From d439da1345822fe25f58adb631f7d0cd9749ecfc Mon Sep 17 00:00:00 2001 From: skachano Date: Wed, 5 Oct 2016 17:06:15 +0000 Subject: Modified existing tests and examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1647 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cd187fe5bc9174403aa5dc96c74871c697b3a5e6 --- .../example/example_witness_complex_off.cpp | 86 ++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 src/Witness_complex/example/example_witness_complex_off.cpp (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp new file mode 100644 index 00000000..6b0060d9 --- /dev/null +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -0,0 +1,86 @@ +/* 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) 2015 INRIA Sophia Antipolis-Méditerranée (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 . + */ + +#include +#include + +#include +#include +#include +#include + +#include + +#include +#include +#include +#include +#include + +typedef CGAL::Epick_d K; +typedef typename K::Point_d Point_d; +typedef typename Gudhi::witness_complex::Witness_complex Witness_complex; +typedef std::vector< Vertex_handle > typeVectorVertex; +typedef std::vector< Point_d > Point_vector; + +int main(int argc, char * const argv[]) { + if (argc != 4) { + std::cerr << "Usage: " << argv[0] + << " path_to_point_file nbL alpha^2\n"; + return 0; + } + + std::string file_name = argv[1]; + int nbL = atoi(argv[2]); + double alpha2 = atof(argv[3]); + clock_t start, end; + + // Construct the Simplex Tree + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "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.begin(), + landmarks.end(), + point_vector.begin(), + point_vector.end()); + witness_complex.create_complex(simplex_tree, alpha2); + end = clock(); + std::cout << "Witness complex took " + << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; +} -- cgit v1.2.3 From 07e6b3d053144329a03bf7c8f52538d221e6ea6d Mon Sep 17 00:00:00 2001 From: skachano Date: Thu, 6 Oct 2016 18:11:50 +0000 Subject: Added persistence examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1670 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c7762be9b79ba70cca84a378915c2deef13211fd --- src/Witness_complex/example/CMakeLists.txt | 7 +- .../example/example_strong_witness_persistence.cpp | 172 +++++++++++++++++++++ .../example/example_witness_complex_off.cpp | 3 +- .../example_witness_complex_persistence.cpp | 172 +++++++++++++++++++++ .../include/gudhi/Strong_witness_complex.h | 12 +- .../include/gudhi/Witness_complex.h | 2 +- 6 files changed, 361 insertions(+), 7 deletions(-) create mode 100644 src/Witness_complex/example/example_strong_witness_persistence.cpp create mode 100644 src/Witness_complex/example/example_witness_complex_persistence.cpp (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 469c9aac..38cfa821 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -7,7 +7,12 @@ if(CGAL_FOUND) if (EIGEN3_FOUND) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) - #add_executable ( relaxed_witness_persistence relaxed_witness_persistence.cpp ) + add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) + target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + add_test(Witness_complex_test_torus_persistence src/Witness_complex/example/Witness_complex_example_witncess_complex_persistence ../data/points/tore3D_1307.off -l 20 -a 0.5) + 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_test(Witness_complex_test_torus_persistence src/Witness_complex/example/Witness_complex_example_strong_witness_persistence ../data/points/tore3D_1307.off -l 20 -a 0.5) endif(EIGEN3_FOUND) endif (NOT CGAL_VERSION VERSION_LESS 4.6.0) endif() diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp new file mode 100644 index 00000000..bf6b4011 --- /dev/null +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -0,0 +1,172 @@ +/* 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 Sophia Antipolis-Méditerranée (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 . + */ + +#include +#include +#include +#include +#include + +#include + +#include + +#include +#include +#include // infinity + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +typedef CGAL::Epick_d K; +typedef typename K::Point_d Point_d; + +typedef typename std::vector Point_vector; +typedef typename Gudhi::witness_complex::Strong_witness_complex Strong_witness_complex; +typedef Gudhi::Simplex_tree<> SimplexTree; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , 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; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader 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 + Strong_witness_complex strong_witness_complex(landmarks.begin(), + landmarks.end(), + witnesses.begin(), + witnesses.end()); + + strong_witness_complex.create_complex(simplex_tree, max_squared_alpha); + + 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::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 + , Filtration_value & min_persistence) { + + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&file_name), + "Name of file containing a point set in off format."); + + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value(&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(&max_squared_alpha)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::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"); + + 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 Strong 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(); + } +} + diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 6b0060d9..849a0a40 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -53,8 +53,6 @@ int main(int argc, char * const argv[]) { int nbL = atoi(argv[2]); double alpha2 = atof(argv[3]); clock_t start, end; - - // Construct the Simplex Tree Gudhi::Simplex_tree<> simplex_tree; // Read the point file @@ -78,6 +76,7 @@ int main(int argc, char * const argv[]) { landmarks.end(), point_vector.begin(), point_vector.end()); + witness_complex.create_complex(simplex_tree, alpha2); end = clock(); std::cout << "Witness complex took " diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp new file mode 100644 index 00000000..9b06b504 --- /dev/null +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -0,0 +1,172 @@ +/* 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 Sophia Antipolis-Méditerranée (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 . + */ + +#include +#include +#include +#include +#include + +#include + +#include + +#include +#include +#include // infinity + +using namespace Gudhi; +using namespace Gudhi::persistent_cohomology; + +typedef CGAL::Epick_d K; +typedef typename K::Point_d Point_d; + +typedef typename std::vector Point_vector; +typedef typename Gudhi::witness_complex::Witness_complex Witness_complex; +typedef Gudhi::Simplex_tree<> SimplexTree; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options(int argc, char * argv[] + , int & nbL + , std::string & file_name + , std::string & filediag + , Filtration_value & max_squared_alpha + , int & p + , 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; + Filtration_value min_persistence; + SimplexTree simplex_tree; + + program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence); + + // Extract the points from the file file_name + Point_vector witnesses, landmarks; + Gudhi::Points_off_reader 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.begin(), + landmarks.end(), + witnesses.begin(), + witnesses.end()); + + witness_complex.create_complex(simplex_tree, max_squared_alpha); + + 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::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 + , Filtration_value & min_persistence) { + + namespace po = boost::program_options; + + po::options_description hidden("Hidden options"); + hidden.add_options() + ("input-file", po::value(&file_name), + "Name of file containing a point set in off format."); + + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("landmarks,l", po::value(&nbL), + "Number of landmarks to choose from the point cloud.") + ("output-file,o", po::value(&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(&max_squared_alpha)->default_value(std::numeric_limits::infinity()), + "Maximal length of an edge for the Rips complex construction.") + ("field-charac,p", po::value(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::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"); + + 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(); + } +} + diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index f5633a98..3a862d71 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -27,9 +27,6 @@ #include #include #include -#include "gudhi/reader_utils.h" -#include "gudhi/distance_functions.h" -#include "gudhi/Simplex_tree.h" #include #include #include @@ -39,6 +36,11 @@ #include #include +#include "Active_witness/Active_witness.h" +#include +#include + + // Needed for nearest neighbours #include #include @@ -142,6 +144,7 @@ private: FT max_alpha_square) { unsigned nbL = landmarks_.size(); + unsigned complex_dim = 0; if (complex.num_vertices() > 0) { std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; return false; @@ -168,7 +171,10 @@ private: complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second); aw_it++; } + if (simplex.size() - 1 > complex_dim) + complex_dim = simplex.size() - 1; } + complex.set_dimension(complex_dim); return true; } diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index a16f9270..7d8fce86 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -31,7 +31,6 @@ #include #include "Active_witness/Active_witness.h" -#include #include #include @@ -175,6 +174,7 @@ private: } k++; } + complex.set_dimension(k-1); return true; } -- cgit v1.2.3 From 1bcd448f6e217655fae4bfbf62d8d3b6caa52503 Mon Sep 17 00:00:00 2001 From: skachano Date: Fri, 7 Oct 2016 09:49:47 +0000 Subject: Added the possibility to limit dimension git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1676 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 16ec8706ffb981ff892960468cc4b809e61612e2 --- .../example/example_strong_witness_persistence.cpp | 10 +++++++--- .../example/example_witness_complex_off.cpp | 6 +++--- .../example_witness_complex_persistence.cpp | 12 +++++++---- .../include/gudhi/Active_witness/Active_witness.h | 3 +++ .../gudhi/Active_witness/Active_witness_iterator.h | 7 +++++++ .../include/gudhi/Strong_witness_complex.h | 23 ++++++++++++++-------- .../include/gudhi/Witness_complex.h | 23 +++++++++++++--------- 7 files changed, 57 insertions(+), 27 deletions(-) (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index bf6b4011..4e06867d 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -53,17 +53,18 @@ void program_options(int argc, char * argv[] , 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; + int p, nbL, lim_d; Filtration_value min_persistence; SimplexTree simplex_tree; - program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence); + 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; @@ -119,6 +120,7 @@ void program_options(int argc, char * argv[] , std::string & filediag , Filtration_value & max_squared_alpha , int & p + , int & dim_max , Filtration_value & min_persistence) { namespace po = boost::program_options; @@ -141,7 +143,9 @@ void program_options(int argc, char * argv[] ("field-charac,p", po::value(&p)->default_value(11), "Characteristic p of the coefficient field Z/pZ for computing homology.") ("min-persistence,m", po::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"); + "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(&dim_max)->default_value(std::numeric_limits::max()), + "Maximal dimension of the strong witness complex we want to compute."); po::positional_options_description pos; pos.add("input-file", 1); diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 849a0a40..37646faf 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -45,12 +45,12 @@ typedef std::vector< Point_d > Point_vector; int main(int argc, char * const argv[]) { if (argc != 4) { std::cerr << "Usage: " << argv[0] - << " path_to_point_file nbL alpha^2\n"; + << " 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]); + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); double alpha2 = atof(argv[3]); clock_t start, end; Gudhi::Simplex_tree<> simplex_tree; @@ -77,7 +77,7 @@ int main(int argc, char * const argv[]) { point_vector.begin(), point_vector.end()); - witness_complex.create_complex(simplex_tree, alpha2); + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); end = clock(); std::cout << "Witness complex took " << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index 9b06b504..a4388047 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -53,17 +53,18 @@ void program_options(int argc, char * argv[] , 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; + int p, nbL, lim_d; Filtration_value min_persistence; SimplexTree simplex_tree; - program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, min_persistence); + 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; @@ -119,6 +120,7 @@ void program_options(int argc, char * argv[] , std::string & filediag , Filtration_value & max_squared_alpha , int & p + , int & dim_max , Filtration_value & min_persistence) { namespace po = boost::program_options; @@ -141,8 +143,10 @@ void program_options(int argc, char * argv[] ("field-charac,p", po::value(&p)->default_value(11), "Characteristic p of the coefficient field Z/pZ for computing homology.") ("min-persistence,m", po::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"); - + "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(&dim_max)->default_value(std::numeric_limits::max()), + "Maximal dimension of the weak witness complex we want to compute."); + po::positional_options_description pos; pos.add("input-file", 1); diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index 9ae41a69..e52410e4 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -31,6 +31,9 @@ namespace Gudhi { namespace witness_complex { + /** \brief Class representing a list of nearest neighbors to a given witness. + * \detail Every element is a pair of a landmark identifier and the squared distance to it. + */ template< typename Id_distance_pair, typename INS_range > class Active_witness { diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 5d4f3d75..9c96f7e8 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -31,6 +31,13 @@ namespace Gudhi { namespace witness_complex { + /** \brief Iterator in the nearest landmark list. + * \detail After the iterator reaches the end of the list, + * the list is augmented by a (nearest landmark, distance) pair if possible. + * If all the landmarks are present in the list, iterator returns the specific end value + * of the corresponding 'Active_witness' object. + */ + template< typename Active_witness, typename Id_distance_pair, typename INS_iterator > diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index 3a862d71..e125d307 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -138,19 +138,26 @@ private: /** \brief Outputs the (weak) witness complex with * squared relaxation parameter 'max_alpha_square' * to simplicial complex 'complex'. + * The parameter 'limit_dimension' represents the maximal dimension of the simplicial complex + * (default value = no limit). */ template < typename SimplicialComplexForWitness > bool create_complex(SimplicialComplexForWitness& complex, - FT max_alpha_square) + FT max_alpha_square, + Landmark_id limit_dimension = std::numeric_limits::max()) { - unsigned nbL = landmarks_.size(); - unsigned complex_dim = 0; + std::size_t nbL = landmarks_.size(); + Landmark_id complex_dim = 0; if (complex.num_vertices() > 0) { - std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; + std::cerr << "Strong witness complex cannot create complex - complex is not empty.\n"; return false; } if (max_alpha_square < 0) { - std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; + std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; + return false; + } + if (limit_dimension < 0) { + std::cerr << "Strong witness complex cannot create complex - limit dimension must be non-negative.\n"; return false; } typeVectorVertex vv; @@ -165,13 +172,13 @@ private: ActiveWitness aw(landmark_tree_.query_incremental_nearest_neighbors(w)); typeVectorVertex simplex; typename ActiveWitness::iterator aw_it = aw.begin(); - float lim_d2 = aw.begin()->second + max_alpha_square; - while (aw_it != aw.end() && aw_it->second < lim_d2) { + float lim_dist2 = aw.begin()->second + max_alpha_square; + while ((Landmark_id)simplex.size() <= limit_dimension + 1 && aw_it != aw.end() && aw_it->second < lim_dist2) { simplex.push_back(aw_it->first); complex.insert_simplex_and_subfaces(simplex, aw_it->second - aw.begin()->second); aw_it++; } - if (simplex.size() - 1 > complex_dim) + if ((Landmark_id)simplex.size() - 1 > complex_dim) complex_dim = simplex.size() - 1; } complex.set_dimension(complex_dim); diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 7d8fce86..2a89306d 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -129,7 +129,8 @@ private: */ template < typename SimplicialComplexForWitness > bool create_complex(SimplicialComplexForWitness& complex, - FT max_alpha_square) + FT max_alpha_square, + Landmark_id limit_dimension = std::numeric_limits::max()) { std::size_t nbL = landmarks_.size(); if (complex.num_vertices() > 0) { @@ -140,6 +141,10 @@ private: std::cerr << "Witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; return false; } + if (limit_dimension < 0) { + std::cerr << "Witness complex cannot create complex - limit dimension must be non-negative.\n"; + return false; + } typeVectorVertex vv; ActiveWitnessList active_witnesses;// = new ActiveWitnessList(); for (unsigned i = 0; i != nbL; ++i) { @@ -150,13 +155,13 @@ private: complex.insert_simplex(vv, Filtration_value(0.0)); /* TODO Error if not inserted : normally no need here though*/ } - unsigned k = 1; /* current dimension in iterative construction */ + Landmark_id k = 1; /* current dimension in iterative construction */ for (auto w: witnesses_) active_witnesses.push_back(ActiveWitness(landmark_tree_.query_incremental_nearest_neighbors(w))); ActiveWitness aw_copy(active_witnesses.front()); - while (!active_witnesses.empty() && k < nbL ) { + while (!active_witnesses.empty() && k <= limit_dimension ) { typename ActiveWitnessList::iterator aw_it = active_witnesses.begin(); - std::vector simplex; + std::vector simplex; simplex.reserve(k+1); while (aw_it != active_witnesses.end()) { bool ok = add_all_faces_of_dimension(k, @@ -191,7 +196,7 @@ private: double alpha2, double norelax_dist2, typename ActiveWitness::iterator curr_l, - std::vector& simplex, + std::vector& simplex, SimplicialComplexForWitness& sc, typename ActiveWitness::iterator end) { @@ -251,17 +256,17 @@ private: * inserted_vertex is the handle of the (k+1)-th vertex witnessed by witness_id */ template < typename SimplicialComplexForWitness > - bool all_faces_in(std::vector& simplex, + bool all_faces_in(typeVectorVertex& simplex, double* filtration_value, SimplicialComplexForWitness& sc) { typedef typename SimplicialComplexForWitness::Simplex_handle Simplex_handle; - std::vector< int > facet; - for (std::vector::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) + typeVectorVertex facet; + for (typename typeVectorVertex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) { facet.clear(); - for (std::vector::iterator it = simplex.begin(); it != simplex.end(); ++it) + for (typename typeVectorVertex::iterator it = simplex.begin(); it != simplex.end(); ++it) if (it != not_it) facet.push_back(*it); Simplex_handle facet_sh = sc.find(facet); -- cgit v1.2.3 From 4473c9fd8d23097ed7b5570b800db245539e91d2 Mon Sep 17 00:00:00 2001 From: skachano Date: Tue, 18 Oct 2016 12:32:40 +0000 Subject: Removed Sophia Antipolis from copyrights git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1731 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f97758e943397259712ad76c4db117df3d3415b6 --- src/Witness_complex/example/example_strong_witness_persistence.cpp | 2 +- src/Witness_complex/example/example_witness_complex_off.cpp | 2 +- src/Witness_complex/example/example_witness_complex_persistence.cpp | 2 +- src/Witness_complex/example/example_witness_complex_sphere.cpp | 2 +- src/Witness_complex/include/gudhi/Active_witness/Active_witness.h | 2 +- .../include/gudhi/Active_witness/Active_witness_iterator.h | 2 +- src/Witness_complex/include/gudhi/Strong_witness_complex.h | 2 +- src/Witness_complex/include/gudhi/Witness_complex.h | 2 +- src/Witness_complex/test/test_simple_witness_complex.cpp | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index 4e06867d..f43cba52 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * 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 diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 37646faf..94088370 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index a4388047..b1b415fa 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * 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 diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 8e2c5ff6..d21195fa 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index c6113442..fce7d3d1 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * 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 diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 25897de6..ae051bea 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * 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 diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index 73de580d..7ef8d3e5 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index e336dc4f..ac0e8f66 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2015 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 diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp index 759ee14d..90b6cfa2 100644 --- a/src/Witness_complex/test/test_simple_witness_complex.cpp +++ b/src/Witness_complex/test/test_simple_witness_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA Sophia Antipolis-Méditerranée (France) + * 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 -- cgit v1.2.3 From fe79f2dcfd8b1540485d8a81fa7cedd07f5c8fac Mon Sep 17 00:00:00 2001 From: skachano Date: Wed, 19 Oct 2016 08:19:49 +0000 Subject: Clément's remarks MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1735 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c3bc66a081a0bc73874246e1e12ab98c6bf2a53e --- src/Witness_complex/doc/Witness_complex_doc.h | 10 +++++-- .../example/example_strong_witness_persistence.cpp | 28 ++---------------- .../example/example_witness_complex_off.cpp | 28 ++---------------- .../example_witness_complex_persistence.cpp | 28 ++---------------- .../example/example_witness_complex_sphere.cpp | 27 ++--------------- .../include/gudhi/Strong_witness_complex.h | 27 ++++++++--------- .../include/gudhi/Witness_complex.h | 32 +++++++------------- .../test/test_simple_witness_complex.cpp | 34 +++------------------- 8 files changed, 43 insertions(+), 171 deletions(-) (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 4f3671e5..2831f107 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -17,7 +17,7 @@ Even though often the set of landmarks \f$L\f$ is a subset of the set of witnesses \f$ W\f$, it is not a requirement for the current implementation. - The simplices are based on landmarks + Landmarks are the vertices of the simplicial complex and witnesses help to decide on which simplices are inserted via a predicate "is witnessed". De Silva and Carlsson in their paper \cite de2004topological differentiate **weak witnessing** and **strong witnessing**: @@ -47,7 +47,13 @@ The constructors take on the step 1, while the function 'create_complex' executes the steps 2 and 3. - \section witnessexamples Examples + \section witnessexample1 Example 1: Constructing weak relaxed witness complex from an off file + + Let's start with a simple example, which reads an off point file and computes a weak witness complex. + + \include Witness_complex/example_witness_complex_off.cpp + + \section witnessexample2 Example2: Computing persistence using strong relaxed witness complex Here is an example of constructing a strong witness complex filtration and computing persistence on it: diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index f43cba52..a0563ee2 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -1,25 +1,3 @@ -/* 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 . - */ - #include #include #include @@ -81,10 +59,8 @@ int main(int argc, char * argv[]) { Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); // Compute witness complex - Strong_witness_complex strong_witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + Strong_witness_complex strong_witness_complex(landmarks, + witnesses); strong_witness_complex.create_complex(simplex_tree, max_squared_alpha); diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 94088370..2677499a 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -1,25 +1,3 @@ -/* 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) 2015 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 . - */ - #include #include @@ -72,10 +50,8 @@ int main(int argc, char * const argv[]) { // Compute witness complex start = clock(); - Witness_complex witness_complex(landmarks.begin(), - landmarks.end(), - point_vector.begin(), - point_vector.end()); + Witness_complex witness_complex(landmarks, + point_vector); witness_complex.create_complex(simplex_tree, alpha2, lim_dim); end = clock(); diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index b1b415fa..00f00aae 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -1,25 +1,3 @@ -/* 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 . - */ - #include #include #include @@ -81,10 +59,8 @@ int main(int argc, char * argv[]) { Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + Witness_complex witness_complex(landmarks, + witnesses); witness_complex.create_complex(simplex_tree, max_squared_alpha); diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index d21195fa..42fb9f8d 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -1,24 +1,3 @@ -/* 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) 2015 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 . - */ #define BOOST_PARAMETER_MAX_ARITY 12 @@ -80,10 +59,8 @@ int main(int argc, char * const argv[]) { Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks.begin(), - landmarks.end(), - point_vector.begin(), - point_vector.end()); + Witness_complex witness_complex(landmarks, + point_vector); witness_complex.create_complex(simplex_tree, 0); end = clock(); double time = static_cast(end - start) / CLOCKS_PER_SEC; diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index 7ef8d3e5..c7b8c27b 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -94,22 +94,18 @@ private: /** * \brief Initializes member variables before constructing simplicial complex. - * \details Records landmarks from the range [landmarks_first, landmarks_last) into a - * table internally, as well as witnesses from the range [witnesses_first, witnesses_last). - * All iterator parameters should satisfy InputIterator - * C++ concept. + * \details Records landmarks from the range 'landmarks' into a + * table internally, as well as witnesses from the range 'witnesses'. */ - template< typename InputIteratorLandmarks, - typename InputIteratorWitnesses > - Strong_witness_complex(InputIteratorLandmarks landmarks_first, - InputIteratorLandmarks landmarks_last, - InputIteratorWitnesses witnesses_first, - InputIteratorWitnesses witnesses_last) - : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_) + template< typename LandmarkRange, + typename WitnessRange > + Strong_witness_complex(const LandmarkRange & landmarks, + const WitnessRange & witnesses) + : witnesses_(witnesses), landmarks_(landmarks), landmark_tree_(landmarks_) { } + /** \brief Returns the point corresponding to the given vertex. */ template @@ -118,9 +114,10 @@ private: return landmarks_[vertex]; } - /** \brief Outputs the strong witness complex in a simplicial complex data structure. - * @param[out] complex Simplicial complex data structure compatible with 'find' and 'insert' operations. - * (Cf SimplicialComplexForWitness) + /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' + * in a simplicial complex data structure. + * @param[out] complex Simplicial complex data structure, which is a model of + * SimplicialComplexForWitness concept. * @param[in] max_alpha_square Maximal squared relaxation parameter. * @param[in] limit_dimension Represents the maximal dimension of the simplicial complex * (default value = no limit). diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index ac0e8f66..c1d402c6 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -46,12 +46,6 @@ namespace witness_complex { * \tparam Kernel_ requires a CGAL::Epick_d class, which * can be static if you know the ambiant dimension at compile-time, or dynamic if you don't. - * \tparam DimensionTag can be either Dimension_tag - * if you know the intrinsic dimension at compile-time, - * or CGAL::Dynamic_dimension_tag - * if you don't. */ template< class Kernel_ > class Witness_complex { @@ -94,19 +88,14 @@ private: /** * \brief Initializes member variables before constructing simplicial complex. - * \details Records landmarks from the range [landmarks_first, landmarks_last) into a - * table internally, as well as witnesses from the range [witnesses_first, witnesses_last). - * All iterator parameters should satisfy InputIterator - * C++ concept. + * \details Records landmarks from the range 'landmarks' into a + * table internally, as well as witnesses from the range 'witnesses'. */ - template< typename InputIteratorLandmarks, - typename InputIteratorWitnesses > - Witness_complex(InputIteratorLandmarks landmarks_first, - InputIteratorLandmarks landmarks_last, - InputIteratorWitnesses witnesses_first, - InputIteratorWitnesses witnesses_last) - : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_) + template< typename LandmarkRange, + typename WitnessRange > + Witness_complex(const LandmarkRange & landmarks, + const WitnessRange & witnesses) + : witnesses_(witnesses), landmarks_(landmarks), landmark_tree_(landmarks_) { } @@ -118,9 +107,10 @@ private: return landmarks_[vertex]; } - /** \brief Outputs the (weak) witness complex in a simplicial complex data structure. - * @param[out] complex Simplicial complex data structure compatible with 'find' and 'insert' operations. - * (Cf SimplicialComplexForWitness) + /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square' + * in a simplicial complex data structure. + * @param[out] complex Simplicial complex data structure compatible which is a model of + * SimplicialComplexForWitness concept. * @param[in] max_alpha_square Maximal squared relaxation parameter. * @param[in] limit_dimension Represents the maximal dimension of the simplicial complex * (default value = no limit). diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp index 90b6cfa2..a0a1b36c 100644 --- a/src/Witness_complex/test/test_simple_witness_complex.cpp +++ b/src/Witness_complex/test/test_simple_witness_complex.cpp @@ -1,25 +1,3 @@ -/* 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 . - */ - #define BOOST_TEST_DYN_LINK #define BOOST_TEST_MODULE "simple_witness_complex" #include @@ -79,10 +57,8 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) { witnesses.push_back(Point_d(std::vector{ 2,-1})); witnesses.push_back(Point_d(std::vector{ 2, 1})); - WitnessComplex witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + WitnessComplex witness_complex(landmarks, + witnesses); witness_complex.create_complex(complex, 0); std::cout << "complex.num_simplices() = " << complex.num_simplices() << std::endl; @@ -93,10 +69,8 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) { std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex.num_simplices() << std::endl; BOOST_CHECK(relaxed_complex.num_simplices() == 239); - StrongWitnessComplex strong_witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + StrongWitnessComplex strong_witness_complex(landmarks, + witnesses); strong_witness_complex.create_complex(strong_relaxed_complex, 9.1); -- cgit v1.2.3 From 22f0bc7f98e4ead21616fa10a3b3c3279a922ee4 Mon Sep 17 00:00:00 2001 From: skachano Date: Mon, 21 Nov 2016 16:15:13 +0000 Subject: Fixed small bug in an example. Thanks to Clément MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1765 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ef71f8be01c177a6b0da8ff58849f1041659e523 --- src/Witness_complex/doc/Witness_complex_doc.h | 2 +- src/Witness_complex/example/example_witness_complex_off.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index ba258ddc..fa45e359 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -34,7 +34,7 @@ which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and **strong relaxed witness complex** respectively. - \image html "swit.svg" "Strong witness witnesses the whole simplex in the witnessing ball" + \image html "swit.svg" "Strongly witnessed simplex" In particular case of 0-relaxation, weak complex corresponds to **witness complex** introduced in \cite de2004topological, whereas 0-relaxed strong witness complex consists of just vertices and is not very interesting. Hence for small relaxation weak version is preferable. diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 2677499a..c057c118 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -21,7 +21,7 @@ typedef std::vector< Vertex_handle > typeVectorVertex; typedef std::vector< Point_d > Point_vector; int main(int argc, char * const argv[]) { - if (argc != 4) { + if (argc != 5) { std::cerr << "Usage: " << argv[0] << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; return 0; -- cgit v1.2.3 From 82132d5dce57c85c183d62d423f26771f7775440 Mon Sep 17 00:00:00 2001 From: skachano Date: Wed, 18 Jan 2017 22:03:13 +0000 Subject: Changed some examples git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@1955 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ce1d18aa2eceb5c3be7eaf4b420081ec16875ea7 --- src/Witness_complex/example/example_strong_witness_persistence.cpp | 4 ++-- src/Witness_complex/example/example_witness_complex_off.cpp | 4 ++-- src/Witness_complex/example/example_witness_complex_persistence.cpp | 4 ++-- src/Witness_complex/example/example_witness_complex_sphere.cpp | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index c81cafd1..d42603aa 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -1,5 +1,5 @@ #include -#include +#include #include #include #include @@ -19,7 +19,7 @@ typedef CGAL::Epick_d K; typedef typename K::Point_d Point_d; typedef typename std::vector Point_vector; -typedef typename Gudhi::witness_complex::Strong_witness_complex Strong_witness_complex; +typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex Strong_witness_complex; typedef Gudhi::Simplex_tree<> SimplexTree; typedef int Vertex_handle; diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index c057c118..751d2d4c 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -2,7 +2,7 @@ #include #include -#include +#include #include #include @@ -16,7 +16,7 @@ typedef CGAL::Epick_d K; typedef typename K::Point_d Point_d; -typedef typename Gudhi::witness_complex::Witness_complex Witness_complex; +typedef typename Gudhi::witness_complex::Euclidean_witness_complex Witness_complex; typedef std::vector< Vertex_handle > typeVectorVertex; typedef std::vector< Point_d > Point_vector; diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index 0350b9cc..fbb18cb4 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -1,5 +1,5 @@ #include -#include +#include #include #include #include @@ -19,7 +19,7 @@ typedef CGAL::Epick_d K; typedef typename K::Point_d Point_d; typedef typename std::vector Point_vector; -typedef typename Gudhi::witness_complex::Witness_complex Witness_complex; +typedef typename Gudhi::witness_complex::Euclidean_witness_complex Witness_complex; typedef Gudhi::Simplex_tree<> SimplexTree; typedef int Vertex_handle; diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 42fb9f8d..90e0339a 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -5,7 +5,7 @@ #include #include -#include +#include #include #include @@ -32,7 +32,7 @@ void write_data(Data_range & data, std::string filename) { } int main(int argc, char * const argv[]) { - typedef Gudhi::witness_complex::Witness_complex> Witness_complex; + typedef Gudhi::witness_complex::Euclidean_witness_complex> Witness_complex; if (argc != 2) { std::cerr << "Usage: " << argv[0] -- cgit v1.2.3 From f2b63bcaa647d1ec839dbe2e5edbe5c4fde1b304 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 28 Feb 2017 16:16:08 +0000 Subject: Fix cppcheck git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@2120 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 49a5c2c6e94d9fbf235eecc92fa30e62980c7c70 --- .../example/example_nearest_landmark_table.cpp | 34 ++++++++++---- .../example/example_strong_witness_complex_off.cpp | 28 +++++++++-- .../example/example_strong_witness_persistence.cpp | 54 ++++++++++++++-------- .../example/example_witness_complex_off.cpp | 11 ++--- .../example_witness_complex_persistence.cpp | 22 +++++++++ .../example/example_witness_complex_sphere.cpp | 33 +++++++++---- src/Witness_complex/example/generators.h | 14 +++--- .../include/gudhi/Active_witness/Active_witness.h | 22 ++++----- .../gudhi/Active_witness/Active_witness_iterator.h | 41 ++++++++-------- .../gudhi/Euclidean_strong_witness_complex.h | 29 ++++++------ .../include/gudhi/Strong_witness_complex.h | 54 ++++++++++------------ .../include/gudhi/Witness_complex.h | 42 ++++++++--------- .../include/gudhi/Witness_complex/all_faces_in.h | 30 ++++++++++-- 13 files changed, 250 insertions(+), 164 deletions(-) (limited to 'src/Witness_complex/example/example_witness_complex_off.cpp') diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp index b3883248..65b675f9 100644 --- a/src/Witness_complex/example/example_nearest_landmark_table.cpp +++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp @@ -1,16 +1,31 @@ -#define BOOST_PARAMETER_MAX_ARITY 12 - +/* 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 . + */ -#include -#include +#define BOOST_PARAMETER_MAX_ARITY 12 #include #include -#include #include -#include - #include #include #include @@ -24,6 +39,8 @@ int main(int argc, char * const argv[]) { using Nearest_landmark_table = std::vector; using Witness_complex = Gudhi::witness_complex::Witness_complex; using Simplex_tree = Gudhi::Simplex_tree<>; + using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; + using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; Simplex_tree simplex_tree; Nearest_landmark_table nlt; @@ -45,8 +62,7 @@ int main(int argc, char * const argv[]) { std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl; - using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; - Gudhi::persistent_cohomology::Persistent_cohomology pcoh(simplex_tree); + Persistent_cohomology pcoh(simplex_tree); // initializes the coefficient field for homology pcoh.init_coefficients(11); diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index 6a4925b8..0ee9ee90 100644 --- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -1,5 +1,24 @@ -#include -#include +/* 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 . + */ #include #include @@ -16,9 +35,8 @@ using K = CGAL::Epick_d; using Point_d = typename K::Point_d; -typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex Witness_complex; -using typeVectorVertex = std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle >; -using Point_vector = std::vector< Point_d >; +using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using Point_vector = std::vector; int main(int argc, char * const argv[]) { if (argc != 5) { diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index d42603aa..5efe69fd 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -1,3 +1,25 @@ +/* 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 . + */ + #include #include #include @@ -12,18 +34,17 @@ #include #include // infinity -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; +using K = CGAL::Epick_d; +using Point_d = K::Point_d; -typedef CGAL::Epick_d K; -typedef typename K::Point_d Point_d; +using Point_vector = std::vector; +using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using SimplexTree = Gudhi::Simplex_tree<>; -typedef typename std::vector Point_vector; -typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex Strong_witness_complex; -typedef Gudhi::Simplex_tree<> SimplexTree; +using Filtration_value = SimplexTree::Filtration_value; -typedef int Vertex_handle; -typedef double Filtration_value; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; void program_options(int argc, char * argv[] , int & nbL @@ -61,9 +82,9 @@ int main(int argc, char * argv[]) { // Compute witness complex Strong_witness_complex strong_witness_complex(landmarks, witnesses); - + strong_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"; @@ -71,7 +92,7 @@ int main(int argc, char * argv[]) { simplex_tree.initialize_filtration(); // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology pcoh(simplex_tree); + Persistent_cohomology pcoh(simplex_tree); // initializes the coefficient field for homology pcoh.init_coefficients(p); @@ -89,7 +110,6 @@ int main(int argc, char * argv[]) { return 0; } - void program_options(int argc, char * argv[] , int & nbL , std::string & file_name @@ -98,14 +118,12 @@ void program_options(int argc, char * argv[] , 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(&file_name), "Name of file containing a point set in off format."); - po::options_description visible("Allowed options", 100); visible.add_options() @@ -122,7 +140,7 @@ void program_options(int argc, char * argv[] "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(&dim_max)->default_value(std::numeric_limits::max()), "Maximal dimension of the strong witness complex we want to compute."); - + po::positional_options_description pos; pos.add("input-file", 1); @@ -133,7 +151,7 @@ void program_options(int argc, char * argv[] 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"; diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 38c6bedc..b36dac0d 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -14,11 +14,10 @@ #include #include -typedef CGAL::Epick_d K; -typedef typename K::Point_d Point_d; -typedef typename Gudhi::witness_complex::Euclidean_witness_complex Witness_complex; -typedef std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle > typeVectorVertex; -typedef std::vector< Point_d > Point_vector; +using K = CGAL::Epick_d; +using Point_d = K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; +using Point_vector = std::vector< Point_d >; int main(int argc, char * const argv[]) { if (argc != 5) { @@ -41,7 +40,7 @@ int main(int argc, char * const argv[]) { 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"; diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index fbb18cb4..364a114a 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -1,3 +1,25 @@ +/* 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 . + */ + #include #include #include diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 1ea9408c..06fe3889 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -1,8 +1,26 @@ -#define BOOST_PARAMETER_MAX_ARITY 12 - +/* 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 . + */ -#include -#include +#define BOOST_PARAMETER_MAX_ARITY 12 #include #include @@ -32,8 +50,9 @@ void write_data(Data_range & data, std::string filename) { } int main(int argc, char * const argv[]) { - typedef Gudhi::witness_complex::Euclidean_witness_complex> Witness_complex; - + using Kernel = CGAL::Epick_d; + using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; + if (argc != 2) { std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n"; @@ -66,8 +85,6 @@ int main(int argc, char * const argv[]) { double time = static_cast(end - start) / CLOCKS_PER_SEC; std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " << time << " s. \n"; - //assert(1 == 0); - //std::cout << simplex_tree << "\n"; std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; l_time.push_back(std::make_pair(nbP, time)); } diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index 731a52b0..7df43db5 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -32,12 +32,12 @@ #include #include -typedef CGAL::Epick_d K; -typedef K::FT FT; -typedef K::Point_d Point_d; -typedef std::vector Point_Vector; -typedef CGAL::Random_points_in_cube_d Random_cube_iterator; -typedef CGAL::Random_points_in_ball_d Random_point_iterator; +using K = CGAL::Epick_d; +using FT = K::FT; +using Point_d = K::Point_d; +using Point_Vector = std::vector; +using Random_cube_iterator = CGAL::Random_points_in_cube_d; +using Random_point_iterator = CGAL::Random_points_in_ball_d; /** * \brief Rock age method of reading off file @@ -155,7 +155,7 @@ void generate_points_torus(Point_Vector& W, int nbP, int dim) { for (int i = 0; i < nbP; i++) { std::vector point; for (int j = 0; j < dim; j++) { - double alpha = rand.uniform_real((double)0, 2*pi); + double alpha = rand.uniform_real(static_cast(0), 2*pi); point.push_back(sin(alpha)); point.push_back(cos(alpha)); } diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index ffc1750f..d41a6811 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -24,8 +24,7 @@ #define ACTIVE_WITNESS_ACTIVE_WITNESS_H_ #include -#include -#include +#include namespace Gudhi { @@ -38,7 +37,7 @@ namespace witness_complex { template< typename Id_distance_pair, typename INS_range > class Active_witness { -public: + public: typedef Active_witness ActiveWitness; typedef typename INS_range::iterator INS_iterator; typedef Active_witness_iterator< ActiveWitness, Id_distance_pair, INS_iterator > iterator; @@ -50,22 +49,19 @@ public: INS_iterator iterator_end_; Active_witness(const INS_range& search_range) - : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) - { + : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) { } - - iterator begin() - { + + iterator begin() { return iterator(this, nearest_landmark_table_.begin()); } - iterator end() - { + iterator end() { return iterator(this); } }; -} -} - +} // namespace witness_complex +} // namespace Gudhi + #endif // ACTIVE_WITNESS_ACTIVE_WITNESS_H_ diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 69a335fa..4e29a40d 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -24,7 +24,7 @@ #define ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_ #include -#include +#include namespace Gudhi { @@ -41,30 +41,29 @@ template< typename Active_witness, typename Id_distance_pair, typename INS_iterator > class Active_witness_iterator - : public boost::iterator_facade< Active_witness_iterator -, Id_distance_pair const -, boost::forward_traversal_tag -, Id_distance_pair const> { + : public boost::iterator_facade< Active_witness_iterator , + Id_distance_pair const, + boost::forward_traversal_tag, + Id_distance_pair const> { friend class boost::iterator_core_access; - + //typedef Active_witness Active_witness; typedef typename std::list::iterator Pair_iterator; - typedef typename Gudhi::witness_complex::Active_witness_iterator Iterator; - - + typedef typename Gudhi::witness_complex::Active_witness_iterator Iterator; + Active_witness *aw_; Pair_iterator lh_; // landmark handle bool is_end_; // true only if the pointer is end and there are no more neighbors to add -public: + public: Active_witness_iterator(Active_witness* aw) - : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) - { + : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) { } Active_witness_iterator(Active_witness* aw, const Pair_iterator& lh) - : aw_(aw), lh_(lh) - { + : aw_(aw), lh_(lh) { is_end_ = false; if (lh_ == aw_->nearest_landmark_table_.end()) { if (aw_->iterator_next_ == aw_->iterator_end_) { @@ -76,21 +75,17 @@ public: } } } - -private : - Id_distance_pair& dereference() const - { + private : + Id_distance_pair& dereference() const { return *lh_; } - bool equal(const Iterator& other) const - { + bool equal(const Iterator& other) const { return (is_end_ == other.is_end_) || (lh_ == other.lh_); } - - void increment() - { + + void increment() { // the neighbor search can't be at the end iterator of a list GUDHI_CHECK(!is_end_ && lh_ != aw_->nearest_landmark_table_.end(), std::logic_error("Wrong active witness increment.")); // if the id of the current landmark is the same as the last one diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h index aad05547..6870c183 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -23,17 +23,15 @@ #ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ #define EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ -#include -#include -#include -#include - #include #include #include +#include +#include + namespace Gudhi { - + namespace witness_complex { /** @@ -46,8 +44,10 @@ namespace witness_complex { * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d class. */ template< class Kernel_ > -class Euclidean_strong_witness_complex : public Strong_witness_complex>::INS_range>> { -private: +class Euclidean_strong_witness_complex + : public Strong_witness_complex>::INS_range>> { + private: typedef Kernel_ K; typedef typename K::Point_d Point_d; typedef std::vector Point_range; @@ -58,12 +58,12 @@ private: typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair; typedef typename Id_distance_pair::first_type Landmark_id; typedef Landmark_id Vertex_handle; - + private: Point_range landmarks_; Kd_tree landmark_tree_; using Strong_witness_complex::nearest_landmark_table_; - + public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /* @name Constructor @@ -81,22 +81,19 @@ private: typename WitnessRange > Euclidean_strong_witness_complex(const LandmarkRange & landmarks, const WitnessRange & witnesses) - : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) - { + : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) { nearest_landmark_table_.reserve(boost::size(witnesses)); for (auto w: witnesses) nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); } - /** \brief Returns the point corresponding to the given vertex. */ template - Point_d get_point( Vertex_handle vertex ) const - { + Point_d get_point(Vertex_handle vertex) const { return landmarks_[vertex]; } - + //@} }; diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index ad741794..3fbbb366 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -23,20 +23,19 @@ #ifndef STRONG_WITNESS_COMPLEX_H_ #define STRONG_WITNESS_COMPLEX_H_ +#include +#include + #include #include #include #include -#include -#include - namespace Gudhi { - + namespace witness_complex { -/** - * \private +/* \private * \class Strong_witness_complex * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses. * \ingroup witness_complex @@ -48,7 +47,7 @@ namespace witness_complex { */ template< class Nearest_landmark_table_ > class Strong_witness_complex { -private: + private: typedef typename Nearest_landmark_table_::value_type Nearest_landmark_range; typedef std::size_t Witness_id; typedef std::size_t Landmark_id; @@ -57,12 +56,11 @@ private: typedef std::list< ActiveWitness > ActiveWitnessList; typedef std::vector< Landmark_id > typeVectorVertex; typedef std::vector Nearest_landmark_table_internal; - typedef Landmark_id Vertex_handle; - + protected: Nearest_landmark_table_internal nearest_landmark_table_; - + public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /* @name Constructor @@ -70,11 +68,9 @@ private: //@{ - Strong_witness_complex() - { + Strong_witness_complex() { } - /** * \brief Initializes member variables before constructing simplicial complex. * \details Records nearest landmark table. @@ -84,10 +80,9 @@ private: * of the pair range iterator needs to be 'std::pair'. */ Strong_witness_complex(Nearest_landmark_table_ const & nearest_landmark_table) - : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) - { + : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) { } - + /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' * in a simplicial complex data structure. * \details The function returns true if the construction is successful and false otherwise. @@ -100,15 +95,15 @@ private: template < typename SimplicialComplexForWitness > bool create_complex(SimplicialComplexForWitness& complex, double max_alpha_square, - Landmark_id limit_dimension = std::numeric_limits::max()) const - { + Landmark_id limit_dimension = std::numeric_limits::max()) const { Landmark_id complex_dim = 0; if (complex.num_vertices() > 0) { std::cerr << "Strong witness complex cannot create complex - complex is not empty.\n"; return false; } if (max_alpha_square < 0) { - std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; + std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be " + << "non-negative.\n"; return false; } if (limit_dimension < 0) { @@ -129,7 +124,8 @@ private: typeVectorVertex& vertices = simplex; //'simplex' now will be called vertices while (aw_it != aw.end() && aw_it->second < lim_dist2) { typeVectorVertex facet = {}; - add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it, aw_it->second - aw.begin()->second, facet, complex); + add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it, + aw_it->second - aw.begin()->second, facet, complex); vertices.push_back(aw_it->first); aw_it++; } @@ -140,13 +136,12 @@ private: return true; } -private: - + private: /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness. - * Iterator is needed to know until how far we can take landmarks to form simplexes. - * simplex is the prefix of the simplexes to insert. - * The landmark pointed by aw_it is added to all formed simplices. - */ + * Iterator is needed to know until how far we can take landmarks to form simplexes. + * simplex is the prefix of the simplexes to insert. + * The landmark pointed by aw_it is added to all formed simplices. + */ template < typename SimplicialComplexForWitness > void add_all_faces_of_dimension(Landmark_id dim, typeVectorVertex& vertices, @@ -154,9 +149,8 @@ private: typename ActiveWitness::iterator aw_it, double filtration_value, typeVectorVertex& simplex, - SimplicialComplexForWitness& sc) const - { - if (dim > 0) + SimplicialComplexForWitness& sc) const { + if (dim > 0) { while (curr_it != vertices.end()) { simplex.push_back(*curr_it); ++curr_it; @@ -176,7 +170,7 @@ private: simplex, sc); } - else if (dim == 0) { + } else if (dim == 0) { simplex.push_back(aw_it->first); sc.insert_simplex_and_subfaces(simplex, filtration_value); simplex.pop_back(); diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index c09e6af9..c0506367 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -33,7 +33,7 @@ #include namespace Gudhi { - + namespace witness_complex { /** @@ -49,7 +49,7 @@ namespace witness_complex { */ template< class Nearest_landmark_table_ > class Witness_complex { -private: + private: typedef typename Nearest_landmark_table_::value_type Nearest_landmark_range; typedef std::size_t Witness_id; typedef std::size_t Landmark_id; @@ -58,12 +58,11 @@ private: typedef std::list< ActiveWitness > ActiveWitnessList; typedef std::vector< Landmark_id > typeVectorVertex; typedef std::vector Nearest_landmark_table_internal; - typedef Landmark_id Vertex_handle; protected: Nearest_landmark_table_internal nearest_landmark_table_; - + public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /* @name Constructor @@ -71,10 +70,9 @@ private: //@{ - Witness_complex() - { + Witness_complex() { } - + /** * \brief Initializes member variables before constructing simplicial complex. * \details Records nearest landmark table. @@ -85,11 +83,9 @@ private: */ Witness_complex(Nearest_landmark_table_ const & nearest_landmark_table) - : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) - { + : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) { } - /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square' * in a simplicial complex data structure. * \details The function returns true if the construction is successful and false otherwise. @@ -102,8 +98,7 @@ private: template < typename SimplicialComplexForWitness > bool create_complex(SimplicialComplexForWitness& complex, double max_alpha_square, - std::size_t limit_dimension = std::numeric_limits::max()) const - { + std::size_t limit_dimension = std::numeric_limits::max()) const { if (complex.num_vertices() > 0) { std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; return false; @@ -118,9 +113,9 @@ private: } ActiveWitnessList active_witnesses; Landmark_id k = 0; /* current dimension in iterative construction */ - for (auto w: nearest_landmark_table_) + for (auto w : nearest_landmark_table_) active_witnesses.push_back(ActiveWitness(w)); - while (!active_witnesses.empty() && k <= limit_dimension ) { + while (!active_witnesses.empty() && k <= limit_dimension) { typename ActiveWitnessList::iterator aw_it = active_witnesses.begin(); std::vector simplex; simplex.reserve(k+1); @@ -134,10 +129,10 @@ private: aw_it->end()); assert(simplex.empty()); if (!ok) - active_witnesses.erase(aw_it++); //First increase the iterator and then erase the previous element + active_witnesses.erase(aw_it++); // First increase the iterator and then erase the previous element else aw_it++; - } + } k++; } complex.set_dimension(k-1); @@ -159,13 +154,12 @@ private: typename ActiveWitness::iterator curr_l, std::vector& simplex, SimplicialComplexForWitness& sc, - typename ActiveWitness::iterator end) const - { + typename ActiveWitness::iterator end) const { if (curr_l == end) return false; bool will_be_active = false; typename ActiveWitness::iterator l_it = curr_l; - if (dim > 0) + if (dim > 0) { for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) { simplex.push_back(l_it->first); if (sc.find(simplex) != sc.null_simplex()) { @@ -183,8 +177,8 @@ private: // If norelax_dist is infinity, change to first omitted distance if (l_it->second <= norelax_dist2) norelax_dist2 = l_it->second; - } - else if (dim == 0) + } + } else if (dim == 0) { for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) { simplex.push_back(l_it->first); double filtration_value = 0; @@ -200,12 +194,12 @@ private: // If norelax_dist is infinity, change to first omitted distance if (l_it->second < norelax_dist2) norelax_dist2 = l_it->second; - } + } + } return will_be_active; } - }; - + } // namespace witness_complex } // namespace Gudhi diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h index d009caca..b68d75a1 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h +++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h @@ -1,3 +1,25 @@ +/* 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) 2015 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 . + */ + #ifndef WITNESS_COMPLEX_ALL_FACES_IN_H_ #define WITNESS_COMPLEX_ALL_FACES_IN_H_ @@ -9,16 +31,14 @@ template < typename SimplicialComplexForWitness, typename Simplex > bool all_faces_in(Simplex& simplex, double* filtration_value, - SimplicialComplexForWitness& sc) - { + SimplicialComplexForWitness& sc) { typedef typename SimplicialComplexForWitness::Simplex_handle Simplex_handle; if (simplex.size() == 1) return true; /* Add vertices unconditionally */ - + Simplex facet; - for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) - { + for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) { facet.clear(); for (typename Simplex::iterator it = simplex.begin(); it != simplex.end(); ++it) if (it != not_it) -- cgit v1.2.3