diff options
author | Hind Montassif <hind.montassif@gmail.com> | 2021-05-05 13:58:30 +0200 |
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committer | Hind Montassif <hind.montassif@gmail.com> | 2021-05-05 13:58:30 +0200 |
commit | 2b694f9beae0e5fa78ae5b8923e7f2905c58777f (patch) | |
tree | 7b3c874390fde4c93abce181f199290edae6e73f /src | |
parent | d68ddc94bd82c48a4433ae0b3b1b3f10c167ed0b (diff) |
Add __init__ files at every level in modules
Remove last modules level and add sample type argument
Rename num_points to n_samples
Diffstat (limited to 'src')
-rw-r--r-- | src/python/CMakeLists.txt | 7 | ||||
-rw-r--r-- | src/python/example/alpha_complex_from_generated_points_on_sphere_example.py | 7 | ||||
-rw-r--r-- | src/python/gudhi/datasets/__init__.py (renamed from src/python/gudhi/datasets/generators/points/__init__.py) | 0 | ||||
-rw-r--r-- | src/python/gudhi/datasets/generators/__init__.py | 0 | ||||
-rw-r--r-- | src/python/gudhi/datasets/generators/points.cc (renamed from src/python/gudhi/datasets/generators/points/sphere.cc) | 29 |
5 files changed, 24 insertions, 19 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index ef9dc3ab..8dd4ea5d 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -46,7 +46,7 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ") set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'hera', ") set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'clustering', ") - set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets/generators/points', ") + set(GUDHI_PYTHON_MODULES_EXTRA "${GUDHI_PYTHON_MODULES_EXTRA}'datasets', ") endif() if(CYTHON_FOUND) set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ") @@ -152,7 +152,7 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ") if (NOT CGAL_VERSION VERSION_LESS 4.11.0) - set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/points/sphere', ") + set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/points', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ") set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ") endif () @@ -264,8 +264,7 @@ if(PYTHONINTERP_FOUND) file(COPY "gudhi/weighted_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") file(COPY "gudhi/dtm_rips_complex.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi") file(COPY "gudhi/hera/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera") - file(COPY "gudhi/datasets/generators/points/__init__.py" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi/datasets/generators/points") - + file(COPY "gudhi/datasets" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi" FILES_MATCHING PATTERN "*.py") # Some files for pip package file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") diff --git a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py index 2b023bbe..e73584d3 100644 --- a/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py +++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -from gudhi.datasets.generators.points import sphere +from gudhi.datasets.generators import points from gudhi import AlphaComplex @@ -22,11 +22,10 @@ print("#####################################################################") print("AlphaComplex creation from generated points on sphere") -# Generate a circle: 50 points; dim 2; radius 1 -points = sphere.generate_random_points(50, 2, 1) +gen_points = points.sphere(n_samples = 50, dim = 2, radius = 1, sample = "random") # Create an alpha complex -alpha_complex = AlphaComplex(points=points) +alpha_complex = AlphaComplex(points = gen_points) simplex_tree = alpha_complex.create_simplex_tree() result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \ diff --git a/src/python/gudhi/datasets/generators/points/__init__.py b/src/python/gudhi/datasets/__init__.py index e69de29b..e69de29b 100644 --- a/src/python/gudhi/datasets/generators/points/__init__.py +++ b/src/python/gudhi/datasets/__init__.py diff --git a/src/python/gudhi/datasets/generators/__init__.py b/src/python/gudhi/datasets/generators/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/src/python/gudhi/datasets/generators/__init__.py diff --git a/src/python/gudhi/datasets/generators/points/sphere.cc b/src/python/gudhi/datasets/generators/points.cc index 79392ef0..f02c7d73 100644 --- a/src/python/gudhi/datasets/generators/points/sphere.cc +++ b/src/python/gudhi/datasets/generators/points.cc @@ -21,40 +21,47 @@ namespace py = pybind11; typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern; -py::array_t<double> generate_points_on_sphere(size_t num_points, int dim, double radius) { +py::array_t<double> generate_points_on_sphere(size_t n_samples, int dim, double radius, std::string sample) { + + if (sample != "random") { + throw pybind11::value_error("sample type is not supported"); + } - py::array_t<double> points({num_points, (size_t)dim}); + py::array_t<double> points({n_samples, (size_t)dim}); py::buffer_info buf = points.request(); double *ptr = static_cast<double *>(buf.ptr); - GUDHI_CHECK(num_points == buf.shape[0], "Py array first dimension not matching num_points on sphere"); + GUDHI_CHECK(n_samples == buf.shape[0], "Py array first dimension not matching n_samples on sphere"); GUDHI_CHECK(dim == buf.shape[1], "Py array second dimension not matching the ambient space dimension"); py::gil_scoped_release release; - auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(num_points, dim, radius); + auto points_generated = Gudhi::generate_points_on_sphere_d<Kern>(n_samples, dim, radius); - for (size_t i = 0; i < num_points; i++) + for (size_t i = 0; i < n_samples; i++) for (int j = 0; j < dim; j++) ptr[i*dim+j] = points_generated[i][j]; return points; } -PYBIND11_MODULE(sphere, m) { +PYBIND11_MODULE(points, m) { m.attr("__license__") = "LGPL v3"; - m.def("generate_random_points", &generate_points_on_sphere, - py::arg("num_points"), py::arg("dim"), py::arg("radius") = 1, + m.def("sphere", &generate_points_on_sphere, + py::arg("n_samples"), py::arg("dim"), + py::arg("radius") = 1, py::arg("sample") = "random", R"pbdoc( Generate random i.i.d. points uniformly on a (d-1)-sphere in R^d - :param num_points: The number of points to be generated. - :type num_points: unsigned integer - :param dim: The dimension. + :param n_samples: The number of points to be generated. + :type n_samples: integer + :param dim: The ambient dimension d. :type dim: integer :param radius: The radius. :type radius: float + :param sample: The sample type. + :type sample: string :rtype: numpy array of float :returns: the generated points on a sphere. )pbdoc"); 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