/* 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 .
*/
#ifndef READ_PERSISTENCE_FROM_FILE_H_
#define READ_PERSISTENCE_FROM_FILE_H_
#include
#include
#include
#include
#include
#include
#include
#include
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 > 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 > barcode_initial = read_persistence_intervals_in_dimension(filename,(int)dimension);
std::vector > 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::infinity()
{
if ( dbg )std::cout << "Swap and enter \n";
//swap them to make sure that birth < death
final_barcode.push_back( std::pair( barcode_initial[i].second , barcode_initial[i].first ) );
continue;
}
else
{
if ( barcode_initial[i].second != std::numeric_limits::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( barcode_initial[i].first , barcode_initial[i].second ) );
}
}
if ( (barcode_initial[i].second == std::numeric_limits::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( 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_