diff options
| -rw-r--r-- | src/Bottleneck_distance/doc/Intro_bottleneck_distance.h | 5 | ||||
| -rw-r--r-- | src/Bottleneck_distance/doc/bottleneck_distance_example.ipe | 8 | ||||
| -rw-r--r-- | src/Bottleneck_distance/doc/bottleneck_distance_example.png | bin | 21465 -> 19485 bytes | |||
| -rw-r--r-- | src/common/doc/main_page.md | 4 | ||||
| -rw-r--r-- | src/cython/doc/bottleneck_distance_sum.inc | 4 | ||||
| -rw-r--r-- | src/cython/doc/bottleneck_distance_user.rst | 10 |
6 files changed, 19 insertions, 12 deletions
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 <gudhi/Bottleneck.h> 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 @@ <?xml version="1.0"?> <!DOCTYPE ipe SYSTEM "ipe.dtd"> <ipe version="70206" creator="Ipe 7.2.7"> -<info created="D:20190606115351" modified="D:20190606115351"/> +<info created="D:20190606115351" modified="D:20190607172542"/> <ipestyle name="basic"> <symbol name="arrow/arc(spx)"> <path stroke="sym-stroke" fill="sym-stroke" pen="sym-pen"> @@ -220,13 +220,13 @@ h <dashstyle name="dash dotted" value="[4 2 1 2] 0"/> <dashstyle name="dash dot dotted" value="[4 2 1 2 1 2] 0"/> <textsize name="large" value="\large"/> +<textsize name="small" value="\small"/> +<textsize name="tiny" value="\tiny"/> <textsize name="Large" value="\Large"/> <textsize name="LARGE" value="\LARGE"/> <textsize name="huge" value="\huge"/> <textsize name="Huge" value="\Huge"/> -<textsize name="small" value="\small"/> <textsize name="footnote" value="\footnotesize"/> -<textsize name="tiny" value="\tiny"/> <textstyle name="center" begin="\begin{center}" end="\end{center}"/> <textstyle name="itemize" begin="\begin{itemize}" end="\end{itemize}"/> <textstyle name="item" begin="\begin{itemize}\item{}" end="\end{itemize}"/> @@ -274,7 +274,7 @@ h 224 320 l </path> <text matrix="1 0 0 1 -32 8" transformations="translations" pos="164 248" stroke="red" type="label" width="23.8" height="7.473" depth="2.49" valign="baseline">(0, 0)</text> -<text matrix="1 0 0 1 -4 4" transformations="translations" pos="132 356" stroke="navy" type="label" width="28.781" height="7.473" depth="2.49" valign="baseline">(13, 0)</text> +<text matrix="1 0 0 1 -4 4" transformations="translations" pos="132 356" stroke="navy" type="label" width="28.781" height="7.473" depth="2.49" valign="baseline">(0, 13)</text> <text transformations="translations" pos="216 300" stroke="black" type="label" width="39.297" height="7.473" depth="2.49" valign="baseline">(6.5, 6.5)</text> <path stroke="black" arrow="normal/normal" rarrow="normal/normal"> 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 Binary files differindex b56ee791..1d3b91aa 100644 --- a/src/Bottleneck_distance/doc/bottleneck_distance_example.png +++ b/src/Bottleneck_distance/doc/bottleneck_distance_example.png 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). </td> <td width="15%"> <b>Author:</b> François Godi<br> 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:: |
