From b9160fb8410bbb999913b0b4e91f1aa1ff58d2cd Mon Sep 17 00:00:00 2001 From: Hind-M Date: Mon, 7 Jun 2021 17:07:55 +0200 Subject: Replace 'uniform' flag of torus generation with 'sample' taking two possible values: 'grid'(i.e uniform==True) or 'random' (i.e uniform==False) --- src/common/include/gudhi/random_point_generators.h | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'src/common/include') diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 33fb182d..07e4f3da 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -185,7 +185,7 @@ std::vector generate_points_on_torus_3D(std::size_t nu // "Private" function used by generate_points_on_torus_d template -static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices, +static void generate_grid_points_on_torus_d(const Kernel &k, int dim, std::size_t num_slices, OutputIterator out, double radius_noise_percentage = 0., std::vector current_point = @@ -208,14 +208,14 @@ static void generate_uniform_points_on_torus_d(const Kernel &k, int dim, std::si double alpha = two_pi * slice_idx / num_slices; cp2.push_back(radius_noise_ratio * std::cos(alpha)); cp2.push_back(radius_noise_ratio * std::sin(alpha)); - generate_uniform_points_on_torus_d( + generate_grid_points_on_torus_d( k, dim, num_slices, out, radius_noise_percentage, cp2); } } } template -std::vector generate_points_on_torus_d(std::size_t num_points, int dim, bool uniform = false, +std::vector generate_points_on_torus_d(std::size_t num_points, int dim, std::string sample = "random", double radius_noise_percentage = 0.) { using namespace boost::math::double_constants; @@ -226,9 +226,9 @@ std::vector generate_points_on_torus_d(std::size_t num std::vector points; points.reserve(num_points); - if (uniform) { + if (sample == "grid") { std::size_t num_slices = (std::size_t)std::pow(num_points, 1. / dim); - generate_uniform_points_on_torus_d( + generate_grid_points_on_torus_d( k, dim, num_slices, std::back_inserter(points), radius_noise_percentage); } else { for (std::size_t i = 0; i < num_points;) { -- cgit v1.2.3 From 575beed582f9288d83a403f4f578731f172f7f5f Mon Sep 17 00:00:00 2001 From: Hind-M Date: Wed, 11 Aug 2021 14:35:25 +0200 Subject: Add test for sphere and torus Fix numerical approximations inconsistencies with dim fraction exponent when generating points as grid on torus Add notes in doc regarding the torus versions use cases --- src/common/include/gudhi/random_point_generators.h | 2 +- src/python/CMakeLists.txt | 3 ++ src/python/doc/datasets_generators.rst | 5 +++ src/python/gudhi/datasets/generators/_points.cc | 4 +++ src/python/gudhi/datasets/generators/points.py | 5 +-- src/python/test/test_datasets_generators.py | 40 ++++++++++++++++++++++ 6 files changed, 54 insertions(+), 5 deletions(-) create mode 100755 src/python/test/test_datasets_generators.py (limited to 'src/common/include') diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 07e4f3da..25a7392d 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -227,7 +227,7 @@ std::vector generate_points_on_torus_d(std::size_t num std::vector points; points.reserve(num_points); if (sample == "grid") { - std::size_t num_slices = (std::size_t)std::pow(num_points, 1. / dim); + std::size_t num_slices = (std::size_t)std::pow(num_points + .5, 1. / dim); // add .5 to avoid rounding down with numerical approximations generate_grid_points_on_torus_d( k, dim, num_slices, std::back_inserter(points), radius_noise_percentage); } else { diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 8c46004a..f30dfe6d 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -443,6 +443,9 @@ if(PYTHONINTERP_FOUND) # Euclidean witness add_gudhi_py_test(test_euclidean_witness_complex) + # Datasets generators + add_gudhi_py_test(test_datasets_generators) # TODO separate full python datasets generators in another test file independant from CGAL ? + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) # Cubical diff --git a/src/python/doc/datasets_generators.rst b/src/python/doc/datasets_generators.rst index 2802eccd..e63dde82 100644 --- a/src/python/doc/datasets_generators.rst +++ b/src/python/doc/datasets_generators.rst @@ -60,6 +60,9 @@ Otherwise, if set to **'grid'**, the points are generated on a grid and would be ( [n\_samples^{1 \over {dim}}]^{dim}, 2*dim ) + +**Note:** This version is recommended when the user wishes to use **'grid'** as sample type, or **'random'** with a relatively small number of samples (~ less than 150). + Example """"""" .. code-block:: python @@ -81,6 +84,8 @@ The user should provide the number of points to be generated on the torus :code: The :code:`sample` argument is optional and is set to **'random'** by default. The other allowed value of sample type is **'grid'**. +**Note:** This version is recommended when the user wishes to use **'random'** as sample type with a great number of samples and a low dimension. + Example """"""" .. code-block:: python diff --git a/src/python/gudhi/datasets/generators/_points.cc b/src/python/gudhi/datasets/generators/_points.cc index 6bbdf284..3d38ff90 100644 --- a/src/python/gudhi/datasets/generators/_points.cc +++ b/src/python/gudhi/datasets/generators/_points.cc @@ -48,6 +48,10 @@ py::array_t generate_points_on_sphere(size_t n_samples, int ambient_dim, py::array_t generate_points_on_torus(size_t n_samples, int dim, std::string sample) { + if ( (sample != "random") && (sample != "grid")) { + throw pybind11::value_error("This sample type is not supported"); + } + std::vector points_generated; { diff --git a/src/python/gudhi/datasets/generators/points.py b/src/python/gudhi/datasets/generators/points.py index 3870dea6..daada486 100644 --- a/src/python/gudhi/datasets/generators/points.py +++ b/src/python/gudhi/datasets/generators/points.py @@ -23,7 +23,7 @@ def _generate_random_points_on_torus(n_samples, dim): def _generate_grid_points_on_torus(n_samples, dim): # Generate points on a dim-torus as a grid - n_samples_grid = int(n_samples**(1./dim)) + n_samples_grid = int((n_samples+.5)**(1./dim)) # add .5 to avoid rounding down with numerical approximations alpha = np.linspace(0, 2*np.pi, n_samples_grid, endpoint=False) array_points_inter = np.column_stack([np.cos(alpha), np.sin(alpha)]) @@ -45,12 +45,9 @@ def torus(n_samples, dim, sample='random'): """ if sample == 'random': # Generate points randomly - print("Sample is random") return _generate_random_points_on_torus(n_samples, dim) elif sample == 'grid': # Generate points on a grid - print("Sample is grid") return _generate_grid_points_on_torus(n_samples, dim) else: raise ValueError("Sample type '{}' is not supported".format(sample)) - return diff --git a/src/python/test/test_datasets_generators.py b/src/python/test/test_datasets_generators.py new file mode 100755 index 00000000..656c30ee --- /dev/null +++ b/src/python/test/test_datasets_generators.py @@ -0,0 +1,40 @@ +""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + Author(s): Hind Montassif + + Copyright (C) 2021 Inria + + Modification(s): + - YYYY/MM Author: Description of the modification +""" + +from gudhi.datasets.generators import points +from gudhi.datasets.generators import _points + +import pytest + +def test_sphere(): + assert _points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'random').shape == (10, 2) + + with pytest.raises(ValueError): + _points.sphere(n_samples = 10, ambient_dim = 2, radius = 1., sample = 'other') + +def test_torus(): + assert _points.torus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) + assert _points.torus(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) + + assert _points.torus(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) + assert _points.torus(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) + + with pytest.raises(ValueError): + _points.torus(n_samples = 10, dim = 4, sample = 'other') + +def test_torus_full_python(): + assert points.torus(n_samples = 64, dim = 3, sample = 'random').shape == (64, 6) + assert points.torus(n_samples = 64, dim = 3, sample = 'grid').shape == (64, 6) + + assert points.torus(n_samples = 10, dim = 4, sample = 'random').shape == (10, 8) + assert points.torus(n_samples = 10, dim = 4, sample = 'grid').shape == (1, 8) + + with pytest.raises(ValueError): + points.torus(n_samples = 10, dim = 4, sample = 'other') -- cgit v1.2.3 From dac3b045c38ace5085049d1caac9cc4bf174229a Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau Date: Tue, 30 Nov 2021 17:33:29 +0100 Subject: Fix this boost deprecated include --- src/common/include/gudhi/reader_utils.h | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'src/common/include') diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 0938f5c1..a1b104e2 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -14,7 +14,11 @@ #include #include -#include +#if BOOST_VERSION < 106600 +# include +#else +# include +#endif #include #include -- cgit v1.2.3 From 4fc331267735a3368160ea7cd001b7fa45d720f7 Mon Sep 17 00:00:00 2001 From: Vincent Rouvreau Date: Thu, 10 Feb 2022 10:32:18 +0100 Subject: Boost 1.66.0 is now the minimal version as required from cgal 5.1 - Also remove useless include boost/version.h --- .github/next_release.md | 3 +++ src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 1 - src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h | 1 - src/Subsampling/include/gudhi/sparsify_point_set.h | 5 ----- src/cmake/modules/GUDHI_third_party_libraries.cmake | 2 +- src/common/doc/installation.h | 2 +- src/common/include/gudhi/reader_utils.h | 4 ---- src/python/doc/installation.rst | 2 +- 8 files changed, 6 insertions(+), 14 deletions(-) (limited to 'src/common/include') diff --git a/.github/next_release.md b/.github/next_release.md index 65a92816..e21b25c7 100644 --- a/.github/next_release.md +++ b/.github/next_release.md @@ -13,6 +13,9 @@ Below is a list of changes made since GUDHI 3.5.0: - [Representations](https://gudhi.inria.fr/python/latest/representations.html#gudhi.representations.vector_methods.BettiCurve) - A more flexible Betti curve class capable of computing exact curves +- Installation + - Boost ≥ 1.66.0 is now required (was ≥ 1.56.0). + - [Module](link) - ... diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index ccc3d852..df5c630e 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -12,7 +12,6 @@ #ifndef ALPHA_COMPLEX_3D_H_ #define ALPHA_COMPLEX_3D_H_ -#include #include #include #include diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index ee64a277..e5522cc7 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -14,7 +14,6 @@ #include #include -#include #include #include diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 4571b8f3..b325fe3c 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -11,12 +11,7 @@ #ifndef SPARSIFY_POINT_SET_H_ #define SPARSIFY_POINT_SET_H_ -#include -#if BOOST_VERSION < 106600 -# include -#else # include -#endif #include #ifdef GUDHI_SUBSAMPLING_PROFILING diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index b316740d..68ffaee1 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -1,6 +1,6 @@ # This files manage third party libraries required by GUDHI -find_package(Boost 1.56.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) +find_package(Boost 1.66.0 QUIET OPTIONAL_COMPONENTS filesystem unit_test_framework program_options) # Boost_FOUND is not reliable if(NOT Boost_VERSION) diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index ef668dfb..67d026bd 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -5,7 +5,7 @@ * Examples of GUDHI headers inclusion can be found in \ref utilities. * * \section compiling Compiling - * The library uses c++14 and requires Boost ≥ 1.56.0 + * The library uses c++14 and requires Boost ≥ 1.66.0 * and CMake ≥ 3.5. * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index a1b104e2..29d5423d 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -14,11 +14,7 @@ #include #include -#if BOOST_VERSION < 106600 -# include -#else # include -#endif #include #include diff --git a/src/python/doc/installation.rst b/src/python/doc/installation.rst index 35c344e3..c2c3db34 100644 --- a/src/python/doc/installation.rst +++ b/src/python/doc/installation.rst @@ -39,7 +39,7 @@ If you are instead using a git checkout, beware that the paths are a bit different, and in particular the `python/` subdirectory is actually `src/python/` there. -The library uses c++14 and requires `Boost `_ :math:`\geq` 1.56.0, +The library uses c++14 and requires `Boost `_ :math:`\geq` 1.66.0, `CMake `_ :math:`\geq` 3.5 to generate makefiles, `NumPy `_ :math:`\geq` 1.15.0, `Cython `_ and `pybind11 `_ to compile -- cgit v1.2.3