diff options
Diffstat (limited to 'src/Persistent_cohomology')
9 files changed, 35 insertions, 30 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 40eb3576..594efb45 100644 --- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp @@ -76,8 +76,9 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(const std::string& progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; exit(-1); } @@ -202,7 +203,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; @@ -215,7 +215,6 @@ 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 9881debf..08f3b334 100644 --- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp @@ -77,8 +77,9 @@ using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; using PCOH = Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; exit(-1); } @@ -204,7 +205,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; @@ -217,7 +217,6 @@ 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 71faebd7..74940387 100644 --- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp @@ -84,8 +84,16 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph path_to_iso_cuboid_3_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_iso_cuboid_3_file coeff_field_characteristic[" << + "integer > 0] min_persistence[float >= -1.0]\n" << + " path_to_OFF_file is the path to your points cloud in OFF format.\n" << + " path_to_iso_cuboid_3_file is the path to the iso cuboid file with the following format :\n" << + " x_min y_min z_min x_max y_max z_max\n" << + " In this example, the periodic cube will be " << + "{ x = [x_min,x_max]; y = [y_min,y_max]; z = [z_min,z_max] }.\n" << + " For more information, please refer to\n" << + " https://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Iso__cuboid__3.html\n"; + exit(-1); } @@ -221,7 +229,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; @@ -234,7 +241,6 @@ 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 7809d5ff..8ef479d4 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -142,11 +142,10 @@ int main(int argc, char * const argv[]) { /* An edge [11,6] */ /* An edge [10,12,2] */ - 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 968db753..16b44094 100644 --- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp @@ -81,8 +81,13 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog ST, Gudhi::persistent_cohomology::Field_Zp >; void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_file_graph path_to_weight_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + std::cerr << "Usage:\n" << progName << " path_to_OFF_file path_to_weight_file coeff_field_characteristic[integer " << + "> 0] min_persistence[float >= -1.0]\n"; + std::cerr << " path_to_OFF_file is the path to your points cloud in OFF format.\n"; + std::cerr << " path_to_weight_file is the path to the weights of your points cloud (one value per line.)\n"; + std::cerr << " Weights values are explained on CGAL documentation:\n"; + std::cerr << " https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0\n"; + std::cerr << " https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation\n"; exit(-1); } @@ -115,6 +120,7 @@ int main(int argc, char * const argv[]) { if (weights_ifstr.good()) { double weight = 0.0; std::size_t index = 0; + wp.reserve(lp.size()); // Attempt read the weight in a double format, return false if it fails while ((weights_ifstr >> weight) && (index < lp.size())) { wp.push_back(Weighted_point_3(lp[index], weight)); @@ -130,7 +136,7 @@ int main(int argc, char * const argv[]) { } // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); + Alpha_shape_3 as(wp.begin(), wp.end(), 0, Alpha_shape_3::GENERAL); #ifdef DEBUG_TRACES std::cout << "Alpha shape computed in GENERAL mode" << std::endl; #endif // DEBUG_TRACES @@ -222,7 +228,6 @@ int main(int argc, char * const argv[]) { else std::cout << "This shall not happen" << std::endl; } - simplex_tree.set_filtration(filtration_max); #ifdef DEBUG_TRACES std::cout << "vertices \t\t" << count_vertices << std::endl; @@ -235,7 +240,6 @@ 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 887aa25f..a1c106d5 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(); |