diff options
Diffstat (limited to 'cython/doc/fileformats.rst')
| -rw-r--r-- | cython/doc/fileformats.rst | 90 |
1 files changed, 0 insertions, 90 deletions
diff --git a/cython/doc/fileformats.rst b/cython/doc/fileformats.rst deleted file mode 100644 index ff20f26e..00000000 --- a/cython/doc/fileformats.rst +++ /dev/null @@ -1,90 +0,0 @@ -:orphan: - -.. To get rid of WARNING: document isn't included in any toctree - -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 -: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 -******* - -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). - -.. 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. |