From 16aaf4cda5fd97da12a7f1da8b0a5168fac2e289 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 11 Oct 2016 13:57:03 +0000 Subject: Problem of merge with tangentialcomplex branch. Redo in an integration branch git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tangential_integration@1701 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fa029e8e90b3e203ea675f02098ec6fe95596f9f --- src/Tangential_complex/example/CMakeLists.txt | 30 ++++++++++++ src/Tangential_complex/example/example_basic.cpp | 46 +++++++++++++++++++ .../example/example_with_perturb.cpp | 53 ++++++++++++++++++++++ 3 files changed, 129 insertions(+) create mode 100644 src/Tangential_complex/example/CMakeLists.txt create mode 100644 src/Tangential_complex/example/example_basic.cpp create mode 100644 src/Tangential_complex/example/example_with_perturb.cpp (limited to 'src/Tangential_complex/example') diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt new file mode 100644 index 00000000..7ba043f0 --- /dev/null +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required(VERSION 2.6) +project(Tangential_complex_examples) + +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.8.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + + add_executable( Tangential_complex_example_basic example_basic.cpp ) + target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) + target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) + target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) + endif() + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for the Tangential_complex examples.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Tangential_complex examples. Version 4.8.0 is required.") + endif () +else() + message(WARNING "CGAL not found. It is required for the Tangential_complex examples.") +endif() diff --git a/src/Tangential_complex/example/example_basic.cpp b/src/Tangential_complex/example/example_basic.cpp new file mode 100644 index 00000000..4f2b859e --- /dev/null +++ b/src/Tangential_complex/example/example_basic.cpp @@ -0,0 +1,46 @@ +#include +#include + +#include +#include + +#include +#include + +namespace tc = Gudhi::tangential_complex; + +typedef CGAL::Epick_d Kernel; +typedef Kernel::FT FT; +typedef Kernel::Point_d Point; +typedef Kernel::Vector_d Vector; +typedef tc::Tangential_complex< +Kernel, CGAL::Dynamic_dimension_tag, +CGAL::Parallel_tag> TC; + +int main(void) { + const int INTRINSIC_DIM = 2; + const int AMBIENT_DIM = 3; + const int NUM_POINTS = 1000; + + Kernel k; + + // Generate points on a 2-sphere + CGAL::Random_points_on_sphere_d generator(AMBIENT_DIM, 3.); + std::vector points; + points.reserve(NUM_POINTS); + for (int i = 0; i < NUM_POINTS; ++i) + points.push_back(*generator++); + + // Compute the TC + TC tc(points, INTRINSIC_DIM, k); + tc.compute_tangential_complex(); + + // Export the TC into a Simplex_tree + Gudhi::Simplex_tree<> stree; + tc.create_complex(stree); + + // Display stats about inconsistencies + tc.number_of_inconsistent_simplices(true); // verbose + + return 0; +} diff --git a/src/Tangential_complex/example/example_with_perturb.cpp b/src/Tangential_complex/example/example_with_perturb.cpp new file mode 100644 index 00000000..d0d877ea --- /dev/null +++ b/src/Tangential_complex/example/example_with_perturb.cpp @@ -0,0 +1,53 @@ +#include +#include + +#include +#include + +#include +#include + +namespace subsampl = Gudhi::subsampling; +namespace tc = Gudhi::tangential_complex; + +typedef CGAL::Epick_d> Kernel; +typedef Kernel::FT FT; +typedef Kernel::Point_d Point; +typedef Kernel::Vector_d Vector; +typedef tc::Tangential_complex< +Kernel, CGAL::Dimension_tag<2>, +CGAL::Parallel_tag> TC; + +int main(void) { + const int INTRINSIC_DIM = 2; + const int AMBIENT_DIM = 3; + const int NUM_POINTS = 50; + + Kernel k; + + // Generate points on a 2-sphere + CGAL::Random_points_on_sphere_d generator(AMBIENT_DIM, 3.); + std::vector points; + points.reserve(NUM_POINTS); + for (int i = 0; i < NUM_POINTS; ++i) + points.push_back(*generator++); + + // Sparsify the point set + std::vector sparsified_points; + subsampl::sparsify_point_set(k, points, 0.1 * 0.1, + std::back_inserter(sparsified_points)); + sparsified_points.swap(points); + + // Compute the TC + TC tc(points, INTRINSIC_DIM, k); + tc.compute_tangential_complex(); + + // Try to fix inconsistencies. Give it 10 seconds to succeed + tc.fix_inconsistencies_using_perturbation(0.05, 10); + + // Export the TC into a Simplex_tree + Gudhi::Simplex_tree<> stree; + tc.create_complex(stree); + + return 0; +} -- cgit v1.2.3 From 92479a53aa228c4e212067b375ab1b665116834e Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 11 Oct 2016 15:24:42 +0000 Subject: Fix doxygen warning CMake message fix CMake test tangential examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@1704 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: efa3c76e767d6ba55367b57c10ab87844c968457 --- src/Simplex_tree/doc/Intro_simplex_tree.h | 4 ++-- src/Tangential_complex/benchmark/CMakeLists.txt | 22 ++++---------------- src/Tangential_complex/example/CMakeLists.txt | 27 +++++++++---------------- src/common/doc/main_page.h | 10 ++++----- 4 files changed, 21 insertions(+), 42 deletions(-) (limited to 'src/Tangential_complex/example') diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index be061785..940dd694 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -66,8 +66,8 @@ Expand the simplex tree in 3.8e-05 s. Information of the Simplex Tree: Number of vertices = 10 Number of simplices = 98 \endcode * - * \li - * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp - Simplex tree is computed and displayed from a 3D alpha + * \li + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp - Simplex tree is computed and displayed from a 3D alpha * complex (Requires CGAL, GMP and GMPXX to be installed) * * diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt index 12488201..a217d6e6 100644 --- a/src/Tangential_complex/benchmark/CMakeLists.txt +++ b/src/Tangential_complex/benchmark/CMakeLists.txt @@ -13,28 +13,14 @@ endif() # need CGAL 4.8 if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - - find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - add_executable(Tangential_complex_benchmark benchmark_tc.cpp) target_link_libraries(Tangential_complex_benchmark ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES}) - endif() - - # Do not forget to copy test files in current binary dir - #file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - - else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required for Tangential complex feature.") - endif() - else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Tangential complex feature. Version 4.8.0 is required.") - endif () -endif() + endif(TBB_FOUND) + endif(EIGEN3_FOUND) + endif (NOT CGAL_VERSION VERSION_LESS 4.8.0) +endif(CGAL_FOUND) diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 7ba043f0..a75ccd5b 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -3,14 +3,7 @@ project(Tangential_complex_examples) if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.8.0) - message(STATUS "CGAL version: ${CGAL_VERSION}.") - - find_package(Eigen3 3.1.0) if (EIGEN3_FOUND) - message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") - include( ${EIGEN3_USE_FILE} ) - include_directories (BEFORE "../../include") - add_executable( Tangential_complex_example_basic example_basic.cpp ) target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY}) add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp ) @@ -18,13 +11,13 @@ if(CGAL_FOUND) if (TBB_FOUND) target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES}) target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES}) - endif() - else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required for the Tangential_complex examples.") - endif() - else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Tangential_complex examples. Version 4.8.0 is required.") - endif () -else() - message(WARNING "CGAL not found. It is required for the Tangential_complex examples.") -endif() + endif(TBB_FOUND) + + add_test(Tangential_complex_example_basic + ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic) + + add_test(Tangential_complex_example_with_perturb + ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb) + endif(EIGEN3_FOUND) + endif(NOT CGAL_VERSION VERSION_LESS 4.8.0) +endif(CGAL_FOUND) diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index fe23c4e7..1a2cb6ba 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -220,8 +220,8 @@ make \endverbatim * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: * \li * Persistent_cohomology/alpha_complex_3d_persistence.cpp - * \li - * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * \li + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * * The following example requires CGAL version ≥ 4.6: * \li @@ -281,8 +281,8 @@ make \endverbatim * Persistent_cohomology/alpha_complex_persistence.cpp * \li * Simplex_tree/simple_simplex_tree.cpp - * \li - * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * \li + * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * \li * Simplex_tree/simplex_tree_from_cliques_of_graph.cpp * \li @@ -351,7 +351,7 @@ make \endverbatim * @example Persistent_cohomology/custom_persistence_sort.cpp * @example Simplex_tree/mini_simplex_tree.cpp * @example Simplex_tree/simple_simplex_tree.cpp - * @example Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp + * @example Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @example Simplex_tree/simplex_tree_from_cliques_of_graph.cpp * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp -- cgit v1.2.3