diff options
Diffstat (limited to 'src')
26 files changed, 511 insertions, 124 deletions
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index ccc3d852..b3dbc9bb 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -12,7 +12,6 @@ #ifndef ALPHA_COMPLEX_3D_H_ #define ALPHA_COMPLEX_3D_H_ -#include <boost/version.hpp> #include <boost/variant.hpp> #include <boost/range/size.hpp> #include <boost/range/combine.hpp> @@ -58,8 +57,6 @@ namespace Gudhi { namespace alpha_complex { -thread_local double RELATIVE_PRECISION_OF_TO_DOUBLE = 0.00001; - // Value_from_iterator returns the filtration value from an iterator on alpha shapes values // // FAST SAFE EXACT diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index 85790baf..d48f6616 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -1283,6 +1283,7 @@ class Simplex_tree { Siblings * new_sib = new Siblings(siblings, // oncles simplex->first, // parent boost::adaptors::reverse(intersection)); // boost::container::ordered_unique_range_t + simplex->second.assign_children(new_sib); std::vector<Vertex_handle> blocked_new_sib_vertex_list; // As all intersections are inserted, we can call the blocker function on all new_sib members for (auto new_sib_member = new_sib->members().begin(); @@ -1305,7 +1306,6 @@ class Simplex_tree { new_sib->members().erase(blocked_new_sib_member); } // ensure recursive call - simplex->second.assign_children(new_sib); siblings_expansion_with_blockers(new_sib, max_dim, k - 1, block_simplex); } } else { diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index ee64a277..e5522cc7 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -14,7 +14,6 @@ #include <gudhi/Debug_utils.h> #include <boost/iterator/iterator_facade.hpp> -#include <boost/version.hpp> #include <boost/container/static_vector.hpp> #include <vector> diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index cf2b0153..25b562e0 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -34,3 +34,9 @@ if (TBB_FOUND) target_link_libraries(Simplex_tree_make_filtration_non_decreasing_test_unit ${TBB_LIBRARIES}) endif() gudhi_add_boost_test(Simplex_tree_make_filtration_non_decreasing_test_unit) + +add_executable ( Simplex_tree_graph_expansion_test_unit simplex_tree_graph_expansion_unit_test.cpp ) +if (TBB_FOUND) + target_link_libraries(Simplex_tree_graph_expansion_test_unit ${TBB_LIBRARIES}) +endif() +gudhi_add_boost_test(Simplex_tree_graph_expansion_test_unit) diff --git a/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp index 881a06ae..6d63d8ae 100644 --- a/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp +++ b/src/Simplex_tree/test/simplex_tree_graph_expansion_unit_test.cpp @@ -9,33 +9,62 @@ */ #include <iostream> -#include <fstream> -#include <string> -#include <algorithm> -#include <utility> // std::pair, std::make_pair -#include <cmath> // float comparison -#include <limits> -#include <functional> // greater +#include <vector> #define BOOST_TEST_DYN_LINK -#define BOOST_TEST_MODULE "simplex_tree" +#define BOOST_TEST_MODULE "simplex_tree_graph_expansion" #include <boost/test/unit_test.hpp> #include <boost/mpl/list.hpp> -// ^ -// /!\ Nothing else from Simplex_tree shall be included to test includes are well defined. #include "gudhi/Simplex_tree.h" +#include <gudhi/Unitary_tests_utils.h> using namespace Gudhi; typedef boost::mpl::list<Simplex_tree<>, Simplex_tree<Simplex_tree_options_fast_persistence>> list_of_tested_variants; +BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_all_is_blocked, typeST, list_of_tested_variants) { + std::clog << "********************************************************************\n"; + std::clog << "simplex_tree_expansion_all_is_blocked\n"; + std::clog << "********************************************************************\n"; + using Simplex_handle = typename typeST::Simplex_handle; + // Construct the Simplex Tree with a 1-skeleton graph example + typeST simplex_tree; + + simplex_tree.insert_simplex({0, 1}, 0.); + simplex_tree.insert_simplex({0, 2}, 1.); + simplex_tree.insert_simplex({0, 3}, 2.); + simplex_tree.insert_simplex({1, 2}, 3.); + simplex_tree.insert_simplex({1, 3}, 4.); + simplex_tree.insert_simplex({2, 3}, 5.); + simplex_tree.insert_simplex({2, 4}, 6.); + simplex_tree.insert_simplex({3, 6}, 7.); + simplex_tree.insert_simplex({4, 5}, 8.); + simplex_tree.insert_simplex({4, 6}, 9.); + simplex_tree.insert_simplex({5, 6}, 10.); + simplex_tree.insert_simplex({6}, 10.); -bool AreAlmostTheSame(float a, float b) { - return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); + typeST stree_copy = simplex_tree; + + simplex_tree.expansion_with_blockers(3, [&](Simplex_handle sh){ return true; }); + + std::clog << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; + std::clog << " - dimension " << simplex_tree.dimension() << "\n"; + std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + std::clog << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) + std::clog << "(" << vertex << ")"; + std::clog << std::endl; + } + + BOOST_CHECK(stree_copy == simplex_tree); } BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_3, typeST, list_of_tested_variants) { + std::clog << "********************************************************************\n"; + std::clog << "simplex_tree_expansion_with_blockers_3\n"; + std::clog << "********************************************************************\n"; using Simplex_handle = typename typeST::Simplex_handle; // Construct the Simplex Tree with a 1-skeleton graph example typeST simplex_tree; @@ -72,9 +101,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_3, typeST, li return result; }); - std::clog << "********************************************************************\n"; - std::clog << "simplex_tree_expansion_with_blockers_3\n"; - std::clog << "********************************************************************\n"; std::clog << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; std::clog << " - dimension " << simplex_tree.dimension() << "\n"; std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; @@ -89,15 +115,23 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_3, typeST, li BOOST_CHECK(simplex_tree.dimension() == 3); // {4, 5, 6} shall be blocked BOOST_CHECK(simplex_tree.find({4, 5, 6}) == simplex_tree.null_simplex()); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,2})), 4.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,3})), 5.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,2,3})), 6.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({1,2,3})), 6.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,2,3})), 7.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,2})), + static_cast<typename typeST::Filtration_value>(4.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,3})), + static_cast<typename typeST::Filtration_value>(5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,2,3})), + static_cast<typename typeST::Filtration_value>(6.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({1,2,3})), + static_cast<typename typeST::Filtration_value>(6.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,2,3})), + static_cast<typename typeST::Filtration_value>(7.)); } BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_2, typeST, list_of_tested_variants) { + std::clog << "********************************************************************\n"; + std::clog << "simplex_tree_expansion_with_blockers_2\n"; + std::clog << "********************************************************************\n"; using Simplex_handle = typename typeST::Simplex_handle; // Construct the Simplex Tree with a 1-skeleton graph example typeST simplex_tree; @@ -134,9 +168,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_2, typeST, li return result; }); - std::clog << "********************************************************************\n"; - std::clog << "simplex_tree_expansion_with_blockers_2\n"; - std::clog << "********************************************************************\n"; std::clog << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; std::clog << " - dimension " << simplex_tree.dimension() << "\n"; std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; @@ -151,14 +182,22 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_blockers_2, typeST, li BOOST_CHECK(simplex_tree.dimension() == 2); // {4, 5, 6} shall be blocked BOOST_CHECK(simplex_tree.find({4, 5, 6}) == simplex_tree.null_simplex()); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,2})), 4.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,3})), 5.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,2,3})), 6.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({1,2,3})), 6.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,2})), + static_cast<typename typeST::Filtration_value>(4.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,3})), + static_cast<typename typeST::Filtration_value>(5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,2,3})), + static_cast<typename typeST::Filtration_value>(6.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({1,2,3})), + static_cast<typename typeST::Filtration_value>(6.)); BOOST_CHECK(simplex_tree.find({0,1,2,3}) == simplex_tree.null_simplex()); } -BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion, typeST, list_of_tested_variants) { +BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_with_find_simplex_blockers, typeST, list_of_tested_variants) { + std::clog << "********************************************************************\n"; + std::clog << "simplex_tree_expansion_with_find_simplex_blockers\n"; + std::clog << "********************************************************************\n"; + using Simplex_handle = typename typeST::Simplex_handle; // Construct the Simplex Tree with a 1-skeleton graph example typeST simplex_tree; @@ -175,10 +214,66 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion, typeST, list_of_tested_var simplex_tree.insert_simplex({5, 6}, 10.); simplex_tree.insert_simplex({6}, 10.); - simplex_tree.expansion(3); + simplex_tree.expansion_with_blockers(3, [&](Simplex_handle sh){ + bool result = false; + std::clog << "Blocker on ["; + std::vector<typename typeST::Vertex_handle> simplex; + // User can loop on the vertices from the given simplex_handle i.e. + for (auto vertex : simplex_tree.simplex_vertex_range(sh)) { + // We block the expansion, if the vertex '1' is in the given list of vertices + if (vertex == 1) + result = true; + std::clog << vertex << ", "; + simplex.push_back(vertex); + } + std::clog << "] => " << result << std::endl; + // Not efficient but test it works - required by the python interface + BOOST_CHECK(simplex_tree.find(simplex) == sh); + return result; + }); + + std::clog << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; + std::clog << " - dimension " << simplex_tree.dimension() << "\n"; + std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + std::clog << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) + std::clog << "(" << vertex << ")"; + std::clog << std::endl; + } + + BOOST_CHECK(simplex_tree.num_simplices() == 20); + BOOST_CHECK(simplex_tree.dimension() == 2); + + // {1, 2, 3}, {0, 1, 2} and {0, 1, 3} shall be blocked as it contains vertex 1 + BOOST_CHECK(simplex_tree.find({4, 5, 6}) != simplex_tree.null_simplex()); + BOOST_CHECK(simplex_tree.find({1, 2, 3}) == simplex_tree.null_simplex()); + BOOST_CHECK(simplex_tree.find({0, 2, 3}) != simplex_tree.null_simplex()); + BOOST_CHECK(simplex_tree.find({0, 1, 2}) == simplex_tree.null_simplex()); + BOOST_CHECK(simplex_tree.find({0, 1, 3}) == simplex_tree.null_simplex()); +} + +BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_3, typeST, list_of_tested_variants) { std::clog << "********************************************************************\n"; std::clog << "simplex_tree_expansion_3\n"; std::clog << "********************************************************************\n"; + // Construct the Simplex Tree with a 1-skeleton graph example + typeST simplex_tree; + + simplex_tree.insert_simplex({0, 1}, 0.); + simplex_tree.insert_simplex({0, 2}, 1.); + simplex_tree.insert_simplex({0, 3}, 2.); + simplex_tree.insert_simplex({1, 2}, 3.); + simplex_tree.insert_simplex({1, 3}, 4.); + simplex_tree.insert_simplex({2, 3}, 5.); + simplex_tree.insert_simplex({2, 4}, 6.); + simplex_tree.insert_simplex({3, 6}, 7.); + simplex_tree.insert_simplex({4, 5}, 8.); + simplex_tree.insert_simplex({4, 6}, 9.); + simplex_tree.insert_simplex({5, 6}, 10.); + simplex_tree.insert_simplex({6}, 10.); + + simplex_tree.expansion(3); std::clog << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; std::clog << " - dimension " << simplex_tree.dimension() << "\n"; std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; @@ -192,16 +287,25 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion, typeST, list_of_tested_var BOOST_CHECK(simplex_tree.num_simplices() == 24); BOOST_CHECK(simplex_tree.dimension() == 3); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({4,5,6})), 10.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,2})), 3.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,3})), 4.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,2,3})), 5.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({1,2,3})), 5.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,2,3})), 5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({4,5,6})), + static_cast<typename typeST::Filtration_value>(10.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,2})), + static_cast<typename typeST::Filtration_value>(3.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,3})), + static_cast<typename typeST::Filtration_value>(4.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,2,3})), + static_cast<typename typeST::Filtration_value>(5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({1,2,3})), + static_cast<typename typeST::Filtration_value>(5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,2,3})), + static_cast<typename typeST::Filtration_value>(5.)); } BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_2, typeST, list_of_tested_variants) { + std::clog << "********************************************************************\n"; + std::clog << "simplex_tree_expansion_2\n"; + std::clog << "********************************************************************\n"; // Construct the Simplex Tree with a 1-skeleton graph example typeST simplex_tree; @@ -220,9 +324,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_2, typeST, list_of_tested_v simplex_tree.expansion(2); - std::clog << "********************************************************************\n"; - std::clog << "simplex_tree_expansion_2\n"; - std::clog << "********************************************************************\n"; std::clog << "* The complex contains " << simplex_tree.num_simplices() << " simplices"; std::clog << " - dimension " << simplex_tree.dimension() << "\n"; std::clog << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; @@ -236,10 +337,15 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_expansion_2, typeST, list_of_tested_v BOOST_CHECK(simplex_tree.num_simplices() == 23); BOOST_CHECK(simplex_tree.dimension() == 2); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({4,5,6})), 10.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,2})), 3.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,1,3})), 4.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({0,2,3})), 5.)); - BOOST_CHECK(AreAlmostTheSame(simplex_tree.filtration(simplex_tree.find({1,2,3})), 5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({4,5,6})), + static_cast<typename typeST::Filtration_value>(10.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,2})), + static_cast<typename typeST::Filtration_value>(3.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,1,3})), + static_cast<typename typeST::Filtration_value>(4.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({0,2,3})), + static_cast<typename typeST::Filtration_value>(5.)); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(simplex_tree.filtration(simplex_tree.find({1,2,3})), + static_cast<typename typeST::Filtration_value>(5.)); BOOST_CHECK(simplex_tree.find({0,1,2,3}) == simplex_tree.null_simplex()); } diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 4571b8f3..b325fe3c 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -11,12 +11,7 @@ #ifndef SPARSIFY_POINT_SET_H_ #define SPARSIFY_POINT_SET_H_ -#include <boost/version.hpp> -#if BOOST_VERSION < 106600 -# include <boost/function_output_iterator.hpp> -#else # include <boost/iterator/function_output_iterator.hpp> -#endif #include <gudhi/Kd_tree_search.h> #ifdef GUDHI_SUBSAMPLING_PROFILING diff --git a/src/Tangential_complex/benchmark/benchmark_tc.cpp b/src/Tangential_complex/benchmark/benchmark_tc.cpp index 6da1425f..8e7c72ff 100644 --- a/src/Tangential_complex/benchmark/benchmark_tc.cpp +++ b/src/Tangential_complex/benchmark/benchmark_tc.cpp @@ -33,6 +33,7 @@ const std::size_t ONLY_LOAD_THE_FIRST_N_POINTS = 20000000; #include <gudhi/sparsify_point_set.h> #include <gudhi/random_point_generators.h> #include <gudhi/Tangential_complex/utilities.h> +#include <gudhi/Simplex_tree.h> #include <CGAL/assertions_behaviour.h> #include <CGAL/Epick_d.h> diff --git a/src/Tangential_complex/example/example_basic.cpp b/src/Tangential_complex/example/example_basic.cpp index ab35edf0..c50b9b8c 100644 --- a/src/Tangential_complex/example/example_basic.cpp +++ b/src/Tangential_complex/example/example_basic.cpp @@ -1,7 +1,6 @@ #include <gudhi/Tangential_complex.h> #include <gudhi/sparsify_point_set.h> -//#include <gudhi/Fake_simplex_tree.h> - +#include <gudhi/Simplex_tree.h> #include <CGAL/Epick_d.h> #include <CGAL/Random.h> @@ -39,7 +38,6 @@ int main(void) { // Export the TC into a Simplex_tree Gudhi::Simplex_tree<> stree; - //Gudhi::Fake_simplex_tree stree; tc.create_complex(stree); // Display stats about inconsistencies diff --git a/src/Tangential_complex/example/example_with_perturb.cpp b/src/Tangential_complex/example/example_with_perturb.cpp index d0d877ea..e70e2980 100644 --- a/src/Tangential_complex/example/example_with_perturb.cpp +++ b/src/Tangential_complex/example/example_with_perturb.cpp @@ -1,5 +1,6 @@ #include <gudhi/Tangential_complex.h> #include <gudhi/sparsify_point_set.h> +#include <gudhi/Simplex_tree.h> #include <CGAL/Epick_d.h> #include <CGAL/Random.h> diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp index 023c1e1a..a24b9ae2 100644 --- a/src/Tangential_complex/test/test_tangential_complex.cpp +++ b/src/Tangential_complex/test/test_tangential_complex.cpp @@ -14,6 +14,7 @@ #include <gudhi/Tangential_complex.h> #include <gudhi/sparsify_point_set.h> +#include <gudhi/Simplex_tree.h> #include <CGAL/Epick_d.h> #include <CGAL/Random.h> diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index b316740d..6a94d1f5 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,12 +1,14 @@ # This files manage third party libraries required by GUDHI -find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) +find_package(Boost 1.66.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) # Boost_FOUND is not reliable if(NOT Boost_VERSION) message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.") endif(NOT Boost_VERSION) include_directories(${Boost_INCLUDE_DIRS}) +message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) +message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) find_package(GMP) if(GMP_FOUND) @@ -17,6 +19,15 @@ if(GMP_FOUND) endif() endif() +# from windows vcpkg eigen 3.4.0#2 : build fails with +# error C2440: '<function-style-cast>': cannot convert from 'Eigen::EigenBase<Derived>::Index' to '__gmp_expr<mpq_t,mpq_t>' +# cf. https://gitlab.com/libeigen/eigen/-/issues/2476 +# Workaround is to compile with '-DEIGEN_DEFAULT_DENSE_INDEX_TYPE=int' +if (FORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT) + message("++ User explicit demand to force EIGEN_DEFAULT_DENSE_INDEX_TYPE to int") + add_definitions(-DEIGEN_DEFAULT_DENSE_INDEX_TYPE=int) +endif() + # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten. # cf. http://doc.cgal.org/latest/Manual/installation.html#title40 # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11". @@ -90,9 +101,6 @@ add_definitions( -DBOOST_ALL_DYN_LINK ) # problem on Mac with boost_system and boost_thread add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED ) -message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS}) -message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS}) - if (WITH_GUDHI_PYTHON) # Find the correct Python interpreter. # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance. @@ -181,4 +189,4 @@ if (WITH_GUDHI_PYTHON) endif(NOT SPHINX_PATH) endif(SPHINX_FOUND) endif(PYTHONINTERP_FOUND AND CYTHON_FOUND) -endif (WITH_GUDHI_PYTHON)
\ No newline at end of file +endif (WITH_GUDHI_PYTHON) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 6c42fbb4..afbad14d 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -5,7 +5,7 @@ * Examples of GUDHI headers inclusion can be found in \ref utilities. * * \section compiling Compiling - * The library uses c++14 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.56.0 + * The library uses c++14 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.66.0 * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index a1b104e2..29d5423d 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -14,11 +14,7 @@ #include <gudhi/graph_simplicial_complex.h> #include <gudhi/Debug_utils.h> -#if BOOST_VERSION < 106600 -# include <boost/function_output_iterator.hpp> -#else # include <boost/iterator/function_output_iterator.hpp> -#endif #include <boost/graph/adjacency_list.hpp> #include <iostream> diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index e3119cfc..63a9bbea 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -180,6 +180,16 @@ if(PYTHONINTERP_FOUND) set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'alpha_complex', ") endif () + # from windows vcpkg eigen 3.4.0#2 : build fails with + # error C2440: '<function-style-cast>': cannot convert from 'Eigen::EigenBase<Derived>::Index' to '__gmp_expr<mpq_t,mpq_t>' + # cf. https://gitlab.com/libeigen/eigen/-/issues/2476 + # Workaround is to compile with '-DEIGEN_DEFAULT_DENSE_INDEX_TYPE=int' + if (FORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT) + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DEIGEN_DEFAULT_DENSE_INDEX_TYPE=int', ") + endif() + + + add_gudhi_debug_info("Boost version ${Boost_VERSION}") if(CGAL_FOUND) if(NOT CGAL_VERSION VERSION_LESS 5.3.0) # CGAL_HEADER_ONLY has been dropped for CGAL >= 5.3. Only the header-only version is supported. @@ -214,13 +224,14 @@ if(PYTHONINTERP_FOUND) endif(NOT GMP_LIBRARIES_DIR) add_GUDHI_PYTHON_lib_dir(${GMP_LIBRARIES_DIR}) message("** Add gmp ${GMP_LIBRARIES_DIR}") + # When FORCE_CGAL_NOT_TO_BUILD_WITH_GMPXX is set, not defining CGAL_USE_GMPXX is sufficient enough if(GMPXX_FOUND) add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}") set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ") add_GUDHI_PYTHON_lib("${GMPXX_LIBRARIES}") add_GUDHI_PYTHON_lib_dir(${GMPXX_LIBRARIES_DIR}) message("** Add gmpxx ${GMPXX_LIBRARIES_DIR}") - endif(GMPXX_FOUND) + endif() endif(GMP_FOUND) if(MPFR_FOUND) add_gudhi_debug_info("MPFR_LIBRARIES = ${MPFR_LIBRARIES}") @@ -264,6 +275,10 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYTHON_INCLUDE_DIRS "${GUDHI_PYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ") endif() + if(DEBUG_TRACES) + set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-DDEBUG_TRACES', ") + endif(DEBUG_TRACES) + if(UNIX AND WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS) set( GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}") endif(UNIX AND WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS) diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index cfd22742..b060c86e 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -27,7 +27,8 @@ Remarks If you pass :code:`precision = 'exact'` to :func:`~gudhi.AlphaComplex.__init__`, the filtration values are the exact ones converted to float. This can be very slow. If you pass :code:`precision = 'safe'` (the default), the filtration values are only - guaranteed to have a small multiplicative error compared to the exact value. + guaranteed to have a small multiplicative error compared to the exact value, see + :func:`~gudhi.AlphaComplex.set_float_relative_precision` to modify the precision. A drawback, when computing persistence, is that an empty exact interval [10^12,10^12] may become a non-empty approximate interval [10^12,10^12+10^6]. Using :code:`precision = 'fast'` makes the computations slightly faster, and the combinatorics are still exact, but diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 35c344e3..cff84691 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -33,25 +33,19 @@ Compiling These instructions are for people who want to compile gudhi from source, they are unnecessary if you installed a binary package of Gudhi as above. They assume that you have downloaded a `release <https://github.com/GUDHI/gudhi-devel/releases>`_, -with a name like `gudhi.3.2.0.tar.gz`, then run `tar xf gudhi.3.2.0.tar.gz`, which -created a directory `gudhi.3.2.0`, hereinafter referred to as `/path-to-gudhi/`. +with a name like `gudhi.3.X.Y.tar.gz`, then run `tar xf gudhi.3.X.Y.tar.gz`, which +created a directory `gudhi.3.X.Y`, hereinafter referred to as `/path-to-gudhi/`. If you are instead using a git checkout, beware that the paths are a bit different, and in particular the `python/` subdirectory is actually `src/python/` there. -The library uses c++14 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.56.0, +The library uses c++14 and requires `Boost <https://www.boost.org/>`_ :math:`\geq` 1.66.0, `CMake <https://www.cmake.org/>`_ :math:`\geq` 3.5 to generate makefiles, -`NumPy <http://numpy.org>`_ :math:`\geq` 1.15.0, `Cython <https://www.cython.org/>`_ and -`pybind11 <https://github.com/pybind/pybind11>`_ to compile -the GUDHI Python module. -It is a multi-platform library and compiles on Linux, Mac OSX and Visual -Studio 2017 or later. +Python :math:`\geq` 3.5, `NumPy <http://numpy.org>`_ :math:`\geq` 1.15.0, `Cython <https://www.cython.org/>`_ +:math:`\geq` 0.27 and `pybind11 <https://github.com/pybind/pybind11>`_ to compile the GUDHI Python module. +It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2017 or later. -On `Windows <https://wiki.python.org/moin/WindowsCompilers>`_ , only Python -:math:`\geq` 3.5 are available because of the required Visual Studio version. - -On other systems, if you have several Python/python installed, the version 2.X -will be used by default, but you can force it by adding +If you have several Python/python installed, the version 2.X may be used by default, but you can force it by adding :code:`-DPython_ADDITIONAL_VERSIONS=3` to the cmake command. GUDHI Python module compilation @@ -142,54 +136,63 @@ If :code:`import gudhi` succeeds, please have a look to debug information: .. code-block:: python - import gudhi - print(gudhi.__debug_info__) + import gudhi as gd + print(gd.__debug_info__) + print("+ Installed modules are: " + gd.__available_modules) + print("+ Missing modules are: " + gd.__missing_modules) You shall have something like: .. code-block:: none - Python version 2.7.15 - Cython version 0.26.1 - Numpy version 1.14.1 - Eigen3 version 3.1.1 - Installed modules are: off_reader;simplex_tree;rips_complex; - cubical_complex;periodic_cubical_complex;reader_utils;witness_complex; - strong_witness_complex;alpha_complex; - Missing modules are: bottleneck_distance;nerve_gic;subsampling; - tangential_complex;persistence_graphical_tools; - euclidean_witness_complex;euclidean_strong_witness_complex; - CGAL version 4.7.1000 - GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so - GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so - TBB version 9107 found and used + Pybind11 version 2.8.1 + Python version 3.7.12 + Cython version 0.29.25 + Numpy version 1.21.4 + Boost version 1.77.0 + + Installed modules are: off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex; + + Missing modules are: bottleneck;nerve_gic;subsampling;tangential_complex;alpha_complex;euclidean_witness_complex; + euclidean_strong_witness_complex; -Here, you can see that bottleneck_distance, nerve_gic, subsampling and -tangential_complex are missing because of the CGAL version. -persistence_graphical_tools is not available as matplotlib is not -available. +Here, you can see that the modules that need CGAL are missing, because CGAL is not installed. +:code:`persistence_graphical_tools` is installed, but +`its functions <https://gudhi.inria.fr/python/latest/persistence_graphical_tools_ref.html>`_ will produce an error as +matplotlib is not available. Unitary tests cannot be run as pytest is missing. A complete configuration would be : .. code-block:: none - Python version 3.6.5 - Cython version 0.28.2 - Pytest version 3.3.2 - Matplotlib version 2.2.2 - Numpy version 1.14.5 - Eigen3 version 3.3.4 - Installed modules are: off_reader;simplex_tree;rips_complex; - cubical_complex;periodic_cubical_complex;persistence_graphical_tools; - reader_utils;witness_complex;strong_witness_complex; - persistence_graphical_tools;bottleneck_distance;nerve_gic;subsampling; - tangential_complex;alpha_complex;euclidean_witness_complex; - euclidean_strong_witness_complex; - CGAL header only version 4.11.0 + Pybind11 version 2.8.1 + Python version 3.9.7 + Cython version 0.29.24 + Pytest version 6.2.5 + Matplotlib version 3.5.0 + Numpy version 1.21.4 + Scipy version 1.7.3 + Scikit-learn version 1.0.1 + POT version 0.8.0 + HNSWlib found + PyKeOps version [pyKeOps]: 1.5 + EagerPy version 0.30.0 + TensorFlow version 2.7.0 + Sphinx version 4.3.0 + Sphinx-paramlinks version 0.5.2 + python_docs_theme found + Eigen3 version 3.4.0 + Boost version 1.74.0 + CGAL version 5.3 GMP_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmp.so GMPXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libgmpxx.so + MPFR_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpfr.so TBB version 9107 found and used + + Installed modules are: bottleneck;off_reader;simplex_tree;rips_complex;cubical_complex;periodic_cubical_complex; + persistence_graphical_tools;reader_utils;witness_complex;strong_witness_complex;nerve_gic;subsampling; + tangential_complex;alpha_complex;euclidean_witness_complex;euclidean_strong_witness_complex; + + Missing modules are: + Documentation ============= @@ -345,8 +348,8 @@ You can still deactivate LaTeX rendering by saying: .. code-block:: python - import gudhi - gudhi.persistence_graphical_tools._gudhi_matplotlib_use_tex=False + import gudhi as gd + gd.persistence_graphical_tools._gudhi_matplotlib_use_tex=False PyKeOps ------- diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index a4888914..375e1561 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -31,6 +31,10 @@ cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": Alpha_complex_interface(vector[vector[double]] points, vector[double] weights, bool fast_version, bool exact_version) nogil except + vector[double] get_point(int vertex) nogil except + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, bool default_filtration_value) nogil except + + @staticmethod + void set_float_relative_precision(double precision) nogil + @staticmethod + double get_float_relative_precision() nogil # AlphaComplex python interface cdef class AlphaComplex: @@ -133,3 +137,28 @@ cdef class AlphaComplex: self.this_ptr.create_simplex_tree(<Simplex_tree_interface_full_featured*>stree_int_ptr, mas, compute_filtration) return stree + + @staticmethod + def set_float_relative_precision(precision): + """ + :param precision: When the AlphaComplex is constructed with :code:`precision = 'safe'` (the default), + one can set the float relative precision of filtration values computed in + :func:`~gudhi.AlphaComplex.create_simplex_tree`. + Default is :code:`1e-5` (cf. :func:`~gudhi.AlphaComplex.get_float_relative_precision`). + For more details, please refer to + `CGAL::Lazy_exact_nt<NT>::set_relative_precision_of_to_double <https://doc.cgal.org/latest/Number_types/classCGAL_1_1Lazy__exact__nt.html>`_ + :type precision: float + """ + if precision <=0. or precision >= 1.: + raise ValueError("Relative precision value must be strictly greater than 0 and strictly lower than 1") + Alpha_complex_interface.set_float_relative_precision(precision) + + @staticmethod + def get_float_relative_precision(): + """ + :returns: The float relative precision of filtration values computation in + :func:`~gudhi.AlphaComplex.create_simplex_tree` when the AlphaComplex is constructed with + :code:`precision = 'safe'` (the default). + :rtype: float + """ + return Alpha_complex_interface.get_float_relative_precision() diff --git a/src/python/gudhi/simplex_tree.pxd b/src/python/gudhi/simplex_tree.pxd index 006a24ed..4f229663 100644 --- a/src/python/gudhi/simplex_tree.pxd +++ b/src/python/gudhi/simplex_tree.pxd @@ -45,6 +45,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_interface_full_featured "Gudhi::Simplex_tree_interface<Gudhi::Simplex_tree_options_full_featured>": Simplex_tree_interface_full_featured() nogil + Simplex_tree_interface_full_featured(Simplex_tree_interface_full_featured&) nogil double simplex_filtration(vector[int] simplex) nogil void assign_simplex_filtration(vector[int] simplex, double filtration) nogil void initialize_filtration() nogil @@ -65,6 +66,7 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": vector[vector[pair[int, pair[double, double]]]] compute_extended_persistence_subdiagrams(vector[pair[int, pair[double, double]]] dgm, double min_persistence) nogil Simplex_tree_interface_full_featured* collapse_edges(int nb_collapse_iteration) nogil except + void reset_filtration(double filtration, int dimension) nogil + bint operator==(Simplex_tree_interface_full_featured) nogil # Iterators over Simplex tree pair[vector[int], double] get_simplex_and_filtration(Simplex_tree_simplex_handle f_simplex) nogil Simplex_tree_simplices_iterator get_simplices_iterator_begin() nogil @@ -74,6 +76,9 @@ cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": Simplex_tree_skeleton_iterator get_skeleton_iterator_begin(int dimension) nogil Simplex_tree_skeleton_iterator get_skeleton_iterator_end(int dimension) nogil pair[Simplex_tree_boundary_iterator, Simplex_tree_boundary_iterator] get_boundary_iterators(vector[int] simplex) nogil except + + # Expansion with blockers + ctypedef bool (*blocker_func_t)(vector[int], void *user_data) + void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) cdef extern from "Persistent_cohomology_interface.h" namespace "Gudhi": cdef cppclass Simplex_tree_persistence_interface "Gudhi::Persistent_cohomology_interface<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>": diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx index c3720936..a4914184 100644 --- a/src/python/gudhi/simplex_tree.pyx +++ b/src/python/gudhi/simplex_tree.pyx @@ -16,6 +16,9 @@ __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" __license__ = "MIT" +cdef bool callback(vector[int] simplex, void *blocker_func): + return (<object>blocker_func)(simplex) + # SimplexTree python interface cdef class SimplexTree: """The simplex tree is an efficient and flexible data structure for @@ -38,13 +41,29 @@ cdef class SimplexTree: cdef Simplex_tree_persistence_interface * pcohptr # Fake constructor that does nothing but documenting the constructor - def __init__(self): + def __init__(self, other = None): """SimplexTree constructor. + + :param other: If `other` is `None` (default value), an empty `SimplexTree` is created. + If `other` is a `SimplexTree`, the `SimplexTree` is constructed from a deep copy of `other`. + :type other: SimplexTree (Optional) + :returns: An empty or a copy simplex tree. + :rtype: SimplexTree + + :raises TypeError: In case `other` is neither `None`, nor a `SimplexTree`. + :note: If the `SimplexTree` is a copy, the persistence information is not copied. If you need it in the clone, + you have to call :func:`compute_persistence` on it even if you had already computed it in the original. """ # The real cython constructor - def __cinit__(self): - self.thisptr = <intptr_t>(new Simplex_tree_interface_full_featured()) + def __cinit__(self, other = None): + if other: + if isinstance(other, SimplexTree): + self.thisptr = _get_copy_intptr(other) + else: + raise TypeError("`other` argument requires to be of type `SimplexTree`, or `None`.") + else: + self.thisptr = <intptr_t>(new Simplex_tree_interface_full_featured()) def __dealloc__(self): cdef Simplex_tree_interface_full_featured* ptr = self.get_ptr() @@ -63,6 +82,21 @@ cdef class SimplexTree: """ return self.pcohptr != NULL + def copy(self): + """ + :returns: A simplex tree that is a deep copy of itself. + :rtype: SimplexTree + + :note: The persistence information is not copied. If you need it in the clone, you have to call + :func:`compute_persistence` on it even if you had already computed it in the original. + """ + stree = SimplexTree() + stree.thisptr = _get_copy_intptr(self) + return stree + + def __deepcopy__(self): + return self.copy() + def filtration(self, simplex): """This function returns the filtration value for a given N-simplex in this simplicial complex, or +infinity if it is not in the complex. @@ -443,6 +477,27 @@ cdef class SimplexTree: persistence_result = self.pcohptr.get_persistence() return self.get_ptr().compute_extended_persistence_subdiagrams(persistence_result, min_persistence) + def expansion_with_blocker(self, max_dim, blocker_func): + """Expands the Simplex_tree containing only a graph. Simplices corresponding to cliques in the graph are added + incrementally, faces before cofaces, unless the simplex has dimension larger than `max_dim` or `blocker_func` + returns `True` for this simplex. + + The function identifies a candidate simplex whose faces are all already in the complex, inserts it with a + filtration value corresponding to the maximum of the filtration values of the faces, then calls `blocker_func` + with this new simplex (represented as a list of int). If `blocker_func` returns `True`, the simplex is removed, + otherwise it is kept. The algorithm then proceeds with the next candidate. + + .. warning:: + Several candidates of the same dimension may be inserted simultaneously before calling `block_simplex`, so + if you examine the complex in `block_simplex`, you may hit a few simplices of the same dimension that have + not been vetted by `block_simplex` yet, or have already been rejected but not yet removed. + + :param max_dim: Expansion maximal dimension value. + :type max_dim: int + :param blocker_func: Blocker oracle. + :type blocker_func: Callable[[List[int]], bool] + """ + self.get_ptr().expansion_with_blockers_callback(max_dim, callback, <void*>blocker_func) def persistence(self, homology_coeff_field=11, min_persistence=0, persistence_dim_max = False): """This function computes and returns the persistence of the simplicial complex. @@ -642,3 +697,13 @@ cdef class SimplexTree: self.thisptr = <intptr_t>(ptr.collapse_edges(nb_iter)) # Delete old pointer del ptr + + def __eq__(self, other:SimplexTree): + """Test for structural equality + :returns: True if the 2 simplex trees are equal, False otherwise. + :rtype: bool + """ + return dereference(self.get_ptr()) == dereference(other.get_ptr()) + +cdef intptr_t _get_copy_intptr(SimplexTree stree) nogil: + return <intptr_t>(new Simplex_tree_interface_full_featured(dereference(stree.get_ptr()))) diff --git a/src/python/gudhi/weighted_rips_complex.py b/src/python/gudhi/weighted_rips_complex.py index 0541572b..16f63c3d 100644 --- a/src/python/gudhi/weighted_rips_complex.py +++ b/src/python/gudhi/weighted_rips_complex.py @@ -12,9 +12,11 @@ from gudhi import SimplexTree class WeightedRipsComplex: """ Class to generate a weighted Rips complex from a distance matrix and weights on vertices, - in the way described in :cite:`dtmfiltrations`. + in the way described in :cite:`dtmfiltrations` with `p=1`. The filtration value of vertex `i` is `2*weights[i]`, + and the filtration value of edge `ij` is `distance_matrix[i][j]+weights[i]+weights[j]`, + or the maximum of the filtrations of its extremities, whichever is largest. Remark that all the filtration values are doubled compared to the definition in the paper - for the consistency with RipsComplex. + for consistency with RipsComplex. """ def __init__(self, distance_matrix, diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h index 671af4a4..469b91ce 100644 --- a/src/python/include/Alpha_complex_interface.h +++ b/src/python/include/Alpha_complex_interface.h @@ -57,6 +57,16 @@ class Alpha_complex_interface { alpha_ptr_->create_simplex_tree(simplex_tree, max_alpha_square, default_filtration_value); } + static void set_float_relative_precision(double precision) { + // cf. Exact_alpha_complex_dD kernel type in Alpha_complex_factory.h + CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>::FT::set_relative_precision_of_to_double(precision); + } + + static double get_float_relative_precision() { + // cf. Exact_alpha_complex_dD kernel type in Alpha_complex_factory.h + return CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>::FT::get_relative_precision_of_to_double(); + } + private: std::unique_ptr<Abstract_alpha_complex> alpha_ptr_; }; diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index 629f6083..aa3dac18 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -42,6 +42,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { using Complex_simplex_iterator = typename Base::Complex_simplex_iterator; using Extended_filtration_data = typename Base::Extended_filtration_data; using Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator; + typedef bool (*blocker_func_t)(Simplex simplex, void *user_data); public: @@ -195,6 +196,13 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { #endif } + void expansion_with_blockers_callback(int dimension, blocker_func_t user_func, void *user_data) { + Base::expansion_with_blockers(dimension, [&](Simplex_handle sh){ + Simplex simplex(Base::simplex_vertex_range(sh).begin(), Base::simplex_vertex_range(sh).end()); + return user_func(simplex, user_data); + }); + } + // Iterator over the simplex tree Complex_simplex_iterator get_simplices_iterator_begin() { // this specific case works because the range is just a pair of iterators - won't work if range was a vector diff --git a/src/python/pyproject.toml b/src/python/pyproject.toml index a9fb4985..55b64466 100644 --- a/src/python/pyproject.toml +++ b/src/python/pyproject.toml @@ -1,3 +1,3 @@ [build-system] -requires = ["setuptools", "wheel", "numpy>=1.15.0", "cython", "pybind11"] +requires = ["setuptools>=24.2.0", "wheel", "numpy>=1.15.0", "cython>=0.27", "pybind11"] build-backend = "setuptools.build_meta" diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 23746998..2c67c2c5 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -5,6 +5,7 @@ Copyright (C) 2019 Inria Modification(s): + - 2021/12 Vincent Rouvreau: Python 3.5 as minimal version - YYYY/MM Author: Description of the modification """ @@ -43,7 +44,7 @@ for module in cython_modules: include_dirs=include_dirs, runtime_library_dirs=runtime_library_dirs,)) -ext_modules = cythonize(ext_modules, compiler_directives={'language_level': str(sys.version_info[0])}) +ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'}) for module in pybind11_modules: my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)] @@ -86,6 +87,7 @@ setup( long_description_content_type='text/x-rst', long_description=long_description, ext_modules = ext_modules, + python_requires='>=3.5.0', install_requires = ['numpy >= 1.15.0',], package_data={"": ["*.dll"], }, ) diff --git a/src/python/test/test_alpha_complex.py b/src/python/test/test_alpha_complex.py index f15284f3..f81e6137 100755 --- a/src/python/test/test_alpha_complex.py +++ b/src/python/test/test_alpha_complex.py @@ -286,3 +286,30 @@ def _weighted_doc_example(precision): def test_weighted_doc_example(): for precision in ['fast', 'safe', 'exact']: _weighted_doc_example(precision) + +def test_float_relative_precision(): + assert AlphaComplex.get_float_relative_precision() == 1e-5 + # Must be > 0. + with pytest.raises(ValueError): + AlphaComplex.set_float_relative_precision(0.) + # Must be < 1. + with pytest.raises(ValueError): + AlphaComplex.set_float_relative_precision(1.) + + points = [[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]] + st = AlphaComplex(points=points).create_simplex_tree() + filtrations = list(st.get_filtration()) + + # Get a better precision + AlphaComplex.set_float_relative_precision(1e-15) + assert AlphaComplex.get_float_relative_precision() == 1e-15 + + st = AlphaComplex(points=points).create_simplex_tree() + filtrations_better_resolution = list(st.get_filtration()) + + assert len(filtrations) == len(filtrations_better_resolution) + for idx in range(len(filtrations)): + # check simplex is the same + assert filtrations[idx][0] == filtrations_better_resolution[idx][0] + # check filtration is about the same with a relative precision of the worst case + assert filtrations[idx][1] == pytest.approx(filtrations_better_resolution[idx][1], rel=1e-5) diff --git a/src/python/test/test_simplex_tree.py b/src/python/test/test_simplex_tree.py index 31c46213..eb481a49 100755 --- a/src/python/test/test_simplex_tree.py +++ b/src/python/test/test_simplex_tree.py @@ -447,4 +447,116 @@ def test_persistence_intervals_in_dimension(): assert np.array_equal(H2, np.array([[ 0., float("inf")]])) # Test empty case assert st.persistence_intervals_in_dimension(3).shape == (0, 2) -
\ No newline at end of file + +def test_equality_operator(): + st1 = SimplexTree() + st2 = SimplexTree() + + assert st1 == st2 + + st1.insert([1,2,3], 4.) + assert st1 != st2 + + st2.insert([1,2,3], 4.) + assert st1 == st2 + +def test_simplex_tree_deep_copy(): + st = SimplexTree() + st.insert([1, 2, 3], 0.) + # compute persistence only on the original + st.compute_persistence() + + st_copy = st.copy() + assert st_copy == st + st_filt_list = list(st.get_filtration()) + + # check persistence is not copied + assert st.__is_persistence_defined() == True + assert st_copy.__is_persistence_defined() == False + + # remove something in the copy and check the copy is included in the original + st_copy.remove_maximal_simplex([1, 2, 3]) + a_filt_list = list(st_copy.get_filtration()) + assert len(a_filt_list) < len(st_filt_list) + + for a_splx in a_filt_list: + assert a_splx in st_filt_list + + # test double free + del st + del st_copy + +def test_simplex_tree_deep_copy_constructor(): + st = SimplexTree() + st.insert([1, 2, 3], 0.) + # compute persistence only on the original + st.compute_persistence() + + st_copy = SimplexTree(st) + assert st_copy == st + st_filt_list = list(st.get_filtration()) + + # check persistence is not copied + assert st.__is_persistence_defined() == True + assert st_copy.__is_persistence_defined() == False + + # remove something in the copy and check the copy is included in the original + st_copy.remove_maximal_simplex([1, 2, 3]) + a_filt_list = list(st_copy.get_filtration()) + assert len(a_filt_list) < len(st_filt_list) + + for a_splx in a_filt_list: + assert a_splx in st_filt_list + + # test double free + del st + del st_copy + +def test_simplex_tree_constructor_exception(): + with pytest.raises(TypeError): + st = SimplexTree(other = "Construction from a string shall raise an exception") + +def test_expansion_with_blocker(): + st=SimplexTree() + st.insert([0,1],0) + st.insert([0,2],1) + st.insert([0,3],2) + st.insert([1,2],3) + st.insert([1,3],4) + st.insert([2,3],5) + st.insert([2,4],6) + st.insert([3,6],7) + st.insert([4,5],8) + st.insert([4,6],9) + st.insert([5,6],10) + st.insert([6],10) + + def blocker(simplex): + try: + # Block all simplices that countains vertex 6 + simplex.index(6) + print(simplex, ' is blocked') + return True + except ValueError: + print(simplex, ' is accepted') + st.assign_filtration(simplex, st.filtration(simplex) + 1.) + return False + + st.expansion_with_blocker(2, blocker) + assert st.num_simplices() == 22 + assert st.dimension() == 2 + assert st.find([4,5,6]) == False + assert st.filtration([0,1,2]) == 4. + assert st.filtration([0,1,3]) == 5. + assert st.filtration([0,2,3]) == 6. + assert st.filtration([1,2,3]) == 6. + + st.expansion_with_blocker(3, blocker) + assert st.num_simplices() == 23 + assert st.dimension() == 3 + assert st.find([4,5,6]) == False + assert st.filtration([0,1,2]) == 4. + assert st.filtration([0,1,3]) == 5. + assert st.filtration([0,2,3]) == 6. + assert st.filtration([1,2,3]) == 6. + assert st.filtration([0,1,2,3]) == 7. |