diff options
Diffstat (limited to 'src/Persistent_cohomology')
10 files changed, 12 insertions, 26 deletions
diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index e17e5926..6400116b 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -189,10 +189,10 @@ and a weights file. \code $> ./weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights 2 0.45 \endcode \code Simplex_tree dim: 3 -2 -0 0 inf -2 1 0.0682162 1.0001 -2 1 0.0934117 1.00003 -2 2 0.56444 1.03938 \endcode +2 0 -1 inf +2 1 -0.931784 0.000103311 +2 1 -0.906588 2.60165e-05 +2 2 -0.43556 0.0393798 \endcode \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html"> Persistent_cohomology/alpha_complex_persistence.cpp</a> computes the persistent homology with @@ -208,7 +208,8 @@ Simplex_tree dim: 3 \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html"> Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a> computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the periodic alpha complex on points sampling from an OFF file. -\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 \endcode +\code $> ./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off +../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 \endcode \code Periodic Delaunay computed. Simplex_tree dim: 3 3 0 0 inf diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp index df96fcfd..de9b8cdf 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -185,7 +185,7 @@ int main(int argc, char* const argv[]) { } } // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); + Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES @@ -198,7 +198,6 @@ int main(int argc, char* const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -211,7 +210,6 @@ int main(int argc, char* const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp index b189e980..5f078251 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -66,7 +66,7 @@ using Cell_handle = Alpha_shape_3::Cell_handle; using Facet = Alpha_shape_3::Facet; using Edge_3 = Alpha_shape_3::Edge; using Vertex_handle = Alpha_shape_3::Vertex_handle; -using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; +using Vertex_list = std::list<Vertex_handle>; // gudhi type definition using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; @@ -200,7 +200,6 @@ int main(int argc, char* const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -213,7 +212,6 @@ int main(int argc, char* const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp index 63731a4a..e6355e6b 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -220,7 +220,6 @@ int main(int argc, char* const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -233,7 +232,6 @@ int main(int argc, char* const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index 67235467..eafa3fd5 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -61,8 +61,7 @@ int main(int argc, char * argv[]) { simplex_tree_stream >> simplex_tree; std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() - << std::endl; + std::cout << " - dimension " << simplex_tree.dimension() << std::endl; /* std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index 7ca9410a..8214d66a 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -143,11 +143,10 @@ int main(int argc, char * const argv[]) { /* An edge [10,12,2] */ st.set_dimension(2); - st.set_filtration(0.4); std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << std::endl; - std::cout << " - dimension " << st.dimension() << " - filtration " << st.filtration() << std::endl; + std::cout << " - dimension " << st.dimension() << std::endl; std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; std::cout << "**************************************************************" << std::endl; diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp index 96cc57e9..4bddbe82 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -245,7 +245,6 @@ int main(int argc, char* const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -258,7 +257,6 @@ int main(int argc, char* const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp index a4a2a9f8..13634ff7 100644 --- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -244,8 +244,6 @@ int main(int argc, char* const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; @@ -257,7 +255,6 @@ int main(int argc, char* const argv[]) { std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; #endif // DEBUG_TRACES #ifdef DEBUG_TRACES diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index f8174020..f53987b6 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -31,12 +31,11 @@ std::string test_rips_persistence(int coefficient, int min_persistence) { // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() - << " - filtration= " << st.filtration() << std::endl; + << std::endl; // Check BOOST_CHECK(st.num_simplices() == 98); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 1.89); // Sort the simplices in the order of the filtration st.initialize_filtration(); diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp index 3537cfa4..9e767943 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test_multi_field.cpp @@ -31,12 +31,11 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub // Display the Simplex_tree std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() - << " - filtration= " << st.filtration() << std::endl; + << std::endl; // Check BOOST_CHECK(st.num_simplices() == 58); BOOST_CHECK(st.dimension() == 3); - BOOST_CHECK(st.filtration() == 0.4); // Sort the simplices in the order of the filtration st.initialize_filtration(); |