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Diffstat (limited to 'include/gudhi/reader_utils.h')
| -rw-r--r-- | include/gudhi/reader_utils.h | 198 |
1 files changed, 198 insertions, 0 deletions
diff --git a/include/gudhi/reader_utils.h b/include/gudhi/reader_utils.h new file mode 100644 index 00000000..899f9df6 --- /dev/null +++ b/include/gudhi/reader_utils.h @@ -0,0 +1,198 @@ +/* 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 Sophia Antipolis-Méditerranée (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/>. + */ + +#ifndef READER_UTILS_H_ +#define READER_UTILS_H_ + +#include <gudhi/graph_simplicial_complex.h> + +#include <boost/graph/adjacency_list.hpp> + +#include <iostream> +#include <fstream> +#include <map> +#include <limits> // for numeric_limits<> +#include <string> +#include <vector> + +/** + * \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 + */ +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); + if (!in_file.is_open()) { + std::cerr << "Unable to open file " << file_name << std::endl; + return; + } + + std::string line; + double x; + while (getline(in_file, line)) { + std::vector< double > point; + std::istringstream iss(line); + while (iss >> x) { + point.push_back(x); + } + // Check for empty lines + if (!point.empty()) + points.push_back(point); + } + in_file.close(); +} + +/** + * \brief Read a graph from a file. + * + * File format: 1 simplex per line + * Dim1 X11 X12 ... X1d Fil1 + * Dim2 X21 X22 ... X2d Fil2 + * etc + * + * 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) { + std::ifstream in_(file_name.c_str(), std::ios::in); + if (!in_.is_open()) { + std::cerr << "Unable to open file " << file_name << std::endl; + } + + std::vector< Edge_t > edges; + std::vector< Filtration_value > edges_fil; + std::map< Vertex_handle, Filtration_value > vertices; + + std::string line; + int dim; + Vertex_handle u, v, max_h = -1; + Filtration_value fil; + while (getline(in_, line)) { + std::istringstream iss(line); + while (iss >> dim) { + switch (dim) { + case 0: + { + iss >> u; + iss >> fil; + vertices[u] = fil; + if (max_h < u) { + max_h = u; + } + break; + } + case 1: + { + iss >> u; + iss >> v; + iss >> fil; + edges.push_back(Edge_t(u, v)); + edges_fil.push_back(fil); + break; + } + default: + { + break; + } + } + } + } + in_.close(); + + if ((size_t) (max_h + 1) != vertices.size()) { + std::cerr << "Error: vertices must be labeled from 0 to n-1 \n"; + } + + 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; + 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); + } + + return skel_graph; +} + +/** + * \brief Read a face from a file. + * + * File format: 1 simplex per line + * Dim1 X11 X12 ... X1d Fil1 + * Dim2 X21 X22 ... X2d Fil2 + * etc + * + * The vertices must be labeled from 0 to n-1. + * Every simplex must appear exactly once. + * Simplices of dimension more than 1 are ignored. + */ +template< typename Vertex_handle, typename Filtration_value > +bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Filtration_value & fil) { + int dim = 0; + if (!(in_ >> dim)) return false; + Vertex_handle v; + for (int i = 0; i < dim + 1; ++i) { + in_ >> v; + simplex.push_back(v); + } + in_ >> fil; + in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return + return true; +} + +/** + * \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.*/ +template< typename Simplex_key, typename Filtration_value > +bool read_hasse_simplex(std::istream & in_, std::vector< Simplex_key > & boundary, Filtration_value & fil) { + int dim; + if (!(in_ >> dim)) return false; + if (dim == 0) { + in_ >> fil; + return true; + } + Simplex_key key; + for (int i = 0; i < dim + 1; ++i) { + in_ >> key; + boundary.push_back(key); + } + in_ >> fil; + return true; +} + +#endif // READER_UTILS_H_ |