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-rw-r--r--example/Witness_complex/CMakeLists.txt16
-rw-r--r--example/Witness_complex/generators.h147
-rw-r--r--example/Witness_complex/witness_complex_from_file.cpp100
-rw-r--r--example/Witness_complex/witness_complex_sphere.cpp90
4 files changed, 353 insertions, 0 deletions
diff --git a/example/Witness_complex/CMakeLists.txt b/example/Witness_complex/CMakeLists.txt
new file mode 100644
index 00000000..4d67e0d0
--- /dev/null
+++ b/example/Witness_complex/CMakeLists.txt
@@ -0,0 +1,16 @@
+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 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)
+ endif(EIGEN3_FOUND)
+ endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
+endif()
diff --git a/example/Witness_complex/generators.h b/example/Witness_complex/generators.h
new file mode 100644
index 00000000..ac445261
--- /dev/null
+++ b/example/Witness_complex/generators.h
@@ -0,0 +1,147 @@
+/* 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 <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+#define EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/point_generators_d.h>
+
+#include <fstream>
+#include <string>
+#include <vector>
+
+typedef CGAL::Epick_d<CGAL::Dynamic_dimension_tag> K;
+typedef K::FT FT;
+typedef K::Point_d Point_d;
+typedef std::vector<Point_d> Point_Vector;
+typedef CGAL::Random_points_in_cube_d<Point_d> Random_cube_iterator;
+typedef CGAL::Random_points_in_ball_d<Point_d> Random_point_iterator;
+
+/**
+ * \brief Rock age method of reading off file
+ *
+ */
+inline void
+off_reader_cust(std::string file_name, std::vector<Point_d> & points) {
+ std::ifstream in_file(file_name.c_str(), std::ios::in);
+ if (!in_file.is_open()) {
+ std::cerr << "Unable to open file " << file_name << std::endl;
+ return;
+ }
+ std::string line;
+ double x;
+ // Line OFF. No need in it
+ if (!getline(in_file, line)) {
+ std::cerr << "No line OFF\n";
+ return;
+ }
+ // Line with 3 numbers. No need
+ if (!getline(in_file, line)) {
+ std::cerr << "No line with 3 numbers\n";
+ return;
+ }
+ // Reading points
+ while (getline(in_file, line)) {
+ std::vector< double > point;
+ std::istringstream iss(line);
+ while (iss >> x) {
+ point.push_back(x);
+ }
+ points.push_back(Point_d(point));
+ }
+ in_file.close();
+}
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust(std::string file_name, Point_Vector & points) {
+ std::ifstream in_file(file_name.c_str(), std::ios::in);
+ if (!in_file.is_open()) {
+ std::cerr << "Unable to open file " << file_name << std::endl;
+ return;
+ }
+ std::string line;
+ double x;
+ while (getline(in_file, line)) {
+ std::vector< double > point;
+ std::istringstream iss(line);
+ while (iss >> x) {
+ point.push_back(x);
+ }
+ Point_d p(point.begin(), point.end());
+ if (point.size() != 1)
+ points.push_back(p);
+ }
+ in_file.close();
+}
+
+/** \brief Generate points on a grid in a cube of side 2
+ * having {+-1}^D as vertices and insert them in W.
+ * The grid has "width" points on each side.
+ * If torus is true then it is supposed that the cube represents
+ * a flat torus, hence the opposite borders are associated.
+ * The points on border in this case are not placed twice.
+ */
+void generate_points_grid(Point_Vector& W, int width, int D, bool torus) {
+ int nb_points = 1;
+ for (int i = 0; i < D; ++i)
+ nb_points *= width;
+ for (int i = 0; i < nb_points; ++i) {
+ std::vector<double> point;
+ int cell_i = i;
+ for (int l = 0; l < D; ++l) {
+ if (torus)
+ point.push_back(-1 + (2.0 / (width - 1))*(cell_i % width));
+ else
+ point.push_back(-1 + (2.0 / width)*(cell_i % width));
+ // attention: the bottom and the right are covered too!
+ cell_i /= width;
+ }
+ W.push_back(point);
+ }
+}
+
+/** \brief Generate nbP points uniformly in a cube of side 2
+ * having {+-1}^dim as its vertices and insert them in W.
+ */
+void generate_points_random_box(Point_Vector& W, int nbP, int dim) {
+ Random_cube_iterator rp(dim, 1.0);
+ for (int i = 0; i < nbP; i++) {
+ W.push_back(*rp++);
+ }
+}
+
+/** \brief Generate nbP points uniformly on a (dim-1)-sphere
+ * and insert them in W.
+ */
+void generate_points_sphere(Point_Vector& W, int nbP, int dim) {
+ CGAL::Random_points_on_sphere_d<Point_d> rp(dim, 1);
+ for (int i = 0; i < nbP; i++)
+ W.push_back(*rp++);
+}
+
+#endif // EXAMPLE_WITNESS_COMPLEX_GENERATORS_H_
diff --git a/example/Witness_complex/witness_complex_from_file.cpp b/example/Witness_complex/witness_complex_from_file.cpp
new file mode 100644
index 00000000..53207ad2
--- /dev/null
+++ b/example/Witness_complex/witness_complex_from_file.cpp
@@ -0,0 +1,100 @@
+/* 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 <http://www.gnu.org/licenses/>.
+ */
+
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Witness_complex.h>
+#include <gudhi/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <string>
+#include <vector>
+
+typedef std::vector< Vertex_handle > typeVectorVertex;
+typedef std::vector< std::vector <double> > Point_Vector;
+
+/**
+ * \brief Customized version of read_points
+ * which takes into account a possible nbP first line
+ *
+ */
+inline void
+read_points_cust(std::string file_name, std::vector< std::vector< double > > & points) {
+ std::ifstream in_file(file_name.c_str(), std::ios::in);
+ if (!in_file.is_open()) {
+ std::cerr << "Unable to open file " << file_name << std::endl;
+ return;
+ }
+ std::string line;
+ double x;
+ while (getline(in_file, line)) {
+ std::vector< double > point;
+ std::istringstream iss(line);
+ while (iss >> x) {
+ point.push_back(x);
+ }
+ if (point.size() != 1)
+ points.push_back(point);
+ }
+ in_file.close();
+}
+
+int main(int argc, char * const argv[]) {
+ if (argc != 3) {
+ std::cerr << "Usage: " << argv[0]
+ << " path_to_point_file nbL \n";
+ return 0;
+ }
+
+ std::string file_name = argv[1];
+ int nbL = atoi(argv[2]);
+ clock_t start, end;
+
+ // Construct the Simplex Tree
+ Gudhi::Simplex_tree<> simplex_tree;
+
+ // Read the point file
+ Point_Vector point_vector;
+ read_points_cust(file_name, point_vector);
+ 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;
+ Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, nbL, 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";
+}
diff --git a/example/Witness_complex/witness_complex_sphere.cpp b/example/Witness_complex/witness_complex_sphere.cpp
new file mode 100644
index 00000000..b26c9f36
--- /dev/null
+++ b/example/Witness_complex/witness_complex_sphere.cpp
@@ -0,0 +1,90 @@
+/* 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 <http://www.gnu.org/licenses/>.
+ */
+#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/Landmark_choice_by_random_point.h>
+#include <gudhi/reader_utils.h>
+
+#include <iostream>
+#include <fstream>
+#include <ctime>
+#include <utility>
+#include <string>
+#include <vector>
+
+#include "generators.h"
+
+/** Write a gnuplot readable file.
+ * Data range is a random access range of pairs (arg, value)
+ */
+template < typename Data_range >
+void write_data(Data_range & data, std::string filename) {
+ std::ofstream ofs(filename, std::ofstream::out);
+ for (auto entry : data)
+ ofs << entry.first << ", " << entry.second << "\n";
+ ofs.close();
+}
+
+int main(int argc, char * const argv[]) {
+ if (argc != 2) {
+ std::cerr << "Usage: " << argv[0]
+ << " number_of_landmarks \n";
+ return 0;
+ }
+
+ int number_of_landmarks = atoi(argv[1]);
+ clock_t start, end;
+
+ // Construct the Simplex Tree
+ Gudhi::Simplex_tree<> simplex_tree;
+
+ std::vector< std::pair<int, double> > l_time;
+
+ // Read the point file
+ for (int nbP = 500; nbP < 10000; nbP += 500) {
+ Point_Vector point_vector;
+ generate_points_sphere(point_vector, nbP, 4);
+ std::cout << "Successfully generated " << 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;
+ Gudhi::witness_complex::landmark_choice_by_random_point(point_vector, number_of_landmarks, knn);
+
+ // Compute witness complex
+ Gudhi::witness_complex::witness_complex(knn, number_of_landmarks, point_vector[0].size(), simplex_tree);
+ 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";
+ std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n";
+ l_time.push_back(std::make_pair(nbP, time));
+ }
+ write_data(l_time, "w_time.dat");
+}
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