From d17d140addd5c88200a983609e7d11a5571d7e7b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 28 May 2019 22:24:04 +0200 Subject: Use markdown for main page. Fix some doxyfile --- src/common/doc/main_page.h | 289 -------------------------------- src/common/doc/main_page.md | 391 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 391 insertions(+), 289 deletions(-) delete mode 100644 src/common/doc/main_page.h create mode 100644 src/common/doc/main_page.md (limited to 'src/common/doc') diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h deleted file mode 100644 index afe9b68c..00000000 --- a/src/common/doc/main_page.h +++ /dev/null @@ -1,289 +0,0 @@ -/*! \mainpage The C++ library - * \tableofcontents - * \image html "Gudhi_banner.png" "" width=20cm - * - * \section Introduction Introduction - * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source - * C++ library for - * Computational Topology and Topological Data Analysis - * (TDA). - * The GUDHI library intends to help the development of new algorithmic solutions in TDA and their transfer to - * applications. It provides robust, efficient, flexible and easy to use implementations of state-of-the-art - * algorithms and data structures. - * - * The current release of the GUDHI library includes: - * - * \li Data structures to represent, construct and manipulate simplicial complexes. - * \li Simplification of simplicial complexes by edge contraction. - * \li Algorithms to compute persistent homology and bottleneck distance. - * - * All data-structures are generic and several of their aspects can be parameterized via template classes. - * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library. - * - \section DataStructures Data structures - \subsection AlphaComplexDataStructure Alpha complex - \image html "alpha_complex_representation.png" "Alpha complex representation" - - - - - -
- Author: Vincent Rouvreau
- Introduced in: GUDHI 1.3.0
- Copyright: GPL v3
- Requires: \ref eigen3 and
- \ref cgal ≥ 4.7.0 for Alpha_complex
- \ref cgal ≥ 4.11.0 for Alpha_complex_3d - 		- Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
- The filtration value of each simplex is computed as the square of the circumradius of the simplex if the - circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration - values of the codimension 1 cofaces that make it not Gabriel otherwise. - All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into - the complex.
- User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex and - Gudhi::alpha_complex::Alpha_complex_3d -
- \subsection CechComplexDataStructure Čech complex - \image html "cech_complex_representation.png" "Čech complex representation" - - - - - -
- Author: Vincent Rouvreau
- Introduced in: GUDHI 2.2.0
- Copyright: GPL v3
- 		- The Čech complex is a simplicial complex constructed from a proximity graph.
- The set of all simplices is filtered by the radius of their minimal enclosing ball.
- User manual: \ref cech_complex - Reference manual: Gudhi::cech_complex::Cech_complex -
- \subsection CubicalComplexDataStructure Cubical complex - \image html "Cubical_complex_representation.png" "Cubical complex representation" - - - - - -
- Author: Pawel Dlotko
- Introduced in: GUDHI 1.3.0
- Copyright: GPL v3
- 		- The cubical complex is an example of a structured complex useful in computational mathematics (specially - rigorous numerics) and image analysis.
- User manual: \ref cubical_complex - Reference manual: Gudhi::cubical_complex::Bitmap_cubical_complex -
- \subsection RipsComplexDataStructure Rips complex - \image html "rips_complex_representation.png" "Rips complex representation" - - - - - -
- Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse
- Introduced in: GUDHI 2.0.0
- Copyright: GPL v3
- 		- Rips_complex is a simplicial complex constructed from a one skeleton graph.
- The filtration value of each edge is computed from a user-given distance function and is inserted until a - user-given threshold value.
- This complex can be built from a point cloud and a distance function, or from a distance matrix.
- User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex -
- \subsection SimplexTreeDataStructure Simplex tree - \image html "Simplex_tree_representation.png" "Simplex tree representation" - - - - - -
- Author: Clément Maria
- Introduced in: GUDHI 1.0.0
- Copyright: GPL v3
- 		- The simplex tree is an efficient and flexible - data structure for representing general (filtered) simplicial complexes. The data structure - is described in \cite boissonnatmariasimplextreealgorithmica .
- User manual: \ref simplex_tree - Reference manual: Gudhi::Simplex_tree -
- \subsection CoverComplexDataStructure Cover Complexes - \image html "gicvisu.jpg" "Graph Induced Complex of a point cloud." - - - - - -
- Author: Mathieu Carrière
- Introduced in: GUDHI 2.1.0
- Copyright: GPL v3
- Requires: \ref cgal ≥ 4.8.1 - 		- Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain - topological information about the input data. They can be computed with a cover of the - data, that comes i.e. from the preimage of a family of intervals covering the image - of a scalar-valued function defined on the data.
- User manual: \ref cover_complex - Reference manual: Gudhi::cover_complex::Cover_complex -
- \subsection SkeletonBlockerDataStructure Skeleton blocker - \image html "ds_representation.png" "Skeleton blocker representation" - - - - - -
- Author: David Salinas
- Introduced in: GUDHI 1.1.0
- Copyright: GPL v3
- 		- The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* - representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the - 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. - This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but - operations that are particularly efficient are operations that do not require simplex enumeration such as edge - iteration, link computation or simplex contraction.
- User manual: \ref skbl - Reference manual: Gudhi::skeleton_blocker::Skeleton_blocker_complex -
- \subsection TangentialComplexDataStructure Tangential complex - \image html "tc_examples.png" "Tangential complex representation" - - - - - -
- Author: Clément Jamin
- Introduced in: GUDHI 2.0.0
- Copyright: GPL v3
- Requires: \ref cgal ≥ 4.8.1 and \ref eigen3 - 		- A Tangential Delaunay complex is a simplicial complex - designed to reconstruct a \f$ k \f$-dimensional manifold embedded in \f$ d \f$-dimensional Euclidean space. - The input is a point sample coming from an unknown manifold. - The running time depends only linearly on the extrinsic dimension \f$ d \f$ - and exponentially on the intrinsic dimension \f$ k \f$.
- User manual: \ref tangential_complex - Reference manual: Gudhi::tangential_complex::Tangential_complex -
- \subsection ToplexMapDataStructure Toplex Map - \image html "map.png" "Toplex map representation" - - - - - - - \subsection WitnessComplexDataStructure Witness complex - \image html "Witness_complex_representation.png" "Witness complex representation" -
- Author: François Godi
- Introduced in: GUDHI 2.1.0
- Copyright: GPL v3
- 		- The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) - and secondly of a map which associate any vertex to a set of pointers toward all toplices - containing this vertex. - User manual: \ref toplex_map - Reference manual: Gudhi::Toplex_map -
- - - - -
- Author: Siargey Kachanovich
- Introduced in: GUDHI 1.3.0
- Copyright: GPL v3
- Euclidean version requires: \ref cgal ≥ 4.6.0 and \ref eigen3 - 		- Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. - The data structure is described in \cite boissonnatmariasimplextreealgorithmica .
- User manual: \ref witness_complex - Reference manual: Gudhi::witness_complex::SimplicialComplexForWitness -
- - \section Toolbox Toolbox - - \subsection BottleneckDistanceToolbox Bottleneck distance - \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" - - - - - -
- Author: François Godi
- Introduced in: GUDHI 2.0.0
- Copyright: GPL v3
- Requires: \ref cgal ≥ 4.8.1 - 		- Bottleneck distance measures the similarity between two persistence diagrams. - It's the shortest distance b for which there exists a perfect matching between - the points of the two diagrams (+ all the diagonal points) such that - any couple of matched points are at distance at most b. -
- User manual: \ref bottleneck_distance -
- \subsection ContractionToolbox Contraction - \image html "sphere_contraction_representation.png" "Sphere contraction example" - - - - - -
- Author: David Salinas
- Introduced in: GUDHI 1.1.0
- Copyright: GPL v3
- 		- The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge - simplicial complexes. It uses the \ref skbl data-structure whose size remains small during simplification of most - used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, - the size of this data-structure is even much lower than the total number of simplices.
- User manual: \ref contr -
- \subsection PersistentCohomologyToolbox Persistent Cohomology - \image html "3DTorus_poch.png" "Rips Persistent Cohomology on a 3D Torus" - - - - - -
- Author: Clément Maria
- Introduced in: GUDHI 1.0.0
- Copyright: GPL v3
- 		- The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing - global topological features like connected components, holes, cavities, etc. Persistent homology studies the - evolution -- birth, life and death -- of these features when the topological space is changing. Consequently, the - theory is essentially composed of three elements: topological spaces, their homology groups and an evolution - scheme. - Computation of persistent cohomology using the algorithm of \cite DBLP:journals/dcg/SilvaMV11 and - \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of - \cite DBLP:conf/esa/BoissonnatDM13 .
- User manual: \ref persistent_cohomology - Reference manual: Gudhi::persistent_cohomology::Persistent_cohomology -
- \subsection PersistenceRepresentationsToolbox Persistence representations - \image html "average_landscape.png" "Persistence representations" - - - - - -
- Author: Pawel Dlotko
- Introduced in: GUDHI 2.1.0
- Copyright: GPL v3
- 		- It contains implementation of various representations of persistence diagrams; diagrams themselves, persistence - landscapes (rigorous and grid version), persistence heath maps, vectors and others. It implements basic - functionalities which are neccessary to use persistence in statistics and machine learning.
- User manual: \ref Persistence_representations -
- -*/ diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md new file mode 100644 index 00000000..61efd582 --- /dev/null +++ b/src/common/doc/main_page.md @@ -0,0 +1,391 @@ +[TOC] + +# The C++ library {#main_page} +\image html "Gudhi_banner.png" +



+ +## Complexes {#Complexes} +### Cubical complex + + + + + + + + + + +
+ \image html "Cubical_complex_representation.png" + + The cubical complex is an example of a structured complex useful in computational mathematics (specially + rigorous numerics) and image analysis.
+ 		+ Author: Pawel Dlotko
+ Introduced in: GUDHI 1.3.0
+ Copyright: GPL v3
+
+ User manual: \ref cubical_complex - Reference manual: Gudhi::cubical_complex::Bitmap_cubical_complex +
+ +### Simplicial complex + +#### Alpha complex + + + + + + + + + + +
+ \image html "alpha_complex_representation.png" + + Alpha complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
+ The filtration value of each simplex is computed as the square of the circumradius of the simplex if the + circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration + values of the codimension 1 cofaces that make it not Gabriel otherwise. + All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into + the complex.
+ 		+ Author: Vincent Rouvreau
+ Introduced in: GUDHI 1.3.0
+ Copyright: GPL v3
+ Requires: \ref eigen3 and
+ \ref cgal ≥ 4.7.0 for Alpha_complex
+ \ref cgal ≥ 4.11.0 for Alpha_complex_3d +
+ User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex and + Gudhi::alpha_complex::Alpha_complex_3d +
+ +#### Čech complex + + + + + + + + + + +
+ \image html "cech_complex_representation.png" + + The Čech complex is a simplicial complex constructed from a proximity graph. + The set of all simplices is filtered by the radius of their minimal enclosing ball. + + Author: Vincent Rouvreau
+ Introduced in: GUDHI 2.2.0
+ Copyright: GPL v3
+
+ User manual: \ref cech_complex - Reference manual: Gudhi::cech_complex::Cech_complex +
+ +#### Rips complex + + + + + + + + + + +
+ \image html "rips_complex_representation.png" + + Rips_complex is a simplicial complex constructed from a one skeleton graph.
+ The filtration value of each edge is computed from a user-given distance function and is inserted until a + user-given threshold value.
+ This complex can be built from a point cloud and a distance function, or from a distance matrix. + 		+ Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+
+ User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex +
+ +#### Witness complex + + + + + + + + + + +
+ \image html "Witness_complex_representation.png" + + Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. + The data structure is described in \cite boissonnatmariasimplextreealgorithmica . + + Author: Siargey Kachanovich
+ Introduced in: GUDHI 1.3.0
+ Copyright: GPL v3
+ Euclidean version requires: \ref cgal ≥ 4.6.0 and \ref eigen3 +
+ User manual: \ref witness_complex - Reference manual: Gudhi::witness_complex::SimplicialComplexForWitness +
+ +### Cover Complexes + + + + + + + + + +
+ \image html "gicvisu.jpg" + + Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain + topological information about the input data. They can be computed with a cover of the + data, that comes i.e. from the preimage of a family of intervals covering the image + of a scalar-valued function defined on the data.
+ User manual: \ref cover_complex - Reference manual: Gudhi::cover_complex::Cover_complex + 		+ Author: Mathieu Carrière
+ Introduced in: GUDHI 2.1.0
+ Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.8.1 +
+ User manual: \ref cover_complex - Reference manual: Gudhi::cover_complex::Cover_complex +
+ +## Data structures and basic operations {#DataStructuresAndBasicOperations} + +### Data structures + +#### Simplex tree + + + + + + + + + +
+ \image html "Simplex_tree_representation.png" + + The simplex tree is an efficient and flexible + data structure for representing general (filtered) simplicial complexes. The data structure + is described in \cite boissonnatmariasimplextreealgorithmica . + + Author: Clément Maria
+ Introduced in: GUDHI 1.0.0
+ Copyright: GPL v3
+
+ User manual: \ref simplex_tree - Reference manual: Gudhi::Simplex_tree +
+ +#### Skeleton blocker + + + + + + + + + + +
+ \image html "ds_representation.png" + + The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* + representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the + 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. + This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but + operations that are particularly efficient are operations that do not require simplex enumeration such as edge + iteration, link computation or simplex contraction. + + Author: David Salinas
+ Introduced in: GUDHI 1.1.0
+ Copyright: GPL v3
+
+ User manual: \ref skbl - Reference manual: Gudhi::skeleton_blocker::Skeleton_blocker_complex +
+ +#### Toplex Map + + + + + + + + + + +
+ \image html "map.png" + + The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices) + and secondly of a map which associate any vertex to a set of pointers toward all toplices + containing this vertex. + + Author: François Godi
+ Introduced in: GUDHI 2.1.0
+ Copyright: GPL v3
+
+ User manual: \ref toplex_map - Reference manual: Gudhi::Toplex_map +
+ +### Basic operations + +#### Contraction + + + + + + + + + + +
+ \image html "sphere_contraction_representation.png" + + Author: David Salinas
+ Introduced in: GUDHI 1.1.0
+ Copyright: GPL v3
+ 		+ The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge + simplicial complexes. It uses the \ref skbl data-structure whose size remains small during simplification of most + used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, + the size of this data-structure is even much lower than the total number of simplices. +
+ User manual: \ref contr +
+ +## Topological descriptors computation {#TopologicalDescriptorsComputation} + +### Persistent Cohomology + + + + + + + + + + +
+ \image html "3DTorus_poch.png" + + The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing + global topological features like connected components, holes, cavities, etc. Persistent homology studies the + evolution -- birth, life and death -- of these features when the topological space is changing. Consequently, the + theory is essentially composed of three elements: topological spaces, their homology groups and an evolution + scheme. + Computation of persistent cohomology using the algorithm of \cite DBLP:journals/dcg/SilvaMV11 and + \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of + \cite DBLP:conf/esa/BoissonnatDM13 . + + Author: Clément Maria
+ Introduced in: GUDHI 1.0.0
+ Copyright: GPL v3
+
+ User manual: \ref persistent_cohomology - Reference manual: Gudhi::persistent_cohomology::Persistent_cohomology +
+ +## Manifold reconstruction {#ManifoldReconstruction} + +### Tangential complex + + + + + + + + + + +
+ \image html "tc_examples.png" + + A Tangential Delaunay complex is a simplicial complex + designed to reconstruct a \f$ k \f$-dimensional manifold embedded in \f$ d \f$-dimensional Euclidean space. + The input is a point sample coming from an unknown manifold. + The running time depends only linearly on the extrinsic dimension \f$ d \f$ + and exponentially on the intrinsic dimension \f$ k \f$. + + Author: Clément Jamin
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.8.1 and \ref eigen3 +
+ User manual: \ref tangential_complex - Reference manual: Gudhi::tangential_complex::Tangential_complex +
+ +## Topological descriptors tools {#TopologicalDescriptorsTools} + +### Bottleneck distance + + + + + + + + + + +
+ \image html "perturb_pd.png" + + Bottleneck distance measures the similarity between two persistence diagrams. + It's the shortest distance b for which there exists a perfect matching between + the points of the two diagrams (+ all the diagonal points) such that + any couple of matched points are at distance at most b. + + Author: François Godi
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.8.1 +
+ User manual: \ref bottleneck_distance +
+ +### Persistence representations + + + + + + + + + + +
+ \image html "average_landscape.png" + + It contains implementation of various representations of persistence diagrams; diagrams themselves, persistence + landscapes (rigorous and grid version), persistence heath maps, vectors and others. It implements basic + functionalities which are neccessary to use persistence in statistics and machine learning. + + Author: Pawel Dlotko
+ Introduced in: GUDHI 2.1.0
+ Copyright: GPL v3
+
+ User manual: \ref Persistence_representations +
-- cgit v1.2.3 From 617129f0e45e4a019b5d6facb8d2679629e34efd Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Tue, 28 May 2019 22:26:03 +0200 Subject: fix typo --- src/common/doc/main_page.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/common/doc') diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 61efd582..a74ebd26 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -95,7 +95,7 @@ \image html "rips_complex_representation.png" - Rips_complex is a simplicial complex constructed from a one skeleton graph.
+ Rips complex is a simplicial complex constructed from a one skeleton graph.
The filtration value of each edge is computed from a user-given distance function and is inserted until a user-given threshold value.
This complex can be built from a point cloud and a distance function, or from a distance matrix. -- cgit v1.2.3 From 1d53826baf9f2bccb96a7242dbabcc55d8977b19 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 3 Jun 2019 15:10:07 +0200 Subject: modify cells height for C++ doc. Use bullet lists to have the same font height on main page --- src/common/doc/main_page.md | 28 +++++++++++----------- src/cython/doc/alpha_complex_sum.inc | 2 +- src/cython/doc/bottleneck_distance_sum.inc | 4 ++-- src/cython/doc/cubical_complex_sum.inc | 2 +- src/cython/doc/nerve_gic_complex_sum.inc | 2 +- src/cython/doc/persistence_graphical_tools_sum.inc | 4 ++-- src/cython/doc/persistent_cohomology_sum.inc | 14 +++++------ src/cython/doc/rips_complex_sum.inc | 2 +- src/cython/doc/simplex_tree_sum.inc | 2 +- src/cython/doc/tangential_complex_sum.inc | 4 ++-- src/cython/doc/witness_complex_sum.inc | 10 ++++---- 11 files changed, 37 insertions(+), 37 deletions(-) (limited to 'src/common/doc') diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index a74ebd26..e61eee81 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -23,7 +23,7 @@ - + User manual: \ref cubical_complex - Reference manual: Gudhi::cubical_complex::Bitmap_cubical_complex @@ -56,7 +56,7 @@ - + User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex and Gudhi::alpha_complex::Alpha_complex_3d @@ -81,7 +81,7 @@ - + User manual: \ref cech_complex - Reference manual: Gudhi::cech_complex::Cech_complex @@ -107,7 +107,7 @@ - + User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex @@ -132,7 +132,7 @@ - + User manual: \ref witness_complex - Reference manual: Gudhi::witness_complex::SimplicialComplexForWitness @@ -159,7 +159,7 @@ - + User manual: \ref cover_complex - Reference manual: Gudhi::cover_complex::Cover_complex @@ -187,7 +187,7 @@ - + User manual: \ref simplex_tree - Reference manual: Gudhi::Simplex_tree @@ -215,7 +215,7 @@ - + User manual: \ref skbl - Reference manual: Gudhi::skeleton_blocker::Skeleton_blocker_complex @@ -240,7 +240,7 @@ - + User manual: \ref toplex_map - Reference manual: Gudhi::Toplex_map @@ -268,7 +268,7 @@ - + User manual: \ref contr @@ -300,7 +300,7 @@ - + User manual: \ref persistent_cohomology - Reference manual: Gudhi::persistent_cohomology::Persistent_cohomology @@ -330,7 +330,7 @@ - + User manual: \ref tangential_complex - Reference manual: Gudhi::tangential_complex::Tangential_complex @@ -359,7 +359,7 @@ - + User manual: \ref bottleneck_distance @@ -384,7 +384,7 @@ - + User manual: \ref Persistence_representations diff --git a/src/cython/doc/alpha_complex_sum.inc b/src/cython/doc/alpha_complex_sum.inc index 100edbbd..806988bb 100644 --- a/src/cython/doc/alpha_complex_sum.inc +++ b/src/cython/doc/alpha_complex_sum.inc @@ -16,5 +16,5 @@ | | 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` | + | * :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 4fedb744..41b9c5a3 100644 --- a/src/cython/doc/bottleneck_distance_sum.inc +++ b/src/cython/doc/bottleneck_distance_sum.inc @@ -10,5 +10,5 @@ | the longest edge | | | | | | :Requires: CGAL :math:`\geq` 4.8.0 | +-----------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------+ - | :doc:`bottleneck_distance_user` | | | - +-----------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------+ + | * :doc:`bottleneck_distance_user` | | + +-----------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/cubical_complex_sum.inc b/src/cython/doc/cubical_complex_sum.inc index 6dcc1fda..6dcf8e48 100644 --- a/src/cython/doc/cubical_complex_sum.inc +++ b/src/cython/doc/cubical_complex_sum.inc @@ -9,6 +9,6 @@ | | | :Copyright: GPL v3 | | | | | +--------------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------+ - | :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | + | * :doc:`cubical_complex_user` | * :doc:`cubical_complex_ref` | | | * :doc:`periodic_cubical_complex_ref` | +--------------------------------------------------------------------------+----------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/nerve_gic_complex_sum.inc b/src/cython/doc/nerve_gic_complex_sum.inc index 47bf84fd..0e606fe1 100644 --- a/src/cython/doc/nerve_gic_complex_sum.inc +++ b/src/cython/doc/nerve_gic_complex_sum.inc @@ -12,5 +12,5 @@ | | | | | | | | +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ - | :doc:`nerve_gic_complex_user` | :doc:`nerve_gic_complex_ref` | + | * :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 ee164652..b412de56 100644 --- a/src/cython/doc/persistence_graphical_tools_sum.inc +++ b/src/cython/doc/persistence_graphical_tools_sum.inc @@ -10,5 +10,5 @@ | | | | | | | :Requires: matplotlib, numpy and scipy | +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ - | :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` | | - +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ + | * :doc:`persistence_graphical_tools_user` | * :doc:`persistence_graphical_tools_ref` | + +-----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/persistent_cohomology_sum.inc b/src/cython/doc/persistent_cohomology_sum.inc index 5bf1a7bf..20ca073c 100644 --- a/src/cython/doc/persistent_cohomology_sum.inc +++ b/src/cython/doc/persistent_cohomology_sum.inc @@ -17,10 +17,10 @@ | | :cite:`DBLP:conf/esa/BoissonnatDM13`. | | | | | | +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ - | :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence | | - | | feature for reference: | | - | | | | - | | * :doc:`simplex_tree_ref` | | - | | * :doc:`cubical_complex_ref` | | - | | * :doc:`periodic_cubical_complex_ref` | | - +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+ + | * :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence | + | | feature for reference: | + | | | + | | * :doc:`simplex_tree_ref` | + | | * :doc:`cubical_complex_ref` | + | | * :doc:`periodic_cubical_complex_ref` | + +-----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/rips_complex_sum.inc b/src/cython/doc/rips_complex_sum.inc index b32b810e..e8e505e2 100644 --- a/src/cython/doc/rips_complex_sum.inc +++ b/src/cython/doc/rips_complex_sum.inc @@ -12,5 +12,5 @@ | | This complex can be built from a point cloud and a distance function, | | | | or from a distance matrix. | | +----------------------------------------------------------------+------------------------------------------------------------------------+----------------------------------------------------------------------+ - | :doc:`rips_complex_user` | :doc:`rips_complex_ref` | + | * :doc:`rips_complex_user` | * :doc:`rips_complex_ref` | +----------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/src/cython/doc/simplex_tree_sum.inc b/src/cython/doc/simplex_tree_sum.inc index 7e10e366..086c69d5 100644 --- a/src/cython/doc/simplex_tree_sum.inc +++ b/src/cython/doc/simplex_tree_sum.inc @@ -9,5 +9,5 @@ | | :cite:`boissonnatmariasimplextreealgorithmica` | :Copyright: GPL v3 | | | | | +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------+ - | :doc:`simplex_tree_user` | :doc:`simplex_tree_ref` | + | * :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 db1c5ab1..0f03ffb3 100644 --- a/src/cython/doc/tangential_complex_sum.inc +++ b/src/cython/doc/tangential_complex_sum.inc @@ -10,5 +10,5 @@ | | dimension :math:`k`. | | | | | :Requires: CGAL :math:`\geq` 4.8.0 | +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ - | :doc:`tangential_complex_user` | :doc:`tangential_complex_ref` | | - +----------------------------------------------------------------+------------------------------------------------------------------------+------------------------------------+ + | * :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 9dc9aef6..49577745 100644 --- a/src/cython/doc/witness_complex_sum.inc +++ b/src/cython/doc/witness_complex_sum.inc @@ -10,8 +10,8 @@ | | | | | | | :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` | | - +-------------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------------------------------------+ + | * :doc:`witness_complex_user` | * :doc:`witness_complex_ref` | + | | * :doc:`strong_witness_complex_ref` | + | | * :doc:`euclidean_witness_complex_ref` | + | | * :doc:`euclidean_strong_witness_complex_ref` | + +-------------------------------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------+ -- cgit v1.2.3 From 5d2095ce1bb0907cc1de2d97c3b056d00f29a83d Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 3 Jun 2019 16:00:08 +0200 Subject: Fix #56 --- src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 2 +- src/common/doc/installation.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'src/common/doc') diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index 32dfcc16..0bf12b1a 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -58,7 +58,7 @@ #include // for numeric_limits<> #if CGAL_VERSION_NR < 1041101000 -// Make compilation fail - required for external projects - https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/10 +// Make compilation fail - required for external projects - https://github.com/GUDHI/gudhi-devel/issues/10 # error Alpha_complex_3d is only available for CGAL >= 4.11 #endif diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 8fb8b330..5d581b08 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -44,7 +44,7 @@ make doxygen \endverbatim * * \subsection helloworld Hello world ! - * The Hello world for GUDHI + * The Hello world for GUDHI * project is an example to help developers to make their own C++ project on top of the GUDHI library. * * \section optionallibrary Optional third-party library -- cgit v1.2.3 From 5661593ab3d8f7bd4cda867fc0348c86d26106e3 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 5 Jun 2019 07:57:54 +0200 Subject: Fix #20: Add OFF section in file format and all documents target to it instead of geomview.org documentation. Modify data/points/alphacomplexdoc.off in dimension 3 to be used as an example for OFF section in file format. --- data/points/alphacomplexdoc.off | 22 ++++++++-------- src/Alpha_complex/utilities/alphacomplex.md | 4 +-- src/Doxyfile.in | 3 ++- src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 3 +-- src/common/doc/file_formats.h | 26 +++++++++++++++++++ .../example/vectordoubleoffreader_result.txt | 14 +++++------ src/common/include/gudhi/Off_reader.h | 3 +-- src/common/test/test_points_off_reader.cpp | 14 +++++------ src/cython/doc/fileformats.rst | 29 ++++++++++++++++++++++ src/cython/doc/nerve_gic_complex_user.rst | 3 +-- 10 files changed, 88 insertions(+), 33 deletions(-) (limited to 'src/common/doc') diff --git a/data/points/alphacomplexdoc.off b/data/points/alphacomplexdoc.off index bb790193..a90db49a 100644 --- a/data/points/alphacomplexdoc.off +++ b/data/points/alphacomplexdoc.off @@ -1,10 +1,12 @@ -nOFF -2 7 0 0 -1.0 1.0 -7.0 0.0 -4.0 6.0 -9.0 6.0 -0.0 14.0 -2.0 19.0 -9.0 17.0 - +# Default is 3 dimension +OFF +# 7 vertices - 0 face - 0 edge +7 0 0 +# Point set: +1.0 1.0 0.0 +7.0 0.0 0.0 +4.0 6.0 0.0 +9.0 6.0 0.0 +0.0 14.0 0.0 +2.0 19.0 0.0 +9.0 17.0 0.0 diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md index b77656ff..fcd16a3b 100644 --- a/src/Alpha_complex/utilities/alphacomplex.md +++ b/src/Alpha_complex/utilities/alphacomplex.md @@ -33,7 +33,7 @@ a prime number). where `` is the path to the input point cloud in -[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF). **Allowed options** @@ -87,7 +87,7 @@ a prime number). ``` where `` is the path to the input point cloud in -[nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html). +[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF). **Allowed options** diff --git a/src/Doxyfile.in b/src/Doxyfile.in index 54a438d4..5b1b8ecc 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -821,7 +821,8 @@ EXCLUDE_SYMBOLS = EXAMPLE_PATH = biblio/ \ example/ \ - utilities/ + utilities/ \ + data/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index bc8aecc3..e72d63dd 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -37,8 +37,7 @@ namespace cover_complex { * neato (from graphviz), * geomview, * KeplerMapper. - * Input point clouds are assumed to be - * OFF files. + * Input point clouds are assumed to be \ref FileFormatsOFF "OFF files" * * \section covers Covers * diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index 23214e25..235296d3 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -29,6 +29,32 @@ namespace Gudhi { \tableofcontents + \section FileFormatsOFF 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): + + \include points/alphacomplexdoc.off + + For dimensions bigger than 3, the dimension can be set like here: + \verbatim + # 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 + \endverbatim + + \section FileFormatsPers Persistence Diagram Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.
diff --git a/src/common/example/vectordoubleoffreader_result.txt b/src/common/example/vectordoubleoffreader_result.txt index 1deb8dbd..b399425a 100644 --- a/src/common/example/vectordoubleoffreader_result.txt +++ b/src/common/example/vectordoubleoffreader_result.txt @@ -1,7 +1,7 @@ -Point[0] = 1 1 -Point[1] = 7 0 -Point[2] = 4 6 -Point[3] = 9 6 -Point[4] = 0 14 -Point[5] = 2 19 -Point[6] = 9 17 +Point[0] = 1 1 0 +Point[1] = 7 0 0 +Point[2] = 4 6 0 +Point[3] = 9 6 0 +Point[4] = 0 14 0 +Point[5] = 2 19 0 +Point[6] = 9 17 0 diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index 05a1e145..fc951fe7 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -37,8 +37,7 @@ namespace Gudhi { /** \brief OFF file reader top class visitor. * - * OFF file must be conform to format described here : - * http://www.geomview.org/docs/html/OFF.html + * OFF file must be conform to \ref FileFormatsOFF */ class Off_reader { public: diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp index ba3bab71..e4b76ed7 100644 --- a/src/common/test/test_points_off_reader.cpp +++ b/src/common/test/test_points_off_reader.cpp @@ -44,19 +44,19 @@ BOOST_AUTO_TEST_CASE( points_doc_test ) BOOST_CHECK(point_cloud.size() == 7); std::vector expected_points; - std::vector point = {1.0, 1.0}; + std::vector point = {1.0, 1.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); - point = {7.0, 0.0}; + point = {7.0, 0.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); - point = {4.0, 6.0}; + point = {4.0, 6.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); - point = {9.0, 6.0}; + point = {9.0, 6.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); - point = {0.0, 14.0}; + point = {0.0, 14.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); - point = {2.0, 19.0}; + point = {2.0, 19.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); - point = {9.0, 17.0}; + point = {9.0, 17.0, 0.0}; expected_points.push_back(Point_d(point.begin(), point.end())); BOOST_CHECK(point_cloud == expected_points); diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst index e205cc8b..345dfdba 100644 --- a/src/cython/doc/fileformats.rst +++ b/src/cython/doc/fileformats.rst @@ -5,6 +5,35 @@ 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 ******************* diff --git a/src/cython/doc/nerve_gic_complex_user.rst b/src/cython/doc/nerve_gic_complex_user.rst index 94a2b246..9101f45d 100644 --- a/src/cython/doc/nerve_gic_complex_user.rst +++ b/src/cython/doc/nerve_gic_complex_user.rst @@ -13,8 +13,7 @@ Visualizations of the simplicial complexes can be done with either neato (from `graphviz `_), `geomview `_, `KeplerMapper `_. -Input point clouds are assumed to be -`OFF files `_. +Input point clouds are assumed to be OFF files (cf. :doc:`fileformats`). Covers ------ -- cgit v1.2.3 From 18e07282a3b9b1e8616ca871d79d7dc820e94a85 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 7 Jun 2019 15:50:31 +0200 Subject: MathJax.js no more required --- src/common/doc/MathJax.js | 53 ----------------------------------------------- 1 file changed, 53 deletions(-) delete mode 100644 src/common/doc/MathJax.js (limited to 'src/common/doc') diff --git a/src/common/doc/MathJax.js b/src/common/doc/MathJax.js deleted file mode 100644 index 35e1994e..00000000 --- a/src/common/doc/MathJax.js +++ /dev/null @@ -1,53 +0,0 @@ -(function () { - var newMathJax = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js'; - var oldMathJax = 'cdn.mathjax.org/mathjax/latest/MathJax.js'; - - var replaceScript = function (script, src) { - // - // Make redirected script - // - var newScript = document.createElement('script'); - newScript.src = newMathJax + src.replace(/.*?(\?|$)/, '$1'); - // - // Move onload and onerror handlers to new script - // - newScript.onload = script.onload; - newScript.onerror = script.onerror; - script.onload = script.onerror = null; - // - // Move any content (old-style configuration scripts) - // - while (script.firstChild) newScript.appendChild(script.firstChild); - // - // Copy script id - // - if (script.id != null) newScript.id = script.id; - // - // Replace original script with new one - // - script.parentNode.replaceChild(newScript, script); - // - // Issue a console warning - // - console.warn('WARNING: cdn.mathjax.org has been retired. Check https://www.mathjax.org/cdn-shutting-down/ for migration tips.') - } - - if (document.currentScript) { - var script = document.currentScript; - replaceScript(script, script.src); - } else { - // - // Look for current script by searching for one with the right source - // - var n = oldMathJax.length; - var scripts = document.getElementsByTagName('script'); - for (var i = 0; i < scripts.length; i++) { - var script = scripts[i]; - var src = (script.src || '').replace(/.*?:\/\//,''); - if (src.substr(0, n) === oldMathJax) { - replaceScript(script, src); - break; - } - } - } -})(); \ No newline at end of file -- cgit v1.2.3