diff options
| author | Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com> | 2022-06-08 09:20:18 +0200 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2022-06-08 09:20:18 +0200 |
| commit | f045b0fe772e2c690d80aebcd31734700790c8a8 (patch) | |
| tree | 627e41947a1ff275c92441a8b953b829d8311d70 | |
| parent | 91b21f6cfdf8e225070514c34bd6fcae296e3d52 (diff) | |
| parent | e66ad01ed9fefd2fd4584c5e7928f808e3f257f5 (diff) | |
Merge branch 'master' into feature/bug_class_diagrams
79 files changed, 297 insertions, 350 deletions
diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index 8462e731..0a3ef43d 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -1151,7 +1151,7 @@ language={English} editor = {Lars Arge and J{\'a}nos Pach}, publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, address = {Dagstuhl, Germany}, - URL = {https://drops.dagstuhl.de/opus/volltexte/2015/5098}, + URL = {https://drops.dagstuhl.de/opus/volltexte/2015/5098/}, URN = {urn:nbn:de:0030-drops-50981}, doi = {10.4230/LIPIcs.SOCG.2015.642}, annote = {Keywords: Simplicial complex, Compact data structures, Automaton, NP-hard} @@ -1341,7 +1341,7 @@ doi="10.1007/978-3-030-43408-3_2", editor = {Sergio Cabello and Danny Z. Chen}, publisher = {Schloss Dagstuhl--Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, - URL = {https://drops.dagstuhl.de/opus/volltexte/2020/12177}, + URL = {https://drops.dagstuhl.de/opus/volltexte/2020/12177/}, URN = {urn:nbn:de:0030-drops-121777}, doi = {10.4230/LIPIcs.SoCG.2020.19}, annote = {Keywords: Computational Topology, Topological Data Analysis, Edge Collapse, Simple Collapse, Persistent homology} diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 7f14f423..41e5e16d 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -107,6 +107,7 @@ Table of Contents * \subsection filtrationcomputation Filtration value computation algorithm * <br> * \f$ + * \begin{array}{l} * \textbf{for } \text{i : dimension } \rightarrow 0 \textbf{ do}\\ * \quad \textbf{for all } \sigma \text{ of dimension i}\\ * \quad\quad \textbf{if } \text{filtration(} \sigma ) \text{ is NaN} \textbf{ then}\\ @@ -127,6 +128,7 @@ Table of Contents * \textbf{end for}\\ * \text{make_filtration_non_decreasing()}\\ * \text{prune_above_filtration()}\\ + * \end{array} * \f$ * * \subsubsection dimension2 Dimension 2 diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 028ec9bb..b1a9407b 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -69,7 +69,7 @@ template<typename D> struct Is_Epeck_D<CGAL::Epeck_d<D>> { static const bool val * \ingroup alpha_complex * * \details - * The data structure is constructing a CGAL Delaunay triangulation (for more informations on CGAL Delaunay + * The data structure is constructing a CGAL Delaunay triangulation (for more information on CGAL Delaunay * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) from a * range of points or from an OFF file (cf. Points_off_reader). * diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h index aa255ec2..4a6af3a4 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h @@ -237,7 +237,7 @@ class Bitmap_cubical_complex : public T { * Filtration_simplex_iterator class provides an iterator though the whole structure in the order of filtration. * Secondary criteria for filtration are: * (1) Dimension of a cube (lower dimensional comes first). - * (2) Position in the data structure (the ones that are earlies in the data structure comes first). + * (2) Position in the data structure (the ones that are earliest in the data structure come first). **/ class Filtration_simplex_range; diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h index f8f80ded..bafe7981 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -43,7 +43,7 @@ namespace cubical_complex { * Each cell is represented by a single * bit (in case of black and white bitmaps, or by a single element of a type T * (here T is a filtration type of a bitmap, typically a double). - * All the informations needed for homology and + * All the information needed for homology and * persistent homology computations (like dimension of a cell, boundary and * coboundary elements of a cell, are then obtained from the * position of the element in C. diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index c65e6082..1d56f0b4 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -86,7 +86,7 @@ class Neighbors_finder { }; /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U - * (which can be a projection) in a layered graph layer given as parmeter. + * (which can be a projection) in a layered graph layer given as parameter. * * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically * removed. diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h index 698f9749..095fd320 100644 --- a/src/Cech_complex/doc/Intro_cech_complex.h +++ b/src/Cech_complex/doc/Intro_cech_complex.h @@ -70,9 +70,8 @@ namespace cech_complex { * This radius computation is the reason why the Cech_complex is taking much more time to be computed than the * \ref rips_complex but it offers more topological guarantees. * - * If the Cech_complex interfaces are not detailed enough for your need, please refer to - * <a href="cech_complex_step_by_step_8cpp-example.html"> - * cech_complex_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed. + * If the Cech_complex interfaces are not detailed enough for your need, please refer to the example + * \gudhi_example_link{Cech_complex,cech_complex_step_by_step.cpp}, where the graph construction over the Simplex_tree is more detailed. * * \subsection cechpointscloudexample Example from a point cloud * diff --git a/src/Cech_complex/include/gudhi/Miniball.hpp b/src/Cech_complex/include/gudhi/Miniball.hpp index ce6cbb5b..55387a8a 100644 --- a/src/Cech_complex/include/gudhi/Miniball.hpp +++ b/src/Cech_complex/include/gudhi/Miniball.hpp @@ -1,4 +1,4 @@ -// Copright (C) 1999-2013, Bernd Gaertner +// Copyright (C) 1999-2013, Bernd Gaertner // $Rev: 3581 $ // // This program is free software: you can redistribute it and/or modify diff --git a/src/Collapse/example/edge_collapse_conserve_persistence.cpp b/src/Collapse/example/edge_collapse_conserve_persistence.cpp index b2c55e7a..19960597 100644 --- a/src/Collapse/example/edge_collapse_conserve_persistence.cpp +++ b/src/Collapse/example/edge_collapse_conserve_persistence.cpp @@ -103,7 +103,7 @@ int main(int argc, char* argv[]) { Gudhi::Euclidean_distance()); if (num_edges(proximity_graph) <= 0) { - std::cerr << "Total number of egdes are zero." << std::endl; + std::cerr << "Total number of edges is zero." << std::endl; exit(-1); } diff --git a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h index c823901f..d0b3fe4a 100644 --- a/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h +++ b/src/Collapse/include/gudhi/Flag_complex_edge_collapser.h @@ -53,7 +53,7 @@ struct Flag_complex_edge_collapser { #ifdef GUDHI_COLLAPSE_USE_DENSE_ARRAY // Minimal matrix interface // Using this matrix generally helps performance, but the memory use may be excessive for a very sparse graph - // (and in extreme cases the constant initialization of the matrix may start to dominate the runnning time). + // (and in extreme cases the constant initialization of the matrix may start to dominate the running time). // Are there cases where the matrix is too big but a hash table would help? std::vector<Filtration_value> neighbors_data; void init_neighbors_dense(){ diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp index 11ee5871..38efb9e6 100644 --- a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp +++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp @@ -45,7 +45,7 @@ int main(int argc, char* argv[]) { min_persistence); Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); - std::cout << "Read the distance matrix succesfully, of size: " << distances.size() << std::endl; + std::cout << "Read the distance matrix successfully, of size: " << distances.size() << std::endl; Proximity_graph proximity_graph = Gudhi::compute_proximity_graph<Simplex_tree>(boost::irange((size_t)0, distances.size()), diff --git a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp index 0eea742c..d8f42ab6 100644 --- a/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp +++ b/src/Collapse/utilities/point_cloud_edge_collapse_rips_persistence.cpp @@ -77,7 +77,7 @@ int main(int argc, char* argv[]) { Gudhi::Euclidean_distance()); if (num_edges(proximity_graph) <= 0) { - std::cerr << "Total number of egdes are zero." << std::endl; + std::cerr << "Total number of edges is zero." << std::endl; exit(-1); } diff --git a/src/Contraction/doc/so3.svg b/src/Contraction/doc/so3.svg index adea3f38..f10cab98 100644 --- a/src/Contraction/doc/so3.svg +++ b/src/Contraction/doc/so3.svg @@ -177,7 +177,7 @@ x="309.4176" y="300.58682" id="tspan4515-4" - style="text-align:center;text-anchor:middle">Rips complex built uppon these points</tspan><tspan + style="text-align:center;text-anchor:middle">Rips complex built upon these points</tspan><tspan sodipodi:role="line" x="309.4176" y="308.96704" diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h index 49250d7a..ae46232c 100644 --- a/src/Contraction/example/Garland_heckbert/Error_quadric.h +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -29,7 +29,7 @@ template <typename Point> class Error_quadric { * Quadric corresponding to the L2 distance to the plane. * * According to the notation of Garland Heckbert, they - * denote a quadric symetric matrix as : + * denote a quadric symmetric matrix as : * Q = [ q11 q12 q13 q14] * [ q12 q22 q23 q24] * [ q13 q23 q33 q34] diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index 58d627c2..0b43c3b3 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -46,7 +46,7 @@ the operations needed for edge contraction algorithms have polynomial complexity Therefore, the simplification can be done without enumerating the set of simplices that is often non tracktable in high-dimension and is then very efficient (sub-linear with regards to the number of simplices in practice). -A typical application of this package is homology group computation. It is illustrated in the next figure where a Rips complex is built uppon a set of high-dimensional points and +A typical application of this package is homology group computation. It is illustrated in the next figure where a Rips complex is built upon a set of high-dimensional points and simplified with edge contractions. It has initially a big number of simplices (around 20 millions) but simplifying it to a much reduced form with only 15 vertices (and 714 simplices) takes only few seconds on a desktop machine (see the example bellow). One can then compute homology group with a simplicial complex having very few simplices instead of running the homology algorithm on the much bigger initial set of @@ -65,7 +65,7 @@ This class design is policy based and heavily inspired from the similar edge col Four policies can be customized in this package: \li Cost_policy: specify how much cost an edge contraction of a given edge. The edge with lowest cost is iteratively picked and contracted if valid. -\li Valid_contraction_policy: specify if a given edge contraction is valid. For instance, this policy can check the link condition which ensures that the homotopy type is preserved afer the edge contraction. +\li Valid_contraction_policy: specify if a given edge contraction is valid. For instance, this policy can check the link condition which ensures that the homotopy type is preserved after the edge contraction. \li Placement_policy: every time an edge is contracted, its points are merge to one point specified by this policy. This may be the middle of the edge of some more sophisticated point such as the minimum of a cost as in \cite Garland. @@ -92,7 +92,7 @@ Despite this package is able to deal with \a arbitrary simplicial complexes (any it is still \a 65% times faster than the CGAL package which is focused on 2-manifold. The main reason is that few blockers appears during the simplification and hence, the algorithm only have to deal with the graph and not higher-dimensional simplices -(in this case triangles). However, we recall that higher-dimensional simplices are \a implicitely +(in this case triangles). However, we recall that higher-dimensional simplices are \a implicitly stored in the \ref skbl data-structure. Hence, one has to store simplices in an external map if some information needs to be associated with them (information that could be a filtration value or an orientation for instance). @@ -153,7 +153,7 @@ void build_rips(ComplexType& complex, double offset){ int main (int argc, char *argv[]) { if (argc!=3){ - std::cerr << "Usage "<<argv[0]<<" ../../data/SO3_10000.off 0.3 to load the file ../../data/SO3_10000.off and contract the Rips complex built with paremeter 0.3.\n"; + std::cerr << "Usage "<<argv[0]<<" ../../data/SO3_10000.off 0.3 to load the file ../../data/SO3_10000.off and contract the Rips complex built with parameter 0.3.\n"; return -1; } diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h index a0d9f2b2..56b76318 100644 --- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h +++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h @@ -280,7 +280,7 @@ typename GeometricSimplifiableComplex::Vertex_handle> { std::size_t id = 0; - // xxx do a parralel for + // xxx do a parallel for for (auto edge : complex_.edge_range()) { complex_[edge].index() = id++; Profile const& profile = create_profile(edge); @@ -474,7 +474,7 @@ typename GeometricSimplifiableComplex::Vertex_handle> { } void update_changed_edges() { - // xxx do a parralel for + // xxx do a parallel for DBG("update edges"); // sequential loop @@ -530,7 +530,7 @@ typename GeometricSimplifiableComplex::Vertex_handle> { // by definition of a blocker // todo uniqument utile pour la link condition - // laisser a l'utilisateur ? booleen update_heap_on_removed_blocker? + // laisser a l'utilisateur ? boolean update_heap_on_removed_blocker? Simplex blocker_copy(*blocker); for (auto x = blocker_copy.begin(); x != blocker_copy.end(); ++x) { for (auto y = x; ++y != blocker_copy.end();) { diff --git a/src/Coxeter_triangulation/include/gudhi/Coxeter_triangulation/Cell_complex/Hasse_diagram_cell.h b/src/Coxeter_triangulation/include/gudhi/Coxeter_triangulation/Cell_complex/Hasse_diagram_cell.h index 59e9a350..9b57da3c 100644 --- a/src/Coxeter_triangulation/include/gudhi/Coxeter_triangulation/Cell_complex/Hasse_diagram_cell.h +++ b/src/Coxeter_triangulation/include/gudhi/Coxeter_triangulation/Cell_complex/Hasse_diagram_cell.h @@ -95,7 +95,7 @@ class Hasse_diagram_cell { deleted_(false) {} /** - * Construcor of a cell of dimension dim having given additional information. + * Constructor of a cell of dimension dim having given additional information. **/ Hasse_diagram_cell(Additional_information ai, int dim) : dimension(dim), additional_info(ai), position(0), deleted_(false) {} @@ -125,7 +125,7 @@ class Hasse_diagram_cell { inline Additional_information& get_additional_information() { return this->additional_info; } /** - * Procedure to retrive position of the cell in the structure. It is used in + * Procedure to retrieve the position of the cell in the structure. It is used in * the implementation of Hasse diagram and set by it. Note that removal of * cell and subsequent call of clean_up_the_structure will change those * positions. @@ -186,7 +186,7 @@ class Hasse_diagram_cell { friend std::ostream& operator<<( std::ostream& out, const Hasse_diagram_cell<Incidence_type, Filtration_type, Additional_information>& c) { // cout << "position : " << c.position << ", dimension : " << c.dimension << ", filtration: " << c.filtration << ", - // size of boudary : " << c.boundary.size() << "\n"; + // size of boundary : " << c.boundary.size() << "\n"; out << c.position << " " << c.dimension << " " << c.filtration << std::endl; for (std::size_t bd = 0; bd != c.boundary.size(); ++bd) { // do not write out the cells that has been deleted diff --git a/src/Coxeter_triangulation/include/gudhi/Functions/Function_affine_plane_in_Rd.h b/src/Coxeter_triangulation/include/gudhi/Functions/Function_affine_plane_in_Rd.h index b29f0906..dc6f5f90 100644 --- a/src/Coxeter_triangulation/include/gudhi/Functions/Function_affine_plane_in_Rd.h +++ b/src/Coxeter_triangulation/include/gudhi/Functions/Function_affine_plane_in_Rd.h @@ -51,7 +51,7 @@ struct Function_affine_plane_in_Rd { * plane in the d-dimensional Euclidean space. * * @param[in] normal_matrix A normal matrix of the affine plane. The number of rows should - * correspond to the ambient dimension, the number of columns should corespond to + * correspond to the ambient dimension, the number of columns should correspond to * the size of the normal basis (codimension). * @param[in] offset The offset vector of the affine plane. * The dimension of the vector should be the ambient dimension of the manifold. @@ -66,7 +66,7 @@ struct Function_affine_plane_in_Rd { * plane in the d-dimensional Euclidean space that passes through origin. * * @param[in] normal_matrix A normal matrix of the affine plane. The number of rows should - * correspond to the ambient dimension, the number of columns should corespond to + * correspond to the ambient dimension, the number of columns should correspond to * the size of the normal basis (codimension). */ Function_affine_plane_in_Rd(const Eigen::MatrixXd& normal_matrix) diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h index db145741..1a63d2f7 100644 --- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h +++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Permutahedral_representation_iterators.h @@ -26,12 +26,12 @@ namespace Gudhi { namespace coxeter_triangulation { -/* \addtogroup coxeter_triangulation +/** \addtogroup coxeter_triangulation * Iterator types for Permutahedral_representation * @{ */ -/* \brief Iterator over the vertices of a simplex +/** \brief Iterator over the vertices of a simplex * represented by its permutahedral representation. * * Forward iterator, 'value_type' is Permutahedral_representation::Vertex.*/ @@ -83,7 +83,7 @@ class Vertex_iterator }; // Vertex_iterator /*---------------------------------------------------------------------------*/ -/* \brief Iterator over the k-faces of a simplex +/** \brief Iterator over the k-faces of a simplex * given by its permutahedral representation. * * Forward iterator, value_type is Permutahedral_representation. */ @@ -141,7 +141,7 @@ class Face_iterator : public boost::iterator_facade<Face_iterator<Permutahedral_ }; // Face_iterator /*---------------------------------------------------------------------------*/ -/* \brief Iterator over the k-cofaces of a simplex +/** \brief Iterator over the k-cofaces of a simplex * given by its permutahedral representation. * * Forward iterator, value_type is Permutahedral_representation. */ @@ -247,6 +247,8 @@ class Coface_iterator }; // Coface_iterator +/** @} */ + } // namespace coxeter_triangulation } // namespace Gudhi diff --git a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h index c43effc8..6b137744 100644 --- a/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h +++ b/src/Coxeter_triangulation/include/gudhi/Permutahedral_representation/Size_range.h @@ -19,7 +19,7 @@ namespace Gudhi { namespace coxeter_triangulation { -/** \brief Auxillary iterator class for sizes of parts in an ordered set partition. +/** \brief Auxiliary iterator class for sizes of parts in an ordered set partition. */ template <class T_it> class Size_iterator diff --git a/src/Doxyfile.in b/src/Doxyfile.in index 13668993..06a74012 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -229,7 +229,7 @@ TAB_SIZE = 2 # "Side Effects:". You can put \n's in the value part of an alias to insert # newlines. -ALIASES = +ALIASES = gudhi_example_link{2}="@ref \2 \"\1/\2\"" # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources # only. Doxygen will then generate output that is more tailored for C. For @@ -1473,6 +1473,17 @@ FORMULA_TRANSPARENT = YES USE_MATHJAX = YES +# With MATHJAX_VERSION it is possible to specify the MathJax version to be used. +# Note that the different versions of MathJax have different requirements with +# regards to the different settings, so it is possible that also other MathJax +# settings have to be changed when switching between the different MathJax +# versions. +# Possible values are: MathJax_2 and MathJax_3. +# The default value is: MathJax_2. +# This tag requires that the tag USE_MATHJAX is set to YES. + +@GUDHI_DOXYGEN_MATHJAX_VERSION@ + # When MathJax is enabled you can set the default output format to be used for # the MathJax output. See the MathJax site (see: # http://docs.mathjax.org/en/latest/output.html) for more details. @@ -1494,15 +1505,14 @@ MATHJAX_FORMAT = HTML-CSS # The default value is: http://cdn.mathjax.org/mathjax/latest. # This tag requires that the tag USE_MATHJAX is set to YES. -MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2 +MATHJAX_RELPATH = # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax # extension names that should be enabled during MathJax rendering. For example # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols # This tag requires that the tag USE_MATHJAX is set to YES. -MATHJAX_EXTENSIONS = TeX/AMSmath \ - TeX/AMSsymbols +MATHJAX_EXTENSIONS = @GUDHI_DOXYGEN_MATHJAX_EXTENSIONS@ # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces # of code that will be used on startup of the MathJax code. See the MathJax site diff --git a/src/GudhUI/todo.txt b/src/GudhUI/todo.txt index 19d99a77..e59d06d4 100644 --- a/src/GudhUI/todo.txt +++ b/src/GudhUI/todo.txt @@ -18,5 +18,5 @@ x faire le lien MainWindow - Model -- bug -x bug ordre contraction -> just that first vertex placement dont work great +x bug ordre contraction -> just that first vertex placement doesn't work great x pb construction rips diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h index 97e58737..65695434 100644 --- a/src/GudhUI/utils/Critical_points.h +++ b/src/GudhUI/utils/Critical_points.h @@ -103,7 +103,7 @@ template<typename SkBlComplex> class Critical_points { // reduced to one point -> contractible return 1; else - // we dont know + // we don't know return 2; } diff --git a/src/GudhUI/utils/Edge_contractor.h b/src/GudhUI/utils/Edge_contractor.h index 0707b186..a71d0742 100644 --- a/src/GudhUI/utils/Edge_contractor.h +++ b/src/GudhUI/utils/Edge_contractor.h @@ -65,7 +65,7 @@ template<typename SkBlComplex> class Edge_contractor { /** * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. + * symmetric graph. */ Edge_contractor(SkBlComplex& complex, unsigned num_contractions) : complex_(complex), num_contractions_(num_contractions) { diff --git a/src/GudhUI/utils/Furthest_point_epsilon_net.h b/src/GudhUI/utils/Furthest_point_epsilon_net.h index 6eb71071..195d0014 100644 --- a/src/GudhUI/utils/Furthest_point_epsilon_net.h +++ b/src/GudhUI/utils/Furthest_point_epsilon_net.h @@ -27,7 +27,7 @@ template<typename SkBlComplex> class Furthest_point_epsilon_net { /** * Let V be the set of vertices. - * Initially v0 is one arbitrarly vertex and the set V0 is {v0}. + * Initially v0 is one, arbitrary, vertex and the set V0 is {v0}. * Then Vk is computed as follows. * First we compute the vertex pk that is the furthest from Vk * then Vk = Vk \cup pk. @@ -54,7 +54,7 @@ template<typename SkBlComplex> class Furthest_point_epsilon_net { /** * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. + * symmetric graph. */ Furthest_point_epsilon_net(SkBlComplex& complex) : complex_(complex) { diff --git a/src/GudhUI/utils/K_nearest_builder.h b/src/GudhUI/utils/K_nearest_builder.h index 34483e58..454b2587 100644 --- a/src/GudhUI/utils/K_nearest_builder.h +++ b/src/GudhUI/utils/K_nearest_builder.h @@ -41,7 +41,7 @@ template<typename SkBlComplex> class K_nearest_builder { public: /** * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. + * symmetric graph. */ K_nearest_builder(SkBlComplex& complex, unsigned k) : complex_(complex) { complex.keep_only_vertices(); diff --git a/src/GudhUI/utils/Lloyd_builder.h b/src/GudhUI/utils/Lloyd_builder.h index c042564f..57e3dc0f 100644 --- a/src/GudhUI/utils/Lloyd_builder.h +++ b/src/GudhUI/utils/Lloyd_builder.h @@ -27,7 +27,7 @@ template<typename SkBlComplex> class Lloyd_builder { /** * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. + * symmetric graph. */ Lloyd_builder(SkBlComplex& complex, unsigned num_iterations) : complex_(complex), dim(-1) { if (!complex_.empty()) { diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h index 030e4bb0..b1c48efd 100644 --- a/src/GudhUI/utils/Vertex_collapsor.h +++ b/src/GudhUI/utils/Vertex_collapsor.h @@ -31,7 +31,7 @@ template<typename SkBlComplex> class Vertex_collapsor { /** * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. + * symmetric graph. */ Vertex_collapsor(SkBlComplex& complex, size_t num_collapses) : complex_(complex), num_collapses_(num_collapses) { diff --git a/src/Nerve_GIC/utilities/km.py.COPYRIGHT b/src/Nerve_GIC/utilities/km.py.COPYRIGHT index bef7b121..5358d287 100644 --- a/src/Nerve_GIC/utilities/km.py.COPYRIGHT +++ b/src/Nerve_GIC/utilities/km.py.COPYRIGHT @@ -1,7 +1,7 @@ km.py is a fork of https://github.com/MLWave/kepler-mapper. Only the visualization part has been kept (Mapper part has been removed). -This file has te following Copyright : +This file has the following Copyright : The MIT License (MIT) diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h index a6c1d6f0..f4324cb2 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h @@ -109,7 +109,7 @@ class Persistence_intervals { std::vector<size_t> cumulative_histogram_of_lengths(size_t number_of_bins = 10) const; /** - * In this procedure we assume that each barcode is a characteristic function of a hight equal to its length. The + * In this procedure we assume that each barcode is a characteristic function of a height equal to its length. The *persistence diagram is a sum of such a functions. The procedure below construct a function being a * sum of the characteristic functions of persistence intervals. The first two parameters are the range in which the *function is to be computed and the last parameter is the number of bins in @@ -207,7 +207,7 @@ class Persistence_intervals { /** * This is a simple function projecting the persistence intervals to a real number. The function we use here is a sum *of squared lengths of intervals. It can be naturally interpreted as - * sum of step function, where the step hight it equal to the length of the interval. + * sum of step function, where the step height it equal to the length of the interval. * At the moment this function is not tested, since it is quite likely to be changed in the future. Given this, when *using it, keep in mind that it * will be most likely changed in the next versions. diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp index 030b072a..3bec8830 100644 --- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp +++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp @@ -49,7 +49,7 @@ void timing_persistence(FilteredComplex & cpx * with a Hasse diagram. The Hasse diagram represents explicitly all * codimension 1 incidence relations in the complex, and hence leads to * a faster computation of persistence because boundaries are precomputed. - * Hovewer, the simplex tree may be constructed directly from a point cloud and + * However, the simplex tree may be constructed directly from a point cloud and * is more compact. * We compute persistent homology with coefficient fields Z/2Z and Z/1223Z. * We present also timings for the computation of multi-field persistent diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h index 26ac7ac8..59ce25e3 100644 --- a/src/Persistent_cohomology/concept/FilteredComplex.h +++ b/src/Persistent_cohomology/concept/FilteredComplex.h @@ -103,7 +103,7 @@ Filtration_simplex_range filtration_simplex_range(); /** @} */ -/* \brief Iterator over the simplices of the complex, +/** \brief Iterator over the simplices of the complex, * in an arbitrary order. * * 'value_type' must be 'Simplex_handle'.*/ diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index a3613d0d..94579564 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -131,8 +131,7 @@ namespace persistent_cohomology { We provide several example files: run these examples with -h for details on their use, and read the README file. -\li <a href="rips_persistence_8cpp-example.html"> -Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence +\li \gudhi_example_link{Rips_complex,rips_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode \code The complex contains 177838 simplices @@ -144,12 +143,10 @@ diagram. More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="rips_multifield_persistence_8cpp-example.html"> -Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its +\li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li <a href="rips_distance_matrix_persistence_8cpp-example.html"> -Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and +\li \gudhi_example_link{Rips_complex,rips_distance_matrix_persistence.cpp} computes the Rips complex of a distance matrix and outputs its persistence diagram. The file should contain square or lower triangular distance matrix with semicolons as separators. @@ -158,8 +155,7 @@ Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="rips_correlation_matrix_persistence_8cpp-example.html"> -Rips_complex/rips_correlation_matrix_persistence.cpp</a> +\li \gudhi_example_link{Rips_complex,rips_correlation_matrix_persistence.cpp} computes the Rips complex of a correlation matrix and outputs its persistence diagram. Note that no check is performed if the matrix given as the input is a correlation matrix. @@ -169,8 +165,7 @@ Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="alpha_complex_3d_persistence_8cpp-example.html"> -Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 @@ -235,8 +230,7 @@ Note that the lengths of the sides of the periodic cuboid have to be the same.<b 3 2 36.8838 inf 3 3 58.6783 inf \endcode -\li <a href="alpha_complex_persistence_8cpp-example.html"> -Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with +\li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. @@ -248,8 +242,7 @@ Simplex_tree dim: 3 More details on the <a href="../../alphacomplex/">Alpha complex utilities</a> dedicated page. -\li <a href="plain_homology_8cpp-example.html"> -Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without +\li \gudhi_example_link{Persistent_cohomology,plain_homology.cpp} computes the plain homology of a simple simplicial complex without filtration values. */ diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index 410cd987..bba0b2f7 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -33,7 +33,7 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog Gudhi::persistent_cohomology::Field_Zp >; std::vector<Point> random_points() { - // Instanciate a random point generator + // Instantiate a random point generator CGAL::Random rng(0); // Generate "points_number" random points in a vector diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index bffaabdd..3da6771e 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -95,7 +95,7 @@ int main(int argc, char * const argv[]) { SimplexVector = {9, 10, 11}; st.insert_simplex_and_subfaces(SimplexVector, 0.3); - // ++ NINETH + // ++ NINTH std::clog << " - INSERT (2,10,12)" << std::endl; SimplexVector = {2, 10, 12}; st.insert_simplex_and_subfaces(SimplexVector, 0.3); diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index 2edf5bc4..ca26a5b9 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -104,7 +104,7 @@ void program_options(int argc, char * argv[] ("min-field-charac,p", po::value<int>(&min_p)->default_value(2), "Minimal characteristic p of the coefficient field Z/pZ.") ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223), - "Minimial characteristic q of the coefficient field Z/pZ.") + "Maximal characteristic q of the coefficient field Z/pZ.") ("min-persistence,m", po::value<Filtration_value>(&min_persistence), "Minimal lifetime of homology feature to be recorded. Default is 0"); diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index d428e497..2301a66b 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -211,7 +211,7 @@ class Persistent_cohomology { /** \brief Update the cohomology groups under the insertion of an edge. * * The 0-homology is maintained with a simple Union-Find data structure, which - * explains the existance of a specific function of edge insertions. */ + * explains the existence of a specific function of edge insertions. */ void update_cohomology_groups_edge(Simplex_handle sigma) { Simplex_handle u, v; boost::tie(u, v) = cpx_->endpoints(sigma); diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 3888ec8f..cd77b327 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -63,9 +63,8 @@ namespace rips_complex { * value set with \f$max(filtration(4,5), filtration(4,6), filtration(5,6))\f$. * And so on for simplex (0,1,2,3). * - * If the Rips_complex interfaces are not detailed enough for your need, please refer to - * <a href="rips_persistence_step_by_step_8cpp-example.html"> - * rips_persistence_step_by_step.cpp</a> example, where the constructions of the graph and + * If the Rips_complex interfaces are not detailed enough for your need, please refer to the example + * \gudhi_example_link{Persistent_cohomology,rips_persistence_step_by_step.cpp} , where the constructions of the graph and * the Simplex_tree are more detailed. * * \section sparserips Sparse Rips complex diff --git a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp index 3d2ba54f..3811d1f1 100644 --- a/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp +++ b/src/Rips_complex/example/example_one_skeleton_rips_from_correlation_matrix.cpp @@ -40,7 +40,7 @@ int main() { throw "The input matrix is not a correlation matrix. The program will now terminate.\n"; } correlations[i][j] = 1 - correlations[i][j]; - // Here we make sure that we will get the treshold value equal to maximal + // Here we make sure that we will get the threshold value equal to maximal // distance in the matrix. if (correlations[i][j] > threshold) threshold = correlations[i][j]; } diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index ef8dec91..2d3ecdec 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -39,11 +39,9 @@ namespace Gudhi { * \subsubsection filteredcomplexessimplextreeexamples Examples * * Here is a list of simplex tree examples : - * \li <a href="simple_simplex_tree_8cpp-example.html"> - * Simplex_tree/simple_simplex_tree.cpp</a> - Simple simplex tree construction and basic function use. + * \li \gudhi_example_link{Simplex_tree,simple_simplex_tree.cpp} - Simple simplex tree construction and basic function use. * - * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html"> - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - Simplex tree construction from cliques of graph read in + * \li \gudhi_example_link{Simplex_tree,simplex_tree_from_cliques_of_graph.cpp} - Simplex tree construction from cliques of graph read in * a file. * * Simplex tree construction with \f$\mathbb{Z}/3\mathbb{Z}\f$ coefficients on weighted graph Klein bottle file: @@ -54,12 +52,10 @@ Expand the simplex tree in 3.8e-05 s. Information of the Simplex Tree: Number of vertices = 10 Number of simplices = 98 \endcode * - * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - Simplex tree is computed and displayed + * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp} - Simplex tree is computed and displayed * from a 3D alpha complex (Requires CGAL, GMP and GMPXX to be installed). * - * \li <a href="graph_expansion_with_blocker_8cpp-example.html"> - * Simplex_tree/graph_expansion_with_blocker.cpp</a> - Simple simplex tree construction from a one-skeleton graph with + * \li \gudhi_example_link{Simplex_tree,graph_expansion_with_blocker.cpp} - Simple simplex tree construction from a one-skeleton graph with * a simple blocker expansion method. * * \subsection filteredcomplexeshassecomplex Hasse complex diff --git a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp index df52bf43..eef8b665 100644 --- a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp +++ b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp @@ -42,7 +42,7 @@ int main(int argc, char* const argv[]) { std::clog << vertex << ", "; } std::clog << "] ( " << stree.filtration(sh); - // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries) + // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boundaries) stree.assign_filtration(sh, stree.filtration(sh) + 1.); std::clog << " + 1. ) = " << result << std::endl; diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index e8bec596..965711da 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -129,7 +129,7 @@ int main(int argc, char* const argv[]) { std::clog << " - 3 NOT INSERTED" << std::endl; } - // ++ NINETH + // ++ NINTH std::clog << " * INSERT (3,0)" << std::endl; typeVectorVertex ninethSimplexVector = {3, 0}; returnValue = simplexTree.insert_simplex(ninethSimplexVector, Filtration_value(SECOND_FILTRATION_VALUE)); diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 6dce947c..9059219c 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -42,6 +42,10 @@ namespace Gudhi { +/** \addtogroup simplex_tree + * @{ + */ + /** * \class Extended_simplex_type Simplex_tree.h gudhi/Simplex_tree.h * \brief Extended simplex type data structure for representing the type of simplices in an extended filtration. @@ -97,8 +101,7 @@ class Simplex_tree { // Simplex_key next to each other). typedef typename boost::container::flat_map<Vertex_handle, Node> Dictionary; - /* \brief Set of nodes sharing a same parent in the simplex tree. */ - /* \brief Set of nodes sharing a same parent in the simplex tree. */ + /** \brief Set of nodes sharing a same parent in the simplex tree. */ typedef Simplex_tree_siblings<Simplex_tree, Dictionary> Siblings; @@ -965,7 +968,7 @@ class Simplex_tree { // If we reached the end of the vertices, and the simplex has more vertices than the given simplex // => we found a coface - // Add a coface if we wan't the star or if the number of vertices of the current simplex matches with nbVertices + // Add a coface if we want the star or if the number of vertices of the current simplex matches with nbVertices bool addCoface = (star || curr_nbVertices == nbVertices); if (addCoface) cofaces.push_back(simplex); @@ -1338,7 +1341,7 @@ class Simplex_tree { } } - /* \private Returns the Simplex_handle composed of the vertex list (from the Simplex_handle), plus the given + /** \private Returns the Simplex_handle composed of the vertex list (from the Simplex_handle), plus the given * Vertex_handle if the Vertex_handle is found in the Simplex_handle children list. * Returns null_simplex() if it does not exist */ @@ -1491,7 +1494,7 @@ class Simplex_tree { int sh_dimension = dimension(sh); if (sh_dimension >= dimension_) - // Stop browsing as soon as the dimension is reached, no need to go furter + // Stop browsing as soon as the dimension is reached, no need to go further return false; new_dimension = (std::max)(new_dimension, sh_dimension); } @@ -1801,7 +1804,7 @@ struct Simplex_tree_options_fast_persistence { static const bool contiguous_vertices = true; }; -/** @} */ // end defgroup simplex_tree +/** @}*/ // end addtogroup simplex_tree } // namespace Gudhi diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index 394c6ee1..b63a5595 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -22,12 +22,12 @@ namespace Gudhi { -/* \addtogroup simplex_tree +/** \addtogroup simplex_tree * Iterators and range types for the Simplex_tree. - * @{ + * @{ */ -/* \brief Iterator over the vertices of a simplex +/** \brief Iterator over the vertices of a simplex * in a SimplexTree. * * Forward iterator, 'value_type' is SimplexTree::Vertex_handle.*/ @@ -73,7 +73,7 @@ class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade< }; /*---------------------------------------------------------------------------*/ -/* \brief Iterator over the simplices of the boundary of a +/** \brief Iterator over the simplices of the boundary of a * simplex. * * Forward iterator, value_type is SimplexTree::Simplex_handle.*/ @@ -181,7 +181,7 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade< SimplexTree * st_; // simplex containing the simplicial complex }; -/* \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices. +/** \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices. * * Forward iterator, value_type is std::pair<SimplexTree::Simplex_handle, SimplexTree::Vertex_handle>.*/ template<class SimplexTree> @@ -291,7 +291,7 @@ class Simplex_tree_boundary_opposite_vertex_simplex_iterator : public boost::ite }; /*---------------------------------------------------------------------------*/ -/* \brief Iterator over the simplices of a simplicial complex. +/** \brief Iterator over the simplices of a simplicial complex. * * Forward iterator, value_type is SimplexTree::Simplex_handle.*/ template<class SimplexTree> @@ -364,7 +364,7 @@ class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade< SimplexTree * st_; }; -/* \brief Iterator over the simplices of the skeleton of a given +/** \brief Iterator over the simplices of the skeleton of a given * dimension of the simplicial complex. * * Forward iterator, value_type is SimplexTree::Simplex_handle.*/ @@ -447,7 +447,8 @@ class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade< int curr_dim_; }; -/* @} */ // end addtogroup simplex_tree +/** @}*/ // end addtogroup simplex_tree + } // namespace Gudhi #endif // SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_ diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h index ae140859..63023daa 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h @@ -15,16 +15,15 @@ namespace Gudhi { -/* \addtogroup simplex_tree +/** \addtogroup simplex_tree * Represents a node of a Simplex_tree. * @{ */ -/* - * \brief Node of a simplex tree with filtration value +/** \brief Node of a simplex tree with filtration value * and simplex key. * - * It stores explicitely its own filtration value and its own Simplex_key. + * It stores explicitly its own filtration value and its own Simplex_key. */ template<class SimplexTree> struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base, SimplexTree::Key_simplex_base { @@ -54,7 +53,8 @@ struct Simplex_tree_node_explicit_storage : SimplexTree::Filtration_simplex_base Siblings * children_; }; -/* @} */ // end addtogroup simplex_tree +/** @}*/ // end addtogroup simplex_tree + } // namespace Gudhi #endif // SIMPLEX_TREE_SIMPLEX_TREE_NODE_EXPLICIT_STORAGE_H_ diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h index ae25d290..d849eeba 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h @@ -20,12 +20,12 @@ namespace Gudhi { -/* \addtogroup simplex_tree +/** \addtogroup simplex_tree * Represents a set of node of a Simplex_tree that share the same parent. * @{ */ -/* \brief Data structure to store a set of nodes in a SimplexTree sharing +/** \brief Data structure to store a set of nodes in a SimplexTree sharing * the same parent node.*/ template<class SimplexTree, class MapContainer> class Simplex_tree_siblings { @@ -58,7 +58,7 @@ class Simplex_tree_siblings { members_() { } - /* \brief Constructor with initialized set of members. + /** \brief Constructor with initialized set of members. * * 'members' must be sorted and unique.*/ template<typename RandomAccessVertexRange> @@ -72,8 +72,7 @@ class Simplex_tree_siblings { } } - /* - * \brief Inserts a Node in the set of siblings nodes. + /** \brief Inserts a Node in the set of siblings nodes. * * If already present, assigns the minimal filtration value * between input filtration_value and the value already @@ -114,7 +113,8 @@ class Simplex_tree_siblings { Dictionary members_; }; -/* @} */ // end addtogroup simplex_tree +/** @}*/ // end addtogroup simplex_tree + } // namespace Gudhi #endif // SIMPLEX_TREE_SIMPLEX_TREE_SIBLINGS_H_ diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h index 3e395ae2..29c76e50 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h @@ -20,7 +20,7 @@ namespace Gudhi { struct linear_indexing_tag { }; -/* \brief Tag for a zigzag ordering of simplices. */ +/** \brief Tag for a zigzag ordering of simplices. */ // struct zigzag_indexing_tag {}; } // namespace Gudhi diff --git a/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp index 6d63d8ae..54e23204 100644 --- a/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp @@ -93,7 +93,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_3, typeST, li std::clog << vertex << ", "; } std::clog << "] ( " << simplex_tree.filtration(sh); - // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries) + // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boundaries) simplex_tree.assign_filtration(sh, simplex_tree.filtration(sh) + 1.); std::clog << " + 1. ) = " << result << std::endl; @@ -160,7 +160,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_2, typeST, li std::clog << vertex << ", "; } std::clog << "] ( " << simplex_tree.filtration(sh); - // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries) + // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boundaries) simplex_tree.assign_filtration(sh, simplex_tree.filtration(sh) + 1.); std::clog << " + 1. ) = " << result << std::endl; diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp index b18e2ec4..79bb5a93 100644 --- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp @@ -287,7 +287,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var set_and_test_simplex_tree_dim_fil(st, eighthSimplexVector.size(), eighthSimplex.second); BOOST_CHECK(st.num_vertices() == (size_t) 4); - // ++ NINETH + // ++ NINTH std::clog << " - INSERT (3,0)" << std::endl; typeVectorVertex ninethSimplexVector{3, 0}; BOOST_CHECK(ninethSimplexVector.size() == 2); @@ -361,7 +361,7 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var test_simplex_tree_contains(st, seventhSimplex, 8); // (2,1,0) -> 8 std::clog << "simplex_tree_insertion - eighth - 3" << std::endl; test_simplex_tree_contains(st, eighthSimplex, 3); // (3) -> 3 - std::clog << "simplex_tree_insertion - nineth - 7" << std::endl; + std::clog << "simplex_tree_insertion - ninth - 7" << std::endl; test_simplex_tree_contains(st, ninethSimplex, 7); // (3,0) -> 7 // Display the Simplex_tree - Can not be done in the middle of 2 inserts diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h index 12fe6469..d83c0ab3 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h @@ -134,7 +134,7 @@ class Skeleton_blocker_simplex { } /** - * Substracts a from the simplex. + * Subtracts a from the simplex. */ void difference(const Skeleton_blocker_simplex & a) { std::vector<T> v; diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h index 4c48ff31..5abd64d7 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h @@ -76,8 +76,8 @@ class Skeleton_blocker_sub_complex : public ComplexType { public: /** * Add a vertex 'global' of K to L. When added to L, this vertex will receive - * another number, addresses(global), its local adress. - * return the adress where the vertex lay on L. + * another number, addresses(global), its local address. + * return the address where the vertex lay on L. * The vertex corresponding to 'global' must not be already present * in the complex. */ @@ -174,7 +174,7 @@ class Skeleton_blocker_sub_complex : public ComplexType { // /** // * Allocates a simplex in L corresponding to the simplex s in K - // * with its local adresses and returns an AddressSimplex. + // * with its local addresses and returns an AddressSimplex. // */ // boost::optional<Simplex> get_address(const Root_simplex_handle & s) const; @@ -226,7 +226,7 @@ bool proper_face_in_union( } // Remark: this function should be friend in order to leave get_adresses private -// however doing so seemes currently not possible due to a visual studio bug c2668 +// however doing so seems currently not possible due to a visual studio bug c2668 // "the compiler does not support partial ordering of template functions as specified in the C++ Standard" // http://www.serkey.com/error-c2668-ambiguous-call-to-overloaded-function-bb45ft.html diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h index a43fa034..18ae6a92 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h @@ -107,7 +107,7 @@ struct Trie { } /** - * Goes to the root in the trie to consitute simplex + * Goes to the root in the trie to constitute simplex */ void add_vertices_up_to_the_root(Simplex& res) const { res.add_vertex(v); diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h index 37c0b4d3..2c49a1b8 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h @@ -21,7 +21,7 @@ namespace skeleton_blocker { /** * \brief Iterator over the triangles that are * adjacent to a vertex of the simplicial complex. - * \remark Will be removed soon -> dont look + * \remark Will be removed soon -> don't look */ template<typename Complex, typename LinkType> class Triangle_around_vertex_iterator : public boost::iterator_facade @@ -95,7 +95,7 @@ class Triangle_around_vertex_iterator : public boost::iterator_facade /** * \brief Iterator over the triangles of the * simplicial complex. - * \remark Will be removed soon -> dont look + * \remark Will be removed soon -> don't look * */ template<typename SkeletonBlockerComplex> diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h index 031bcb9c..8ceaa480 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h @@ -438,7 +438,7 @@ class Skeleton_blocker_complex { } /** - * return the id of a vertex of adress local present in the graph + * return the id of a vertex of address local present in the graph */ Root_vertex_handle get_id(Vertex_handle local) const { assert(0 <= local.vertex && local.vertex < boost::num_vertices(skeleton)); @@ -740,7 +740,7 @@ class Skeleton_blocker_complex { * complex to the smallest flag complex that contains it. */ void remove_blockers() { - // Desallocate the blockers + // Deallocate the blockers while (!blocker_map_.empty()) { delete_blocker(blocker_map_.begin()->second); } @@ -764,8 +764,8 @@ class Skeleton_blocker_complex { public: /** - * Removes the simplex s from the set of blockers - * and desallocate s. + * Removes the simplex sigma from the set of blockers + * and deallocate sigma. */ void delete_blocker(Blocker_handle sigma) { if (visitor) @@ -960,7 +960,7 @@ class Skeleton_blocker_complex { } /* - * @brief returnrs true iff the complex is empty. + * @brief returns true iff the complex is empty. */ bool empty() const { return num_vertices() == 0; @@ -1043,7 +1043,7 @@ class Skeleton_blocker_complex { if (num_vertices() == 1) return true; for (auto vi : vertex_range()) { - // xxx todo faire une methode bool is_in_blocker(Vertex_handle) + // xxx todo create a method: bool is_in_blocker(Vertex_handle) if (blocker_map_.find(vi) == blocker_map_.end()) { // no blocker passes through the vertex, we just need to // check if the current vertex is linked to all others vertices of the complex diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index f3491f91..cc424810 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -1152,7 +1152,7 @@ class Tangential_complex { #ifdef GUDHI_TC_VERY_VERBOSE std::cerr << "Inserted " << num_inserted_points << " points / " << num_attempts_to_insert_points - << " attemps to compute the star\n"; + << " attempts to compute the star\n"; #endif update_star(i); diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index 2ae1d6e0..1aebb045 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -18,7 +18,7 @@ namespace Gudhi { namespace witness_complex { - /* \class Active_witness + /** \class Active_witness * \brief Class representing a list of nearest neighbors to a given witness. * \details Every element is a pair of a landmark identifier and the squared distance to it. */ diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 4f8fddba..18f19650 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -18,7 +18,7 @@ namespace Gudhi { namespace witness_complex { -/* \brief Iterator in the nearest landmark list. +/** \brief Iterator in the nearest landmark list. * \details After the iterator reaches the end of the list, * the list is augmented by a (nearest landmark, distance) pair if possible. * If all the landmarks are present in the list, iterator returns the specific end value diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index b3699f77..ddc0da32 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -125,7 +125,7 @@ class Strong_witness_complex { //@} private: - /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness. + /** \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness. * Iterator is needed to know until how far we can take landmarks to form simplexes. * simplex is the prefix of the simplexes to insert. * The landmark pointed by aw_it is added to all formed simplices. diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index d655c7f6..66ae7af2 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -127,7 +127,7 @@ class Witness_complex { //@} private: - /* \brief Adds recursively all the faces of a certain dimension dim witnessed by the same witness. + /** \brief Adds recursively all the faces of a certain dimension dim witnessed by the same witness. * Iterator is needed to know until how far we can take landmarks to form simplexes. * simplex is the prefix of the simplexes to insert. * The output value indicates if the witness rests active or not. diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h index 5845728a..007ab084 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h +++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h @@ -11,7 +11,7 @@ #ifndef WITNESS_COMPLEX_ALL_FACES_IN_H_ #define WITNESS_COMPLEX_ALL_FACES_IN_H_ -/* \brief Check if the facets of the k-dimensional simplex witnessed +/** \brief Check if the facets of the k-dimensional simplex witnessed * by witness witness_id are already in the complex. * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id */ diff --git a/src/cmake/modules/FindTBB.cmake b/src/cmake/modules/FindTBB.cmake index 13f4d929..e6c42dc7 100644 --- a/src/cmake/modules/FindTBB.cmake +++ b/src/cmake/modules/FindTBB.cmake @@ -34,7 +34,7 @@ # # GvdB: Mac OS X distribution places libraries directly in lib directory. # -# For backwards compatibility, you may explicitely set the CMake variables TBB_ARCHITECTURE and TBB_COMPILER. +# For backwards compatibility, you may explicitly set the CMake variables TBB_ARCHITECTURE and TBB_COMPILER. # TBB_ARCHITECTURE [ ia32 | em64t | itanium ] # which architecture to use # TBB_COMPILER e.g. vc9 or cc3.2.3_libc2.3.2_kernel2.4.21 or cc4.0.1_os10.4.9 @@ -54,8 +54,8 @@ # TBB_MALLOC_DEBUG_LIBRARY, the TBB debug malloc library # TBB_FOUND, If false, don't try to use TBB. # TBB_INTERFACE_VERSION, as defined in tbb/tbb_stddef.h -# TBB_MALLOCPROXY_DEBUG_LIBRARY, the TBB debug malloc_proxy library (not included in TBB_LIBRARIES since it's optionnal) -# TBB_MALLOCPROXY_RELEASE_LIBRARY, the TBB release malloc_proxy library (not included in TBB_LIBRARIES since it's optionnal) +# TBB_MALLOCPROXY_DEBUG_LIBRARY, the TBB debug malloc_proxy library (not included in TBB_LIBRARIES since it's optional) +# TBB_MALLOCPROXY_RELEASE_LIBRARY, the TBB release malloc_proxy library (not included in TBB_LIBRARIES since it's optional) include(CheckCXXSourceCompiles) diff --git a/src/cmake/modules/GUDHI_doxygen_target.cmake b/src/cmake/modules/GUDHI_doxygen_target.cmake index e8064466..327513da 100644 --- a/src/cmake/modules/GUDHI_doxygen_target.cmake +++ b/src/cmake/modules/GUDHI_doxygen_target.cmake @@ -44,11 +44,19 @@ if(DOXYGEN_FOUND) set(GUDHI_DOXYGEN_UTILS_PATH "utilities/*") endif() + message("++ Doxygen version ${DOXYGEN_VERSION}") if (DOXYGEN_VERSION VERSION_LESS 1.9.3) set(GUDHI_DOXYGEN_CLASS_DIAGRAMS "CLASS_DIAGRAMS = NO") else() set(GUDHI_DOXYGEN_CLASS_DIAGRAMS "") endif() + if (DOXYGEN_VERSION VERSION_LESS 1.9.2) + set(GUDHI_DOXYGEN_MATHJAX_VERSION "MATHJAX_VERSION = MathJax_2") + set(GUDHI_DOXYGEN_MATHJAX_EXTENSIONS "TeX/AMSmath TeX/AMSsymbols") + else() + set(GUDHI_DOXYGEN_MATHJAX_VERSION "MATHJAX_VERSION = MathJax_3") + set(GUDHI_DOXYGEN_MATHJAX_EXTENSIONS "ams") + endif() configure_file(${GUDHI_DOXYGEN_SOURCE_PREFIX}/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile" @ONLY) diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake index 13248f7e..ec1f756b 100644 --- a/src/cmake/modules/GUDHI_modules.cmake +++ b/src/cmake/modules/GUDHI_modules.cmake @@ -2,7 +2,7 @@ set(GUDHI_MODULES_FULL_LIST "") function(add_gudhi_module file_path) - option("WITH_MODULE_GUDHI_${file_path}" "Activate/desactivate ${file_path} compilation and installation" ON) + option("WITH_MODULE_GUDHI_${file_path}" "Activate/deactivate ${file_path} compilation and installation" ON) if (WITH_MODULE_GUDHI_${file_path}) set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} CACHE INTERNAL "GUDHI_MODULES") else() @@ -10,7 +10,7 @@ function(add_gudhi_module file_path) endif() # Required by user_version set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE) - # Include module headers is independant - You may ask for no Alpha complex module but Python interface i.e. + # Include module headers is independent - You may ask for no Alpha complex module but Python interface i.e. if(IS_DIRECTORY ${CMAKE_SOURCE_DIR}/src/${file_path}/include/) include_directories(src/${file_path}/include/) endif() diff --git a/src/cmake/modules/GUDHI_options.cmake b/src/cmake/modules/GUDHI_options.cmake index 3cd0a489..bffb3ffc 100644 --- a/src/cmake/modules/GUDHI_options.cmake +++ b/src/cmake/modules/GUDHI_options.cmake @@ -1,5 +1,5 @@ -option(WITH_GUDHI_BENCHMARK "Activate/desactivate benchmark compilation" OFF) -option(WITH_GUDHI_EXAMPLE "Activate/desactivate examples compilation and installation" OFF) -option(WITH_GUDHI_PYTHON "Activate/desactivate python module compilation and installation" ON) -option(WITH_GUDHI_TEST "Activate/desactivate examples compilation and installation" ON) -option(WITH_GUDHI_UTILITIES "Activate/desactivate utilities compilation and installation" ON) +option(WITH_GUDHI_BENCHMARK "Activate/deactivate benchmark compilation" OFF) +option(WITH_GUDHI_EXAMPLE "Activate/deactivate examples compilation and installation" OFF) +option(WITH_GUDHI_PYTHON "Activate/deactivate python module compilation and installation" ON) +option(WITH_GUDHI_TEST "Activate/deactivate examples compilation and installation" ON) +option(WITH_GUDHI_UTILITIES "Activate/deactivate utilities compilation and installation" ON) diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index 6a94d1f5..6ba822ad 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -174,7 +174,7 @@ if (WITH_GUDHI_PYTHON) message(FATAL_ERROR "ERROR: GUDHI_PYTHON_PATH is not valid.") endif(NOT GUDHI_PYTHON_PATH) - option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Usefull when setting rpath is not allowed" ON) + option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Useful when setting rpath is not allowed" ON) if(PYTHONINTERP_FOUND AND CYTHON_FOUND) if(SPHINX_FOUND) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 1953c946..24a7fc7a 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -58,8 +58,7 @@ make \endverbatim * * The following example requires the <a target="_blank" href="https://gmplib.org/">GNU Multiple Precision Arithmetic * Library</a> (GMP) and will not be built if GMP is not installed: - * \li <a href="rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> + * \li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} * * Having GMP version 4.2 or higher installed is recommended. * @@ -76,58 +75,32 @@ make \endverbatim * * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms * Library</a> (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed: - * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * \li <a href="strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="example_strong_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_strong_witness_complex_off.cpp</a> - * \li <a href="example_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_witness_complex_off.cpp</a> - * \li <a href="example_witness_complex_sphere_8cpp-example.html"> - * Witness_complex/example_witness_complex_sphere.cpp</a> - * \li <a href="_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="bottleneck_basic_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/bottleneck_distance.cpp</a> - * \li <a href="_coord_g_i_c_8cpp-example.html"> - * Nerve_GIC/CoordGIC.cpp</a> - * \li <a href="_func_g_i_c_8cpp-example.html"> - * Nerve_GIC/FuncGIC.cpp</a> - * \li <a href="_nerve_8cpp-example.html"> - * Nerve_GIC/Nerve.cpp</a> - * \li <a href="_voronoi_g_i_c_8cpp-example.html"> - * Nerve_GIC/VoronoiGIC.cpp</a> - * \li <a href="example_spatial_searching_8cpp-example.html"> - * Spatial_searching/example_spatial_searching.cpp</a> - * \li <a href="example_choose_n_farthest_points_8cpp-example.html"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * \li <a href="_weighted_alpha_complex_3d_from_points_8cpp-example.html"> - * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a> - * \li <a href="alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_coxeter_triangulation_2manifold_tracing_flat_torus_with_boundary_8cpp-example.html"> - * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a> + * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp} + * \li \gudhi_example_link{Witness_complex,strong_witness_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,weak_witness_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,example_strong_witness_complex_off.cpp} + * \li \gudhi_example_link{Witness_complex,example_witness_complex_off.cpp} + * \li \gudhi_example_link{Witness_complex,example_witness_complex_sphere.cpp} + * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_off.cpp} + * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_points.cpp} + * \li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} + * \li \gudhi_example_link{Persistent_cohomology,custom_persistence_sort.cpp} + * \li \gudhi_example_link{Bottleneck_distance,alpha_rips_persistence_bottleneck_distance.cpp} + * \li \gudhi_example_link{Bottleneck_distance,bottleneck_basic_example.cpp} + * \li \gudhi_example_link{Bottleneck_distance,bottleneck_distance.cpp} + * \li \gudhi_example_link{Nerve_GIC,CoordGIC.cpp} + * \li \gudhi_example_link{Nerve_GIC,FuncGIC.cpp} + * \li \gudhi_example_link{Nerve_GIC,Nerve.cpp} + * \li \gudhi_example_link{Nerve_GIC,VoronoiGIC.cpp} + * \li \gudhi_example_link{Spatial_searching,example_spatial_searching.cpp} + * \li \gudhi_example_link{Subsampling,example_choose_n_farthest_points.cpp} + * \li \gudhi_example_link{Subsampling,example_pick_n_random_points.cpp} + * \li \gudhi_example_link{Subsampling,example_sparsify_point_set.cpp} + * \li \gudhi_example_link{Tangential_complex,example_basic.cpp} + * \li \gudhi_example_link{Tangential_complex,example_with_perturb.cpp} + * \li \gudhi_example_link{Alpha_complex,Weighted_alpha_complex_3d_from_points.cpp} + * \li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} + * \li \gudhi_example_link{Coxeter_triangulation,manifold_tracing_flat_torus_with_boundary.cpp} * * \subsection eigen Eigen * Some GUDHI modules (cf. \ref main_page "modules list"), and few examples require @@ -136,48 +109,27 @@ make \endverbatim * * The following examples/utilities require the <a target="_blank" href="https://eigen.tuxfamily.org">Eigen</a> and will not be * built if Eigen is not installed: - * \li <a href="_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_weighted_alpha_complex_3d_from_points_8cpp-example.html"> - * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a> - * \li <a href="alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> - * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="example_spatial_searching_8cpp-example.html"> - * Spatial_searching/example_spatial_searching.cpp</a> - * \li <a href="example_choose_n_farthest_points_8cpp-example.html"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * \li <a href="strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="example_strong_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_strong_witness_complex_off.cpp</a> - * \li <a href="example_witness_complex_off_8cpp-example.html"> - * Witness_complex/example_witness_complex_off.cpp</a> - * \li <a href="example_witness_complex_sphere_8cpp-example.html"> - * Witness_complex/example_witness_complex_sphere.cpp</a> - * \li <a href="_coxeter_triangulation_2cell_complex_from_basic_circle_manifold_8cpp-example.html"> - * Coxeter_triangulation/cell_complex_from_basic_circle_manifold.cpp</a> - * \li <a href="_coxeter_triangulation_2manifold_tracing_custom_function_8cpp-example.html"> - * Coxeter_triangulation/manifold_tracing_custom_function.cpp</a> - * \li <a href="_coxeter_triangulation_2manifold_tracing_flat_torus_with_boundary_8cpp-example.html"> - * Coxeter_triangulation/manifold_tracing_flat_torus_with_boundary.cpp</a> + * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_off.cpp} + * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_points.cpp} + * \li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} + * \li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} + * \li \gudhi_example_link{Alpha_complex,Weighted_alpha_complex_3d_from_points.cpp} + * \li \gudhi_example_link{Bottleneck_distance,alpha_rips_persistence_bottleneck_distance.cpp} + * \li \gudhi_example_link{Persistent_cohomology,custom_persistence_sort.cpp} + * \li \gudhi_example_link{Spatial_searching,example_spatial_searching.cpp} + * \li \gudhi_example_link{Subsampling,example_choose_n_farthest_points.cpp} + * \li \gudhi_example_link{Subsampling,example_pick_n_random_points.cpp} + * \li \gudhi_example_link{Subsampling,example_sparsify_point_set.cpp} + * \li \gudhi_example_link{Tangential_complex,example_basic.cpp} + * \li \gudhi_example_link{Tangential_complex,example_with_perturb.cpp} + * \li \gudhi_example_link{Witness_complex,strong_witness_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,weak_witness_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,example_strong_witness_complex_off.cpp} + * \li \gudhi_example_link{Witness_complex,example_witness_complex_off.cpp} + * \li \gudhi_example_link{Witness_complex,example_witness_complex_sphere.cpp} + * \li \gudhi_example_link{Coxeter_triangulation,cell_complex_from_basic_circle_manifold.cpp} + * \li \gudhi_example_link{Coxeter_triangulation,manifold_tracing_custom_function.cpp} + * \li \gudhi_example_link{Coxeter_triangulation,manifold_tracing_flat_torus_with_boundary.cpp} * * \subsection tbb Threading Building Blocks * <a target="_blank" href="https://github.com/oneapi-src/oneTBB">Intel® TBB</a> lets you easily write parallel @@ -187,68 +139,37 @@ make \endverbatim * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * * The following examples/utilities are using Intel® TBB if installed: - * \li <a href="_alpha_complex_from_off_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_off.cpp</a> - * \li <a href="_alpha_complex_from_points_8cpp-example.html"> - * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="alpha_complex_3d_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_3d_persistence.cpp</a> - * \li <a href="alpha_complex_persistence_8cpp-example.html"> - * Alpha_complex/alpha_complex_persistence.cpp</a> - * \li <a href="cubical_complex_persistence_8cpp-example.html"> - * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> - * \li <a href="periodic_cubical_complex_persistence_8cpp-example.html"> - * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a> - * \li <a href="_random_bitmap_cubical_complex_8cpp-example.html"> - * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> - * \li <a href="_coord_g_i_c_8cpp-example.html"> - * Nerve_GIC/CoordGIC.cpp</a> - * \li <a href="_func_g_i_c_8cpp-example.html"> - * Nerve_GIC/FuncGIC.cpp</a> - * \li <a href="_nerve_8cpp-example.html"> - * Nerve_GIC/Nerve.cpp</a> - * \li <a href="_voronoi_g_i_c_8cpp-example.html"> - * Nerve_GIC/VoronoiGIC.cpp</a> - * \li <a href="simple_simplex_tree_8cpp-example.html"> - * Simplex_tree/simple_simplex_tree.cpp</a> - * \li <a href="example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * \li <a href="simplex_tree_from_cliques_of_graph_8cpp-example.html"> - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - * \li <a href="graph_expansion_with_blocker_8cpp-example.html"> - * Simplex_tree/graph_expansion_with_blocker.cpp</a> - * \li <a href="alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="rips_persistence_via_boundary_matrix_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> - * \li <a href="persistence_from_file_8cpp-example.html"> - * Persistent_cohomology/persistence_from_file.cpp</a> - * \li <a href="persistence_from_simple_simplex_tree_8cpp-example.html"> - * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> - * \li <a href="plain_homology_8cpp-example.html"> - * Persistent_cohomology/plain_homology.cpp</a> - * \li <a href="rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * \li <a href="rips_persistence_step_by_step_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> - * \li <a href="custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.cpp</a> - * \li <a href="example_one_skeleton_rips_from_points_8cpp-example.html"> - * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> - * \li <a href="example_rips_complex_from_off_file_8cpp-example.html"> - * Rips_complex/example_rips_complex_from_off_file.cpp</a> - * \li <a href="rips_distance_matrix_persistence_8cpp-example.html"> - * Rips_complex/rips_distance_matrix_persistence.cpp</a> - * \li <a href="rips_persistence_8cpp-example.html"> - * Rips_complex/rips_persistence.cpp</a> - * \li <a href="strong_witness_persistence_8cpp-example.html"> - * Witness_complex/strong_witness_persistence.cpp</a> - * \li <a href="weak_witness_persistence_8cpp-example.html"> - * Witness_complex/weak_witness_persistence.cpp</a> - * \li <a href="example_nearest_landmark_table_8cpp-example.html"> - * Witness_complex/example_nearest_landmark_table.cpp</a> + * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_off.cpp} + * \li \gudhi_example_link{Alpha_complex,Alpha_complex_from_points.cpp} + * \li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} + * \li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} + * \li \gudhi_example_link{Bitmap_cubical_complex,cubical_complex_persistence.cpp} + * \li \gudhi_example_link{Bitmap_cubical_complex,periodic_cubical_complex_persistence.cpp} + * \li \gudhi_example_link{Bitmap_cubical_complex,Random_bitmap_cubical_complex.cpp} + * \li \gudhi_example_link{Nerve_GIC,CoordGIC.cpp} + * \li \gudhi_example_link{Nerve_GIC,FuncGIC.cpp} + * \li \gudhi_example_link{Nerve_GIC,Nerve.cpp} + * \li \gudhi_example_link{Nerve_GIC,VoronoiGIC.cpp} + * \li \gudhi_example_link{Simplex_tree,simple_simplex_tree.cpp} + * \li \gudhi_example_link{Simplex_tree,example_alpha_shapes_3_simplex_tree_from_off_file.cpp} + * \li \gudhi_example_link{Simplex_tree,simplex_tree_from_cliques_of_graph.cpp} + * \li \gudhi_example_link{Simplex_tree,graph_expansion_with_blocker.cpp} + * \li \gudhi_example_link{Persistent_cohomology,alpha_complex_3d_persistence.cpp} + * \li \gudhi_example_link{Persistent_cohomology,alpha_complex_persistence.cpp} + * \li \gudhi_example_link{Persistent_cohomology,rips_persistence_via_boundary_matrix.cpp} + * \li \gudhi_example_link{Persistent_cohomology,persistence_from_file.cpp} + * \li \gudhi_example_link{Persistent_cohomology,persistence_from_simple_simplex_tree.cpp} + * \li \gudhi_example_link{Persistent_cohomology,plain_homology.cpp} + * \li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} + * \li \gudhi_example_link{Persistent_cohomology,rips_persistence_step_by_step.cpp} + * \li \gudhi_example_link{Persistent_cohomology,custom_persistence_sort.cpp} + * \li \gudhi_example_link{Rips_complex,example_one_skeleton_rips_from_points.cpp} + * \li \gudhi_example_link{Rips_complex,example_rips_complex_from_off_file.cpp} + * \li \gudhi_example_link{Rips_complex,rips_distance_matrix_persistence.cpp} + * \li \gudhi_example_link{Rips_complex,rips_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,strong_witness_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,weak_witness_persistence.cpp} + * \li \gudhi_example_link{Witness_complex,example_nearest_landmark_table.cpp} * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 29d5423d..a7d82541 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -231,7 +231,7 @@ std::vector<std::vector<Filtration_value>> read_lower_triangular_matrix_from_csv std::string line; - // the first line is emtpy, so we ignore it: + // the first line is empty, so we ignore it: std::getline(in, line); std::vector<Filtration_value> values_in_this_line; result.push_back(values_in_this_line); diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h index 2e36b831..3a0df1a8 100644 --- a/src/common/include/gudhi/writing_persistence_to_file.h +++ b/src/common/include/gudhi/writing_persistence_to_file.h @@ -48,7 +48,7 @@ class Persistence_interval_common { : birth_(birth), death_(death), dimension_(dim), arith_element_(field) {} /** - * Operator to compare two persistence pairs. During the comparision all the + * Operator to compare two persistence pairs. During the comparison all the * fields: birth, death, dimensiona and arith_element_ are taken into account * and they all have to be equal for two pairs to be equal. **/ @@ -65,7 +65,7 @@ class Persistence_interval_common { /** * Operator to compare objects of a type Persistence_interval_common. * One intervals is smaller than the other if it has lower persistence. - * Note that this operator do not take Arith_element into account when doing comparisions. + * Note that this operator do not take Arith_element into account when doing comparisons. **/ bool operator<(const Persistence_interval_common& i2) const { return fabs(this->death_ - this->birth_) < fabs(i2.death_ - i2.birth_); diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 54221151..af0b6115 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -329,9 +329,9 @@ if(PYTHONINTERP_FOUND) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/") # User warning - Sphinx is a static pages generator, and configured to work fine with user_version - # Images and biblio warnings because not found on developper version + # Images and biblio warnings because not found on developer version if (GUDHI_PYTHON_PATH STREQUAL "src/python") - set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss") + set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developer version. Images and biblio will miss") endif() # sphinx target requires gudhi.so, because conf.py reads gudhi version from it add_custom_target(sphinx @@ -484,7 +484,7 @@ if(PYTHONINTERP_FOUND) add_gudhi_py_test(test_euclidean_witness_complex) # Datasets generators - add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independant from CGAL ? + add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independent from CGAL ? endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index ea2eb7e1..0b35dbc5 100755 --- a/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/python/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -40,7 +40,7 @@ parser.add_argument( args = parser.parse_args() if not (-1.0 < args.min_edge_correlation < 1.0): - print("Wrong value of the treshold corelation (should be between -1 and 1).") + print("Wrong value of the threshold corelation (should be between -1 and 1).") sys.exit(1) print("#####################################################################") diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc index 1a21f02f..fa0cf8aa 100644 --- a/src/python/gudhi/hera/wasserstein.cc +++ b/src/python/gudhi/hera/wasserstein.cc @@ -29,7 +29,7 @@ double wasserstein_distance( if(std::isinf(internal_p)) internal_p = hera::get_infinity<double>(); params.internal_p = internal_p; params.delta = delta; - // The extra parameters are purposedly not exposed for now. + // The extra parameters are purposely not exposed for now. return hera::wasserstein_dist(diag1, diag2, params); } diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py index 7ed11360..21275cdd 100644 --- a/src/python/gudhi/persistence_graphical_tools.py +++ b/src/python/gudhi/persistence_graphical_tools.py @@ -332,7 +332,7 @@ def plot_persistence_diagram( axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha) # Infinity label yt = axes.get_yticks() - yt = yt[np.where(yt < axis_end)] # to avoid ploting ticklabel higher than infinity + yt = yt[np.where(yt < axis_end)] # to avoid plotting ticklabel higher than infinity yt = np.append(yt, infinity) ytl = ["%.3f" % e for e in yt] # to avoid float precision error ytl[-1] = r"$+\infty$" diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 4f229663..5642f82d 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -63,7 +63,6 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": bool prune_above_filtration(double filtration) nogil bool make_filtration_non_decreasing() nogil void compute_extended_filtration() nogil - vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) nogil Simplex_tree_interface_full_featured* collapse_edges(int nb_collapse_iteration) nogil except + void reset_filtration(double filtration, int dimension) nogil bint operator==(Simplex_tree_interface_full_featured) nogil @@ -81,7 +80,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": - cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": + cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>>": Simplex_tree_persistence_interface(Simplex_tree_interface_full_featured * st, bool persistence_dim_max) nogil void compute_persistence(int homology_coeff_field, double min_persistence) nogil except + vector[pair[int, pair[double, double]]] get_persistence() nogil @@ -92,3 +91,4 @@ cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": vector[pair[vector[int], vector[int]]] persistence_pairs() nogil pair[vector[vector[int]], vector[vector[int]]] lower_star_generators() nogil pair[vector[vector[int]], vector[vector[int]]] flag_generators() nogil + vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(double min_persistence) nogil diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index 2c53a872..521a7763 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -474,8 +474,7 @@ cdef class SimplexTree: del self.pcohptr self.pcohptr = new Simplex_tree_persistence_interface(self.get_ptr(), False) self.pcohptr.compute_persistence(homology_coeff_field, -1.) - persistence_result = self.pcohptr.get_persistence() - return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence) + return self.pcohptr.compute_extended_persistence_subdiagrams(min_persistence) def expansion_with_blocker(self, max_dim, blocker_func): """Expands the Simplex_tree containing only a graph. Simplices corresponding to cliques in the graph are added diff --git a/src/python/gudhi/wasserstein/barycenter.py b/src/python/gudhi/wasserstein/barycenter.py index d67bcde7..bb6e641e 100644 --- a/src/python/gudhi/wasserstein/barycenter.py +++ b/src/python/gudhi/wasserstein/barycenter.py @@ -37,7 +37,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False): :param init: The initial value for barycenter estimate. If ``None``, init is made on a random diagram from the dataset. Otherwise, it can be an ``int`` (then initialization is made on ``pdiagset[init]``) - or a `(n x 2)` ``numpy.array`` enconding a persistence diagram with `n` points. + or a `(n x 2)` ``numpy.array`` encoding a persistence diagram with `n` points. :type init: ``int``, or (n x 2) ``np.array`` :param verbose: if ``True``, returns additional information about the barycenter. :type verbose: boolean @@ -45,7 +45,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False): (local minimum of the energy function). If ``pdiagset`` is empty, returns ``None``. If verbose, returns a couple ``(Y, log)`` where ``Y`` is the barycenter estimate, - and ``log`` is a ``dict`` that contains additional informations: + and ``log`` is a ``dict`` that contains additional information: - `"groupings"`, a list of list of pairs ``(i,j)``. Namely, ``G[k] = [...(i, j)...]``, where ``(i,j)`` indicates that `pdiagset[k][i]`` is matched to ``Y[j]`` if ``i = -1`` or ``j = -1``, it means they represent the diagonal. @@ -73,7 +73,7 @@ def lagrangian_barycenter(pdiagset, init=None, verbose=False): nb_iter = 0 - converged = False # stoping criterion + converged = False # stopping criterion while not converged: nb_iter += 1 K = len(Y) # current nb of points in Y (some might be on diagonal) diff --git a/src/python/include/Persistent_cohomology_interface.h b/src/python/include/Persistent_cohomology_interface.h index e5a3dfba..945378a0 100644 --- a/src/python/include/Persistent_cohomology_interface.h +++ b/src/python/include/Persistent_cohomology_interface.h @@ -12,6 +12,8 @@ #define INCLUDE_PERSISTENT_COHOMOLOGY_INTERFACE_H_ #include <gudhi/Persistent_cohomology.h> +#include <gudhi/Simplex_tree.h> // for Extended_simplex_type + #include <cstdlib> #include <vector> @@ -223,6 +225,44 @@ persistent_cohomology::Persistent_cohomology<FilteredComplex, persistent_cohomol return out; } + using Filtration_value = typename FilteredComplex::Filtration_value; + using Birth_death = std::pair<Filtration_value, Filtration_value>; + using Persistence_subdiagrams = std::vector<std::vector<std::pair<int, Birth_death>>>; + + Persistence_subdiagrams compute_extended_persistence_subdiagrams(Filtration_value min_persistence){ + Persistence_subdiagrams pers_subs(4); + auto const& persistent_pairs = Base::get_persistent_pairs(); + for (auto pair : persistent_pairs) { + std::pair<Filtration_value, Extended_simplex_type> px = stptr_->decode_extended_filtration(stptr_->filtration(get<0>(pair)), + stptr_->efd); + std::pair<Filtration_value, Extended_simplex_type> py = stptr_->decode_extended_filtration(stptr_->filtration(get<1>(pair)), + stptr_->efd); + std::pair<int, Birth_death> pd_point = std::make_pair(stptr_->dimension(get<0>(pair)), + std::make_pair(px.first, py.first)); + if(std::abs(px.first - py.first) > min_persistence){ + //Ordinary + if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){ + pers_subs[0].push_back(pd_point); + } + // Relative + else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){ + pers_subs[1].push_back(pd_point); + } + else{ + // Extended+ + if (px.first < py.first){ + pers_subs[2].push_back(pd_point); + } + //Extended- + else{ + pers_subs[3].push_back(pd_point); + } + } + } + } + return pers_subs; + } + private: // A copy FilteredComplex* stptr_; diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index 7f9b0067..3848c5ad 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -132,36 +132,6 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { return; } - std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> compute_extended_persistence_subdiagrams(const std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>& dgm, Filtration_value min_persistence){ - std::vector<std::vector<std::pair<int, std::pair<Filtration_value, Filtration_value>>>> new_dgm(4); - for (unsigned int i = 0; i < dgm.size(); i++){ - std::pair<Filtration_value, Extended_simplex_type> px = this->decode_extended_filtration(dgm[i].second.first, this->efd); - std::pair<Filtration_value, Extended_simplex_type> py = this->decode_extended_filtration(dgm[i].second.second, this->efd); - std::pair<int, std::pair<Filtration_value, Filtration_value>> pd_point = std::make_pair(dgm[i].first, std::make_pair(px.first, py.first)); - if(std::abs(px.first - py.first) > min_persistence){ - //Ordinary - if (px.second == Extended_simplex_type::UP && py.second == Extended_simplex_type::UP){ - new_dgm[0].push_back(pd_point); - } - // Relative - else if (px.second == Extended_simplex_type::DOWN && py.second == Extended_simplex_type::DOWN){ - new_dgm[1].push_back(pd_point); - } - else{ - // Extended+ - if (px.first < py.first){ - new_dgm[2].push_back(pd_point); - } - //Extended- - else{ - new_dgm[3].push_back(pd_point); - } - } - } - } - return new_dgm; - } - Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) { using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>; std::vector<Filtered_edge> edges; diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 688f4fd6..54bafed5 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -320,6 +320,10 @@ def test_extend_filtration(): ] dgms = st.extended_persistence(min_persistence=-1.) + assert len(dgms) == 4 + # Sort by (death-birth) descending - we are only interested in those with the longest life span + for idx in range(4): + dgms[idx] = sorted(dgms[idx], key=lambda x:(-abs(x[1][0]-x[1][1]))) assert dgms[0][0][1][0] == pytest.approx(2.) assert dgms[0][0][1][1] == pytest.approx(3.) @@ -528,7 +532,7 @@ def test_expansion_with_blocker(): def blocker(simplex): try: - # Block all simplices that countains vertex 6 + # Block all simplices that contain vertex 6 simplex.index(6) print(simplex, ' is blocked') return True diff --git a/src/python/test/test_subsampling.py b/src/python/test/test_subsampling.py index 4019852e..3431f372 100755 --- a/src/python/test/test_subsampling.py +++ b/src/python/test/test_subsampling.py @@ -91,7 +91,7 @@ def test_simple_choose_n_farthest_points_randomed(): assert gudhi.choose_n_farthest_points(points=[], nb_points=1) == [] assert gudhi.choose_n_farthest_points(points=point_set, nb_points=0) == [] - # Go furter than point set on purpose + # Go further than point set on purpose for iter in range(1, 10): sub_set = gudhi.choose_n_farthest_points(points=point_set, nb_points=iter) for sub in sub_set: @@ -117,7 +117,7 @@ def test_simple_pick_n_random_points(): assert gudhi.pick_n_random_points(points=[], nb_points=1) == [] assert gudhi.pick_n_random_points(points=point_set, nb_points=0) == [] - # Go furter than point set on purpose + # Go further than point set on purpose for iter in range(1, 10): sub_set = gudhi.pick_n_random_points(points=point_set, nb_points=iter) for sub in sub_set: |
