From 4e33acbac51c8c2348dc88a16eb38e14c8ef724a Mon Sep 17 00:00:00 2001 From: Marc Glisse Date: Wed, 5 Jun 2019 09:46:58 +0200 Subject: typo --- src/common/doc/main_page.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'src/common/doc/main_page.md') diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index e61eee81..88e761df 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -374,8 +374,8 @@ 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. + landscapes (rigorous and grid version), persistence heat maps, vectors and others. It implements basic + functionalities which are necessary to use persistence in statistics and machine learning. Author: Pawel Dlotko
-- cgit v1.2.3 From 4b401e9a51cbcbb44d47f4819b57ec7787088df4 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 7 Jun 2019 17:27:29 +0200 Subject: Fix doc review. Add citations for python doc version. Replace (13,0) with (0,13) in figure --- .../doc/Intro_bottleneck_distance.h | 5 +++-- .../doc/bottleneck_distance_example.ipe | 8 ++++---- .../doc/bottleneck_distance_example.png | Bin 21465 -> 19485 bytes src/common/doc/main_page.md | 4 +++- src/cython/doc/bottleneck_distance_sum.inc | 4 ++-- src/cython/doc/bottleneck_distance_user.rst | 10 +++++++--- 6 files changed, 19 insertions(+), 12 deletions(-) (limited to 'src/common/doc/main_page.md') diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 520aab4f..7cb0752e 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -40,7 +40,8 @@ namespace persistence_diagram { * * The bottleneck distance measures the similarity between two persistence diagrams. It is the shortest distance b for * which there exists a perfect matching between the points of the two diagrams (completed with all the points on the - * diagonal in order to ignore cardinality mismatchs) such that any couple of matched points are at distance at most b. + * diagonal in order to ignore cardinality mismatchs) such that any couple of matched points are at distance at most b, + * where the distance between points is the sup norm in \f$\mathbb{R}^2\f$ (not the Euclidean distance). * * \image html perturb_pd.png On this picture, the red edges represent the matching. The bottleneck distance is the length of the longest edge. * @@ -50,7 +51,7 @@ namespace persistence_diagram { * * \section bottleneckdistanceprecision Distance computation * - * Bottleneck distance does not use Euclidean distance, like explained in the following example: + * The following example explains how the distance is computed: * * \code{.cpp} #include diff --git a/src/Bottleneck_distance/doc/bottleneck_distance_example.ipe b/src/Bottleneck_distance/doc/bottleneck_distance_example.ipe index 9dc5420e..2033ea56 100644 --- a/src/Bottleneck_distance/doc/bottleneck_distance_example.ipe +++ b/src/Bottleneck_distance/doc/bottleneck_distance_example.ipe @@ -1,7 +1,7 @@ - + @@ -220,13 +220,13 @@ h + + - - @@ -274,7 +274,7 @@ h 224 320 l (0, 0) -(13, 0) +(0, 13) (6.5, 6.5) 160.433 359.995 m diff --git a/src/Bottleneck_distance/doc/bottleneck_distance_example.png b/src/Bottleneck_distance/doc/bottleneck_distance_example.png index b56ee791..1d3b91aa 100644 Binary files a/src/Bottleneck_distance/doc/bottleneck_distance_example.png and b/src/Bottleneck_distance/doc/bottleneck_distance_example.png differ diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index e61eee81..a0a3496d 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -349,7 +349,9 @@ 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. + any couple of matched points are at distance at most b, + where the distance between points is the sup norm in \f$\mathbb{R}^2\f$ + (not the Euclidean distance). Author: François Godi
diff --git a/src/cython/doc/bottleneck_distance_sum.inc b/src/cython/doc/bottleneck_distance_sum.inc index 41b9c5a3..6840e838 100644 --- a/src/cython/doc/bottleneck_distance_sum.inc +++ b/src/cython/doc/bottleneck_distance_sum.inc @@ -6,8 +6,8 @@ | ../../doc/Bottleneck_distance/perturb_pd.png | diagrams. It's the shortest distance b for which there exists a | | | :figclass: align-center | perfect matching between the points of the two diagrams (+ all the | :Introduced in: GUDHI 2.0.0 | | | diagonal points) such that any couple of matched points are at | | - | Bottleneck distance is the length of | distance at most b. | :Copyright: GPL v3 | - | the longest edge | | | + | Bottleneck distance is the length of | distance at most b, where the distance between points is the sup | :Copyright: GPL v3 | + | the longest edge | norm in :math:`\mathbb{R}^2`. | | | | | :Requires: CGAL :math:`\geq` 4.8.0 | +-----------------------------------------------------------------+----------------------------------------------------------------------+-----------------------------------------------+ | * :doc:`bottleneck_distance_user` | | diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst index a6a4426f..9435c7f1 100644 --- a/src/cython/doc/bottleneck_distance_user.rst +++ b/src/cython/doc/bottleneck_distance_user.rst @@ -9,6 +9,10 @@ Definition .. include:: bottleneck_distance_sum.inc +This implementation is based on ideas from "Geometry Helps in Bottleneck Matching and Related Problems" +:cite:`DBLP:journals/algorithmica/EfratIK01`. Another relevant publication, although it was not used is +"Geometry Helps to Compare Persistence Diagrams" :cite:`Kerber:2017:GHC:3047249.3064175`. + Function -------- .. autofunction:: gudhi.bottleneck_distance @@ -16,7 +20,7 @@ Function Distance computation -------------------- -Bottleneck distance does not use Euclidean distance, like explained in the following example: +The following example explains how the distance is computed: .. testcode:: @@ -33,14 +37,14 @@ Bottleneck distance does not use Euclidean distance, like explained in the follo ../../doc/Bottleneck_distance/bottleneck_distance_example.png :figclass: align-center - The point (0, 13) is at 6.5 distance from the diagonal and more + The point (0, 13) is at distance 6.5 from the diagonal and more specifically from the point (6.5, 6.5) Basic example ------------- -This another example computes the bottleneck distance from 2 persistence diagrams: +This other example computes the bottleneck distance from 2 persistence diagrams: .. testcode:: -- cgit v1.2.3 From 27d0f9c592181845e38f85da6a62c6a129b56122 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 12 Jun 2019 07:50:39 +0200 Subject: Remove references manual --- src/common/doc/main_page.md | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) (limited to 'src/common/doc/main_page.md') diff --git a/src/common/doc/main_page.md b/src/common/doc/main_page.md index 88e761df..47d0583a 100644 --- a/src/common/doc/main_page.md +++ b/src/common/doc/main_page.md @@ -24,7 +24,7 @@ - User manual: \ref cubical_complex - Reference manual: Gudhi::cubical_complex::Bitmap_cubical_complex + User manual: \ref cubical_complex @@ -57,8 +57,7 @@ - User manual: \ref alpha_complex - Reference manual: Gudhi::alpha_complex::Alpha_complex and - Gudhi::alpha_complex::Alpha_complex_3d + User manual: \ref alpha_complex @@ -82,7 +81,7 @@ - User manual: \ref cech_complex - Reference manual: Gudhi::cech_complex::Cech_complex + User manual: \ref cech_complex @@ -108,7 +107,7 @@ - User manual: \ref rips_complex - Reference manual: Gudhi::rips_complex::Rips_complex + User manual: \ref rips_complex @@ -133,7 +132,7 @@ - User manual: \ref witness_complex - Reference manual: Gudhi::witness_complex::SimplicialComplexForWitness + User manual: \ref witness_complex @@ -149,7 +148,6 @@ 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.
- User manual: \ref cover_complex - Reference manual: Gudhi::cover_complex::Cover_complex Author: Mathieu Carrière
@@ -160,7 +158,7 @@ - User manual: \ref cover_complex - Reference manual: Gudhi::cover_complex::Cover_complex + User manual: \ref cover_complex @@ -188,7 +186,7 @@ - User manual: \ref simplex_tree - Reference manual: Gudhi::Simplex_tree + User manual: \ref simplex_tree @@ -216,7 +214,7 @@ - User manual: \ref skbl - Reference manual: Gudhi::skeleton_blocker::Skeleton_blocker_complex + User manual: \ref skbl @@ -241,7 +239,7 @@ - User manual: \ref toplex_map - Reference manual: Gudhi::Toplex_map + User manual: \ref toplex_map @@ -301,7 +299,7 @@ - User manual: \ref persistent_cohomology - Reference manual: Gudhi::persistent_cohomology::Persistent_cohomology + User manual: \ref persistent_cohomology @@ -331,7 +329,7 @@ - User manual: \ref tangential_complex - Reference manual: Gudhi::tangential_complex::Tangential_complex + User manual: \ref tangential_complex -- cgit v1.2.3