: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 ******* This file format is a format inspired from 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). .. 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).