diff options
Diffstat (limited to 'example/Persistent_cohomology')
9 files changed, 62 insertions, 40 deletions
diff --git a/example/Persistent_cohomology/CMakeLists.txt b/example/Persistent_cohomology/CMakeLists.txt index 3c45e79b..f47de4c3 100644 --- a/example/Persistent_cohomology/CMakeLists.txt +++ b/example/Persistent_cohomology/CMakeLists.txt @@ -2,25 +2,23 @@ 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_distance_matrix_persistence rips_distance_matrix_persistence.cpp) -target_link_libraries(rips_distance_matrix_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_distance_matrix_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(rips_persistence rips_persistence.cpp) -target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) +target_link_libraries(rips_persistence ${Boost_PROGRAM_OPTIONS_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}) @@ -47,27 +45,36 @@ add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FIL "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "2" "-m" "0") add_test(NAME Persistent_cohomology_example_from_file_3_3_100 COMMAND $<TARGET_FILE:persistence_from_file> "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc" "-p" "3" "-m" "100") - + +install(TARGETS plain_homology DESTINATION bin) +install(TARGETS persistence_from_simple_simplex_tree DESTINATION bin) +install(TARGETS rips_distance_matrix_persistence DESTINATION bin) +install(TARGETS rips_persistence DESTINATION bin) +install(TARGETS rips_persistence_step_by_step DESTINATION bin) +install(TARGETS rips_persistence_via_boundary_matrix DESTINATION bin) +install(TARGETS persistence_from_file DESTINATION bin) + 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) - add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $<TARGET_FILE:rips_multifield_persistence> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71") + add_test(NAME Persistent_cohomology_example_multifield_2_71 COMMAND $<TARGET_FILE:rips_multifield_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "2" "-q" "71") + install(TARGETS rips_multifield_persistence DESTINATION bin) endif(GMPXX_FOUND) endif(GMP_FOUND) if(CGAL_FOUND) add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp) - target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY}) 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(alpha_complex_3d_persistence ${TBB_LIBRARIES}) @@ -81,16 +88,20 @@ if(CGAL_FOUND) add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45") + install(TARGETS alpha_complex_3d_persistence DESTINATION bin) + install(TARGETS exact_alpha_complex_3d_persistence DESTINATION bin) + install(TARGETS weighted_alpha_complex_3d_persistence DESTINATION bin) + if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) add_executable (alpha_complex_persistence alpha_complex_persistence.cpp) target_link_libraries(alpha_complex_persistence - ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) + ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY}) add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp) - target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + target_link_libraries(periodic_alpha_complex_3d_persistence ${CGAL_LIBRARY}) 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(alpha_complex_persistence ${TBB_LIBRARIES}) @@ -102,5 +113,10 @@ if(CGAL_FOUND) add_test(NAME Persistent_cohomology_example_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:periodic_alpha_complex_3d_persistence> "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "2" "0") add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>) + + install(TARGETS alpha_complex_persistence DESTINATION bin) + install(TARGETS periodic_alpha_complex_3d_persistence DESTINATION bin) + install(TARGETS custom_persistence_sort DESTINATION bin) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) endif(CGAL_FOUND) diff --git a/example/Persistent_cohomology/README b/example/Persistent_cohomology/README index 2ac79398..794b94ae 100644 --- a/example/Persistent_cohomology/README +++ b/example/Persistent_cohomology/README @@ -121,7 +121,7 @@ N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension. 3) 3D periodic special case --------------------------- -./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off 3 1.0 +./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 output: Periodic Delaunay computed. diff --git a/example/Persistent_cohomology/alpha_complex_3d_persistence.cpp b/example/Persistent_cohomology/alpha_complex_3d_persistence.cpp index fd227b82..f63ff0f6 100644 --- a/example/Persistent_cohomology/alpha_complex_3d_persistence.cpp +++ b/example/Persistent_cohomology/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); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -216,7 +216,6 @@ 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/example/Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp b/example/Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp index 8a335075..09561d03 100644 --- a/example/Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp +++ b/example/Persistent_cohomology/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/example/Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp b/example/Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp index 8928cfc2..8140a3c5 100644 --- a/example/Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp +++ b/example/Persistent_cohomology/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); simplex_tree.set_dimension(dim_max); #ifdef DEBUG_TRACES @@ -235,7 +242,6 @@ 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/example/Persistent_cohomology/persistence_from_file.cpp b/example/Persistent_cohomology/persistence_from_file.cpp index 67235467..eafa3fd5 100644 --- a/example/Persistent_cohomology/persistence_from_file.cpp +++ b/example/Persistent_cohomology/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/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp b/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp index 7ca9410a..8214d66a 100644 --- a/example/Persistent_cohomology/persistence_from_simple_simplex_tree.cpp +++ b/example/Persistent_cohomology/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/example/Persistent_cohomology/rips_distance_matrix_persistence.cpp b/example/Persistent_cohomology/rips_distance_matrix_persistence.cpp index 8517e7f6..d38808c7 100644 --- a/example/Persistent_cohomology/rips_distance_matrix_persistence.cpp +++ b/example/Persistent_cohomology/rips_distance_matrix_persistence.cpp @@ -57,7 +57,7 @@ int main(int argc, char * argv[]) { program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, min_persistence); - Distance_matrix distances = read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); Rips_complex rips_complex_from_file(distances, threshold); // Construct the Rips complex in a Simplex Tree diff --git a/example/Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp b/example/Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp index 34b90933..72268511 100644 --- a/example/Persistent_cohomology/weighted_alpha_complex_3d_persistence.cpp +++ b/example/Persistent_cohomology/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 |