.filtration(st3.find({1, 2, 3})); + Simplex_tree::Filtration_value f013 = st3.filtration(st3.find({0, 1, 3})); + Simplex_tree::Filtration_value f023 = st3.filtration(st3.find({0, 2, 3})); + Simplex_tree::Filtration_value f0123 = st3.filtration(st3.find({0, 1, 2, 3})); + std::cout << "f0123= " << f0123 << " | f012= " << f012 << " - f123= " << f123 << " - f013= " << f013 << + " - f023= " << f023 << std::endl; + BOOST_CHECK(are_almost_the_same(f0123, std::max(f012, std::max(f123, std::max(f013, f023))))); + +} + +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE(Rips_create_complex_throw) { + // ---------------------------------------------------------------------------- + // + // Init of a rips complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double rips_threshold = 12.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - rips threshold=" << + rips_threshold << "==========" << std::endl; + + Gudhi::Points_off_reader<Point> off_reader(off_file_name); + Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), rips_threshold, Euclidean_distance()); + + Simplex_tree stree; + std::vector<int> simplex = {0, 1, 2}; + stree.insert_simplex_and_subfaces(simplex); + std::cout << "Check exception throw in debug mode" << std::endl; + // throw excpt because stree is not empty + BOOST_CHECK_THROW (rips_complex_from_file.create_complex(stree, 1), std::invalid_argument); +} +#endif |
