diff options
Diffstat (limited to 'src/cython/doc')
| -rw-r--r-- | src/cython/doc/alpha_complex_sum.inc | 34 | ||||
| -rw-r--r-- | src/cython/doc/bottleneck_distance_sum.inc | 22 | ||||
| -rwxr-xr-x | src/cython/doc/conf.py | 2 | ||||
| -rw-r--r-- | src/cython/doc/cubical_complex_sum.inc | 2 | ||||
| -rw-r--r-- | src/cython/doc/installation.rst | 15 | ||||
| -rw-r--r-- | src/cython/doc/nerve_gic_complex_sum.inc | 26 | ||||
| -rw-r--r-- | src/cython/doc/persistence_graphical_tools_sum.inc | 2 | ||||
| -rw-r--r-- | src/cython/doc/persistent_cohomology_sum.inc | 2 | ||||
| -rw-r--r-- | src/cython/doc/rips_complex_sum.inc | 2 | ||||
| -rw-r--r-- | src/cython/doc/simplex_tree_sum.inc | 2 | ||||
| -rw-r--r-- | src/cython/doc/tangential_complex_sum.inc | 22 | ||||
| -rw-r--r-- | src/cython/doc/witness_complex_sum.inc | 29 |
12 files changed, 75 insertions, 85 deletions
diff --git a/src/cython/doc/alpha_complex_sum.inc b/src/cython/doc/alpha_complex_sum.inc index 806988bb..9049e654 100644 --- a/src/cython/doc/alpha_complex_sum.inc +++ b/src/cython/doc/alpha_complex_sum.inc @@ -1,20 +1,20 @@ .. table:: :widths: 30 50 20 - +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------+ - | .. figure:: | Alpha complex is a simplicial complex constructed from the finite | :Author: Vincent Rouvreau | - | ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | - | :alt: Alpha complex representation | | :Introduced in: GUDHI 2.0.0 | - | :figclass: align-center | The filtration value of each simplex is computed as the square of the | | - | | circumradius of the simplex if the circumsphere is empty (the simplex | :Copyright: GPL v3 | - | | is then said to be Gabriel), and as the minimum of the filtration | | - | | values of the codimension 1 cofaces that make it not Gabriel | :Requires: Eigen3 and CGAL :math:`\geq` 4.7.0 | - | | otherwise. All simplices that have a filtration value strictly | | - | | greater than a given alpha squared value are not inserted into the | | - | | complex. | | - | | | | - | | This package requires having CGAL version 4.7 or higher (4.8.1 is | | - | | advised for better performance). | | - +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------+ - | * :doc:`alpha_complex_user` | * :doc:`alpha_complex_ref` | - +----------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+ + +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------+ + | .. figure:: | Alpha complex is a simplicial complex constructed from the finite | :Author: Vincent Rouvreau | + | ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | + | :alt: Alpha complex representation | | :Introduced in: GUDHI 2.0.0 | + | :figclass: align-center | The filtration value of each simplex is computed as the square of the | | + | | circumradius of the simplex if the circumsphere is empty (the simplex | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | is then said to be Gabriel), and as the minimum of the filtration | | + | | values of the codimension 1 cofaces that make it not Gabriel | :Requires: `Eigen3 <installation.html#eigen3>`__ and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | + | | otherwise. All simplices that have a filtration value strictly | | + | | greater than a given alpha squared value are not inserted into the | | + | | complex. | | + | | | | + | | This package requires having CGAL version 4.7 or higher (4.8.1 is | | + | | advised for better performance). | | + +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------+ + | * :doc:`alpha_complex_user` | * :doc:`alpha_complex_ref` | + +----------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/bottleneck_distance_sum.inc b/src/cython/doc/bottleneck_distance_sum.inc index 6840e838..6eb0ac19 100644 --- a/src/cython/doc/bottleneck_distance_sum.inc +++ b/src/cython/doc/bottleneck_distance_sum.inc @@ -1,14 +1,14 @@ .. table:: :widths: 30 50 20 - +-----------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------+ - | .. figure:: | Bottleneck distance measures the similarity between two persistence | :Author: François Godi | - | ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | | - | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | :Introduced in: GUDHI 2.0.0 | - | | diagonal points) such that any couple of matched points are at | | - | Bottleneck distance is the length of | distance at most b, where the distance between points is the sup | :Copyright: GPL v3 | - | the longest edge | norm in :math:`\mathbb{R}^2`. | | - | | | :Requires: CGAL :math:`\geq` 4.8.0 | - +-----------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------+ - | * :doc:`bottleneck_distance_user` | | - +-----------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------+ + +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+ + | .. figure:: | Bottleneck distance measures the similarity between two persistence | :Author: François Godi | + | ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | | + | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | :Introduced in: GUDHI 2.0.0 | + | | diagonal points) such that any couple of matched points are at | | + | Bottleneck distance is the length of | distance at most b, where the distance between points is the sup | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | the longest edge | norm in :math:`\mathbb{R}^2`. | | + | | | :Requires: `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | + +-----------------------------------------------------------------+----------------------------------------------------------------------+------------------------------------------------------------------+ + | * :doc:`bottleneck_distance_user` | | + +-----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py index ce08f679..e4c718c3 100755 --- a/src/cython/doc/conf.py +++ b/src/cython/doc/conf.py @@ -62,7 +62,7 @@ import gudhi # General information about the project. project = gudhi.__name__ -copyright = gudhi.__copyright__ + ' - ' + gudhi.__license__ +copyright = gudhi.__copyright__ + ' - MIT' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff --git a/src/cython/doc/cubical_complex_sum.inc b/src/cython/doc/cubical_complex_sum.inc index 6dcf8e48..f200e695 100644 --- a/src/cython/doc/cubical_complex_sum.inc +++ b/src/cython/doc/cubical_complex_sum.inc @@ -6,7 +6,7 @@ | ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image | | | :alt: Cubical complex representation | analysis. | :Introduced in: GUDHI 2.0.0 | | :figclass: align-center | | | - | | | :Copyright: GPL v3 | + | | | :Copyright: MIT | | | | | +--------------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------+ | * :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index 855dea44..02b889d0 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -151,29 +151,18 @@ The :doc:`Alpha complex </alpha_complex_user>`, C++ library which provides easy access to efficient and reliable geometric algorithms. -Having CGAL, the Computational Geometry Algorithms Library, version 4.7.0 or -higher installed is recommended. The procedure to install this library +The procedure to install this library according to your operating system is detailed `here <http://doc.cgal.org/latest/Manual/installation.html>`_. -The following examples requires CGAL version ≥ 4.7.0: +The following examples requires CGAL version ≥ 4.11.0: .. only:: builder_html * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>` * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>` - -The following examples requires CGAL version ≥ 4.8.0: - -.. only:: builder_html - * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>` * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>` - -The following examples requires CGAL version ≥ 4.8.1: - -.. only:: builder_html - * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>` * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>` diff --git a/src/cython/doc/nerve_gic_complex_sum.inc b/src/cython/doc/nerve_gic_complex_sum.inc index 0e606fe1..d633c4ff 100644 --- a/src/cython/doc/nerve_gic_complex_sum.inc +++ b/src/cython/doc/nerve_gic_complex_sum.inc @@ -1,16 +1,16 @@ .. table:: :widths: 30 50 20 - +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ - | .. figure:: | Nerves and Graph Induced Complexes are cover complexes, i.e. | :Author: Mathieu Carrière | - | ../../doc/Nerve_GIC/gicvisu.jpg | simplicial complexes that provably contain topological information | | - | :alt: Graph Induced Complex of a point cloud. | about the input data. They can be computed with a cover of the data, | :Introduced in: GUDHI 2.3.0 | - | :figclass: align-center | that comes i.e. from the preimage of a family of intervals covering | | - | | the image of a scalar-valued function defined on the data. | :Copyright: GPL v3 | - | | | | - | | | :Requires: CGAL :math:`\geq` 4.8.1 | - | | | | - | | | | - +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ - | * :doc:`nerve_gic_complex_user` | * :doc:`nerve_gic_complex_ref` | - +----------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------+ + +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------+ + | .. figure:: | Nerves and Graph Induced Complexes are cover complexes, i.e. | :Author: Mathieu Carrière | + | ../../doc/Nerve_GIC/gicvisu.jpg | simplicial complexes that provably contain topological information | | + | :alt: Graph Induced Complex of a point cloud. | about the input data. They can be computed with a cover of the data, | :Introduced in: GUDHI 2.3.0 | + | :figclass: align-center | that comes i.e. from the preimage of a family of intervals covering | | + | | the image of a scalar-valued function defined on the data. | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | | | + | | | :Requires: `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | + | | | | + | | | | + +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------+ + | * :doc:`nerve_gic_complex_user` | * :doc:`nerve_gic_complex_ref` | + +----------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc index b412de56..0cdf8072 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.inc +++ b/src/cython/doc/persistence_graphical_tools_sum.inc @@ -6,7 +6,7 @@ | img/graphical_tools_representation.png | the user to build easily persistence barcode, diagram or density. | | | | | :Introduced in: GUDHI 2.0.0 | | | | | - | | | :Copyright: GPL v3 | + | | | :Copyright: MIT | | | | | | | | :Requires: matplotlib, numpy and scipy | +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ diff --git a/src/cython/doc/persistent_cohomology_sum.inc b/src/cython/doc/persistent_cohomology_sum.inc index 20ca073c..4d7b077e 100644 --- a/src/cython/doc/persistent_cohomology_sum.inc +++ b/src/cython/doc/persistent_cohomology_sum.inc @@ -6,7 +6,7 @@ | ../../doc/Persistent_cohomology/3DTorus_poch.png | a sequence of (homology) groups, capturing global topological | | | :figclass: align-center | features like connected components, holes, cavities, etc. Persistent | :Introduced in: GUDHI 2.0.0 | | | homology studies the evolution -- birth, life and death -- of these | | - | Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | :Copyright: GPL v3 | + | Rips Persistent Cohomology on a 3D | features when the topological space is changing. Consequently, the | :Copyright: MIT | | Torus | theory is essentially composed of three elements: topological spaces, | | | | their homology groups and an evolution scheme. | | | | | | diff --git a/src/cython/doc/rips_complex_sum.inc b/src/cython/doc/rips_complex_sum.inc index e8e505e2..857c6893 100644 --- a/src/cython/doc/rips_complex_sum.inc +++ b/src/cython/doc/rips_complex_sum.inc @@ -6,7 +6,7 @@ | ../../doc/Rips_complex/rips_complex_representation.png | graph. | | | :figclass: align-center | | :Introduced in: GUDHI 2.0.0 | | | The filtration value of each edge is computed from a user-given | | - | | distance function and is inserted until a user-given threshold | :Copyright: GPL v3 | + | | distance function and is inserted until a user-given threshold | :Copyright: MIT | | | value. | | | | | | | | This complex can be built from a point cloud and a distance function, | | diff --git a/src/cython/doc/simplex_tree_sum.inc b/src/cython/doc/simplex_tree_sum.inc index 086c69d5..5ba58d2b 100644 --- a/src/cython/doc/simplex_tree_sum.inc +++ b/src/cython/doc/simplex_tree_sum.inc @@ -6,7 +6,7 @@ | ../../doc/Simplex_tree/Simplex_tree_representation.png | representing general (filtered) simplicial complexes. | | | :alt: Simplex tree representation | | :Introduced in: GUDHI 2.0.0 | | :figclass: align-center | The data structure is described in | | - | | :cite:`boissonnatmariasimplextreealgorithmica` | :Copyright: GPL v3 | + | | :cite:`boissonnatmariasimplextreealgorithmica` | :Copyright: MIT | | | | | +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------+ | * :doc:`simplex_tree_user` | * :doc:`simplex_tree_ref` | diff --git a/src/cython/doc/tangential_complex_sum.inc b/src/cython/doc/tangential_complex_sum.inc index 0f03ffb3..c8bc1177 100644 --- a/src/cython/doc/tangential_complex_sum.inc +++ b/src/cython/doc/tangential_complex_sum.inc @@ -1,14 +1,14 @@ .. table:: :widths: 30 50 20 - +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ - | .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | :Author: Clément Jamin | - | ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | | - | :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | :Introduced in: GUDHI 2.0.0 | - | | an unknown manifold. The running time depends only linearly on the | | - | | extrinsic dimension :math:`d` and exponentially on the intrinsic | :Copyright: GPL v3 | - | | dimension :math:`k`. | | - | | | :Requires: CGAL :math:`\geq` 4.8.0 | - +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ - | * :doc:`tangential_complex_user` | * :doc:`tangential_complex_ref` | - +----------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------+ + +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------+ + | .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to | :Author: Clément Jamin | + | ../../doc/Tangential_complex/tc_examples.png | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`- | | + | :figclass: align-center | dimensional Euclidean space. The input is a point sample coming from | :Introduced in: GUDHI 2.0.0 | + | | an unknown manifold. The running time depends only linearly on the | | + | | extrinsic dimension :math:`d` and exponentially on the intrinsic | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | dimension :math:`k`. | | + | | | :Requires: `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | + +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------------------------------------+ + | * :doc:`tangential_complex_user` | * :doc:`tangential_complex_ref` | + +----------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/witness_complex_sum.inc b/src/cython/doc/witness_complex_sum.inc index 49577745..2be8b220 100644 --- a/src/cython/doc/witness_complex_sum.inc +++ b/src/cython/doc/witness_complex_sum.inc @@ -1,17 +1,18 @@ .. table:: :widths: 30 50 20 - +-------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------------------------------------+ - | .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | :Author: Siargey Kachanovich | - | ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | | - | :alt: Witness complex representation | | :Introduced in: GUDHI 2.0.0 | - | :figclass: align-center | The data structure is described in | | - | | :cite:`boissonnatmariasimplextreealgorithmica`. | :Copyright: GPL v3 | - | | | | - | | | :Requires: Eigen3 and CGAL :math:`\geq` 4.6.0 for Euclidean versions only | - +-------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------------------------------------+ - | * :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | - | | * :doc:`strong_witness_complex_ref` | - | | * :doc:`euclidean_witness_complex_ref` | - | | * :doc:`euclidean_strong_witness_complex_ref` | - +-------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------+ + +-------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ + | .. figure:: | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on | :Author: Siargey Kachanovich | + | ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`. | | + | :alt: Witness complex representation | | :Introduced in: GUDHI 2.0.0 | + | :figclass: align-center | The data structure is described in | | + | | :cite:`boissonnatmariasimplextreealgorithmica`. | :Copyright: MIT (`GPL v3 </licensing/>`_ for Euclidean versions only) | + | | | | + | | | :Requires: `Eigen3 <installation.html#eigen3>`__ and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 for Euclidean versions only | + +-------------------------------------------------------------------+----------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+ + | * :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | + | | * :doc:`strong_witness_complex_ref` | + | | * :doc:`euclidean_witness_complex_ref` | + | | * :doc:`euclidean_strong_witness_complex_ref` | + +-------------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ + |