diff options
Diffstat (limited to 'src/Nerve_GIC/doc/Intro_graph_induced_complex.h')
| -rw-r--r-- | src/Nerve_GIC/doc/Intro_graph_induced_complex.h | 58 |
1 files changed, 40 insertions, 18 deletions
diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 95c0ca40..c03d37d8 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -33,7 +33,10 @@ namespace graph_induced_complex { * * @{ * - * Visualizations of the simplicial complexes require neato, python and firefox!! + * Visualizations of the simplicial complexes can be done with either + * <a target="_blank" href=""> neato </a>, + * <a target="_blank" href=""> geomview </a>, or + * <a target="_blank" href=""> python </a> + <a target="_blank" href=""> firefox </a>. * * \section covers Covers * @@ -65,19 +68,27 @@ namespace graph_induced_complex { * * When launching: * - * \code $> ./Nerve ../../../data/points/human.off 2 10 0.3 --v + * \code $> ./Nerve ../../../../data/points/human.off 2 10 0.3 --v * \endcode * * the program output is: * * \include Nerve_GIC/Nerve.txt * - * The first three lines are requirements for visualization with Kepler-Mapper. + * The program also writes a file SC.txt. + * The first three lines in this file are requirements for visualization with Kepler-Mapper. * The fourth line contains the number of vertices nv and edges ne of the Nerve. * The next nv lines represent the vertices. Each line contains the vertex ID, * the number of data points it contains, and their average color function value. * Finally, the next ne lines represent the edges, characterized by the ID of their vertices. + * Using e.g. * + * \code $> python visu.py && firefox SC.html + * \endcode + * + * one can obtain the following visualization: + * + * \image html "nervevisu.png" "Visualization with Kepler Mapper" * * \section gic Graph Induced Complexes (GIC) * @@ -90,7 +101,8 @@ namespace graph_induced_complex { * See <a target="_blank" href="https://arxiv.org/abs/1304.0662"> this article </a> * for more details. * - * \image html "gic_complex.png" "GIC of a point cloud." + * \image html "gic_complex.png" "GIC of a point cloud. Image taken from + * <a target="_blank" href="https://arxiv.org/abs/1304.0662"> this article </a>" * * \subsection gicexample Example with cover from function * @@ -105,12 +117,12 @@ namespace graph_induced_complex { * * When launching: * - * \code $> ./GIC ../../../data/points/human.off 0.075 2 0.075 0 --v + * \code $> ./GIC ../../../../data/points/human.off 0.075 2 0.075 0 --v * \endcode * - * the program output is: + * the program outputs SC.txt, which can be visualized with python and firefox as before: * - * \include Nerve_GIC/GIC.txt + * \image html "gicvisu.png" "Visualization with Kepler Mapper" * * \subsection gicexamplevor Example with cover from Voronoï * @@ -124,12 +136,17 @@ namespace graph_induced_complex { * * When launching: * - * \code $> ./GICvoronoi ../../../data/points/human.off 100 --v + * \code $> ./GICvoronoi ../../../../data/points/human.off 100 --v * \endcode * - * the program output is: + * the program outputs SC.off. Using e.g. + * + * \code $> geomview SC.off + * \endcode * - * \include Nerve_GIC/GICvoronoi.txt + * one can obtain the following visualization: + * + * \image html "gicvoronoivisu.png" "Visualization with Geomview" * * \subsection mapperdeltadefinition Mapper Delta * @@ -143,9 +160,9 @@ namespace graph_induced_complex { * * Mapper Delta comes with optimal selection for the Rips threshold, * the resolution and the gain of the function cover. In this example, - * we compute the Mapper Delta of a point cloud sampled on a 3D human shape (human.off), + * we compute the Mapper Delta of a Klein bottle embedded in R^5, * where the graph G comes from a Rips complex with optimal threshold, - * and the cover C comes from the preimages of intervals covering the height function (coordinate 2), + * and the cover C comes from the preimages of intervals covering the first coordinate, * with optimal resolution and gain. Note that optimal threshold, resolution and gain * also exist for the Nerve of this cover. * @@ -153,12 +170,17 @@ namespace graph_induced_complex { * * When launching: * - * \code $> ./MapperDeltaCoord ../../../data/points/human.off 2 --v + * \code $> ./MapperDeltaCoord ../../../../data/points/KleinBottle5D.off 0 --v * \endcode * - * the program output is: + * the program outputs SC.dot. Using e.g. + * + * \code $> neato SC.dot -Tpdf -o SC.pdf + * \endcode + * + * one can obtain the following visualization: * - * \include MapperDeltaCoord.txt + * \image html "mapperdeltacoordvisu2.pdf" "Visualization with Neato" * * We also provide an example on a set of 72 pictures taken around the same object (lucky_cat.off). * The function is now the first eigenfunction given by PCA, whose values @@ -168,12 +190,12 @@ namespace graph_induced_complex { * * When launching: * - * \code $> ./MapperDeltaFunc ../../../data/points/COIL_database/lucky_cat.off ../../../data/points/COIL_database/lucky_cat_PCA1 --v + * \code $> ./MapperDeltaFunc ../../../../data/points/COIL_database/lucky_cat.off ../../../../data/points/COIL_database/lucky_cat_PCA1 --v * \endcode * - * the program output is: + * the program outputs again SC.dot which gives the following visualization after using neato: * - * \include MapperDeltaFunc.dot + * \image html "mapperdeltafuncvisu.pdf" "Visualization with Neato" * * \copyright GNU General Public License v3. * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim |