diff options
author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-02-05 07:43:52 +0100 |
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committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2020-02-05 07:43:52 +0100 |
commit | 8e888b8be306c32c561396ca80b47a0aa9f9f859 (patch) | |
tree | c745eca4eeeeeac45551e80e3732b78e42759c7c /src | |
parent | bf4b4eeda9762ed9e99c2b24f19331fa0111fcfe (diff) | |
parent | 33540d9b4c4d320ee1482d876a10200d89ff4f49 (diff) |
Merge last master modification and fix merge conflict
Diffstat (limited to 'src')
-rw-r--r-- | src/Nerve_GIC/include/gudhi/GIC.h | 8 | ||||
-rw-r--r-- | src/Simplex_tree/example/CMakeLists.txt | 3 | ||||
-rw-r--r-- | src/Tangential_complex/include/gudhi/Tangential_complex.h | 4 | ||||
-rw-r--r-- | src/Witness_complex/example/CMakeLists.txt | 10 | ||||
-rw-r--r-- | src/python/doc/alpha_complex_sum.inc | 15 |
5 files changed, 24 insertions, 16 deletions
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index ab099c04..61db6508 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -14,7 +14,7 @@ #ifdef GUDHI_USE_TBB #include <tbb/parallel_for.h> -#include <tbb/mutex.h> +#include <mutex> #endif #include <gudhi/Debug_utils.h> @@ -459,7 +459,7 @@ class Cover_complex { // This cannot be parallelized if thread_local is not defined // thread_local is not defined for XCode < v.8 #if defined(GUDHI_USE_TBB) && defined(GUDHI_CAN_USE_CXX11_THREAD_LOCAL) - tbb::mutex deltamutex; + std::mutex deltamutex; tbb::parallel_for(0, N, [&](int i){ std::vector<int> samples(m); SampleWithoutReplacement(n, m, samples); @@ -765,7 +765,7 @@ class Cover_complex { #ifdef GUDHI_USE_TBB if (verbose) std::clog << "Computing connected components (parallelized)..." << std::endl; - tbb::mutex covermutex, idmutex; + std::mutex covermutex, idmutex; tbb::parallel_for(0, res, [&](int i){ // Compute connected components Graph G = one_skeleton.create_subgraph(); @@ -895,7 +895,7 @@ class Cover_complex { // Compute the geodesic distances to subsamples with Dijkstra #ifdef GUDHI_USE_TBB if (verbose) std::clog << "Computing geodesic distances (parallelized)..." << std::endl; - tbb::mutex coverMutex; tbb::mutex mindistMutex; + std::mutex coverMutex; tbb::mutex mindistMutex; tbb::parallel_for(0, m, [&](int i){ int seed = voronoi_subsamples[i]; std::vector<double> dmap(n); diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index f99b164c..8a8cac58 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -16,6 +16,9 @@ endif() add_test(NAME Simplex_tree_example_simple_simplex_tree COMMAND $<TARGET_FILE:Simplex_tree_example_simple_simplex_tree>) add_executable ( Simplex_tree_example_mini_simplex_tree mini_simplex_tree.cpp ) +if (TBB_FOUND) + target_link_libraries(Simplex_tree_example_mini_simplex_tree ${TBB_LIBRARIES}) +endif() add_test(NAME Simplex_tree_example_mini_simplex_tree COMMAND $<TARGET_FILE:Simplex_tree_example_mini_simplex_tree>) # An example with Simplex-tree using CGAL alpha_shapes_3 diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index f058fa9f..f007bdd5 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -60,7 +60,7 @@ #ifdef GUDHI_USE_TBB #include <tbb/parallel_for.h> #include <tbb/combinable.h> -#include <tbb/mutex.h> +#include <mutex> #endif // #define GUDHI_TC_EXPORT_NORMALS // Only for 3D surfaces (k=2, d=3) @@ -147,7 +147,7 @@ class Tangential_complex { typedef typename Tr_traits::Vector_d Tr_vector; #if defined(GUDHI_USE_TBB) - typedef tbb::mutex Mutex_for_perturb; + typedef std::mutex Mutex_for_perturb; typedef Vector Translation_for_perturb; typedef std::vector<Atomic_wrapper<FT> > Weights; #else diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 5860f3a3..2659798e 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -12,10 +12,18 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) # CGAL and Eigen3 are required for Euclidean version of Witness if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_off ${TBB_LIBRARIES}) + endif() add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_sphere ${TBB_LIBRARIES}) + endif() add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_strong_off) + if (TBB_FOUND) + target_link_libraries(Witness_complex_example_strong_off ${TBB_LIBRARIES}) + endif() add_test(NAME Witness_complex_example_off_test_torus COMMAND $<TARGET_FILE:Witness_complex_example_off> diff --git a/src/python/doc/alpha_complex_sum.inc b/src/python/doc/alpha_complex_sum.inc index a1184663..b5af0d27 100644 --- a/src/python/doc/alpha_complex_sum.inc +++ b/src/python/doc/alpha_complex_sum.inc @@ -5,16 +5,13 @@ | .. figure:: | Alpha complex is a simplicial complex constructed from the finite | :Author: Vincent Rouvreau | | ../../doc/Alpha_complex/alpha_complex_representation.png | cells of a Delaunay Triangulation. | | | :alt: Alpha complex representation | | :Introduced in: GUDHI 2.0.0 | - | :figclass: align-center | The filtration value of each simplex is computed as the square of the | | - | | circumradius of the simplex if the circumsphere is empty (the simplex | :Copyright: MIT (`GPL v3 </licensing/>`_) | - | | is then said to be Gabriel), and as the minimum of the filtration | | - | | values of the codimension 1 cofaces that make it not Gabriel | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | - | | otherwise. All simplices that have a filtration value | | - | | :math:`> \alpha^2` are removed from the Delaunay complex | | - | | when creating the simplicial complex if it is specified. | | + | :figclass: align-center | The filtration value of each simplex is computed as the **square** of | | + | | the circumradius of the simplex if the circumsphere is empty (the | :Copyright: MIT (`GPL v3 </licensing/>`_) | + | | simplex is then said to be Gabriel), and as the minimum of the | | + | | filtration values of the codimension 1 cofaces that make it not | :Requires: `Eigen <installation.html#eigen>`__ :math:`\geq` 3.1.0 and `CGAL <installation.html#cgal>`__ :math:`\geq` 4.11.0 | + | | Gabriel otherwise. | | | | | | - | | This package requires having CGAL version 4.7 or higher (4.8.1 is | | - | | advised for better performance). | | + | | For performances reasons, it is advised to use CGAL ≥ 5.0.0. | | +----------------------------------------------------------------+------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------+ | * :doc:`alpha_complex_user` | * :doc:`alpha_complex_ref` | +----------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ |