From 8d7329f3e5ad843e553c3c5503cecc28ef2eead6 Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Thu, 20 Apr 2017 11:10:45 +0200 Subject: GUDHI 2.0.0 as released by upstream in a tarball. --- doc/common/main_page.h | 190 +++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 159 insertions(+), 31 deletions(-) (limited to 'doc/common/main_page.h') diff --git a/doc/common/main_page.h b/doc/common/main_page.h index 0983051d..2e45e5aa 100644 --- a/doc/common/main_page.h +++ b/doc/common/main_page.h @@ -3,7 +3,9 @@ * \image html "Gudhi_banner.png" "" width=20cm * * \section Introduction Introduction - * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library for + * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source + * C++ library, with a + * Python interface, for * Computational Topology and Topological Data Analysis * (TDA). * The GUDHI library intends to help the development of new algorithmic solutions in TDA and their transfer to @@ -28,6 +30,7 @@ Author: Vincent Rouvreau
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.7.0 and \ref eigen3 Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.
@@ -55,6 +58,24 @@ User manual: \ref cubical_complex - Reference manual: Gudhi::cubical_complex::Bitmap_cubical_complex + \subsection RipsComplexDataStructure Rips complex + \image html "rips_complex_representation.png" "Rips complex representation" + + + + + +
+ Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+ 		+ Rips_complex is a simplicial complex constructed from a one skeleton graph.
+ The filtration value of each edge is computed from a user-given distance function and is inserted until a + user-given threshold value.
+ This complex can be built from a point cloud and a distance function, or from a distance matrix.
+ User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex +
\subsection SimplexTreeDataStructure Simplex tree \image html "Simplex_tree_representation.png" "Simplex tree representation" @@ -92,6 +113,26 @@ User manual: \ref skbl - Reference manual: Gudhi::skeleton_blocker::Skeleton_blocker_complex + + \subsection TangentialComplexDataStructure Tangential complex + \image html "tc_examples.png" "Tangential complex representation" + + + + +
+ Author: Clément Jamin
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.8.1 and \ref eigen3 + 		+ A Tangential Delaunay complex is a simplicial complex + designed to reconstruct a \f$ k \f$-dimensional manifold embedded in \f$ d \f$-dimensional Euclidean space. + The input is a point sample coming from an unknown manifold. + The running time depends only linearly on the extrinsic dimension \f$ d \f$ + and exponentially on the intrinsic dimension \f$ k \f$.
+ User manual: \ref tangential_complex - Reference manual: Gudhi::tangential_complex::Tangential_complex +
\subsection WitnessComplexDataStructure Witness complex \image html "Witness_complex_representation.png" "Witness complex representation" @@ -101,6 +142,7 @@ Author: Siargey Kachanovich
Introduced in: GUDHI 1.3.0
Copyright: GPL v3
+ Euclidean version requires: \ref cgal ≥ 4.6.0 and \ref eigen3 Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. @@ -111,6 +153,26 @@ \section Toolbox Toolbox + \subsection BottleneckDistanceToolbox Bottleneck distance + \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" + + + + + +
+ Author: François Godi
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+ Requires: \ref cgal ≥ 4.8.1 and \ref eigen3 + 		+ Bottleneck distance measures the similarity between two persistence diagrams. + It's the shortest distance b for which there exists a perfect matching between + the points of the two diagrams (+ all the diagonal points) such that + any couple of matched points are at distance at most b. +
+ User manual: \ref bottleneck_distance +
\subsection ContractionToolbox Contraction \image html "sphere_contraction_representation.png" "Sphere contraction example" @@ -153,11 +215,11 @@
*/ -/*! \page installation Gudhi installation +/*! \page installation GUDHI installation * \tableofcontents - * As Gudhi is a header only library, there is no need to install the library. + * As GUDHI is a header only library, there is no need to install the library. * - * Examples of Gudhi headers inclusion can be found in \ref demos. + * Examples of GUDHI headers inclusion can be found in \ref demos. * * \section compiling Compiling * The library uses c++11 and requires Boost with version 1.48.0 or @@ -176,39 +238,54 @@ make \endverbatim * To test your build, run the following command in a terminal: * \verbatim make test \endverbatim * + * \subsection documentationgeneration Documentation + * To generate the documentation, Doxygen is required. + * Run the following command in a terminal: +\verbatim +make doxygen +# Documentation will be generated in the folder YYYY-MM-DD-hh-mm-ss_GUDHI_X.Y.Z/doc/html/ +# You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder` +\endverbatim + * * \section optionallibrary Optional third-party library - * \subsection gmp GMP: + * \subsection gmp GMP * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision * arithmetic, operating on signed integers, rational numbers, and floating point numbers. * * The following example requires the GNU Multiple Precision Arithmetic * Library (GMP) and will not be built if GMP is not installed: - * \li - * Persistent_cohomology/performance_rips_persistence.cpp * \li * Persistent_cohomology/rips_multifield_persistence.cpp * * Having GMP version 4.2 or higher installed is recommended. * - * \subsection cgal CGAL: - * The \ref alpha_complex data structure and few examples requires CGAL, which is a C++ library which provides easy - * access to efficient and reliable geometric algorithms. + * \subsection cgal CGAL + * The \ref alpha_complex data structure, \ref bottleneck_distance, and few examples requires CGAL, which is a C++ + * library which provides easy access to efficient and reliable geometric algorithms. + * + * \note There is no need to install CGAL, you can just cmake . && make CGAL (or even + * cmake -DCGAL_HEADER_ONLY=ON . for CGAL version ≥ 4.8.0), thereafter you will be able to compile + * GUDHI by calling cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make * - * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to + * Having CGAL version 4.4.0 or higher installed is recommended. The procedure to install this library according to * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html * * The following examples require the Computational Geometry Algorithms * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: * \li * Persistent_cohomology/alpha_complex_3d_persistence.cpp - * \li - * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * \li + * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp + * \li + * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp + * \li + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * - * The following example requires CGAL version ≥ 4.6: + * The following example requires CGAL version ≥ 4.6.0: * \li * Witness_complex/witness_complex_sphere.cpp * - * The following example requires CGAL version ≥ 4.7: + * The following example requires CGAL version ≥ 4.7.0: * \li * Alpha_complex/Alpha_complex_from_off.cpp * \li @@ -220,7 +297,29 @@ make \endverbatim * \li * Persistent_cohomology/custom_persistence_sort.cpp * - * \subsection eigen3 Eigen3: + * The following example requires CGAL version ≥ 4.8.1: + * \li + * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp + * \li + * Bottleneck_distance/bottleneck_basic_example.cpp + * \li + * Bottleneck_distance/bottleneck_read_file_example.cpp + * \li + * Spatial_searching/example_spatial_searching.cpp + * \li + * Subsampling/example_choose_n_farthest_points.cpp + * \li + * Subsampling/example_custom_kernel.cpp + * \li + * Subsampling/example_pick_n_random_points.cpp + * \li + * Subsampling/example_sparsify_point_set.cpp + * \li + * Tangential_complex/example_basic.cpp + * \li + * Tangential_complex/example_with_perturb.cpp + * + * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires * Eigen3 is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. @@ -228,9 +327,9 @@ make \endverbatim * The following example requires the Eigen3 and will not be * built if Eigen3 is not installed: * \li - * Alpha_complex/Alpha_complex_from_off.cpp (requires also Eigen3) + * Alpha_complex/Alpha_complex_from_off.cpp * \li - * Alpha_complex/Alpha_complex_from_points.cpp (requires also Eigen3) + * Alpha_complex/Alpha_complex_from_points.cpp * \li * Persistent_cohomology/alpha_complex_persistence.cpp * \li @@ -238,7 +337,7 @@ make \endverbatim * \li * Persistent_cohomology/custom_persistence_sort.cpp * - * \subsection tbb Threading Building Blocks: + * \subsection tbb Threading Building Blocks * Intel® TBB lets you easily write parallel * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have * future-proof scalability. @@ -262,8 +361,8 @@ make \endverbatim * Persistent_cohomology/alpha_complex_persistence.cpp * \li * Simplex_tree/simple_simplex_tree.cpp - * \li - * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * \li + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * \li * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp * \li @@ -272,28 +371,38 @@ make \endverbatim * Persistent_cohomology/alpha_complex_persistence.cpp * \li * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * \li - * Persistent_cohomology/performance_rips_persistence.cpp * \li * Persistent_cohomology/persistence_from_file.cpp * \li * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * \li * Persistent_cohomology/plain_homology.cpp + * \li + * Persistent_cohomology/rips_distance_matrix_persistence.cpp * \li * Persistent_cohomology/rips_multifield_persistence.cpp * \li * Persistent_cohomology/rips_persistence.cpp + * \li + * Persistent_cohomology/rips_persistence_step_by_step.cpp + * \li + * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp + * \li + * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * \li * Persistent_cohomology/custom_persistence_sort.cpp + * \li + * Rips_complex/example_one_skeleton_rips_from_points.cpp + * \li + * Rips_complex/example_rips_complex_from_off_file.cpp * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim * - * Gudhi is open to external contributions. If you want to join our development team, please contact us. + * GUDHI is open to external contributions. If you want to join our development team, please contact us. * */ @@ -308,36 +417,55 @@ make \endverbatim * \verbinclude biblio/how_to_cite_gudhi.bib */ -// List of Gudhi examples - Doxygen needs at least a file tag to analyse comments +// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp + * @example Bottleneck_distance/bottleneck_basic_example.cpp + * @example Bottleneck_distance/bottleneck_read_file_example.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * @example common/CGAL_3D_points_off_reader.cpp - * @example common/CGAL_points_off_reader.cpp + * @example common/example_CGAL_3D_points_off_reader.cpp + * @example common/example_CGAL_points_off_reader.cpp * @example Contraction/Garland_heckbert.cpp * @example Contraction/Rips_contraction.cpp * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/performance_rips_persistence.cpp + * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp + * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/persistence_from_file.cpp * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * @example Persistent_cohomology/plain_homology.cpp * @example Persistent_cohomology/rips_multifield_persistence.cpp + * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp * @example Persistent_cohomology/rips_persistence.cpp * @example Persistent_cohomology/custom_persistence_sort.cpp + * @example Persistent_cohomology/rips_persistence_step_by_step.cpp + * @example Rips_complex/example_one_skeleton_rips_from_points.cpp + * @example Rips_complex/example_rips_complex_from_off_file.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp - * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp * @example Skeleton_blocker/Skeleton_blocker_link.cpp - * @example Witness_complex/witness_complex_from_file.cpp - * @example Witness_complex/witness_complex_sphere.cpp + * @example Spatial_searching/example_spatial_searching.cpp + * @example Subsampling/example_choose_n_farthest_points.cpp + * @example Subsampling/example_custom_kernel.cpp + * @example Subsampling/example_pick_n_random_points.cpp + * @example Subsampling/example_sparsify_point_set.cpp + * @example Tangential_complex/example_basic.cpp + * @example Tangential_complex/example_with_perturb.cpp + * @example Witness_complex/example_nearest_landmark_table.cpp + * @example Witness_complex/example_strong_witness_complex_off.cpp + * @example Witness_complex/example_strong_witness_persistence.cpp + * @example Witness_complex/example_witness_complex_off.cpp + * @example Witness_complex/example_witness_complex_persistence.cpp + * @example Witness_complex/example_witness_complex_sphere.cpp */ -- cgit v1.2.3