From f2b63bcaa647d1ec839dbe2e5edbe5c4fde1b304 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 28 Feb 2017 16:16:08 +0000 Subject: Fix cppcheck git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/relaxed-witness@2120 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 49a5c2c6e94d9fbf235eecc92fa30e62980c7c70 --- .../example/example_nearest_landmark_table.cpp | 34 ++++++++++---- .../example/example_strong_witness_complex_off.cpp | 28 +++++++++-- .../example/example_strong_witness_persistence.cpp | 54 ++++++++++++++-------- .../example/example_witness_complex_off.cpp | 11 ++--- .../example_witness_complex_persistence.cpp | 22 +++++++++ .../example/example_witness_complex_sphere.cpp | 33 +++++++++---- src/Witness_complex/example/generators.h | 14 +++--- .../include/gudhi/Active_witness/Active_witness.h | 22 ++++----- .../gudhi/Active_witness/Active_witness_iterator.h | 41 ++++++++-------- .../gudhi/Euclidean_strong_witness_complex.h | 29 ++++++------ .../include/gudhi/Strong_witness_complex.h | 54 ++++++++++------------ .../include/gudhi/Witness_complex.h | 42 ++++++++--------- .../include/gudhi/Witness_complex/all_faces_in.h | 30 ++++++++++-- 13 files changed, 250 insertions(+), 164 deletions(-) diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp index b3883248..65b675f9 100644 --- a/src/Witness_complex/example/example_nearest_landmark_table.cpp +++ b/src/Witness_complex/example/example_nearest_landmark_table.cpp @@ -1,16 +1,31 @@ -#define BOOST_PARAMETER_MAX_ARITY 12 - +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (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 . + */ -#include -#include +#define BOOST_PARAMETER_MAX_ARITY 12 #include #include -#include #include -#include - #include #include #include @@ -24,6 +39,8 @@ int main(int argc, char * const argv[]) { using Nearest_landmark_table = std::vector; using Witness_complex = Gudhi::witness_complex::Witness_complex; using Simplex_tree = Gudhi::Simplex_tree<>; + using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; + using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; Simplex_tree simplex_tree; Nearest_landmark_table nlt; @@ -45,8 +62,7 @@ int main(int argc, char * const argv[]) { std::cout << "Number of simplices: " << simplex_tree.num_simplices() << std::endl; - using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; - Gudhi::persistent_cohomology::Persistent_cohomology pcoh(simplex_tree); + Persistent_cohomology pcoh(simplex_tree); // initializes the coefficient field for homology pcoh.init_coefficients(11); diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp index 6a4925b8..0ee9ee90 100644 --- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -1,5 +1,24 @@ -#include -#include +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (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 . + */ #include #include @@ -16,9 +35,8 @@ using K = CGAL::Epick_d; using Point_d = typename K::Point_d; -typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex Witness_complex; -using typeVectorVertex = std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle >; -using Point_vector = std::vector< Point_d >; +using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using Point_vector = std::vector; int main(int argc, char * const argv[]) { if (argc != 5) { diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index d42603aa..5efe69fd 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -1,3 +1,25 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (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 . + */ + #include #include #include @@ -12,18 +34,17 @@ #include #include // infinity -using namespace Gudhi; -using namespace Gudhi::persistent_cohomology; +using K = CGAL::Epick_d; +using Point_d = K::Point_d; -typedef CGAL::Epick_d K; -typedef typename K::Point_d Point_d; +using Point_vector = std::vector; +using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using SimplexTree = Gudhi::Simplex_tree<>; -typedef typename std::vector Point_vector; -typedef typename Gudhi::witness_complex::Euclidean_strong_witness_complex Strong_witness_complex; -typedef Gudhi::Simplex_tree<> SimplexTree; +using Filtration_value = SimplexTree::Filtration_value; -typedef int Vertex_handle; -typedef double Filtration_value; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; void program_options(int argc, char * argv[] , int & nbL @@ -61,9 +82,9 @@ int main(int argc, char * argv[]) { // Compute witness complex Strong_witness_complex strong_witness_complex(landmarks, witnesses); - + strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); - + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; @@ -71,7 +92,7 @@ int main(int argc, char * argv[]) { simplex_tree.initialize_filtration(); // Compute the persistence diagram of the complex - persistent_cohomology::Persistent_cohomology pcoh(simplex_tree); + Persistent_cohomology pcoh(simplex_tree); // initializes the coefficient field for homology pcoh.init_coefficients(p); @@ -89,7 +110,6 @@ int main(int argc, char * argv[]) { return 0; } - void program_options(int argc, char * argv[] , int & nbL , std::string & file_name @@ -98,14 +118,12 @@ void program_options(int argc, char * argv[] , int & p , int & dim_max , Filtration_value & min_persistence) { - namespace po = boost::program_options; - + po::options_description hidden("Hidden options"); hidden.add_options() ("input-file", po::value(&file_name), "Name of file containing a point set in off format."); - po::options_description visible("Allowed options", 100); visible.add_options() @@ -122,7 +140,7 @@ void program_options(int argc, char * argv[] "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") ("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), "Maximal dimension of the strong witness complex we want to compute."); - + po::positional_options_description pos; pos.add("input-file", 1); @@ -133,7 +151,7 @@ void program_options(int argc, char * argv[] po::store(po::command_line_parser(argc, argv). options(all).positional(pos).run(), vm); po::notify(vm); - + if (vm.count("help") || !vm.count("input-file")) { std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 38c6bedc..b36dac0d 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -14,11 +14,10 @@ #include #include -typedef CGAL::Epick_d K; -typedef typename K::Point_d Point_d; -typedef typename Gudhi::witness_complex::Euclidean_witness_complex Witness_complex; -typedef std::vector< typename Gudhi::Simplex_tree<>::Vertex_handle > typeVectorVertex; -typedef std::vector< Point_d > Point_vector; +using K = CGAL::Epick_d; +using Point_d = K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; +using Point_vector = std::vector< Point_d >; int main(int argc, char * const argv[]) { if (argc != 5) { @@ -41,7 +40,7 @@ int main(int argc, char * const argv[]) { exit(-1); // ----- >> } point_vector = Point_vector(off_reader.get_point_cloud()); - + std::cout << "Successfully read " << point_vector.size() << " points.\n"; std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index fbb18cb4..364a114a 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -1,3 +1,25 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (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 . + */ + #include #include #include diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index 1ea9408c..06fe3889 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -1,8 +1,26 @@ -#define BOOST_PARAMETER_MAX_ARITY 12 - +/* 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): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (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 . + */ -#include -#include +#define BOOST_PARAMETER_MAX_ARITY 12 #include #include @@ -32,8 +50,9 @@ void write_data(Data_range & data, std::string filename) { } int main(int argc, char * const argv[]) { - typedef Gudhi::witness_complex::Euclidean_witness_complex> Witness_complex; - + using Kernel = CGAL::Epick_d; + using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; + if (argc != 2) { std::cerr << "Usage: " << argv[0] << " number_of_landmarks \n"; @@ -66,8 +85,6 @@ int main(int argc, char * const argv[]) { double time = static_cast(end - start) / CLOCKS_PER_SEC; std::cout << "Witness complex for " << number_of_landmarks << " landmarks took " << time << " s. \n"; - //assert(1 == 0); - //std::cout << simplex_tree << "\n"; std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; l_time.push_back(std::make_pair(nbP, time)); } diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index 731a52b0..7df43db5 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -32,12 +32,12 @@ #include #include -typedef CGAL::Epick_d K; -typedef K::FT FT; -typedef K::Point_d Point_d; -typedef std::vector Point_Vector; -typedef CGAL::Random_points_in_cube_d Random_cube_iterator; -typedef CGAL::Random_points_in_ball_d Random_point_iterator; +using K = CGAL::Epick_d; +using FT = K::FT; +using Point_d = K::Point_d; +using Point_Vector = std::vector; +using Random_cube_iterator = CGAL::Random_points_in_cube_d; +using Random_point_iterator = CGAL::Random_points_in_ball_d; /** * \brief Rock age method of reading off file @@ -155,7 +155,7 @@ void generate_points_torus(Point_Vector& W, int nbP, int dim) { for (int i = 0; i < nbP; i++) { std::vector point; for (int j = 0; j < dim; j++) { - double alpha = rand.uniform_real((double)0, 2*pi); + double alpha = rand.uniform_real(static_cast(0), 2*pi); point.push_back(sin(alpha)); point.push_back(cos(alpha)); } diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h index ffc1750f..d41a6811 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -24,8 +24,7 @@ #define ACTIVE_WITNESS_ACTIVE_WITNESS_H_ #include -#include -#include +#include namespace Gudhi { @@ -38,7 +37,7 @@ namespace witness_complex { template< typename Id_distance_pair, typename INS_range > class Active_witness { -public: + public: typedef Active_witness ActiveWitness; typedef typename INS_range::iterator INS_iterator; typedef Active_witness_iterator< ActiveWitness, Id_distance_pair, INS_iterator > iterator; @@ -50,22 +49,19 @@ public: INS_iterator iterator_end_; Active_witness(const INS_range& search_range) - : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) - { + : search_range_(search_range), iterator_next_(search_range_.begin()), iterator_end_(search_range_.end()) { } - - iterator begin() - { + + iterator begin() { return iterator(this, nearest_landmark_table_.begin()); } - iterator end() - { + iterator end() { return iterator(this); } }; -} -} - +} // namespace witness_complex +} // namespace Gudhi + #endif // ACTIVE_WITNESS_ACTIVE_WITNESS_H_ diff --git a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h index 69a335fa..4e29a40d 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness_iterator.h @@ -24,7 +24,7 @@ #define ACTIVE_WITNESS_ACTIVE_WITNESS_ITERATOR_H_ #include -#include +#include namespace Gudhi { @@ -41,30 +41,29 @@ template< typename Active_witness, typename Id_distance_pair, typename INS_iterator > class Active_witness_iterator - : public boost::iterator_facade< Active_witness_iterator -, Id_distance_pair const -, boost::forward_traversal_tag -, Id_distance_pair const> { + : public boost::iterator_facade< Active_witness_iterator , + Id_distance_pair const, + boost::forward_traversal_tag, + Id_distance_pair const> { friend class boost::iterator_core_access; - + //typedef Active_witness Active_witness; typedef typename std::list::iterator Pair_iterator; - typedef typename Gudhi::witness_complex::Active_witness_iterator Iterator; - - + typedef typename Gudhi::witness_complex::Active_witness_iterator Iterator; + Active_witness *aw_; Pair_iterator lh_; // landmark handle bool is_end_; // true only if the pointer is end and there are no more neighbors to add -public: + public: Active_witness_iterator(Active_witness* aw) - : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) - { + : aw_(aw), lh_(aw_->nearest_landmark_table_.end()), is_end_(true) { } Active_witness_iterator(Active_witness* aw, const Pair_iterator& lh) - : aw_(aw), lh_(lh) - { + : aw_(aw), lh_(lh) { is_end_ = false; if (lh_ == aw_->nearest_landmark_table_.end()) { if (aw_->iterator_next_ == aw_->iterator_end_) { @@ -76,21 +75,17 @@ public: } } } - -private : - Id_distance_pair& dereference() const - { + private : + Id_distance_pair& dereference() const { return *lh_; } - bool equal(const Iterator& other) const - { + bool equal(const Iterator& other) const { return (is_end_ == other.is_end_) || (lh_ == other.lh_); } - - void increment() - { + + void increment() { // the neighbor search can't be at the end iterator of a list GUDHI_CHECK(!is_end_ && lh_ != aw_->nearest_landmark_table_.end(), std::logic_error("Wrong active witness increment.")); // if the id of the current landmark is the same as the last one diff --git a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h index aad05547..6870c183 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -23,17 +23,15 @@ #ifndef EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ #define EUCLIDEAN_STRONG_WITNESS_COMPLEX_H_ -#include -#include -#include -#include - #include #include #include +#include +#include + namespace Gudhi { - + namespace witness_complex { /** @@ -46,8 +44,10 @@ namespace witness_complex { * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d class. */ template< class Kernel_ > -class Euclidean_strong_witness_complex : public Strong_witness_complex>::INS_range>> { -private: +class Euclidean_strong_witness_complex + : public Strong_witness_complex>::INS_range>> { + private: typedef Kernel_ K; typedef typename K::Point_d Point_d; typedef std::vector Point_range; @@ -58,12 +58,12 @@ private: typedef typename Nearest_landmark_range::Point_with_transformed_distance Id_distance_pair; typedef typename Id_distance_pair::first_type Landmark_id; typedef Landmark_id Vertex_handle; - + private: Point_range landmarks_; Kd_tree landmark_tree_; using Strong_witness_complex::nearest_landmark_table_; - + public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /* @name Constructor @@ -81,22 +81,19 @@ private: typename WitnessRange > Euclidean_strong_witness_complex(const LandmarkRange & landmarks, const WitnessRange & witnesses) - : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) - { + : landmarks_(std::begin(landmarks), std::end(landmarks)), landmark_tree_(landmarks_) { nearest_landmark_table_.reserve(boost::size(witnesses)); for (auto w: witnesses) nearest_landmark_table_.push_back(landmark_tree_.query_incremental_nearest_neighbors(w)); } - /** \brief Returns the point corresponding to the given vertex. */ template - Point_d get_point( Vertex_handle vertex ) const - { + Point_d get_point(Vertex_handle vertex) const { return landmarks_[vertex]; } - + //@} }; diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index ad741794..3fbbb366 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -23,20 +23,19 @@ #ifndef STRONG_WITNESS_COMPLEX_H_ #define STRONG_WITNESS_COMPLEX_H_ +#include +#include + #include #include #include #include -#include -#include - namespace Gudhi { - + namespace witness_complex { -/** - * \private +/* \private * \class Strong_witness_complex * \brief Constructs strong witness complex for a given table of nearest landmarks with respect to witnesses. * \ingroup witness_complex @@ -48,7 +47,7 @@ namespace witness_complex { */ template< class Nearest_landmark_table_ > class Strong_witness_complex { -private: + private: typedef typename Nearest_landmark_table_::value_type Nearest_landmark_range; typedef std::size_t Witness_id; typedef std::size_t Landmark_id; @@ -57,12 +56,11 @@ private: typedef std::list< ActiveWitness > ActiveWitnessList; typedef std::vector< Landmark_id > typeVectorVertex; typedef std::vector Nearest_landmark_table_internal; - typedef Landmark_id Vertex_handle; - + protected: Nearest_landmark_table_internal nearest_landmark_table_; - + public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /* @name Constructor @@ -70,11 +68,9 @@ private: //@{ - Strong_witness_complex() - { + Strong_witness_complex() { } - /** * \brief Initializes member variables before constructing simplicial complex. * \details Records nearest landmark table. @@ -84,10 +80,9 @@ private: * of the pair range iterator needs to be 'std::pair'. */ Strong_witness_complex(Nearest_landmark_table_ const & nearest_landmark_table) - : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) - { + : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) { } - + /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' * in a simplicial complex data structure. * \details The function returns true if the construction is successful and false otherwise. @@ -100,15 +95,15 @@ private: template < typename SimplicialComplexForWitness > bool create_complex(SimplicialComplexForWitness& complex, double max_alpha_square, - Landmark_id limit_dimension = std::numeric_limits::max()) const - { + Landmark_id limit_dimension = std::numeric_limits::max()) const { Landmark_id complex_dim = 0; if (complex.num_vertices() > 0) { std::cerr << "Strong witness complex cannot create complex - complex is not empty.\n"; return false; } if (max_alpha_square < 0) { - std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be non-negative.\n"; + std::cerr << "Strong witness complex cannot create complex - squared relaxation parameter must be " + << "non-negative.\n"; return false; } if (limit_dimension < 0) { @@ -129,7 +124,8 @@ private: typeVectorVertex& vertices = simplex; //'simplex' now will be called vertices while (aw_it != aw.end() && aw_it->second < lim_dist2) { typeVectorVertex facet = {}; - add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it, aw_it->second - aw.begin()->second, facet, complex); + add_all_faces_of_dimension(limit_dimension, vertices, vertices.begin(), aw_it, + aw_it->second - aw.begin()->second, facet, complex); vertices.push_back(aw_it->first); aw_it++; } @@ -140,13 +136,12 @@ private: return true; } -private: - + private: /* \brief Adds recursively all the faces of a certain dimension dim-1 witnessed by the same witness. - * Iterator is needed to know until how far we can take landmarks to form simplexes. - * simplex is the prefix of the simplexes to insert. - * The landmark pointed by aw_it is added to all formed simplices. - */ + * Iterator is needed to know until how far we can take landmarks to form simplexes. + * simplex is the prefix of the simplexes to insert. + * The landmark pointed by aw_it is added to all formed simplices. + */ template < typename SimplicialComplexForWitness > void add_all_faces_of_dimension(Landmark_id dim, typeVectorVertex& vertices, @@ -154,9 +149,8 @@ private: typename ActiveWitness::iterator aw_it, double filtration_value, typeVectorVertex& simplex, - SimplicialComplexForWitness& sc) const - { - if (dim > 0) + SimplicialComplexForWitness& sc) const { + if (dim > 0) { while (curr_it != vertices.end()) { simplex.push_back(*curr_it); ++curr_it; @@ -176,7 +170,7 @@ private: simplex, sc); } - else if (dim == 0) { + } else if (dim == 0) { simplex.push_back(aw_it->first); sc.insert_simplex_and_subfaces(simplex, filtration_value); simplex.pop_back(); diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index c09e6af9..c0506367 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -33,7 +33,7 @@ #include namespace Gudhi { - + namespace witness_complex { /** @@ -49,7 +49,7 @@ namespace witness_complex { */ template< class Nearest_landmark_table_ > class Witness_complex { -private: + private: typedef typename Nearest_landmark_table_::value_type Nearest_landmark_range; typedef std::size_t Witness_id; typedef std::size_t Landmark_id; @@ -58,12 +58,11 @@ private: typedef std::list< ActiveWitness > ActiveWitnessList; typedef std::vector< Landmark_id > typeVectorVertex; typedef std::vector Nearest_landmark_table_internal; - typedef Landmark_id Vertex_handle; protected: Nearest_landmark_table_internal nearest_landmark_table_; - + public: ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /* @name Constructor @@ -71,10 +70,9 @@ private: //@{ - Witness_complex() - { + Witness_complex() { } - + /** * \brief Initializes member variables before constructing simplicial complex. * \details Records nearest landmark table. @@ -85,11 +83,9 @@ private: */ Witness_complex(Nearest_landmark_table_ const & nearest_landmark_table) - : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) - { + : nearest_landmark_table_(std::begin(nearest_landmark_table), std::end(nearest_landmark_table)) { } - /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square' * in a simplicial complex data structure. * \details The function returns true if the construction is successful and false otherwise. @@ -102,8 +98,7 @@ private: template < typename SimplicialComplexForWitness > bool create_complex(SimplicialComplexForWitness& complex, double max_alpha_square, - std::size_t limit_dimension = std::numeric_limits::max()) const - { + std::size_t limit_dimension = std::numeric_limits::max()) const { if (complex.num_vertices() > 0) { std::cerr << "Witness complex cannot create complex - complex is not empty.\n"; return false; @@ -118,9 +113,9 @@ private: } ActiveWitnessList active_witnesses; Landmark_id k = 0; /* current dimension in iterative construction */ - for (auto w: nearest_landmark_table_) + for (auto w : nearest_landmark_table_) active_witnesses.push_back(ActiveWitness(w)); - while (!active_witnesses.empty() && k <= limit_dimension ) { + while (!active_witnesses.empty() && k <= limit_dimension) { typename ActiveWitnessList::iterator aw_it = active_witnesses.begin(); std::vector simplex; simplex.reserve(k+1); @@ -134,10 +129,10 @@ private: aw_it->end()); assert(simplex.empty()); if (!ok) - active_witnesses.erase(aw_it++); //First increase the iterator and then erase the previous element + active_witnesses.erase(aw_it++); // First increase the iterator and then erase the previous element else aw_it++; - } + } k++; } complex.set_dimension(k-1); @@ -159,13 +154,12 @@ private: typename ActiveWitness::iterator curr_l, std::vector& simplex, SimplicialComplexForWitness& sc, - typename ActiveWitness::iterator end) const - { + typename ActiveWitness::iterator end) const { if (curr_l == end) return false; bool will_be_active = false; typename ActiveWitness::iterator l_it = curr_l; - if (dim > 0) + if (dim > 0) { for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) { simplex.push_back(l_it->first); if (sc.find(simplex) != sc.null_simplex()) { @@ -183,8 +177,8 @@ private: // If norelax_dist is infinity, change to first omitted distance if (l_it->second <= norelax_dist2) norelax_dist2 = l_it->second; - } - else if (dim == 0) + } + } else if (dim == 0) { for (; l_it->second - alpha2 <= norelax_dist2 && l_it != end; ++l_it) { simplex.push_back(l_it->first); double filtration_value = 0; @@ -200,12 +194,12 @@ private: // If norelax_dist is infinity, change to first omitted distance if (l_it->second < norelax_dist2) norelax_dist2 = l_it->second; - } + } + } return will_be_active; } - }; - + } // namespace witness_complex } // namespace Gudhi diff --git a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h index d009caca..b68d75a1 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h +++ b/src/Witness_complex/include/gudhi/Witness_complex/all_faces_in.h @@ -1,3 +1,25 @@ +/* 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): Siargey Kachanovich + * + * Copyright (C) 2015 INRIA (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 . + */ + #ifndef WITNESS_COMPLEX_ALL_FACES_IN_H_ #define WITNESS_COMPLEX_ALL_FACES_IN_H_ @@ -9,16 +31,14 @@ template < typename SimplicialComplexForWitness, typename Simplex > bool all_faces_in(Simplex& simplex, double* filtration_value, - SimplicialComplexForWitness& sc) - { + SimplicialComplexForWitness& sc) { typedef typename SimplicialComplexForWitness::Simplex_handle Simplex_handle; if (simplex.size() == 1) return true; /* Add vertices unconditionally */ - + Simplex facet; - for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) - { + for (typename Simplex::iterator not_it = simplex.begin(); not_it != simplex.end(); ++not_it) { facet.clear(); for (typename Simplex::iterator it = simplex.begin(); it != simplex.end(); ++it) if (it != not_it) -- cgit v1.2.3