diff options
Diffstat (limited to 'src/Persistent_cohomology/example')
5 files changed, 21 insertions, 22 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index eb31e050..98ed753d 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -2,19 +2,17 @@ cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) -target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY}) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) -target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY}) add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) -target_link_libraries(rips_persistence_step_by_step ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) -target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence_via_boundary_matrix ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(persistence_from_file persistence_from_file.cpp) -target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) target_link_libraries(plain_homology ${TBB_LIBRARIES}) @@ -46,7 +44,7 @@ if(GMP_FOUND) if(GMPXX_FOUND) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence - ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) if (TBB_FOUND) target_link_libraries(rips_multifield_persistence ${TBB_LIBRARIES}) endif(TBB_FOUND) @@ -58,9 +56,9 @@ endif(GMP_FOUND) if(CGAL_FOUND) add_executable(exact_alpha_complex_3d_persistence exact_alpha_complex_3d_persistence.cpp) - target_link_libraries(exact_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(exact_alpha_complex_3d_persistence ${CGAL_LIBRARY}) add_executable(weighted_alpha_complex_3d_persistence weighted_alpha_complex_3d_persistence.cpp) - target_link_libraries(weighted_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(weighted_alpha_complex_3d_persistence ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(exact_alpha_complex_3d_persistence ${TBB_LIBRARIES}) @@ -76,7 +74,7 @@ if(CGAL_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable(custom_persistence_sort custom_persistence_sort.cpp) - target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY}) if (TBB_FOUND) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) 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 fa49dcee..8ce68406 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); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -218,7 +218,6 @@ 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 4a2b10f3..a4ecf9da 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); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -236,7 +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 |