From f44d72644fc31bc863d0c81d0ae80630ebc506e5 Mon Sep 17 00:00:00 2001 From: skachano Date: Thu, 14 Jan 2016 16:17:51 +0000 Subject: Added example stuff git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@968 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a769b41f7d2d784a2740c149da08dac8124e3df9 --- src/Witness_complex/example/CMakeLists.txt | 11 +- src/Witness_complex/example/generators.h | 134 +++++++++++++++++++++ .../example/witness_complex_sphere.cpp | 126 +++++++++++++++++++ .../include/gudhi/Witness_complex.h | 2 +- .../test/simple_witness_complex.cpp | 5 +- .../test/witness_complex_points.cpp | 9 +- 6 files changed, 271 insertions(+), 16 deletions(-) create mode 100644 src/Witness_complex/example/generators.h create mode 100644 src/Witness_complex/example/witness_complex_sphere.cpp (limited to 'src/Witness_complex') diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index 4473078a..b5770ba6 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -4,9 +4,6 @@ project(GUDHIWitnessComplex) # 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) - - add_executable( witness_complex_bench witness_complex_bench.cpp ) - add_test( witness_complex_bench_from_bunny &{CMAKE_CURRENT_BINARY_DIR}/witness_complex_bench ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 100) if(CGAL_FOUND) if (NOT CGAL_VERSION VERSION_LESS 4.6.0) @@ -21,12 +18,12 @@ if(CGAL_FOUND) message(STATUS "Eigen3 use file: ${EIGEN3_USE_FILE}.") include_directories (BEFORE "../../include") - add_executable ( witness_complex_bench2 witness_complex_bench2.cpp ) - target_link_libraries(witness_complex_bench2 ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_executable ( witness_complex_sphere witness_complex_sphere.cpp ) + target_link_libraries(witness_complex_sphere ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) else() - message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + message(WARNING "Eigen3 not found. Version 3.1.0 is required for witness_complex_sphere example.") endif() else() - message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile witness_complex_sphere example. Version 4.6.0 is required.") endif () endif() diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h new file mode 100644 index 00000000..0d42cda2 --- /dev/null +++ b/src/Witness_complex/example/generators.h @@ -0,0 +1,134 @@ +#ifndef GENERATORS_H +#define GENERATORS_H + +#include + +#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; + +/** + * \brief Rock age method of reading off file + * + */ +inline void +off_reader_cust ( std::string file_name , std::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; + // 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 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 rp(dim,1); + for (int i = 0; i < nbP; i++) + W.push_back(*rp++); +} + + +#endif diff --git a/src/Witness_complex/example/witness_complex_sphere.cpp b/src/Witness_complex/example/witness_complex_sphere.cpp new file mode 100644 index 00000000..1fa0fc42 --- /dev/null +++ b/src/Witness_complex/example/witness_complex_sphere.cpp @@ -0,0 +1,126 @@ +/* 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 . + */ +#define BOOST_PARAMETER_MAX_ARITY 12 + + +#include +#include +#include +#include + +#include +#include + +#include +#include +#include +#include + +#include "generators.h" + +using namespace Gudhi; + +typedef std::vector< Vertex_handle > typeVectorVertex; +//typedef std::vector< std::vector > Point_Vector; + +typedef Witness_complex< Simplex_tree<> > WitnessComplex; + +/** + * \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(); +} + +/** 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 != 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 + Simplex_tree<> simplex_tree; + + std::vector< std::pair > 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 > knn; + Landmark_choice_by_random_point(point_vector, nbL, knn); + + // Compute witness complex + WitnessComplex(knn, simplex_tree, nbL, point_vector[0].size()); + end = clock(); + double time = (double)(end-start)/CLOCKS_PER_SEC; + std::cout << "Witness complex for " << nbL << " landmarks took " + << time << " s. \n"; + l_time.push_back(std::make_pair(nbP,time)); + } + write_data(l_time, "w_time.dat"); +} diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 791d0e45..915e445c 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -27,7 +27,7 @@ #include #include #include -#include "gudhi/distance_functions.h" +#include #include #include #include diff --git a/src/Witness_complex/test/simple_witness_complex.cpp b/src/Witness_complex/test/simple_witness_complex.cpp index c7d85a4d..ea38b5c0 100644 --- a/src/Witness_complex/test/simple_witness_complex.cpp +++ b/src/Witness_complex/test/simple_witness_complex.cpp @@ -22,9 +22,8 @@ #include #include -//#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Witness_complex.h" +#include +#include using namespace Gudhi; diff --git a/src/Witness_complex/test/witness_complex_points.cpp b/src/Witness_complex/test/witness_complex_points.cpp index a86bf493..0a50101d 100644 --- a/src/Witness_complex/test/witness_complex_points.cpp +++ b/src/Witness_complex/test/witness_complex_points.cpp @@ -22,11 +22,10 @@ #include #include -//#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Witness_complex.h" -#include "gudhi/Landmark_choice_by_random_point.h" -#include "gudhi/Landmark_choice_by_furthest_point.h" +#include +#include +#include +#include using namespace Gudhi; -- cgit v1.2.3