1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
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_
|
