diff options
author | Gard Spreemann <gspr@nonempty.org> | 2023-01-20 13:47:30 +0100 |
---|---|---|
committer | Gard Spreemann <gspr@nonempty.org> | 2023-01-20 13:47:30 +0100 |
commit | 688cbc5c29d0a6aaf233eee185a06cef5cb2e745 (patch) | |
tree | cb13b84e9f7cddea48b903d24014f63d1dfda7e3 /src/Cech_complex | |
parent | 2b3caf86fc6500a9fca9e9085012a2315fbbac3b (diff) | |
parent | ed492f09ca3c9d7cd972bbbbec37f680cd624fbe (diff) |
Merge tag 'tags/gudhi-release-3.7.1' into dfsg/latestdfsg/latest
Diffstat (limited to 'src/Cech_complex')
-rw-r--r-- | src/Cech_complex/doc/Intro_cech_complex.h | 2 | ||||
-rw-r--r-- | src/Cech_complex/include/gudhi/Cech_complex.h | 3 | ||||
-rw-r--r-- | src/Cech_complex/utilities/CMakeLists.txt | 20 | ||||
-rw-r--r-- | src/Cech_complex/utilities/cech_persistence.cpp | 69 | ||||
-rw-r--r-- | src/Cech_complex/utilities/cechcomplex.md | 12 |
5 files changed, 80 insertions, 26 deletions
diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h index 595fb64b..73093c07 100644 --- a/src/Cech_complex/doc/Intro_cech_complex.h +++ b/src/Cech_complex/doc/Intro_cech_complex.h @@ -17,7 +17,7 @@ namespace cech_complex { /** \defgroup cech_complex Čech complex * - * \author Vincent Rouvreau + * \author Vincent Rouvreau, Hind montassif * * @{ * diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h index 625f7c9c..dbdf5e93 100644 --- a/src/Cech_complex/include/gudhi/Cech_complex.h +++ b/src/Cech_complex/include/gudhi/Cech_complex.h @@ -1,11 +1,12 @@ /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. - * Author(s): Vincent Rouvreau + * Author(s): Vincent Rouvreau, Hind Montassif * * Copyright (C) 2018 Inria * * Modification(s): * - YYYY/MM Author: Description of the modification + * - 2022/02 Hind Montassif : Replace MiniBall with Sphere_circumradius */ #ifndef CECH_COMPLEX_H_ 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 $<TARGET_FILE:cech_persistence> - "${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 $<TARGET_FILE:cech_persistence> + "${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 $<TARGET_FILE:cech_persistence> + "${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 $<TARGET_FILE:cech_persistence> + "${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..e6419f3d 100644 --- a/src/Cech_complex/utilities/cech_persistence.cpp +++ b/src/Cech_complex/utilities/cech_persistence.cpp @@ -16,6 +16,7 @@ #include <boost/program_options.hpp> #include <CGAL/Epeck_d.h> // For EXACT or SAFE version +#include <CGAL/Epick_d.h> // For FAST version #include <string> #include <vector> @@ -25,41 +26,66 @@ using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; using Filtration_value = Simplex_tree::Filtration_value; -using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>; -using Point = typename Kernel::Point_d; -using Points_off_reader = Gudhi::Points_off_reader<Point>; -using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; -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<class Kernel> +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<Point>; + using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>; + + 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<CGAL::Dynamic_dimension_tag>; + stree = create_simplex_tree<Fast_kernel>(off_file_points, exact_version, max_radius, dim_max); + } else { + using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>; + stree = create_simplex_tree<Kernel>(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<std::string>(&off_file_points), @@ -86,8 +113,12 @@ 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<std::string>(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::clog")( + "Name of file in which the persistence diagram is written. Default print in standard output")( "max-radius,r", po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), "Maximal length of an edge for the Cech complex construction.")( diff --git a/src/Cech_complex/utilities/cechcomplex.md b/src/Cech_complex/utilities/cechcomplex.md index 821e4dad..54c4e88d 100644 --- a/src/Cech_complex/utilities/cechcomplex.md +++ b/src/Cech_complex/utilities/cechcomplex.md @@ -26,18 +26,24 @@ a prime number). **Usage** -`cech_persistence [options] <OFF input file>` +`cech_persistence [options] <input OFF file>` + +where +`<input OFF file>` is the path to the input point cloud in +[nOFF ASCII format]({{ site.officialurl }}/doc/latest/fileformats.html#FileFormatsOFF). **Allowed options** * `-h [ --help ]` Produce help message * `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. -* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Čech complex construction. +* `-r [ --max-radius ]` (default = inf) Maximal radius for the Čech complex construction. * `-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. +Beware: this program may use a lot of RAM and take a lot of time if `max-radius` is set to a large value. **Example 1 with Z/2Z coefficients** |