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-rw-r--r--src/Witness_complex/example/CMakeLists.txt30
-rw-r--r--src/Witness_complex/example/example_nearest_landmark_table.cpp48
-rw-r--r--src/Witness_complex/example/example_strong_witness_complex_off.cpp61
-rw-r--r--src/Witness_complex/example/example_strong_witness_persistence.cpp152
-rw-r--r--src/Witness_complex/example/example_witness_complex_off.cpp61
-rw-r--r--src/Witness_complex/example/example_witness_complex_persistence.cpp152
-rw-r--r--src/Witness_complex/example/example_witness_complex_sphere.cpp (renamed from src/Witness_complex/example/witness_complex_sphere.cpp)47
-rw-r--r--src/Witness_complex/example/generators.h19
-rw-r--r--src/Witness_complex/example/witness_complex_from_file.cpp84
9 files changed, 530 insertions, 124 deletions
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 857ec819..320f3fba 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -1,17 +1,33 @@
cmake_minimum_required(VERSION 2.6)
project(Witness_complex_examples)
-# A simple example
- add_executable( witness_complex_from_file witness_complex_from_file.cpp )
- add_test( witness_complex_from_bunny ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_from_file
- ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.off 100)
if(CGAL_FOUND)
if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
if (EIGEN3_FOUND)
- add_executable ( witness_complex_sphere witness_complex_sphere.cpp )
- target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
- add_test( witness_complex_sphere_10 ${CMAKE_CURRENT_BINARY_DIR}/witness_complex_sphere 10)
+ add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
+ add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
+ add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.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_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
+ target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+ add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp )
+ if (TBB_FOUND)
+ target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
+ target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
+ target_link_libraries(Witness_complex_example_nearest_landmark_table ${TBB_LIBRARIES})
+ endif()
+
+ add_test(Witness_complex_test_torus_persistence
+ ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_witness_persistence
+ ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
+ add_test(Witness_complex_test_torus_persistence
+ ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_witness_persistence
+ ${CMAKE_SOURCE_DIR}/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_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp
new file mode 100644
index 00000000..becf74e7
--- /dev/null
+++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp
@@ -0,0 +1,48 @@
+#define BOOST_PARAMETER_MAX_ARITY 12
+
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/reader_utils.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility>
+#include <string>
+#include <vector>
+#include <list>
+
+int main(int argc, char * const argv[]) {
+ typedef std::vector<std::pair<std::size_t, double>> Nearest_landmark_range;
+ typedef std::vector<Nearest_landmark_range> Nearest_landmark_table;
+ typedef Gudhi::witness_complex::Witness_complex<Nearest_landmark_table> Witness_complex;
+
+ Gudhi::Simplex_tree<> simplex_tree;
+ Nearest_landmark_table nlt;
+
+ // Example contains 5 witnesses and 5 landmarks
+ Nearest_landmark_range w0 = {std::make_pair(0,0), std::make_pair(1,1), std::make_pair(2,2), std::make_pair(3,3), std::make_pair(4,4)}; nlt.push_back(w0);
+ Nearest_landmark_range w1 = {std::make_pair(1,0), std::make_pair(2,1), std::make_pair(3,2), std::make_pair(4,3), std::make_pair(0,4)}; nlt.push_back(w1);
+ Nearest_landmark_range w2 = {std::make_pair(2,0), std::make_pair(3,1), std::make_pair(4,2), std::make_pair(0,3), std::make_pair(1,4)}; nlt.push_back(w2);
+ Nearest_landmark_range w3 = {std::make_pair(3,0), std::make_pair(4,1), std::make_pair(0,2), std::make_pair(1,3), std::make_pair(2,4)}; nlt.push_back(w3);
+ Nearest_landmark_range w4 = {std::make_pair(4,0), std::make_pair(0,1), std::make_pair(1,2), std::make_pair(2,3), std::make_pair(3,4)}; nlt.push_back(w4);
+
+ Witness_complex witness_complex(nlt);
+ witness_complex.create_complex(simplex_tree, 4.1);
+
+ std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl;
+
+ Gudhi::persistent_cohomology::Persistent_cohomology<Gudhi::Simplex_tree<>, Gudhi::persistent_cohomology::Field_Zp > pcoh(simplex_tree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(11);
+
+ pcoh.compute_persistent_cohomology(-0.1);
+ pcoh.output_diagram();
+}
diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
new file mode 100644
index 00000000..c9a3b543
--- /dev/null
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
@@ -0,0 +1,61 @@
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
+#include <gudhi/pick_n_random_points.h>
+#include <gudhi/Points_off_io.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <string>
+#include <vector>
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef typename K::Point_d Point_d;
+typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex<K> Witness_complex;
+typedef std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle > typeVectorVertex;
+typedef std::vector< Point_d > Point_vector;
+
+int main(int argc, char * const argv[]) {
+ if (argc != 5) {
+ std::cerr << "Usage: " << argv[0]
+ << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
+ return 0;
+ }
+
+ std::string file_name = argv[1];
+ int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
+ double alpha2 = atof(argv[3]);
+ clock_t start, end;
+ Gudhi::Simplex_tree<> simplex_tree;
+
+ // Read the point file
+ Point_vector point_vector, landmarks;
+ Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+ if (!off_reader.is_valid()) {
+ std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
+ }
+ point_vector = Point_vector(off_reader.get_point_cloud());
+
+ std::cout << "Successfully read " << point_vector.size() << " points.\n";
+ std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
+
+ // Choose landmarks
+ Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+
+ // Compute witness complex
+ start = clock();
+ Witness_complex witness_complex(landmarks,
+ point_vector);
+
+ witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
+ end = clock();
+ std::cout << "Strong witness complex took "
+ << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+ std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
+}
diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp
new file mode 100644
index 00000000..d42603aa
--- /dev/null
+++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp
@@ -0,0 +1,152 @@
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_strong_witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits> // infinity
+
+using namespace Gudhi;
+using namespace Gudhi::persistent_cohomology;
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef typename K::Point_d Point_d;
+
+typedef typename std::vector<Point_d> Point_vector;
+typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex<K> 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
+ , int & dim_max
+ , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+ std::string file_name;
+ std::string filediag;
+ Filtration_value max_squared_alpha;
+ int p, nbL, lim_d;
+ Filtration_value min_persistence;
+ SimplexTree simplex_tree;
+
+ program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence);
+
+ // Extract the points from the file file_name
+ Point_vector witnesses, landmarks;
+ Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+ if (!off_reader.is_valid()) {
+ std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
+ }
+ witnesses = Point_vector(off_reader.get_point_cloud());
+ std::cout << "Successfully read " << witnesses.size() << " points.\n";
+ std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+ // Choose landmarks from witnesses
+ Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+ // Compute witness complex
+ 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";
+
+ // Sort the simplices in the order of the filtration
+ simplex_tree.initialize_filtration();
+
+ // Compute the persistence diagram of the complex
+ persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p);
+
+ pcoh.compute_persistent_cohomology(min_persistence);
+
+ // Output the diagram in filediag
+ if (filediag.empty()) {
+ pcoh.output_diagram();
+ } else {
+ std::ofstream out(filediag);
+ pcoh.output_diagram(out);
+ out.close();
+ }
+
+ return 0;
+}
+
+
+void program_options(int argc, char * argv[]
+ , int & nbL
+ , std::string & file_name
+ , std::string & filediag
+ , Filtration_value & max_squared_alpha
+ , int & p
+ , int & dim_max
+ , Filtration_value & min_persistence) {
+
+ namespace po = boost::program_options;
+
+ po::options_description hidden("Hidden options");
+ hidden.add_options()
+ ("input-file", po::value<std::string>(&file_name),
+ "Name of file containing a point set in off format.");
+
+
+ po::options_description visible("Allowed options", 100);
+ visible.add_options()
+ ("help,h", "produce help message")
+ ("landmarks,l", po::value<int>(&nbL),
+ "Number of landmarks to choose from the point cloud.")
+ ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")
+ ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+ "Maximal squared relaxation parameter.")
+ ("field-charac,p", po::value<int>(&p)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")
+ ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
+ ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+ "Maximal dimension of the strong witness complex we want to compute.");
+
+ po::positional_options_description pos;
+ pos.add("input-file", 1);
+
+ po::options_description all;
+ all.add(visible).add(hidden);
+ po::variables_map vm;
+
+ po::store(po::command_line_parser(argc, argv).
+ options(all).positional(pos).run(), vm);
+ po::notify(vm);
+
+ if (vm.count("help") || !vm.count("input-file")) {
+ std::cout << std::endl;
+ std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+ std::cout << "of a 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
new file mode 100644
index 00000000..38c6bedc
--- /dev/null
+++ b/src/Witness_complex/example/example_witness_complex_off.cpp
@@ -0,0 +1,61 @@
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/pick_n_random_points.h>
+#include <gudhi/Points_off_io.h>
+
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <string>
+#include <vector>
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef typename K::Point_d Point_d;
+typedef typename Gudhi::witness_complex::Euclidean_witness_complex<K> Witness_complex;
+typedef std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle > typeVectorVertex;
+typedef std::vector< Point_d > Point_vector;
+
+int main(int argc, char * const argv[]) {
+ if (argc != 5) {
+ std::cerr << "Usage: " << argv[0]
+ << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n";
+ return 0;
+ }
+
+ std::string file_name = argv[1];
+ int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]);
+ double alpha2 = atof(argv[3]);
+ clock_t start, end;
+ Gudhi::Simplex_tree<> simplex_tree;
+
+ // Read the point file
+ Point_vector point_vector, landmarks;
+ Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+ if (!off_reader.is_valid()) {
+ std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
+ }
+ point_vector = Point_vector(off_reader.get_point_cloud());
+
+ std::cout << "Successfully read " << point_vector.size() << " points.\n";
+ std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n";
+
+ // Choose landmarks
+ Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks));
+
+ // Compute witness complex
+ start = clock();
+ Witness_complex witness_complex(landmarks,
+ point_vector);
+
+ witness_complex.create_complex(simplex_tree, alpha2, lim_dim);
+ end = clock();
+ std::cout << "Witness complex took "
+ << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
+ std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
+}
diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp
new file mode 100644
index 00000000..fbb18cb4
--- /dev/null
+++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp
@@ -0,0 +1,152 @@
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Euclidean_witness_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+#include <gudhi/Points_off_io.h>
+#include <gudhi/pick_n_random_points.h>
+
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <string>
+#include <vector>
+#include <limits> // infinity
+
+using namespace Gudhi;
+using namespace Gudhi::persistent_cohomology;
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef typename K::Point_d Point_d;
+
+typedef typename std::vector<Point_d> Point_vector;
+typedef typename Gudhi::witness_complex::Euclidean_witness_complex<K> 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
+ , int & dim_max
+ , Filtration_value & min_persistence);
+
+int main(int argc, char * argv[]) {
+ std::string file_name;
+ std::string filediag;
+ Filtration_value max_squared_alpha;
+ int p, nbL, lim_d;
+ Filtration_value min_persistence;
+ SimplexTree simplex_tree;
+
+ program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence);
+
+ // Extract the points from the file file_name
+ Point_vector witnesses, landmarks;
+ Gudhi::Points_off_reader<Point_d> off_reader(file_name);
+ if (!off_reader.is_valid()) {
+ std::cerr << "Witness complex - Unable to read file " << file_name << "\n";
+ exit(-1); // ----- >>
+ }
+ witnesses = Point_vector(off_reader.get_point_cloud());
+ std::cout << "Successfully read " << witnesses.size() << " points.\n";
+ std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n";
+
+ // Choose landmarks from witnesses
+ Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks));
+
+ // Compute witness complex
+ Witness_complex witness_complex(landmarks,
+ witnesses);
+
+ witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d);
+
+ std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n";
+ std::cout << " and has dimension " << simplex_tree.dimension() << " \n";
+
+ // Sort the simplices in the order of the filtration
+ simplex_tree.initialize_filtration();
+
+ // Compute the persistence diagram of the complex
+ persistent_cohomology::Persistent_cohomology<SimplexTree, Field_Zp > pcoh(simplex_tree);
+ // initializes the coefficient field for homology
+ pcoh.init_coefficients(p);
+
+ pcoh.compute_persistent_cohomology(min_persistence);
+
+ // Output the diagram in filediag
+ if (filediag.empty()) {
+ pcoh.output_diagram();
+ } else {
+ std::ofstream out(filediag);
+ pcoh.output_diagram(out);
+ out.close();
+ }
+
+ return 0;
+}
+
+
+void program_options(int argc, char * argv[]
+ , int & nbL
+ , std::string & file_name
+ , std::string & filediag
+ , Filtration_value & max_squared_alpha
+ , int & p
+ , int & dim_max
+ , Filtration_value & min_persistence) {
+
+ namespace po = boost::program_options;
+
+ po::options_description hidden("Hidden options");
+ hidden.add_options()
+ ("input-file", po::value<std::string>(&file_name),
+ "Name of file containing a point set in off format.");
+
+
+ po::options_description visible("Allowed options", 100);
+ visible.add_options()
+ ("help,h", "produce help message")
+ ("landmarks,l", po::value<int>(&nbL),
+ "Number of landmarks to choose from the point cloud.")
+ ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
+ "Name of file in which the persistence diagram is written. Default print in std::cout")
+ ("max-sq-alpha,a", po::value<Filtration_value>(&max_squared_alpha)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+ "Maximal squared relaxation parameter.")
+ ("field-charac,p", po::value<int>(&p)->default_value(11),
+ "Characteristic p of the coefficient field Z/pZ for computing homology.")
+ ("min-persistence,m", po::value<Filtration_value>(&min_persistence)->default_value(0),
+ "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals")
+ ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(std::numeric_limits<int>::max()),
+ "Maximal dimension of the weak witness complex we want to compute.");
+
+ po::positional_options_description pos;
+ pos.add("input-file", 1);
+
+ po::options_description all;
+ all.add(visible).add(hidden);
+ po::variables_map vm;
+
+ po::store(po::command_line_parser(argc, argv).
+ options(all).positional(pos).run(), vm);
+ po::notify(vm);
+
+ if (vm.count("help") || !vm.count("input-file")) {
+ std::cout << std::endl;
+ std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+ std::cout << "of a Weak witness complex defined on a set of input points.\n \n";
+ std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+ std::cout << " p dim b d \n";
+ std::cout << "where dim is the dimension of the homological feature,\n";
+ std::cout << "b and d are respectively the birth and death of the feature and \n";
+ std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+ std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+ std::cout << visible << std::endl;
+ std::abort();
+ }
+}
+
diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp
index 60e02225..1ea9408c 100644
--- a/src/Witness_complex/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
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
#define BOOST_PARAMETER_MAX_ARITY 12
@@ -26,11 +5,12 @@
#include <sys/stat.h>
#include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Construct_closest_landmark_table.h>
+#include <gudhi/Euclidean_witness_complex.h>
#include <gudhi/pick_n_random_points.h>
#include <gudhi/reader_utils.h>
+#include <CGAL/Epick_d.h>
+
#include <iostream>
#include <fstream>
#include <ctime>
@@ -40,8 +20,6 @@
#include "generators.h"
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-
/** Write a gnuplot readable file.
* Data range is a random access range of pairs (arg, value)
*/
@@ -54,6 +32,8 @@ void write_data(Data_range & data, std::string filename) {
}
int main(int argc, char * const argv[]) {
+ typedef Gudhi::witness_complex::Euclidean_witness_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>> Witness_complex;
+
if (argc != 2) {
std::cerr << "Usage: " << argv[0]
<< " number_of_landmarks \n";
@@ -63,13 +43,12 @@ int main(int argc, char * const argv[]) {
int number_of_landmarks = atoi(argv[1]);
clock_t start, end;
- // Construct the Simplex Tree
- Simplex_tree simplex_tree;
-
std::vector< std::pair<int, double> > l_time;
- // Read the point file
+ // Generate points
for (int nbP = 500; nbP < 10000; nbP += 500) {
+ // Construct the Simplex Tree
+ Gudhi::Simplex_tree<> simplex_tree;
Point_Vector point_vector, landmarks;
generate_points_sphere(point_vector, nbP, 4);
std::cout << "Successfully generated " << point_vector.size() << " points.\n";
@@ -77,16 +56,18 @@ int main(int argc, char * const argv[]) {
// Choose landmarks
start = clock();
- std::vector<std::vector< int > > knn;
- Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks));
- Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(point_vector, landmarks, knn);
+ Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks));
// Compute witness complex
- Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
+ Witness_complex witness_complex(landmarks,
+ point_vector);
+ witness_complex.create_complex(simplex_tree, 0);
end = clock();
double time = static_cast<double>(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 ac445261..731a52b0 100644
--- a/src/Witness_complex/example/generators.h
+++ b/src/Witness_complex/example/generators.h
@@ -25,10 +25,12 @@
#include <CGAL/Epick_d.h>
#include <CGAL/point_generators_d.h>
+#include <CGAL/Random.h>
#include <fstream>
#include <string>
#include <vector>
+#include <cmath>
typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
typedef K::FT FT;
@@ -144,4 +146,21 @@ void generate_points_sphere(Point_Vector& W, int nbP, int dim) {
W.push_back(*rp++);
}
+/** \brief Generate nbP points on a (flat) d-torus embedded in R^{2d}
+ *
+ */
+void generate_points_torus(Point_Vector& W, int nbP, int dim) {
+ CGAL::Random rand;
+ const double pi = std::acos(-1);
+ for (int i = 0; i < nbP; i++) {
+ std::vector<FT> point;
+ for (int j = 0; j < dim; j++) {
+ double alpha = rand.uniform_real((double)0, 2*pi);
+ point.push_back(sin(alpha));
+ point.push_back(cos(alpha));
+ }
+ W.push_back(Point_d(point));
+ }
+}
+
#endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
diff --git a/src/Witness_complex/example/witness_complex_from_file.cpp b/src/Witness_complex/example/witness_complex_from_file.cpp
deleted file mode 100644
index 5dd18d0a..00000000
--- a/src/Witness_complex/example/witness_complex_from_file.cpp
+++ /dev/null
@@ -1,84 +0,0 @@
-/* This file is part of the Gudhi Library. The Gudhi library
- * (Geometric Understanding in Higher Dimensions) is a generic C++
- * library for computational topology.
- *
- * Author(s): Siargey Kachanovich
- *
- * Copyright (C) 2015 INRIA
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include <gudhi/Points_off_io.h>
-#include <gudhi/Simplex_tree.h>
-#include <gudhi/Witness_complex.h>
-#include <gudhi/Construct_closest_landmark_table.h>
-#include <gudhi/pick_n_random_points.h>
-#include <gudhi/reader_utils.h>
-
-#include <iostream>
-#include <fstream>
-#include <ctime>
-#include <string>
-#include <vector>
-
-typedef Gudhi::Simplex_tree<> Simplex_tree;
-typedef std::vector< Simplex_tree::Vertex_handle > typeVectorVertex;
-typedef std::vector< std::vector <double> > Point_Vector;
-
-int main(int argc, char * const argv[]) {
- if (argc != 3) {
- std::cerr << "Usage: " << argv[0]
- << " path_to_point_file.off nbL \n";
- return 0;
- }
-
- std::string off_file_name = argv[1];
- int nbL = atoi(argv[2]);
- clock_t start, end;
-
- // Construct the Simplex Tree
- Simplex_tree simplex_tree;
-
- // Read the OFF file (input file name given as parameter) and triangulate points
- Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name);
- // Check the read operation was correct
- if (!off_reader.is_valid()) {
- std::cerr << "Unable to read file " << off_file_name << std::endl;
- }
- // Read the point file
- 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].size() << ".\n";
-
- // Choose landmarks
- start = clock();
- std::vector<std::vector< int > > knn;
- Point_Vector landmarks;
- Gudhi::subsampling::pick_n_random_points(point_vector, 100, std::back_inserter(landmarks));
- Gudhi::witness_complex::construct_closest_landmark_table<Simplex_tree::Filtration_value>(point_vector, landmarks, knn);
- end = clock();
- std::cout << "Landmark choice for " << nbL << " landmarks took "
- << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
-
- // Compute witness complex
- start = clock();
- Gudhi::witness_complex::witness_complex(knn, nbL, point_vector[0].size(), simplex_tree);
- end = clock();
- std::cout << "Witness complex took "
- << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
-}
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-02 12:24:29 +0000