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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
|
/* 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) 2017 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>
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::ifstream in;
in.open( filename );
//checking if the file exist:
if ( !in.good() )
{
std::cerr << "The file : " << filename << " do not exist. The program will now terminate \n";
throw "The file from which you are trying to read the persistence landscape do not exist. The program will now terminate \n";
}
std::string line;
std::vector< std::pair<double,double> > barcode;
int number_of_entries_per_line = -1;
while (!in.eof())
{
getline(in,line);
if ( dbg )std::cerr << "Reading line : " << line << std::endl;
if ( !(line.length() == 0 || line[0] == '#') )
{
//If we do not know how many entries per line we have, we check it in below.
if ( number_of_entries_per_line == -1 )
{
number_of_entries_per_line = 0;
std::string line_copy(line);
if ( line_copy.find("inf") != std::string::npos )
{
size_t np = line_copy.find("inf");
//replace symbols 'inf' in line_copy with white spaces:
line_copy[np] = ' ';
line_copy[np+1] = ' ';
line_copy[np+2] = ' ';
number_of_entries_per_line = 1;
}
//check how many entries we have in the line.
std::stringstream ss( line_copy );
double number;
std::vector<double> this_line;
while ( ss >> number )
{
this_line.push_back( number );
}
number_of_entries_per_line += (int)this_line.size();
if ( dbg )
{
std::cerr << "number_of_entries_per_line : " << number_of_entries_per_line << ". This number was obtained by analyzing this line : " << line << std::endl;
}
if ( (number_of_entries_per_line < 2) || ( number_of_entries_per_line > 4 ) )
{
std::cerr << "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
throw "The input file you have provided have wrong number of numerical entries per line. The program will now terminate. \n";
}
}
//In case there is an 'inf' string in this line, we are dealing with this situation in below.
if ( line.find("inf") != std::string::npos )
{
if ( dbg )
{
std::cerr << "This line: " << line << " contains infinite interval. \n";
}
//first we substitute inf by white spaces:
size_t np = line.find("inf");
line[np] = ' ';
line[np+1] = ' ';
line[np+2] = ' ';
if ( what_to_substitute_for_infinite_bar != -1 )
{
double beginn, field, dim;
std::stringstream lineSS(line);
if ( number_of_entries_per_line == 4 )lineSS >> field;
if ( number_of_entries_per_line >= 3 )
{
lineSS >> dim;
}
else
{
dim = dimension;
}
lineSS >> beginn;
if ( dim == dimension )
{
if ( beginn > what_to_substitute_for_infinite_bar )
{
barcode.push_back( std::make_pair( what_to_substitute_for_infinite_bar , beginn ) );
}
else
{
barcode.push_back( std::make_pair( beginn , what_to_substitute_for_infinite_bar ) );
}
if (dbg)
{
std::cerr << "this is the line that is going to the output : " << beginn << " , " << what_to_substitute_for_infinite_bar << std::endl;
}
}
}
else
{
//this is a line with infinity. Since the variable what_to_substitute_for_infinite_bar have not been set up, it means that this line will be skipped.
if ( dbg )
{
std::cerr << "We will skip it \n";
}
}
continue;
}
else
{
//Then, we read the content of the line. We know that it do not contain 'inf' substring.
std::stringstream lineSS(line);
double beginn, endd, field, dim;
if ( number_of_entries_per_line == 4 )lineSS >> field;
if ( number_of_entries_per_line >= 3 )
{
lineSS >> dim;
}
else
{
dim = dimension;
}
lineSS >> beginn;
lineSS >> endd;
if ( beginn > endd )
{
std::swap(beginn,endd);
}
if ( dim == dimension )
{
barcode.push_back( std::make_pair( beginn , endd ) );
if (dbg)
{
std::cerr << "This is a line that is going to the output : " << beginn << " , " << endd << std::endl;
}
}
else
{
if ( (number_of_entries_per_line==3) && (dimension == -1) )
{
barcode.push_back( std::make_pair( beginn , endd ) );
}
}
}
}
else
{
if ( dbg )
{
std::cerr << "This is a comment line \n";
}
}
}
in.close();
if ( dbg )std::cerr << "End of reading \n";
return barcode;
} // read_persistence_intervals_in_one_dimension_from_file
} // namespace Persistence_representations
} // namespace Gudhi
#endif // READ_PERSISTENCE_FROM_FILE_H_
|
