diff options
Diffstat (limited to 'src/common/include')
| -rw-r--r-- | src/common/include/gudhi/distance_functions.h | 34 | ||||
| -rw-r--r-- | src/common/include/gudhi/graph_simplicial_complex.h | 59 | ||||
| -rw-r--r-- | src/common/include/gudhi/reader_utils.h | 163 |
3 files changed, 152 insertions, 104 deletions
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index cd518581..5891ef0e 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 @@ -25,19 +25,25 @@ #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. */ -template< typename Point > -double euclidean_distance(Point &p1, Point &p2) { - double dist = 0.; - auto it1 = p1.begin(); - auto it2 = p2.begin(); - for (; it1 != p1.end(); ++it1, ++it2) { - double tmp = *it1 - *it2; - dist += tmp*tmp; +/** @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. */ +class Euclidean_distance { + public: + template< typename Point > + auto operator()(const Point& p1, const Point& p2) -> typename std::decay<decltype(*std::begin(p1))>::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 std::sqrt(dist); } - return std::sqrt(dist); -} +}; #endif // DISTANCE_FUNCTIONS_H_ diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index 042ef516..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 @@ -39,61 +39,4 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; -typedef int Vertex_handle; -typedef double Filtration_value; -typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS -, boost::property < vertex_filtration_t, Filtration_value > -, boost::property < edge_filtration_t, Filtration_value > -> Graph_t; -typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; - -/** \brief Output 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. - * - * The type PointCloud furnishes .begin() and .end() methods, that return - * iterators with value_type Point. - */ -template< typename PointCloud -, typename Point > -Graph_t compute_proximity_graph(PointCloud &points - , Filtration_value threshold - , Filtration_value distance(Point p1, Point p2)) { - std::vector< Edge_t > edges; - std::vector< Filtration_value > edges_fil; - std::map< Vertex_handle, Filtration_value > vertices; - - Vertex_handle idx_u, idx_v; - Filtration_value fil; - idx_u = 0; - for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { - idx_v = idx_u + 1; - for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { - fil = distance(*it_u, *it_v); - if (fil <= threshold) { - edges.emplace_back(idx_u, idx_v); - edges_fil.push_back(fil); - } - } - ++idx_u; - } - - Graph_t skel_graph(edges.begin() - , edges.end() - , edges_fil.begin() - , idx_u); // number of points labeled from 0 to idx_u-1 - - auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - - boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end; - for (std::tie(vi, vi_end) = boost::vertices(skel_graph); - vi != vi_end; ++vi) { - boost::put(vertex_prop, *vi, 0.); - } - - return skel_graph; -} - #endif // GRAPH_SIMPLICIAL_COMPLEX_H_ diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 899f9df6..4c8d85cd 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria + * Author(s): Clement Maria, Pawel Dlotko * - * 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 @@ -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); @@ -66,23 +72,29 @@ 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. + * + * \tparam Graph_t Type for the return graph. Must be constructible from iterators on pairs of Vertex_handle + * \tparam Filtration_value Type for the value of the read filtration + * \tparam Vertex_handle Type for the value of the read vertices * - * 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. * Simplices of dimension more than 1 are ignored. */ -inline Graph_t read_graph(std::string file_name) { +template< typename Graph_t, typename Filtration_value, typename Vertex_handle > +Graph_t read_graph(std::string file_name) { std::ifstream in_(file_name.c_str(), std::ios::in); if (!in_.is_open()) { std::cerr << "Unable to open file " << file_name << std::endl; } + typedef std::pair< Vertex_handle, Vertex_handle > Edge_t; std::vector< Edge_t > edges; std::vector< Filtration_value > edges_fil; std::map< Vertex_handle, Filtration_value > vertices; @@ -130,7 +142,7 @@ inline Graph_t read_graph(std::string file_name) { Graph_t skel_graph(edges.begin(), edges.end(), edges_fil.begin(), vertices.size()); auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end; + typename boost::graph_traits<Graph_t>::vertex_iterator vi, vi_end; auto v_it = vertices.begin(); for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi, ++v_it) { boost::put(vertex_prop, *vi, v_it->second); @@ -140,12 +152,12 @@ 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. @@ -166,18 +178,16 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi } /** - * \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 - * - * 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.*/ + * @brief Read a hasse simplex from a file. + * + * 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.*/ template< typename Simplex_key, typename Filtration_value > bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) { int dim; @@ -195,4 +205,93 @@ bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundar return true; } +/** + * @brief Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole + * (square) matrix. + * + * @author Pawel Dlotko + * + * Square matrix file format:<br> + * 0;D12;...;D1j<br> + * D21;0;...;D2j<br> + * ...<br> + * Dj1;Dj2;...;0<br> + * + * 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(const std::string& filename, + const char separator = ';') { +#ifdef DEBUG_TRACES + std::cout << "Using procedure read_lower_triangular_matrix_from_csv_file \n"; +#endif // DEBUG_TRACES + std::vector< std::vector< Filtration_value > > result; + std::ifstream in; + in.open(filename.c_str()); + if (!in.is_open()) { + return result; + } + + std::string line; + + // the first line is emtpy, so we ignore it: + std::getline(in, line); + std::vector< Filtration_value > values_in_this_line; + result.push_back(values_in_this_line); + + int number_of_line = 0; + + // first, read the file line by line to a string: + while (std::getline(in, line)) { + // if line is empty, break + if (line.size() == 0) + break; + + // if the last element of a string is comma: + if (line[ line.size() - 1 ] == separator) { + // then shrink the string by one + line.pop_back(); + } + + // replace all commas with spaces + std::replace(line.begin(), line.end(), separator, ' '); + + // put the new line to a stream + std::istringstream iss(line); + // and now read the doubles. + + int number_of_entry = 0; + std::vector< Filtration_value > values_in_this_line; + while (iss.good()) { + double entry; + iss >> entry; + if (number_of_entry <= number_of_line) { + values_in_this_line.push_back(entry); + } + ++number_of_entry; + } + if (!values_in_this_line.empty())result.push_back(values_in_this_line); + ++number_of_line; + } + in.close(); + +#ifdef DEBUG_TRACES + std::cerr << "Here is the matrix we read : \n"; + for (size_t i = 0; i != result.size(); ++i) { + for (size_t j = 0; j != result[i].size(); ++j) { + std::cerr << result[i][j] << " "; + } + std::cerr << std::endl; + } +#endif // DEBUG_TRACES + + return result; +} // read_lower_triangular_matrix_from_csv_file + #endif // READER_UTILS_H_ |