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Diffstat (limited to 'src/common/include/gudhi/reader_utils.h')
| -rw-r--r-- | src/common/include/gudhi/reader_utils.h | 181 |
1 files changed, 181 insertions, 0 deletions
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h new file mode 100644 index 00000000..5c8cbeb7 --- /dev/null +++ b/src/common/include/gudhi/reader_utils.h @@ -0,0 +1,181 @@ + /* 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 GUDHI_READER_UTILS_H +#define GUDHI_READER_UTILS_H + +#include <iostream> +#include <fstream> +#include <boost/graph/adjacency_list.hpp> +#include "gudhi/graph_simplicial_complex.h" + +/** + * \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); } + 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 (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 // GUDHI_READER_UTILS_H |