diff options
Diffstat (limited to 'src/Persistent_cohomology')
17 files changed, 371 insertions, 400 deletions
diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index 2bb3b0c7..ad8dc84b 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -2,11 +2,13 @@ project(Persistent_cohomology_benchmark) if(GMP_FOUND) if(GMPXX_FOUND) - add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) - target_link_libraries(performance_rips_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) - if (TBB_FOUND) - target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) - endif(TBB_FOUND) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + if (TARGET Boost::program_options) + add_executable ( performance_rips_persistence EXCLUDE_FROM_ALL performance_rips_persistence.cpp ) + target_link_libraries(performance_rips_persistence Boost::program_options ${GMPXX_LIBRARIES} ${GMP_LIBRARIES}) + if (TBB_FOUND) + target_link_libraries(performance_rips_persistence ${TBB_LIBRARIES}) + endif(TBB_FOUND) + file(COPY "${CMAKE_SOURCE_DIR}/data/points/Kl.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + endif() endif(GMPXX_FOUND) endif(GMP_FOUND) diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp index 45757002..3bec8830 100644 --- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp +++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp @@ -49,7 +49,7 @@ void timing_persistence(FilteredComplex & cpx * with a Hasse diagram. The Hasse diagram represents explicitly all * codimension 1 incidence relations in the complex, and hence leads to * a faster computation of persistence because boundaries are precomputed. - * Hovewer, the simplex tree may be constructed directly from a point cloud and + * However, the simplex tree may be constructed directly from a point cloud and * is more compact. * We compute persistent homology with coefficient fields Z/2Z and Z/1223Z. * We present also timings for the computation of multi-field persistent @@ -74,7 +74,7 @@ int main(int argc, char * argv[]) { Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n"; + std::clog << "Compute Rips graph in " << elapsed_sec << " ms.\n"; // Construct the Rips complex in a Simplex Tree Simplex_tree st; @@ -86,16 +86,16 @@ int main(int argc, char * argv[]) { end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n"; - std::cout << " - dimension = " << st.dimension() << std::endl; - std::cout << " - number of simplices = " << st.num_simplices() << std::endl; + std::clog << "Compute Rips complex in " << elapsed_sec << " ms.\n"; + std::clog << " - dimension = " << st.dimension() << std::endl; + std::clog << " - number of simplices = " << st.num_simplices() << std::endl; // Sort the simplices in the order of the filtration start = std::chrono::system_clock::now(); st.initialize_filtration(); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n"; + std::clog << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n"; // Copy the keys inside the simplices start = std::chrono::system_clock::now(); @@ -106,22 +106,22 @@ int main(int argc, char * argv[]) { } end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n"; + std::clog << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n"; // Convert the simplex tree into a hasse diagram start = std::chrono::system_clock::now(); Gudhi::Hasse_complex<> hcpx(st); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n"; + std::clog << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n"; - std::cout << "Timings when using a simplex tree: \n"; + std::clog << "Timings when using a simplex tree: \n"; timing_persistence(st, p); timing_persistence(st, q); timing_persistence(st, p, q); - std::cout << "Timings when using a Hasse complex: \n"; + std::clog << "Timings when using a Hasse complex: \n"; timing_persistence(hcpx, p); timing_persistence(hcpx, q); timing_persistence(hcpx, p, q); @@ -130,7 +130,7 @@ int main(int argc, char * argv[]) { } end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n"; + std::clog << "Running the complex destructors in " << elapsed_sec << " ms.\n"; return 0; } @@ -145,13 +145,13 @@ timing_persistence(FilteredComplex & cpx Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n"; + std::clog << " Initialize pcoh in " << elapsed_sec << " ms.\n"; // initializes the coefficient field for homology start = std::chrono::system_clock::now(); pcoh.init_coefficients(p); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; + std::clog << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; start = std::chrono::system_clock::now(); @@ -159,12 +159,12 @@ timing_persistence(FilteredComplex & cpx end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n"; + std::clog << " Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n"; start = std::chrono::system_clock::now(); } end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; + std::clog << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; } template< typename FilteredComplex> @@ -179,13 +179,13 @@ timing_persistence(FilteredComplex & cpx Gudhi::persistent_cohomology::Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n"; + std::clog << " Initialize pcoh in " << elapsed_sec << " ms.\n"; // initializes the coefficient field for homology start = std::chrono::system_clock::now(); pcoh.init_coefficients(p, q); end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; + std::clog << " Initialize the coefficient field in " << elapsed_sec << " ms.\n"; // compute persistent homology, disgarding persistent features of life shorter than min_persistence start = std::chrono::system_clock::now(); @@ -194,11 +194,11 @@ timing_persistence(FilteredComplex & cpx end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ " + std::clog << " Compute multi-field persistent homology in all coefficient fields Z/pZ " << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n"; start = std::chrono::system_clock::now(); } end = std::chrono::system_clock::now(); elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count(); - std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; + std::clog << " Run the persistence destructors in " << elapsed_sec << " ms.\n"; } diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h index 26ac7ac8..59ce25e3 100644 --- a/src/Persistent_cohomology/concept/FilteredComplex.h +++ b/src/Persistent_cohomology/concept/FilteredComplex.h @@ -103,7 +103,7 @@ Filtration_simplex_range filtration_simplex_range(); /** @} */ -/* \brief Iterator over the simplices of the complex, +/** \brief Iterator over the simplices of the complex, * in an arbitrary order. * * 'value_type' must be 'Simplex_handle'.*/ diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 46b784d8..94579564 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -21,7 +21,7 @@ namespace persistent_cohomology { \author Clément Maria Computation of persistent cohomology using the algorithm of - \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 + \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:conf/compgeom/DeyFW14 and the Compressed Annotation Matrix implementation of \cite DBLP:conf/esa/BoissonnatDM13 @@ -131,8 +131,7 @@ namespace persistent_cohomology { We provide several example files: run these examples with -h for details on their use, and read the README file. -\li <a href="_rips_complex_2rips_persistence_8cpp-example.html"> -Rips_complex/rips_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its persistence +\li \gudhi_example_link{Rips_complex,rips_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence diagram. \code $> ./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 \endcode \code The complex contains 177838 simplices @@ -144,12 +143,10 @@ diagram. More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="_persistent_cohomology_2rips_multifield_persistence_8cpp-example.html"> -Persistent_cohomology/rips_multifield_persistence.cpp</a> computes the Rips complex of a point cloud and outputs its +\li \gudhi_example_link{Persistent_cohomology,rips_multifield_persistence.cpp} computes the Rips complex of a point cloud and outputs its persistence diagram with a family of field coefficients. -\li <a href="_rips_complex_2rips_distance_matrix_persistence_8cpp-example.html"> -Rips_complex/rips_distance_matrix_persistence.cpp</a> computes the Rips complex of a distance matrix and +\li \gudhi_example_link{Rips_complex,rips_distance_matrix_persistence.cpp} computes the Rips complex of a distance matrix and outputs its persistence diagram. The file should contain square or lower triangular distance matrix with semicolons as separators. @@ -158,8 +155,7 @@ Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="_rips_complex_2rips_correlation_matrix_persistence_8cpp-example.html"> -Rips_complex/rips_correlation_matrix_persistence.cpp</a> +\li \gudhi_example_link{Rips_complex,rips_correlation_matrix_persistence.cpp} computes the Rips complex of a correlation matrix and outputs its persistence diagram. Note that no check is performed if the matrix given as the input is a correlation matrix. @@ -169,8 +165,7 @@ Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv More details on the <a href="../../ripscomplex/">Rips complex utilities</a> dedicated page. -\li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html"> -Alpha_complex/alpha_complex_3d_persistence.cpp</a> computes the persistent homology with +\li \gudhi_example_link{Alpha_complex,alpha_complex_3d_persistence.cpp} computes the persistent homology with \f$\mathbb{Z}/2\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45 \endcode \code Simplex_tree dim: 3 @@ -235,8 +230,7 @@ Note that the lengths of the sides of the periodic cuboid have to be the same.<b 3 2 36.8838 inf 3 3 58.6783 inf \endcode -\li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html"> -Alpha_complex/alpha_complex_persistence.cpp</a> computes the persistent homology with +\li \gudhi_example_link{Alpha_complex,alpha_complex_persistence.cpp} computes the persistent homology with \f$\mathbb{Z}/p\mathbb{Z}\f$ coefficients of the alpha complex on points sampling from an OFF file. \code $> ./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off \endcode \code Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. @@ -248,8 +242,7 @@ Simplex_tree dim: 3 More details on the <a href="../../alphacomplex/">Alpha complex utilities</a> dedicated page. -\li <a href="_persistent_cohomology_2plain_homology_8cpp-example.html"> -Persistent_cohomology/plain_homology.cpp</a> computes the plain homology of a simple simplicial complex without +\li \gudhi_example_link{Persistent_cohomology,plain_homology.cpp} computes the plain homology of a simple simplicial complex without filtration values. */ 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); } } diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index 0f1876d0..c00bd33d 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -100,7 +100,7 @@ class Persistent_cohomology { ds_rank_(num_simplices_), // union-find ds_parent_(num_simplices_), // union-find ds_repr_(num_simplices_, NULL), // union-find -> annotation vectors - dsets_(&ds_rank_[0], &ds_parent_[0]), // union-find + dsets_(ds_rank_.data(), ds_parent_.data()), // union-find cam_(), // collection of annotation vectors zero_cocycles_(), // union-find -> Simplex_key of creator for 0-homology transverse_idx_(), // key -> row @@ -211,7 +211,7 @@ class Persistent_cohomology { /** \brief Update the cohomology groups under the insertion of an edge. * * The 0-homology is maintained with a simple Union-Find data structure, which - * explains the existance of a specific function of edge insertions. */ + * explains the existence of a specific function of edge insertions. */ void update_cohomology_groups_edge(Simplex_handle sigma) { Simplex_handle u, v; boost::tie(u, v) = cpx_->endpoints(sigma); @@ -288,10 +288,7 @@ class Persistent_cohomology { // with multiplicity. We used to sum the coefficients directly in // annotations_in_boundary by using a map, we now do it later. typedef std::pair<Column *, int> annotation_t; -#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL - thread_local -#endif // GUDHI_CAN_USE_CXX11_THREAD_LOCAL - std::vector<annotation_t> annotations_in_boundary; + thread_local std::vector<annotation_t> annotations_in_boundary; annotations_in_boundary.clear(); int sign = 1 - 2 * (dim_sigma % 2); // \in {-1,1} provides the sign in the // alternate sum in the boundary. @@ -564,35 +561,22 @@ class Persistent_cohomology { void output_diagram(std::ostream& ostream = std::cout) { cmp_intervals_by_length cmp(cpx_); std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); - bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity; for (auto pair : persistent_pairs_) { - // Special case on windows, inf is "1.#INF" (cf. unitary tests and R package TDA) - if (has_infinity && cpx_->filtration(get<1>(pair)) == std::numeric_limits<Filtration_value>::infinity()) { - ostream << get<2>(pair) << " " << cpx_->dimension(get<0>(pair)) << " " - << cpx_->filtration(get<0>(pair)) << " inf " << std::endl; - } else { - ostream << get<2>(pair) << " " << cpx_->dimension(get<0>(pair)) << " " - << cpx_->filtration(get<0>(pair)) << " " - << cpx_->filtration(get<1>(pair)) << " " << std::endl; - } + ostream << get<2>(pair) << " " << cpx_->dimension(get<0>(pair)) << " " + << cpx_->filtration(get<0>(pair)) << " " + << cpx_->filtration(get<1>(pair)) << " " << std::endl; } } void write_output_diagram(std::string diagram_name) { std::ofstream diagram_out(diagram_name.c_str()); + diagram_out.exceptions(diagram_out.failbit); cmp_intervals_by_length cmp(cpx_); std::sort(std::begin(persistent_pairs_), std::end(persistent_pairs_), cmp); - bool has_infinity = std::numeric_limits<Filtration_value>::has_infinity; for (auto pair : persistent_pairs_) { - // Special case on windows, inf is "1.#INF" - if (has_infinity && cpx_->filtration(get<1>(pair)) == std::numeric_limits<Filtration_value>::infinity()) { - diagram_out << cpx_->dimension(get<0>(pair)) << " " - << cpx_->filtration(get<0>(pair)) << " inf" << std::endl; - } else { - diagram_out << cpx_->dimension(get<0>(pair)) << " " - << cpx_->filtration(get<0>(pair)) << " " - << cpx_->filtration(get<1>(pair)) << std::endl; - } + diagram_out << cpx_->dimension(get<0>(pair)) << " " + << cpx_->filtration(get<0>(pair)) << " " + << cpx_->filtration(get<1>(pair)) << std::endl; } } @@ -739,7 +723,7 @@ class Persistent_cohomology { boost::disjoint_sets<int *, Simplex_key *> dsets_; /* The compressed annotation matrix fields.*/ Cam cam_; - /* Dictionary establishing the correspondance between the Simplex_key of + /* Dictionary establishing the correspondence between the Simplex_key of * the root vertex in the union-find ds and the Simplex_key of the vertex which * created the connected component as a 0-dimension homology feature.*/ std::map<Simplex_key, Simplex_key> zero_cocycles_; diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h index 0673625c..f442b632 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h @@ -13,6 +13,7 @@ #include <utility> #include <vector> +#include <stdexcept> namespace Gudhi { @@ -33,15 +34,28 @@ class Field_Zp { } void init(int charac) { - assert(charac > 0); // division by zero + non negative values Prime = charac; + + // Check that the provided prime is less than the maximum allowed as int, calculation below, and 'plus_times_equal' function : 46337 ; i.e (max_prime-1)*max_prime <= INT_MAX + if(Prime > 46337) + throw std::invalid_argument("Maximum homology_coeff_field allowed value is 46337"); + + // Check for primality + if (Prime <= 1) + throw std::invalid_argument("homology_coeff_field must be a prime number"); + inverse_.clear(); inverse_.reserve(charac); inverse_.push_back(0); for (int i = 1; i < Prime; ++i) { int inv = 1; - while (((inv * i) % Prime) != 1) + int mult = inv * i; + while ( (mult % Prime) != 1) { ++inv; + if(mult == Prime) + throw std::invalid_argument("homology_coeff_field must be a prime number"); + mult = inv * i; + } inverse_.push_back(inv); } } diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp index b9f11607..7a2feeff 100644 --- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp +++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp @@ -82,7 +82,7 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) // 2 1 0 inf // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1. - std::cout << "BETTI NUMBERS" << std::endl; + std::clog << "BETTI NUMBERS" << std::endl; BOOST_CHECK(pcoh.betti_number(0) == 2); BOOST_CHECK(pcoh.betti_number(1) == 1); @@ -94,7 +94,7 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) BOOST_CHECK(bns[1] == 1); BOOST_CHECK(bns[2] == 0); - std::cout << "GET PERSISTENT PAIRS" << std::endl; + std::clog << "GET PERSISTENT PAIRS" << std::endl; // Custom sort and output persistence cmp_intervals_by_dim_then_length<Mini_simplex_tree> cmp(&st); @@ -118,12 +118,12 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 0); BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex()); - std::cout << "INTERVALS IN DIMENSION" << std::endl; + std::clog << "INTERVALS IN DIMENSION" << std::endl; auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0); - std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; + std::clog << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; for (std::size_t i = 0; i < intervals_in_dimension_0.size(); i++) - std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << + std::clog << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << intervals_in_dimension_0[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_0.size() == 2); BOOST_CHECK(intervals_in_dimension_0[0].first == 0); @@ -133,16 +133,16 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers ) auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1); - std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; + std::clog << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; for (std::size_t i = 0; i < intervals_in_dimension_1.size(); i++) - std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << + std::clog << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << intervals_in_dimension_1[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_1.size() == 1); BOOST_CHECK(intervals_in_dimension_1[0].first == 0); BOOST_CHECK(intervals_in_dimension_1[0].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity()); auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2); - std::cout << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl; + std::clog << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl; BOOST_CHECK(intervals_in_dimension_2.size() == 0); } @@ -259,12 +259,12 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) BOOST_CHECK(st.filtration(get<0>(persistent_pairs[2])) == 1); BOOST_CHECK(get<1>(persistent_pairs[2]) == st.null_simplex()); - std::cout << "INTERVALS IN DIMENSION" << std::endl; + std::clog << "INTERVALS IN DIMENSION" << std::endl; auto intervals_in_dimension_0 = pcoh.intervals_in_dimension(0); - std::cout << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; + std::clog << "intervals_in_dimension_0.size() = " << intervals_in_dimension_0.size() << std::endl; for (std::size_t i = 0; i < intervals_in_dimension_0.size(); i++) - std::cout << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << + std::clog << "intervals_in_dimension_0[" << i << "] = [" << intervals_in_dimension_0[i].first << "," << intervals_in_dimension_0[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_0.size() == 2); BOOST_CHECK(intervals_in_dimension_0[0].first == 2); @@ -273,19 +273,19 @@ BOOST_AUTO_TEST_CASE( betti_numbers ) BOOST_CHECK(intervals_in_dimension_0[1].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity()); auto intervals_in_dimension_1 = pcoh.intervals_in_dimension(1); - std::cout << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; + std::clog << "intervals_in_dimension_1.size() = " << intervals_in_dimension_1.size() << std::endl; for (std::size_t i = 0; i < intervals_in_dimension_1.size(); i++) - std::cout << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << + std::clog << "intervals_in_dimension_1[" << i << "] = [" << intervals_in_dimension_1[i].first << "," << intervals_in_dimension_1[i].second << "]" << std::endl; BOOST_CHECK(intervals_in_dimension_1.size() == 1); BOOST_CHECK(intervals_in_dimension_1[0].first == 4); BOOST_CHECK(intervals_in_dimension_1[0].second == std::numeric_limits<Mini_simplex_tree::Filtration_value>::infinity()); auto intervals_in_dimension_2 = pcoh.intervals_in_dimension(2); - std::cout << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl; + std::clog << "intervals_in_dimension_2.size() = " << intervals_in_dimension_2.size() << std::endl; BOOST_CHECK(intervals_in_dimension_2.size() == 0); - std::cout << "EMPTY COMPLEX" << std::endl; + std::clog << "EMPTY COMPLEX" << std::endl; Simplex_tree empty; empty.initialize_filtration(); St_persistence pcoh_empty(empty, false); diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp index a1c106d5..ea41a8aa 100644 --- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp +++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp @@ -21,7 +21,7 @@ using namespace boost::unit_test; typedef Simplex_tree<> typeST; -std::string test_rips_persistence(int coefficient, int min_persistence) { +std::string test_persistence(int coefficient, int min_persistence) { // file is copied in CMakeLists.txt std::ifstream simplex_tree_stream; simplex_tree_stream.open("simplex_tree_file_for_unit_test.txt"); @@ -30,7 +30,7 @@ std::string test_rips_persistence(int coefficient, int min_persistence) { simplex_tree_stream.close(); // Display the Simplex_tree - std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() + std::clog << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() << std::endl; // Check @@ -44,16 +44,16 @@ std::string test_rips_persistence(int coefficient, int min_persistence) { Persistent_cohomology<Simplex_tree<>, Field_Zp> pcoh(st); pcoh.init_coefficients( coefficient ); // initializes the coefficient field for homology - // Check infinite rips + // Compute the persistent homology of the complex pcoh.compute_persistent_cohomology( min_persistence ); // Minimal lifetime of homology feature to be recorded. - std::ostringstream ossInfinite; + std::ostringstream ossPers; - pcoh.output_diagram(ossInfinite); - std::string strInfinite = ossInfinite.str(); - return strInfinite; + pcoh.output_diagram(ossPers); + std::string strPers = ossPers.str(); + return strPers; } -void test_rips_persistence_in_dimension(int dimension) { +void test_persistence_with_coeff_field(int coeff_field) { std::string value0(" 0 0.02 1.12"); std::string value1(" 0 0.03 1.13"); std::string value2(" 0 0.04 1.14"); @@ -65,112 +65,104 @@ void test_rips_persistence_in_dimension(int dimension) { std::string value8(" 0 0 inf" ); std::string value9(" 0 0.01 inf" ); - value0.insert(0,std::to_string(dimension)); - value1.insert(0,std::to_string(dimension)); - value2.insert(0,std::to_string(dimension)); - value3.insert(0,std::to_string(dimension)); - value4.insert(0,std::to_string(dimension)); - value5.insert(0,std::to_string(dimension)); - value6.insert(0,std::to_string(dimension)); - value7.insert(0,std::to_string(dimension)); - value8.insert(0,std::to_string(dimension)); - value9.insert(0,std::to_string(dimension)); - - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=0" << std::endl; - - std::string str_rips_persistence = test_rips_persistence(dimension, 0); - std::cout << str_rips_persistence << std::endl; + value0.insert(0,std::to_string(coeff_field)); + value1.insert(0,std::to_string(coeff_field)); + value2.insert(0,std::to_string(coeff_field)); + value3.insert(0,std::to_string(coeff_field)); + value4.insert(0,std::to_string(coeff_field)); + value5.insert(0,std::to_string(coeff_field)); + value6.insert(0,std::to_string(coeff_field)); + value7.insert(0,std::to_string(coeff_field)); + value8.insert(0,std::to_string(coeff_field)); + value9.insert(0,std::to_string(coeff_field)); + + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST OF PERSISTENT_COHOMOLOGY_SINGLE_FIELD COEFF_FIELD=" << coeff_field << " MIN_PERS=0" << std::endl; + + std::string str_persistence = test_persistence(coeff_field, 0); + std::clog << str_persistence << std::endl; - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value4) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value5) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value6) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value7) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; - - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=1" << std::endl; - - str_rips_persistence = test_rips_persistence(dimension, 1); - - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value4) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value5) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value6) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value7) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; - - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=2" << std::endl; - - str_rips_persistence = test_rips_persistence(dimension, 2); - - BOOST_CHECK(str_rips_persistence.find(value0) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value1) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value2) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value3) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value4) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value5) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value6) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value7) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; - - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_SINGLE_FIELD DIM=" << dimension << " MIN_PERS=Inf" << std::endl; - - str_rips_persistence = test_rips_persistence(dimension, (std::numeric_limits<int>::max)()); - - BOOST_CHECK(str_rips_persistence.find(value0) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value1) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value2) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value3) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value4) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value5) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value6) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value7) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value8) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value9) != std::string::npos); // Check found - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; + BOOST_CHECK(str_persistence.find(value0) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value1) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value2) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value3) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value4) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value5) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value6) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value7) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value8) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value9) != std::string::npos); // Check found + std::clog << "str_persistence=" << str_persistence << std::endl; + + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST OF PERSISTENT_COHOMOLOGY_SINGLE_FIELD COEFF_FIELD=" << coeff_field << " MIN_PERS=1" << std::endl; + + str_persistence = test_persistence(coeff_field, 1); + + BOOST_CHECK(str_persistence.find(value0) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value1) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value2) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value3) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value4) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value5) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value6) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value7) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value8) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value9) != std::string::npos); // Check found + std::clog << "str_persistence=" << str_persistence << std::endl; + + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST OF PERSISTENT_COHOMOLOGY_SINGLE_FIELD COEFF_FIELD=" << coeff_field << " MIN_PERS=2" << std::endl; + + str_persistence = test_persistence(coeff_field, 2); + + BOOST_CHECK(str_persistence.find(value0) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value1) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value2) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value3) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value4) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value5) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value6) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value7) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value8) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value9) != std::string::npos); // Check found + std::clog << "str_persistence=" << str_persistence << std::endl; + + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST OF PERSISTENT_COHOMOLOGY_SINGLE_FIELD COEFF_FIELD=" << coeff_field << " MIN_PERS=Inf" << std::endl; + + str_persistence = test_persistence(coeff_field, (std::numeric_limits<int>::max)()); + + BOOST_CHECK(str_persistence.find(value0) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value1) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value2) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value3) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value4) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value5) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value6) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value7) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value8) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value9) != std::string::npos); // Check found + std::clog << "str_persistence=" << str_persistence << std::endl; } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_1 ) +BOOST_AUTO_TEST_CASE( persistent_cohomology_single_field_coeff_not_prime ) { - test_rips_persistence_in_dimension(1); + for (auto non_prime : {0, 1, 4, 6}) + BOOST_CHECK_THROW(test_persistence_with_coeff_field(non_prime), std::invalid_argument); } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_2 ) +BOOST_AUTO_TEST_CASE( persistent_cohomology_single_field_coeff_prime ) { - test_rips_persistence_in_dimension(2); + for (auto prime : {2, 3, 5, 11, 13}) + test_persistence_with_coeff_field(prime); } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_3 ) +BOOST_AUTO_TEST_CASE( persistent_cohomology_single_field_coeff_limit ) { - test_rips_persistence_in_dimension(3); + BOOST_CHECK_THROW(test_persistence_with_coeff_field(46349), std::invalid_argument); } -BOOST_AUTO_TEST_CASE( rips_persistent_cohomology_single_field_dim_5 ) -{ - test_rips_persistence_in_dimension(5); -} - -// TODO(VR): not working from 6 -// std::string str_rips_persistence = test_rips_persistence(6, 0); -// TODO(VR): division by zero -// std::string str_rips_persistence = test_rips_persistence(0, 0); - /** SimplexTree minimal options to test the limits. * * Maximum number of simplices to compute persistence is <CODE>std::numeric_limits<std::uint8_t>::max()<\CODE> = 256.*/ 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 9e767943..c6c0bfaf 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 @@ -21,7 +21,7 @@ using namespace boost::unit_test; typedef Simplex_tree<> typeST; -std::string test_rips_persistence(int min_coefficient, int max_coefficient, double min_persistence) { +std::string test_persistence(int min_coefficient, int max_coefficient, double min_persistence) { // file is copied in CMakeLists.txt std::ifstream simplex_tree_stream; simplex_tree_stream.open("simplex_tree_file_for_multi_field_unit_test.txt"); @@ -30,7 +30,7 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub simplex_tree_stream.close(); // Display the Simplex_tree - std::cout << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() + std::clog << "The complex contains " << st.num_simplices() << " simplices" << " - dimension= " << st.dimension() << std::endl; // Check @@ -44,17 +44,17 @@ std::string test_rips_persistence(int min_coefficient, int max_coefficient, doub Persistent_cohomology<Simplex_tree<>, Multi_field> pcoh(st); pcoh.init_coefficients(min_coefficient, max_coefficient); // initializes the coefficient field for homology - // Check infinite rips + // Compute the persistent homology of the complex pcoh.compute_persistent_cohomology(min_persistence); // Minimal lifetime of homology feature to be recorded. - std::ostringstream ossRips; - pcoh.output_diagram(ossRips); + std::ostringstream ossPers; + pcoh.output_diagram(ossPers); - std::string strRips = ossRips.str(); - return strRips; + std::string strPers = ossPers.str(); + return strPers; } -void test_rips_persistence_in_dimension(int min_dimension, int max_dimension) { +void test_persistence_with_coeff_field(int min_coefficient, int max_coefficient) { // there are 2 discontinued ensembles std::string value0(" 0 0.25 inf"); std::string value1(" 1 0.4 inf"); @@ -68,48 +68,60 @@ void test_rips_persistence_in_dimension(int min_dimension, int max_dimension) { std::string value6(" 2 0.3 inf"); std::string value7(" 2 0.4 inf"); - std::cout << "********************************************************************" << std::endl; - std::cout << "TEST OF RIPS_PERSISTENT_COHOMOLOGY_MULTI_FIELD MIN_DIM=" << min_dimension << " MAX_DIM=" << max_dimension << " MIN_PERS=0" << std::endl; + std::clog << "********************************************************************" << std::endl; + std::clog << "TEST OF PERSISTENT_COHOMOLOGY_MULTI_FIELD MIN_COEFF=" << min_coefficient << " MAX_COEFF=" << max_coefficient << " MIN_PERS=0" << std::endl; - std::string str_rips_persistence = test_rips_persistence(min_dimension, max_dimension, 0.0); - std::cout << "str_rips_persistence=" << str_rips_persistence << std::endl; + std::string str_persistence = test_persistence(min_coefficient, max_coefficient, 0.0); + std::clog << "str_persistence=" << str_persistence << std::endl; - BOOST_CHECK(str_rips_persistence.find(value0) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value1) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value2) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value0) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value1) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value2) != std::string::npos); // Check found - if ((min_dimension < 2) && (max_dimension < 2)) { - BOOST_CHECK(str_rips_persistence.find(value3) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value4) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value5) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value6) != std::string::npos); // Check found - BOOST_CHECK(str_rips_persistence.find(value7) != std::string::npos); // Check found + if ((min_coefficient < 2) && (max_coefficient < 2)) { + BOOST_CHECK(str_persistence.find(value3) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value4) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value5) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value6) != std::string::npos); // Check found + BOOST_CHECK(str_persistence.find(value7) != std::string::npos); // Check found } else { - BOOST_CHECK(str_rips_persistence.find(value3) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value4) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value5) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value6) == std::string::npos); // Check not found - BOOST_CHECK(str_rips_persistence.find(value7) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value3) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value4) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value5) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value6) == std::string::npos); // Check not found + BOOST_CHECK(str_persistence.find(value7) == std::string::npos); // Check not found } } -BOOST_AUTO_TEST_CASE(rips_persistent_cohomology_multi_field_dim_1_2) { - test_rips_persistence_in_dimension(0, 1); +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_0_0) { + test_persistence_with_coeff_field(0, 0); } -BOOST_AUTO_TEST_CASE(rips_persistent_cohomology_multi_field_dim_2_3) { - test_rips_persistence_in_dimension(1, 3); +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_0_1) { + test_persistence_with_coeff_field(0, 1); } -BOOST_AUTO_TEST_CASE(rips_persistent_cohomology_multi_field_dim_1_5) { - test_rips_persistence_in_dimension(1, 5); +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_0_6) { + test_persistence_with_coeff_field(0, 6); } -// TODO(VR): not working from 6 -// std::string str_rips_persistence = test_rips_persistence(6, 0); -// TODO(VR): division by zero -// std::string str_rips_persistence = test_rips_persistence(0, 0); -// TODO(VR): is result OK of : -// test_rips_persistence_in_dimension(3, 4); +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_1_2) { + test_persistence_with_coeff_field(1, 2); +} + +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_1_3) { + test_persistence_with_coeff_field(1, 3); +} + +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_1_5) { + test_persistence_with_coeff_field(1, 5); +} + +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_2_3) { + test_persistence_with_coeff_field(2, 3); +} +BOOST_AUTO_TEST_CASE(persistent_cohomology_multi_field_coeff_3_4) { + test_persistence_with_coeff_field(3, 4); +} |