diff options
author | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-05 08:26:50 +0000 |
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committer | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-05 08:26:50 +0000 |
commit | 300914816e3e5d347efd9eaa5d06c236ad81511e (patch) | |
tree | be2b6484191bd40bfaf66c634889fcb91466282f /src | |
parent | b2160d53d6b94979cb62c0369e62aad83a4cb8c7 (diff) |
Move some utils + update doc so that utilities are shown as examples
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2756 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: a707d174a382da7efad3d12a73bb66d2c90da599
Diffstat (limited to 'src')
-rw-r--r-- | src/Doxyfile | 3 | ||||
-rw-r--r-- | src/Persistent_cohomology/doc/Intro_persistent_cohomology.h | 20 | ||||
-rw-r--r-- | src/Rips_complex/utilities/CMakeLists.txt (renamed from src/Persistent_cohomology/utilities/CMakeLists.txt) | 6 | ||||
-rw-r--r-- | src/Rips_complex/utilities/README (renamed from src/Persistent_cohomology/utilities/README) | 2 | ||||
-rw-r--r-- | src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp (renamed from src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp) | 0 | ||||
-rw-r--r-- | src/Rips_complex/utilities/rips_persistence.cpp (renamed from src/Persistent_cohomology/utilities/rips_persistence.cpp) | 0 | ||||
-rw-r--r-- | src/common/doc/main_page.h | 54 |
7 files changed, 41 insertions, 44 deletions
diff --git a/src/Doxyfile b/src/Doxyfile index 7f5975eb..7b506e42 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -819,7 +819,8 @@ EXCLUDE_SYMBOLS = # command). EXAMPLE_PATH = biblio/ \ - example/ + example/ \ + utilities/ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index e17e5926..576a1af8 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -143,8 +143,8 @@ namespace persistent_cohomology { We provide several example files: run these examples with -h for details on their use, and read the README file. -\li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html"> -Persistent_cohomology/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence +\li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> +Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode \code The complex contains 177838 simplices @@ -158,12 +158,12 @@ diagram. Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html"> -Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and +\li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> +Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and outputs its persistence diagram. -\li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> -Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> +Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 \endcode \code Simplex_tree dim: 3 @@ -194,8 +194,8 @@ and a weights file. 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> -Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with +\li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> +Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. @@ -205,8 +205,8 @@ Simplex_tree dim: 3 2 1 0.0934117 1.00003 2 2 0.56444 1.03938 \endcode -\li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> -Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> +Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. \code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode \code Periodic Delaunay computed. diff --git a/src/Persistent_cohomology/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index 9a506b3f..baa571fa 100644 --- a/src/Persistent_cohomology/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -1,5 +1,5 @@ cmake_minimum_required(VERSION 2.6) -project(Persistent_cohomology_utilities) +project(Rips_complex_utilities) add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) @@ -12,9 +12,9 @@ if (TBB_FOUND) target_link_libraries(rips_persistence ${TBB_LIBRARIES}) endif() -add_test(NAME Persistent_cohomology_example_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence> +add_test(NAME Rips_complex_utility_from_rips_distance_matrix COMMAND $<TARGET_FILE:rips_distance_matrix_persistence> "${CMAKE_SOURCE_DIR}/data/distance_matrix/full_square_distance_matrix.csv" "-r" "1.0" "-d" "3" "-p" "3" "-m" "0") -add_test(NAME Persistent_cohomology_example_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence> +add_test(NAME Rips_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") install(TARGETS rips_distance_matrix_persistence DESTINATION bin) diff --git a/src/Persistent_cohomology/utilities/README b/src/Rips_complex/utilities/README index eecee7ee..ddb7860f 100644 --- a/src/Persistent_cohomology/utilities/README +++ b/src/Rips_complex/utilities/README @@ -1,4 +1,4 @@ -# Persistent_cohomology # +# Rips_complex # ## `rips_persistence` ## This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention: diff --git a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp index d38808c7..d38808c7 100644 --- a/src/Persistent_cohomology/utilities/rips_distance_matrix_persistence.cpp +++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp diff --git a/src/Persistent_cohomology/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp index d504798b..d504798b 100644 --- a/src/Persistent_cohomology/utilities/rips_persistence.cpp +++ b/src/Rips_complex/utilities/rips_persistence.cpp diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index cee0c28b..466236ad 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -271,8 +271,8 @@ make doxygen * * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> @@ -289,10 +289,10 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * @@ -329,12 +329,12 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html"> * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html"> @@ -364,26 +364,24 @@ make doxygen * Alpha_complex/Alpha_complex_from_off.cpp</a> * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html"> * Alpha_complex/Alpha_complex_from_points.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_3d_persistence.cpp</a> + * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> + * Alpha_complex/alpha_complex_persistence.cpp</a> + * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> + * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html"> * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a> * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html"> * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a> * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html"> * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html"> * Simplex_tree/simple_simplex_tree.cpp</a> * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html"> * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a> * \li <a href="_simplex_tree_2simplex_tree_from_cliques_of_graph_8cpp-example.html"> * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> - * Persistent_cohomology/alpha_complex_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_via_boundary_matrix_8cpp-example.html"> * Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp</a> * \li <a href="_persistent_cohomology_2persistence_from_file_8cpp-example.html"> @@ -392,26 +390,24 @@ make doxygen * Persistent_cohomology/persistence_from_simple_simplex_tree.cpp</a> * \li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> * Persistent_cohomology/plain_homology.cpp</a> - * \li <a href="_persistent_cohomology_2rips_distance_matrix_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_distance_matrix_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> * Persistent_cohomology/rips_multifield_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2rips_persistence_8cpp-example.html"> - * Persistent_cohomology/rips_persistence.cpp</a> * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html"> * Persistent_cohomology/rips_persistence_step_by_step.cpp</a> * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html"> * Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp</a> - * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> - * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html"> * Persistent_cohomology/custom_persistence_sort.cpp</a> * \li <a href="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html"> * Rips_complex/example_one_skeleton_rips_from_points.cpp</a> * \li <a href="_rips_complex_2example_rips_complex_from_off_file_8cpp-example.html"> * Rips_complex/example_rips_complex_from_off_file.cpp</a> + * \li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> + * Rips_complex/rips_distance_matrix_persistence.cpp</a> + * \li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> + * Rips_complex/rips_persistence.cpp</a> * * \section Contributions Bug reports and contributions * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to: @@ -436,6 +432,9 @@ make doxygen /*! @file Examples * @example Alpha_complex/Alpha_complex_from_off.cpp * @example Alpha_complex/Alpha_complex_from_points.cpp + * @example Alpha_complex/alpha_complex_3d_persistence.cpp + * @example Alpha_complex/alpha_complex_persistence.cpp + * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp * @example Bottleneck_distance/bottleneck_basic_example.cpp * @example Bottleneck_distance/bottleneck_read_file_example.cpp @@ -446,22 +445,19 @@ make doxygen * @example common/example_CGAL_points_off_reader.cpp * @example Contraction/Garland_heckbert.cpp * @example Contraction/Rips_contraction.cpp - * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/alpha_complex_persistence.cpp * @example Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp * @example Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp - * @example Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp * @example Persistent_cohomology/persistence_from_file.cpp * @example Persistent_cohomology/persistence_from_simple_simplex_tree.cpp * @example Persistent_cohomology/plain_homology.cpp * @example Persistent_cohomology/rips_multifield_persistence.cpp - * @example Persistent_cohomology/rips_distance_matrix_persistence.cpp - * @example Persistent_cohomology/rips_persistence.cpp * @example Persistent_cohomology/custom_persistence_sort.cpp * @example Persistent_cohomology/rips_persistence_step_by_step.cpp * @example Rips_complex/example_one_skeleton_rips_from_points.cpp * @example Rips_complex/example_rips_complex_from_off_file.cpp + * @example Rips_complex/rips_persistence.cpp + * @example Rips_complex/rips_distance_matrix_persistence.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp |