From 1aaa09bab10ccc6ca56e31b1f49f420aad5d6f50 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Fri, 3 Mar 2017 10:47:59 +0000 Subject: changes to the doc, towards building a doc... git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2145 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ced0884e23fdac7301bc379c8533bb3b2fc4ae53 --- src/cmake/modules/GUDHI_user_version_target.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/cmake/modules') diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 805f0a83..0d0b8767 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -48,7 +48,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) - set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex") + set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex;Gudhi_stat") foreach(GUDHI_MODULE ${GUDHI_MODULES}) # doc files -- cgit v1.2.3 From ca2ad986b9925ab7006597f0f7045f7be47a42b2 Mon Sep 17 00:00:00 2001 From: pdlotko Date: Fri, 7 Apr 2017 09:10:52 +0000 Subject: Answers to Marc's comments git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/gudhi_stat@2317 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f941a6b20210282408d0ef95b84daa973add2513 --- biblio/bibliography.bib | 16 ++++++++-------- .../Persistence_landscape_on_grid.h | 8 +++++--- src/cmake/modules/GUDHI_user_version_target.txt | 2 +- src/common/doc/main_page.h | 17 +++++++++++++++++ src/cython/doc/img/average_landscape.png | Bin 0 -> 14917 bytes 5 files changed, 31 insertions(+), 12 deletions(-) create mode 100644 src/cython/doc/img/average_landscape.png (limited to 'src/cmake/modules') diff --git a/biblio/bibliography.bib b/biblio/bibliography.bib index dbd0cb42..37aa8198 100644 --- a/biblio/bibliography.bib +++ b/biblio/bibliography.bib @@ -988,14 +988,14 @@ language={English} } @ARTICLE{bubenik_dlotko_landscapes_2016, - author = {P. Bubenik, P. Dlotko}, + author = {P. Bubenik and P. Dlotko}, title = {A persistence landscapes toolbox for topological statistics.}, journal = {Journal of Symbolic Computation.}, year = {2016} } @ARTICLE{Fasy_Kim_Lecci_Maria_tda, - author = {B. Fasy, J. Kim, F. Lecci, C. Maria}, + author = {B. Fasy and J. Kim and F. Lecci and C. Maria}, title = {Introduction to the R package TDA.}, journal = {arXiv:1411.1830.}, year = {2016} @@ -1003,7 +1003,7 @@ language={English} @ARTICLE{Ferri_Frosini_comparision_sheme_1, - author = {P. Donatini, P. Frosini, A. Lovato}, + author = {P. Donatini and P. Frosini and A. Lovato}, title = {Size functions for signature recognition.}, journal = {Proceedings of SPIE, Vision Geometry VII, vol. 3454}, year = {1998} @@ -1011,14 +1011,14 @@ language={English} @ARTICLE{Ferri_Frosini_comparision_sheme_2, - author = {M. Ferri, P. Frosini, A. Lovato, C. Zambelli}, + author = {M. Ferri and P. Frosini and A. Lovato and C. Zambelli}, title = {Point selection: A new comparison scheme for size functions (With an application to monogram recognition).}, journal = {Proceedings Third Asian Conference on Computer Vision, Lecture Notes in Computer Science 1351.}, year = {1998} } @ARTICLE{Persistence_Images_2017, - author = {H. Adams, S. Chepushtanova, T. Emerson, E. Hanson, M. Kirby, F. Motta, R. Neville, C. Peterson, P. Shipman, L. Ziegelmeier}, + author = {H. Adams and S. Chepushtanova and T. Emerson and E. Hanson and M. Kirby and F. Motta and R. Neville and C. Peterson and P. Shipman and L. Ziegelmeier}, title = {Persistence Images: A Stable Vector Representation of Persistent Homology.}, journal = {Journal of Machine Learning Research}, year = {2017} @@ -1026,21 +1026,21 @@ language={English} @ARTICLE{Kusano_Fukumizu_Hiraoka_PWGK, - author = {G. Kusano, K. Fukumizu, Y. Hiraoka}, + author = {G. Kusano and K. Fukumizu and Y. Hiraoka}, title = {Persistence weighted Gaussian kernel for topological data analysis.}, journal = {ICML'16 Proceedings of the 33rd International Conference on International Conference on Machine Learning - Volume 48}, year = {2016} } @ARTICLE{Reininghaus_Huber_ALL_PSSK, - author = {J. Reininghaus, S. Huber, U. Bauer, R. Kwitt}, + author = {J. Reininghaus and S. Huber and U. Bauer and R. Kwitt}, title = {A Stable Multi-Scale Kernel for Topological Machine Learning.}, journal = {Proc. 2015 IEEE Conf. Comp. Vision & Pat. Rec. (CVPR '15)}, year = {2015} } @ARTICLE{Carriere_Oudot_Ovsjanikov_top_signatures_3d, - author = {M. Carrière, S. Oudot, M. Ovsjanikov}, + author = {M. Carrière and S. Oudot and M. Ovsjanikov}, title = {Stable Topological Signatures for Points on 3D Shapes.}, journal = {Proc. Sympos. on Geometry Processing}, year = {2015} diff --git a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h index 422699ef..b70ef1d9 100644 --- a/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h +++ b/src/Gudhi_stat/include/gudhi/persistence_representations/Persistence_landscape_on_grid.h @@ -313,8 +313,11 @@ public: //compute the value of the linear function parametrized by line on a point x: return line.first*x+line.second; } + + protected: + template < typename oper > friend Persistence_landscape_on_grid operation_on_pair_of_landscapes_on_grid( const Persistence_landscape_on_grid& land1 , const Persistence_landscape_on_grid& land2 ); - + public: /** *\private A function that compute sum of two landscapes. **/ @@ -1024,8 +1027,7 @@ protected: this->number_of_functions_for_projections_to_reals = this->values_of_landscapes.size(); } - void set_up_values_of_landscapes( const std::vector< std::pair< double , double > >& p , double grid_min_ , double grid_max_ , size_t number_of_points_ ); - template < typename oper > friend Persistence_landscape_on_grid operation_on_pair_of_landscapes_on_grid( const Persistence_landscape_on_grid& land1 , const Persistence_landscape_on_grid& land2 ); + void set_up_values_of_landscapes( const std::vector< std::pair< double , double > >& p , double grid_min_ , double grid_max_ , size_t number_of_points_ ); Persistence_landscape_on_grid multiply_lanscape_by_real_number_not_overwrite( double x )const; }; diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index b6a60dd1..a971f1d9 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -50,7 +50,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Gudhi_stat;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex") - set(GUDHI_DIRECTORIES "doc;example;concept") + set(GUDHI_DIRECTORIES "doc;example;concept;utilities") set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") foreach(GUDHI_MODULE ${GUDHI_MODULES}) diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index e6f29fa8..55673f60 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -151,6 +151,23 @@ + + \subsection Gudhi_stat Gudhi statistical sublibrary + \image html "average_landscape.png" "Gudhi statistical sublibrary" + + + + + +
+ Author: Pawel Dlotko
+ Introduced in: GUDHI 2.0.0
+ Copyright: GPL v3
+ 		+ This is a statistical library for gudhi. It contain 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. + User manual: \ref gudhi_stat - Reference manual: Gudhi::Gudhi_stat +
\section Toolbox Toolbox \subsection BottleneckDistanceToolbox Bottleneck distance diff --git a/src/cython/doc/img/average_landscape.png b/src/cython/doc/img/average_landscape.png new file mode 100644 index 00000000..ea59926b Binary files /dev/null and b/src/cython/doc/img/average_landscape.png differ -- cgit v1.2.3