diff options
Diffstat (limited to 'src/Persistence_representations/include/gudhi/read_persistence_from_file.h')
| -rw-r--r-- | src/Persistence_representations/include/gudhi/read_persistence_from_file.h | 133 |
1 files changed, 133 insertions, 0 deletions
diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h new file mode 100644 index 00000000..770da15b --- /dev/null +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -0,0 +1,133 @@ +/* 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): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (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 READ_PERSISTENCE_FROM_FILE_H_ +#define READ_PERSISTENCE_FROM_FILE_H_ + +#include <iostream> +#include <fstream> +#include <sstream> +#include <vector> +#include <algorithm> +#include <string> +#include <utility> +#include <gudhi/reader_utils.h> + +namespace Gudhi { +namespace Persistence_representations { + +/** + * Universal procedure to read files with persistence. It ignores the lines starting from # (treat them as comments). + * It reads the fist line which is not a comment and assume that there are some numerical entries over there. The + *program assume + * that each other line in the file, which is not a comment, have the same number of numerical entries (2, 3 or 4). + * If there are two numerical entries per line, then the function assume that they are birth/death coordinates. + * If there are three numerical entries per line, then the function assume that they are: dimension and birth/death + *coordinates. + * If there are four numerical entries per line, then the function assume that they are: the characteristic of a filed + *over which + * persistence was computed, dimension and birth/death coordinates. + * The 'inf' string can appear only as a last element of a line. + * The procedure returns vector of persistence pairs. +**/ +std::vector<std::pair<double, double> > read_persistence_intervals_in_one_dimension_from_file( + std::string const& filename, int dimension = -1, double what_to_substitute_for_infinite_bar = -1) { + bool dbg = false; + + std::string line; + std::vector<std::pair<double, double> > barcode_initial = read_persistence_intervals_in_dimension(filename,(int)dimension); + std::vector<std::pair<double, double> > final_barcode; + final_barcode.reserve( barcode_initial.size() ); + + if ( dbg ) + { + std::cerr << "Here are the intervals that we read from the file : \n"; + for ( size_t i = 0 ; i != barcode_initial.size() ; ++i ) + { + std::cout << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl; + } + getchar(); + } + + for ( size_t i = 0 ; i != barcode_initial.size() ; ++i ) + { + if ( dbg ) + { + std::cout << "COnsidering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl; + } + // if ( barcode_initial[i].first == barcode_initial[i].second ) + //{ + // if ( dbg )std::cout << "It has zero length \n"; + // continue;//zero length intervals are not relevant, so we skip all of them. + //} + + if ( barcode_initial[i].first > barcode_initial[i].second )//note that in this case barcode_initial[i].second != std::numeric_limits<double>::infinity() + { + if ( dbg )std::cout << "Swap and enter \n"; + //swap them to make sure that birth < death + final_barcode.push_back( std::pair<double,double>( barcode_initial[i].second , barcode_initial[i].first ) ); + continue; + } + else + { + if ( barcode_initial[i].second != std::numeric_limits<double>::infinity() ) + { + if ( dbg )std::cout << "Simply enters\n"; + //in this case, due to the previous conditions we know that barcode_initial[i].first < barcode_initial[i].second, so we put them as they are + final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , barcode_initial[i].second ) ); + } + } + + if ( (barcode_initial[i].second == std::numeric_limits<double>::infinity() ) && ( what_to_substitute_for_infinite_bar != -1 ) ) + { + if ( barcode_initial[i].first < what_to_substitute_for_infinite_bar )//if only birth < death. + { + final_barcode.push_back( std::pair<double,double>( barcode_initial[i].first , what_to_substitute_for_infinite_bar ) ); + } + } + else + { + //if the variable what_to_substitute_for_infinite_bar is not set, then we ignore all the infinite bars. + } + } + + + if ( dbg ) + { + std::cerr << "Here are the final bars that we are sending further : \n"; + for ( size_t i = 0 ; i != final_barcode.size() ; ++i ) + { + std::cout << final_barcode[i].first << " " << final_barcode[i].second << std::endl; + } + std::cerr << "final_barcode.size() : " << final_barcode.size() << std::endl; + getchar(); + } + + + + return final_barcode; +} // read_persistence_intervals_in_one_dimension_from_file + +} // namespace Persistence_representations +} // namespace Gudhi + +#endif // READ_PERSISTENCE_FROM_FILE_H_ |