From db938dbd74460e7a0fd705be8628984052f71dc0 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 4 Sep 2020 17:23:16 +0200 Subject: Alpha_kernel_d, its tests and Alpha complex to use it --- .../example/Weighted_alpha_complex_from_points.cpp | 54 ++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp (limited to 'src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp') diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp new file mode 100644 index 00000000..19a04282 --- /dev/null +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -0,0 +1,54 @@ +#include +// to construct a simplex_tree from alpha complex +#include + +#include + +#include +#include + +// Explicit dimension 2 Epeck_d kernel +using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<2> >; +using Bare_point = Kernel::Point_d; +using Weighted_point = Kernel::Weighted_point_d; +using Vector_of_points = std::vector; + +int main() { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); + points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); + points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); + points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex alpha_complex_from_weighted_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_weighted_points.create_complex(simplex)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::clog << "Weighted alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.num_vertices() << " vertices." << std::endl; + + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : simplex.filtration_simplex_range()) { + std::clog << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::clog << vertex << " "; + } + std::clog << ") -> " << "[" << simplex.filtration(f_simplex) << "] "; + std::clog << std::endl; + } + } + return 0; +} -- cgit v1.2.3 From 9922407fe6f5d8872522157555c3573e95930ac3 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 7 Sep 2020 10:31:11 +0200 Subject: Fix compilation error and test with 0. weights --- src/Alpha_complex/example/CMakeLists.txt | 4 +++- .../example/Weighted_alpha_complex_from_points.cpp | 14 +++++++------- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 11 ++++------- 3 files changed, 14 insertions(+), 15 deletions(-) (limited to 'src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 08eb979e..17dc896c 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -28,6 +28,8 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt") + add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $) + if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) @@ -47,7 +49,7 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) endif() - endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) if (NOT CGAL_VERSION VERSION_LESS 4.11.0) add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp ) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index 19a04282..05858084 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -18,13 +18,13 @@ int main() { // Init of a list of points // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); - points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); - points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); - points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); + points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 0.)); + points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 0.)); + points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 0.)); + points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 0.)); + points.push_back(Weighted_point(Bare_point(0.0, 14.0), 0.)); + points.push_back(Weighted_point(Bare_point(2.0, 19.0), 0.)); + points.push_back(Weighted_point(Bare_point(9.0, 17.0), 0.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index 87604ec4..a3e3845a 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -71,8 +71,7 @@ class Alpha_kernel_d { return sph.second; } - template - Point get_circumcenter(const Sphere& sph) const { + auto get_circumcenter(const Sphere& sph) const { return sph.first; } @@ -117,13 +116,11 @@ class Alpha_kernel_d { return sph.weight(); } - template - Point get_circumcenter(const Sphere& sph) const { - return sph.point(); + auto get_circumcenter(const Sphere& sph) const { + return sph; } - template - FT get_squared_distance(const Point& first, const Point& second) const { + FT get_squared_distance(const Weighted_point_d& first, const Weighted_point_d& second) const { return kernel_.power_distance_d_object()(first, second); } }; -- cgit v1.2.3 From 171ddab9b7a50f0303d7201fa547dbfb445f9698 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Fri, 11 Sep 2020 11:55:55 +0200 Subject: Requires CGAL >= 5.1. Fix is_gabriel computation --- src/Alpha_complex/example/CMakeLists.txt | 14 +++++++++----- .../example/Weighted_alpha_complex_from_points.cpp | 14 +++++++------- src/Alpha_complex/include/gudhi/Alpha_complex.h | 8 ++++++-- .../include/gudhi/Alpha_complex/Alpha_kernel_d.h | 17 ++++------------- src/Alpha_complex/test/CMakeLists.txt | 13 +++++++++---- 5 files changed, 35 insertions(+), 31 deletions(-) (limited to 'src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp') diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 17dc896c..1fc2330a 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -7,13 +7,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY}) add_executable ( Alpha_complex_example_fast_from_off Fast_alpha_complex_from_off.cpp ) target_link_libraries(Alpha_complex_example_fast_from_off ${CGAL_LIBRARY}) - add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp ) - target_link_libraries(Weighted_alpha_complex_example_from_points ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_example_from_points ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_from_off ${TBB_LIBRARIES}) target_link_libraries(Alpha_complex_example_fast_from_off ${TBB_LIBRARIES}) - target_link_libraries(Weighted_alpha_complex_example_from_points ${TBB_LIBRARIES}) endif() add_test(NAME Alpha_complex_example_from_points COMMAND $) @@ -28,8 +25,6 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) add_test(NAME Alpha_complex_example_fast_from_off_32 COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" "32.0" "${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt") - add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $) - if (DIFF_PATH) # Do not forget to copy test results files in current binary dir file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) @@ -69,3 +64,12 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) COMMAND $) endif(NOT CGAL_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp ) + target_link_libraries(Weighted_alpha_complex_example_from_points ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Weighted_alpha_complex_example_from_points ${TBB_LIBRARIES}) + endif() + add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $) +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index 05858084..19a04282 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -18,13 +18,13 @@ int main() { // Init of a list of points // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 0.)); - points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 0.)); - points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 0.)); - points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 0.)); - points.push_back(Weighted_point(Bare_point(0.0, 14.0), 0.)); - points.push_back(Weighted_point(Bare_point(2.0, 19.0), 0.)); - points.push_back(Weighted_point(Bare_point(9.0, 17.0), 0.)); + points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); + points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); + points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); + points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); + points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); + points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 8e9fe773..4316d9bc 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -210,6 +210,11 @@ class Alpha_complex { << std::endl; #endif +#if CGAL_VERSION_NR < 1050101000 + // Make compilation fail if weighted and CGAL < 5.1 + static_assert(!Weighted, "Weighted Alpha_complex is only available for CGAL >= 5.1"); +#endif + auto first = std::begin(points); auto last = std::end(points); @@ -457,8 +462,7 @@ class Alpha_complex { while(shortiter != enditer && *longiter == *shortiter) { ++longiter; ++shortiter; } Vertex_handle extra = *longiter; auto const& cache=get_cache(complex, f_boundary); - bool is_gab = kernel_.get_squared_distance(kernel_.get_circumcenter(cache), get_point_(extra)) >= - kernel_.get_squared_radius(cache); + bool is_gab = kernel_.is_gabriel(cache, get_point_(extra)); #ifdef DEBUG_TRACES std::clog << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << extra << std::endl; #endif // DEBUG_TRACES diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h index a3e3845a..b64e4f59 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex/Alpha_kernel_d.h @@ -71,13 +71,8 @@ class Alpha_kernel_d { return sph.second; } - auto get_circumcenter(const Sphere& sph) const { - return sph.first; - } - - template - FT get_squared_distance(const Point& first, const Point& second) const { - return kernel_.squared_distance_d_object()(first, second); + bool is_gabriel(const Sphere& circumcenter, const Point_d& point) { + return kernel_.squared_distance_d_object()(circumcenter.first, point) >= circumcenter.second; } }; @@ -116,12 +111,8 @@ class Alpha_kernel_d { return sph.weight(); } - auto get_circumcenter(const Sphere& sph) const { - return sph; - } - - FT get_squared_distance(const Weighted_point_d& first, const Weighted_point_d& second) const { - return kernel_.power_distance_d_object()(first, second); + bool is_gabriel(const Sphere& circumcenter, const Weighted_point_d& point) { + return kernel_.power_distance_d_object()(circumcenter, point) >= 0; } }; diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 71e4ea7c..837d2948 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -10,17 +10,13 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) target_link_libraries(Alpha_complex_test_unit ${CGAL_LIBRARY}) add_executable ( Delaunay_complex_test_unit Delaunay_complex_unit_test.cpp ) target_link_libraries(Delaunay_complex_test_unit ${CGAL_LIBRARY}) - add_executable ( Alpha_kernel_d_test_unit Alpha_kernel_d_unit_test.cpp ) - target_link_libraries(Alpha_kernel_d_test_unit ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(Alpha_complex_test_unit ${TBB_LIBRARIES}) target_link_libraries(Delaunay_complex_test_unit ${TBB_LIBRARIES}) - target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) endif() gudhi_add_boost_test(Alpha_complex_test_unit) gudhi_add_boost_test(Delaunay_complex_test_unit) - gudhi_add_boost_test(Alpha_kernel_d_test_unit) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) @@ -47,3 +43,12 @@ if (NOT CGAL_VERSION VERSION_LESS 4.11.0) gudhi_add_boost_test(Weighted_periodic_alpha_complex_3d_test_unit) endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) + add_executable ( Alpha_kernel_d_test_unit Alpha_kernel_d_unit_test.cpp ) + target_link_libraries(Alpha_kernel_d_test_unit ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(Alpha_kernel_d_test_unit ${TBB_LIBRARIES}) + endif() + gudhi_add_boost_test(Alpha_kernel_d_test_unit) +endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) \ No newline at end of file -- cgit v1.2.3 From cb68f3e4c8ce7724ccb693e5c67dd9928d12d84b Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 16 Sep 2020 12:39:00 +0200 Subject: Some documentation about weighted dD Alpha complex. Make examples 3d/dD consistents --- src/Alpha_complex/doc/Intro_alpha_complex.h | 35 +++++++++++++++++++++- .../Weighted_alpha_complex_3d_from_points.cpp | 4 +-- .../example/Weighted_alpha_complex_from_points.cpp | 16 +++++----- .../example/weightedalpha3dfrompoints_for_doc.txt | 4 +-- 4 files changed, 45 insertions(+), 14 deletions(-) (limited to 'src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp') diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 60da7169..f14adee6 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -22,6 +22,17 @@ namespace alpha_complex { * * @{ * +
+Table of Contents + +
+ * \section definition Definition * * Alpha_complex is a simplicial complex @@ -146,6 +157,28 @@ namespace alpha_complex { * `SimplicialComplexForAlpha::prune_above_filtration()`). * In the following example, the value is given by the user as argument of the program. * + * \section weightedversion Weighted specific version + * Requires: \ref eigen ≥ 3.1.0 and \ref cgal ≥ 5.1.0. + * For performances reasons, it is advised to use \ref eigen ≥ 3.5.8 and \ref cgal ≥ 5.2.0 + * A weighted version for Alpha complex is available (cf. Alpha_complex). + * + * This example builds the CGAL weighted alpha shapes from a small molecule, and initializes the alpha complex with + * it. This example is taken from CGAL 3d + * weighted alpha shapes. + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex/Weighted_alpha_complex_from_points.cpp + * + * When launching: + * + * \code $> ./Weighted_alpha_complex_example_from_points + * \endcode + * + * the program output is: + * + * \include Alpha_complex/weightedalpha3dfrompoints_for_doc.txt + * * * \section offexample Example from OFF file * @@ -166,7 +199,7 @@ namespace alpha_complex { * \include Alpha_complex/alphaoffreader_for_doc_32.txt * * - * \section weighted3dexample 3d specific example + * \section weighted3dexample 3d specific version * * A specific module for Alpha complex is available in 3d (cf. Alpha_complex_3d) and allows to construct standard, * weighted, periodic or weighted and periodic versions of alpha complexes. Alpha values computation can be diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index c044194e..74f0cf30 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -34,10 +34,10 @@ int main(int argc, char **argv) { // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::clog << "Alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + std::clog << "Weighted alpha complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; - std::clog << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; for (auto f_simplex : simplex.filtration_simplex_range()) { std::clog << " ( "; for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index 19a04282..d49d3e93 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -8,23 +8,21 @@ #include // Explicit dimension 2 Epeck_d kernel -using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<2> >; +using Kernel = CGAL::Epeck_d< CGAL::Dimension_tag<3> >; using Bare_point = Kernel::Point_d; using Weighted_point = Kernel::Weighted_point_d; using Vector_of_points = std::vector; int main() { // ---------------------------------------------------------------------------- - // Init of a list of points + // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1.0, 1.0) , 1.)); - points.push_back(Weighted_point(Bare_point(7.0, 0.0) , 1.)); - points.push_back(Weighted_point(Bare_point(4.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 6.0) , 1.)); - points.push_back(Weighted_point(Bare_point(0.0, 14.0), 1.)); - points.push_back(Weighted_point(Bare_point(2.0, 19.0), 1.)); - points.push_back(Weighted_point(Bare_point(9.0, 17.0), 1.)); + points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); + points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); + points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); + points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); + points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt index 7a09998d..f0695f1a 100644 --- a/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt +++ b/src/Alpha_complex/example/weightedalpha3dfrompoints_for_doc.txt @@ -1,5 +1,5 @@ -Alpha complex is of dimension 3 - 29 simplices - 5 vertices. -Iterator on alpha complex simplices in the filtration order, with [filtration value]: +Weighted alpha complex is of dimension 3 - 29 simplices - 5 vertices. +Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]: ( 0 ) -> [-4] ( 1 ) -> [-4] ( 2 ) -> [-4] -- cgit v1.2.3 From c1b317640f81fefff7f7a774b239957fb632fa43 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Wed, 30 Sep 2020 09:18:36 +0200 Subject: code review: emplace_back versus push_back --- .../Weighted_alpha_complex_3d_from_points.cpp | 10 +++++----- .../example/Weighted_alpha_complex_from_points.cpp | 10 +++++----- src/Alpha_complex/include/gudhi/Alpha_complex.h | 6 +++--- src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp | 20 ++++++++++---------- .../utilities/alpha_complex_persistence.cpp | 2 +- 5 files changed, 24 insertions(+), 24 deletions(-) (limited to 'src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp') diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp index a8d00272..09431d6e 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_3d_from_points.cpp @@ -18,11 +18,11 @@ int main(int argc, char **argv) { // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- std::vector weighted_points; - weighted_points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); - weighted_points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); + weighted_points.emplace_back(Bare_point(1, -1, -1), 4.); + weighted_points.emplace_back(Bare_point(-1, 1, -1), 4.); + weighted_points.emplace_back(Bare_point(-1, -1, 1), 4.); + weighted_points.emplace_back(Bare_point(1, 1, 1), 4.); + weighted_points.emplace_back(Bare_point(2, 2, 2), 1.); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp index d49d3e93..d1f3e436 100644 --- a/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Weighted_alpha_complex_from_points.cpp @@ -18,11 +18,11 @@ int main() { // Init of a list of points and weights from a small molecule // ---------------------------------------------------------------------------- Vector_of_points points; - points.push_back(Weighted_point(Bare_point(1, -1, -1), 4.)); - points.push_back(Weighted_point(Bare_point(-1, 1, -1), 4.)); - points.push_back(Weighted_point(Bare_point(-1, -1, 1), 4.)); - points.push_back(Weighted_point(Bare_point(1, 1, 1), 4.)); - points.push_back(Weighted_point(Bare_point(2, 2, 2), 1.)); + points.emplace_back(Bare_point(1, -1, -1), 4.); + points.emplace_back(Bare_point(-1, 1, -1), 4.); + points.emplace_back(Bare_point(-1, -1, 1), 4.); + points.emplace_back(Bare_point(1, 1, 1), 4.); + points.emplace_back(Bare_point(2, 2, 2), 1.); // ---------------------------------------------------------------------------- // Init of an alpha complex from the list of points diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index a692dbc6..4f8e3d54 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -310,7 +310,7 @@ class Alpha_complex { thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) - v.push_back(get_point_(vertex)); + v.emplace_back(get_point_(vertex)); cache_.emplace_back(kernel_.get_sphere(v.cbegin(), v.cend())); } return cache_[k]; @@ -326,7 +326,7 @@ class Alpha_complex { thread_local std::vector v; v.clear(); for (auto vertex : cplx.simplex_vertex_range(s)) - v.push_back(get_point_(vertex)); + v.emplace_back(get_point_(vertex)); return kernel_.get_squared_radius(v.cbegin(), v.cend()); } @@ -394,7 +394,7 @@ class Alpha_complex { std::clog << " " << (*vit)->data(); #endif // DEBUG_TRACES // Vector of vertex construction for simplex_tree structure - vertexVector.push_back((*vit)->data()); + vertexVector.emplace_back((*vit)->data()); } } #ifdef DEBUG_TRACES diff --git a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp index 192834b3..6eae103d 100644 --- a/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_kernel_d_unit_test.cpp @@ -63,11 +63,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kerne using Point_d = typename Unweighted_kernel::Point_d; std::vector unw_pts; - unw_pts.push_back(Point_d(p0.begin(), p0.end())); - unw_pts.push_back(Point_d(p1.begin(), p1.end())); - unw_pts.push_back(Point_d(p2.begin(), p2.end())); - unw_pts.push_back(Point_d(p3.begin(), p3.end())); - unw_pts.push_back(Point_d(p4.begin(), p4.end())); + unw_pts.emplace_back(p0.begin(), p0.end()); + unw_pts.emplace_back(p1.begin(), p1.end()); + unw_pts.emplace_back(p2.begin(), p2.end()); + unw_pts.emplace_back(p3.begin(), p3.end()); + unw_pts.emplace_back(p4.begin(), p4.end()); Unweighted_kernel kernel; auto unw_sphere = kernel.get_sphere(unw_pts.cbegin(), unw_pts.cend()); @@ -79,11 +79,11 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_kernel_d_sphere, TestedKernel, list_of_kerne using Weighted_point_d = typename Weighted_kernel::Weighted_point_d; using Bare_point_d = typename Weighted_kernel::Bare_point_d; std::vector w_pts; - w_pts.push_back(Weighted_point_d(Bare_point_d(p0.begin(), p0.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p1.begin(), p1.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p2.begin(), p2.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p3.begin(), p3.end()), 0.)); - w_pts.push_back(Weighted_point_d(Bare_point_d(p4.begin(), p4.end()), 0.)); + w_pts.emplace_back(Bare_point_d(p0.begin(), p0.end()), 0.); + w_pts.emplace_back(Bare_point_d(p1.begin(), p1.end()), 0.); + w_pts.emplace_back(Bare_point_d(p2.begin(), p2.end()), 0.); + w_pts.emplace_back(Bare_point_d(p3.begin(), p3.end()), 0.); + w_pts.emplace_back(Bare_point_d(p4.begin(), p4.end()), 0.); Weighted_kernel w_kernel; auto w_sphere = w_kernel.get_sphere(w_pts.cbegin(), w_pts.cend()); diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index e86b34e2..3ce7b440 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -50,7 +50,7 @@ std::vector read_weight_file(const std::string &weight_file) { double weight = 0.0; // Attempt read the weight in a double format, return false if it fails while (weights_ifstr >> weight) { - weights.push_back(weight); + weights.emplace_back(weight); } } else { std::cerr << "Unable to read weights file " << weight_file << std::endl; -- cgit v1.2.3