diff options
Diffstat (limited to 'src/common')
-rw-r--r-- | src/common/doc/main_page.h | 3 | ||||
-rw-r--r-- | src/common/include/gudhi/distance_functions.h | 11 | ||||
-rw-r--r-- | src/common/include/gudhi/graph_simplicial_complex.h | 2 | ||||
-rw-r--r-- | src/common/include/gudhi/reader_utils.h | 84 | ||||
-rw-r--r-- | src/common/test/test_distance_matrix_reader.cpp | 16 |
5 files changed, 62 insertions, 54 deletions
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 85310f66..85ae8679 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -60,7 +60,7 @@ <table border="0"> <tr> <td width="25%"> - <b>Author:</b> Clément Maria<br> + <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau<br> <b>Introduced in:</b> GUDHI 1.4.0<br> <b>Copyright:</b> GPL v3<br> </td> @@ -68,6 +68,7 @@ Rips_complex is a simplicial complex constructed from a one skeleton graph.<br> The filtration value of each edge is computed from a user-given distance function and is inserted until a user-given threshold value.<br> + This complex can be built from a point cloud and a distance function, or from a distance matrix.<br> <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex </td> </tr> diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index 006df275..ed2c1f5d 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * 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 @@ -25,9 +25,12 @@ #include <cmath> // for std::sqrt -/* Compute the Euclidean distance between two Points given - * by a range of coordinates. The points are assumed to have - * the same dimension. */ +/** @file + * @brief Global distance functions + */ + +/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to + * have the same dimension. */ template< typename Filtration_value, typename Point > Filtration_value euclidean_distance(const Point &p1,const Point &p2) { Filtration_value dist = 0.; diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 9dbcd891..5fe7c826 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * 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/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 40d566d8..3799e583 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -34,14 +34,20 @@ #include <string> #include <vector> +// Keep this file tag for Doxygen to parse the code, otherwise, functions are not documented. +// It is required for global functions and variables. + +/** @file + * @brief This file includes common file reader for GUDHI + */ + /** - * \brief Read a set of points to turn it - * into a vector< vector<double> > by filling points + * @brief Read a set of points to turn it into a vector< vector<double> > by filling points. * - * File format: 1 point per line - * X11 X12 ... X1d - * X21 X22 ... X2d - * etc + * File format: 1 point per line<br> + * X11 X12 ... X1d<br> + * X21 X22 ... X2d<br> + * etc<br> */ inline void read_points(std::string file_name, std::vector< std::vector< double > > & points) { std::ifstream in_file(file_name.c_str(), std::ios::in); @@ -66,12 +72,12 @@ inline void read_points(std::string file_name, std::vector< std::vector< double } /** - * \brief Read a graph from a file. + * @brief Read a graph from a file. * - * File format: 1 simplex per line - * Dim1 X11 X12 ... X1d Fil1 - * Dim2 X21 X22 ... X2d Fil2 - * etc + * File format: 1 simplex per line<br> + * Dim1 X11 X12 ... X1d Fil1<br> + * Dim2 X21 X22 ... X2d Fil2<br> + * etc<br> * * The vertices must be labeled from 0 to n-1. * Every simplex must appear exactly once. @@ -141,12 +147,12 @@ inline Graph_t read_graph(std::string file_name) { } /** - * \brief Read a face from a file. + * @brief Read a face from a file. * - * File format: 1 simplex per line - * Dim1 X11 X12 ... X1d Fil1 - * Dim2 X21 X22 ... X2d Fil2 - * etc + * File format: 1 simplex per line<br> + * Dim1 X11 X12 ... X1d Fil1<br> + * Dim2 X21 X22 ... X2d Fil2<br> + * etc<br> * * The vertices must be labeled from 0 to n-1. * Every simplex must appear exactly once. @@ -167,18 +173,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi } /** - * \brief Read a hasse simplex from a file. + * @brief Read a hasse simplex from a file. * - * File format: 1 simplex per line - * Dim1 k11 k12 ... k1Dim1 Fil1 - * Dim2 k21 k22 ... k2Dim2 Fil2 - * etc + * File format: 1 simplex per line<br> + * Dim1 k11 k12 ... k1Dim1 Fil1<br> + * Dim2 k21 k22 ... k2Dim2 Fil2<br> + * etc<br> * - * The key of a simplex is its position in the filtration order - * and also the number of its row in the file. - * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the - * filtration has dimension Dimi, filtration value fil1 and simplices with - * key ki1 ... kiDimi in its boundary.*/ + * The key of a simplex is its position in the filtration order and also the number of its row in the file. + * Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value + * fil1 and simplices with key ki1 ... kiDimi in its boundary.*/ template< typename Simplex_key, typename Filtration_value > bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) { int dim; @@ -197,27 +201,27 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar } /** - * \brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole + * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole * (square) matrix. * - * \author Pawel Dlotko + * @author Pawel Dlotko * - * Square matrix file format: - * 0;D12;...;D1j - * D21;0;...;D2j - * ... - * Dj1;Dj2;...;0 + * Square matrix file format:<br> + * 0;D12;...;D1j<br> + * D21;0;...;D2j<br> + * ...<br> + * Dj1;Dj2;...;0<br> * - * lower matrix file format: - * 0 - * D21; - * D31;D32; - * ... - * Dj1;Dj2;...;Dj(j-1); + * lower matrix file format:<br> + * 0<br> + * D21;<br> + * D31;D32;<br> + * ...<br> + * Dj1;Dj2;...;Dj(j-1);<br> * **/ template< typename Filtration_value > -std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(std::string filename, +std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string& filename, const char separator=';') { bool dbg = false; if (dbg) { diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index 7eb7e846..a4c46bb1 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -47,21 +47,21 @@ BOOST_AUTO_TEST_CASE( lower_triangular_distance_matrix ) std::cout << "from_lower_triangular size = " << from_lower_triangular.size() << std::endl; BOOST_CHECK(from_lower_triangular.size() == 5); - for (int i = 0; i < from_lower_triangular.size(); i++) { + for (std::size_t i = 0; i < from_lower_triangular.size(); i++) { std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl; BOOST_CHECK(from_lower_triangular[i].size() == i); } std::vector<double> expected = {1}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[1] == expected); expected = {2,3}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[2] == expected); expected = {4,5,6}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[3] == expected); expected = {7,8,9,10}; - BOOST_CHECK(from_lower_triangular[0] == expected); + BOOST_CHECK(from_lower_triangular[4] == expected); } @@ -78,8 +78,8 @@ BOOST_AUTO_TEST_CASE( full_square_distance_matrix ) } std::cout << "from_full_square size = " << from_full_square.size() << std::endl; BOOST_CHECK(from_full_square.size() == 5); - for (int i = 0; i < from_lower_triangular.size(); i++) { - std::cout << "from_lower_triangular[" << i << "] size = " << from_lower_triangular[i].size() << std::endl; - BOOST_CHECK(from_lower_triangular[i].size() == i); + for (std::size_t i = 0; i < from_full_square.size(); i++) { + std::cout << "from_full_square[" << i << "] size = " << from_full_square[i].size() << std::endl; + BOOST_CHECK(from_full_square[i].size() == i); } } |