File formats¶
Persistence Diagram¶
Such a file, whose extension is usually .pers
, contains a list of
persistence intervals.
Lines starting with #
are ignored (comments).
Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
[[field] dimension] birth death
Here is a simple sample file:
# Persistence diagram example
2 2.7 3.7
2 9.6 14.
# Some comments
3 34.2 34.974
4 3. inf
Other sample files can be found in the data/persistence_diagram folder.
Such files can be generated with
gudhi.SimplexTree.write_persistence_diagram()
, read with
gudhi.read_persistence_intervals_grouped_by_dimension()
, or
gudhi.read_persistence_intervals_in_dimension()
and displayed with
gudhi.plot_persistence_barcode()
or
gudhi.plot_persistence_diagram()
.
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:
min_x min_y [min_z ...]
max_x max_y [max_z ...]
Here is a simple sample file in the 3D case:
-1. -1. -1.
1. 1. 1.
Perseus¶
This file format is the format used by the Perseus software 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).

Example of a input data.
The input file for the following complex is:
2
3
3
1
4
6
8
20
4
7
6
5
../../data/bitmap/cubicalcomplexdoc.txt
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:
2
-3
3
1
4
6
8
20
4
7
6
5
../../data/bitmap/periodiccubicalcomplexdoc.txt
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.