From a034f774490ea06c018726ed58a0cfbe9d12d97c Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau Date: Mon, 26 Sep 2022 13:40:57 +0200 Subject: Cech_persistence utility for safe/exact/fast mode --- src/Cech_complex/utilities/CMakeLists.txt | 20 +++++++- src/Cech_complex/utilities/cech_persistence.cpp | 67 ++++++++++++++++++------- src/Cech_complex/utilities/cechcomplex.md | 8 ++- 3 files changed, 74 insertions(+), 21 deletions(-) diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt index e80a698e..64557cee 100644 --- a/src/Cech_complex/utilities/CMakeLists.txt +++ b/src/Cech_complex/utilities/CMakeLists.txt @@ -9,8 +9,24 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.0.1) target_link_libraries(cech_persistence ${TBB_LIBRARIES}) endif() - add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D_safe COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "safe.pers") + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D_fast COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "fast.pers" "-f") + add_test(NAME Cech_complex_utility_from_rips_on_tore_3D_exact COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3" "-o" "exact.pers" "-e") + + if (DIFF_PATH) + add_test(Cech_complex_utilities_diff_exact ${DIFF_PATH} + "exact.pers" "safe.pers") + set_tests_properties(Cech_complex_utilities_diff_exact PROPERTIES DEPENDS + "Cech_complex_utility_from_rips_on_tore_3D_safe;Cech_complex_utility_from_rips_on_tore_3D_exact") + + add_test(Cech_complex_utilities_diff_fast ${DIFF_PATH} + "fast.pers" "safe.pers") + set_tests_properties(Cech_complex_utilities_diff_fast PROPERTIES DEPENDS + "Cech_complex_utility_from_rips_on_tore_3D_safe;Cech_complex_utility_from_rips_on_tore_3D_fast") + endif() install(TARGETS cech_persistence DESTINATION bin) endif() diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp index 75d10c0f..a07ba212 100644 --- a/src/Cech_complex/utilities/cech_persistence.cpp +++ b/src/Cech_complex/utilities/cech_persistence.cpp @@ -16,6 +16,7 @@ #include #include // For EXACT or SAFE version +#include // For FAST version #include #include @@ -25,41 +26,66 @@ using Simplex_tree = Gudhi::Simplex_tree; using Filtration_value = Simplex_tree::Filtration_value; -using Kernel = CGAL::Epeck_d; -using Point = typename Kernel::Point_d; -using Points_off_reader = Gudhi::Points_off_reader; -using Cech_complex = Gudhi::cech_complex::Cech_complex; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; -void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, - Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence); +void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast, + std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p, + Filtration_value& min_persistence); + +template +Simplex_tree create_simplex_tree(const std::string &off_file_points, bool exact_version, + Filtration_value max_radius, int dim_max) { + using Point = typename Kernel::Point_d; + using Points_off_reader = Gudhi::Points_off_reader; + using Cech_complex = Gudhi::cech_complex::Cech_complex; + + Simplex_tree stree; + + Points_off_reader off_reader(off_file_points); + Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius, exact_version); + cech_complex_from_file.create_complex(stree, dim_max); + + return stree; +} int main(int argc, char* argv[]) { std::string off_file_points; std::string filediag; + bool exact_version = false; + bool fast_version = false; Filtration_value max_radius; int dim_max; int p; Filtration_value min_persistence; - program_options(argc, argv, off_file_points, filediag, max_radius, dim_max, p, min_persistence); + program_options(argc, argv, off_file_points, exact_version, fast_version, filediag, max_radius, dim_max, p, + min_persistence); - Points_off_reader off_reader(off_file_points); - Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius); + if ((exact_version) && (fast_version)) { + std::cerr << "You cannot set the exact and the fast version." << std::endl; + exit(-1); + } - // Construct the Cech complex in a Simplex Tree - Simplex_tree simplex_tree; + Simplex_tree stree; + if (fast_version) { + // WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d) + // (i.e. when the points are on a grid) + using Fast_kernel = CGAL::Epick_d; + stree = create_simplex_tree(off_file_points, exact_version, max_radius, dim_max); + } else { + using Kernel = CGAL::Epeck_d; + stree = create_simplex_tree(off_file_points, exact_version, max_radius, dim_max); + } - cech_complex_from_file.create_complex(simplex_tree, dim_max); - std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::clog << " and has dimension " << simplex_tree.dimension() << " \n"; + std::clog << "The complex contains " << stree.num_simplices() << " simplices \n"; + std::clog << " and has dimension " << stree.dimension() << " \n"; // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); + stree.initialize_filtration(); // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); + Persistent_cohomology pcoh(stree); // initializes the coefficient field for homology pcoh.init_coefficients(p); @@ -77,8 +103,9 @@ int main(int argc, char* argv[]) { return 0; } -void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, - Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence) { +void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast, + std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p, + Filtration_value& min_persistence) { namespace po = boost::program_options; po::options_description hidden("Hidden options"); hidden.add_options()("input-file", po::value(&off_file_points), @@ -86,6 +113,10 @@ void program_options(int argc, char* argv[], std::string& off_file_points, std:: po::options_description visible("Allowed options", 100); visible.add_options()("help,h", "produce help message")( + "exact,e", po::bool_switch(&exact), + "To activate exact version of Cech complex (default is false, not available if fast is set)")( + "fast,f", po::bool_switch(&fast), + "To activate fast version of Cech complex (default is false, not available if exact is set)")( "output-file,o", po::value(&filediag)->default_value(std::string()), "Name of file in which the persistence diagram is written. Default print in std::clog")( "max-radius,r", diff --git a/src/Cech_complex/utilities/cechcomplex.md b/src/Cech_complex/utilities/cechcomplex.md index 821e4dad..0e82674d 100644 --- a/src/Cech_complex/utilities/cechcomplex.md +++ b/src/Cech_complex/utilities/cechcomplex.md @@ -26,7 +26,11 @@ a prime number). **Usage** -`cech_persistence [options] ` +`cech_persistence [options] ` + +where +`` is the path to the input point cloud in +[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF). **Allowed options** @@ -36,6 +40,8 @@ a prime number). * `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Čech complex we want to compute. * `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. +* `-e [ --exact ]` for the exact computation version. +* `-f [ --fast ]` for the fast computation version. Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. -- cgit v1.2.3