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
|
/* 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): Clément Jamin
*
* Copyright (C) 2017 Inria
*
* 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 DOC_COMMON_FILE_FORMAT_H_
#define DOC_COMMON_FILE_FORMAT_H_
namespace Gudhi {
/*! \page fileformats File formats
\tableofcontents
\section FileFormatsPers Persistence Diagram
Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
Lines starting with `#` are ignored (comments).<br>
Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
\verbatim
[[field] dimension] birth death
\endverbatim
Here is a simple sample file:
\verbatim
# Persistence diagram example
2 2.7 3.7
2 9.6 14.
# Some comments
3 34.2 34.974
4 3. inf
\endverbatim
Other sample files can be found in the `data/persistence_diagram` folder.
Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
`Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
`Gudhi::read_persistence_intervals_in_dimension()`.
\section FileFormatsIsoCuboid Iso-cuboid
Such a file describes an iso-oriented cuboid with diagonal opposite vertices (min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:<br>
\verbatim
min_x min_y [min_z ...]
max_x max_y [max_z ...]
\endverbatim
Here is a simple sample file in the 3D case:
\verbatim
-1. -1. -1.
1. 1. 1.
\endverbatim
\section FileFormatsPerseus Perseus
This file format is the format used by the Perseus software
(http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
The first line contains a number d begin the dimension of the
bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
20 4 7 6 5 in the example below).
\image html "exampleBitmap.png" "Example of a input data."
The input file for the following complex is:
\verbatim
2
3
3
1
4
6
8
20
4
7
6
5
\endverbatim
To indicate periodic boundary conditions in a
given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance:
\verbatim
2
-3
3
1
4
6
8
20
4
7
6
5
\endverbatim
Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
Other sample files can be found in the `data/bitmap` folder.
*/
} // namespace Gudhi
#endif // DOC_COMMON_FILE_FORMAT_H_
|
