diff options
8 files changed, 43 insertions, 171 deletions
diff --git a/src/Witness_complex/doc/Witness_complex_doc.h b/src/Witness_complex/doc/Witness_complex_doc.h index 4f3671e5..2831f107 100644 --- a/src/Witness_complex/doc/Witness_complex_doc.h +++ b/src/Witness_complex/doc/Witness_complex_doc.h @@ -17,7 +17,7 @@ Even though often the set of landmarks \f$L\f$ is a subset of the set of witnesses \f$ W\f$, it is not a requirement for the current implementation. - The simplices are based on landmarks + Landmarks are the vertices of the simplicial complex and witnesses help to decide on which simplices are inserted via a predicate "is witnessed". De Silva and Carlsson in their paper \cite de2004topological differentiate **weak witnessing** and **strong witnessing**: @@ -47,7 +47,13 @@ The constructors take on the step 1, while the function 'create_complex' executes the steps 2 and 3. - \section witnessexamples Examples + \section witnessexample1 Example 1: Constructing weak relaxed witness complex from an off file + + Let's start with a simple example, which reads an off point file and computes a weak witness complex. + + \include Witness_complex/example_witness_complex_off.cpp + + \section witnessexample2 Example2: Computing persistence using strong relaxed witness complex Here is an example of constructing a strong witness complex filtration and computing persistence on it: diff --git a/src/Witness_complex/example/example_strong_witness_persistence.cpp b/src/Witness_complex/example/example_strong_witness_persistence.cpp index f43cba52..a0563ee2 100644 --- a/src/Witness_complex/example/example_strong_witness_persistence.cpp +++ b/src/Witness_complex/example/example_strong_witness_persistence.cpp @@ -1,25 +1,3 @@ -/* 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 <http://www.gnu.org/licenses/>. - */ - #include <gudhi/Simplex_tree.h> #include <gudhi/Strong_witness_complex.h> #include <gudhi/Persistent_cohomology.h> @@ -81,10 +59,8 @@ int main(int argc, char * argv[]) { Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); // Compute witness complex - Strong_witness_complex strong_witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + Strong_witness_complex strong_witness_complex(landmarks, + witnesses); strong_witness_complex.create_complex(simplex_tree, max_squared_alpha); diff --git a/src/Witness_complex/example/example_witness_complex_off.cpp b/src/Witness_complex/example/example_witness_complex_off.cpp index 94088370..2677499a 100644 --- a/src/Witness_complex/example/example_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_witness_complex_off.cpp @@ -1,25 +1,3 @@ -/* 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 <http://www.gnu.org/licenses/>. - */ - #include <sys/types.h> #include <sys/stat.h> @@ -72,10 +50,8 @@ int main(int argc, char * const argv[]) { // Compute witness complex start = clock(); - Witness_complex witness_complex(landmarks.begin(), - landmarks.end(), - point_vector.begin(), - point_vector.end()); + Witness_complex witness_complex(landmarks, + point_vector); witness_complex.create_complex(simplex_tree, alpha2, lim_dim); end = clock(); diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp index b1b415fa..00f00aae 100644 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ b/src/Witness_complex/example/example_witness_complex_persistence.cpp @@ -1,25 +1,3 @@ -/* 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 <http://www.gnu.org/licenses/>. - */ - #include <gudhi/Simplex_tree.h> #include <gudhi/Witness_complex.h> #include <gudhi/Persistent_cohomology.h> @@ -81,10 +59,8 @@ int main(int argc, char * argv[]) { Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + Witness_complex witness_complex(landmarks, + witnesses); witness_complex.create_complex(simplex_tree, max_squared_alpha); diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index d21195fa..42fb9f8d 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.cpp @@ -1,24 +1,3 @@ -/* 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 <http://www.gnu.org/licenses/>. - */ #define BOOST_PARAMETER_MAX_ARITY 12 @@ -80,10 +59,8 @@ int main(int argc, char * const argv[]) { Gudhi::subsampling::pick_n_random_points(point_vector, number_of_landmarks, std::back_inserter(landmarks)); // Compute witness complex - Witness_complex witness_complex(landmarks.begin(), - landmarks.end(), - point_vector.begin(), - point_vector.end()); + Witness_complex witness_complex(landmarks, + point_vector); witness_complex.create_complex(simplex_tree, 0); end = clock(); double time = static_cast<double>(end - start) / CLOCKS_PER_SEC; diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index 7ef8d3e5..c7b8c27b 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -94,22 +94,18 @@ private: /** * \brief Initializes member variables before constructing simplicial complex. - * \details Records landmarks from the range [landmarks_first, landmarks_last) into a - * table internally, as well as witnesses from the range [witnesses_first, witnesses_last). - * All iterator parameters should satisfy <a target="_blank" - * href="http://en.cppreference.com/w/cpp/concept/InputIterator">InputIterator</a> - * C++ concept. + * \details Records landmarks from the range 'landmarks' into a + * table internally, as well as witnesses from the range 'witnesses'. */ - template< typename InputIteratorLandmarks, - typename InputIteratorWitnesses > - Strong_witness_complex(InputIteratorLandmarks landmarks_first, - InputIteratorLandmarks landmarks_last, - InputIteratorWitnesses witnesses_first, - InputIteratorWitnesses witnesses_last) - : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_) + template< typename LandmarkRange, + typename WitnessRange > + Strong_witness_complex(const LandmarkRange & landmarks, + const WitnessRange & witnesses) + : witnesses_(witnesses), landmarks_(landmarks), landmark_tree_(landmarks_) { } + /** \brief Returns the point corresponding to the given vertex. */ template <typename Vertex_handle> @@ -118,9 +114,10 @@ private: return landmarks_[vertex]; } - /** \brief Outputs the strong witness complex in a simplicial complex data structure. - * @param[out] complex Simplicial complex data structure compatible with 'find' and 'insert' operations. - * (Cf SimplicialComplexForWitness) + /** \brief Outputs the strong witness complex of relaxation 'max_alpha_square' + * in a simplicial complex data structure. + * @param[out] complex Simplicial complex data structure, which is a model of + * SimplicialComplexForWitness concept. * @param[in] max_alpha_square Maximal squared relaxation parameter. * @param[in] limit_dimension Represents the maximal dimension of the simplicial complex * (default value = no limit). diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index ac0e8f66..c1d402c6 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -46,12 +46,6 @@ namespace witness_complex { * \tparam Kernel_ requires a <a target="_blank" * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a> class, which * can be static if you know the ambiant dimension at compile-time, or dynamic if you don't. - * \tparam DimensionTag can be either <a target="_blank" - * href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dimension__tag.html">Dimension_tag<d></a> - * if you know the intrinsic dimension at compile-time, - * or <a target="_blank" - * href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html">CGAL::Dynamic_dimension_tag</a> - * if you don't. */ template< class Kernel_ > class Witness_complex { @@ -94,19 +88,14 @@ private: /** * \brief Initializes member variables before constructing simplicial complex. - * \details Records landmarks from the range [landmarks_first, landmarks_last) into a - * table internally, as well as witnesses from the range [witnesses_first, witnesses_last). - * All iterator parameters should satisfy <a target="_blank" - * href="http://en.cppreference.com/w/cpp/concept/InputIterator">InputIterator</a> - * C++ concept. + * \details Records landmarks from the range 'landmarks' into a + * table internally, as well as witnesses from the range 'witnesses'. */ - template< typename InputIteratorLandmarks, - typename InputIteratorWitnesses > - Witness_complex(InputIteratorLandmarks landmarks_first, - InputIteratorLandmarks landmarks_last, - InputIteratorWitnesses witnesses_first, - InputIteratorWitnesses witnesses_last) - : witnesses_(witnesses_first, witnesses_last), landmarks_(landmarks_first, landmarks_last), landmark_tree_(landmarks_) + template< typename LandmarkRange, + typename WitnessRange > + Witness_complex(const LandmarkRange & landmarks, + const WitnessRange & witnesses) + : witnesses_(witnesses), landmarks_(landmarks), landmark_tree_(landmarks_) { } @@ -118,9 +107,10 @@ private: return landmarks_[vertex]; } - /** \brief Outputs the (weak) witness complex in a simplicial complex data structure. - * @param[out] complex Simplicial complex data structure compatible with 'find' and 'insert' operations. - * (Cf SimplicialComplexForWitness) + /** \brief Outputs the (weak) witness complex of relaxation 'max_alpha_square' + * in a simplicial complex data structure. + * @param[out] complex Simplicial complex data structure compatible which is a model of + * SimplicialComplexForWitness concept. * @param[in] max_alpha_square Maximal squared relaxation parameter. * @param[in] limit_dimension Represents the maximal dimension of the simplicial complex * (default value = no limit). diff --git a/src/Witness_complex/test/test_simple_witness_complex.cpp b/src/Witness_complex/test/test_simple_witness_complex.cpp index 90b6cfa2..a0a1b36c 100644 --- a/src/Witness_complex/test/test_simple_witness_complex.cpp +++ b/src/Witness_complex/test/test_simple_witness_complex.cpp @@ -1,25 +1,3 @@ -/* 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 <http://www.gnu.org/licenses/>. - */ - #define BOOST_TEST_DYN_LINK #define BOOST_TEST_MODULE "simple_witness_complex" #include <boost/test/unit_test.hpp> @@ -79,10 +57,8 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) { witnesses.push_back(Point_d(std::vector<FT>{ 2,-1})); witnesses.push_back(Point_d(std::vector<FT>{ 2, 1})); - WitnessComplex witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + WitnessComplex witness_complex(landmarks, + witnesses); witness_complex.create_complex(complex, 0); std::cout << "complex.num_simplices() = " << complex.num_simplices() << std::endl; @@ -93,10 +69,8 @@ BOOST_AUTO_TEST_CASE(simple_witness_complex) { std::cout << "relaxed_complex.num_simplices() = " << relaxed_complex.num_simplices() << std::endl; BOOST_CHECK(relaxed_complex.num_simplices() == 239); - StrongWitnessComplex strong_witness_complex(landmarks.begin(), - landmarks.end(), - witnesses.begin(), - witnesses.end()); + StrongWitnessComplex strong_witness_complex(landmarks, + witnesses); strong_witness_complex.create_complex(strong_relaxed_complex, 9.1); |