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-rw-r--r--CMakeGUDHIVersion.txt2
-rw-r--r--src/Bitmap_cubical_complex/doc/Cubical_complex_representation.ipe732
-rw-r--r--src/Bitmap_cubical_complex/doc/Cubical_complex_representation.pngbin0 -> 19167 bytes
-rw-r--r--src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h2
-rw-r--r--src/Contraction/doc/sphere_contraction_representation.pngbin0 -> 44839 bytes
-rw-r--r--src/Contraction/include/gudhi/Edge_contraction.h2
-rw-r--r--src/Doxyfile24
-rw-r--r--src/Persistent_cohomology/doc/3DTorus_poch.pngbin0 -> 40164 bytes
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h9
-rw-r--r--src/Simplex_tree/doc/Simplex_tree_representation.pngbin0 -> 39217 bytes
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree.h2
-rw-r--r--src/Witness_complex/doc/Witness_complex_doc.h6
-rw-r--r--src/Witness_complex/doc/Witness_complex_representation.pngbin0 -> 48899 bytes
-rw-r--r--src/common/doc/footer.html29
-rw-r--r--src/common/doc/header.html82
-rw-r--r--src/common/doc/main_page.h143
-rw-r--r--src/common/doc/stylesheet.css1367
17 files changed, 2351 insertions, 49 deletions
diff --git a/CMakeGUDHIVersion.txt b/CMakeGUDHIVersion.txt
index 19d10535..20767813 100644
--- a/CMakeGUDHIVersion.txt
+++ b/CMakeGUDHIVersion.txt
@@ -1,5 +1,5 @@
set (GUDHI_MAJOR_VERSION 1)
-set (GUDHI_MINOR_VERSION 2)
+set (GUDHI_MINOR_VERSION 3)
set (GUDHI_PATCH_VERSION 0)
set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
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new file mode 100644
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diff --git a/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
new file mode 100644
index 00000000..afb2a75e
--- /dev/null
+++ b/src/Bitmap_cubical_complex/doc/Cubical_complex_representation.png
Binary files differ
diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index cde0b2fc..be4caaad 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -76,7 +76,7 @@ namespace Cubical_complex {
* directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube \f$C \in
* \mathcal{K}\f$.
*
- * \image html "bitmapAllCubes.png" "Cubical complex.
+ * \image html "Cubical_complex_representation.png" Cubical complex.
*
* Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical
* complexes in \f$\mathbb{R}\f$. The number of all cubes in each direction is equal \f$2n+1\f$, where \f$n\f$ is the
diff --git a/src/Contraction/doc/sphere_contraction_representation.png b/src/Contraction/doc/sphere_contraction_representation.png
new file mode 100644
index 00000000..edf37bf3
--- /dev/null
+++ b/src/Contraction/doc/sphere_contraction_representation.png
Binary files differ
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index ee3e3de1..73236db9 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -46,7 +46,7 @@ namespace contraction {
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 uch lower than the total number of simplices.
+size of this data-structure is even much lower than the total number of simplices.
The edge contraction operation consists in identifying two vertices of a simplicial complex.
A lot of algorithms have been developed in computer graphics that allows to reduce efficiently the size of 2-dimensional simplicial complexes
diff --git a/src/Doxyfile b/src/Doxyfile
index a93578c5..8fe41755 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -32,19 +32,19 @@ DOXYFILE_ENCODING = UTF-8
# title of most generated pages and in a few other places.
# The default value is: My Project.
-PROJECT_NAME = "Gudhi"
+PROJECT_NAME = "GUDHI"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = "1.2.0"
+PROJECT_NUMBER = "1.3.0"
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
-PROJECT_BRIEF =
+PROJECT_BRIEF = "C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding."
# With the PROJECT_LOGO tag one can specify an logo or icon that is included in
# the documentation. The maximum height of the logo should not exceed 55 pixels
@@ -580,27 +580,27 @@ STRICT_PROTO_MATCHING = NO
# documentation.
# The default value is: YES.
-GENERATE_TODOLIST = YES
+GENERATE_TODOLIST = NO
# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the
# test list. This list is created by putting \test commands in the
# documentation.
# The default value is: YES.
-GENERATE_TESTLIST = YES
+GENERATE_TESTLIST = NO
# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
-GENERATE_BUGLIST = YES
+GENERATE_BUGLIST = NO
# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
-GENERATE_DEPRECATEDLIST= YES
+GENERATE_DEPRECATEDLIST= NO
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
@@ -835,6 +835,8 @@ EXAMPLE_RECURSIVE = NO
IMAGE_PATH = doc/Skeleton_blocker/ \
doc/common/ \
doc/Contraction/ \
+ doc/Simplex_tree/ \
+ doc/Persistent_cohomology/ \
doc/Witness_complex/ \
doc/Bitmap_cubical_complex/
@@ -1040,7 +1042,7 @@ HTML_FILE_EXTENSION = .html
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_HEADER =
+HTML_HEADER = doc/common/header.html
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1050,7 +1052,7 @@ HTML_HEADER =
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_FOOTER =
+HTML_FOOTER = doc/common/footer.html
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1062,7 +1064,7 @@ HTML_FOOTER =
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
-HTML_STYLESHEET =
+HTML_STYLESHEET = doc/common/stylesheet.css
# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
# defined cascading style sheet that is included after the standard style sheets
@@ -1545,7 +1547,7 @@ EXTRA_SEARCH_MAPPINGS =
# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output.
# The default value is: YES.
-GENERATE_LATEX = YES
+GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
diff --git a/src/Persistent_cohomology/doc/3DTorus_poch.png b/src/Persistent_cohomology/doc/3DTorus_poch.png
new file mode 100644
index 00000000..1c9d8328
--- /dev/null
+++ b/src/Persistent_cohomology/doc/3DTorus_poch.png
Binary files differ
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 643b810c..3c331f0f 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -63,15 +63,6 @@ namespace persistent_cohomology {
composed of three elements:
topological spaces, their homology groups and an evolution scheme.
- 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.
-
<DT>Topological Spaces:</DT>
Topological spaces are represented by simplicial complexes.
Let \f$V = \{1, \cdots ,|V|\}\f$ be a set of <EM>vertices</EM>.
diff --git a/src/Simplex_tree/doc/Simplex_tree_representation.png b/src/Simplex_tree/doc/Simplex_tree_representation.png
new file mode 100644
index 00000000..9d401520
--- /dev/null
+++ b/src/Simplex_tree/doc/Simplex_tree_representation.png
Binary files differ
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 8a1a1344..46670b85 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -68,6 +68,7 @@ namespace Gudhi {
The simplex tree is an efficient and flexible
data structure for representing general (filtered) simplicial complexes. The data structure
is described in \cite boissonnatmariasimplextreealgorithmica
+ \image html "Simplex_tree_representation.png" "Simplex tree representation"
The second one is the Hasse_complex. The Hasse complex is a data structure representing
explicitly all co-dimension 1 incidence relations in a complex. It is consequently faster
@@ -85,6 +86,7 @@ namespace Gudhi {
struct Simplex_tree_options_full_featured;
/**
+ * \class Simplex_tree Simplex_tree.h gudhi/Simplex_tree.h
* \brief Simplex Tree data structure for representing simplicial complexes.
*
* \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h
index e9f78170..60dfd27b 100644
--- a/src/Witness_complex/doc/Witness_complex_doc.h
+++ b/src/Witness_complex/doc/Witness_complex_doc.h
@@ -6,6 +6,8 @@
\author Siargey Kachanovich
+ \image html "Witness_complex_representation.png" "Witness complex representation"
+
\section Definitions
Witness complex \f$ Wit(W,L) \f$ is a simplicial complex defined on two sets of points in \f$\mathbb{R}^D\f$:
@@ -18,7 +20,9 @@
\f$ \sigma \subset L \f$ is witnessed if there exists a point \f$w \in W\f$ such that
w is closer to the vertices of \f$ \sigma \f$ than other points in \f$ L \f$ and all of its faces are witnessed as well.
-
+
+ The data structure is described in \cite boissonnatmariasimplextreealgorithmica .
+
\section Implementation
The principal class of this module is Gudhi::Witness_complex.
diff --git a/src/Witness_complex/doc/Witness_complex_representation.png b/src/Witness_complex/doc/Witness_complex_representation.png
new file mode 100644
index 00000000..1d31a490
--- /dev/null
+++ b/src/Witness_complex/doc/Witness_complex_representation.png
Binary files differ
diff --git a/src/common/doc/footer.html b/src/common/doc/footer.html
new file mode 100644
index 00000000..7b4cdc5c
--- /dev/null
+++ b/src/common/doc/footer.html
@@ -0,0 +1,29 @@
+<!-- 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-->
+<!--END PROJECT_NAME-->
+ </td>
+ <td class="network-entypo">
+<!--BEGIN GENERATE_TREEVIEW-->
+ $generatedby
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion
+<!--END GENERATE_TREEVIEW-->
+ </td>
+ </tr>
+</table>
+
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small> tralala
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
new file mode 100644
index 00000000..c958390c
--- /dev/null
+++ b/src/common/doc/header.html
@@ -0,0 +1,82 @@
+<!-- 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="http://gudhi.gforge.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" />
+$extrastylesheet
+</head>
+<body>
+
+<!-- GUDHI website header BEGIN -->
+<div id="navigation" class="sticky">
+ <nav class="top-bar" role="navigation" data-topbar>
+ <section class="top-bar-section">
+ <ul class="right">
+ <li class="divider"></li>
+ <li><a href="http://gudhi.gforge.inria.fr/contact/">Contact</a></li>
+ </ul>
+ <ul class="left">
+ <li><a href="http://gudhi.gforge.inria.fr/"> <img src="http://gudhi.gforge.inria.fr/assets/img/home.png" alt="&nbsp;&nbsp;GUDHI">&nbsp;&nbsp;GUDHI </a></li>
+ <li class="divider"></li>
+ <li class="has-dropdown">
+ <a href="#">Project</a>
+ <ul class="dropdown">
+ <li><a href="http://gudhi.gforge.inria.fr/people/">People</a></li>
+ <li><a href="http://gudhi.gforge.inria.fr/getinvolved/">Get involved</a></li>
+ <li><a href="http://gudhi.gforge.inria.fr/partners/">Partners and Funding</a></li>
+ <li><a href="http://gudhi.gforge.inria.fr/relatedprojects/">Related projects</a></li>
+ </ul>
+ </li>
+ <li class="divider"></li>
+ <li class="has-dropdown">
+ <a href="#">Download</a>
+ <ul class="dropdown">
+ <li><a href="http://gudhi.gforge.inria.fr/licensing/">Licensing</a></li>
+ <li><a href="https://gforge.inria.fr/frs/?group_id=3865" target="_blank">Get the sources</a></li>
+ <li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">Installation manual</a></li>
+ </ul>
+ </li>
+ <li class="divider"></li>
+ <li><a href="http://gudhi.gforge.inria.fr/doc/latest/modules.html">Documentation</a></li>
+ <li class="divider"></li>
+ <li><a href="http://gudhi.gforge.inria.fr/interfaces/">Interfaces</a></li>
+ <li class="divider"></li>
+ </ul>
+ </section>
+ </nav>
+</div><!-- /#navigation -->
+<!-- GUDHI website header BEGIN -->
+
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 30px;">
+ <!--BEGIN DISABLE_INDEX-->
+ <!--BEGIN SEARCHENGINE-->
+ <td>$searchbox</td>
+ <!--END SEARCHENGINE-->
+ <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 41b8ba1e..56cb82bb 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,15 +1,14 @@
/*! \mainpage
+ * \tableofcontents
* \image html "Gudhi_banner.jpg" "" width=20cm
*
* \section Introduction Introduction
- * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for
+ * The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic open source C++ library 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 is developed as part of the
- * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
- * Research Council. 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 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:
*
@@ -20,24 +19,118 @@
* 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.
*
- * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
- * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
- * webpage</a>.
- *
- * The library comes with data sets, \ref demos and \ref testsuites.
- *
- * Gudhi is also accessible though the
- * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
- * (Statistical Tools for Topological Data Analysis).
- *
- * The development of the GUDHI library is steered by an Editorial Board composed of:
- *
- * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/">
- * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée
- * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France
- * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
- * \li Vincent Rouvreau | INRIA Saclay - Ile de France
- *
+ \section DataStructures Data structures
+ \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 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 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::skbl::Skeleton_blocker_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>
+ </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 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
+ </td>
+ </tr>
+</table>
*/
/*! \page installation Gudhi installation
@@ -47,7 +140,7 @@
*
* \section compiling Compiling
* The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
- * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
*
* \subsection gmp GMP:
* The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
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+ -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+ -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+ box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+ padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+ white-space: nowrap;
+ border-right: 1px solid #A8B8D9;
+ border-bottom: 1px solid #A8B8D9;
+ vertical-align: top;
+}
+
+.fieldtable td.fieldname {
+ padding-top: 3px;
+}
+
+.fieldtable td.fielddoc {
+ border-bottom: 1px solid #A8B8D9;
+ /*width: 100%;*/
+}
+
+.fieldtable td.fielddoc p:first-child {
+ margin-top: 0px;
+}
+
+.fieldtable td.fielddoc p:last-child {
+ margin-bottom: 2px;
+}
+
+.fieldtable tr:last-child td {
+ border-bottom: none;
+}
+
+.fieldtable th {
+ background-image:url('nav_f.png');
+ background-repeat:repeat-x;
+ background-color: #E2E8F2;
+ font-size: 90%;
+ color: #253555;
+ padding-bottom: 4px;
+ padding-top: 5px;
+ text-align:left;
+ -moz-border-radius-topleft: 4px;
+ -moz-border-radius-topright: 4px;
+ -webkit-border-top-left-radius: 4px;
+ -webkit-border-top-right-radius: 4px;
+ border-top-left-radius: 4px;
+ border-top-right-radius: 4px;
+ border-bottom: 1px solid #A8B8D9;
+}
+
+
+.tabsearch {
+ top: 0px;
+ left: 10px;
+ height: 36px;
+ background-image: url('tab_b.png');
+ z-index: 101;
+ overflow: hidden;
+ font-size: 13px;
+}
+
+.navpath ul
+{
+ font-size: 11px;
+ background-image:url('tab_b.png');
+ background-repeat:repeat-x;
+ background-position: 0 -5px;
+ height:30px;
+ line-height:30px;
+ color:#8AA0CC;
+ border:solid 1px #C2CDE4;
+ overflow:hidden;
+ margin:0px;
+ padding:0px;
+}
+
+.navpath li
+{
+ list-style-type:none;
+ float:left;
+ padding-left:10px;
+ padding-right:15px;
+ background-image:url('bc_s.png');
+ background-repeat:no-repeat;
+ background-position:right;
+ color:#364D7C;
+}
+
+.navpath li.navelem a
+{
+ height:32px;
+ display:block;
+ text-decoration: none;
+ outline: none;
+ color: #283A5D;
+ font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+ text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
+ text-decoration: none;
+}
+
+.navpath li.navelem a:hover
+{
+ color:#6884BD;
+}
+
+.navpath li.footer
+{
+ list-style-type:none;
+ float:right;
+ padding-left:10px;
+ padding-right:15px;
+ background-image:none;
+ background-repeat:no-repeat;
+ background-position:right;
+ color:#364D7C;
+ font-size: 8pt;
+}
+
+
+div.summary
+{
+ float: right;
+ font-size: 8pt;
+ padding-right: 5px;
+ width: 50%;
+ text-align: right;
+}
+
+div.summary a
+{
+ white-space: nowrap;
+}
+
+div.ingroups
+{
+ font-size: 8pt;
+ width: 50%;
+ text-align: left;
+}
+
+div.ingroups a
+{
+ white-space: nowrap;
+}
+
+div.header
+{
+ background-image:url('nav_h.png');
+ background-repeat:repeat-x;
+ background-color: #F9FAFC;
+ margin: 0px;
+ border-bottom: 1px solid #C4CFE5;
+}
+
+div.headertitle
+{
+ padding: 5px 5px 5px 10px;
+}
+
+dl
+{
+ padding: 0 0 0 10px;
+}
+
+/* dl.note, dl.warning, dl.attention, dl.pre, dl.post, dl.invariant, dl.deprecated, dl.todo, dl.test, dl.bug */
+dl.section
+{
+ margin-left: 0px;
+ padding-left: 0px;
+}
+
+dl.note
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #D0C000;
+}
+
+dl.warning, dl.attention
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #FF0000;
+}
+
+dl.pre, dl.post, dl.invariant
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #00D000;
+}
+
+dl.deprecated
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #505050;
+}
+
+dl.todo
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #00C0E0;
+}
+
+dl.test
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #3030E0;
+}
+
+dl.bug
+{
+ margin-left:-7px;
+ padding-left: 3px;
+ border-left:4px solid;
+ border-color: #C08050;
+}
+
+dl.section dd {
+ margin-bottom: 6px;
+}
+
+
+#projectlogo
+{
+ text-align: center;
+ vertical-align: bottom;
+ border-collapse: separate;
+}
+
+#projectlogo img
+{
+ border: 0px none;
+}
+
+#projectname
+{
+ border: 0px none;
+ font: 300% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 2px 0px;
+}
+
+#projectbrief
+{
+ font: 60% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 0px;
+}
+
+#projectnumber
+{
+ font: 80% Tahoma, Arial,sans-serif;
+ margin: 0px;
+ padding: 0px;
+}
+
+#titlearea
+{
+ padding: 0px;
+ margin: 0px;
+ width: 100%;
+ border-bottom: 1px solid #5373B4;
+}
+
+.image
+{
+ text-align: center;
+}
+
+.dotgraph
+{
+ text-align: center;
+}
+
+.mscgraph
+{
+ text-align: center;
+}
+
+.diagraph
+{
+ text-align: center;
+}
+
+.caption
+{
+ font-weight: bold;
+}
+
+div.zoom
+{
+ border: 1px solid #90A5CE;
+}
+
+dl.citelist {
+ margin-bottom:50px;
+}
+
+dl.citelist dt {
+ color:#334975;
+ float:left;
+ font-weight:bold;
+ margin-right:10px;
+ padding:5px;
+}
+
+dl.citelist dd {
+ margin:2px 0;
+ padding:5px 0;
+}
+
+div.toc {
+ padding: 14px 25px;
+ background-color: #F4F6FA;
+ border: 1px solid #D8DFEE;
+ border-radius: 7px 7px 7px 7px;
+ float: right;
+ height: auto;
+ margin: 0 20px 10px 10px;
+ width: 200px;
+}
+
+div.toc li {
+ background: url("bdwn.png") no-repeat scroll 0 5px transparent;
+ font: 10px/1.2 Verdana,DejaVu Sans,Geneva,sans-serif;
+ margin-top: 5px;
+ padding-left: 10px;
+ padding-top: 2px;
+}
+
+div.toc h3 {
+ font: bold 12px/1.2 Arial,FreeSans,sans-serif;
+ color: #4665A2;
+ border-bottom: 0 none;
+ margin: 0;
+}
+
+div.toc ul {
+ list-style: none outside none;
+ border: medium none;
+ padding: 0px;
+}
+
+div.toc li.level1 {
+ margin-left: 0px;
+}
+
+div.toc li.level2 {
+ margin-left: 15px;
+}
+
+div.toc li.level3 {
+ margin-left: 30px;
+}
+
+div.toc li.level4 {
+ margin-left: 45px;
+}
+
+.inherit_header {
+ font-weight: bold;
+ color: gray;
+ cursor: pointer;
+ -webkit-touch-callout: none;
+ -webkit-user-select: none;
+ -khtml-user-select: none;
+ -moz-user-select: none;
+ -ms-user-select: none;
+ user-select: none;
+}
+
+.inherit_header td {
+ padding: 6px 0px 2px 5px;
+}
+
+.inherit {
+ display: none;
+}
+
+tr.heading h2 {
+ margin-top: 12px;
+ margin-bottom: 4px;
+}
+
+/* tooltip related style info */
+
+.ttc {
+ position: absolute;
+ display: none;
+}
+
+#powerTip {
+ cursor: default;
+ white-space: nowrap;
+ background-color: white;
+ border: 1px solid gray;
+ border-radius: 4px 4px 4px 4px;
+ box-shadow: 1px 1px 7px gray;
+ display: none;
+ font-size: smaller;
+ max-width: 80%;
+ opacity: 0.9;
+ padding: 1ex 1em 1em;
+ position: absolute;
+ z-index: 2147483647;
+}
+
+#powerTip div.ttdoc {
+ color: grey;
+ font-style: italic;
+}
+
+#powerTip div.ttname a {
+ font-weight: bold;
+}
+
+#powerTip div.ttname {
+ font-weight: bold;
+}
+
+#powerTip div.ttdeci {
+ color: #006318;
+}
+
+#powerTip div {
+ margin: 0px;
+ padding: 0px;
+ font: 12px/16px Roboto,sans-serif;
+}
+
+#powerTip:before, #powerTip:after {
+ content: "";
+ position: absolute;
+ margin: 0px;
+}
+
+#powerTip.n:after, #powerTip.n:before,
+#powerTip.s:after, #powerTip.s:before,
+#powerTip.w:after, #powerTip.w:before,
+#powerTip.e:after, #powerTip.e:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.nw:after, #powerTip.nw:before,
+#powerTip.sw:after, #powerTip.sw:before {
+ border: solid transparent;
+ content: " ";
+ height: 0;
+ width: 0;
+ position: absolute;
+}
+
+#powerTip.n:after, #powerTip.s:after,
+#powerTip.w:after, #powerTip.e:after,
+#powerTip.nw:after, #powerTip.ne:after,
+#powerTip.sw:after, #powerTip.se:after {
+ border-color: rgba(255, 255, 255, 0);
+}
+
+#powerTip.n:before, #powerTip.s:before,
+#powerTip.w:before, #powerTip.e:before,
+#powerTip.nw:before, #powerTip.ne:before,
+#powerTip.sw:before, #powerTip.se:before {
+ border-color: rgba(128, 128, 128, 0);
+}
+
+#powerTip.n:after, #powerTip.n:before,
+#powerTip.ne:after, #powerTip.ne:before,
+#powerTip.nw:after, #powerTip.nw:before {
+ top: 100%;
+}
+
+#powerTip.n:after, #powerTip.ne:after, #powerTip.nw:after {
+ border-top-color: #ffffff;
+ border-width: 10px;
+ margin: 0px -10px;
+}
+#powerTip.n:before {
+ border-top-color: #808080;
+ border-width: 11px;
+ margin: 0px -11px;
+}
+#powerTip.n:after, #powerTip.n:before {
+ left: 50%;
+}
+
+#powerTip.nw:after, #powerTip.nw:before {
+ right: 14px;
+}
+
+#powerTip.ne:after, #powerTip.ne:before {
+ left: 14px;
+}
+
+#powerTip.s:after, #powerTip.s:before,
+#powerTip.se:after, #powerTip.se:before,
+#powerTip.sw:after, #powerTip.sw:before {
+ bottom: 100%;
+}
+
+#powerTip.s:after, #powerTip.se:after, #powerTip.sw:after {
+ border-bottom-color: #ffffff;
+ border-width: 10px;
+ margin: 0px -10px;
+}
+
+#powerTip.s:before, #powerTip.se:before, #powerTip.sw:before {
+ border-bottom-color: #808080;
+ border-width: 11px;
+ margin: 0px -11px;
+}
+
+#powerTip.s:after, #powerTip.s:before {
+ left: 50%;
+}
+
+#powerTip.sw:after, #powerTip.sw:before {
+ right: 14px;
+}
+
+#powerTip.se:after, #powerTip.se:before {
+ left: 14px;
+}
+
+#powerTip.e:after, #powerTip.e:before {
+ left: 100%;
+}
+#powerTip.e:after {
+ border-left-color: #ffffff;
+ border-width: 10px;
+ top: 50%;
+ margin-top: -10px;
+}
+#powerTip.e:before {
+ border-left-color: #808080;
+ border-width: 11px;
+ top: 50%;
+ margin-top: -11px;
+}
+
+#powerTip.w:after, #powerTip.w:before {
+ right: 100%;
+}
+#powerTip.w:after {
+ border-right-color: #ffffff;
+ border-width: 10px;
+ top: 50%;
+ margin-top: -10px;
+}
+#powerTip.w:before {
+ border-right-color: #808080;
+ border-width: 11px;
+ top: 50%;
+ margin-top: -11px;
+}
+
+@media print
+{
+ #top { display: none; }
+ #side-nav { display: none; }
+ #nav-path { display: none; }
+ body { overflow:visible; }
+ h1, h2, h3, h4, h5, h6 { page-break-after: avoid; }
+ .summary { display: none; }
+ .memitem { page-break-inside: avoid; }
+ #doc-content
+ {
+ margin-left:0 !important;
+ height:auto !important;
+ width:auto !important;
+ overflow:inherit;
+ display:inline;
+ }
+}
+