diff options
author | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-04 10:24:04 +0000 |
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committer | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-10-04 10:24:04 +0000 |
commit | 73efba37dfcab3f9b8589cb3b0b80f6d7dd7bd0b (patch) | |
tree | 8ed0cf77fafbf47f0cb5bdea97d49b6611a1ef48 /src/Witness_complex/utilities | |
parent | f45959484fb85299d9ac60c43de9325e5c06e730 (diff) |
Document utilies in README files using Markdown + move/rename some utilities
Only missing doc for now: Garland_heckbert
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8
Diffstat (limited to 'src/Witness_complex/utilities')
-rw-r--r-- | src/Witness_complex/utilities/CMakeLists.txt | 26 | ||||
-rw-r--r-- | src/Witness_complex/utilities/README | 72 | ||||
-rw-r--r-- | src/Witness_complex/utilities/example_strong_witness_complex_off.cpp | 79 | ||||
-rw-r--r-- | src/Witness_complex/utilities/strong_witness_persistence.cpp (renamed from src/Witness_complex/utilities/example_strong_witness_persistence.cpp) | 0 | ||||
-rw-r--r-- | src/Witness_complex/utilities/weak_witness_persistence.cpp | 171 |
5 files changed, 257 insertions, 91 deletions
diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index 918ab864..125a41ff 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -3,24 +3,26 @@ project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) - add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) - target_link_libraries(Witness_complex_example_strong_off) + + add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp ) + target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp ) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp ) + target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) if (TBB_FOUND) - target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES}) + target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES}) endif() - add_test(NAME Witness_complex_example_strong_off_test_torus - COMMAND $<TARGET_FILE:Witness_complex_example_strong_off> - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") - add_test(NAME Witness_complex_example_strong_test_torus_persistence - COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence> + add_test(NAME Witness_complex_strong_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") + add_test(NAME Witness_complex_weak_test_torus_persistence + COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence> "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - install(TARGETS Witness_complex_example_strong_off DESTINATION bin) - install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin) endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README new file mode 100644 index 00000000..d8dc9ca7 --- /dev/null +++ b/src/Witness_complex/utilities/README @@ -0,0 +1,72 @@ +# Witness_complex #
+
+## `weak_witness_persistence` ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+`p dim b d`
+
+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+*Usage*
+`weak_witness_persistence [options] <OFF input file>`
+
+*Allowed options*
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-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.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+*Example*
+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`
+
+outputs:
+```
+Successfully read 1307 points.
+Ambient dimension is 3.
+The complex contains 732 simplices and has dimension 8
+11 0 0 inf
+11 1 0 inf
+11 2 0.0275251 0.0534586
+11 1 0 0.0239952
+```
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
+
+## `strong_witness_persistence` ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+`p dim b d`
+
+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.
+
+*Usage*
+`strong_witness_persistence [options] <OFF input file>`
+
+*Allowed options*
+
+* `-h [ --help ]` Produce help message
+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.
+* `-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.
+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.
+
+*Example*
+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`
+
+outputs:
+```
+Successfully read 1307 points.
+Ambient dimension is 3.
+The complex contains 1836 simplices and has dimension 8
+11 0 0 inf
+11 1 0.00674748 inf
+11 2 0.0937751 0.235354
+```
+
+N.B.: output is random as the 20 landmarks are chosen randomly.
diff --git a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp b/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp deleted file mode 100644 index 0ee9ee90..00000000 --- a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp +++ /dev/null @@ -1,79 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see <http://www.gnu.org/licenses/>. - */ - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Euclidean_strong_witness_complex.h> -#include <gudhi/pick_n_random_points.h> -#include <gudhi/Points_off_io.h> - -#include <CGAL/Epick_d.h> - -#include <iostream> -#include <fstream> -#include <ctime> -#include <string> -#include <vector> - -using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; -using Point_d = typename K::Point_d; -using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex<K>; -using Point_vector = std::vector<Point_d>; - -int main(int argc, char * const argv[]) { - if (argc != 5) { - std::cerr << "Usage: " << argv[0] - << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; - return 0; - } - - std::string file_name = argv[1]; - int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); - double alpha2 = atof(argv[3]); - clock_t start, end; - Gudhi::Simplex_tree<> simplex_tree; - - // Read the point file - Point_vector point_vector, landmarks; - Gudhi::Points_off_reader<Point_d> off_reader(file_name); - if (!off_reader.is_valid()) { - std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n"; - exit(-1); // ----- >> - } - point_vector = Point_vector(off_reader.get_point_cloud()); - - std::cout << "Successfully read " << point_vector.size() << " points.\n"; - std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; - - // Choose landmarks - Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - - // Compute witness complex - start = clock(); - Witness_complex witness_complex(landmarks, - point_vector); - - witness_complex.create_complex(simplex_tree, alpha2, lim_dim); - end = clock(); - std::cout << "Strong witness complex took " - << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n"; - std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; -} diff --git a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp index f786fe7b..f786fe7b 100644 --- a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp new file mode 100644 index 00000000..a1146922 --- /dev/null +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp @@ -0,0 +1,171 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Euclidean_witness_complex.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> +#include <gudhi/pick_n_random_points.h> + +#include <boost/program_options.hpp> + +#include <CGAL/Epick_d.h> + +#include <string> +#include <vector> +#include <limits> // infinity + +using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; +using Point_d = K::Point_d; + +using Point_vector = std::vector<Point_d>; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex<K>; +using SimplexTree = Gudhi::Simplex_tree<>; + +using Filtration_value = SimplexTree::Filtration_value; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp>; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence); + +int main(int argc, char * argv[]) { + std::string file_name; + std::string filediag; + Filtration_value max_squared_alpha; + int p, nbL, lim_d; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader<Point_d> off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + witnesses = Point_vector(off_reader.get_point_cloud()); + std::cout << "Successfully read " << witnesses.size() << " points.\n"; + std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; + + // Choose landmarks from witnesses + Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + Witness_complex witness_complex(landmarks, + witnesses); + + witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); + + 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(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , int & dim_max + , Filtration_value & min_persistence) { + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value<std::string>(&file_name), + "Name of file containing a point set in off format."); + + Filtration_value default_alpha = std::numeric_limits<Filtration_value>::infinity(); + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value<int>(&nbL), + "Number of landmarks to choose from the point cloud.") + ("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") + ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(default_alpha), + "Maximal squared relaxation parameter.") + ("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)->default_value(0), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") + ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()), + "Maximal dimension of the weak witness complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + po::variables_map vm; + + po::store(po::command_line_parser(argc, argv). + options(all).positional(pos).run(), vm); + 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 Weak witness 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::abort(); + } +} |