diff options
Diffstat (limited to 'src')
-rw-r--r-- | src/CMakeLists.txt | 34 | ||||
-rw-r--r-- | src/cmake/modules/GUDHI_modules.cmake | 43 | ||||
-rw-r--r-- | src/cmake/modules/GUDHI_user_version_target.cmake (renamed from src/cmake/modules/GUDHI_user_version_target.txt) | 1 | ||||
-rw-r--r-- | src/common/include/gudhi/random_point_generators.h | 32 | ||||
-rw-r--r-- | src/common/utilities/CMakeLists.txt | 15 | ||||
-rw-r--r-- | src/common/utilities/README | 19 | ||||
-rw-r--r-- | src/common/utilities/hypergenerator.cpp | 189 |
7 files changed, 314 insertions, 19 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index ebcb6888..77a03c17 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -7,6 +7,9 @@ enable_testing() list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/") +# To be done first - Modules list can be found in CMAKE_MODULE_PATH/GUDHI_modules.cmake +include(GUDHI_modules) + # For "make doxygen" set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR}) include(GUDHI_doxygen_target) @@ -39,27 +42,22 @@ endif() # Gudhi compilation part include_directories(include) -add_subdirectory(example/common) -add_subdirectory(example/Simplex_tree) -add_subdirectory(example/Persistent_cohomology) -add_subdirectory(example/Skeleton_blocker) -add_subdirectory(example/Contraction) -add_subdirectory(example/Bitmap_cubical_complex) -add_subdirectory(example/Witness_complex) -add_subdirectory(example/Alpha_complex) -add_subdirectory(example/Rips_complex) -add_subdirectory(example/Spatial_searching) -add_subdirectory(example/Subsampling) -add_subdirectory(example/Tangential_complex) -add_subdirectory(example/Bottleneck_distance) - -# data points generator -add_subdirectory(data/points/generator) +# Include module CMake subdirectories +# GUDHI_SUB_DIRECTORIES is managed in CMAKE_MODULE_PATH/GUDHI_modules.cmake +foreach(GUDHI_MODULE ${GUDHI_MODULES}) + foreach(GUDHI_SUB_DIRECTORY ${GUDHI_SUB_DIRECTORIES}) + if(EXISTS ${CMAKE_SOURCE_DIR}/${GUDHI_SUB_DIRECTORY}/${GUDHI_MODULE}/CMakeLists.txt) + add_subdirectory(src/${GUDHI_MODULE}/${GUDHI_SUB_DIRECTORY}/) + endif(EXISTS ${CMAKE_SOURCE_DIR}/${GUDHI_SUB_DIRECTORY}/${GUDHI_MODULE}/CMakeLists.txt) + endforeach(GUDHI_SUB_DIRECTORY ${GUDHI_SUB_DIRECTORIES}) +endforeach(GUDHI_MODULE ${GUDHI_MODULES}) add_subdirectory(GudhUI) -# specific for cython module -add_subdirectory(${GUDHI_CYTHON_PATH}) +if (NOT WITHOUT_GUDHI_PYTHON) + # specific for cython module + add_subdirectory(${GUDHI_CYTHON_PATH}) +endif() #--------------------------------------------------------------------------------------- #--------------------------------------------------------------------------------------- diff --git a/src/cmake/modules/GUDHI_modules.cmake b/src/cmake/modules/GUDHI_modules.cmake new file mode 100644 index 00000000..6a26d7bf --- /dev/null +++ b/src/cmake/modules/GUDHI_modules.cmake @@ -0,0 +1,43 @@ +# A function to add a new module in GUDHI + +set(GUDHI_MODULES "") +function(add_gudhi_module file_path) + set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE) +endfunction(add_gudhi_module) + +# Add your new module in the list, order is not important + +add_gudhi_module(common) +add_gudhi_module(Alpha_complex) +add_gudhi_module(Bitmap_cubical_complex) +add_gudhi_module(Bottleneck_distance) +add_gudhi_module(Contraction) +add_gudhi_module(Hasse_complex) +add_gudhi_module(Persistent_cohomology) +add_gudhi_module(Rips_complex) +add_gudhi_module(Simplex_tree) +add_gudhi_module(Skeleton_blocker) +add_gudhi_module(Spatial_searching) +add_gudhi_module(Subsampling) +add_gudhi_module(Tangential_complex) +add_gudhi_module(Witness_complex) + +# message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") + +if (WITH_GUDHI_BENCHMARK) + set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};benchmark") +endif() +if (WITH_GUDHI_EXAMPLE) + set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example") +endif() +if (NOT WITHOUT_GUDHI_TEST) + set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test") +endif() +if (NOT WITHOUT_GUDHI_UTILITIES) + set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities") +endif() + +message("++ GUDHI_SUB_DIRECTORIES list is:\"${GUDHI_SUB_DIRECTORIES}\"") + + + diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.cmake index ca6bcd34..a764e88a 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.cmake @@ -47,7 +47,6 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) - set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex") set(GUDHI_DIRECTORIES "doc;example;concept") set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 2ec465ef..9df77760 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -282,6 +282,38 @@ std::vector<typename Kernel::Point_d> generate_points_on_sphere_d(std::size_t nu } template <typename Kernel> +std::vector<typename Kernel::Point_d> generate_points_in_ball_d(std::size_t num_points, int dim, double radius) { + typedef typename Kernel::Point_d Point; + Kernel k; + CGAL::Random rng; + CGAL::Random_points_in_ball_d<Point> generator(dim, radius); + std::vector<Point> points; + points.reserve(num_points); + for (std::size_t i = 0; i < num_points;) { + Point p = *generator++; + points.push_back(p); + ++i; + } + return points; +} + +template <typename Kernel> +std::vector<typename Kernel::Point_d> generate_points_in_cube_d(std::size_t num_points, int dim, double radius) { + typedef typename Kernel::Point_d Point; + Kernel k; + CGAL::Random rng; + CGAL::Random_points_in_cube_d<Point> generator(dim, radius); + std::vector<Point> points; + points.reserve(num_points); + for (std::size_t i = 0; i < num_points;) { + Point p = *generator++; + points.push_back(p); + ++i; + } + return points; +} + +template <typename Kernel> std::vector<typename Kernel::Point_d> generate_points_on_two_spheres_d(std::size_t num_points, int dim, double radius, double distance_between_centers, double radius_noise_percentage = 0.) { diff --git a/src/common/utilities/CMakeLists.txt b/src/common/utilities/CMakeLists.txt new file mode 100644 index 00000000..88d377a7 --- /dev/null +++ b/src/common/utilities/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 2.6) +project(data_points_generator) + +if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) + add_executable ( data_points_generator hypergenerator.cpp ) + target_link_libraries(data_points_generator ${Boost_SYSTEM_LIBRARY}) + add_test(NAME data_points_generator_on_sphere_1000_3_15.2 COMMAND $<TARGET_FILE:data_points_generator> + "on" "sphere" "onSphere.off" "1000" "3" "15.2") + add_test(NAME data_points_generator_in_sphere_100_2 COMMAND $<TARGET_FILE:data_points_generator> + "in" "sphere" "inSphere.off" "100" "2") + + # on cube is not available in CGAL + add_test(NAME data_points_generator_in_cube_10000_3_5.8 COMMAND $<TARGET_FILE:data_points_generator> + "in" "cube" "inCube.off" "10000" "3" "5.8") +endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/common/utilities/README b/src/common/utilities/README new file mode 100644 index 00000000..f2ece556 --- /dev/null +++ b/src/common/utilities/README @@ -0,0 +1,19 @@ +======================= data_points_generator ================================== + +Example of use : + +*** Hyper sphere|cube generator + +./data_points_generator on sphere onSphere.off 1000 3 15.2 + + => generates a onSphere.off file with 1000 points randomized on a sphere of dimension 3 and radius 15.2 + +./data_points_generator in sphere inSphere.off 100 2 + + => generates a inSphere.off file with 100 points randomized in a sphere of dimension 2 (circle) and radius 1.0 (default) + +./data_points_generator in cube inCube.off 10000 3 5.8 + + => generates a inCube.off file with 10000 points randomized in a cube of dimension 3 and side 5.8 + +!! Warning: hypegenerator on cube is not available !! diff --git a/src/common/utilities/hypergenerator.cpp b/src/common/utilities/hypergenerator.cpp new file mode 100644 index 00000000..0f310a13 --- /dev/null +++ b/src/common/utilities/hypergenerator.cpp @@ -0,0 +1,189 @@ +/* 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): Vincent Rouvreau + * + * Copyright (C) 2014 INRIA Saclay (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/random_point_generators.h> + +#include <CGAL/Epick_d.h> +#include <CGAL/algorithm.h> +#include <CGAL/assertions.h> + +#include <iostream> +#include <iterator> +#include <vector> +#include <fstream> // for std::ofstream +#include <cstdlib> + +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K; +typedef K::Point_d Point; + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " in|on sphere|cube off_file_name points_number[integer > 0] " << + "dimension[integer > 1] radius[double > 0.0 | default = 1.0]" << std::endl; + exit(-1); +} + +int main(int argc, char **argv) { + // program args management + if ((argc != 6) && (argc != 7)) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl; + usage(argv[0]); + } + + int points_number = atoi(argv[4]); + if (points_number <= 0) { + std::cerr << "Error: " << argv[4] << " is not correct" << std::endl; + usage(argv[0]); + } + + int dimension = atoi(argv[5]); + if (dimension <= 0) { + std::cerr << "Error: " << argv[5] << " is not correct" << std::endl; + usage(argv[0]); + } + + double radius = 1.0; + if (argc == 7) { + radius = atof(argv[6]); + if (radius <= 0.0) { + std::cerr << "Error: " << argv[6] << " is not correct" << std::endl; + usage(argv[0]); + } + } + + bool in = false; + if (strcmp(argv[1], "in") == 0) { + in = true; + } else if (strcmp(argv[1], "on") != 0) { + std::cerr << "Error: " << argv[1] << " is not correct" << std::endl; + usage(argv[0]); + } + + enum class Data_shape { sphere, cube, curve, torus, klein, undefined } ; + + Data_shape shape = Data_shape::undefined; + if (memcmp(argv[2], "sphere", sizeof("sphere")) == 0) { + shape = Data_shape::sphere; + } else if (memcmp(argv[2], "cube", sizeof("cube")) == 0) { + shape = Data_shape::cube; + } else if (memcmp(argv[2], "curve", sizeof("curve")) == 0) { + shape = Data_shape::curve; + } else if (memcmp(argv[2], "torus", sizeof("torus")) == 0) { + shape = Data_shape::torus; + } else if (memcmp(argv[2], "klein", sizeof("klein")) == 0) { + shape = Data_shape::klein; + } else { + std::cerr << "Error: " << argv[2] << " is not correct" << std::endl; + usage(argv[0]); + } + + std::ofstream diagram_out(argv[3]); + if (dimension == 3) { + diagram_out << "OFF" << std::endl; + diagram_out << points_number << " 0 0" << std::endl; + } else { + diagram_out << "nOFF" << std::endl; + diagram_out << dimension << " " << points_number << " 0 0" << std::endl; + } + + if (diagram_out.is_open()) { + // Generate "points_number" random points in a vector + std::vector<Point> points; + if (in) { + switch (shape) { + case Data_shape::sphere: + points = Gudhi::generate_points_in_ball_d<K>(points_number, dimension, radius); + break; + case Data_shape::cube: + points = Gudhi::generate_points_in_ball_d<K>(points_number, dimension, radius); + break; + case Data_shape::curve: + std::cerr << "Sorry: in curve is not available" << std::endl; + usage(argv[0]); + break; + case Data_shape::torus: + std::cerr << "Sorry: in torus is not available" << std::endl; + usage(argv[0]); + break; + case Data_shape::klein: + std::cerr << "Sorry: in klein is not available" << std::endl; + usage(argv[0]); + break; + default: + usage(argv[0]); + break; + } + } else { // means "on" + switch (shape) { + case Data_shape::sphere: + points = Gudhi::generate_points_on_sphere_d<K>(points_number, dimension, radius); + break; + case Data_shape::cube: + std::cerr << "Sorry: on cube is not available" << std::endl; + usage(argv[0]); + break; + case Data_shape::curve: + points = Gudhi::generate_points_on_moment_curve<K>(points_number, dimension, -radius/2., radius/2.); + break; + case Data_shape::torus: + if (dimension == 3) + points = Gudhi::generate_points_on_torus_3D<K>(points_number, dimension, radius, radius/2.); + else + points = Gudhi::generate_points_on_torus_d<K>(points_number, dimension, true); + break; + case Data_shape::klein: + switch (dimension) { + case 3: + points = Gudhi::generate_points_on_klein_bottle_3D<K>(points_number, radius, radius/2., true); + break; + case 4: + points = Gudhi::generate_points_on_klein_bottle_4D<K>(points_number, radius, radius/2., 0., true); + break; + case 5: + points = Gudhi::generate_points_on_klein_bottle_variant_5D<K>(points_number, radius, radius/2., true); + break; + default: + std::cerr << "Sorry: on klein is only available for dimension 3, 4 and 5" << std::endl; + usage(argv[0]); + break; + } + break; + default: + usage(argv[0]); + break; + } + } + + for (auto thePoint : points) { + int i = 0; + for (; i < dimension - 1; i++) { + diagram_out << thePoint[i] << " "; + } + diagram_out << thePoint[i] << std::endl; // last point + Carriage Return + } + } else { + std::cerr << "Error: " << argv[3] << " cannot be opened" << std::endl; + usage(argv[0]); + } + + return 0; +} + |