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-rw-r--r--doc/common/examples.h99
-rw-r--r--doc/common/file_formats.h125
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-rw-r--r--doc/common/header.html102
-rw-r--r--doc/common/installation.h280
-rw-r--r--doc/common/main_page.h269
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diff --git a/doc/common/Gudhi_banner.png b/doc/common/Gudhi_banner.png
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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-->&#160;Version $projectnumber<!--END PROJECT_NUMBER-->
-<!--BEGIN PROJECT_BRIEF-->&#160;-&#160;$projectbrief<!--END PROJECT_BRIEF-->
-<!--BEGIN PROJECT_BRIEF-->&#160;-&#160;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
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--- 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="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;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-->
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-<!--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> &ge; 1.48.0
- * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 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 &ge; 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 &ge; 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 &ge; 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 &ge; 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&reg; 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&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
- *
- * The following examples/utilities are using Intel&reg; 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
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--- 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 &ge; 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> Cl&eacute;ment 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> Cl&eacute;ment 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 Carri&egrave;re<br>
- <b>Introduced in:</b> GUDHI 2.1.0<br>
- <b>Copyright:</b> GPL v3<br>
- <b>Requires:</b> \ref cgal &ge; 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> Cl&eacute;ment Jamin<br>
- <b>Introduced in:</b> GUDHI 2.0.0<br>
- <b>Copyright:</b> GPL v3<br>
- <b>Requires:</b> \ref cgal &ge; 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$.<br>
- <b>User manual:</b> \ref tangential_complex - <b>Reference manual:</b> Gudhi::tangential_complex::Tangential_complex
- </td>
- </tr>
-</table>
- \subsection WitnessComplexDataStructure Witness complex
- \image html "Witness_complex_representation.png" "Witness complex representation"
-<table border="0">
- <tr>
- <td width="25%">
- <b>Author:</b> Siargey Kachanovich<br>
- <b>Introduced in:</b> GUDHI 1.3.0<br>
- <b>Copyright:</b> GPL v3<br>
- <b>Euclidean version requires:</b> \ref cgal &ge; 4.6.0 and \ref eigen3
- </td>
- <td width="75%">
- Witness complex \f$ 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> Fran&ccedil;ois Godi<br>
- <b>Introduced in:</b> GUDHI 2.0.0<br>
- <b>Copyright:</b> GPL v3<br>
- <b>Requires:</b> \ref cgal &ge; 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> Cl&eacute;ment 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>
-
-*/
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