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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
* Author(s): Pawel Dlotko
*
* Copyright (C) 2016 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#ifndef READ_PERSISTENCE_FROM_FILE_H_
#define READ_PERSISTENCE_FROM_FILE_H_
#include <gudhi/reader_utils.h>
#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <algorithm>
#include <string>
#include <utility>
#include <limits> // for std::numeric_limits<>
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, static_cast<int>(dimension));
std::vector<std::pair<double, double> > final_barcode;
final_barcode.reserve(barcode_initial.size());
if (dbg) {
std::clog << "Here are the intervals that we read from the file : \n";
for (size_t i = 0; i != barcode_initial.size(); ++i) {
std::clog << barcode_initial[i].first << " " << barcode_initial[i].second << std::endl;
}
getchar();
}
for (size_t i = 0; i != barcode_initial.size(); ++i) {
if (dbg) {
std::clog << "Considering interval : " << barcode_initial[i].first << " " << barcode_initial[i].second
<< std::endl;
}
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::clog << "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::clog << "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::clog << "Here are the final bars that we are sending further : \n";
for (size_t i = 0; i != final_barcode.size(); ++i) {
std::clog << final_barcode[i].first << " " << final_barcode[i].second << std::endl;
}
std::clog << "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_
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