diff options
Diffstat (limited to 'src/common/doc')
-rw-r--r-- | src/common/doc/file_formats.h | 66 | ||||
-rw-r--r-- | src/common/doc/main_page.h | 147 |
2 files changed, 163 insertions, 50 deletions
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index d715aa4d..c60ed15a 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -53,6 +53,72 @@ namespace Gudhi { Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or `Gudhi::read_persistence_intervals_in_dimension()`. + + + \section FileFormatsIsoCuboid Iso-cuboid + + Such a file describes an iso-oriented cuboid with diagonal opposite vertices (min_x, min_y, min_z,...) and (max_x, max_y, max_z, ...). The format is:<br> + \verbatim + min_x min_y [min_z ...] + max_x max_y [max_z ...] + \endverbatim + + Here is a simple sample file in the 3D case: + \verbatim + -1. -1. -1. + 1. 1. 1. + \endverbatim + + + \section FileFormatsPerseus Perseus + + This file format is the format used by the Perseus software + (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda. + The first line contains a number d begin the dimension of the + bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3 + in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8 + 20 4 7 6 5 in the example below). + + \image html "exampleBitmap.png" "Example of a input data." + + The input file for the following complex is: + \verbatim + 2 + 3 + 3 + 1 + 4 + 6 + 8 + 20 + 4 + 7 + 6 + 5 + \endverbatim + + To indicate periodic boundary conditions in a + given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance: + + \verbatim + 2 + -3 + 3 + 1 + 4 + 6 + 8 + 20 + 4 + 7 + 6 + 5 + \endverbatim + + Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y. + + Other sample files can be found in the `data/bitmap` folder. + */ } // namespace Gudhi diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index 34bf6c22..148ee670 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -99,7 +99,7 @@ <tr> <td width="25%"> <b>Author:</b> Mathieu Carrière<br> - <b>Introduced in:</b> GUDHI 2.0.1<br> + <b>Introduced in:</b> GUDHI 2.1.0<br> <b>Copyright:</b> GPL v3<br> </td> <td width="75%"> @@ -170,6 +170,7 @@ </table> \section Toolbox Toolbox + \subsection BottleneckDistanceToolbox Bottleneck distance \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge" <table border="0"> @@ -229,7 +230,25 @@ <b>User manual:</b> \ref persistent_cohomology - <b>Reference manual:</b> Gudhi::persistent_cohomology::Persistent_cohomology </td> </tr> +</table> + \subsection PersistenceRepresentationsToolbox Persistence representations + \image html "average_landscape.png" "Persistence representations" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> Pawel Dlotko<br> + <b>Introduced in:</b> GUDHI 2.1.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + It contains implementation of various representations of persistence diagrams; diagrams themselves, persistence + landscapes (rigorous and grid version), persistence heath maps, vectors and others. It implements basic + functionalities which are neccessary to use persistence in statistics and machine learning.<br> + <b>User manual:</b> \ref Persistence_representations + </td> + </tr> </table> + */ /*! \page installation GUDHI installation @@ -287,30 +306,38 @@ make doxygen * 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 <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms + * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> * - * The following example requires CGAL version ≥ 4.6.0: - * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html"> - * Witness_complex/witness_complex_sphere.cpp</a> - * + * The following examples/utilities require CGAL version ≥ 4.6.0: + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_strong_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> + * Witness_complex/example_witness_complex_sphere.cpp</a> + * * The following example requires CGAL version ≥ 4.7.0: * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * @@ -319,8 +346,8 @@ make doxygen * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="_bottleneck_distance_2bottleneck_read_file_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_read_file_example.cpp</a> + * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html"> + * Bottleneck_distance/bottleneck_distance.cpp</a> * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> * Spatial_searching/example_spatial_searching.cpp</a> * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html"> @@ -341,18 +368,18 @@ make doxygen * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra: * matrices, vectors, numerical solvers, and related algorithms. * - * The following example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be + * The following examples/utilities require the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be * built if Eigen3 is not installed: * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> @@ -369,6 +396,16 @@ make doxygen * Tangential_complex/example_basic.cpp</a> * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> * Tangential_complex/example_with_perturb.cpp</a> + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_strong_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_strong_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_off_8cpp-example.html"> + * Witness_complex/example_witness_complex_off.cpp</a> + * \li <a href="_witness_complex_2example_witness_complex_sphere_8cpp-example.html"> + * Witness_complex/example_witness_complex_sphere.cpp</a> * * \subsection tbb Threading Building Blocks * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel® TBB</a> lets you easily write parallel @@ -377,21 +414,27 @@ make doxygen * * Having Intel® TBB installed is recommended to parallelize and accelerate some GUDHI computations. * - * The following examples are using Intel® TBB if installed: + * The following examples/utilities are using Intel® TBB if installed: * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a> * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> - * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a> + * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a> * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> - * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a> + * Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp</a> * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html"> * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html"> * Simplex_tree/simple_simplex_tree.cpp</a> * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> @@ -412,27 +455,31 @@ make doxygen * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> * Persistent_cohomology/plain_homology.cpp</a> - * \li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> * Rips_complex/example_rips_complex_from_off_file.cpp</a> - * + * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> + * Rips_complex/rips_distance_matrix_persistence.cpp</a> + * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> + * Rips_complex/rips_persistence.cpp</a> + * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html"> + * Witness_complex/strong_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2weak_witness_persistence_8cpp-example.html"> + * Witness_complex/weak_witness_persistence.cpp</a> + * \li <a href="_witness_complex_2example_nearest_landmark_table_8cpp-example.html"> + * Witness_complex/example_nearest_landmark_table.cpp</a> + * * \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 @@ -456,32 +503,32 @@ make doxygen /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Alpha_complex/alpha_complex_3d_persistence.cpp + * @example Alpha_complex/alpha_complex_persistence.cpp + * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp + * @example Alpha_complex/weighted_alpha_complex_3d_persistence.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 Bottleneck_distance/bottleneck_distance.cpp + * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp + * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.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/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 Rips_complex/rips_persistence.cpp + * @example Rips_complex/rips_distance_matrix_persistence.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -499,9 +546,9 @@ make doxygen * @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 + * @example Witness_complex/weak_witness_persistence.cpp + * @example Witness_complex/strong_witness_persistence.cpp */ - + |