diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-06-23 13:50:46 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-06-23 13:50:46 +0000 |
commit | 01b0bf84f780b9998a48f0dbe338319da1c6d6f2 (patch) | |
tree | edff3e5ac2536e112ad7f14830fa5a566467ae80 /src | |
parent | ea986c68192c7536716d139e5a5f0a30a76f0fc1 (diff) |
Alpha complex documentation - 2nd part
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@633 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 023b5aaa57593a4e8e77cf12f388559b638f0eb1
Diffstat (limited to 'src')
-rw-r--r-- | src/Alpha_complex/doc/alpha_complex_doc.ipe | 438 | ||||
-rw-r--r-- | src/Alpha_complex/doc/alpha_complex_doc.png | bin | 0 -> 46226 bytes | |||
-rw-r--r-- | src/Alpha_complex/doc/alpha_complex_doc_135.ipe | 514 | ||||
-rw-r--r-- | src/Alpha_complex/doc/alpha_complex_doc_135.png | bin | 0 -> 94098 bytes | |||
-rw-r--r-- | src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.ipe | 493 | ||||
-rw-r--r-- | src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png | bin | 0 -> 70425 bytes | |||
-rw-r--r-- | src/Alpha_complex/include/gudhi/Alpha_complex.h | 90 | ||||
-rw-r--r-- | src/Doxyfile | 3 |
8 files changed, 1521 insertions, 17 deletions
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size="normal" stroke="darkcyan" fill="white"/> +<path matrix="1 0 0 1 0 80" stroke="darkcyan"> +243.428 591.569 m +186.061 643.28 l +</path> +<text matrix="1 0 0 1 0 80" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="18.785" height="4.294" depth="1.49" valign="baseline">$\alpha_{531}$</text> +<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="280 660" size="normal" stroke="black" fill="white"/> +<use matrix="1 0 0 1 -263.3 -172.154" name="mark/fdisk(sfx)" pos="300 720" size="normal" stroke="black" fill="white"/> +<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="370 690" size="normal" stroke="black" fill="white"/> +<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="290 530" size="normal" stroke="black" fill="white"/> +<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="350 520" size="normal" stroke="black" fill="white"/> +<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="320 580" size="normal" stroke="black" fill="white"/> +<use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="370 580" size="normal" stroke="black" fill="white"/> +<path matrix="1 0 0 1 -264 -162" stroke="lightgray"> +320 580 m +350 520 l +290 530 l +320 580 l +320 580 l +</path> +<path matrix="1 0 0 1 -264 -162" stroke="lightgray"> +320 580 m +280 660 l +290 530 l +320 580 l +320 580 l +</path> +<path matrix="1 0 0 1 -264 -162" stroke="lightgray"> +320 580 m +370 580 l +350 520 l +320 580 l +</path> +<text matrix="0.582962 0 0 1 -211.265 -209.555" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[3,1] is Gabriel $\rightarrow$ $\alpha_{31}$ is not$\\$ +modified (NaN) +</text> +<text matrix="1 0 0 1 -266.155 -165.501" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> +<text matrix="1 0 0 1 -264 -162" 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225.859 -165.729" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="14.814" height="4.294" depth="1.49" valign="baseline">$\alpha_{35}$</text> +<text matrix="1 0 0 1 122 -164" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> +<path stroke="darkcyan" pen="heavier"> +406.093 497.775 m +446.094 418.092 l +</path> +<path stroke="darkcyan"> +44.5799 0 0 44.5799 425.934 457.774 e +</path> +<use name="mark/fdisk(sfx)" pos="425.934 457.774" size="normal" stroke="darkcyan" fill="white"/> +<path stroke="darkcyan"> +425.854 457.774 m +470.795 457.774 l +</path> +<text matrix="1 0 0 1 -48.9756 -209.799" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[3,5] is Gabriel $\rightarrow$ $\alpha_{35}$ is not modified (NaN) +</text> +<path stroke="darkblue" 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differnew file mode 100644 index 00000000..516de126 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_doc_alpha_shape.png diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 44741e3b..191ff853 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -51,47 +51,105 @@ namespace alphacomplex { #define Kinit(f) =k.f() -/** \defgroup alpha_complex Alpha complex in dimension N - * @{ +/** \tableofcontents + * \defgroup alpha_complex Alpha complex + * * \author Vincent Rouvreau - * - * \section Definition * - * Alpha_complex is a Simplex_tree constructed from each finite cell of a Delaunay Triangulation in dimension N. + * @{ + * + * \section definition Definition + * + * Alpha_complex is a Simplex_tree constructed from each finite cell of a Delaunay Triangulation. * * The filtration value of each simplex is computed from the alpha value of the simplex if it is Gabriel or * from the alpha value of the simplex coface that makes the simplex not Gabriel. * - * Please refer to \cite AlphaShapesDefinition for the alpha complex definition or to - * \cite AlphaShapesIntroduction for alpha complex concept vulgarization. + * Please refer to \cite AlphaShapesDefinition for a more complete alpha complex definition. * - * \section Example + * Alpha complex are interesting because it looks like an \ref alpha-shape "Alpha shape" as described in + * \cite AlphaShapesIntroduction (an alpha complex concept vulgarization). + * + * \section example Example + * + * This example loads points from an OFF file, builds the Delaunay triangulation from the points, and finally + * initialize the alpha complex with it. * - * This example loads points from an OFF file, builds the Delaunay triangulation, and finally initialize the - * alpha complex with it. * Then, it is asked to display information about the alpha complex. * * \include Alpha_complex_from_off.cpp * * When launching: * - * \code $> ./alphaoffreader ../../data/points/alphashapedoc.off + * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off * \endcode * * the program output is: * * \include alphaoffreader_for_doc.txt + * + * \section algorithm Algorithm + * + * <b>Data structure</b> + * + * In order to build the alpha complex, first, a Simplex tree is build from the cells of a Delaunay Triangulation. + * (The filtration value is set to NaN, which stands for unknown value): + * \image html "alpha_complex_doc.png" "Simplex tree structure construction example" + * + * <b>Filtration value computation algorithm</b> + * + * \f{algorithm}{ + * \caption{Filtration value computation algorithm}\label{alpha} + * \begin{algorithmic} + * \For{i : dimension $\rightarrow$ 1} + * \ForAll{$\sigma$ of dimension i} + * \If {filtration($\sigma$) is NaN} + * \State filtration($\sigma$) = $\alpha(\sigma)$ + * \EndIf + * \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value} + * \If {filtration($\tau$) is not NaN} + * \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$)) + * \Else + * \If {$\tau$ is not Gabriel for $\sigma$} + * \State filtration($\tau$) = filtration($\sigma$) + * \EndIf + * \EndIf + * \EndFor + * \EndFor + * \EndFor + * \end{algorithmic} + * \f} + * + * From the example above, it means the algorithm will look into each triangulation ([1,2,3], [2,3,4], [1,3,5], ...), + * will compute the filtration value of the triangulation, and then will propagate the filtration value as described + * here : + * \image html "alpha_complex_doc_135.png" "Filtration value propagation example" + * Then, the algorithm will look into each edge ([1,2], [2,3], [1,3], ...), + * will compute the filtration value of the edge (in this case, propagation will have no effect). + * + * Finally, the algorithm will look into each vertex ([1], [2], [3], [4], [5], [6] and [7]), + * will set the filtration value (0 in case of a vertex - propagation will have no effect). + * + * \section alpha-shape Alpha shape + * + * In the example above, the alpha shape of \f$\alpha_{74} < \alpha < \alpha_{73}\f$ is the alpha complex where the + * \f$\alpha_{74} <\f$ filtration value \f$< \alpha_{73}\f$ as described in \cite AlphaShapesIntroduction + * + * \image html "alpha_complex_doc_alpha_shape.png" "Alpha shape example" + * \copyright GNU General Public License v3. + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim */ /** @} */ // end defgroup alpha_complex /** * \brief Alpha complex data structure. * - * \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation - * induced by the order relation on vertices \f$ v_0 < \cdots < v_d \f$. - * - * Details may be found in \cite boissonnatmariasimplextreealgorithmica. - * + * \details + * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay + * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from + * an OFF file (cf. Delaunay_triangulation_off_reader). + * + * Please refer to \ref alpha_complex for examples. * */ template<typename IndexingTag = linear_indexing_tag, diff --git a/src/Doxyfile b/src/Doxyfile index 49ec4768..a84c4897 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -834,6 +834,7 @@ EXAMPLE_RECURSIVE = NO # \image command). IMAGE_PATH = Skeleton_blocker/doc/ \ + Alpha_complex/doc/ \ common/doc/ \ Contraction/doc/ @@ -1597,7 +1598,7 @@ PAPER_TYPE = a4 # If left blank no extra packages will be included. # This tag requires that the tag GENERATE_LATEX is set to YES. -EXTRA_PACKAGES = amsfonts amsmath amssymb +EXTRA_PACKAGES = amsfonts amsmath amssymb algorithm algpseudocode # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the # generated LaTeX document. The header should contain everything until the first |