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diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h new file mode 100644 index 00000000..b109956d --- /dev/null +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -0,0 +1,169 @@ +/* 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) 2015 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/>. + */ + +#ifndef INTRO_ALPHA_COMPLEX_H_ +#define INTRO_ALPHA_COMPLEX_H_ + +// needs namespace for Doxygen to link on classes +namespace Gudhi { +// needs namespace for Doxygen to link on classes +namespace alphacomplex { + +/** \defgroup alpha_complex Alpha complex + * + * \author Vincent Rouvreau + * + * @{ + * + * \section definition Definition + * + * Alpha_complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> + * constructed from the finite cells of a Delaunay Triangulation. + * + * The filtration value of each simplex is computed from the circumradius of the simplex if it is Gabriel or + * from the alpha value of the simplex cofaces that make it not Gabriel. + * + * All simplices that have a filtration value strictly greater than a given alpha square value are not inserted into + * the simplex. + * + * \image html "alpha_complex_representation.png" "Alpha simplicial complex representation" + * + * Alpha_complex is constructing a `Simplex_tree` using <a target="_blank" + * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations">Delaunay Triangulation</a> + * \cite cgal:hdj-t-15b from <a target="_blank" href="http://www.cgal.org/">CGAL</a> (the Computational Geometry + * Algorithms Library \cite cgal:eb-15b). + * + * The complex is a template class requiring an Epick_d <a target="_blank" + * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a> + * \cite cgal:s-gkd-15b from CGAL as template. + * + * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * + * \section pointsexample Example from points + * + * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and initializes the + * alpha complex with it. + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex_from_points.cpp + * + * When launching: + * + * \code $> ./alphapoints + * \endcode + * + * the program output is: + * + * \include alphaoffreader_for_doc_60.txt + * + * \section algorithm Algorithm + * + * \subsection datastructure Data structure + * + * In order to build the alpha complex, first, a Simplex tree is built from the cells of a Delaunay Triangulation. + * (The filtration value is set to NaN, which stands for unknown value): + * \image html "alpha_complex_doc.png" "Simplex tree structure construction example" + * + * \subsection filtrationcomputation Filtration value computation algorithm + * + * \f{algorithm}{ + * \caption{Filtration value computation algorithm}\label{alpha} + * \begin{algorithmic} + * \For{i : dimension $\rightarrow$ 0} + * \ForAll{$\sigma$ of dimension i} + * \If {filtration($\sigma$) is NaN} + * \State filtration($\sigma$) = $\alpha^2(\sigma)$ + * \EndIf + * \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value} + * \If {filtration($\tau$) is not NaN} + * \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$)) + * \Else + * \If {$\tau$ is not Gabriel for $\sigma$} + * \State filtration($\tau$) = filtration($\sigma$) + * \EndIf + * \EndIf + * \EndFor + * \EndFor + * \EndFor + * \State make\_filtration\_non\_decreasing() + * \State prune\_above\_filtration() + * \end{algorithmic} + * \f} + * + * \subsubsection dimension2 Dimension 2 + * + * From the example above, it means the algorithm looks into each triangle ([1,2,3], [2,3,4], [1,3,5], ...), + * computes the filtration value of the triangle, and then propagates the filtration value as described + * here : + * \image html "alpha_complex_doc_135.png" "Filtration value propagation example" + * + * \subsubsection dimension1 Dimension 1 + * + * Then, the algorithm looks into each edge ([1,2], [2,3], [1,3], ...), + * computes the filtration value of the edge (in this case, propagation will have no effect). + * + * \subsubsection dimension0 Dimension 0 + * + * Finally, the algorithm looks into each vertex ([1], [2], [3], [4], [5], [6] and [7]) and + * sets the filtration value (0 in case of a vertex - propagation will have no effect). + * + * \subsubsection nondecreasing Non decreasing filtration values + * + * As Alpha square value computed from CGAL is an approximation, we have to make filtration non decreasing while + * increasing the dimension for our simplicial complex to be valid (cf. + * `Simplex_tree::make_filtration_non_decreasing()`). + * + * \subsubsection pruneabove Prune above given filtration value + * + * The simplex tree is pruned from the given maximum alpha square value (cf. `Simplex_tree::prune_above_filtration()`). + * In this example, the value is given by the user as argument of the program. + * + * + * \section offexample Example from OFF file + * + * This example builds the Delaunay triangulation in a dynamic kernel, and initializes the alpha complex with it. + * + * + * Then, it is asked to display information about the alpha complex. + * + * \include Alpha_complex_from_off.cpp + * + * When launching: + * + * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 32.0 + * \endcode + * + * the program output is: + * + * \include alphaoffreader_for_doc_32.txt + * + * \copyright GNU General Public License v3. + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + */ +/** @} */ // end defgroup alpha_complex + +} // namespace alphacomplex + +} // namespace Gudhi + +#endif // INTRO_ALPHA_COMPLEX_H_ diff --git a/src/Alpha_complex/doc/alpha_complex_doc.ipe b/src/Alpha_complex/doc/alpha_complex_doc.ipe new file mode 100644 index 00000000..e74f9bc4 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_doc.ipe @@ -0,0 +1,438 @@ +<?xml version="1.0"?> +<!DOCTYPE ipe SYSTEM "ipe.dtd"> +<ipe version="70107" creator="Ipe 7.1.10"> +<info created="D:20150603143945" modified="D:20151130095407"/> +<ipestyle name="basic"> +<symbol 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--- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -0,0 +1,58 @@ +#include <gudhi/Alpha_complex.h> +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <string> + +void usage(char * const progName) { + std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n"; + std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 3) && (argc != 4)) { + std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; + usage(argv[0]); + } + + std::string off_file_name(argv[1]); + double alpha_square_max_value = atof(argv[2]); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel; + Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value); + + std::streambuf* streambufffer; + std::ofstream ouput_file_stream; + + if (argc == 4) { + ouput_file_stream.open(std::string(argv[3])); + streambufffer = ouput_file_stream.rdbuf(); + } else { + streambufffer = std::cout.rdbuf(); + } + + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + output_stream << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() << + " - " << alpha_complex_from_file.num_simplices() << " simplices - " << + alpha_complex_from_file.num_vertices() << " vertices." << std::endl; + + output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] "; + output_stream << std::endl; + } + ouput_file_stream.close(); + return 0; +} diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp new file mode 100644 index 00000000..815e40d7 --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -0,0 +1,49 @@ +#include <CGAL/Epick_d.h> +#include <gudhi/Alpha_complex.h> + +#include <iostream> +#include <string> +#include <vector> + +typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; +typedef Kernel::Point_d Point; +typedef std::vector<Point> Vector_of_points; + +int main(int argc, char **argv) { + double alpha_square_max_value = 60.0; + + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + points.push_back(Point(1.0, 1.0)); + points.push_back(Point(7.0, 0.0)); + points.push_back(Point(4.0, 6.0)); + points.push_back(Point(9.0, 6.0)); + points.push_back(Point(0.0, 14.0)); + points.push_back(Point(2.0, 19.0)); + points.push_back(Point(9.0, 17.0)); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_points(points, alpha_square_max_value); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << alpha_complex_from_points.dimension() << + " - " << alpha_complex_from_points.num_simplices() << " simplices - " << + alpha_complex_from_points.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + return 0; +} diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt new file mode 100644 index 00000000..e904133b --- /dev/null +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -0,0 +1,39 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIAlphaShapesExample) + +# need CGAL 4.7 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + + add_executable ( alphapoints Alpha_complex_from_points.cpp ) + target_link_libraries(alphapoints ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints) + + # Do not forget to copy test files in current binary dir + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + # Do not forget to copy test results files in current binary dir + file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) + target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY}) + add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt) + add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt) + if (DIFF_PATH) + add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt) + add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt) + endif() + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.") + endif () +endif() diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt new file mode 100644 index 00000000..13183e86 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt @@ -0,0 +1,22 @@ +Alpha complex is of dimension 2 - 20 simplices - 7 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt new file mode 100644 index 00000000..71f29a00 --- /dev/null +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt @@ -0,0 +1,27 @@ +Alpha complex is of dimension 2 - 25 simplices - 7 vertices. +Iterator on alpha complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h new file mode 100644 index 00000000..0898c6cd --- /dev/null +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -0,0 +1,393 @@ +/* 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) 2015 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/>. + */ + +#ifndef ALPHA_COMPLEX_H_ +#define ALPHA_COMPLEX_H_ + +// to construct a simplex_tree from Delaunay_triangulation +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Debug_utils.h> +// to construct a Delaunay_triangulation from a OFF file +#include <gudhi/Delaunay_triangulation_off_io.h> + +#include <stdlib.h> +#include <math.h> // isnan, fmax + +#include <CGAL/Delaunay_triangulation.h> + +#include <iostream> +#include <vector> +#include <string> +#include <limits> // NaN +#include <map> +#include <utility> // std::pair +#include <stdexcept> + +namespace Gudhi { + +namespace alphacomplex { + +/** + * \brief Alpha complex data structure. + * + * \details + * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay + * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from + * an OFF file (cf. Delaunay_triangulation_off_reader). + * + * Please refer to \ref alpha_complex for examples. + * + * The complex is a template class requiring an Epick_d <a target="_blank" + * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a> + * \cite cgal:s-gkd-15b from CGAL as template. + * + * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * + */ +template<class Kernel> +class Alpha_complex : public Simplex_tree<> { + private: + // From Simplex_tree + // Type required to insert into a simplex_tree (with or without subfaces). + typedef std::vector<Vertex_handle> Vector_vertex; + + // Simplex_result is the type returned from simplex_tree insert function. + typedef typename std::pair<Simplex_handle, bool> Simplex_result; + + // Delaunay_triangulation type required to create an alpha-complex. + typedef typename CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation; + + typedef typename Kernel::Compute_squared_radius_d Squared_Radius; + typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel; + typedef typename Kernel::Point_dimension_d Point_Dimension; + + typedef typename Kernel::Point_d Point_d; + + // Type required to compute squared radius, or side of bounded sphere on a vector of points. + typedef typename std::vector<Point_d> Vector_of_CGAL_points; + + // Vertex_iterator type from CGAL. + typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator; + + // size_type type from CGAL. + typedef typename Delaunay_triangulation::size_type size_type; + + // Double map type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa. + typedef typename std::map< CGAL_vertex_iterator, Vertex_handle > Map_vertex_iterator_to_handle; + //typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Map_vertex_handle_to_iterator; + typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator; + + private: + /** \brief Map to switch from CGAL vertex iterator to simplex tree vertex handle.*/ + Map_vertex_iterator_to_handle vertex_iterator_to_handle_; + /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator. + * Vertex handles are inserted sequentially, starting at 0.*/ + Vector_vertex_iterator vertex_handle_to_iterator_; + /** \brief Pointer on the CGAL Delaunay triangulation.*/ + Delaunay_triangulation* triangulation_; + /** \brief Kernel for triangulation_ functions access.*/ + Kernel kernel_; + + public: + /** \brief Alpha_complex constructor from an OFF file name. + * Uses the Delaunay_triangulation_off_reader to construct the Delaunay triangulation required to initialize + * the Alpha_complex. + * + * @param[in] off_file_name OFF file [path and] name. + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + */ + Alpha_complex(const std::string& off_file_name, + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) + : triangulation_(nullptr) { + Gudhi::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name); + if (!off_reader.is_valid()) { + std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; + exit(-1); // ----- >> + } + triangulation_ = off_reader.get_complex(); + init(max_alpha_square); + } + + /** \brief Alpha_complex constructor from a Delaunay triangulation. + * + * @param[in] triangulation_ptr Pointer on a <a target="_blank" + * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations"> + * CGAL::Delaunay_triangulation<Kernel></a> \cite cgal:hdj-t-15b. + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + */ + Alpha_complex(Delaunay_triangulation* triangulation_ptr, + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) + : triangulation_(triangulation_ptr) { + init(max_alpha_square); + } + + /** \brief Alpha_complex constructor from a list of points. + * + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a Kernel::Point_d. + * \warning In debug mode, the exception std::invalid_argument is thrown if an empty input point range is passed as + * argument. + */ + template<typename InputPointRange > + Alpha_complex(const InputPointRange& points, + Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) + : triangulation_(nullptr) { + auto first = std::begin(points); + auto last = std::end(points); + + GUDHI_CHECK((first == last), + std::invalid_argument ("Alpha_complex::Alpha_complex(InputPointRange) - Empty input point range")); + + if (first != last) { + // point_dimension function initialization + Point_Dimension point_dimension = kernel_.point_dimension_d_object(); + + // Delaunay triangulation is point dimension minus one. + triangulation_ = new Delaunay_triangulation(point_dimension(*first) - 1); + + size_type inserted = triangulation_->insert(first, last); + if (inserted != (last -first)) { + std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << "\n"; + exit(-1); // ----- >> + } + init(max_alpha_square); + } + } + + /** \brief Alpha_complex destructor. + * + * @warning Deletes the Delaunay triangulation. + */ + ~Alpha_complex() { + delete triangulation_; + } + + /** \brief get_point returns the point corresponding to the vertex given as parameter. + * + * @param[in] vertex Vertex handle of the point to retrieve. + * @return The point found. + * @warning Exception std::out_of_range is thrown in case vertex is not found. + */ + Point_d get_point(Vertex_handle vertex) const { + return vertex_handle_to_iterator_.at(vertex)->point(); + } + + private: + /** \brief Initialize the Alpha_complex from the Delaunay triangulation. + * + * @param[in] max_alpha_square maximum for alpha square value. + * + * @warning Delaunay triangulation must be already constructed with at least one vertex and dimension must be more + * than 0. + * + * Initialization can be launched once. + */ + void init(Filtration_value max_alpha_square) { + if (triangulation_ == nullptr) { + std::cerr << "Alpha_complex init - Cannot init from a NULL triangulation\n"; + return; // ----- >> + } + if (triangulation_->number_of_vertices() < 1) { + std::cerr << "Alpha_complex init - Cannot init from a triangulation without vertices\n"; + return; // ----- >> + } + if (triangulation_->maximal_dimension() < 1) { + std::cerr << "Alpha_complex init - Cannot init from a zero-dimension triangulation\n"; + return; // ----- >> + } + if (num_vertices() > 0) { + std::cerr << "Alpha_complex init - Cannot init twice\n"; + return; // ----- >> + } + + set_dimension(triangulation_->maximal_dimension()); + // set_filtration to +inf for prune_above_filtration to be done (if necessary) + set_filtration(std::numeric_limits<Filtration_value>::infinity()); + + // -------------------------------------------------------------------------------------------- + // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa + // Start to insert at handle = 0 - default integer value + Vertex_handle vertex_handle = Vertex_handle(); + // Loop on triangulation vertices list + for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) { + if (!triangulation_->is_infinite(*vit)) { +#ifdef DEBUG_TRACES + std::cout << "Vertex insertion - " << vertex_handle << " -> " << vit->point() << std::endl; +#endif // DEBUG_TRACES + + vertex_iterator_to_handle_.emplace(vit, vertex_handle); + vertex_handle_to_iterator_.push_back(vit); + vertex_handle++; + } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // Simplex_tree construction from loop on triangulation finite full cells list + for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) { + Vector_vertex vertexVector; +#ifdef DEBUG_TRACES + std::cout << "Simplex_tree insertion "; +#endif // DEBUG_TRACES + for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) { + if (*vit != nullptr) { +#ifdef DEBUG_TRACES + std::cout << " " << vertex_iterator_to_handle_[*vit]; +#endif // DEBUG_TRACES + // Vector of vertex construction for simplex_tree structure + vertexVector.push_back(vertex_iterator_to_handle_[*vit]); + } + } +#ifdef DEBUG_TRACES + std::cout << std::endl; +#endif // DEBUG_TRACES + // Insert each simplex and its subfaces in the simplex tree - filtration is NaN + Simplex_result insert_result = insert_simplex_and_subfaces(vertexVector, + std::numeric_limits<double>::quiet_NaN()); + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // ### For i : d -> 0 + for (int decr_dim = dimension(); decr_dim >= 0; decr_dim--) { + // ### Foreach Sigma of dim i + for (auto f_simplex : skeleton_simplex_range(decr_dim)) { + int f_simplex_dim = dimension(f_simplex); + if (decr_dim == f_simplex_dim) { + Vector_of_CGAL_points pointVector; +#ifdef DEBUG_TRACES + std::cout << "Sigma of dim " << decr_dim << " is"; +#endif // DEBUG_TRACES + for (auto vertex : simplex_vertex_range(f_simplex)) { + pointVector.push_back(get_point(vertex)); +#ifdef DEBUG_TRACES + std::cout << " " << vertex; +#endif // DEBUG_TRACES + } +#ifdef DEBUG_TRACES + std::cout << std::endl; +#endif // DEBUG_TRACES + // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma) + if (isnan(filtration(f_simplex))) { + Filtration_value alpha_complex_filtration = 0.0; + // No need to compute squared_radius on a single point - alpha is 0.0 + if (f_simplex_dim > 0) { + // squared_radius function initialization + Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object(); + + alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end()); + } + assign_filtration(f_simplex, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << filtration(f_simplex) << std::endl; +#endif // DEBUG_TRACES + } + propagate_alpha_filtration(f_simplex, decr_dim); + } + } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension + if (make_filtration_non_decreasing()) { + initialize_filtration(); + } + // Remove all simplices that have a filtration value greater than max_alpha_square + prune_above_filtration(max_alpha_square); + // -------------------------------------------------------------------------------------------- + } + + template<typename Simplex_handle> + void propagate_alpha_filtration(Simplex_handle f_simplex, int decr_dim) { + // ### Foreach Tau face of Sigma + for (auto f_boundary : boundary_simplex_range(f_simplex)) { +#ifdef DEBUG_TRACES + std::cout << " | --------------------------------------------------\n"; + std::cout << " | Tau "; + for (auto vertex : simplex_vertex_range(f_boundary)) { + std::cout << vertex << " "; + } + std::cout << "is a face of Sigma\n"; + std::cout << " | isnan(filtration(Tau)=" << isnan(filtration(f_boundary)) << std::endl; +#endif // DEBUG_TRACES + // ### If filt(Tau) is not NaN + if (!isnan(filtration(f_boundary))) { + // ### filt(Tau) = fmin(filt(Tau), filt(Sigma)) + Filtration_value alpha_complex_filtration = fmin(filtration(f_boundary), filtration(f_simplex)); + assign_filtration(f_boundary, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << filtration(f_boundary) << std::endl; +#endif // DEBUG_TRACES + // ### Else + } else { + // No need to compute is_gabriel for dimension <= 2 + // i.e. : Sigma = (3,1) => Tau = 1 + if (decr_dim > 1) { + // insert the Tau points in a vector for is_gabriel function + Vector_of_CGAL_points pointVector; + Vertex_handle vertexForGabriel = Vertex_handle(); + for (auto vertex : simplex_vertex_range(f_boundary)) { + pointVector.push_back(get_point(vertex)); + } + // Retrieve the Sigma point that is not part of Tau - parameter for is_gabriel function + Point_d point_for_gabriel; + for (auto vertex : simplex_vertex_range(f_simplex)) { + point_for_gabriel = get_point(vertex); + if (std::find(pointVector.begin(), pointVector.end(), point_for_gabriel) == pointVector.end()) { + // vertex is not found in Tau + vertexForGabriel = vertex; + // No need to continue loop + break; + } + } + // is_gabriel function initialization + Is_Gabriel is_gabriel = kernel_.side_of_bounded_sphere_d_object(); + bool is_gab = is_gabriel(pointVector.begin(), pointVector.end(), point_for_gabriel) + != CGAL::ON_BOUNDED_SIDE; +#ifdef DEBUG_TRACES + std::cout << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl; +#endif // DEBUG_TRACES + // ### If Tau is not Gabriel of Sigma + if (false == is_gab) { + // ### filt(Tau) = filt(Sigma) + Filtration_value alpha_complex_filtration = filtration(f_simplex); + assign_filtration(f_boundary, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(f_boundary) << std::endl; +#endif // DEBUG_TRACES + } + } + } + } + } +}; + +} // namespace alphacomplex + +} // namespace Gudhi + +#endif // ALPHA_COMPLEX_H_ diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp new file mode 100644 index 00000000..2912019d --- /dev/null +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -0,0 +1,239 @@ +/* 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) 2015 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/>. + */ + +#define BOOST_TEST_DYN_LINK +#define BOOST_TEST_MODULE "alpha_complex" +#include <boost/test/unit_test.hpp> + +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> + +#include <cmath> // float comparison +#include <limits> +#include <string> +#include <vector> + +// to construct a Delaunay_triangulation from a OFF file +#include <gudhi/Delaunay_triangulation_off_io.h> +#include <gudhi/Alpha_complex.h> + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d; +// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter + +BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) { + // ---------------------------------------------------------------------------- + // + // Init of an alpha-complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double max_alpha_square_value = 60.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << + max_alpha_square_value << "==========" << std::endl; + + Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); + + const int DIMENSION = 2; + std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES); + + const int NUMBER_OF_SIMPLICES = 25; + std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); + +} + +BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) { + // ---------------------------------------------------------------------------- + // + // Init of an alpha-complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double max_alpha_square_value = 59.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << + max_alpha_square_value << "==========" << std::endl; + + Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value); + + const int DIMENSION = 2; + std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION); + + const int NUMBER_OF_VERTICES = 7; + std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES); + + const int NUMBER_OF_SIMPLICES = 23; + std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES); +} + +bool are_almost_the_same(float a, float b) { + return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); +} + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_s; +typedef Kernel_s::Point_d Point; +typedef std::vector<Point> Vector_of_points; + + +bool is_point_in_list(Vector_of_points points_list, Point point) { + for (auto& point_in_list : points_list) { + if (point_in_list == point) { + return true; // point found + } + } + return false; // point not found +} + +BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Vector_of_points points; + std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 0.0, 0.0, 1.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 0.0, 1.0, 0.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + coords = { 1.0, 0.0, 0.0, 0.0 }; + points.push_back(Point(coords.begin(), coords.end())); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(points); + + std::cout << "========== Alpha_complex_from_points ==========" << std::endl; + + // Another way to check num_simplices + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15); + + std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_points.dimension() == 4); + std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4); + + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + switch (alpha_complex_from_points.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0)); + break; + case 1: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0)); + break; + case 2: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 2.0/3.0)); + break; + case 3: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 3.0/4.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } + + Point p0 = alpha_complex_from_points.get_point(0); + std::cout << "alpha_complex_from_points.get_point(0)=" << p0 << std::endl; + BOOST_CHECK(4 == p0.dimension()); + BOOST_CHECK(is_point_in_list(points, p0)); + + Point p1 = alpha_complex_from_points.get_point(1); + std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl; + BOOST_CHECK(4 == p1.dimension()); + BOOST_CHECK(is_point_in_list(points, p1)); + + Point p2 = alpha_complex_from_points.get_point(2); + std::cout << "alpha_complex_from_points.get_point(2)=" << p2 << std::endl; + BOOST_CHECK(4 == p2.dimension()); + BOOST_CHECK(is_point_in_list(points, p2)); + + Point p3 = alpha_complex_from_points.get_point(3); + std::cout << "alpha_complex_from_points.get_point(3)=" << p3 << std::endl; + BOOST_CHECK(4 == p3.dimension()); + BOOST_CHECK(is_point_in_list(points, p3)); + + // Test to the limit + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(4), std::out_of_range); + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(-1), std::out_of_range); + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range); + + // Test after prune_above_filtration + alpha_complex_from_points.prune_above_filtration(0.6); + // Another way to check num_simplices + std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl; + num_simplices = 0; + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 10); + std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_simplices() == 10); + + std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl; + BOOST_CHECK(alpha_complex_from_points.dimension() == 4); + std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl; + BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4); + + for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) { + switch (alpha_complex_from_points.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0)); + break; + case 1: + BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } + +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt new file mode 100644 index 00000000..2e5d6c3d --- /dev/null +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -0,0 +1,42 @@ +cmake_minimum_required(VERSION 2.6) +project(GUDHIAlphaComplexTest) + +if (GCOVR_PATH) + # for gcovr to make coverage reports - Corbera Jenkins plugin + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage") +endif() +if (GPROF_PATH) + # for gprof to make coverage reports - Jenkins + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg") +endif() + +# need CGAL 4.7 +# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../.. +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + message(STATUS "CGAL version: ${CGAL_VERSION}.") + + find_package(Eigen3 3.1.0) + if (EIGEN3_FOUND) + message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.") + include( ${EIGEN3_USE_FILE} ) + include_directories (BEFORE "../../include") + + add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp ) + target_link_libraries(AlphaComplexUT ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + + # Do not forget to copy test files in current binary dir + file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + + add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT + # XML format for Jenkins xUnit plugin + --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no) + + else() + message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha complex feature.") + endif() + else() + message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex feature. Version 4.6.0 is required.") + endif () +endif() + diff --git a/src/Alpha_complex/test/README b/src/Alpha_complex/test/README new file mode 100644 index 00000000..45b87d91 --- /dev/null +++ b/src/Alpha_complex/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./AlphaComplexUnitTest --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) |
