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:orphan:
.. To get rid of WARNING: document isn't included in any toctree
File formats
############
OFF file format
***************
OFF files must be conform to format described here:
http://www.geomview.org/docs/html/OFF.html
OFF files are mainly used as point cloud inputs. Here is an example of 7 points
in a 3-dimensional space. As edges and faces are not used for point set, there
is no need to specify them (just set their numbers to 0):
.. literalinclude:: ../../data/points/alphacomplexdoc.off
.. centered:: ../../points/alphacomplexdoc.off
For dimensions bigger than 3, the dimension can be set like here::
# Dimension is no more 3
nOFF
# dimension 4 - 7 vertices - 0 face - 0 edge
4 7 0 0
# Point set:
1.0 1.0 0.0 0.0
7.0 0.0 0.0 0.0
4.0 6.0 0.0 0.0
9.0 6.0 0.0 0.0
0.0 14.0 0.0 0.0
2.0 19.0 0.0 0.0
9.0 17.0 0.0 0.0
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
:meth:`gudhi.SimplexTree.write_persistence_diagram`, read with
:meth:`gudhi.read_persistence_intervals_grouped_by_dimension`, or
:meth:`gudhi.read_persistence_intervals_in_dimension` and displayed with
:meth:`gudhi.plot_persistence_barcode` or
:meth:`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 file format:
Perseus
*******
This file format is a format inspired from 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).
.. figure::
../../doc/Bitmap_cubical_complex/exampleBitmap.png
:alt: Example of a input data.
:figclass: align-center
Example of a input data.
The input file for the following complex is:
.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
.. centered:: ../../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:
.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
.. centered:: ../../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.
.. note::
Unlike in Perseus format the filtration on the maximal cubes can be any
double precision number. Consequently one cannot mark the cubes that are
not present with ``-1``'s. To do that please set their filtration value to
:math:`+\infty` (aka. ``inf`` in the file).
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