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-rw-r--r-- | doc/common/file_formats.h | 125 | ||||
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-rw-r--r-- | doc/common/installation.h | 280 | ||||
-rw-r--r-- | doc/common/main_page.h | 269 | ||||
-rw-r--r-- | doc/common/offline_header.html | 41 | ||||
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diff --git a/doc/common/Gudhi_banner.png b/doc/common/Gudhi_banner.png Binary files differdeleted file mode 100644 index 18e8a672..00000000 --- a/doc/common/Gudhi_banner.png +++ /dev/null diff --git a/doc/common/examples.h b/doc/common/examples.h deleted file mode 100644 index 40f202c7..00000000 --- a/doc/common/examples.h +++ /dev/null @@ -1,99 +0,0 @@ -// List of GUDHI examples - Doxygen needs at least a file tag to analyse comments -// In user_version, `find . -name "*.cpp"` in example and utilities folders -/*! @file Examples - * @example Alpha_complex/Alpha_complex_from_off.cpp - * @example Alpha_complex/Alpha_complex_from_points.cpp - * @example Bottleneck_distance/bottleneck_basic_example.cpp - * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp - * @example Witness_complex/example_nearest_landmark_table.cpp - * @example Witness_complex/example_witness_complex_off.cpp - * @example Witness_complex/example_witness_complex_sphere.cpp - * @example Witness_complex/example_strong_witness_complex_off.cpp - * @example Simplex_tree/mini_simplex_tree.cpp - * @example Simplex_tree/graph_expansion_with_blocker.cpp - * @example Simplex_tree/simple_simplex_tree.cpp - * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp - * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - * @example Simplex_tree/cech_complex_cgal_mini_sphere_3d.cpp - * @example Persistent_cohomology/plain_homology.cpp - * @example Persistent_cohomology/persistence_from_file.cpp - * @example Persistent_cohomology/rips_persistence_step_by_step.cpp - * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp - * @example Persistent_cohomology/custom_persistence_sort.cpp - * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp - * @example Persistent_cohomology/rips_multifield_persistence.cpp - * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp - * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp - * @example Skeleton_blocker/Skeleton_blocker_link.cpp - * @example Contraction/Garland_heckbert.cpp - * @example Contraction/Rips_contraction.cpp - * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp - * @example common/example_CGAL_3D_points_off_reader.cpp - * @example common/example_vector_double_points_off_reader.cpp - * @example common/example_CGAL_points_off_reader.cpp - * @example Rips_complex/example_one_skeleton_rips_from_distance_matrix.cpp - * @example Rips_complex/example_one_skeleton_rips_from_points.cpp - * @example Rips_complex/example_rips_complex_from_csv_distance_matrix_file.cpp - * @example Rips_complex/example_rips_complex_from_off_file.cpp - * @example Persistence_representations/persistence_intervals.cpp - * @example Persistence_representations/persistence_vectors.cpp - * @example Persistence_representations/persistence_heat_maps.cpp - * @example Persistence_representations/persistence_landscape_on_grid.cpp - * @example Persistence_representations/persistence_landscape.cpp - * @example Tangential_complex/example_basic.cpp - * @example Tangential_complex/example_with_perturb.cpp - * @example Subsampling/example_custom_kernel.cpp - * @example Subsampling/example_choose_n_farthest_points.cpp - * @example Subsampling/example_sparsify_point_set.cpp - * @example Subsampling/example_pick_n_random_points.cpp - * @example Nerve_GIC/CoordGIC.cpp - * @example Nerve_GIC/Nerve.cpp - * @example Nerve_GIC/FuncGIC.cpp - * @example Nerve_GIC/VoronoiGIC.cpp - * @example Spatial_searching/example_spatial_searching.cpp - * @example Alpha_complex/alpha_complex_3d_persistence.cpp - * @example Alpha_complex/alpha_complex_persistence.cpp - * @example Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp - * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp - * @example Bottleneck_distance/bottleneck_distance.cpp - * @example Witness_complex/weak_witness_persistence.cpp - * @example Witness_complex/strong_witness_persistence.cpp - * @example Bitmap_cubical_complex/cubical_complex_persistence.cpp - * @example Bitmap_cubical_complex/periodic_cubical_complex_persistence.cpp - * @example common/off_file_from_shape_generator.cpp - * @example Rips_complex/rips_distance_matrix_persistence.cpp - * @example Rips_complex/rips_persistence.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp - * @example Persistence_representations/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp - * @example Persistence_representations/persistence_intervals/compute_number_of_dominant_intervals.cpp - * @example Persistence_representations/persistence_intervals/plot_persistence_Betti_numbers.cpp - * @example Persistence_representations/persistence_intervals/plot_persistence_intervals.cpp - * @example Persistence_representations/persistence_intervals/plot_histogram_of_intervals_lengths.cpp - * @example Persistence_representations/persistence_intervals/compute_bottleneck_distance.cpp - * @example Persistence_representations/persistence_heat_maps/create_pssk.cpp - * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp - * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp - * @example Persistence_representations/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp - * @example Persistence_representations/persistence_heat_maps/average_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_heat_maps/plot_persistence_heat_map.cpp - * @example Persistence_representations/persistence_heat_maps/create_persistence_heat_maps.cpp - * @example Persistence_representations/persistence_vectors/plot_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/compute_distance_of_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/average_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/create_persistence_vectors.cpp - * @example Persistence_representations/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp - * @example Persistence_representations/persistence_landscapes/average_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/compute_scalar_product_of_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/create_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/compute_distance_of_landscapes.cpp - * @example Persistence_representations/persistence_landscapes/plot_landscapes.cpp - */ - diff --git a/doc/common/file_formats.h b/doc/common/file_formats.h deleted file mode 100644 index 523153b8..00000000 --- a/doc/common/file_formats.h +++ /dev/null @@ -1,125 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library -* (Geometric Understanding in Higher Dimensions) is a generic C++ -* library for computational topology. -* -* Author(s): Clément Jamin -* -* Copyright (C) 2017 Inria -* -* This program is free software: you can redistribute it and/or modify -* it under the terms of the GNU General Public License as published by -* the Free Software Foundation, either version 3 of the License, or -* (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program. If not, see <http://www.gnu.org/licenses/>. -*/ - -#ifndef DOC_COMMON_FILE_FORMAT_H_ -#define DOC_COMMON_FILE_FORMAT_H_ - -namespace Gudhi { - -/*! \page fileformats File formats - - \tableofcontents - - \section FileFormatsPers Persistence Diagram - - Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br> - Lines starting with `#` are ignored (comments).<br> - Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines): - \verbatim - [[field] dimension] birth death - \endverbatim - - Here is a simple sample file: - \verbatim - # Persistence diagram example - 2 2.7 3.7 - 2 9.6 14. - # Some comments - 3 34.2 34.974 - 4 3. inf - \endverbatim - - Other sample files can be found in the `data/persistence_diagram` folder. - - 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 - -#endif // DOC_COMMON_FILE_FORMAT_H_ diff --git a/doc/common/footer.html b/doc/common/footer.html deleted file mode 100644 index a557922b..00000000 --- a/doc/common/footer.html +++ /dev/null @@ -1,23 +0,0 @@ -<!-- HTML footer for doxygen 1.8.6--> -<!-- start footer part --> -<table style="width:100%"> - <tr class="no-bullet shadow-black"> - <td class="network-entypo"> -<!--BEGIN PROJECT_NAME--> $projectname -<!--BEGIN PROJECT_NUMBER--> Version $projectnumber<!--END PROJECT_NUMBER--> -<!--BEGIN PROJECT_BRIEF--> - $projectbrief<!--END PROJECT_BRIEF--> -<!--BEGIN PROJECT_BRIEF--> - Copyright : GPL v3<!--END PROJECT_BRIEF--> -<!--END PROJECT_NAME--> - </td> - <td class="network-entypo"> -<!--BEGIN GENERATE_TREEVIEW--> - $generatedby - <a href="http://www.doxygen.org/index.html"> - Doxygen</a> $doxygenversion -<!--END GENERATE_TREEVIEW--> - </td> - </tr> -</table> - -</body> -</html> diff --git a/doc/common/header.html b/doc/common/header.html deleted file mode 100644 index c12d2816..00000000 --- a/doc/common/header.html +++ /dev/null @@ -1,102 +0,0 @@ -<!-- HTML header for doxygen 1.8.6--> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<!-- GUDHI website : class="no-js" lang="en" is necessary --> -<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en"> -<head> -<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> -<meta http-equiv="X-UA-Compatible" content="IE=9"/> -<meta name="generator" content="Doxygen $doxygenversion"/> -<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME--> -<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME--> -<!-- GUDHI website css for header BEGIN --> -<link rel="stylesheet" type="text/css" href="https://gudhi.inria.fr/assets/css/styles_feeling_responsive.css" /> -<!-- GUDHI website css for header END --> -<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/> -<script type="text/javascript" src="$relpath^jquery.js"></script> -<script type="text/javascript" src="$relpath^dynsections.js"></script> -$treeview -$search -$mathjax -<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" /> -$extrastylesheet -</head> -<body> - -<!-- GUDHI website header BEGIN --> -<div id="navigation" class="sticky"> - <nav class="top-bar" role="navigation" data-topbar> - <ul class="title-area"> - <li class="name"> - <h1 class="show-for-small-only"><a href="" class="icon-tree"> GUDHI C++ library</a></h1> - </li> - <!-- Remove the class "menu-icon" to get rid of menu icon. Take out "Menu" to just have icon alone --> - <li class="toggle-topbar menu-icon"><a href="#"><span>Navigation</span></a></li> - </ul> - <section class="top-bar-section"> - <ul class="right"> - <li class="divider"></li> - <li><a href="/contact/">Contact</a></li> - </ul> - <ul class="left"> - <li><a href="/"> <img src="/assets/img/home.png" alt=" GUDHI"> GUDHI </a></li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Project</a> - <ul class="dropdown"> - <li><a href="/people/">People</a></li> - <li><a href="/keepintouch/">Keep in touch</a></li> - <li><a href="/partners/">Partners and Funding</a></li> - <li><a href="/relatedprojects/">Related projects</a></li> - <li><a href="/theyaretalkingaboutus/">They are talking about us</a></li> - </ul> - </li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Download</a> - <ul class="dropdown"> - <li><a href="/licensing/">Licensing</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5253/library-latest.zip" target="_blank">Get the latest sources</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5280/utils_osx-latest.zip" target="_blank">Utils for Mac OSx</a></li> - <li><a href="https://gforge.inria.fr/frs/download.php/latestzip/5279/utils_win64-latest.zip" target="_blank">Utils for Win x64</a></li> - </ul> - </li> - <li class="divider"></li> - <li class="has-dropdown"> - <a href="#">Documentation</a> - <ul class="dropdown"> - <li><a href="/doc/latest/">C++ documentation</a></li> - <li><a href="/doc/latest/installation.html">C++ installation manual</a></li> - <li><a href="/python/latest/">Python documentation</a></li> - <li><a href="/python/latest/installation.html">Python installation manual</a></li> - <li><a href="/utils/">Utilities</a></li> - <li><a href="/tutorials/">Tutorials</a></li> - <li><a href="/dockerfile/">Dockerfile</a></li> - </ul> - </li> - <li class="divider"></li> - <li><a href="/interfaces/">Interfaces</a></li> - <li class="divider"></li> - </ul> - </section> - </nav> -</div><!-- /#navigation --> -<!-- GUDHI website header BEGIN --> - -<div id="top"><!-- do not remove this div, it is closed by doxygen! --> - -<!--BEGIN TITLEAREA--> -<div id="titlearea"> -<table cellspacing="0" cellpadding="0"> - <tbody> - <tr style="height: 30px;"> - <!--BEGIN DISABLE_INDEX--> - <!--BEGIN SEARCHENGINE--> - <td>$searchbox</td> - <!--END SEARCHENGINE--> - <!--END DISABLE_INDEX--> - </tr> - </tbody> -</table> -</div> -<!--END TITLEAREA--> -<!-- end header part --> diff --git a/doc/common/installation.h b/doc/common/installation.h deleted file mode 100644 index c27e4f56..00000000 --- a/doc/common/installation.h +++ /dev/null @@ -1,280 +0,0 @@ -/*! \page installation GUDHI installation - * \tableofcontents - * 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 utilities. - * - * \section compiling Compiling - * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.48.0 - * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.1. - * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. - * - * \subsection utilities Utilities and examples - * To build the utilities, run the following commands in a terminal: -\verbatim cd /path-to-gudhi/ -mkdir build -cd build/ -cmake .. -make \endverbatim - * By default, examples are disabled. You can activate their compilation with - * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX), - * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or y mofifying the - * cmake command as follows : -\verbatim cmake -DWITH_GUDHI_EXAMPLE=ON .. -make \endverbatim - * A list of utilities and examples is available <a href="examples.html">here</a>. - * - * \subsection libraryinstallation Installation - * To install the library (headers and activated utilities), run the following command in a terminal: - * \verbatim make install \endverbatim - * This action may require to be in the sudoer or administrator of the machine in function of the operating system and - * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>. - * - * \subsection testsuites Test suites - * To test your build, run the following command in a terminal: - * \verbatim make test \endverbatim - * - * \subsection documentationgeneration Documentation - * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> 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 - * - * \subsection helloworld Hello world ! - * The <a target="_blank" href="https://gitlab.inria.fr/GUDHI/hello-gudhi-world">Hello world for GUDHI</a> - * project is an example to help developers to make their own C++ project on top of the GUDHI library. - * - * \section optionallibrary Optional third-party library - * \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 <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic - * Library</a> (GMP) and will not be built if GMP is not installed: - * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * - * Having GMP version 4.2 or higher installed is recommended. - * - * \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 <CODE>cmake . && make</CODE> CGAL (or even - * <CODE>cmake -DCGAL_HEADER_ONLY=ON .</CODE> for CGAL version ≥ 4.8.0), thereafter you will be able to compile - * GUDHI by calling <CODE>cmake -DCGAL_DIR=/your/path/to/CGAL-X.Y .. && make</CODE> - * - * 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/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="_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 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="_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> - * - * The following example requires CGAL version ≥ 4.8.1: - * \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="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html"> - * Bottleneck_distance/bottleneck_basic_example.cpp</a> - * \li <a href="_bottleneck_distance_2bottleneck_read_file_8cpp-example.html"> - * Bottleneck_distance/bottleneck_distance.cpp</a> - * \li <a href="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html"> - * Nerve_GIC/CoordGIC.cpp</a> - * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html"> - * Nerve_GIC/FuncGIC.cpp</a> - * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html"> - * Nerve_GIC/Nerve.cpp</a> - * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html"> - * Nerve_GIC/VoronoiGIC.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"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> - * Subsampling/example_custom_kernel.cpp</a> - * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> - * Tangential_complex/example_basic.cpp</a> - * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html"> - * Tangential_complex/example_with_perturb.cpp</a> - * - * \subsection eigen3 Eigen3 - * The \ref alpha_complex data structure and few examples requires - * <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 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_2custom_persistence_sort_8cpp-example.html"> - * Persistent_cohomology/custom_persistence_sort.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"> - * Subsampling/example_choose_n_farthest_points.cpp</a> - * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html"> - * Subsampling/example_custom_kernel.cpp</a> - * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html"> - * Subsampling/example_pick_n_random_points.cpp</a> - * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html"> - * Subsampling/example_sparsify_point_set.cpp</a> - * \li <a href="_tangential_complex_2example_basic_8cpp-example.html"> - * 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 - * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have - * future-proof scalability. - * - * 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_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/cubical_complex_persistence.cpp</a> - * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> - * 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="_nerve__g_i_c_2_coord_g_i_c_8cpp-example.html"> - * Nerve_GIC/CoordGIC.cpp</a> - * \li <a href="_nerve__g_i_c_2_func_g_i_c_8cpp-example.html"> - * Nerve_GIC/FuncGIC.cpp</a> - * \li <a href="_nerve__g_i_c_2_nerve_8cpp-example.html"> - * Nerve_GIC/Nerve.cpp</a> - * \li <a href="_nerve__g_i_c_2_voronoi_g_i_c_8cpp-example.html"> - * Nerve_GIC/VoronoiGIC.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"> - * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> - * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> - * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - * \li <a href="_simplex_tree_2graph_expansion_with_blocker_8cpp-example.html"> - * Simplex_tree/graph_expansion_with_blocker.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="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> - * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> - * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> - * Persistent_cohomology/persistence_from_file.cpp</a> - * \li <a href="_persistent_cohomology_2persistence_from_simple_simplex_tree_8cpp-example.html"> - * 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_multifield_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_multifield_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_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 - * - * GUDHI is open to external contributions. If you want to join our development team, please contact us. - * -*/ - -/*! \page Citation Acknowledging the GUDHI library - * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use - * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages. - * Feel free to contact us in case you have any question or remark on this topic. - * - * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications - * directly related to the GUDHI library. - * \section GudhiBibtex GUDHI bibtex - * \verbinclude biblio/how_to_cite_gudhi.bib -*/ diff --git a/doc/common/main_page.h b/doc/common/main_page.h deleted file mode 100644 index db1e80ce..00000000 --- a/doc/common/main_page.h +++ /dev/null @@ -1,269 +0,0 @@ -/*! \mainpage The C++ library - * \tableofcontents - * \image html "Gudhi_banner.png" "" width=20cm - * - * \section Introduction Introduction - * The GUDHI library (Geometry Understanding in Higher Dimensions) is a generic open source - * <a class="el" target="_blank" href="http://gudhi.gforge.inria.fr/doc/latest/">C++ library</a> for - * Computational Topology and Topological Data Analysis - * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>). - * The GUDHI library intends to help the development of new algorithmic solutions in TDA and their transfer to - * applications. It provides robust, efficient, flexible and easy to use implementations of state-of-the-art - * algorithms and data structures. - * - * The current release of the GUDHI library includes: - * - * \li Data structures to represent, construct and manipulate simplicial complexes. - * \li Simplification of simplicial complexes by edge contraction. - * \li Algorithms to compute persistent homology and bottleneck distance. - * - * All data-structures are generic and several of their aspects can be parameterized via template classes. - * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library. - * - \section DataStructures Data structures - \subsection AlphaComplexDataStructure Alpha complex - \image html "alpha_complex_representation.png" "Alpha complex representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Vincent Rouvreau<br> - <b>Introduced in:</b> GUDHI 1.3.0<br> - <b>Copyright:</b> GPL v3<br> - <b>Requires:</b> \ref cgal ≥ 4.7.0 and \ref eigen3 - </td> - <td width="75%"> - Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br> - The filtration value of each simplex is computed as the square of the circumradius of the simplex if the - circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration - values of the codimension 1 cofaces that make it not Gabriel otherwise. - All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into - the complex.<br> - <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alpha_complex::Alpha_complex - </td> - </tr> -</table> - \subsection CechComplexDataStructure Čech complex - \image html "cech_complex_representation.png" "Čech complex representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Vincent Rouvreau<br> - <b>Introduced in:</b> GUDHI 2.2.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - The Čech complex is a simplicial complex constructed from a proximity graph.<br> - The set of all simplices is filtered by the radius of their minimal enclosing ball.<br> - <b>User manual:</b> \ref cech_complex - <b>Reference manual:</b> Gudhi::cech_complex::Cech_complex - </td> - </tr> -</table> - \subsection CubicalComplexDataStructure Cubical complex - \image html "Cubical_complex_representation.png" "Cubical complex representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Pawel Dlotko<br> - <b>Introduced in:</b> GUDHI 1.3.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - The cubical complex is an example of a structured complex useful in computational mathematics (specially - rigorous numerics) and image analysis.<br> - <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex - </td> - </tr> -</table> - \subsection RipsComplexDataStructure Rips complex - \image html "rips_complex_representation.png" "Rips complex representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Clément Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse<br> - <b>Introduced in:</b> GUDHI 2.0.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - Rips_complex is a simplicial complex constructed from a one skeleton graph.<br> - The filtration value of each edge is computed from a user-given distance function and is inserted until a - user-given threshold value.<br> - This complex can be built from a point cloud and a distance function, or from a distance matrix.<br> - <b>User manual:</b> \ref rips_complex - <b>Reference manual:</b> Gudhi::rips_complex::Rips_complex - </td> - </tr> -</table> - \subsection SimplexTreeDataStructure Simplex tree - \image html "Simplex_tree_representation.png" "Simplex tree representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Clément Maria<br> - <b>Introduced in:</b> GUDHI 1.0.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - The simplex tree is an efficient and flexible - data structure for representing general (filtered) simplicial complexes. The data structure - is described in \cite boissonnatmariasimplextreealgorithmica .<br> - <b>User manual:</b> \ref simplex_tree - <b>Reference manual:</b> Gudhi::Simplex_tree - </td> - </tr> -</table> - \subsection CoverComplexDataStructure Cover Complexes - \image html "gicvisu.jpg" "Graph Induced Complex of a point cloud." -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Mathieu Carrière<br> - <b>Introduced in:</b> GUDHI 2.1.0<br> - <b>Copyright:</b> GPL v3<br> - <b>Requires:</b> \ref cgal ≥ 4.8.1 - </td> - <td width="75%"> - Nerves and Graph Induced Complexes are cover complexes, i.e. simplicial complexes that provably contain - topological information about the input data. They can be computed with a cover of the - data, that comes i.e. from the preimage of a family of intervals covering the image - of a scalar-valued function defined on the data. <br> - <b>User manual:</b> \ref cover_complex - <b>Reference manual:</b> Gudhi::cover_complex::Cover_complex - </td> - </tr> -</table> - \subsection SkeletonBlockerDataStructure Skeleton blocker - \image html "ds_representation.png" "Skeleton blocker representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> David Salinas<br> - <b>Introduced in:</b> GUDHI 1.1.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - The Skeleton-Blocker data-structure proposes a light encoding for simplicial complexes by storing only an *implicit* - representation of its simplices \cite socg_blockers_2011,\cite blockers2012. Intuitively, it just stores the - 1-skeleton of a simplicial complex with a graph and the set of its "missing faces" that is very small in practice. - This data-structure handles all simplicial complexes operations such as simplex enumeration or simplex removal but - operations that are particularly efficient are operations that do not require simplex enumeration such as edge - iteration, link computation or simplex contraction.<br> - <b>User manual:</b> \ref skbl - <b>Reference manual:</b> Gudhi::skeleton_blocker::Skeleton_blocker_complex - </td> - </tr> -</table> - \subsection TangentialComplexDataStructure Tangential complex - \image html "tc_examples.png" "Tangential complex representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Clément Jamin<br> - <b>Introduced in:</b> GUDHI 2.0.0<br> - <b>Copyright:</b> GPL v3<br> - <b>Requires:</b> \ref cgal ≥ 4.8.1 and \ref eigen3 - </td> - <td width="75%"> - A Tangential Delaunay complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> - 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$.<br> - <b>User manual:</b> \ref tangential_complex - <b>Reference manual:</b> Gudhi::tangential_complex::Tangential_complex - </td> - </tr> -</table> - \subsection WitnessComplexDataStructure Witness complex - \image html "Witness_complex_representation.png" "Witness complex representation" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Siargey Kachanovich<br> - <b>Introduced in:</b> GUDHI 1.3.0<br> - <b>Copyright:</b> GPL v3<br> - <b>Euclidean version requires:</b> \ref cgal ≥ 4.6.0 and \ref eigen3 - </td> - <td width="75%"> - Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$. - The data structure is described in \cite boissonnatmariasimplextreealgorithmica .<br> - <b>User manual:</b> \ref witness_complex - <b>Reference manual:</b> Gudhi::witness_complex::SimplicialComplexForWitness - </td> - </tr> -</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"> - <tr> - <td width="25%"> - <b>Author:</b> François Godi<br> - <b>Introduced in:</b> GUDHI 2.0.0<br> - <b>Copyright:</b> GPL v3<br> - <b>Requires:</b> \ref cgal ≥ 4.8.1 - </td> - <td width="75%"> - 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. - <br> - <b>User manual:</b> \ref bottleneck_distance - </td> - </tr> -</table> - \subsection ContractionToolbox Contraction - \image html "sphere_contraction_representation.png" "Sphere contraction example" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> David Salinas<br> - <b>Introduced in:</b> GUDHI 1.1.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - The purpose of this package is to offer a user-friendly interface for edge contraction simplification of huge - simplicial complexes. It uses the \ref skbl data-structure whose size remains small during simplification of most - used geometrical complexes of topological data analysis such as the Rips or the Delaunay complexes. In practice, - the size of this data-structure is even much lower than the total number of simplices.<br> - <b>User manual:</b> \ref contr - </td> - </tr> -</table> - \subsection PersistentCohomologyToolbox Persistent Cohomology - \image html "3DTorus_poch.png" "Rips Persistent Cohomology on a 3D Torus" -<table border="0"> - <tr> - <td width="25%"> - <b>Author:</b> Clément Maria<br> - <b>Introduced in:</b> GUDHI 1.0.0<br> - <b>Copyright:</b> GPL v3<br> - </td> - <td width="75%"> - The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing - global topological features like connected components, holes, cavities, etc. Persistent homology studies the - evolution -- birth, life and death -- of these features when the topological space is changing. Consequently, the - theory is essentially composed of three elements: topological spaces, their homology groups and an evolution - scheme. - Computation of persistent cohomology using the algorithm of \cite DBLP:journals/dcg/SilvaMV11 and - \cite DBLP:journals/corr/abs-1208-5018 and the Compressed Annotation Matrix implementation of - \cite DBLP:conf/esa/BoissonnatDM13 .<br> - <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> - -*/ diff --git a/doc/common/offline_header.html b/doc/common/offline_header.html deleted file mode 100644 index 6a02a895..00000000 --- a/doc/common/offline_header.html +++ /dev/null @@ -1,41 +0,0 @@ -<!-- HTML header for doxygen 1.8.6--> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> -<!-- GUDHI website : class="no-js" lang="en" is necessary --> -<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en"> -<head> -<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/> -<meta http-equiv="X-UA-Compatible" content="IE=9"/> -<meta name="generator" content="Doxygen $doxygenversion"/> -<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME--> -<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME--> -<!-- GUDHI website css for header END --> -<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/> -<script type="text/javascript" src="$relpath^jquery.js"></script> -<script type="text/javascript" src="$relpath^dynsections.js"></script> -$treeview -$search -$mathjax -<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" /> -$extrastylesheet -</head> -<body> - - -<div id="top"><!-- do not remove this div, it is closed by doxygen! --> - -<!--BEGIN TITLEAREA--> -<div id="titlearea"> -<table cellspacing="0" cellpadding="0"> - <tbody> - <tr style="height: 30px;"> - <!--BEGIN DISABLE_INDEX--> - <!--BEGIN SEARCHENGINE--> - <td>$searchbox</td> - <!--END SEARCHENGINE--> - <!--END DISABLE_INDEX--> - </tr> - </tbody> -</table> -</div> -<!--END TITLEAREA--> -<!-- end header part --> diff --git a/doc/common/stylesheet.css b/doc/common/stylesheet.css deleted file mode 100644 index 1df177a4..00000000 --- a/doc/common/stylesheet.css +++ /dev/null @@ -1,1367 +0,0 @@ -/* The standard CSS for doxygen 1.8.6 */ - -body, table, div, p, dl { - font: 400 14px/22px Roboto,sans-serif; 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