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::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().

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 (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).

exampleBitmap.png
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

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

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.

GUDHI  Version 2.3.0  - C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.  - Copyright : GPL v3 Generated on Tue Sep 4 2018 14:33:00 for GUDHI by Doxygen 1.8.13