From 9899ae167f281d10b1684dfcd02c6838c5bf28df Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Fri, 2 Feb 2018 13:51:45 +0100 Subject: GUDHI 2.1.0 as released by upstream in a tarball. --- cython/doc/_templates/layout.html | 6 +++- cython/doc/conf.py | 4 +-- cython/doc/cubical_complex_user.rst | 45 ++++++++++++++---------------- cython/doc/fileformats.rst | 55 ++++++++++++++++++++++++++++++++++++- cython/doc/python3-sphinx-build.py | 2 +- cython/doc/witness_complex_user.rst | 2 +- 6 files changed, 83 insertions(+), 31 deletions(-) (limited to 'cython/doc') diff --git a/cython/doc/_templates/layout.html b/cython/doc/_templates/layout.html index 243f33c6..8e4eba40 100644 --- a/cython/doc/_templates/layout.html +++ b/cython/doc/_templates/layout.html @@ -198,6 +198,8 @@
  • @@ -208,6 +210,8 @@
  • C++ installation manual
  • Python documentation
  • Python installation manual
    • +
  • Utilities
    • +
  • Tutorial
  • @@ -255,7 +259,7 @@ {%- if hasdoc('copyright') %} {% trans path=pathto('copyright'), copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} {%- else %} - {% trans copyright=copyright|e %}© Copyright {{ copyright }}.{% endtrans %} + {% trans copyright=copyright|e %} {{ copyright }}.{% endtrans %} {%- endif %} {%- endif %} {%- if last_updated %} diff --git a/cython/doc/conf.py b/cython/doc/conf.py index 19a880d4..a13c9751 100755 --- a/cython/doc/conf.py +++ b/cython/doc/conf.py @@ -62,7 +62,7 @@ import gudhi # General information about the project. project = gudhi.__name__ -copyright = gudhi.__copyright__ +copyright = gudhi.__copyright__ + ' - ' + gudhi.__license__ # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -158,7 +158,7 @@ html_static_path = ['_static'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. diff --git a/cython/doc/cubical_complex_user.rst b/cython/doc/cubical_complex_user.rst index 2bfac62a..34598f02 100644 --- a/cython/doc/cubical_complex_user.rst +++ b/cython/doc/cubical_complex_user.rst @@ -81,23 +81,7 @@ filtration to all cubes. There are a number of constructors that can be used to who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`. Currently one input from a text file is used. It uses a format used already in `Perseus software `_ by Vidit Nanda. -Below we are providing a description of the format. 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 +The file format is described here: :doc:`Perseus `. .. testcode:: @@ -124,15 +108,9 @@ Imposing periodic boundary conditions in the direction i, means that the left an :math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical -complex with periodic boundary conditions. One can also use Perseus style input files. 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 +complex with periodic boundary conditions. -Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. +One can also use Perseus style input files (see :doc:`Perseus `) for the specific periodic case: .. testcode:: @@ -149,6 +127,23 @@ the program output is: Periodic cubical complex is of dimension 2 - 42 simplices. +Or it can be defined as follows: + +.. testcode:: + + from gudhi import PeriodicCubicalComplex as pcc + periodic_cc = pcc(dimensions=[3,3], + top_dimensional_cells= [0, 0, 0, 0, 1, 0, 0, 0, 0], + periodic_dimensions=[True, False]) + result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \ + repr(periodic_cc.num_simplices()) + ' simplices.' + print(result_str) + +the program output is: + +.. testoutput:: + + Periodic cubical complex is of dimension 2 - 42 simplices. Examples. --------- diff --git a/cython/doc/fileformats.rst b/cython/doc/fileformats.rst index 156ef4e4..4f0b6f6d 100644 --- a/cython/doc/fileformats.rst +++ b/cython/doc/fileformats.rst @@ -23,7 +23,7 @@ Here is a simple sample file:: 3 34.2 34.974 4 3. inf -Other sample files can be found in the data/persistence_diagram folder. +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 @@ -31,3 +31,56 @@ Such files can be generated with :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 `_ 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. diff --git a/cython/doc/python3-sphinx-build.py b/cython/doc/python3-sphinx-build.py index 44b94169..84d158cf 100755 --- a/cython/doc/python3-sphinx-build.py +++ b/cython/doc/python3-sphinx-build.py @@ -1,4 +1,4 @@ -#!/usr/bin/python3 +#!/usr/bin/env python3 """ Emulate sphinx-build for python3 diff --git a/cython/doc/witness_complex_user.rst b/cython/doc/witness_complex_user.rst index 29413269..99be5185 100644 --- a/cython/doc/witness_complex_user.rst +++ b/cython/doc/witness_complex_user.rst @@ -121,7 +121,7 @@ Example2: Computing persistence using strong relaxed witness complex Here is an example of constructing a strong witness complex filtration and computing persistence on it: -* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>` +* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` Bibliography ============ -- cgit v1.2.3