From 10ca6a70ba7ffea5c65d9c045b624da3d4200a63 Mon Sep 17 00:00:00 2001 From: ROUVREAU Vincent Date: Mon, 15 Jun 2020 07:52:15 +0200 Subject: Factory to build python alpha complex. 3d version of alpha complex. Needs change in doc as alphacomplexdoc.off is a fake 3d off data file --- src/python/doc/alpha_complex_user.rst | 47 ++------- src/python/gudhi/alpha_complex.pyx | 27 +++-- src/python/include/Alpha_complex_factory.h | 144 +++++++++++++++++++++++++++ src/python/include/Alpha_complex_interface.h | 74 ++++---------- 4 files changed, 185 insertions(+), 107 deletions(-) create mode 100644 src/python/include/Alpha_complex_factory.h (limited to 'src') diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst index 097470c1..bcc2fc51 100644 --- a/src/python/doc/alpha_complex_user.rst +++ b/src/python/doc/alpha_complex_user.rst @@ -178,49 +178,22 @@ In the following example, a threshold of :math:`\alpha^2 = 32.0` is used. Example from OFF file ^^^^^^^^^^^^^^^^^^^^^ -This example builds the Delaunay triangulation from the points given by an OFF file, and initializes the alpha complex -with it. +This example builds the alpha complex from 300 random points on a 2-torus. +Then, it computes the persistence diagram and diplays it: -Then, it is asked to display information about the alpha complex: - -.. testcode:: +.. plot:: + :include-source: + import matplotlib.pyplot as plt import gudhi alpha_complex = gudhi.AlphaComplex(off_file=gudhi.__root_source_dir__ + \ - '/data/points/alphacomplexdoc.off') - simplex_tree = alpha_complex.create_simplex_tree(max_alpha_square=32.0) + '/data/points/tore3D_300.off') + 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) - fmt = '%s -> %.2f' - for filtered_value in simplex_tree.get_filtration(): - print(fmt % tuple(filtered_value)) - -the program output is: - -.. testoutput:: - - Alpha complex is of dimension 2 - 20 simplices - 7 vertices. - [0] -> 0.00 - [1] -> 0.00 - [2] -> 0.00 - [3] -> 0.00 - [4] -> 0.00 - [5] -> 0.00 - [6] -> 0.00 - [2, 3] -> 6.25 - [4, 5] -> 7.25 - [0, 2] -> 8.50 - [0, 1] -> 9.25 - [1, 3] -> 10.00 - [1, 2] -> 11.25 - [1, 2, 3] -> 12.50 - [0, 1, 2] -> 13.00 - [5, 6] -> 13.25 - [2, 4] -> 20.00 - [4, 6] -> 22.74 - [4, 5, 6] -> 22.74 - [3, 6] -> 30.25 - + diag = simplex_tree.persistence() + gudhi.plot_persistence_diagram(diag) + plt.show() diff --git a/src/python/gudhi/alpha_complex.pyx b/src/python/gudhi/alpha_complex.pyx index a356384d..ac44c61f 100644 --- a/src/python/gudhi/alpha_complex.pyx +++ b/src/python/gudhi/alpha_complex.pyx @@ -20,6 +20,7 @@ import os from gudhi.simplex_tree cimport * from gudhi.simplex_tree import SimplexTree +from gudhi import read_points_from_off_file __author__ = "Vincent Rouvreau" __copyright__ = "Copyright (C) 2016 Inria" @@ -27,11 +28,9 @@ __license__ = "GPL v3" cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": cdef cppclass Alpha_complex_interface "Gudhi::alpha_complex::Alpha_complex_interface": - Alpha_complex_interface(vector[vector[double]] points, bool fast_version) nogil except + - # bool from_file is a workaround for cython to find the correct signature - Alpha_complex_interface(string off_file, bool fast_version, bool from_file) nogil except + + Alpha_complex_interface(vector[vector[double]] points, bool fast_version, bool exact_version) nogil except + vector[double] get_point(int vertex) nogil except + - void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, bool exact_version, bool default_filtration_value) nogil except + + void create_simplex_tree(Simplex_tree_interface_full_featured* simplex_tree, double max_alpha_square, bool default_filtration_value) nogil except + # AlphaComplex python interface cdef class AlphaComplex: @@ -54,7 +53,6 @@ cdef class AlphaComplex: """ cdef Alpha_complex_interface * this_ptr - cdef bool exact # Fake constructor that does nothing but documenting the constructor def __init__(self, points=None, off_file='', precision='safe'): @@ -76,21 +74,20 @@ cdef class AlphaComplex: def __cinit__(self, points = None, off_file = '', precision = 'safe'): assert precision in ['fast', 'safe', 'exact'], "Alpha complex precision can only be 'fast', 'safe' or 'exact'" cdef bool fast = precision == 'fast' - self.exact = precision == 'exact' + cdef bool exact = precision == 'exact' cdef vector[vector[double]] pts if off_file: if os.path.isfile(off_file): - self.this_ptr = new Alpha_complex_interface(off_file.encode('utf-8'), fast, True) + points = read_points_from_off_file(off_file = off_file) else: print("file " + off_file + " not found.") - else: - if points is None: - # Empty Alpha construction - points=[] - pts = points - with nogil: - self.this_ptr = new Alpha_complex_interface(pts, fast) + if points is None: + # Empty Alpha construction + points=[] + pts = points + with nogil: + self.this_ptr = new Alpha_complex_interface(pts, fast, exact) def __dealloc__(self): if self.this_ptr != NULL: @@ -128,5 +125,5 @@ cdef class AlphaComplex: cdef bool compute_filtration = default_filtration_value == True with nogil: self.this_ptr.create_simplex_tree(stree_int_ptr, - mas, self.exact, compute_filtration) + mas, compute_filtration) return stree diff --git a/src/python/include/Alpha_complex_factory.h b/src/python/include/Alpha_complex_factory.h new file mode 100644 index 00000000..7cab73bd --- /dev/null +++ b/src/python/include/Alpha_complex_factory.h @@ -0,0 +1,144 @@ +/* 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): Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#ifndef INCLUDE_ALPHA_COMPLEX_FACTORY_H_ +#define INCLUDE_ALPHA_COMPLEX_FACTORY_H_ + +#include +#include +#include +#include +#include +#include + +#include + +#include "Simplex_tree_interface.h" + +#include +#include +#include +#include // for std::unique_ptr + +namespace Gudhi { + +namespace alpha_complex { + +template +std::vector pt_cgal_to_cython(CgalPointType& point) { + std::vector vd; + for (auto coord = point.cartesian_begin(); coord != point.cartesian_end(); coord++) + vd.push_back(CGAL::to_double(*coord)); + return vd; +} + +template +static CgalPointType pt_cython_to_cgal(std::vector const& vec) { + return CgalPointType(vec.size(), vec.begin(), vec.end()); +} + +class Abstract_alpha_complex { + public: + virtual std::vector get_point(int vh) = 0; + virtual void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, + bool default_filtration_value) = 0; +}; + +class Exact_Alphacomplex_dD : public Abstract_alpha_complex { + private: + using Exact_kernel = CGAL::Epeck_d; + using Point_exact_kernel = typename Exact_kernel::Point_d; + + public: + Exact_Alphacomplex_dD(const std::vector>& points, bool exact_version) + : exact_version_(exact_version) { + ac_exact_ptr_ = std::make_unique>( + boost::adaptors::transform(points, pt_cython_to_cgal)); + } + + std::vector get_point(int vh) { + Point_exact_kernel const& point = ac_exact_ptr_->get_point(vh); + return pt_cgal_to_cython(point); + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, + bool default_filtration_value){ + ac_exact_ptr_->create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value); + } + + private: + bool exact_version_; + std::unique_ptr> ac_exact_ptr_; +}; + +class Inexact_Alphacomplex_dD : public Abstract_alpha_complex { + private: + using Inexact_kernel = CGAL::Epick_d; + using Point_inexact_kernel = typename Inexact_kernel::Point_d; + + public: + Inexact_Alphacomplex_dD(const std::vector>& points, bool exact_version) + : exact_version_(exact_version) { + ac_inexact_ptr_ = std::make_unique>( + boost::adaptors::transform(points, pt_cython_to_cgal)); + } + + std::vector get_point(int vh) { + Point_inexact_kernel const& point = ac_inexact_ptr_->get_point(vh); + return pt_cgal_to_cython(point); + } + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, + bool default_filtration_value){ + ac_inexact_ptr_->create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value); + } + + private: + bool exact_version_; + std::unique_ptr> ac_inexact_ptr_; +}; + +template +class Alphacomplex_3D : public Abstract_alpha_complex { + private: + using Point_3 = typename Alpha_complex_3d::Bare_point_3; + + static Point_3 pt_cython_to_cgal_3(std::vector const& vec) { + return Point_3(vec[0], vec[1], vec[2]); + } + + public: + Alphacomplex_3D(const std::vector>& points) { + alpha3d_ptr_ = std::make_unique>( + boost::adaptors::transform(points, pt_cython_to_cgal_3)); + } + + std::vector get_point(int vh) { + Point_3 const& point = alpha3d_ptr_->get_point(vh); + return pt_cgal_to_cython(point); + } + + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, + bool default_filtration_value){ + alpha3d_ptr_->create_complex(*simplex_tree, max_alpha_square); + if (default_filtration_value) { + // TODO + } + } + + private: + std::unique_ptr> alpha3d_ptr_; +}; + + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // INCLUDE_ALPHA_COMPLEX_FACTORY_H_ diff --git a/src/python/include/Alpha_complex_interface.h b/src/python/include/Alpha_complex_interface.h index 3ac5db1f..c4b9df4b 100644 --- a/src/python/include/Alpha_complex_interface.h +++ b/src/python/include/Alpha_complex_interface.h @@ -11,12 +11,8 @@ #ifndef INCLUDE_ALPHA_COMPLEX_INTERFACE_H_ #define INCLUDE_ALPHA_COMPLEX_INTERFACE_H_ -#include -#include -#include -#include - -#include +#include "Alpha_complex_factory.h" +#include #include "Simplex_tree_interface.h" @@ -30,67 +26,35 @@ namespace Gudhi { namespace alpha_complex { class Alpha_complex_interface { - private: - using Exact_kernel = CGAL::Epeck_d; - using Inexact_kernel = CGAL::Epick_d; - using Point_exact_kernel = typename Exact_kernel::Point_d; - using Point_inexact_kernel = typename Inexact_kernel::Point_d; - - template - std::vector pt_cgal_to_cython(CgalPointType& point) { - std::vector vd; - for (auto coord = point.cartesian_begin(); coord != point.cartesian_end(); coord++) - vd.push_back(CGAL::to_double(*coord)); - return vd; - } - - template - static CgalPointType pt_cython_to_cgal(std::vector const& vec) { - return CgalPointType(vec.size(), vec.begin(), vec.end()); - } - public: - Alpha_complex_interface(const std::vector>& points, bool fast_version) - : fast_version_(fast_version) { - if (fast_version_) { - ac_inexact_ptr_ = std::make_unique>( - boost::adaptors::transform(points, pt_cython_to_cgal)); + Alpha_complex_interface(const std::vector>& points, bool fast_version, bool exact_version) { + if (points[0].size() == 3) { + if (fast_version) + alpha_ptr_ = std::make_unique>(points); + else if (exact_version) + alpha_ptr_ = std::make_unique>(points); + else + alpha_ptr_ = std::make_unique>(points); } else { - ac_exact_ptr_ = std::make_unique>( - boost::adaptors::transform(points, pt_cython_to_cgal)); + if (fast_version) { + alpha_ptr_ = std::make_unique(points, exact_version); + } else { + alpha_ptr_ = std::make_unique(points, exact_version); + } } } - Alpha_complex_interface(const std::string& off_file_name, bool fast_version, bool from_file = true) - : fast_version_(fast_version) { - if (fast_version_) - ac_inexact_ptr_ = std::make_unique>(off_file_name); - else - ac_exact_ptr_ = std::make_unique>(off_file_name); - } - std::vector get_point(int vh) { - if (fast_version_) { - Point_inexact_kernel const& point = ac_inexact_ptr_->get_point(vh); - return pt_cgal_to_cython(point); - } else { - Point_exact_kernel const& point = ac_exact_ptr_->get_point(vh); - return pt_cgal_to_cython(point); - } + return alpha_ptr_->get_point(vh); } - void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, bool exact_version, + void create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, bool default_filtration_value) { - if (fast_version_) - ac_inexact_ptr_->create_complex(*simplex_tree, max_alpha_square, exact_version, default_filtration_value); - else - ac_exact_ptr_->create_complex(*simplex_tree, max_alpha_square, exact_version, default_filtration_value); + alpha_ptr_->create_simplex_tree(simplex_tree, max_alpha_square, default_filtration_value); } private: - bool fast_version_; - std::unique_ptr> ac_exact_ptr_; - std::unique_ptr> ac_inexact_ptr_; + std::unique_ptr alpha_ptr_; }; } // namespace alpha_complex -- cgit v1.2.3