From 093866604f986dded2db6a96d7dbc4b6d1f7194a Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Wed, 5 Jul 2017 15:03:57 +0000 Subject: Fix default filtration value given by the graph_expansion method with blocker git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/graph_expansion_with_blocker_oracle@2585 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 38586e3c9a622c74c6b6658bdc0a6776c5ea5d5a --- src/Simplex_tree/example/CMakeLists.txt | 17 -- src/Simplex_tree/example/block.cpp | 30 ++- .../example/cech_complex_step_by_step.cpp | 230 --------------------- 3 files changed, 12 insertions(+), 265 deletions(-) delete mode 100644 src/Simplex_tree/example/cech_complex_step_by_step.cpp (limited to 'src/Simplex_tree/example') diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index 7a30979f..4557deb3 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -34,25 +34,8 @@ if(GMP_FOUND AND CGAL_FOUND) "${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off") install(TARGETS Simplex_tree_example_alpha_shapes_3_from_off DESTINATION bin) - - # - # TO BE REMOVED !! - # - - add_executable ( Simplex_tree_example_cech_complex_step_by_step cech_complex_step_by_step.cpp ) - target_link_libraries(Simplex_tree_example_cech_complex_step_by_step ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(Simplex_tree_example_cech_complex_step_by_step ${TBB_LIBRARIES}) - endif() - add_test(NAME Simplex_tree_example_cech_complex_step_by_step COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "-d" "3" "-r" "6.0") - endif() -# -# TO BE REMOVED !! -# - add_executable ( Simplex_tree_example_block block.cpp ) if (TBB_FOUND) target_link_libraries(Simplex_tree_example_block ${TBB_LIBRARIES}) diff --git a/src/Simplex_tree/example/block.cpp b/src/Simplex_tree/example/block.cpp index 75b8d1ea..67697b89 100644 --- a/src/Simplex_tree/example/block.cpp +++ b/src/Simplex_tree/example/block.cpp @@ -24,15 +24,13 @@ #include #include -#include // for pair -#include using Simplex_tree = Gudhi::Simplex_tree<>; using Simplex_handle = Simplex_tree::Simplex_handle; int main(int argc, char * const argv[]) { - // Construct the Simplex Tree + // Construct the Simplex Tree with a 1-skeleton graph example Simplex_tree simplexTree; simplexTree.insert_simplex({0, 1}, 0.); @@ -46,31 +44,27 @@ int main(int argc, char * const argv[]) { simplexTree.insert_simplex({4, 5}, 8.); simplexTree.insert_simplex({4, 6}, 9.); simplexTree.insert_simplex({5, 6}, 10.); - simplexTree.insert_simplex({6}, 11.); - - std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n"; - std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << "\n"; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : simplexTree.filtration_simplex_range()) { - std::cout << " " << "[" << simplexTree.filtration(f_simplex) << "] "; - for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) - std::cout << "(" << vertex << ")"; - std::cout << std::endl; - } + simplexTree.insert_simplex({6}, 10.); simplexTree.expansion_with_blockers(3, [&](Simplex_handle sh){ bool result = false; + std::cout << "Blocker on ["; + // User can loop on the vertices from the given simplex_handle i.e. for (auto vertex : simplexTree.simplex_vertex_range(sh)) { + // We block the expansion, if the vertex '6' is in the given list of vertices if (vertex == 6) result = true; - std::cout << "#(" << vertex << ")#"; + std::cout << vertex << ", "; } - std::cout << std::endl; + std::cout << "] ( " << simplexTree.filtration(sh); + // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries) + simplexTree.assign_filtration(sh, simplexTree.filtration(sh) + 1.); + + std::cout << " + 1. ) = " << result << std::endl; + return result; }); - simplexTree.initialize_filtration(); std::cout << "********************************************************************\n"; std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices\n"; std::cout << " - dimension " << simplexTree.dimension() << " - filtration " << simplexTree.filtration() << "\n"; diff --git a/src/Simplex_tree/example/cech_complex_step_by_step.cpp b/src/Simplex_tree/example/cech_complex_step_by_step.cpp deleted file mode 100644 index 1805c792..00000000 --- a/src/Simplex_tree/example/cech_complex_step_by_step.cpp +++ /dev/null @@ -1,230 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Clément Maria - * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include -#include -#include - -// #include -// #include -// #include -#include -#include -#include - -#include - -#include -#include -#include // infinity -#include // for pair -#include - -// ---------------------------------------------------------------------------- -// rips_persistence_step_by_step is an example of each step that is required to -// build a Rips over a Simplex_tree. Please refer to rips_persistence to see -// how to do the same thing with the Rips_complex wrapper for less detailed -// steps. -// ---------------------------------------------------------------------------- - -// Types definition -using Simplex_tree = Gudhi::Simplex_tree; -using Vertex_handle = Simplex_tree::Vertex_handle; -using Simplex_handle = Simplex_tree::Simplex_handle; -using Filtration_value = Simplex_tree::Filtration_value; -using Siblings = Simplex_tree::Siblings; -using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS -, boost::property < vertex_filtration_t, Filtration_value > -, boost::property < edge_filtration_t, Filtration_value > ->; -using Edge_t = std::pair< Vertex_handle, Vertex_handle >; - -using Kernel = CGAL::Epick_d< CGAL::Dimension_tag<2> >;// CGAL::Dynamic_dimension_tag >; -using Point = Kernel::Point_d; -using Traits = CGAL::Min_sphere_of_points_d_traits_d; -using Min_sphere = CGAL::Min_sphere_of_spheres_d; - -using Points_off_reader = Gudhi::Points_off_reader; - -class Cech_blocker { - public: - bool operator()(Simplex_handle sh) { - std::vector points; - for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) { - points.push_back(point_cloud_[vertex]); - std::cout << "#(" << vertex << ")#"; - } - Min_sphere ms(points.begin(),points.end()); - Filtration_value radius = ms.radius(); - std::cout << "radius = " << radius << " - " << (radius > threshold_) << std::endl; - simplex_tree_.assign_filtration(sh, radius); - return (radius > threshold_); - } - Cech_blocker(Simplex_tree& simplex_tree, Filtration_value threshold, const std::vector& point_cloud) - : simplex_tree_(simplex_tree), - threshold_(threshold), - point_cloud_(point_cloud) { } - private: - Simplex_tree simplex_tree_; - Filtration_value threshold_; - std::vector point_cloud_; -}; - -template< typename InputPointRange> -Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold); - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , Filtration_value & threshold - , int & dim_max); - -int main(int argc, char * argv[]) { - std::string off_file_points; - Filtration_value threshold; - int dim_max; - - program_options(argc, argv, off_file_points, threshold, dim_max); - - // Extract the points from the file filepoints - Points_off_reader off_reader(off_file_points); - - // Compute the proximity graph of the points - Graph_t prox_graph = compute_proximity_graph(off_reader.get_point_cloud(), threshold); - - //Min_sphere sph1(off_reader.get_point_cloud()[0], off_reader.get_point_cloud()[1], off_reader.get_point_cloud()[2]); - // Construct the Rips complex in a Simplex Tree - Simplex_tree st; - // insert the proximity graph in the simplex tree - st.insert_graph(prox_graph); - // expand the graph until dimension dim_max - st.expansion_with_blockers(dim_max, Cech_blocker(st, threshold, off_reader.get_point_cloud())); - - std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << st.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - - std::cout << "********************************************************************\n"; - // Display the Simplex_tree - Can not be done in the middle of 2 inserts - std::cout << "* The complex contains " << st.num_simplices() << " simplices\n"; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << "\n"; - std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : st.filtration_simplex_range()) { - std::cout << " " << "[" << st.filtration(f_simplex) << "] "; - for (auto vertex : st.simplex_vertex_range(f_simplex)) { - std::cout << static_cast(vertex) << " "; - } - std::cout << std::endl; - } - - return 0; -} - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , Filtration_value & threshold - , int & dim_max) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&off_file_points), - "Name of an OFF file containing a point set.\n"); - - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("max-edge-length,r", - po::value(&threshold)->default_value(std::numeric_limits::infinity()), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute."); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Construct a Cech complex defined on a set of input points.\n \n"; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} - -/** Output the proximity graph of the points. - * - * If points contains n elements, the proximity graph is the graph - * with n vertices, and an edge [u,v] iff the distance function between - * points u and v is smaller than threshold. - * - * The type PointCloud furnishes .begin() and .end() methods, that return - * iterators with value_type Point. - */ -template< typename InputPointRange> -Graph_t compute_proximity_graph(InputPointRange &points, Filtration_value threshold) { - std::vector< Edge_t > edges; - std::vector< Filtration_value > edges_fil; - - Kernel k; - Vertex_handle idx_u, idx_v; - Filtration_value fil; - idx_u = 0; - for (auto it_u = points.begin(); it_u != points.end(); ++it_u) { - idx_v = idx_u + 1; - for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) { - fil = k.squared_distance_d_object()(*it_u, *it_v); - // For Cech Complex, threshold is a radius (distance /2) - fil = std::sqrt(fil) / 2.; - if (fil <= threshold) { - edges.emplace_back(idx_u, idx_v); - edges_fil.push_back(fil); - } - } - ++idx_u; - } - - Graph_t skel_graph(edges.begin() - , edges.end() - , edges_fil.begin() - , idx_u); // number of points labeled from 0 to idx_u-1 - - auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph); - - boost::graph_traits::vertex_iterator vi, vi_end; - for (std::tie(vi, vi_end) = boost::vertices(skel_graph); - vi != vi_end; ++vi) { - boost::put(vertex_prop, *vi, 0.); - } - - return skel_graph; -} -- cgit v1.2.3