Merge pull request #481 from Hind-M/generate_points_sphere_python

Add random points generator on sphere in python, with an example

5 files changed, 110 insertions, 0 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index bc9a3b7b..98f2b85f 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -46,6 +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', ")
   endif()
   if(CYTHON_FOUND)
     set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'off_reader', ")
@@ -151,6 +152,7 @@ if(PYTHONINTERP_FOUND)
     set(GUDHI_PYBIND11_MODULES "${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', ")
       set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ")
       set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ")
     endif ()
@@ -262,6 +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 "${CMAKE_CURRENT_BINARY_DIR}/gudhi/hera")
+    file(COPY "gudhi/datasets" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi" FILES_MATCHING PATTERN "*.py")
 
     # Some files for pip package
     file(COPY "introduction.rst" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
@@ -423,6 +426,10 @@ if(PYTHONINTERP_FOUND)
                WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
                COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
                ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
+      add_test(NAME alpha_complex_from_generated_points_on_sphere_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_generated_points_on_sphere_example.py")
       add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}"
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
new file mode 100644
index 00000000..267e6436
--- /dev/null
+++ b/src/python/example/alpha_complex_from_generated_points_on_sphere_example.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+
+from gudhi.datasets.generators import points
+from gudhi import AlphaComplex
+
+
+""" 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
+"""
+
+__author__ = "Hind Montassif"
+__copyright__ = "Copyright (C) 2021 Inria"
+__license__ = "MIT"
+
+print("#####################################################################")
+print("AlphaComplex creation from generated points on sphere")
+
+
+gen_points = points.sphere(n_samples = 50, ambient_dim = 2, radius = 1, sample = "random")
+
+# Create an alpha complex
+alpha_complex = AlphaComplex(points = gen_points)
+simplex_tree = alpha_complex.create_simplex_tree()
+
+result_str = 'Alpha complex is of dimension ' + repr(simplex_tree.dimension()) + ' - ' + \
+    repr(simplex_tree.num_simplices()) + ' simplices - ' + \
+    repr(simplex_tree.num_vertices()) + ' vertices.'
+print(result_str)
+
diff --git a/src/python/gudhi/datasets/__init__.py b/src/python/gudhi/datasets/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ 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.cc b/src/python/gudhi/datasets/generators/points.cc
new file mode 100644
index 00000000..d658946b
--- /dev/null
+++ b/src/python/gudhi/datasets/generators/points.cc
@@ -0,0 +1,68 @@
+/*    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
+ */
+
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+
+#include <gudhi/random_point_generators.h>
+#include <gudhi/Debug_utils.h>
+
+#include <CGAL/Epick_d.h>
+
+namespace py = pybind11;
+
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kern;
+
+py::array_t<double> generate_points_on_sphere(size_t n_samples, int ambient_dim, double radius, std::string sample) {
+    
+    if (sample != "random") {
+        throw pybind11::value_error("This sample type is not supported");
+    }
+
+    py::array_t<double> points({n_samples, (size_t)ambient_dim});
+
+    py::buffer_info buf = points.request();
+    double *ptr = static_cast<double *>(buf.ptr);
+
+    GUDHI_CHECK(n_samples == buf.shape[0], "Py array first dimension not matching n_samples on sphere");
+    GUDHI_CHECK(ambient_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>(n_samples, ambient_dim, radius);
+
+    for (size_t i = 0; i < n_samples; i++)
+        for (int j = 0; j < ambient_dim; j++)
+            ptr[i*ambient_dim+j] = points_generated[i][j];
+
+    return points;
+}
+
+PYBIND11_MODULE(points, m) {
+      m.attr("__license__") = "LGPL v3";
+      m.def("sphere", &generate_points_on_sphere,
+          py::arg("n_samples"), py::arg("ambient_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 n_samples: The number of points to be generated.
+    :type n_samples: integer
+    :param ambient_dim: The ambient dimension d.
+    :type ambient_dim: integer
+    :param radius: The radius. Default value is `1.`.
+    :type radius: float
+    :param sample: The sample type. Default and only available value is `"random"`.
+    :type sample: string
+    :rtype: numpy array of float
+    :returns: the generated points on a sphere.
+    )pbdoc");
+}