diff options
Diffstat (limited to 'src/Persistent_cohomology/example')
8 files changed, 149 insertions, 175 deletions
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 94ec13c5..d66954d7 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -1,68 +1,70 @@ project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) +if (TBB_FOUND) + target_link_libraries(plain_homology ${TBB_LIBRARIES}) +endif() +add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>) add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp) - -add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) -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_PROGRAM_OPTIONS_LIBRARY}) - -add_executable(persistence_from_file persistence_from_file.cpp) -target_link_libraries(persistence_from_file ${Boost_PROGRAM_OPTIONS_LIBRARY}) - if (TBB_FOUND) - target_link_libraries(plain_homology ${TBB_LIBRARIES}) target_link_libraries(persistence_from_simple_simplex_tree ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) - target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) - target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) endif() - -add_test(NAME Persistent_cohomology_example_plain_homology COMMAND $<TARGET_FILE:plain_homology>) add_test(NAME Persistent_cohomology_example_from_simple_simplex_tree COMMAND $<TARGET_FILE:persistence_from_simple_simplex_tree> - "1" "0") -add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") -add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix> - "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") -add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file> - "${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") + "2" "0") -install(TARGETS plain_homology DESTINATION bin) -install(TARGETS persistence_from_simple_simplex_tree 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(TARGET Boost::program_options) + add_executable(rips_persistence_step_by_step rips_persistence_step_by_step.cpp) + target_link_libraries(rips_persistence_step_by_step Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence_step_by_step ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_from_rips_step_by_step_on_tore_3D COMMAND $<TARGET_FILE:rips_persistence_step_by_step> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") +endif() + +if(TARGET Boost::program_options) + add_executable(rips_persistence_via_boundary_matrix rips_persistence_via_boundary_matrix.cpp) + target_link_libraries(rips_persistence_via_boundary_matrix Boost::program_options) + if (TBB_FOUND) + target_link_libraries(rips_persistence_via_boundary_matrix ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_via_boundary_matrix COMMAND $<TARGET_FILE:rips_persistence_via_boundary_matrix> + "${CMAKE_SOURCE_DIR}/data/points/Kl.off" "-r" "0.16" "-d" "3" "-p" "3" "-m" "100") +endif() + +if(TARGET Boost::program_options) + add_executable(persistence_from_file persistence_from_file.cpp) + target_link_libraries(persistence_from_file Boost::program_options) + if (TBB_FOUND) + target_link_libraries(persistence_from_file ${TBB_LIBRARIES}) + endif() + add_test(NAME Persistent_cohomology_example_from_file_3_2_0 COMMAND $<TARGET_FILE:persistence_from_file> + "${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/Klein_bottle_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/Klein_bottle_complex.fsc" "-p" "3" "-m" "100") +endif() if(GMP_FOUND) - if(GMPXX_FOUND) + if(GMPXX_FOUND) + if(TARGET Boost::program_options) add_executable(rips_multifield_persistence rips_multifield_persistence.cpp ) target_link_libraries(rips_multifield_persistence - ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + Boost::program_options ${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") - install(TARGETS rips_multifield_persistence DESTINATION bin) - endif(GMPXX_FOUND) + endif() + endif(GMPXX_FOUND) endif(GMP_FOUND) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) - add_executable(custom_persistence_sort custom_persistence_sort.cpp) target_link_libraries(custom_persistence_sort ${CGAL_LIBRARY}) - if (TBB_FOUND) target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES}) endif(TBB_FOUND) add_test(NAME Persistent_cohomology_example_custom_persistence_sort COMMAND $<TARGET_FILE:custom_persistence_sort>) - - install(TARGETS custom_persistence_sort DESTINATION bin) - endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index be74cf50..bba0b2f7 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -33,7 +33,7 @@ using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomolog Gudhi::persistent_cohomology::Field_Zp >; std::vector<Point> random_points() { - // Instanciate a random point generator + // Instantiate a random point generator CGAL::Random rng(0); // Generate "points_number" random points in a vector @@ -70,26 +70,23 @@ struct cmp_intervals_by_dim_then_length { int main(int argc, char **argv) { std::vector<Point> points = random_points(); - std::cout << "Points size=" << points.size() << std::endl; + std::clog << "Points size=" << points.size() << std::endl; // Alpha complex persistence computation from generated points Alpha_complex alpha_complex_from_points(points); - std::cout << "alpha_complex_from_points" << std::endl; + std::clog << "alpha_complex_from_points" << std::endl; Simplex_tree simplex; - std::cout << "simplex" << std::endl; + std::clog << "simplex" << std::endl; if (alpha_complex_from_points.create_complex(simplex, 0.6)) { - std::cout << "simplex" << std::endl; + std::clog << "simplex" << std::endl; // ---------------------------------------------------------------------------- // Display information about the alpha complex // ---------------------------------------------------------------------------- - std::cout << "Simplicial complex is of dimension " << simplex.dimension() << + std::clog << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; - // Sort the simplices in the order of the filtration - simplex.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; + std::clog << "Simplex_tree dim: " << simplex.dimension() << std::endl; Persistent_cohomology pcoh(simplex); @@ -102,23 +99,23 @@ int main(int argc, char **argv) { auto persistent_pairs = pcoh.get_persistent_pairs(); std::sort(std::begin(persistent_pairs), std::end(persistent_pairs), cmp); for (auto pair : persistent_pairs) { - std::cout << simplex.dimension(get<0>(pair)) << " " + std::clog << simplex.dimension(get<0>(pair)) << " " << simplex.filtration(get<0>(pair)) << " " << simplex.filtration(get<1>(pair)) << std::endl; } // Persistent Betti numbers - std::cout << "The persistent Betti numbers in interval [0.40, 0.41] are : "; + std::clog << "The persistent Betti numbers in interval [0.40, 0.41] are : "; for (int dim = 0; dim < simplex.dimension(); dim++) - std::cout << "b" << dim << " = " << pcoh.persistent_betti_number(dim, 0.40, 0.41) << " ; "; - std::cout << std::endl; + std::clog << "b" << dim << " = " << pcoh.persistent_betti_number(dim, 0.40, 0.41) << " ; "; + std::clog << std::endl; // Betti numbers std::vector<int> betti_numbers = pcoh.betti_numbers(); - std::cout << "The Betti numbers are : "; + std::clog << "The Betti numbers are : "; for (std::size_t i = 0; i < betti_numbers.size(); i++) - std::cout << "b" << i << " = " << betti_numbers[i] << " ; "; - std::cout << std::endl; + std::clog << "b" << i << " = " << betti_numbers[i] << " ; "; + std::clog << std::endl; } return 0; } diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index d169cc63..7f89c001 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -37,9 +37,9 @@ int main(int argc, char * argv[]) { program_options(argc, argv, simplex_tree_file, output_file, p, min_persistence); - std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() + std::clog << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() << std::endl; - std::cout << " - p=" << p << " - min_persistence=" << min_persistence << std::endl; + std::clog << " - p=" << p << " - min_persistence=" << min_persistence << std::endl; // Read the list of simplices from a file. Simplex_tree<> simplex_tree; @@ -47,21 +47,18 @@ int main(int argc, char * argv[]) { std::ifstream simplex_tree_stream(simplex_tree_file); simplex_tree_stream >> simplex_tree; - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; - std::cout << " - dimension " << simplex_tree.dimension() << std::endl; + std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; + std::clog << " - dimension " << simplex_tree.dimension() << std::endl; /* - std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + std::clog << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; for( auto f_simplex : simplex_tree.filtration_simplex_range() ) - { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + { std::clog << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) - { std::cout << vertex << " "; } - std::cout << std::endl; + { std::clog << vertex << " "; } + std::clog << std::endl; }*/ - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - // Compute the persistence diagram of the complex Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree); // initializes the coefficient field for homology @@ -96,7 +93,7 @@ void program_options(int argc, char * argv[] visible.add_options() ("help,h", "produce help message") ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") + "Name of file in which the persistence diagram is written. Default print in standard output") ("field-charac,p", po::value<int>(&p)->default_value(11), "Characteristic p of the coefficient field Z/pZ for computing homology.") ("min-persistence,m", po::value<Filtration_value>(&min_persistence), @@ -114,17 +111,17 @@ void program_options(int argc, char * argv[] po::notify(vm); if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; + std::clog << std::endl; + std::clog << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::clog << "of a Rips complex defined on a set of input points.\n \n"; + std::clog << "The output diagram contains one bar per line, written with the convention: \n"; + std::clog << " p dim b d \n"; + std::clog << "where dim is the dimension of the homological feature,\n"; + std::clog << "b and d are respectively the birth and death of the feature and \n"; + std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::clog << visible << std::endl; exit(-1); } } 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 3c91662f..3da6771e 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -51,62 +51,62 @@ int main(int argc, char * const argv[]) { } // TEST OF INSERTION - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF INSERTION" << std::endl; + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST OF INSERTION" << std::endl; Simplex_tree st; // ++ FIRST - std::cout << " - INSERT (0,1,2)" << std::endl; + std::clog << " - INSERT (0,1,2)" << std::endl; typeVectorVertex SimplexVector = {0, 1, 2}; st.insert_simplex_and_subfaces(SimplexVector, 0.3); // ++ SECOND - std::cout << " - INSERT 3" << std::endl; + std::clog << " - INSERT 3" << std::endl; SimplexVector = {3}; st.insert_simplex_and_subfaces(SimplexVector, 0.1); // ++ THIRD - std::cout << " - INSERT (0,3)" << std::endl; + std::clog << " - INSERT (0,3)" << std::endl; SimplexVector = {0, 3}; st.insert_simplex_and_subfaces(SimplexVector, 0.2); // ++ FOURTH - std::cout << " - INSERT (0,1) (already inserted)" << std::endl; + std::clog << " - INSERT (0,1) (already inserted)" << std::endl; SimplexVector = {0, 1}; st.insert_simplex_and_subfaces(SimplexVector, 0.2); // ++ FIFTH - std::cout << " - INSERT (3,4,5)" << std::endl; + std::clog << " - INSERT (3,4,5)" << std::endl; SimplexVector = {3, 4, 5}; st.insert_simplex_and_subfaces(SimplexVector, 0.3); // ++ SIXTH - std::cout << " - INSERT (0,1,6,7)" << std::endl; + std::clog << " - INSERT (0,1,6,7)" << std::endl; SimplexVector = {0, 1, 6, 7}; st.insert_simplex_and_subfaces(SimplexVector, 0.4); // ++ SEVENTH - std::cout << " - INSERT (4,5,8,9)" << std::endl; + std::clog << " - INSERT (4,5,8,9)" << std::endl; SimplexVector = {4, 5, 8, 9}; st.insert_simplex_and_subfaces(SimplexVector, 0.4); // ++ EIGHTH - std::cout << " - INSERT (9,10,11)" << std::endl; + std::clog << " - INSERT (9,10,11)" << std::endl; SimplexVector = {9, 10, 11}; st.insert_simplex_and_subfaces(SimplexVector, 0.3); - // ++ NINETH - std::cout << " - INSERT (2,10,12)" << std::endl; + // ++ NINTH + std::clog << " - INSERT (2,10,12)" << std::endl; SimplexVector = {2, 10, 12}; st.insert_simplex_and_subfaces(SimplexVector, 0.3); // ++ TENTH - std::cout << " - INSERT (11,6)" << std::endl; + std::clog << " - INSERT (11,6)" << std::endl; SimplexVector = {6, 11}; st.insert_simplex_and_subfaces(SimplexVector, 0.2); // ++ ELEVENTH - std::cout << " - INSERT (13,14,15)" << std::endl; + std::clog << " - INSERT (13,14,15)" << std::endl; SimplexVector = {13, 14, 15}; st.insert_simplex_and_subfaces(SimplexVector, 0.25); @@ -131,24 +131,24 @@ int main(int argc, char * const argv[]) { /* An edge [10,12,2] */ - std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " + std::clog << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices " << 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::clog << " - dimension " << st.dimension() << std::endl; + std::clog << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; - std::cout << "**************************************************************" << std::endl; - std::cout << "strict graph G { " << std::endl; + std::clog << "**************************************************************" << std::endl; + std::clog << "strict graph G { " << std::endl; for (auto f_simplex : st.filtration_simplex_range()) { - std::cout << " " << "[" << st.filtration(f_simplex) << "] "; + std::clog << " " << "[" << st.filtration(f_simplex) << "] "; for (auto vertex : st.simplex_vertex_range(f_simplex)) { - std::cout << static_cast<int>(vertex) << " -- "; + std::clog << static_cast<int>(vertex) << " -- "; } - std::cout << ";" << std::endl; + std::clog << ";" << std::endl; } - std::cout << "}" << std::endl; - std::cout << "**************************************************************" << std::endl; + std::clog << "}" << std::endl; + std::clog << "**************************************************************" << std::endl; // Compute the persistence diagram of the complex Persistent_cohomology pcoh(st); diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index 84333e46..236b67de 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -59,9 +59,6 @@ int main() { st.insert_simplex_and_subfaces(edge35); st.insert_simplex(vertex4); - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - // Class for homology computation // By default, since the complex has dimension 1, only 0-dimensional homology would be computed. // Here we also want persistent homology to be computed for the maximal dimension in the complex (persistence_dim_max = true) @@ -83,9 +80,9 @@ int main() { pcoh.output_diagram(); // Print the Betti numbers are b0=2 and b1=2. - std::cout << std::endl; - std::cout << "The Betti numbers are : "; + std::clog << std::endl; + std::clog << "The Betti numbers are : "; for (int i = 0; i < 3; i++) - std::cout << "b" << i << " = " << pcoh.betti_number(i) << " ; "; - std::cout << std::endl; + std::clog << "b" << i << " = " << pcoh.betti_number(i) << " ; "; + std::clog << std::endl; } diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index 9eb5ccfc..84453898 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -56,11 +56,8 @@ int main(int argc, char * argv[]) { Simplex_tree simplex_tree; rips_complex_from_file.create_complex(simplex_tree, dim_max); - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); + std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::clog << " and has dimension " << simplex_tree.dimension() << " \n"; // Compute the persistence diagram of the complex Persistent_cohomology pcoh(simplex_tree); @@ -99,7 +96,7 @@ void program_options(int argc, char * argv[] visible.add_options() ("help,h", "produce help message") ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") + "Name of file in which the persistence diagram is written. Default print in standard output") ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), "Maximal length of an edge for the Rips complex construction.") ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), @@ -107,7 +104,7 @@ void program_options(int argc, char * argv[] ("min-field-charac,p", po::value<int>(&min_p)->default_value(2), "Minimal characteristic p of the coefficient field Z/pZ.") ("max-field-charac,q", po::value<int>(&max_p)->default_value(1223), - "Minimial characteristic q of the coefficient field Z/pZ.") + "Maximal characteristic q of the coefficient field Z/pZ.") ("min-persistence,m", po::value<Filtration_value>(&min_persistence), "Minimal lifetime of homology feature to be recorded. Default is 0"); @@ -123,20 +120,20 @@ void program_options(int argc, char * argv[] po::notify(vm); if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with various coefficient fields \n"; - std::cout << "of a Rips complex defined on a set of input points. The coefficient \n"; - std::cout << "fields are all the Z/rZ for a prime number r contained in the \n"; - std::cout << "specified range [p,q]\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p1*...*pr dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p1*...*pr is the product of prime numbers pi such that the homology \n"; - std::cout << "feature exists in homology with Z/piZ coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; + std::clog << std::endl; + std::clog << "Compute the persistent homology with various coefficient fields \n"; + std::clog << "of a Rips complex defined on a set of input points. The coefficient \n"; + std::clog << "fields are all the Z/rZ for a prime number r contained in the \n"; + std::clog << "specified range [p,q]\n \n"; + std::clog << "The output diagram contains one bar per line, written with the convention: \n"; + std::clog << " p1*...*pr dim b d \n"; + std::clog << "where dim is the dimension of the homological feature,\n"; + std::clog << "b and d are respectively the birth and death of the feature and \n"; + std::clog << "p1*...*pr is the product of prime numbers pi such that the homology \n"; + std::clog << "feature exists in homology with Z/piZ coefficients." << std::endl << std::endl; + + std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::clog << visible << std::endl; exit(-1); } } diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp index 02db05ec..6f37cf5c 100644 --- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp @@ -73,11 +73,8 @@ int main(int argc, char * argv[]) { // expand the graph until dimension dim_max st.expansion(dim_max); - std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << st.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - st.initialize_filtration(); + std::clog << "The complex contains " << st.num_simplices() << " simplices \n"; + std::clog << " and has dimension " << st.dimension() << " \n"; // Compute the persistence diagram of the complex Persistent_cohomology pcoh(st); @@ -115,7 +112,7 @@ void program_options(int argc, char * argv[] visible.add_options() ("help,h", "produce help message") ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") + "Name of file in which the persistence diagram is written. Default print in standard output") ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()), "Maximal length of an edge for the Rips complex construction.") @@ -138,17 +135,17 @@ void program_options(int argc, char * argv[] po::notify(vm); if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; + std::clog << std::endl; + std::clog << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::clog << "of a Rips complex defined on a set of input points.\n \n"; + std::clog << "The output diagram contains one bar per line, written with the convention: \n"; + std::clog << " p dim b d \n"; + std::clog << "where dim is the dimension of the homological feature,\n"; + std::clog << "b and d are respectively the birth and death of the feature and \n"; + std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::clog << visible << std::endl; exit(-1); } } diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp index 37fa5e93..6b60f603 100644 --- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp @@ -17,10 +17,6 @@ #include <boost/program_options.hpp> -#ifdef GUDHI_USE_TBB -#include <tbb/task_scheduler_init.h> -#endif - #include <string> #include <vector> @@ -64,13 +60,8 @@ int main(int argc, char * argv[]) { Simplex_tree& st = *new Simplex_tree; rips_complex_from_file.create_complex(st, dim_max); - std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << st.dimension() << " \n"; - -#ifdef GUDHI_USE_TBB - // Unnecessary, but clarifies which operations are parallel. - tbb::task_scheduler_init ts; -#endif + std::clog << "The complex contains " << st.num_simplices() << " simplices \n"; + std::clog << " and has dimension " << st.dimension() << " \n"; // Sort the simplices in the order of the filtration st.initialize_filtration(); @@ -81,10 +72,6 @@ int main(int argc, char * argv[]) { // Convert to a more convenient representation. Gudhi::Hasse_complex<> hcpx(st); -#ifdef GUDHI_USE_TBB - ts.terminate(); -#endif - // Free some space. delete &st; @@ -122,7 +109,7 @@ void program_options(int argc, char * argv[] visible.add_options() ("help,h", "produce help message") ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") + "Name of file in which the persistence diagram is written. Default print in standard output") ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), "Maximal length of an edge for the Rips complex construction.") ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), @@ -144,17 +131,17 @@ void program_options(int argc, char * argv[] po::notify(vm); if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Rips complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; + std::clog << std::endl; + std::clog << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::clog << "of a Rips complex defined on a set of input points.\n \n"; + std::clog << "The output diagram contains one bar per line, written with the convention: \n"; + std::clog << " p dim b d \n"; + std::clog << "where dim is the dimension of the homological feature,\n"; + std::clog << "b and d are respectively the birth and death of the feature and \n"; + std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::clog << visible << std::endl; exit(-1); } } |