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Diffstat (limited to 'src/Alpha_complex')
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diff --git a/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h b/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h new file mode 100644 index 00000000..2b8bff94 --- /dev/null +++ b/src/Alpha_complex/concept/Simplicial_complex_for_alpha.h @@ -0,0 +1,89 @@ +/* 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) 2016 INRIA + * + * 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 CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ +#define CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ + +namespace Gudhi { + +namespace alpha_complex { + +/** \brief The concept SimplicialComplexForAlpha describes the requirements for a type to implement a simplicial + * complex, that can be created from a `Alpha_complex`. + */ +struct SimplicialComplexForAlpha { + /** Handle to specify a simplex. */ + typedef unspecified Simplex_handle; + /** Handle to specify a vertex. Must be a non-negative integer. */ + typedef unspecified Vertex_handle; + /** Handle to specify the simplex filtration value. */ + typedef unspecified Filtration_value; + + /** Returns the number of vertices in the simplicial complex. */ + std::size_t num_vertices(); + + /** Sets the simplicial complex dimension. */ + void set_dimension(int dimension); + + /** Gets the 'simplex' dimension. */ + int dimension(Simplex_handle simplex); + + /** Assigns the 'simplex' with the given 'filtration' value. */ + int assign_filtration(Simplex_handle simplex, Filtration_value filtration); + + /** \brief Inserts a simplex with vertices from a given simplex (represented by a vector of Vertex_handle) in the + * simplicial complex with the given 'filtration' value. */ + void insert_simplex_and_subfaces(std::vector<Vertex_handle> const & vertex_range, Filtration_value filtration); + + /** Browses the simplicial complex to make the filtration non-decreasing. */ + void make_filtration_non_decreasing(); + + /** Prune the simplicial complex above 'filtration' value given as parameter. */ + void prune_above_filtration(Filtration_value filtration); + + /** \brief Iterator over vertices of a simplex. + * + * 'value type' must be 'Vertex_handle'.*/ + typedef unspecified Simplex_vertex_range; + + /** \brief Returns a range over vertices of a given + * simplex. */ + Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex); + + /** \brief Iterator over the boundaries of the complex, in an arbitrary order. + * + * 'value_type' must be 'Simplex_handle'.*/ + typedef unspecified Boundary_simplex_range; + + /** \brief Returns a range over boundaries of a given simplex. */ + Boundary_simplex_range boundary_simplex_range(Simplex_handle const & simplex); + + /** \brief Return type of an insertion of a simplex + */ + typedef unspecified Insertion_result_type; +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ 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..3ffdae7f --- /dev/null +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -0,0 +1,176 @@ +/* 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 + * + * 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 DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_ +#define DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_ + +// needs namespace for Doxygen to link on classes +namespace Gudhi { +// needs namespace for Doxygen to link on classes +namespace alpha_complex { + +/** \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 as the square of the circumradius of the simplex if the + * circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration + * values of the codimension 1 cofaces that make it not Gabriel otherwise. + * + * All simplices that have a filtration value strictly greater than a given alpha squared value are not inserted into + * the complex. + * + * \image html "alpha_complex_representation.png" "Alpha-complex representation" + * + * Alpha_complex is constructing a <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) and is able to create a `SimplicialComplexForAlpha`. + * + * 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 parameter. + * + * \remark When the simplicial 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 creates a + * `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Alpha_complex/Alpha_complex_from_points.cpp + * + * When launching: + * + * \code $> ./alphapoints + * \endcode + * + * the program output is: + * + * \include Alpha_complex/alphaoffreader_for_doc_60.txt + * + * \section createcomplexalgorithm Create complex algorithm + * + * \subsection datastructure Data structure + * + * In order to create the simplicial complex, first, it is built from the cells of the Delaunay Triangulation. + * The filtration values are set to NaN, which stands for unknown value. + * + * In example, : + * \image html "alpha_complex_doc.png" "Simplicial complex 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 ([0,1,2], [0,2,4], [1,2,3], ...), + * computes the filtration value of the triangle, and then propagates the filtration value as described + * here : + * \image html "alpha_complex_doc_420.png" "Filtration value propagation example" + * + * \subsubsection dimension1 Dimension 1 + * + * Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...), + * 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 ([0], [1], [2], [3], [4], [5] and [6]) and + * sets the filtration value (0 in case of a vertex - propagation will have no effect). + * + * \subsubsection nondecreasing Non decreasing filtration values + * + * As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not + * quite define a proper filtration (i.e. non-decreasing with respect to inclusion). + * We fix that up by calling `SimplicialComplexForAlpha::make_filtration_non_decreasing()`. + * + * \subsubsection pruneabove Prune above given filtration value + * + * The simplex tree is pruned from the given maximum alpha squared value (cf. + * `SimplicialComplexForAlpha::prune_above_filtration()`). + * In the following 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/Alpha_complex_from_off.cpp + * + * When launching: + * + * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 32.0 + * \endcode + * + * the program output is: + * + * \include Alpha_complex/alphaoffreader_for_doc_32.txt + * + * \copyright GNU General Public License v3. + * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim + */ +/** @} */ // end defgroup alpha_complex + +} // namespace alpha_complex + +namespace alphacomplex = alpha_complex; + +} // namespace Gudhi + +#endif // 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+<path matrix="1 0 0 1 0 80" stroke="lightgray"> +280 660 m +300 710 l +370 690 l +280 660 l +</path> +<path matrix="1 0 0 1 0 80" stroke="lightgray"> +320 580 m +370 690 l +370 580 l +320 580 l +</path> +<path matrix="1 0 0 1 0 80" stroke="lightgray"> +280 660 m +370 690 l +320 580 l +280 660 l +</path> +<path matrix="1 0 0 1 0 80" stroke="darkcyan"> +77.2727 0 0 77.2727 243.636 591.818 e +</path> +<path matrix="1 0 0 1 0 80" stroke="darkcyan"> +243.428 591.569 m +186.061 643.28 l +</path> +<text matrix="1 0 0 1 0 80" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="18.785" height="4.294" depth="1.49" valign="baseline">$\alpha_{420}$</text> +<path matrix="1 0 0 1 -264 -162" stroke="lightgray"> +320 580 m +350 520 l +290 530 l +320 580 l +320 580 l +</path> +<path matrix="1 0 0 1 -264 -162" stroke="lightgray"> +320 580 m +280 660 l +290 530 l +320 580 l +320 580 l +</path> +<path matrix="1 0 0 1 -264 -162" stroke="lightgray"> +320 580 m +370 580 l +350 520 l +320 580 l +</path> +<text matrix="0.582962 0 0 1 -211.265 -209.555" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[2,0] is Gabriel $\rightarrow$ $\alpha_{20}$ is not$\\$ +modified (NaN) +</text> +<text matrix="1 0 0 1 -266.155 -165.501" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">0</text> +<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="310.693 578.759" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> +<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> +<text matrix="1 0 0 1 -264 -172" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" 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(" << nbArgs << ") is not correct\n"; + 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)) usage(argc, (argv[0] - 1)); + + 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::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name); + + 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(); + } + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + std::ostream output_stream(streambufffer); + + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + output_stream << "Alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.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 : simplex.filtration_simplex_range()) { + output_stream << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + output_stream << vertex << " "; + } + output_stream << ") -> " << "[" << simplex.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..491b7e6d --- /dev/null +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -0,0 +1,68 @@ +#include <gudhi/Alpha_complex.h> +// to construct a simplex_tree from alpha complex +#include <gudhi/Simplex_tree.h> + +#include <CGAL/Epick_d.h> + +#include <iostream> +#include <string> +#include <vector> +#include <limits> // for numeric limits + +typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; +typedef Kernel::Point_d Point; +typedef std::vector<Point> Vector_of_points; + +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n"; + std::cerr << " i.e.: " << progName << " 60.0\n"; + exit(-1); // ----- >> +} + +int main(int argc, char **argv) { + if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); + + // Delaunay complex if alpha_square_max_value is not given by the user. + double alpha_square_max_value = std::numeric_limits<double>::infinity(); + if (argc == 2) + alpha_square_max_value = atof(argv[1]); + + // ---------------------------------------------------------------------------- + // 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::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_points(points); + + Gudhi::Simplex_tree<> simplex; + if (alpha_complex_from_points.create_complex(simplex, alpha_square_max_value)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Alpha complex is of dimension " << simplex.dimension() << + " - " << simplex.num_simplices() << " simplices - " << + simplex.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 : simplex.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : simplex.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex.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..71a95d61 --- /dev/null +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -0,0 +1,33 @@ +cmake_minimum_required(VERSION 2.6) +project(Alpha_complex_examples) + +# 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) + if (EIGEN3_FOUND) + add_executable ( alphapoints Alpha_complex_from_points.cpp ) + target_link_libraries(alphapoints ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + add_executable ( alphaoffreader Alpha_complex_from_off.cpp ) + target_link_libraries(alphaoffreader ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(alphapoints ${TBB_LIBRARIES}) + target_link_libraries(alphaoffreader ${TBB_LIBRARIES}) + endif() + + 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}/) + 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) + # 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_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() + endif(EIGEN3_FOUND) + endif(NOT CGAL_VERSION VERSION_LESS 4.7.0) +endif(CGAL_FOUND) 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..9d5a9bad --- /dev/null +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -0,0 +1,434 @@ +/* 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 + * + * 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_ + +#include <gudhi/Debug_utils.h> +// to construct Alpha_complex from a OFF file of points +#include <gudhi/Points_off_io.h> + +#include <stdlib.h> +#include <math.h> // isnan, fmax + +#include <CGAL/Delaunay_triangulation.h> +#include <CGAL/Epick_d.h> +#include <CGAL/Spatial_sort_traits_adapter_d.h> +#include <CGAL/property_map.h> // for CGAL::Identity_property_map + +#include <iostream> +#include <vector> +#include <string> +#include <limits> // NaN +#include <map> +#include <utility> // std::pair +#include <stdexcept> +#include <numeric> // for std::iota + +namespace Gudhi { + +namespace alpha_complex { + +/** + * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h + * \brief Alpha complex data structure. + * + * \ingroup alpha_complex + * + * \details + * The data structure is constructing 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/) from a + * range of points or from an OFF file (cf. Points_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, default value is <a target="_blank" + * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> + * < <a target="_blank" href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html"> + * CGAL::Dynamic_dimension_tag </a> > + * + * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex. + * + */ +template<class Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>> +class Alpha_complex { + public: + // Add an int in TDS to save point index in the structure + typedef CGAL::Triangulation_data_structure<typename Kernel::Dimension, + CGAL::Triangulation_vertex<Kernel, std::ptrdiff_t>, + CGAL::Triangulation_full_cell<Kernel> > TDS; + /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ + typedef CGAL::Delaunay_triangulation<Kernel, TDS> Delaunay_triangulation; + + /** \brief A point in Euclidean space.*/ + typedef typename Kernel::Point_d Point_d; + /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay + * triangulations.*/ + typedef Kernel Geom_traits; + + private: + 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; + + // 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; + + // Map type to switch from simplex tree vertex handle to CGAL vertex iterator. + typedef typename std::map< std::size_t, CGAL_vertex_iterator > Vector_vertex_iterator; + + private: + /** \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 Points_off_reader to construct the Delaunay triangulation required to initialize + * the Alpha_complex. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * @param[in] off_file_name OFF file [path and] name. + */ + Alpha_complex(const std::string& off_file_name) + : triangulation_(nullptr) { + Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); + if (!off_reader.is_valid()) { + std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; + exit(-1); // ----- >> + } + + init_from_range(off_reader.get_point_cloud()); + } + + /** \brief Alpha_complex constructor from a list of points. + * + * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous. + * + * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d + * + * The type InputPointRange must be a range for which std::begin and + * std::end return input iterators on a Kernel::Point_d. + */ + template<typename InputPointRange > + Alpha_complex(const InputPointRange& points) + : triangulation_(nullptr) { + init_from_range(points); + } + + /** \brief Alpha_complex destructor deletes the Delaunay triangulation. + */ + ~Alpha_complex() { + delete triangulation_; + } + + // Forbid copy/move constructor/assignment operator + Alpha_complex(const Alpha_complex& other) = delete; + Alpha_complex& operator= (const Alpha_complex& other) = delete; + Alpha_complex (Alpha_complex&& other) = delete; + Alpha_complex& operator= (Alpha_complex&& other) = delete; + + /** \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. + * @exception std::out_of_range In case vertex is not found (cf. std::vector::at). + */ + const Point_d& get_point(std::size_t vertex) const { + return vertex_handle_to_iterator_.at(vertex)->point(); + } + + /** \brief number_of_vertices returns the number of vertices (same as the number of points). + * + * @return The number of vertices. + */ + const std::size_t number_of_vertices() const { + return vertex_handle_to_iterator_.size(); + } + + private: + template<typename InputPointRange > + void init_from_range(const InputPointRange& points) { + auto first = std::begin(points); + auto last = std::end(points); + + if (first != last) { + // point_dimension function initialization + Point_Dimension point_dimension = kernel_.point_dimension_d_object(); + + // Delaunay triangulation is point dimension. + triangulation_ = new Delaunay_triangulation(point_dimension(*first)); + + std::vector<Point_d> point_cloud(first, last); + + // Creates a vector {0, 1, ..., N-1} + std::vector<std::ptrdiff_t> indices(boost::counting_iterator<std::ptrdiff_t>(0), + boost::counting_iterator<std::ptrdiff_t>(point_cloud.size())); + + typedef boost::iterator_property_map<typename std::vector<Point_d>::iterator, + CGAL::Identity_property_map<std::ptrdiff_t>> Point_property_map; + typedef CGAL::Spatial_sort_traits_adapter_d<Kernel, Point_property_map> Search_traits_d; + + CGAL::spatial_sort(indices.begin(), indices.end(), Search_traits_d(std::begin(point_cloud))); + + typename Delaunay_triangulation::Full_cell_handle hint; + for (auto index : indices) { + typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(point_cloud[index], hint); + // Save index value as data to retrieve it after insertion + pos->data() = index; + hint = pos->full_cell(); + } + // -------------------------------------------------------------------------------------------- + // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa + // 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 - " << vit->data() << " -> " << vit->point() << std::endl; +#endif // DEBUG_TRACES + vertex_handle_to_iterator_.emplace(vit->data(), vit); + } + } + // -------------------------------------------------------------------------------------------- + } + } + + public: + template <typename SimplicialComplexForAlpha> + bool create_complex(SimplicialComplexForAlpha& complex) { + typedef typename SimplicialComplexForAlpha::Filtration_value Filtration_value; + return create_complex(complex, std::numeric_limits<Filtration_value>::infinity()); + } + + /** \brief Inserts all Delaunay triangulation into the simplicial complex. + * It also computes the filtration values accordingly to the \ref createcomplexalgorithm + * + * \tparam SimplicialComplexForAlpha must meet `SimplicialComplexForAlpha` concept. + * + * @param[in] complex SimplicialComplexForAlpha to be created. + * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. + * + * @return true if creation succeeds, false otherwise. + * + * @pre Delaunay triangulation must be already constructed with dimension strictly greater than 0. + * @pre The simplicial complex must be empty (no vertices) + * + * Initialization can be launched once. + */ + template <typename SimplicialComplexForAlpha, typename Filtration_value> + bool create_complex(SimplicialComplexForAlpha& complex, Filtration_value max_alpha_square) { + // From SimplicialComplexForAlpha type required to insert into a simplicial complex (with or without subfaces). + typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; + typedef typename SimplicialComplexForAlpha::Simplex_handle Simplex_handle; + typedef std::vector<Vertex_handle> Vector_vertex; + + if (triangulation_ == nullptr) { + std::cerr << "Alpha_complex cannot create_complex from a NULL triangulation\n"; + return false; // ----- >> + } + if (triangulation_->maximal_dimension() < 1) { + std::cerr << "Alpha_complex cannot create_complex from a zero-dimension triangulation\n"; + return false; // ----- >> + } + if (complex.num_vertices() > 0) { + std::cerr << "Alpha_complex create_complex - complex is not empty\n"; + return false; // ----- >> + } + + complex.set_dimension(triangulation_->maximal_dimension()); + + // -------------------------------------------------------------------------------------------- + // Simplex_tree construction from loop on triangulation finite full cells list + if (triangulation_->number_of_vertices() > 0) { + 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 << " " << (*vit)->data(); +#endif // DEBUG_TRACES + // Vector of vertex construction for simplex_tree structure + vertexVector.push_back((*vit)->data()); + } + } +#ifdef DEBUG_TRACES + std::cout << std::endl; +#endif // DEBUG_TRACES + // Insert each simplex and its subfaces in the simplex tree - filtration is NaN + complex.insert_simplex_and_subfaces(vertexVector, std::numeric_limits<double>::quiet_NaN()); + } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // Will be re-used many times + Vector_of_CGAL_points pointVector; + // ### For i : d -> 0 + for (int decr_dim = triangulation_->maximal_dimension(); decr_dim >= 0; decr_dim--) { + // ### Foreach Sigma of dim i + for (Simplex_handle f_simplex : complex.skeleton_simplex_range(decr_dim)) { + int f_simplex_dim = complex.dimension(f_simplex); + if (decr_dim == f_simplex_dim) { + pointVector.clear(); +#ifdef DEBUG_TRACES + std::cout << "Sigma of dim " << decr_dim << " is"; +#endif // DEBUG_TRACES + for (auto vertex : complex.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 (std::isnan(complex.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()); + } + complex.assign_filtration(f_simplex, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << complex.filtration(f_simplex) << std::endl; +#endif // DEBUG_TRACES + } + propagate_alpha_filtration(complex, f_simplex, decr_dim); + } + } + } + // -------------------------------------------------------------------------------------------- + + // -------------------------------------------------------------------------------------------- + // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension + complex.make_filtration_non_decreasing(); + // Remove all simplices that have a filtration value greater than max_alpha_square + complex.prune_above_filtration(max_alpha_square); + // -------------------------------------------------------------------------------------------- + return true; + } + + private: + template <typename SimplicialComplexForAlpha, typename Simplex_handle> + void propagate_alpha_filtration(SimplicialComplexForAlpha& complex, Simplex_handle f_simplex, int decr_dim) { + // From SimplicialComplexForAlpha type required to assign filtration values. + typedef typename SimplicialComplexForAlpha::Filtration_value Filtration_value; +#ifdef DEBUG_TRACES + typedef typename SimplicialComplexForAlpha::Vertex_handle Vertex_handle; +#endif // DEBUG_TRACES + + // ### Foreach Tau face of Sigma + for (auto f_boundary : complex.boundary_simplex_range(f_simplex)) { +#ifdef DEBUG_TRACES + std::cout << " | --------------------------------------------------\n"; + std::cout << " | Tau "; + for (auto vertex : complex.simplex_vertex_range(f_boundary)) { + std::cout << vertex << " "; + } + std::cout << "is a face of Sigma\n"; + std::cout << " | isnan(complex.filtration(Tau)=" << std::isnan(complex.filtration(f_boundary)) << std::endl; +#endif // DEBUG_TRACES + // ### If filt(Tau) is not NaN + if (!std::isnan(complex.filtration(f_boundary))) { + // ### filt(Tau) = fmin(filt(Tau), filt(Sigma)) + Filtration_value alpha_complex_filtration = fmin(complex.filtration(f_boundary), + complex.filtration(f_simplex)); + complex.assign_filtration(f_boundary, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << complex.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; +#ifdef DEBUG_TRACES + Vertex_handle vertexForGabriel = Vertex_handle(); +#endif // DEBUG_TRACES + for (auto vertex : complex.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 : complex.simplex_vertex_range(f_simplex)) { + point_for_gabriel = get_point(vertex); + if (std::find(pointVector.begin(), pointVector.end(), point_for_gabriel) == pointVector.end()) { +#ifdef DEBUG_TRACES + // vertex is not found in Tau + vertexForGabriel = vertex; +#endif // DEBUG_TRACES + // 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 = complex.filtration(f_simplex); + complex.assign_filtration(f_boundary, alpha_complex_filtration); +#ifdef DEBUG_TRACES + std::cout << " | filt(Tau) = filt(Sigma) = " << complex.filtration(f_boundary) << std::endl; +#endif // DEBUG_TRACES + } + } + } + } + } +}; + +} // namespace alpha_complex + +namespace alphacomplex = alpha_complex; + +} // 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..7380547f --- /dev/null +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -0,0 +1,286 @@ +/* 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 + * + * 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> + +#include <gudhi/Alpha_complex.h> +// to construct a simplex_tree from Delaunay_triangulation +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <boost/mpl/list.hpp> + +// Use dynamic_dimension_tag for the user to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d; +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel_s; +// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter + +typedef boost::mpl::list<Kernel_d, Kernel_s> list_of_kernel_variants; + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_OFF_file, TestedKernel, list_of_kernel_variants) { + // ---------------------------------------------------------------------------- + // + // 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::alpha_complex::Alpha_complex<TestedKernel> alpha_complex_from_file(off_file_name); + + std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_file.number_of_vertices() + << std::endl; + BOOST_CHECK(alpha_complex_from_file.number_of_vertices() == 7); + + Gudhi::Simplex_tree<> simplex_tree_60; + BOOST_CHECK(alpha_complex_from_file.create_complex(simplex_tree_60, max_alpha_square_value)); + + std::cout << "simplex_tree_60.dimension()=" << simplex_tree_60.dimension() << std::endl; + BOOST_CHECK(simplex_tree_60.dimension() == 2); + + std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_file.number_of_vertices() + << std::endl; + BOOST_CHECK(alpha_complex_from_file.number_of_vertices() == 7); + + std::cout << "simplex_tree_60.num_vertices()=" << simplex_tree_60.num_vertices() << std::endl; + BOOST_CHECK(simplex_tree_60.num_vertices() == 7); + + std::cout << "simplex_tree_60.num_simplices()=" << simplex_tree_60.num_simplices() << std::endl; + BOOST_CHECK(simplex_tree_60.num_simplices() == 25); + + max_alpha_square_value = 59.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" << + max_alpha_square_value << "==========" << std::endl; + + Gudhi::Simplex_tree<> simplex_tree_59; + BOOST_CHECK(alpha_complex_from_file.create_complex(simplex_tree_59, max_alpha_square_value)); + + std::cout << "simplex_tree_59.dimension()=" << simplex_tree_59.dimension() << std::endl; + BOOST_CHECK(simplex_tree_59.dimension() == 2); + + std::cout << "simplex_tree_59.num_vertices()=" << simplex_tree_59.num_vertices() << std::endl; + BOOST_CHECK(simplex_tree_59.num_vertices() == 7); + + std::cout << "simplex_tree_59.num_simplices()=" << simplex_tree_59.num_simplices() << std::endl; + BOOST_CHECK(simplex_tree_59.num_simplices() == 23); +} + +bool are_almost_the_same(float a, float b) { + return std::fabs(a - b) < std::numeric_limits<float>::epsilon(); +} + +// Use static dimension_tag for the user not to be able to set dimension +typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_4; +typedef Kernel_4::Point_d Point_4; +typedef std::vector<Point_4> Vector_4_Points; + +bool is_point_in_list(Vector_4_Points points_list, Point_4 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_4_Points points; + std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 }; + points.push_back(Point_4(coords.begin(), coords.end())); + coords = { 0.0, 0.0, 1.0, 0.0 }; + points.push_back(Point_4(coords.begin(), coords.end())); + coords = { 0.0, 1.0, 0.0, 0.0 }; + points.push_back(Point_4(coords.begin(), coords.end())); + coords = { 1.0, 0.0, 0.0, 0.0 }; + points.push_back(Point_4(coords.begin(), coords.end())); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex<Kernel_4> alpha_complex_from_points(points); + + std::cout << "========== Alpha_complex_from_points ==========" << std::endl; + + Gudhi::Simplex_tree<> simplex_tree; + BOOST_CHECK(alpha_complex_from_points.create_complex(simplex_tree)); + + std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_points.number_of_vertices() + << std::endl; + BOOST_CHECK(alpha_complex_from_points.number_of_vertices() == points.size()); + + // 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 : simplex_tree.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl; + BOOST_CHECK(simplex_tree.num_simplices() == 15); + + std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl; + BOOST_CHECK(simplex_tree.dimension() == 4); + std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl; + BOOST_CHECK(simplex_tree.num_vertices() == 4); + + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + switch (simplex_tree.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 0.0)); + break; + case 1: + BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 1.0/2.0)); + break; + case 2: + BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 2.0/3.0)); + break; + case 3: + BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 3.0/4.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } + + Point_4 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_4 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_4 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_4 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 + bool modified = simplex_tree.prune_above_filtration(0.6); + if (modified) { + simplex_tree.initialize_filtration(); + } + BOOST_CHECK(modified); + + // 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 : simplex_tree.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 10); + std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl; + BOOST_CHECK(simplex_tree.num_simplices() == 10); + + std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl; + BOOST_CHECK(simplex_tree.dimension() == 4); + std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl; + BOOST_CHECK(simplex_tree.num_vertices() == 4); + + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + switch (simplex_tree.dimension(f_simplex)) { + case 0: + BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 0.0)); + break; + case 1: + BOOST_CHECK(are_almost_the_same(simplex_tree.filtration(f_simplex), 1.0/2.0)); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } + +} + +BOOST_AUTO_TEST_CASE_TEMPLATE(Alpha_complex_from_empty_points, TestedKernel, list_of_kernel_variants) { + std::cout << "========== Alpha_complex_from_empty_points ==========" << std::endl; + + // ---------------------------------------------------------------------------- + // Init of an empty list of points + // ---------------------------------------------------------------------------- + std::vector<typename TestedKernel::Point_d> points; + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from the list of points + // ---------------------------------------------------------------------------- + Gudhi::alpha_complex::Alpha_complex<TestedKernel> alpha_complex_from_points(points); + + // Test to the limit + BOOST_CHECK_THROW (alpha_complex_from_points.get_point(0), std::out_of_range); + + Gudhi::Simplex_tree<> simplex_tree; + BOOST_CHECK(!alpha_complex_from_points.create_complex(simplex_tree)); + + std::cout << "alpha_complex_from_points.number_of_vertices()=" << alpha_complex_from_points.number_of_vertices() + << std::endl; + BOOST_CHECK(alpha_complex_from_points.number_of_vertices() == points.size()); + + std::cout << "simplex_tree.num_simplices()=" << simplex_tree.num_simplices() << std::endl; + BOOST_CHECK(simplex_tree.num_simplices() == 0); + + std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl; + BOOST_CHECK(simplex_tree.dimension() == -1); + + std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl; + BOOST_CHECK(simplex_tree.num_vertices() == 0); +} diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt new file mode 100644 index 00000000..efc0565f --- /dev/null +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -0,0 +1,32 @@ +cmake_minimum_required(VERSION 2.6) +project(Alpha_complex_tests) + +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() + +if(CGAL_FOUND) + if (NOT CGAL_VERSION VERSION_LESS 4.7.0) + if (EIGEN3_FOUND) + add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp ) + target_link_libraries(AlphaComplexUT ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) + if (TBB_FOUND) + target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES}) + endif() + + # Do not forget to copy test files in current binary dir + file(COPY "${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) + + endif(EIGEN3_FOUND) + endif (NOT CGAL_VERSION VERSION_LESS 4.7.0) +endif(CGAL_FOUND) + 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) |
