diff options
| author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-05-30 21:04:22 +0000 |
|---|---|---|
| committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-05-30 21:04:22 +0000 |
| commit | 01cfd13aa84317debb4bf681309533b693322131 (patch) | |
| tree | 178bca6c0fabe13784c1fb695a1713d722c681d9 /src | |
| parent | d0aa6ea5b543c4692f6e42d12252b03d5e43a255 (diff) | |
| parent | 1f1033f14cef0b5b602a23c9f35659fa0168f1b4 (diff) | |
Merge last trunk modifications
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3495 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 4033114216c767ad4028e3f6d4ccb5f5dfb88f78
Diffstat (limited to 'src')
416 files changed, 3154 insertions, 581 deletions
diff --git a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h index 2b8bff94..a51df127 100644 --- a/src/Alpha_complex/concept/SimplicialComplexForAlpha.h +++ b/src/Alpha_complex/concept/SimplicialComplexForAlpha.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Alpha_complex/doc/COPYRIGHT b/src/Alpha_complex/doc/COPYRIGHT index dbad2380..5f1d97cc 100644 --- a/src/Alpha_complex/doc/COPYRIGHT +++ b/src/Alpha_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Vincent Rouvreau -Copyright (C) 2015 INRIA +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 diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index a08663ca..2d55c710 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * 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 @@ -57,9 +57,13 @@ namespace alpha_complex { * 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 + * \remark + * - When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay * complex. - * + * - For people only interested in the topology of the \ref alpha_complex (for instance persistence), + * \ref alpha_complex is equivalent to the \ref cech_complex and much smaller if you do not bound the radii. + * \ref cech_complex can still make sense in higher dimension precisely because you can bound the radii. + * * \section pointsexample Example from points * * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and creates a diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt index 5bf553e9..2fc62452 100644 --- a/src/Alpha_complex/example/CMakeLists.txt +++ b/src/Alpha_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Alpha_complex_examples) # need CGAL 4.7 diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 91305032..4c07eddb 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index c3ad1a9c..622fcae8 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt index 9e0b3b3c..9255d3db 100644 --- a/src/Alpha_complex/test/CMakeLists.txt +++ b/src/Alpha_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Alpha_complex_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0) diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt index a2dfac20..7ace6064 100644 --- a/src/Alpha_complex/utilities/CMakeLists.txt +++ b/src/Alpha_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Alpha_complex_utilities) if(CGAL_FOUND) diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h index a59f0654..a72fd96d 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h +++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 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 diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 8ef5ffb2..8cda0b70 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -35,6 +35,8 @@ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index 2105220a..42390b0e 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_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): 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/>. + */ + #include <boost/program_options.hpp> #include <CGAL/Epick_d.h> diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp index cceac46e..cbe003ff 100644 --- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -30,6 +30,8 @@ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 188cf604..11010701 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -5,7 +5,7 @@ * Author(s): Vincent Rouvreau * Pawel Dlotko - 2017 - Swansea University, UK * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -32,6 +32,8 @@ #include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h> #include <CGAL/Periodic_3_Delaunay_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp index 93be8a05..cdeeabfc 100644 --- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -31,6 +31,8 @@ #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Regular_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> // For CGAL < 4.11 diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp index 5321bb0a..d030c88c 100644 --- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -5,7 +5,7 @@ * Author(s): Vincent Rouvreau * Pawel Dlotko - 2017 - Swansea University, UK * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -31,6 +31,8 @@ #include <CGAL/Periodic_3_regular_triangulation_traits_3.h> #include <CGAL/Periodic_3_regular_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> +#include <CGAL/Alpha_shape_cell_base_3.h> +#include <CGAL/Alpha_shape_vertex_base_3.h> #include <CGAL/iterator.h> #include <fstream> diff --git a/src/Bitmap_cubical_complex/doc/COPYRIGHT b/src/Bitmap_cubical_complex/doc/COPYRIGHT index bcd46b23..2b14dcb9 100644 --- a/src/Bitmap_cubical_complex/doc/COPYRIGHT +++ b/src/Bitmap_cubical_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Pawel Dlotko -Copyright (C) 2015 INRIA +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 diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h index a5d7b60f..d1836ef0 100644 --- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h +++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * 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 diff --git a/src/Bitmap_cubical_complex/example/CMakeLists.txt b/src/Bitmap_cubical_complex/example/CMakeLists.txt index 99304aa4..dc659f2d 100644 --- a/src/Bitmap_cubical_complex/example/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_examples) add_executable ( Random_bitmap_cubical_complex Random_bitmap_cubical_complex.cpp ) diff --git a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp index f70558f2..6eb24040 100644 --- a/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp +++ b/src/Bitmap_cubical_complex/example/Random_bitmap_cubical_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * 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 diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h index 770eb55f..cc19b8b5 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * 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 diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h index 705b68a0..f82d4cc3 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * 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 diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h index bf257be1..9b74e267 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * 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 @@ -492,7 +492,7 @@ class Bitmap_cubical_complex_base { this->multipliers.push_back(multiplier); multiplier *= 2 * sizes[i] + 1; } - this->data = std::vector<T>(multiplier, std::numeric_limits<T>::max()); + this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity()); this->total_number_of_cells = multiplier; } @@ -562,7 +562,7 @@ void Bitmap_cubical_complex_base<T>::put_data_to_bins(T diameter_of_bin) { template <typename T> std::pair<T, T> Bitmap_cubical_complex_base<T>::min_max_filtration() { - std::pair<T, T> min_max(std::numeric_limits<T>::max(), std::numeric_limits<T>::min()); + std::pair<T, T> min_max(std::numeric_limits<T>::infinity(), -std::numeric_limits<T>::infinity()); for (std::size_t i = 0; i != this->data.size(); ++i) { if (this->data[i] < min_max.first) min_max.first = this->data[i]; if (this->data[i] > min_max.second) min_max.second = this->data[i]; diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h index 4a0d1c74..8c35f590 100644 --- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Sophia-Saclay (France) + * 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 @@ -177,7 +177,7 @@ class Bitmap_cubical_complex_periodic_boundary_conditions_base : public Bitmap_c } } // std::reverse( this->sizes.begin() , this->sizes.end() ); - this->data = std::vector<T>(multiplier, std::numeric_limits<T>::max()); + this->data = std::vector<T>(multiplier, std::numeric_limits<T>::infinity()); this->total_number_of_cells = multiplier; } Bitmap_cubical_complex_periodic_boundary_conditions_base(const std::vector<unsigned>& sizes); diff --git a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp index 4af699e9..ca7bd986 100644 --- a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp +++ b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * 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 diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt index 02b026f2..8b43632a 100644 --- a/src/Bitmap_cubical_complex/test/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt index 676a730a..416db67f 100644 --- a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt +++ b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bitmap_cubical_complex_utilities) add_executable ( cubical_complex_persistence cubical_complex_persistence.cpp ) diff --git a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp index 9d1bc08c..170aa684 100644 --- a/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp +++ b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * 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 diff --git a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp index c812cb3a..e9ba5495 100644 --- a/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp +++ b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2015 INRIA Saclay (France) + * 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 diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt index 20a4e47b..3105a1d5 100644 --- a/src/Bottleneck_distance/benchmark/CMakeLists.txt +++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_benchmark) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp b/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp index 456c570b..acafb199 100644 --- a/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/benchmark/bottleneck_chrono.cpp @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index b157f22a..d016faf4 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -4,7 +4,7 @@ * * Author: François Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/doc/COPYRIGHT b/src/Bottleneck_distance/doc/COPYRIGHT index 179740a6..1c2016b1 100644 --- a/src/Bottleneck_distance/doc/COPYRIGHT +++ b/src/Bottleneck_distance/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): François Godi -Copyright (C) 2015 INRIA +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 diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 3998fe8d..f8fce96c 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -4,7 +4,7 @@ * * Author: François Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt index 6095d6eb..c6f10127 100644 --- a/src/Bottleneck_distance/example/CMakeLists.txt +++ b/src/Bottleneck_distance/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp index fd164b22..1e27887c 100644 --- a/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp +++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp index d0ca4e20..3df7d12d 100644 --- a/src/Bottleneck_distance/example/bottleneck_basic_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_basic_example.cpp @@ -4,7 +4,7 @@ * * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h index 7aee07bb..41f8b16a 100644 --- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h +++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index f51e22e9..313e7d9c 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 0b2d26fe..7f350f64 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 87c7cee5..36a63ea0 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h index 622b0691..cb163623 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt index 2676b82c..bb739280 100644 --- a/src/Bottleneck_distance/test/CMakeLists.txt +++ b/src/Bottleneck_distance/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_tests) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index e39613b3..bce88e13 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -4,7 +4,7 @@ * * Author: Francois Godi * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt index d19e3b1c..2f35885c 100644 --- a/src/Bottleneck_distance/utilities/CMakeLists.txt +++ b/src/Bottleneck_distance/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Bottleneck_distance_utilities) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Bottleneck_distance/utilities/bottleneck_distance.cpp b/src/Bottleneck_distance/utilities/bottleneck_distance.cpp index 9dd52b31..8f724f95 100644 --- a/src/Bottleneck_distance/utilities/bottleneck_distance.cpp +++ b/src/Bottleneck_distance/utilities/bottleneck_distance.cpp @@ -4,7 +4,7 @@ * * Authors: Francois Godi, small modifications by Pawel Dlotko * - * Copyright (C) 2015 INRIA + * 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 diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 94587044..c60346d5 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,12 +1,19 @@ -cmake_minimum_required(VERSION 2.6) -project(GUDHI) +cmake_minimum_required(VERSION 3.1) -include("CMakeGUDHIVersion.txt") +project(GUDHI) -enable_testing() +include(CMakeGUDHIVersion.txt) list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/") +# This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path +set(GUDHI_CYTHON_PATH "cython") + +# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH +include(GUDHI_third_party_libraries NO_POLICY_SCOPE) + +include(GUDHI_compilation_flags) + # Add your new module in the list, order is not important include(GUDHI_modules) @@ -14,6 +21,7 @@ add_gudhi_module(common) add_gudhi_module(Alpha_complex) add_gudhi_module(Bitmap_cubical_complex) add_gudhi_module(Bottleneck_distance) +add_gudhi_module(Cech_complex) add_gudhi_module(Contraction) add_gudhi_module(Hasse_complex) add_gudhi_module(Persistence_representations) @@ -33,30 +41,6 @@ message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"") set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR}) include(GUDHI_doxygen_target) -# This variable is used by Cython CMakeLists.txt to know its path -set(GUDHI_CYTHON_PATH "cython") -# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH -include(GUDHI_third_party_libraries) - -if(MSVC) - # Turn off some VC++ warnings - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") -else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic") -endif() - -if(CMAKE_BUILD_TYPE MATCHES Debug) - message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") -else() - message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") -endif() - -if (DEBUG_TRACES) - message(STATUS "DEBUG_TRACES are activated") - # For programs to be more verbose - add_definitions(-DDEBUG_TRACES) -endif() - #--------------------------------------------------------------------------------------- # Gudhi compilation part include_directories(include) diff --git a/src/Cech_complex/benchmark/CMakeLists.txt b/src/Cech_complex/benchmark/CMakeLists.txt new file mode 100644 index 00000000..b7697764 --- /dev/null +++ b/src/Cech_complex/benchmark/CMakeLists.txt @@ -0,0 +1,12 @@ +cmake_minimum_required(VERSION 2.6) +project(Cech_complex_benchmark) + +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + +add_executable(cech_complex_benchmark cech_complex_benchmark.cpp) +target_link_libraries(cech_complex_benchmark ${Boost_SYSTEM_LIBRARY} ${Boost_FILESYSTEM_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(cech_complex_benchmark ${TBB_LIBRARIES}) +endif() diff --git a/src/Cech_complex/benchmark/cech_complex_benchmark.cpp b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp new file mode 100644 index 00000000..86314930 --- /dev/null +++ b/src/Cech_complex/benchmark/cech_complex_benchmark.cpp @@ -0,0 +1,144 @@ +/* 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) 2018 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/>. + */ + +#include <gudhi/Points_off_io.h> +#include <gudhi/distance_functions.h> +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/Clock.h> +#include <gudhi/Rips_complex.h> +#include <gudhi/Cech_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Miniball.hpp> + +#include "boost/filesystem.hpp" // includes all needed Boost.Filesystem declarations + +#include <string> +#include <vector> + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<Filtration_value>; +using Point_cloud = std::vector<Point>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; +using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; +using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; + +class Minimal_enclosing_ball_radius { + public: + // boost::range_value is not SFINAE-friendly so we cannot use it in the return type + template <typename Point> + typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type operator()( + const Point& p1, const Point& p2) const { + // Type def + using Point_cloud = std::vector<Point>; + using Point_iterator = typename Point_cloud::const_iterator; + using Coordinate_iterator = typename Point::const_iterator; + using Min_sphere = + typename Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + + Point_cloud point_cloud; + point_cloud.push_back(p1); + point_cloud.push_back(p2); + + GUDHI_CHECK((p1.end() - p1.begin()) != (p2.end() - p2.begin()), "inconsistent point dimensions"); + Min_sphere min_sphere(p1.end() - p1.begin(), point_cloud.begin(), point_cloud.end()); + + return std::sqrt(min_sphere.squared_radius()); + } +}; + +int main(int argc, char* argv[]) { + std::string off_file_points = "tore3D_1307.off"; + Filtration_value threshold = 1e20; + + // Extract the points from the file filepoints + Points_off_reader off_reader(off_file_points); + + Gudhi::Clock euclidean_clock("Gudhi::Euclidean_distance"); + // Compute the proximity graph of the points + Proximity_graph euclidean_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>( + off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); + + std::cout << euclidean_clock << std::endl; + + Gudhi::Clock miniball_clock("Minimal_enclosing_ball_radius"); + // Compute the proximity graph of the points + Proximity_graph miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>( + off_reader.get_point_cloud(), threshold, Minimal_enclosing_ball_radius()); + std::cout << miniball_clock << std::endl; + + Gudhi::Clock common_miniball_clock("Gudhi::Minimal_enclosing_ball_radius()"); + // Compute the proximity graph of the points + Proximity_graph common_miniball_prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>( + off_reader.get_point_cloud(), threshold, Gudhi::Minimal_enclosing_ball_radius()); + std::cout << common_miniball_clock << std::endl; + + boost::filesystem::path full_path(boost::filesystem::current_path()); + std::cout << "Current path is : " << full_path << std::endl; + + std::cout << "File name;Radius;Rips time;Cech time; Ratio Rips/Cech time;Rips nb simplices;Cech nb simplices;" + << std::endl; + boost::filesystem::directory_iterator end_itr; // default construction yields past-the-end + for (boost::filesystem::directory_iterator itr(boost::filesystem::current_path()); itr != end_itr; ++itr) { + if (!boost::filesystem::is_directory(itr->status())) { + if (itr->path().extension() == ".off") // see below + { + Points_off_reader off_reader(itr->path().string()); + Point p0 = off_reader.get_point_cloud()[0]; + + for (Filtration_value radius = 0.1; radius < 0.4; radius += 0.1) { + std::cout << itr->path().stem() << ";"; + std::cout << radius << ";"; + Gudhi::Clock rips_clock("Rips computation"); + Rips_complex rips_complex_from_points(off_reader.get_point_cloud(), radius, + Gudhi::Minimal_enclosing_ball_radius()); + Simplex_tree rips_stree; + rips_complex_from_points.create_complex(rips_stree, p0.size() - 1); + // ------------------------------------------ + // Display information about the Rips complex + // ------------------------------------------ + double rips_sec = rips_clock.num_seconds(); + std::cout << rips_sec << ";"; + + Gudhi::Clock cech_clock("Cech computation"); + Cech_complex cech_complex_from_points(off_reader.get_point_cloud(), radius); + Simplex_tree cech_stree; + cech_complex_from_points.create_complex(cech_stree, p0.size() - 1); + // ------------------------------------------ + // Display information about the Cech complex + // ------------------------------------------ + double cech_sec = cech_clock.num_seconds(); + std::cout << cech_sec << ";"; + std::cout << cech_sec / rips_sec << ";"; + + assert(rips_stree.num_simplices() >= cech_stree.num_simplices()); + std::cout << rips_stree.num_simplices() << ";"; + std::cout << cech_stree.num_simplices() << ";" << std::endl; + } + } + } + } + + return 0; +} diff --git a/src/Cech_complex/concept/SimplicialComplexForCech.h b/src/Cech_complex/concept/SimplicialComplexForCech.h new file mode 100644 index 00000000..89231eec --- /dev/null +++ b/src/Cech_complex/concept/SimplicialComplexForCech.h @@ -0,0 +1,66 @@ +/* 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) 2018 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_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_ +#define CONCEPT_CECH_COMPLEX_SIMPLICIAL_COMPLEX_FOR_CECH_H_ + +namespace Gudhi { + +namespace cech_complex { + +/** \brief The concept SimplicialComplexForCech describes the requirements for a type to implement a simplicial + * complex, that can be created from a `Cech_complex`. + */ +struct SimplicialComplexForCech { + /** 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; + + /** Assigns the 'simplex' with the given 'filtration' value. */ + int assign_filtration(Simplex_handle simplex, Filtration_value filtration); + + /** \brief Returns a range over vertices of a given + * simplex. */ + Simplex_vertex_range simplex_vertex_range(Simplex_handle const & simplex); + + /** \brief Inserts a given `Gudhi::ProximityGraph` in the simplicial complex. */ + template<class ProximityGraph> + void insert_graph(const ProximityGraph& proximity_graph); + + /** \brief Expands the simplicial complex containing only its one skeleton until a given maximal dimension. + * expansion can be blocked by the blocker oracle. */ + template< typename Blocker > + void expansion_with_blockers(int max_dim, Blocker block_simplex); + + /** Returns the number of vertices in the simplicial complex. */ + std::size_t num_vertices(); + +}; + +} // namespace alpha_complex + +} // namespace Gudhi + +#endif // CONCEPT_ALPHA_COMPLEX_SIMPLICIAL_COMPLEX_FOR_ALPHA_H_ diff --git a/src/Cech_complex/doc/COPYRIGHT b/src/Cech_complex/doc/COPYRIGHT new file mode 100644 index 00000000..5f1d97cc --- /dev/null +++ b/src/Cech_complex/doc/COPYRIGHT @@ -0,0 +1,19 @@ +The files of this directory are 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/>. diff --git a/src/Cech_complex/doc/Intro_cech_complex.h b/src/Cech_complex/doc/Intro_cech_complex.h new file mode 100644 index 00000000..4483bcb9 --- /dev/null +++ b/src/Cech_complex/doc/Intro_cech_complex.h @@ -0,0 +1,114 @@ +/* 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) 2018 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_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_ +#define DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_ + +namespace Gudhi { + +namespace cech_complex { + +/** \defgroup cech_complex Čech complex + * + * \author Vincent Rouvreau + * + * @{ + * + * \section cechdefinition Čech complex definition + * + * Čech complex + * <a target="_blank" href="https://en.wikipedia.org/wiki/%C4%8Cech_cohomology">(Wikipedia)</a> is a + * <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a> constructed + * from a proximity graph. The set of all simplices is filtered by the radius of their minimal enclosing ball. + * + * The input shall be a point cloud in an Euclidean space. + * + * \remark For people only interested in the topology of the \ref cech_complex (for instance persistence), + * \ref alpha_complex is equivalent to the \ref cech_complex and much smaller if you do not bound the radii. + * \ref cech_complex can still make sense in higher dimension precisely because you can bound the radii. + * + * \subsection cechalgorithm Algorithm + * + * Cech_complex first builds a proximity graph from a point cloud. + * The filtration value of each edge of the `Gudhi::Proximity_graph` is computed from + * `Gudhi::Minimal_enclosing_ball_radius` function. + * + * All edges that have a filtration value strictly greater than a user given maximal radius value, \f$max\_radius\f$, + * are not inserted into the complex. + * + * Vertex name correspond to the index of the point in the given range (aka. the point cloud). + * + * \image html "cech_one_skeleton.png" "Čech complex proximity graph representation" + * + * When creating a simplicial complex from this proximity graph, Cech_complex inserts the proximity graph into the + * simplicial complex data structure, and then expands the simplicial complex when required. + * + * On this example, as edges \f$(x,y)\f$, \f$(y,z)\f$ and \f$(z,y)\f$ are in the complex, the minimal ball radius + * containing the points \f$(x,y,z)\f$ is computed. + * + * \f$(x,y,z)\f$ is inserted to the simplicial complex with the filtration value set with + * \f$mini\_ball\_radius(x,y,z))\f$ iff \f$mini\_ball\_radius(x,y,z)) \leq max\_radius\f$. + * + * And so on for higher dimensions. + * + * \image html "cech_complex_representation.png" "Čech complex expansion" + * + * The minimal ball radius computation is insured by + * <a target="_blank" href="https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html"> + * the miniball software (V3.0)</a> - Smallest Enclosing Balls of Points - and distributed with GUDHI. + * Please refer to + * <a target="_blank" href="https://people.inf.ethz.ch/gaertner/subdir/texts/own_work/esa99_final.pdf"> + * the miniball software design description</a> for more information about this computation. + * + * This radius computation is the reason why the Cech_complex is taking much more time to be computed than the + * \ref rips_complex but it offers more topological guarantees. + * + * If the Cech_complex interfaces are not detailed enough for your need, please refer to + * <a href="_cech_complex_2cech_complex_step_by_step_8cpp-example.html"> + * cech_complex_step_by_step.cpp</a> example, where the graph construction over the Simplex_tree is more detailed. + * + * \subsection cechpointscloudexample Example from a point cloud + * + * This example builds the proximity graph from the given points, and maximal radius values. + * Then it creates a `Simplex_tree` with it. + * + * Then, it is asked to display information about the simplicial complex. + * + * \include Cech_complex/cech_complex_example_from_points.cpp + * + * When launching (maximal enclosing ball radius is 1., is expanded until dimension 2): + * + * \code $> ./Cech_complex_example_from_points + * \endcode + * + * the program output is: + * + * \include Cech_complex/cech_complex_example_from_points_for_doc.txt + * + */ +/** @} */ // end defgroup cech_complex + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // DOC_CECH_COMPLEX_INTRO_CECH_COMPLEX_H_ diff --git a/src/Cech_complex/doc/cech_complex_representation.ipe b/src/Cech_complex/doc/cech_complex_representation.ipe new file mode 100644 index 00000000..377745a3 --- /dev/null +++ b/src/Cech_complex/doc/cech_complex_representation.ipe @@ -0,0 +1,330 @@ +<?xml version="1.0"?> +<!DOCTYPE ipe SYSTEM "ipe.dtd"> +<ipe version="70107" creator="Ipe 7.1.10"> +<info created="D:20150603143945" modified="D:20180305162524"/> +<ipestyle name="basic"> +<symbol name="arrow/arc(spx)"> +<path 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Binary files differnew file mode 100644 index 00000000..cc636616 --- /dev/null +++ b/src/Cech_complex/doc/cech_one_skeleton.png diff --git a/src/Cech_complex/example/CMakeLists.txt b/src/Cech_complex/example/CMakeLists.txt new file mode 100644 index 00000000..ab391215 --- /dev/null +++ b/src/Cech_complex/example/CMakeLists.txt @@ -0,0 +1,16 @@ +cmake_minimum_required(VERSION 2.6) +project(Cech_complex_examples) + +add_executable ( Cech_complex_example_step_by_step cech_complex_step_by_step.cpp ) +target_link_libraries(Cech_complex_example_step_by_step ${Boost_PROGRAM_OPTIONS_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Cech_complex_example_step_by_step ${TBB_LIBRARIES}) +endif() +add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:Cech_complex_example_step_by_step> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-d" "3") + +add_executable ( Cech_complex_example_from_points cech_complex_example_from_points.cpp) +if (TBB_FOUND) + target_link_libraries(Cech_complex_example_from_points ${TBB_LIBRARIES}) +endif() +add_test(NAME Cech_complex_example_from_points COMMAND $<TARGET_FILE:Cech_complex_example_from_points>) diff --git a/src/Cech_complex/example/cech_complex_example_from_points.cpp b/src/Cech_complex/example/cech_complex_example_from_points.cpp new file mode 100644 index 00000000..3cc5a4df --- /dev/null +++ b/src/Cech_complex/example/cech_complex_example_from_points.cpp @@ -0,0 +1,54 @@ +#include <gudhi/Cech_complex.h> +#include <gudhi/Simplex_tree.h> + +#include <iostream> +#include <string> +#include <vector> +#include <array> + +int main() { + // Type definitions + using Point_cloud = std::vector<std::array<double, 2>>; + using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; + using Filtration_value = Simplex_tree::Filtration_value; + using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; + + Point_cloud points; + points.push_back({1., 0.}); // 0 + points.push_back({0., 1.}); // 1 + points.push_back({2., 1.}); // 2 + points.push_back({3., 2.}); // 3 + points.push_back({0., 3.}); // 4 + points.push_back({3. + std::sqrt(3.), 3.}); // 5 + points.push_back({1., 4.}); // 6 + points.push_back({3., 4.}); // 7 + points.push_back({2., 4. + std::sqrt(3.)}); // 8 + points.push_back({0., 4.}); // 9 + points.push_back({-0.5, 2.}); // 10 + + // ---------------------------------------------------------------------------- + // Init of a Cech complex from points + // ---------------------------------------------------------------------------- + Filtration_value max_radius = 1.; + Cech_complex cech_complex_from_points(points, max_radius); + + Simplex_tree stree; + cech_complex_from_points.create_complex(stree, 2); + // ---------------------------------------------------------------------------- + // Display information about the one skeleton Cech complex + // ---------------------------------------------------------------------------- + std::cout << "Cech complex is of dimension " << stree.dimension() << " - " << stree.num_simplices() << " simplices - " + << stree.num_vertices() << " vertices." << std::endl; + + std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl; + for (auto f_simplex : stree.filtration_simplex_range()) { + std::cout << " ( "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " + << "[" << stree.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + return 0; +} diff --git a/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt b/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt new file mode 100644 index 00000000..be0afc76 --- /dev/null +++ b/src/Cech_complex/example/cech_complex_example_from_points_for_doc.txt @@ -0,0 +1,31 @@ +Iterator on Cech complex simplices in the filtration order, with [filtration value]: + ( 0 ) -> [0] + ( 1 ) -> [0] + ( 2 ) -> [0] + ( 3 ) -> [0] + ( 4 ) -> [0] + ( 5 ) -> [0] + ( 6 ) -> [0] + ( 7 ) -> [0] + ( 8 ) -> [0] + ( 9 ) -> [0] + ( 10 ) -> [0] + ( 9 4 ) -> [0.5] + ( 9 6 ) -> [0.5] + ( 10 1 ) -> [0.559017] + ( 10 4 ) -> [0.559017] + ( 1 0 ) -> [0.707107] + ( 2 0 ) -> [0.707107] + ( 3 2 ) -> [0.707107] + ( 6 4 ) -> [0.707107] + ( 9 6 4 ) -> [0.707107] + ( 2 1 ) -> [1] + ( 2 1 0 ) -> [1] + ( 4 1 ) -> [1] + ( 5 3 ) -> [1] + ( 7 3 ) -> [1] + ( 7 5 ) -> [1] + ( 7 6 ) -> [1] + ( 8 6 ) -> [1] + ( 8 7 ) -> [1] + ( 10 4 1 ) -> [1] diff --git a/src/Cech_complex/example/cech_complex_step_by_step.cpp b/src/Cech_complex/example/cech_complex_step_by_step.cpp new file mode 100644 index 00000000..d2dc8b65 --- /dev/null +++ b/src/Cech_complex/example/cech_complex_step_by_step.cpp @@ -0,0 +1,166 @@ +/* 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) 2018 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/>. + */ + +#include <gudhi/graph_simplicial_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Points_off_io.h> + +#include <gudhi/Miniball.hpp> + +#include <boost/program_options.hpp> + +#include <string> +#include <vector> +#include <limits> // infinity +#include <utility> // for pair +#include <map> + +// ---------------------------------------------------------------------------- +// rips_persistence_step_by_step is an example of each step that is required to +// build a Rips over a Simplex_tree. Please refer to rips_persistence to see +// how to do the same thing with the Rips_complex wrapper for less detailed +// steps. +// ---------------------------------------------------------------------------- + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<>; +using Simplex_handle = Simplex_tree::Simplex_handle; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<double>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; + +class Cech_blocker { + private: + using Point_cloud = std::vector<Point>; + using Point_iterator = Point_cloud::const_iterator; + using Coordinate_iterator = Point::const_iterator; + using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + + public: + bool operator()(Simplex_handle sh) { + std::vector<Point> points; + for (auto vertex : simplex_tree_.simplex_vertex_range(sh)) { + points.push_back(point_cloud_[vertex]); +#ifdef DEBUG_TRACES + std::cout << "#(" << vertex << ")#"; +#endif // DEBUG_TRACES + } + Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points); +#ifdef DEBUG_TRACES + std::cout << "radius = " << radius << " - " << (radius > max_radius_) << std::endl; +#endif // DEBUG_TRACES + simplex_tree_.assign_filtration(sh, radius); + return (radius > max_radius_); + } + Cech_blocker(Simplex_tree& simplex_tree, Filtration_value max_radius, const std::vector<Point>& point_cloud) + : simplex_tree_(simplex_tree), max_radius_(max_radius), point_cloud_(point_cloud) { + dimension_ = point_cloud_[0].size(); + } + + private: + Simplex_tree simplex_tree_; + Filtration_value max_radius_; + std::vector<Point> point_cloud_; + int dimension_; +}; + +void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max); + +int main(int argc, char* argv[]) { + std::string off_file_points; + Filtration_value max_radius; + int dim_max; + + program_options(argc, argv, off_file_points, max_radius, dim_max); + + // Extract the points from the file filepoints + Points_off_reader off_reader(off_file_points); + + // Compute the proximity graph of the points + Proximity_graph prox_graph = Gudhi::compute_proximity_graph<Simplex_tree>(off_reader.get_point_cloud(), max_radius, + Gudhi::Minimal_enclosing_ball_radius()); + + // Construct the Rips complex in a Simplex Tree + Simplex_tree st; + // insert the proximity graph in the simplex tree + st.insert_graph(prox_graph); + // expand the graph until dimension dim_max + st.expansion_with_blockers(dim_max, Cech_blocker(st, max_radius, off_reader.get_point_cloud())); + + std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << st.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + st.initialize_filtration(); + +#if DEBUG_TRACES + std::cout << "********************************************************************\n"; + std::cout << "* The complex contains " << st.num_simplices() << " simplices - dimension=" << st.dimension() << "\n"; + std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << " " + << "[" << st.filtration(f_simplex) << "] "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << static_cast<int>(vertex) << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES + + return 0; +} + +void program_options(int argc, char* argv[], std::string& off_file_points, Filtration_value& max_radius, int& dim_max) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value<std::string>(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "max-radius,r", + po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Rips complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Rips complex we want to compute."); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + 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 << "Construct a Cech complex defined on a set of input points.\n \n"; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Cech_complex/include/gudhi/Cech_complex.h b/src/Cech_complex/include/gudhi/Cech_complex.h new file mode 100644 index 00000000..f4fb4288 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Cech_complex.h @@ -0,0 +1,129 @@ +/* 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) 2018 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 CECH_COMPLEX_H_ +#define CECH_COMPLEX_H_ + +#include <gudhi/distance_functions.h> // for Gudhi::Minimal_enclosing_ball_radius +#include <gudhi/graph_simplicial_complex.h> // for Gudhi::Proximity_graph +#include <gudhi/Debug_utils.h> // for GUDHI_CHECK +#include <gudhi/Cech_complex_blocker.h> // for Gudhi::cech_complex::Cech_blocker + +#include <iostream> +#include <stdexcept> // for exception management + +namespace Gudhi { + +namespace cech_complex { + +/** + * \class Cech_complex + * \brief Cech complex data structure. + * + * \ingroup cech_complex + * + * \details + * The data structure is a proximity graph, containing edges when the edge length is less or equal + * to a given max_radius. Edge length is computed from `Gudhi::Minimal_enclosing_ball_radius` distance function. + * + * \tparam SimplicialComplexForProximityGraph furnishes `Vertex_handle` and `Filtration_value` type definition required + * by `Gudhi::Proximity_graph`. + * + * \tparam ForwardPointRange must be a range for which `std::begin()` and `std::end()` methods return input + * iterators on a point. `std::begin()` and `std::end()` methods are also required for a point. + */ +template <typename SimplicialComplexForProximityGraph, typename ForwardPointRange> +class Cech_complex { + private: + // Required by compute_proximity_graph + using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle; + using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value; + using Proximity_graph = Gudhi::Proximity_graph<SimplicialComplexForProximityGraph>; + + // Retrieve Coordinate type from ForwardPointRange + using Point_from_range_iterator = typename boost::range_const_iterator<ForwardPointRange>::type; + using Point_from_range = typename std::iterator_traits<Point_from_range_iterator>::value_type; + using Coordinate_iterator = typename boost::range_const_iterator<Point_from_range>::type; + using Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type; + + public: + // Point and Point_cloud type definition + using Point = std::vector<Coordinate>; + using Point_cloud = std::vector<Point>; + + public: + /** \brief Cech_complex constructor from a list of points. + * + * @param[in] points Range of points. + * @param[in] max_radius Maximal radius value. + * + * \tparam ForwardPointRange must be a range of Point. Point must be a range of <b>copyable</b> Cartesian coordinates. + * + */ + Cech_complex(const ForwardPointRange& points, Filtration_value max_radius) : max_radius_(max_radius) { + // Point cloud deep copy + point_cloud_.reserve(boost::size(points)); + for (auto&& point : points) point_cloud_.emplace_back(std::begin(point), std::end(point)); + + cech_skeleton_graph_ = Gudhi::compute_proximity_graph<SimplicialComplexForProximityGraph>( + point_cloud_, max_radius_, Gudhi::Minimal_enclosing_ball_radius()); + } + + /** \brief Initializes the simplicial complex from the proximity graph and expands it until a given maximal + * dimension, using the Cech blocker oracle. + * + * @param[in] complex SimplicialComplexForCech to be created. + * @param[in] dim_max graph expansion until this given maximal dimension. + * @exception std::invalid_argument In debug mode, if `complex.num_vertices()` does not return 0. + * + */ + template <typename SimplicialComplexForCechComplex> + void create_complex(SimplicialComplexForCechComplex& complex, int dim_max) { + GUDHI_CHECK(complex.num_vertices() == 0, + std::invalid_argument("Cech_complex::create_complex - simplicial complex is not empty")); + + // insert the proximity graph in the simplicial complex + complex.insert_graph(cech_skeleton_graph_); + // expand the graph until dimension dim_max + complex.expansion_with_blockers(dim_max, + Cech_blocker<SimplicialComplexForCechComplex, Cech_complex>(&complex, this)); + } + + /** @return max_radius value given at construction. */ + Filtration_value max_radius() const { return max_radius_; } + + /** @param[in] vertex Point position in the range. + * @return The point. + */ + const Point& get_point(Vertex_handle vertex) const { return point_cloud_[vertex]; } + + private: + Proximity_graph cech_skeleton_graph_; + Filtration_value max_radius_; + Point_cloud point_cloud_; +}; + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // CECH_COMPLEX_H_ diff --git a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h new file mode 100644 index 00000000..b0d347b1 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h @@ -0,0 +1,91 @@ +/* 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) 2018 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 CECH_COMPLEX_BLOCKER_H_ +#define CECH_COMPLEX_BLOCKER_H_ + +#include <gudhi/distance_functions.h> // for Gudhi::Minimal_enclosing_ball_radius + +#include <iostream> +#include <vector> +#include <cmath> // for std::sqrt + +namespace Gudhi { + +namespace cech_complex { + +/** \internal + * \class Cech_blocker + * \brief Čech complex blocker. + * + * \ingroup cech_complex + * + * \details + * Čech blocker is an oracle constructed from a Cech_complex and a simplicial complex. + * + * \tparam SimplicialComplexForProximityGraph furnishes `Simplex_handle` and `Filtration_value` type definition, + * `simplex_vertex_range(Simplex_handle sh)`and `assign_filtration(Simplex_handle sh, Filtration_value filt)` methods. + * + * \tparam Chech_complex is required by the blocker. + */ +template <typename SimplicialComplexForCech, typename Cech_complex> +class Cech_blocker { + private: + using Point_cloud = typename Cech_complex::Point_cloud; + + using Simplex_handle = typename SimplicialComplexForCech::Simplex_handle; + using Filtration_value = typename SimplicialComplexForCech::Filtration_value; + + public: + /** \internal \brief Čech complex blocker operator() - the oracle - assigns the filtration value from the simplex + * radius and returns if the simplex expansion must be blocked. + * \param[in] sh The Simplex_handle. + * \return true if the simplex radius is greater than the Cech_complex max_radius*/ + bool operator()(Simplex_handle sh) { + Point_cloud points; + for (auto vertex : sc_ptr_->simplex_vertex_range(sh)) { + points.push_back(cc_ptr_->get_point(vertex)); +#ifdef DEBUG_TRACES + std::cout << "#(" << vertex << ")#"; +#endif // DEBUG_TRACES + } + Filtration_value radius = Gudhi::Minimal_enclosing_ball_radius()(points); +#ifdef DEBUG_TRACES + if (radius > cc_ptr_->max_radius()) std::cout << "radius > max_radius => expansion is blocked\n"; +#endif // DEBUG_TRACES + sc_ptr_->assign_filtration(sh, radius); + return (radius > cc_ptr_->max_radius()); + } + + /** \internal \brief Čech complex blocker constructor. */ + Cech_blocker(SimplicialComplexForCech* sc_ptr, Cech_complex* cc_ptr) : sc_ptr_(sc_ptr), cc_ptr_(cc_ptr) {} + + private: + SimplicialComplexForCech* sc_ptr_; + Cech_complex* cc_ptr_; +}; + +} // namespace cech_complex + +} // namespace Gudhi + +#endif // CECH_COMPLEX_BLOCKER_H_ diff --git a/src/Cech_complex/include/gudhi/Miniball.COPYRIGHT b/src/Cech_complex/include/gudhi/Miniball.COPYRIGHT new file mode 100644 index 00000000..dbe4c553 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Miniball.COPYRIGHT @@ -0,0 +1,4 @@ +The miniball software is available under the GNU General Public License (GPLv3 - https://www.gnu.org/copyleft/gpl.html). +If your intended use is not compliant with this license, please buy a commercial license (EUR 500 - https://people.inf.ethz.ch/gaertner/subdir/software/miniball/license.html). +You need a license if the software that you develop using Miniball V3.0 is not open source. + diff --git a/src/Cech_complex/include/gudhi/Miniball.README b/src/Cech_complex/include/gudhi/Miniball.README new file mode 100644 index 00000000..033d8953 --- /dev/null +++ b/src/Cech_complex/include/gudhi/Miniball.README @@ -0,0 +1,26 @@ +https://people.inf.ethz.ch/gaertner/subdir/software/miniball.html + +Smallest Enclosing Balls of Points - Fast and Robust in C++. +(high-quality software for smallest enclosing balls of balls is available in the computational geometry algorithms library CGAL) + + +This is the miniball software (V3.0) for computing smallest enclosing balls of points in arbitrary dimensions. It consists of a C++ header file Miniball.hpp (around 500 lines of code) and two example programs miniball_example.cpp and miniball_example_containers.cpp that demonstrate the usage. The first example stores the coordinates of the input points in a two-dimensional array, the second example uses a list of vectors to show how generic containers can be used. + +Credits: Aditya Gupta and Alexandros Konstantinakis-Karmis have significantly contributed to this version of the software. + +Changes - https://people.inf.ethz.ch/gaertner/subdir/software/miniball/changes.txt - from previous versions. + +The theory - https://people.inf.ethz.ch/gaertner/subdir/texts/own_work/esa99_final.pdf - behind the miniball software (Proc. 7th Annual European Symposium on Algorithms (ESA), Lecture Notes in Computer Science 1643, Springer-Verlag, pp.325-338, 1999). + +Main Features: + + Very fast in low dimensions. 1 million points in 5-space are processed within 0.05 seconds on any recent machine. + + High numerical stability. Almost all input degeneracies (cospherical points, multiple points, points very close together) are routinely handled. + + Easily integrates into your code. You can freely choose the coordinate type of your points and the container to store the points. If you still need to adapt the code, the header is small and readable and contains documentation for all major methods. + + +Changes done for the GUDHI version of MiniBall: + - Add include guard + - Move Miniball namespace inside a new Gudhi namespace diff --git a/src/Cech_complex/include/gudhi/Miniball.hpp b/src/Cech_complex/include/gudhi/Miniball.hpp new file mode 100644 index 00000000..ce6cbb5b --- /dev/null +++ b/src/Cech_complex/include/gudhi/Miniball.hpp @@ -0,0 +1,523 @@ +// Copright (C) 1999-2013, Bernd Gaertner +// $Rev: 3581 $ +// +// 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/>. +// +// Contact: +// -------- +// Bernd Gaertner +// Institute of Theoretical Computer Science +// ETH Zuerich +// CAB G31.1 +// CH-8092 Zuerich, Switzerland +// http://www.inf.ethz.ch/personal/gaertner + +#ifndef MINIBALL_HPP_ +#define MINIBALL_HPP_ + +#include <cassert> +#include <algorithm> +#include <list> +#include <ctime> +#include <limits> + +namespace Gudhi { + +namespace Miniball { + + // Global Functions + // ================ + template <typename NT> + inline NT mb_sqr (NT r) {return r*r;} + + // Functors + // ======== + + // functor to map a point iterator to the corresponding coordinate iterator; + // generic version for points whose coordinate containers have begin() + template < typename Pit_, typename Cit_ > + struct CoordAccessor { + typedef Pit_ Pit; + typedef Cit_ Cit; + inline Cit operator() (Pit it) const { return (*it).begin(); } + }; + + // partial specialization for points whose coordinate containers are arrays + template < typename Pit_, typename Cit_ > + struct CoordAccessor<Pit_, Cit_*> { + typedef Pit_ Pit; + typedef Cit_* Cit; + inline Cit operator() (Pit it) const { return *it; } + }; + + // Class Declaration + // ================= + + template <typename CoordAccessor> + class Miniball { + private: + // types + // The iterator type to go through the input points + typedef typename CoordAccessor::Pit Pit; + // The iterator type to go through the coordinates of a single point. + typedef typename CoordAccessor::Cit Cit; + // The coordinate type + typedef typename std::iterator_traits<Cit>::value_type NT; + // The iterator to go through the support points + typedef typename std::list<Pit>::iterator Sit; + + // data members... + const int d; // dimension + Pit points_begin; + Pit points_end; + CoordAccessor coord_accessor; + double time; + const NT nt0; // NT(0) + + //...for the algorithms + std::list<Pit> L; + Sit support_end; + int fsize; // number of forced points + int ssize; // number of support points + + // ...for the ball updates + NT* current_c; + NT current_sqr_r; + NT** c; + NT* sqr_r; + + // helper arrays + NT* q0; + NT* z; + NT* f; + NT** v; + NT** a; + + public: + // The iterator type to go through the support points + typedef typename std::list<Pit>::const_iterator SupportPointIterator; + + // PRE: [begin, end) is a nonempty range + // POST: computes the smallest enclosing ball of the points in the range + // [begin, end); the functor a maps a point iterator to an iterator + // through the d coordinates of the point + Miniball (int d_, Pit begin, Pit end, CoordAccessor ca = CoordAccessor()); + + // POST: returns a pointer to the first element of an array that holds + // the d coordinates of the center of the computed ball + const NT* center () const; + + // POST: returns the squared radius of the computed ball + NT squared_radius () const; + + // POST: returns the number of support points of the computed ball; + // the support points form a minimal set with the same smallest + // enclosing ball as the input set; in particular, the support + // points are on the boundary of the computed ball, and their + // number is at most d+1 + int nr_support_points () const; + + // POST: returns an iterator to the first support point + SupportPointIterator support_points_begin () const; + + // POST: returns a past-the-end iterator for the range of support points + SupportPointIterator support_points_end () const; + + // POST: returns the maximum excess of any input point w.r.t. the computed + // ball, divided by the squared radius of the computed ball. The + // excess of a point is the difference between its squared distance + // from the center and the squared radius; Ideally, the return value + // is 0. subopt is set to the absolute value of the most negative + // coefficient in the affine combination of the support points that + // yields the center. Ideally, this is a convex combination, and there + // is no negative coefficient in which case subopt is set to 0. + NT relative_error (NT& subopt) const; + + // POST: return true if the relative error is at most tol, and the + // suboptimality is 0; the default tolerance is 10 times the + // coordinate type's machine epsilon + bool is_valid (NT tol = NT(10) * std::numeric_limits<NT>::epsilon()) const; + + // POST: returns the time in seconds taken by the constructor call for + // computing the smallest enclosing ball + double get_time() const; + + // POST: deletes dynamically allocated arrays + ~Miniball(); + + private: + void mtf_mb (Sit n); + void mtf_move_to_front (Sit j); + void pivot_mb (Pit n); + void pivot_move_to_front (Pit j); + NT excess (Pit pit) const; + void pop (); + bool push (Pit pit); + NT suboptimality () const; + void create_arrays(); + void delete_arrays(); + }; + + // Class Definition + // ================ + template <typename CoordAccessor> + Miniball<CoordAccessor>::Miniball (int d_, Pit begin, Pit end, + CoordAccessor ca) + : d (d_), + points_begin (begin), + points_end (end), + coord_accessor (ca), + time (clock()), + nt0 (NT(0)), + L(), + support_end (L.begin()), + fsize(0), + ssize(0), + current_c (NULL), + current_sqr_r (NT(-1)), + c (NULL), + sqr_r (NULL), + q0 (NULL), + z (NULL), + f (NULL), + v (NULL), + a (NULL) + { + assert (points_begin != points_end); + create_arrays(); + + // set initial center + for (int j=0; j<d; ++j) c[0][j] = nt0; + current_c = c[0]; + + // compute miniball + pivot_mb (points_end); + + // update time + time = (clock() - time) / CLOCKS_PER_SEC; + } + + template <typename CoordAccessor> + Miniball<CoordAccessor>::~Miniball() + { + delete_arrays(); + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::create_arrays() + { + c = new NT*[d+1]; + v = new NT*[d+1]; + a = new NT*[d+1]; + for (int i=0; i<d+1; ++i) { + c[i] = new NT[d]; + v[i] = new NT[d]; + a[i] = new NT[d]; + } + sqr_r = new NT[d+1]; + q0 = new NT[d]; + z = new NT[d+1]; + f = new NT[d+1]; + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::delete_arrays() + { + delete[] f; + delete[] z; + delete[] q0; + delete[] sqr_r; + for (int i=0; i<d+1; ++i) { + delete[] a[i]; + delete[] v[i]; + delete[] c[i]; + } + delete[] a; + delete[] v; + delete[] c; + } + + template <typename CoordAccessor> + const typename Miniball<CoordAccessor>::NT* + Miniball<CoordAccessor>::center () const + { + return current_c; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::squared_radius () const + { + return current_sqr_r; + } + + template <typename CoordAccessor> + int Miniball<CoordAccessor>::nr_support_points () const + { + assert (ssize < d+2); + return ssize; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::SupportPointIterator + Miniball<CoordAccessor>::support_points_begin () const + { + return L.begin(); + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::SupportPointIterator + Miniball<CoordAccessor>::support_points_end () const + { + return support_end; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::relative_error (NT& subopt) const + { + NT e, max_e = nt0; + // compute maximum absolute excess of support points + for (SupportPointIterator it = support_points_begin(); + it != support_points_end(); ++it) { + e = excess (*it); + if (e < nt0) e = -e; + if (e > max_e) { + max_e = e; + } + } + // compute maximum excess of any point + for (Pit i = points_begin; i != points_end; ++i) + if ((e = excess (i)) > max_e) + max_e = e; + + subopt = suboptimality(); + assert (current_sqr_r > nt0 || max_e == nt0); + return (current_sqr_r == nt0 ? nt0 : max_e / current_sqr_r); + } + + template <typename CoordAccessor> + bool Miniball<CoordAccessor>::is_valid (NT tol) const + { + NT suboptimality; + return ( (relative_error (suboptimality) <= tol) && (suboptimality == 0) ); + } + + template <typename CoordAccessor> + double Miniball<CoordAccessor>::get_time() const + { + return time; + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::mtf_mb (Sit n) + { + // Algorithm 1: mtf_mb (L_{n-1}, B), where L_{n-1} = [L.begin, n) + // B: the set of forced points, defining the current ball + // S: the superset of support points computed by the algorithm + // -------------------------------------------------------------- + // from B. Gaertner, Fast and Robust Smallest Enclosing Balls, ESA 1999, + // http://www.inf.ethz.ch/personal/gaertner/texts/own_work/esa99_final.pdf + + // PRE: B = S + assert (fsize == ssize); + + support_end = L.begin(); + if ((fsize) == d+1) return; + + // incremental construction + for (Sit i = L.begin(); i != n;) + { + // INV: (support_end - L.begin() == |S|-|B|) + assert (std::distance (L.begin(), support_end) == ssize - fsize); + + Sit j = i++; + if (excess(*j) > nt0) + if (push(*j)) { // B := B + p_i + mtf_mb (j); // mtf_mb (L_{i-1}, B + p_i) + pop(); // B := B - p_i + mtf_move_to_front(j); + } + } + // POST: the range [L.begin(), support_end) stores the set S\B + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::mtf_move_to_front (Sit j) + { + if (support_end == j) + support_end++; + L.splice (L.begin(), L, j); + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::pivot_mb (Pit n) + { + // Algorithm 2: pivot_mb (L_{n-1}), where L_{n-1} = [L.begin, n) + // -------------------------------------------------------------- + // from B. Gaertner, Fast and Robust Smallest Enclosing Balls, ESA 1999, + // http://www.inf.ethz.ch/personal/gaertner/texts/own_work/esa99_final.pdf + NT old_sqr_r; + const NT* c; + Pit pivot, k; + NT e, max_e, sqr_r; + Cit p; + do { + old_sqr_r = current_sqr_r; + sqr_r = current_sqr_r; + + pivot = points_begin; + max_e = nt0; + for (k = points_begin; k != n; ++k) { + p = coord_accessor(k); + e = -sqr_r; + c = current_c; + for (int j=0; j<d; ++j) + e += mb_sqr<NT>(*p++-*c++); + if (e > max_e) { + max_e = e; + pivot = k; + } + } + + if (max_e > nt0) { + // check if the pivot is already contained in the support set + if (std::find(L.begin(), support_end, pivot) == support_end) { + assert (fsize == 0); + if (push (pivot)) { + mtf_mb(support_end); + pop(); + pivot_move_to_front(pivot); + } + } + } + } while (old_sqr_r < current_sqr_r); + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::pivot_move_to_front (Pit j) + { + L.push_front(j); + if (std::distance(L.begin(), support_end) == d+2) + support_end--; + } + + template <typename CoordAccessor> + inline typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::excess (Pit pit) const + { + Cit p = coord_accessor(pit); + NT e = -current_sqr_r; + NT* c = current_c; + for (int k=0; k<d; ++k){ + e += mb_sqr<NT>(*p++-*c++); + } + return e; + } + + template <typename CoordAccessor> + void Miniball<CoordAccessor>::pop () + { + --fsize; + } + + template <typename CoordAccessor> + bool Miniball<CoordAccessor>::push (Pit pit) + { + int i, j; + NT eps = mb_sqr<NT>(std::numeric_limits<NT>::epsilon()); + + Cit cit = coord_accessor(pit); + Cit p = cit; + + if (fsize==0) { + for (i=0; i<d; ++i) + q0[i] = *p++; + for (i=0; i<d; ++i) + c[0][i] = q0[i]; + sqr_r[0] = nt0; + } + else { + // set v_fsize to Q_fsize + for (i=0; i<d; ++i) + //v[fsize][i] = p[i]-q0[i]; + v[fsize][i] = *p++-q0[i]; + + // compute the a_{fsize,i}, i< fsize + for (i=1; i<fsize; ++i) { + a[fsize][i] = nt0; + for (j=0; j<d; ++j) + a[fsize][i] += v[i][j] * v[fsize][j]; + a[fsize][i]*=(2/z[i]); + } + + // update v_fsize to Q_fsize-\bar{Q}_fsize + for (i=1; i<fsize; ++i) { + for (j=0; j<d; ++j) + v[fsize][j] -= a[fsize][i]*v[i][j]; + } + + // compute z_fsize + z[fsize]=nt0; + for (j=0; j<d; ++j) + z[fsize] += mb_sqr<NT>(v[fsize][j]); + z[fsize]*=2; + + // reject push if z_fsize too small + if (z[fsize]<eps*current_sqr_r) { + return false; + } + + // update c, sqr_r + p=cit; + NT e = -sqr_r[fsize-1]; + for (i=0; i<d; ++i) + e += mb_sqr<NT>(*p++-c[fsize-1][i]); + f[fsize]=e/z[fsize]; + + for (i=0; i<d; ++i) + c[fsize][i] = c[fsize-1][i]+f[fsize]*v[fsize][i]; + sqr_r[fsize] = sqr_r[fsize-1] + e*f[fsize]/2; + } + current_c = c[fsize]; + current_sqr_r = sqr_r[fsize]; + ssize = ++fsize; + return true; + } + + template <typename CoordAccessor> + typename Miniball<CoordAccessor>::NT + Miniball<CoordAccessor>::suboptimality () const + { + NT* l = new NT[d+1]; + NT min_l = nt0; + l[0] = NT(1); + for (int i=ssize-1; i>0; --i) { + l[i] = f[i]; + for (int k=ssize-1; k>i; --k) + l[i]-=a[k][i]*l[k]; + if (l[i] < min_l) min_l = l[i]; + l[0] -= l[i]; + } + if (l[0] < min_l) min_l = l[0]; + delete[] l; + if (min_l < nt0) + return -min_l; + return nt0; + } +} // namespace Miniball + +} // namespace Gudhi + +#endif // MINIBALL_HPP_ diff --git a/src/Cech_complex/test/CMakeLists.txt b/src/Cech_complex/test/CMakeLists.txt new file mode 100644 index 00000000..8db51173 --- /dev/null +++ b/src/Cech_complex/test/CMakeLists.txt @@ -0,0 +1,15 @@ +cmake_minimum_required(VERSION 2.6) +project(Cech_complex_tests) + +include(GUDHI_test_coverage) + +add_executable ( Cech_complex_test_unit test_cech_complex.cpp ) +target_link_libraries(Cech_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY}) +if (TBB_FOUND) + target_link_libraries(Cech_complex_test_unit ${TBB_LIBRARIES}) +endif() + +# Do not forget to copy test files in current binary dir +file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + +gudhi_add_coverage_test(Cech_complex_test_unit) diff --git a/src/Cech_complex/test/README b/src/Cech_complex/test/README new file mode 100644 index 00000000..adf704f7 --- /dev/null +++ b/src/Cech_complex/test/README @@ -0,0 +1,12 @@ +To compile: +*********** + +cmake . +make + +To launch with details: +*********************** + +./Cech_complex_test_unit --report_level=detailed --log_level=all + + ==> echo $? returns 0 in case of success (non-zero otherwise) diff --git a/src/Cech_complex/test/test_cech_complex.cpp b/src/Cech_complex/test/test_cech_complex.cpp new file mode 100644 index 00000000..9039169c --- /dev/null +++ b/src/Cech_complex/test/test_cech_complex.cpp @@ -0,0 +1,264 @@ +/* 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) 2018 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 "cech_complex" +#include <boost/test/unit_test.hpp> + +#include <cmath> // float comparison +#include <limits> +#include <string> +#include <vector> +#include <algorithm> // std::max + +#include <gudhi/Cech_complex.h> +// to construct Cech_complex from a OFF file of points +#include <gudhi/Points_off_io.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Unitary_tests_utils.h> +#include <gudhi/Miniball.hpp> + +// Type definitions +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<Filtration_value>; +using Point_cloud = std::vector<Point>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; + +using Point_iterator = Point_cloud::const_iterator; +using Coordinate_iterator = Point::const_iterator; +using Min_sphere = Gudhi::Miniball::Miniball<Gudhi::Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + +BOOST_AUTO_TEST_CASE(Cech_complex_for_documentation) { + // ---------------------------------------------------------------------------- + // + // Init of a Cech complex from a point cloud + // + // ---------------------------------------------------------------------------- + Point_cloud points; + points.push_back({1., 0.}); // 0 + points.push_back({0., 1.}); // 1 + points.push_back({2., 1.}); // 2 + points.push_back({3., 2.}); // 3 + points.push_back({0., 3.}); // 4 + points.push_back({3. + std::sqrt(3.), 3.}); // 5 + points.push_back({1., 4.}); // 6 + points.push_back({3., 4.}); // 7 + points.push_back({2., 4. + std::sqrt(3.)}); // 8 + points.push_back({0., 4.}); // 9 + points.push_back({-0.5, 2.}); // 10 + + Filtration_value max_radius = 1.0; + std::cout << "========== NUMBER OF POINTS = " << points.size() << " - Cech max_radius = " << max_radius + << "==========" << std::endl; + + Cech_complex cech_complex_for_doc(points, max_radius); + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(cech_complex_for_doc.max_radius(), max_radius); + std::size_t i = 0; + for (; i < points.size(); i++) { + BOOST_CHECK(points[i] == cech_complex_for_doc.get_point(i)); + } + + const int DIMENSION_1 = 1; + Simplex_tree st; + cech_complex_for_doc.create_complex(st, DIMENSION_1); + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION_1); + + const int NUMBER_OF_VERTICES = 11; + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 27); + + // Check filtration values of vertices is 0.0 + for (auto f_simplex : st.skeleton_simplex_range(0)) { + BOOST_CHECK(st.filtration(f_simplex) == 0.0); + } + + // Check filtration values of edges + for (auto f_simplex : st.skeleton_simplex_range(DIMENSION_1)) { + if (DIMENSION_1 == st.dimension(f_simplex)) { + std::vector<Point> vp; + std::cout << "vertex = ("; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << ","; + vp.push_back(points.at(vertex)); + } + std::cout << ") - distance =" << Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1)) + << " - filtration =" << st.filtration(f_simplex) << std::endl; + BOOST_CHECK(vp.size() == 2); + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), + Gudhi::Minimal_enclosing_ball_radius()(vp.at(0), vp.at(1))); + } + } + + const int DIMENSION_2 = 2; + +#ifdef GUDHI_DEBUG + BOOST_CHECK_THROW(cech_complex_for_doc.create_complex(st, DIMENSION_2), std::invalid_argument); +#endif + + Simplex_tree st2; + cech_complex_for_doc.create_complex(st2, DIMENSION_2); + std::cout << "st2.dimension()=" << st2.dimension() << std::endl; + BOOST_CHECK(st2.dimension() == DIMENSION_2); + + std::cout << "st2.num_vertices()=" << st2.num_vertices() << std::endl; + BOOST_CHECK(st2.num_vertices() == NUMBER_OF_VERTICES); + + std::cout << "st2.num_simplices()=" << st2.num_simplices() << std::endl; + BOOST_CHECK(st2.num_simplices() == 30); + + Point_cloud points012; + for (std::size_t vertex = 0; vertex <= 2; vertex++) { + points012.push_back(cech_complex_for_doc.get_point(vertex)); + } + std::size_t dimension = points[0].end() - points[0].begin(); + Min_sphere ms012(dimension, points012.begin(), points012.end()); + + Simplex_tree::Filtration_value f012 = st2.filtration(st2.find({0, 1, 2})); + std::cout << "f012= " << f012 << " | ms012_radius= " << std::sqrt(ms012.squared_radius()) << std::endl; + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f012, std::sqrt(ms012.squared_radius())); + + Point_cloud points1410; + points1410.push_back(cech_complex_for_doc.get_point(1)); + points1410.push_back(cech_complex_for_doc.get_point(4)); + points1410.push_back(cech_complex_for_doc.get_point(10)); + Min_sphere ms1410(dimension, points1410.begin(), points1410.end()); + + Simplex_tree::Filtration_value f1410 = st2.filtration(st2.find({1, 4, 10})); + std::cout << "f1410= " << f1410 << " | ms1410_radius= " << std::sqrt(ms1410.squared_radius()) << std::endl; + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f1410, std::sqrt(ms1410.squared_radius())); + + Point_cloud points469; + points469.push_back(cech_complex_for_doc.get_point(4)); + points469.push_back(cech_complex_for_doc.get_point(6)); + points469.push_back(cech_complex_for_doc.get_point(9)); + Min_sphere ms469(dimension, points469.begin(), points469.end()); + + Simplex_tree::Filtration_value f469 = st2.filtration(st2.find({4, 6, 9})); + std::cout << "f469= " << f469 << " | ms469_radius= " << std::sqrt(ms469.squared_radius()) << std::endl; + + GUDHI_TEST_FLOAT_EQUALITY_CHECK(f469, std::sqrt(ms469.squared_radius())); + + BOOST_CHECK((st2.find({6, 7, 8}) == st2.null_simplex())); + BOOST_CHECK((st2.find({3, 5, 7}) == st2.null_simplex())); +} + +BOOST_AUTO_TEST_CASE(Cech_complex_from_points) { + // ---------------------------------------------------------------------------- + // Init of a list of points + // ---------------------------------------------------------------------------- + Point_cloud points; + std::vector<double> coords = {0.0, 0.0, 0.0, 1.0}; + points.push_back(Point(coords.begin(), coords.end())); + coords = {0.0, 0.0, 1.0, 0.0}; + points.push_back(Point(coords.begin(), coords.end())); + coords = {0.0, 1.0, 0.0, 0.0}; + points.push_back(Point(coords.begin(), coords.end())); + coords = {1.0, 0.0, 0.0, 0.0}; + points.push_back(Point(coords.begin(), coords.end())); + + // ---------------------------------------------------------------------------- + // Init of a Cech complex from the list of points + // ---------------------------------------------------------------------------- + Cech_complex cech_complex_from_points(points, 2.0); + + std::cout << "========== cech_complex_from_points ==========" << std::endl; + Simplex_tree st; + const int DIMENSION = 3; + cech_complex_from_points.create_complex(st, DIMENSION); + + // Another way to check num_simplices + std::cout << "Iterator on Cech complex simplices in the filtration order, with [filtration value]:" << std::endl; + int num_simplices = 0; + for (auto f_simplex : st.filtration_simplex_range()) { + num_simplices++; + std::cout << " ( "; + for (auto vertex : st.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << ") -> " + << "[" << st.filtration(f_simplex) << "] "; + std::cout << std::endl; + } + BOOST_CHECK(num_simplices == 15); + std::cout << "st.num_simplices()=" << st.num_simplices() << std::endl; + BOOST_CHECK(st.num_simplices() == 15); + + std::cout << "st.dimension()=" << st.dimension() << std::endl; + BOOST_CHECK(st.dimension() == DIMENSION); + std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl; + BOOST_CHECK(st.num_vertices() == 4); + + for (auto f_simplex : st.filtration_simplex_range()) { + std::cout << "dimension(" << st.dimension(f_simplex) << ") - f = " << st.filtration(f_simplex) << std::endl; + switch (st.dimension(f_simplex)) { + case 0: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.0); + break; + case 1: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.707107, .00001); + break; + case 2: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.816497, .00001); + break; + case 3: + GUDHI_TEST_FLOAT_EQUALITY_CHECK(st.filtration(f_simplex), 0.866025, .00001); + break; + default: + BOOST_CHECK(false); // Shall not happen + break; + } + } +} + +#ifdef GUDHI_DEBUG +BOOST_AUTO_TEST_CASE(Cech_create_complex_throw) { + // ---------------------------------------------------------------------------- + // + // Init of a Cech complex from a OFF file + // + // ---------------------------------------------------------------------------- + std::string off_file_name("alphacomplexdoc.off"); + double max_radius = 12.0; + std::cout << "========== OFF FILE NAME = " << off_file_name << " - Cech max_radius=" << max_radius + << "==========" << std::endl; + + Gudhi::Points_off_reader<Point> off_reader(off_file_name); + Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius); + + Simplex_tree stree; + std::vector<int> simplex = {0, 1, 2}; + stree.insert_simplex_and_subfaces(simplex); + std::cout << "Check exception throw in debug mode" << std::endl; + // throw excpt because stree is not empty + BOOST_CHECK_THROW(cech_complex_from_file.create_complex(stree, 1), std::invalid_argument); +} +#endif diff --git a/src/Cech_complex/utilities/CMakeLists.txt b/src/Cech_complex/utilities/CMakeLists.txt new file mode 100644 index 00000000..30b99729 --- /dev/null +++ b/src/Cech_complex/utilities/CMakeLists.txt @@ -0,0 +1,14 @@ +cmake_minimum_required(VERSION 2.6) +project(Cech_complex_utilities) + +add_executable(cech_persistence cech_persistence.cpp) +target_link_libraries(cech_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) + +if (TBB_FOUND) + target_link_libraries(cech_persistence ${TBB_LIBRARIES}) +endif() + +add_test(NAME Cech_complex_utility_from_rips_on_tore_3D COMMAND $<TARGET_FILE:cech_persistence> + "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "-r" "0.25" "-m" "0.5" "-d" "3" "-p" "3") + +install(TARGETS cech_persistence DESTINATION bin) diff --git a/src/Cech_complex/utilities/cech_persistence.cpp b/src/Cech_complex/utilities/cech_persistence.cpp new file mode 100644 index 00000000..abd9dbcd --- /dev/null +++ b/src/Cech_complex/utilities/cech_persistence.cpp @@ -0,0 +1,136 @@ +/* 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) 2018 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/>. + */ + +#include <gudhi/Cech_complex.h> +#include <gudhi/distance_functions.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/Points_off_io.h> + +#include <boost/program_options.hpp> + +#include <string> +#include <vector> +#include <limits> // infinity + +// Types definition +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Point = std::vector<double>; +using Point_cloud = std::vector<Point>; +using Points_off_reader = Gudhi::Points_off_reader<Point>; +using Cech_complex = Gudhi::cech_complex::Cech_complex<Simplex_tree, Point_cloud>; +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string off_file_points; + std::string filediag; + Filtration_value max_radius; + int dim_max; + int p; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, filediag, max_radius, dim_max, p, min_persistence); + + Points_off_reader off_reader(off_file_points); + Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius); + + // Construct the Cech complex in a Simplex Tree + Simplex_tree simplex_tree; + + cech_complex_from_file.create_complex(simplex_tree, dim_max); + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; + std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(p); + + pcoh.compute_persistent_cohomology(min_persistence); + + // Output the diagram in filediag + if (filediag.empty()) { + pcoh.output_diagram(); + } else { + std::ofstream out(filediag); + pcoh.output_diagram(out); + out.close(); + } + + return 0; +} + +void program_options(int argc, char* argv[], std::string& off_file_points, std::string& filediag, + Filtration_value& max_radius, int& dim_max, int& p, Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()("input-file", po::value<std::string>(&off_file_points), + "Name of an OFF file containing a point set.\n"); + + po::options_description visible("Allowed options", 100); + visible.add_options()("help,h", "produce help message")( + "output-file,o", po::value<std::string>(&filediag)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout")( + "max-radius,r", + po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()), + "Maximal length of an edge for the Cech complex construction.")( + "cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), + "Maximal dimension of the Cech complex we want to compute.")( + "field-charac,p", po::value<int>(&p)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.")( + "min-persistence,m", po::value<Filtration_value>(&min_persistence), + "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " + "intervals"); + + po::positional_options_description pos; + pos.add("input-file", 1); + + po::options_description all; + all.add(visible).add(hidden); + + po::variables_map vm; + 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"; + std::cout << "of a Cech complex defined on a set of input points.\n \n"; + std::cout << "The output diagram contains one bar per line, written with the convention: \n"; + std::cout << " p dim b d \n"; + std::cout << "where dim is the dimension of the homological feature,\n"; + std::cout << "b and d are respectively the birth and death of the feature and \n"; + std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; + + std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} diff --git a/src/Cech_complex/utilities/cechcomplex.md b/src/Cech_complex/utilities/cechcomplex.md new file mode 100644 index 00000000..f7817dbb --- /dev/null +++ b/src/Cech_complex/utilities/cechcomplex.md @@ -0,0 +1,38 @@ + + +# Čech complex # + +## cech_persistence ## +This program computes the persistent homology with coefficient field *Z/pZ* of +a Čech complex defined on a set of input points, using Euclidean distance. The +output diagram contains one bar per line, written with the convention: + +`p dim birth death` + +where `dim` is the dimension of the homological feature, `birth` and `death` +are respectively the birth and death of the feature, and `p` is the +characteristic of the field *Z/pZ* used for homology coefficients (`p` must be +a prime number). + +**Usage** + +`cech_persistence [options] <OFF input file>` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Čech complex construction. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Čech complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. + +**Example 1 with Z/2Z coefficients** + +`cech_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +**Example 2 with Z/3Z coefficients** + +`cech_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3` diff --git a/src/Contraction/doc/COPYRIGHT b/src/Contraction/doc/COPYRIGHT index 1de850d7..5b606ac2 100644 --- a/src/Contraction/doc/COPYRIGHT +++ b/src/Contraction/doc/COPYRIGHT @@ -3,7 +3,7 @@ The files of this directory are part of the Gudhi Library. The Gudhi library computational topology. Author(s): David Salinas -Copyright (C) 2015 INRIA +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 diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt index a92d1685..582b7ab8 100644 --- a/src/Contraction/example/CMakeLists.txt +++ b/src/Contraction/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Contraction_examples) add_executable(RipsContraction Rips_contraction.cpp) diff --git a/src/Contraction/example/Garland_heckbert.cpp b/src/Contraction/example/Garland_heckbert.cpp index 2b0dc973..08dd932e 100644 --- a/src/Contraction/example/Garland_heckbert.cpp +++ b/src/Contraction/example/Garland_heckbert.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-M�diterran�e (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h index e7dafaa0..8bd9b545 100644 --- a/src/Contraction/example/Garland_heckbert/Error_quadric.h +++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-M�diterran�e (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp index 501b0e87..7f9b150a 100644 --- a/src/Contraction/example/Rips_contraction.cpp +++ b/src/Contraction/example/Rips_contraction.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/Edge_profile.h b/src/Contraction/include/gudhi/Contraction/Edge_profile.h index e4910b27..30b1b80a 100644 --- a/src/Contraction/include/gudhi/Contraction/Edge_profile.h +++ b/src/Contraction/include/gudhi/Contraction/Edge_profile.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h b/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h index 7ee05aad..fa02308b 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Contraction_visitor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h index f4d343ec..04ce36b6 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h index 5d329496..a5567454 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h b/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h index dac2d448..1b7a825b 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Edge_length_cost.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h b/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h index 1f68db0d..0b9f8775 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h +++ b/src/Contraction/include/gudhi/Contraction/policies/First_vertex_placement.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h index 250bba27..8c869830 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h index 4b59f1b5..0ba23a35 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h index 34ffa49f..19509fad 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h index 78d61173..8a91f0b5 100644 --- a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h +++ b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index cf9a2c27..fcd06996 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h index df884c93..13086161 100644 --- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h +++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Doxyfile b/src/Doxyfile index f1981e2e..52de65b0 100644 --- a/src/Doxyfile +++ b/src/Doxyfile @@ -843,7 +843,8 @@ EXAMPLE_RECURSIVE = NO IMAGE_PATH = doc/Skeleton_blocker/ \ doc/Alpha_complex/ \ doc/common/ \ - doc/Contraction/ \ + doc/Cech_complex/ \ + doc/Contraction/ \ doc/Simplex_tree/ \ doc/Persistent_cohomology/ \ doc/Witness_complex/ \ diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt index 2503a03e..b357b8f7 100644 --- a/src/GudhUI/CMakeLists.txt +++ b/src/GudhUI/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.8) project(GudhUI) # Need to find OpenGL first as find_package(Qt5) tries to #include"GL/gl.h" on some platforms @@ -38,4 +37,4 @@ if (OPENGL_FOUND) install(TARGETS GudhUI DESTINATION bin) endif() -endif(OPENGL_FOUND)
\ No newline at end of file +endif(OPENGL_FOUND) diff --git a/src/GudhUI/gui/MainWindow.cpp b/src/GudhUI/gui/MainWindow.cpp index 779ccd33..b11b80e9 100644 --- a/src/GudhUI/gui/MainWindow.cpp +++ b/src/GudhUI/gui/MainWindow.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h index 15664dcb..6076c2ee 100644 --- a/src/GudhUI/gui/MainWindow.h +++ b/src/GudhUI/gui/MainWindow.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_edge_contraction.cpp b/src/GudhUI/gui/Menu_edge_contraction.cpp index a679b0bf..041bdf9e 100644 --- a/src/GudhUI/gui/Menu_edge_contraction.cpp +++ b/src/GudhUI/gui/Menu_edge_contraction.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_edge_contraction.h b/src/GudhUI/gui/Menu_edge_contraction.h index 2d5640e8..0ef7b267 100644 --- a/src/GudhUI/gui/Menu_edge_contraction.h +++ b/src/GudhUI/gui/Menu_edge_contraction.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp b/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp index e24865f2..b1ad15c8 100644 --- a/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp +++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_k_nearest_neighbors.h b/src/GudhUI/gui/Menu_k_nearest_neighbors.h index 77303b67..56b5b63d 100644 --- a/src/GudhUI/gui/Menu_k_nearest_neighbors.h +++ b/src/GudhUI/gui/Menu_k_nearest_neighbors.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_persistence.cpp b/src/GudhUI/gui/Menu_persistence.cpp index 016c076b..ec990559 100644 --- a/src/GudhUI/gui/Menu_persistence.cpp +++ b/src/GudhUI/gui/Menu_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_persistence.h b/src/GudhUI/gui/Menu_persistence.h index 1a2a2408..32f0c5ca 100644 --- a/src/GudhUI/gui/Menu_persistence.h +++ b/src/GudhUI/gui/Menu_persistence.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.cpp b/src/GudhUI/gui/Menu_uniform_neighbors.cpp index 20e4f98f..7f392b6c 100644 --- a/src/GudhUI/gui/Menu_uniform_neighbors.cpp +++ b/src/GudhUI/gui/Menu_uniform_neighbors.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/Menu_uniform_neighbors.h b/src/GudhUI/gui/Menu_uniform_neighbors.h index 61316966..88a3823b 100644 --- a/src/GudhUI/gui/Menu_uniform_neighbors.h +++ b/src/GudhUI/gui/Menu_uniform_neighbors.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/gui/gudhui.cpp b/src/GudhUI/gui/gudhui.cpp index 276c4a5f..2a100fd5 100644 --- a/src/GudhUI/gui/gudhui.cpp +++ b/src/GudhUI/gui/gudhui.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 @@ -28,7 +28,7 @@ int main(int argc, char** argv) { QApplication application(argc, argv); application.setOrganizationDomain("inria.fr"); - application.setOrganizationName("INRIA"); + application.setOrganizationName("Inria"); application.setApplicationName("GudhUI"); MainWindow mw; diff --git a/src/GudhUI/model/Complex_typedefs.h b/src/GudhUI/model/Complex_typedefs.h index a4df2c94..347db1e3 100644 --- a/src/GudhUI/model/Complex_typedefs.h +++ b/src/GudhUI/model/Complex_typedefs.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h index 072d1185..1d5cc087 100644 --- a/src/GudhUI/model/Model.h +++ b/src/GudhUI/model/Model.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h index b527d684..49c87b3c 100644 --- a/src/GudhUI/utils/Bar_code_persistence.h +++ b/src/GudhUI/utils/Bar_code_persistence.h @@ -1,3 +1,26 @@ +/* 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): David Salinas + * + * Copyright (C) 2014 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/>. + * + */ + #include <math.h> // isfinite #include <QtGui/QApplication> diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h index e7b9ef31..fbd690f8 100644 --- a/src/GudhUI/utils/Critical_points.h +++ b/src/GudhUI/utils/Critical_points.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Edge_collapsor.h b/src/GudhUI/utils/Edge_collapsor.h index 151e9b01..b3cc7df7 100644 --- a/src/GudhUI/utils/Edge_collapsor.h +++ b/src/GudhUI/utils/Edge_collapsor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Edge_contractor.h b/src/GudhUI/utils/Edge_contractor.h index 8a29ff4b..090baabe 100644 --- a/src/GudhUI/utils/Edge_contractor.h +++ b/src/GudhUI/utils/Edge_contractor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Furthest_point_epsilon_net.h b/src/GudhUI/utils/Furthest_point_epsilon_net.h index 98346daa..dbb6661c 100644 --- a/src/GudhUI/utils/Furthest_point_epsilon_net.h +++ b/src/GudhUI/utils/Furthest_point_epsilon_net.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h index d0974463..732df607 100644 --- a/src/GudhUI/utils/Is_manifold.h +++ b/src/GudhUI/utils/Is_manifold.h @@ -7,7 +7,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/K_nearest_builder.h b/src/GudhUI/utils/K_nearest_builder.h index 4000a331..14851d96 100644 --- a/src/GudhUI/utils/K_nearest_builder.h +++ b/src/GudhUI/utils/K_nearest_builder.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Lloyd_builder.h b/src/GudhUI/utils/Lloyd_builder.h index 18ec9fac..67595d33 100644 --- a/src/GudhUI/utils/Lloyd_builder.h +++ b/src/GudhUI/utils/Lloyd_builder.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/MClock.h b/src/GudhUI/utils/MClock.h index e8d8918a..992f6fa5 100644 --- a/src/GudhUI/utils/MClock.h +++ b/src/GudhUI/utils/MClock.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h index 2dc03c8e..c8afded9 100644 --- a/src/GudhUI/utils/Persistence_compute.h +++ b/src/GudhUI/utils/Persistence_compute.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Rips_builder.h b/src/GudhUI/utils/Rips_builder.h index 59b4bee2..ed62c1c0 100644 --- a/src/GudhUI/utils/Rips_builder.h +++ b/src/GudhUI/utils/Rips_builder.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/UI_utils.h b/src/GudhUI/utils/UI_utils.h index 9cc209d3..67a02869 100644 --- a/src/GudhUI/utils/UI_utils.h +++ b/src/GudhUI/utils/UI_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/utils/Vertex_collapsor.h b/src/GudhUI/utils/Vertex_collapsor.h index 568dab2f..fca57f7d 100644 --- a/src/GudhUI/utils/Vertex_collapsor.h +++ b/src/GudhUI/utils/Vertex_collapsor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/Color.h b/src/GudhUI/view/Color.h index ba0592e1..808dc2d8 100644 --- a/src/GudhUI/view/Color.h +++ b/src/GudhUI/view/Color.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h index 1333f5d3..3f8a6fd9 100644 --- a/src/GudhUI/view/FirstCoordProjector.h +++ b/src/GudhUI/view/FirstCoordProjector.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/Projector3D.h b/src/GudhUI/view/Projector3D.h index 2a756541..a1421f51 100644 --- a/src/GudhUI/view/Projector3D.h +++ b/src/GudhUI/view/Projector3D.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/View_parameter.h b/src/GudhUI/view/View_parameter.h index 9805abc2..578a0268 100644 --- a/src/GudhUI/view/View_parameter.h +++ b/src/GudhUI/view/View_parameter.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/Viewer.cpp b/src/GudhUI/view/Viewer.cpp index c6c2b345..42e35d6c 100644 --- a/src/GudhUI/view/Viewer.cpp +++ b/src/GudhUI/view/Viewer.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/Viewer.h b/src/GudhUI/view/Viewer.h index 797ddc53..414044ef 100644 --- a/src/GudhUI/view/Viewer.h +++ b/src/GudhUI/view/Viewer.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/Viewer_instructor.cpp b/src/GudhUI/view/Viewer_instructor.cpp index 1ddd4d8b..a9dc4525 100644 --- a/src/GudhUI/view/Viewer_instructor.cpp +++ b/src/GudhUI/view/Viewer_instructor.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/GudhUI/view/Viewer_instructor.h b/src/GudhUI/view/Viewer_instructor.h index 05c5c1fc..4b06acb8 100644 --- a/src/GudhUI/view/Viewer_instructor.h +++ b/src/GudhUI/view/Viewer_instructor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/Hasse_complex/include/gudhi/Hasse_complex.h b/src/Hasse_complex/include/gudhi/Hasse_complex.h index e67f7609..efcaea55 100644 --- a/src/Hasse_complex/include/gudhi/Hasse_complex.h +++ b/src/Hasse_complex/include/gudhi/Hasse_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Nerve_GIC/doc/COPYRIGHT b/src/Nerve_GIC/doc/COPYRIGHT index 0c36a526..6b33053e 100644 --- a/src/Nerve_GIC/doc/COPYRIGHT +++ b/src/Nerve_GIC/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Mathieu Carrière -Copyright (C) 2017 INRIA +Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h index 2b648425..bc8aecc3 100644 --- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h +++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carriere * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 542c6af4..fdecf86e 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Nerve_GIC_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) @@ -17,11 +16,11 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1) file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> - "tore3D_1307.off" "0") + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> - "lucky_cat.off" - "lucky_cat_PCA1") + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") install(TARGETS CoordGIC DESTINATION bin) install(TARGETS FuncGIC DESTINATION bin) diff --git a/src/Nerve_GIC/example/CoordGIC.cpp b/src/Nerve_GIC/example/CoordGIC.cpp index d544db94..73edae18 100644 --- a/src/Nerve_GIC/example/CoordGIC.cpp +++ b/src/Nerve_GIC/example/CoordGIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/example/FuncGIC.cpp b/src/Nerve_GIC/example/FuncGIC.cpp index cb0f0d63..1f5de999 100644 --- a/src/Nerve_GIC/example/FuncGIC.cpp +++ b/src/Nerve_GIC/example/FuncGIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index d6f3ded6..aa6478e5 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -4,7 +4,7 @@ * * Author: Mathieu Carriere * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt index c35cdff7..99263ea0 100644 --- a/src/Nerve_GIC/test/CMakeLists.txt +++ b/src/Nerve_GIC/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Graph_induced_complex_tests) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Nerve_GIC/test/test_GIC.cpp b/src/Nerve_GIC/test/test_GIC.cpp index e3067d35..0db2cce2 100644 --- a/src/Nerve_GIC/test/test_GIC.cpp +++ b/src/Nerve_GIC/test/test_GIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index 7a838a8c..215f9dfd 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Nerve_GIC_examples) if (NOT CGAL_VERSION VERSION_LESS 4.8.1) diff --git a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py index c811f610..701e7a52 100755 --- a/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py +++ b/src/Nerve_GIC/utilities/KeplerMapperVisuFromTxtFile.py @@ -11,7 +11,7 @@ import argparse Author(s): Mathieu Carriere - Copyright (C) 2017 INRIA + Copyright (C) 2017 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 @@ -28,7 +28,7 @@ import argparse """ __author__ = "Mathieu Carriere" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='Creates an html Keppler Mapper ' diff --git a/src/Nerve_GIC/utilities/Nerve.cpp b/src/Nerve_GIC/utilities/Nerve.cpp index aefc3874..667129e0 100644 --- a/src/Nerve_GIC/utilities/Nerve.cpp +++ b/src/Nerve_GIC/utilities/Nerve.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Nerve_GIC/utilities/VoronoiGIC.cpp b/src/Nerve_GIC/utilities/VoronoiGIC.cpp index 54bb871e..33deca40 100644 --- a/src/Nerve_GIC/utilities/VoronoiGIC.cpp +++ b/src/Nerve_GIC/utilities/VoronoiGIC.cpp @@ -4,7 +4,7 @@ * * Author(s): Mathieu Carrière * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/Persistence_representations/concept/Real_valued_topological_data.h b/src/Persistence_representations/concept/Real_valued_topological_data.h index 1d3595ad..22ef6d72 100644 --- a/src/Persistence_representations/concept/Real_valued_topological_data.h +++ b/src/Persistence_representations/concept/Real_valued_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/concept/Topological_data_with_averages.h b/src/Persistence_representations/concept/Topological_data_with_averages.h index 9ebd105f..aa64467f 100644 --- a/src/Persistence_representations/concept/Topological_data_with_averages.h +++ b/src/Persistence_representations/concept/Topological_data_with_averages.h @@ -5,7 +5,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/concept/Topological_data_with_distances.h b/src/Persistence_representations/concept/Topological_data_with_distances.h index a6a62307..c8eb2b34 100644 --- a/src/Persistence_representations/concept/Topological_data_with_distances.h +++ b/src/Persistence_representations/concept/Topological_data_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/concept/Topological_data_with_scalar_product.h b/src/Persistence_representations/concept/Topological_data_with_scalar_product.h index 2e506ca9..0f08b8c6 100644 --- a/src/Persistence_representations/concept/Topological_data_with_scalar_product.h +++ b/src/Persistence_representations/concept/Topological_data_with_scalar_product.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/concept/Vectorized_topological_data.h b/src/Persistence_representations/concept/Vectorized_topological_data.h index b6b5b109..365105d6 100644 --- a/src/Persistence_representations/concept/Vectorized_topological_data.h +++ b/src/Persistence_representations/concept/Vectorized_topological_data.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/doc/Persistence_representations_doc.h b/src/Persistence_representations/doc/Persistence_representations_doc.h index 38bd3a21..4d850a02 100644 --- a/src/Persistence_representations/doc/Persistence_representations_doc.h +++ b/src/Persistence_representations/doc/Persistence_representations_doc.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA Sophia-Saclay (France) + * 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 diff --git a/src/Persistence_representations/example/CMakeLists.txt b/src/Persistence_representations/example/CMakeLists.txt index 54d719ac..33558df3 100644 --- a/src/Persistence_representations/example/CMakeLists.txt +++ b/src/Persistence_representations/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_example) add_executable ( Persistence_representations_example_landscape_on_grid persistence_landscape_on_grid.cpp ) diff --git a/src/Persistence_representations/example/persistence_heat_maps.cpp b/src/Persistence_representations/example/persistence_heat_maps.cpp index 2a472ac6..323b57e9 100644 --- a/src/Persistence_representations/example/persistence_heat_maps.cpp +++ b/src/Persistence_representations/example/persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/example/persistence_intervals.cpp b/src/Persistence_representations/example/persistence_intervals.cpp index c1ceb458..b5dcf25c 100644 --- a/src/Persistence_representations/example/persistence_intervals.cpp +++ b/src/Persistence_representations/example/persistence_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/example/persistence_landscape.cpp b/src/Persistence_representations/example/persistence_landscape.cpp index 400a9ae1..27542cf7 100644 --- a/src/Persistence_representations/example/persistence_landscape.cpp +++ b/src/Persistence_representations/example/persistence_landscape.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp index b201b397..0f471a67 100644 --- a/src/Persistence_representations/example/persistence_landscape_on_grid.cpp +++ b/src/Persistence_representations/example/persistence_landscape_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/example/persistence_vectors.cpp b/src/Persistence_representations/example/persistence_vectors.cpp index 834ae644..072e530d 100644 --- a/src/Persistence_representations/example/persistence_vectors.cpp +++ b/src/Persistence_representations/example/persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/PSSK.h b/src/Persistence_representations/include/gudhi/PSSK.h index 630f5623..e1174455 100644 --- a/src/Persistence_representations/include/gudhi/PSSK.h +++ b/src/Persistence_representations/include/gudhi/PSSK.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h index a80c3c40..35e51e63 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h +++ b/src/Persistence_representations/include/gudhi/Persistence_heat_maps.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals.h b/src/Persistence_representations/include/gudhi/Persistence_intervals.h index 3d04d8b7..76eac7d7 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h index 79908883..f48d1a3b 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h +++ b/src/Persistence_representations/include/gudhi/Persistence_intervals_with_distances.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape.h b/src/Persistence_representations/include/gudhi/Persistence_landscape.h index c5aa7867..4381a55b 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h index 84fd22ed..fd8a181c 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h +++ b/src/Persistence_representations/include/gudhi/Persistence_landscape_on_grid.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/Persistence_vectors.h b/src/Persistence_representations/include/gudhi/Persistence_vectors.h index 63577e46..9c04be1d 100644 --- a/src/Persistence_representations/include/gudhi/Persistence_vectors.h +++ b/src/Persistence_representations/include/gudhi/Persistence_vectors.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/common_persistence_representations.h b/src/Persistence_representations/include/gudhi/common_persistence_representations.h index 44e125a7..3d03f1f6 100644 --- a/src/Persistence_representations/include/gudhi/common_persistence_representations.h +++ b/src/Persistence_representations/include/gudhi/common_persistence_representations.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h index 83b89d0e..e0fc7107 100644 --- a/src/Persistence_representations/include/gudhi/read_persistence_from_file.h +++ b/src/Persistence_representations/include/gudhi/read_persistence_from_file.h @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/CMakeLists.txt b/src/Persistence_representations/test/CMakeLists.txt index 335a71ef..5e2b6910 100644 --- a/src/Persistence_representations/test/CMakeLists.txt +++ b/src/Persistence_representations/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_test) include(GUDHI_test_coverage) diff --git a/src/Persistence_representations/test/persistence_heat_maps_test.cpp b/src/Persistence_representations/test/persistence_heat_maps_test.cpp index e36108b7..5fad8051 100644 --- a/src/Persistence_representations/test/persistence_heat_maps_test.cpp +++ b/src/Persistence_representations/test/persistence_heat_maps_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/persistence_intervals_test.cpp b/src/Persistence_representations/test/persistence_intervals_test.cpp index f555e243..a89db9e3 100644 --- a/src/Persistence_representations/test/persistence_intervals_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp index 631e4d70..6ba9a470 100644 --- a/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp +++ b/src/Persistence_representations/test/persistence_intervals_with_distances_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp index 130ac8cc..7eca413b 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_on_grid_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/persistence_lanscapes_test.cpp b/src/Persistence_representations/test/persistence_lanscapes_test.cpp index e98ef894..27ad0987 100644 --- a/src/Persistence_representations/test/persistence_lanscapes_test.cpp +++ b/src/Persistence_representations/test/persistence_lanscapes_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/read_persistence_from_file_test.cpp b/src/Persistence_representations/test/read_persistence_from_file_test.cpp index 276b92ab..c3e8cb4e 100644 --- a/src/Persistence_representations/test/read_persistence_from_file_test.cpp +++ b/src/Persistence_representations/test/read_persistence_from_file_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/test/vector_representation_test.cpp b/src/Persistence_representations/test/vector_representation_test.cpp index c545dce7..a6b9314e 100644 --- a/src/Persistence_representations/test/vector_representation_test.cpp +++ b/src/Persistence_representations/test/vector_representation_test.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt index 386e9fa5..89ef232f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_heat_maps_utilities) add_persistence_representation_creation_utility(create_pssk "10" "-1" "-1" "4" "-1") diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp index 6739e0b6..2cbd812b 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp index ed8278a2..14d0db8f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp index 63626853..12fceedc 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp index b4a1daa5..21c553b9 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * -* Copyright (C) 2016 INRIA (France) +* 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp index c50f9ddb..99b0bd17 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp index 59ff3c24..a4b6e458 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp index 25cd1067..5960a89f 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp index 97ddb8f0..04f33915 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp index 63711d83..e4402589 100644 --- a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt index 875ff45e..649b72cb 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_intervals_utilities) diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp index 9102da79..3be3de8f 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_birth_death_range_in_persistence_diagram.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp index c8290845..a6953b98 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_bottleneck_distance.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp index b3d126f0..4f052f42 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/compute_number_of_dominant_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp index ccb5b645..f283971b 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_histogram_of_intervals_lengths.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp index b433c2b3..1cacbcd0 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_Betti_numbers.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp index 33387802..f92d5782 100644 --- a/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp +++ b/src/Persistence_representations/utilities/persistence_intervals/plot_persistence_intervals.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt index d7087ed8..6b24d032 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_landscapes_utilities) add_persistence_representation_creation_utility(create_landscapes "-1") diff --git a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp index 1a59be8c..4048f508 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/average_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp index 5062f521..253fa273 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_distance_of_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp index 5b5e9fa3..11fe2886 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/compute_scalar_product_of_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp index 6030e994..59aad2f3 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/create_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp index c797a7a8..f32a92a1 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes/plot_landscapes.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt index c5ea4bbf..36f3196b 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_representations_lanscapes_on_grid_utilities) # Need to set grid min and max for further average, distance and scalar_product diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp index 0b098d1a..47102087 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/average_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp index fd0fcd15..6cf2739d 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_distance_of_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp index 01de3dee..9417be6b 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/compute_scalar_product_of_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp index 78e8ef57..46e229bc 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/create_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp index dddb3615..39e438d2 100644 --- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp +++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/plot_landscapes_on_grid.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt index a401c955..bc982094 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt +++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistence_vectors_utilities) add_persistence_representation_creation_utility(create_persistence_vectors "-1") diff --git a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp index 0144e76f..45199838 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/average_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp index 7e66d25e..0db7dbec 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_distance_of_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp index 303c6e3e..8e99251b 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/compute_scalar_product_of_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp index cc5e5393..364284e5 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/create_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp index aa33107d..550e47c5 100644 --- a/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp +++ b/src/Persistence_representations/utilities/persistence_vectors/plot_persistence_vectors.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Persistent_cohomology/benchmark/CMakeLists.txt b/src/Persistent_cohomology/benchmark/CMakeLists.txt index 8b135ba1..2bb3b0c7 100644 --- a/src/Persistent_cohomology/benchmark/CMakeLists.txt +++ b/src/Persistent_cohomology/benchmark/CMakeLists.txt @@ -1,6 +1,4 @@ -cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_benchmark) - if(GMP_FOUND) if(GMPXX_FOUND) diff --git a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp index 252e8aef..3b00d7a9 100644 --- a/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp +++ b/src/Persistent_cohomology/benchmark/performance_rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/concept/CoefficientField.h b/src/Persistent_cohomology/concept/CoefficientField.h index 953b06c2..9d066cca 100644 --- a/src/Persistent_cohomology/concept/CoefficientField.h +++ b/src/Persistent_cohomology/concept/CoefficientField.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h index d6b662e9..62b9002f 100644 --- a/src/Persistent_cohomology/concept/FilteredComplex.h +++ b/src/Persistent_cohomology/concept/FilteredComplex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 @@ -29,10 +29,6 @@ struct FilteredComplex { /** Handle to specify a simplex. */ typedef unspecified Simplex_handle; -/** \brief Key associated to each simplex. - * - * Must be an integer type. */ - typedef unspecified Simplex_key; /** \brief Type for the value of the filtration function. * * Must be comparable with <. */ @@ -58,20 +54,10 @@ struct FilteredComplex * filtration function on the complex. */ Filtration_value filtration(Simplex_handle sh); -/** \brief Returns a key that is different from the keys associated - * to the simplices. */ - Simplex_key null_key (); -/** \brief Returns the key associated to a simplex. - * - * This is never called on null_simplex(). */ - Simplex_key key ( Simplex_handle sh ); /** \brief Returns the simplex that has index idx in the filtration. * * This is only called on valid indices. */ Simplex_handle simplex ( size_t idx ); -/** \brief Assign a key to a simplex. */ - void assign_key(Simplex_handle sh, Simplex_key key); - /** \brief Iterator on the simplices belonging to the * boundary of a simplex. * @@ -115,6 +101,26 @@ typedef unspecified Filtration_simplex_range; * .begin() and .end() return type Filtration_simplex_iterator.*/ Filtration_simplex_range filtration_simplex_range(); +/** \name Map interface + * Conceptually a `std::unordered_map<Simplex_handle,std::size_t>`. + * @{ */ +/** \brief Data stored for each simplex. + * + * Must be an integer type. */ + typedef unspecified Simplex_key; +/** \brief Returns a constant dummy number that is either negative, + * or at least as large as `num_simplices()`. Suggested value: -1. */ + Simplex_key null_key (); +/** \brief Returns the number stored for a simplex by `assign_key`. + * + * This is never called on null_simplex(). */ + Simplex_key key ( Simplex_handle sh ); +/** \brief Store a number for a simplex, which can later be retrieved with `key(sh)`. + * + * This is never called on null_simplex(). */ + void assign_key(Simplex_handle sh, Simplex_key n); +/** @} */ + /* \brief Iterator over the simplices of the complex, * in an arbitrary order. diff --git a/src/Persistent_cohomology/concept/PersistentHomology.h b/src/Persistent_cohomology/concept/PersistentHomology.h index 111723a5..f9a78763 100644 --- a/src/Persistent_cohomology/concept/PersistentHomology.h +++ b/src/Persistent_cohomology/concept/PersistentHomology.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/doc/COPYRIGHT b/src/Persistent_cohomology/doc/COPYRIGHT index 34345bef..6cde9520 100644 --- a/src/Persistent_cohomology/doc/COPYRIGHT +++ b/src/Persistent_cohomology/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clément Maria -Copyright (C) 2015 INRIA +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 diff --git a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h index 3113a22c..5fb9d4d2 100644 --- a/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h +++ b/src/Persistent_cohomology/doc/Intro_persistent_cohomology.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt index 18e2913b..0f731519 100644 --- a/src/Persistent_cohomology/example/CMakeLists.txt +++ b/src/Persistent_cohomology/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_examples) add_executable(plain_homology plain_homology.cpp) diff --git a/src/Persistent_cohomology/example/custom_persistence_sort.cpp b/src/Persistent_cohomology/example/custom_persistence_sort.cpp index 64f2a4dc..35366144 100644 --- a/src/Persistent_cohomology/example/custom_persistence_sort.cpp +++ b/src/Persistent_cohomology/example/custom_persistence_sort.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/example/persistence_from_file.cpp b/src/Persistent_cohomology/example/persistence_from_file.cpp index eafa3fd5..c40434a4 100644 --- a/src/Persistent_cohomology/example/persistence_from_file.cpp +++ b/src/Persistent_cohomology/example/persistence_from_file.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp index 8ef479d4..ffccfd86 100644 --- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp +++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp index a5ae09c8..a2256060 100644 --- a/src/Persistent_cohomology/example/plain_homology.cpp +++ b/src/Persistent_cohomology/example/plain_homology.cpp @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * 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 diff --git a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp index dae36ed2..626ec2ef 100644 --- a/src/Persistent_cohomology/example/rips_multifield_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_multifield_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp index c1de0ef8..7c81fcfb 100644 --- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp index 9618f278..c7607dce 100644 --- a/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp +++ b/src/Persistent_cohomology/example/rips_persistence_via_boundary_matrix.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria, Marc Glisse * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h index a8c9afa3..c68b5c0b 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h index 6db16e69..e98b4bb4 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Field_Zp.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h index 38bc08d1..2bae8654 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h index 5deb2d88..de6c0750 100644 --- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Persistent_cohomology_column.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt index 45f53eb9..f8baf861 100644 --- a/src/Persistent_cohomology/test/CMakeLists.txt +++ b/src/Persistent_cohomology/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Persistent_cohomology_tests) include(GUDHI_test_coverage) diff --git a/src/Rips_complex/concept/SimplicialComplexForRips.h b/src/Rips_complex/concept/SimplicialComplexForRips.h index 7dab0615..3c5acecf 100644 --- a/src/Rips_complex/concept/SimplicialComplexForRips.h +++ b/src/Rips_complex/concept/SimplicialComplexForRips.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Rips_complex/doc/COPYRIGHT b/src/Rips_complex/doc/COPYRIGHT index 594b7d03..2c31a0d6 100644 --- a/src/Rips_complex/doc/COPYRIGHT +++ b/src/Rips_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau -Copyright (C) 2015 INRIA +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 diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h index 5a551e60..712d3b6e 100644 --- a/src/Rips_complex/doc/Intro_rips_complex.h +++ b/src/Rips_complex/doc/Intro_rips_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt index af86636b..e7772bdb 100644 --- a/src/Rips_complex/example/CMakeLists.txt +++ b/src/Rips_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_examples) # Point cloud diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h index 1e4b76a7..f0fe57f4 100644 --- a/src/Rips_complex/include/gudhi/Rips_complex.h +++ b/src/Rips_complex/include/gudhi/Rips_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria, Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h index 1a9d6ebb..19a44b28 100644 --- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h +++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2018 INRIA + * Copyright (C) 2018 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 diff --git a/src/Rips_complex/test/CMakeLists.txt b/src/Rips_complex/test/CMakeLists.txt index 3da9c90d..745d953c 100644 --- a/src/Rips_complex/test/CMakeLists.txt +++ b/src/Rips_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Rips_complex/test/test_rips_complex.cpp b/src/Rips_complex/test/test_rips_complex.cpp index 4e7b79d2..b8b444c9 100644 --- a/src/Rips_complex/test/test_rips_complex.cpp +++ b/src/Rips_complex/test/test_rips_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA Saclay (France) + * 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 diff --git a/src/Rips_complex/utilities/CMakeLists.txt b/src/Rips_complex/utilities/CMakeLists.txt index deb73ff0..4b565628 100644 --- a/src/Rips_complex/utilities/CMakeLists.txt +++ b/src/Rips_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Rips_complex_utilities) add_executable(rips_distance_matrix_persistence rips_distance_matrix_persistence.cpp) diff --git a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp index c2082fae..d4671b45 100644 --- a/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp +++ b/src/Rips_complex/utilities/rips_correlation_matrix_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp index ca3c0327..53191ca7 100644 --- a/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp +++ b/src/Rips_complex/utilities/rips_distance_matrix_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Pawel Dlotko, Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Rips_complex/utilities/rips_persistence.cpp b/src/Rips_complex/utilities/rips_persistence.cpp index 8405c014..7cee927e 100644 --- a/src/Rips_complex/utilities/rips_persistence.cpp +++ b/src/Rips_complex/utilities/rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Rips_complex/utilities/sparse_rips_persistence.cpp b/src/Rips_complex/utilities/sparse_rips_persistence.cpp index d4bae3ba..bcd5c2c5 100644 --- a/src/Rips_complex/utilities/sparse_rips_persistence.cpp +++ b/src/Rips_complex/utilities/sparse_rips_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse, Clément Maria * - * Copyright (C) 2018 INRIA + * Copyright (C) 2018 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 diff --git a/src/Simplex_tree/concept/FiltrationValue.h b/src/Simplex_tree/concept/FiltrationValue.h index 79ca06cc..f4dcf985 100644 --- a/src/Simplex_tree/concept/FiltrationValue.h +++ b/src/Simplex_tree/concept/FiltrationValue.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/concept/IndexingTag.h b/src/Simplex_tree/concept/IndexingTag.h index 1dcdd756..37e7e294 100644 --- a/src/Simplex_tree/concept/IndexingTag.h +++ b/src/Simplex_tree/concept/IndexingTag.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/concept/SimplexKey.h b/src/Simplex_tree/concept/SimplexKey.h index 9fbed401..c03f7da1 100644 --- a/src/Simplex_tree/concept/SimplexKey.h +++ b/src/Simplex_tree/concept/SimplexKey.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h index 89acdc18..6638da26 100644 --- a/src/Simplex_tree/concept/SimplexTreeOptions.h +++ b/src/Simplex_tree/concept/SimplexTreeOptions.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * 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 diff --git a/src/Simplex_tree/concept/VertexHandle.h b/src/Simplex_tree/concept/VertexHandle.h index 3efbba61..9d0642c3 100644 --- a/src/Simplex_tree/concept/VertexHandle.h +++ b/src/Simplex_tree/concept/VertexHandle.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/doc/COPYRIGHT b/src/Simplex_tree/doc/COPYRIGHT index 34345bef..6cde9520 100644 --- a/src/Simplex_tree/doc/COPYRIGHT +++ b/src/Simplex_tree/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clément Maria -Copyright (C) 2015 INRIA +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 diff --git a/src/Simplex_tree/doc/Intro_simplex_tree.h b/src/Simplex_tree/doc/Intro_simplex_tree.h index 6b80d1c9..db399489 100644 --- a/src/Simplex_tree/doc/Intro_simplex_tree.h +++ b/src/Simplex_tree/doc/Intro_simplex_tree.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt index b33b2d05..857e8518 100644 --- a/src/Simplex_tree/example/CMakeLists.txt +++ b/src/Simplex_tree/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Simplex_tree_examples) add_executable ( Simplex_tree_example_from_cliques_of_graph simplex_tree_from_cliques_of_graph.cpp ) diff --git a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp index 9bd51106..08ed74bb 100644 --- a/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp +++ b/src/Simplex_tree/example/cech_complex_cgal_mini_sphere_3d.cpp @@ -2,9 +2,9 @@ * (Geometric Understanding in Higher Dimensions) is a generic C++ * library for computational topology. * - * Author(s): Clément Maria + * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2017 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 diff --git a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp index d8289ba9..290a9d9b 100644 --- a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp +++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp index 0d458cbd..f39de31f 100644 --- a/src/Simplex_tree/example/graph_expansion_with_blocker.cpp +++ b/src/Simplex_tree/example/graph_expansion_with_blocker.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 + * Copyright (C) 2014 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 @@ -29,33 +29,33 @@ using Simplex_handle = Simplex_tree::Simplex_handle; int main(int argc, char* const argv[]) { // Construct the Simplex Tree with a 1-skeleton graph example - Simplex_tree simplexTree; + Simplex_tree stree; - simplexTree.insert_simplex({0, 1}, 0.); - simplexTree.insert_simplex({0, 2}, 1.); - simplexTree.insert_simplex({0, 3}, 2.); - simplexTree.insert_simplex({1, 2}, 3.); - simplexTree.insert_simplex({1, 3}, 4.); - simplexTree.insert_simplex({2, 3}, 5.); - simplexTree.insert_simplex({2, 4}, 6.); - simplexTree.insert_simplex({3, 6}, 7.); - simplexTree.insert_simplex({4, 5}, 8.); - simplexTree.insert_simplex({4, 6}, 9.); - simplexTree.insert_simplex({5, 6}, 10.); - simplexTree.insert_simplex({6}, 10.); + stree.insert_simplex({0, 1}, 0.); + stree.insert_simplex({0, 2}, 1.); + stree.insert_simplex({0, 3}, 2.); + stree.insert_simplex({1, 2}, 3.); + stree.insert_simplex({1, 3}, 4.); + stree.insert_simplex({2, 3}, 5.); + stree.insert_simplex({2, 4}, 6.); + stree.insert_simplex({3, 6}, 7.); + stree.insert_simplex({4, 5}, 8.); + stree.insert_simplex({4, 6}, 9.); + stree.insert_simplex({5, 6}, 10.); + stree.insert_simplex({6}, 10.); - simplexTree.expansion_with_blockers(3, [&](Simplex_handle sh) { + stree.expansion_with_blockers(3, [&](Simplex_handle sh) { bool result = false; std::cout << "Blocker on ["; // User can loop on the vertices from the given simplex_handle i.e. - for (auto vertex : simplexTree.simplex_vertex_range(sh)) { + for (auto vertex : stree.simplex_vertex_range(sh)) { // We block the expansion, if the vertex '6' is in the given list of vertices if (vertex == 6) result = true; std::cout << vertex << ", "; } - std::cout << "] ( " << simplexTree.filtration(sh); + std::cout << "] ( " << stree.filtration(sh); // User can re-assign a new filtration value directly in the blocker (default is the maximal value of boudaries) - simplexTree.assign_filtration(sh, simplexTree.filtration(sh) + 1.); + stree.assign_filtration(sh, stree.filtration(sh) + 1.); std::cout << " + 1. ) = " << result << std::endl; @@ -63,13 +63,13 @@ int main(int argc, char* const argv[]) { }); std::cout << "********************************************************************\n"; - std::cout << "* The complex contains " << simplexTree.num_simplices() << " simplices"; - std::cout << " - dimension " << simplexTree.dimension() << "\n"; + std::cout << "* The complex contains " << stree.num_simplices() << " simplices"; + std::cout << " - dimension " << stree.dimension() << "\n"; std::cout << "* Iterator on Simplices in the filtration, with [filtration value]:\n"; - for (auto f_simplex : simplexTree.filtration_simplex_range()) { + for (auto f_simplex : stree.filtration_simplex_range()) { std::cout << " " - << "[" << simplexTree.filtration(f_simplex) << "] "; - for (auto vertex : simplexTree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")"; + << "[" << stree.filtration(f_simplex) << "] "; + for (auto vertex : stree.simplex_vertex_range(f_simplex)) std::cout << "(" << vertex << ")"; std::cout << std::endl; } diff --git a/src/Simplex_tree/example/mini_simplex_tree.cpp b/src/Simplex_tree/example/mini_simplex_tree.cpp index 19e45361..e7c7177f 100644 --- a/src/Simplex_tree/example/mini_simplex_tree.cpp +++ b/src/Simplex_tree/example/mini_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France) + * 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 diff --git a/src/Simplex_tree/example/simple_simplex_tree.cpp b/src/Simplex_tree/example/simple_simplex_tree.cpp index 828977c2..d71b5608 100644 --- a/src/Simplex_tree/example/simple_simplex_tree.cpp +++ b/src/Simplex_tree/example/simple_simplex_tree.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp index d1b8b2de..6d70f3d1 100644 --- a/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp +++ b/src/Simplex_tree/example/simplex_tree_from_cliques_of_graph.cpp @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h index d9e2d73e..74a7281d 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h index ab7346d4..335bac1e 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h index 25d4888a..3a75ec72 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h index 1eca7f6f..ab2ca707 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h index 0adeb46d..ec4461f3 100644 --- a/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h +++ b/src/Simplex_tree/include/gudhi/Simplex_tree/indexing_tag.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt index 8684ad2a..c63d8532 100644 --- a/src/Simplex_tree/test/CMakeLists.txt +++ b/src/Simplex_tree/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Simplex_tree_tests) include(GUDHI_test_coverage) diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h index d82425a0..fd806ff1 100644 --- a/src/Skeleton_blocker/concept/SkeletonBlockerDS.h +++ b/src/Skeleton_blocker/concept/SkeletonBlockerDS.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h b/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h index 477464c4..d8521343 100644 --- a/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h +++ b/src/Skeleton_blocker/concept/SkeletonBlockerGeometricDS.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/doc/COPYRIGHT b/src/Skeleton_blocker/doc/COPYRIGHT index 1de850d7..5b606ac2 100644 --- a/src/Skeleton_blocker/doc/COPYRIGHT +++ b/src/Skeleton_blocker/doc/COPYRIGHT @@ -3,7 +3,7 @@ The files of this directory are part of the Gudhi Library. The Gudhi library computational topology. Author(s): David Salinas -Copyright (C) 2015 INRIA +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 diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index de70f089..0e5d2f11 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Skeleton_blocker_examples) add_executable(Skeleton_blocker_example_from_simplices Skeleton_blocker_from_simplices.cpp) diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp index 076c6a53..f288e39c 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp index 08ff0264..4d008450 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_iteration.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp index 58322038..2ec72128 100644 --- a/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp +++ b/src/Skeleton_blocker/example/Skeleton_blocker_link.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index aca2aa57..e8b6fde8 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h index ba3636bc..6c6a8638 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h index d4b60613..feab7b3f 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h index 747e60f1..56009daf 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h index 275376e6..22c1668e 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h index 3835cf77..144f1fd0 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h index aa6f2215..d7193157 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h index fadf6619..dbfb4042 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h index 2b681752..f80ca4fe 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Top_faces.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h index 2c9602fa..7a5d38eb 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/internal/Trie.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h index d2fff960..95c5f7ef 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_blockers_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h index b90dcf34..5c725aae 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_edges_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h index 1351614f..8054e64f 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h index 2acdb555..e2024652 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h index 736941dd..a834fe1d 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_triangles_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h index 9e9ae961..3a638ae6 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_vertices_iterators.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h index 4f052ba5..addd8104 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h index 95331b7a..39b88ceb 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h index 4db075b0..428d4e9b 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h index 544e02e8..d5adb39d 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt index 4a363294..19c65871 100644 --- a/src/Skeleton_blocker/test/CMakeLists.txt +++ b/src/Skeleton_blocker/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Skeleton_blocker_tests) include(GUDHI_test_coverage) diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp index 4f9888ba..9760c74d 100644 --- a/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp +++ b/src/Skeleton_blocker/test/test_skeleton_blocker_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp index d035b2c3..f2d3bb27 100644 --- a/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp +++ b/src/Skeleton_blocker/test/test_skeleton_blocker_geometric_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp b/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp index 360b91db..1f263c98 100644 --- a/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp +++ b/src/Skeleton_blocker/test/test_skeleton_blocker_simplifiable.cpp @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/Spatial_searching/doc/Intro_spatial_searching.h b/src/Spatial_searching/doc/Intro_spatial_searching.h index 52ed65e4..f387ab2f 100644 --- a/src/Spatial_searching/doc/Intro_spatial_searching.h +++ b/src/Spatial_searching/doc/Intro_spatial_searching.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Spatial_searching/example/CMakeLists.txt b/src/Spatial_searching/example/CMakeLists.txt index 4cf3d863..0f799987 100644 --- a/src/Spatial_searching/example/CMakeLists.txt +++ b/src/Spatial_searching/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Spatial_searching_examples) if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Spatial_searching/include/gudhi/Kd_tree_search.h b/src/Spatial_searching/include/gudhi/Kd_tree_search.h index 96bbeb36..ad1054e5 100644 --- a/src/Spatial_searching/include/gudhi/Kd_tree_search.h +++ b/src/Spatial_searching/include/gudhi/Kd_tree_search.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt index b9da7b4e..b60ab1e3 100644 --- a/src/Spatial_searching/test/CMakeLists.txt +++ b/src/Spatial_searching/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Spatial_searching_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Spatial_searching/test/test_Kd_tree_search.cpp b/src/Spatial_searching/test/test_Kd_tree_search.cpp index 8a8334c3..981a5850 100644 --- a/src/Spatial_searching/test/test_Kd_tree_search.cpp +++ b/src/Spatial_searching/test/test_Kd_tree_search.cpp @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/doc/Intro_subsampling.h b/src/Subsampling/doc/Intro_subsampling.h index ab9cdc37..d88f6bf6 100644 --- a/src/Subsampling/doc/Intro_subsampling.h +++ b/src/Subsampling/doc/Intro_subsampling.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt index 34400b1e..f26d107f 100644 --- a/src/Subsampling/example/CMakeLists.txt +++ b/src/Subsampling/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Subsampling_examples) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Subsampling/include/gudhi/choose_n_farthest_points.h b/src/Subsampling/include/gudhi/choose_n_farthest_points.h index 8390b4c9..ab1c4c73 100644 --- a/src/Subsampling/include/gudhi/choose_n_farthest_points.h +++ b/src/Subsampling/include/gudhi/choose_n_farthest_points.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/include/gudhi/pick_n_random_points.h b/src/Subsampling/include/gudhi/pick_n_random_points.h index 8c90b6bf..64821e5d 100644 --- a/src/Subsampling/include/gudhi/pick_n_random_points.h +++ b/src/Subsampling/include/gudhi/pick_n_random_points.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/include/gudhi/sparsify_point_set.h b/src/Subsampling/include/gudhi/sparsify_point_set.h index 7d3b97fb..db10e0b1 100644 --- a/src/Subsampling/include/gudhi/sparsify_point_set.h +++ b/src/Subsampling/include/gudhi/sparsify_point_set.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/test/CMakeLists.txt b/src/Subsampling/test/CMakeLists.txt index dbf97db3..924f0925 100644 --- a/src/Subsampling/test/CMakeLists.txt +++ b/src/Subsampling/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Subsampling_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Subsampling/test/test_choose_n_farthest_points.cpp b/src/Subsampling/test/test_choose_n_farthest_points.cpp index ee9d4c77..0e0eb29c 100644 --- a/src/Subsampling/test/test_choose_n_farthest_points.cpp +++ b/src/Subsampling/test/test_choose_n_farthest_points.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/test/test_pick_n_random_points.cpp b/src/Subsampling/test/test_pick_n_random_points.cpp index 6c8dbea2..4baf4a5d 100644 --- a/src/Subsampling/test/test_pick_n_random_points.cpp +++ b/src/Subsampling/test/test_pick_n_random_points.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Subsampling/test/test_sparsify_point_set.cpp b/src/Subsampling/test/test_sparsify_point_set.cpp index f993d6d6..f414dda3 100644 --- a/src/Subsampling/test/test_sparsify_point_set.cpp +++ b/src/Subsampling/test/test_sparsify_point_set.cpp @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt index 8729e394..f136ab27 100644 --- a/src/Tangential_complex/benchmark/CMakeLists.txt +++ b/src/Tangential_complex/benchmark/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Tangential_complex_benchmark) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/benchmark/RIB_exporter.h b/src/Tangential_complex/benchmark/RIB_exporter.h index 73c14041..59ca138a 100644 --- a/src/Tangential_complex/benchmark/RIB_exporter.h +++ b/src/Tangential_complex/benchmark/RIB_exporter.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/benchmark/XML_exporter.h b/src/Tangential_complex/benchmark/XML_exporter.h index ed44f90a..4db5687f 100644 --- a/src/Tangential_complex/benchmark/XML_exporter.h +++ b/src/Tangential_complex/benchmark/XML_exporter.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/doc/COPYRIGHT b/src/Tangential_complex/doc/COPYRIGHT index c4df0f64..f9f92471 100644 --- a/src/Tangential_complex/doc/COPYRIGHT +++ b/src/Tangential_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Clement Jamin -Copyright (C) 2015 INRIA +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 diff --git a/src/Tangential_complex/doc/Intro_tangential_complex.h b/src/Tangential_complex/doc/Intro_tangential_complex.h index 00e00c52..f4fc8ac7 100644 --- a/src/Tangential_complex/doc/Intro_tangential_complex.h +++ b/src/Tangential_complex/doc/Intro_tangential_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt index 16d1339d..af0dac51 100644 --- a/src/Tangential_complex/example/CMakeLists.txt +++ b/src/Tangential_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Tangential_complex_examples) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h index 6f061922..d8356520 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h index 65c74ca5..f79186b0 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h index ffefcd6b..e1af1ea6 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/config.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/config.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h b/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h index b2d6d674..2dd46118 100644 --- a/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h +++ b/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt index 1948c8f6..902f19af 100644 --- a/src/Tangential_complex/test/CMakeLists.txt +++ b/src/Tangential_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Tangential_complex_tests) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1) diff --git a/src/Tangential_complex/test/test_tangential_complex.cpp b/src/Tangential_complex/test/test_tangential_complex.cpp index 48156440..4e2d4f65 100644 --- a/src/Tangential_complex/test/test_tangential_complex.cpp +++ b/src/Tangential_complex/test/test_tangential_complex.cpp @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/Witness_complex/concept/SimplicialComplexForWitness.h b/src/Witness_complex/concept/SimplicialComplexForWitness.h index d78cc83f..8b85f4e4 100644 --- a/src/Witness_complex/concept/SimplicialComplexForWitness.h +++ b/src/Witness_complex/concept/SimplicialComplexForWitness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France) + * Copyright (C) 2014 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 diff --git a/src/Witness_complex/doc/COPYRIGHT b/src/Witness_complex/doc/COPYRIGHT index 7d032c87..25a700cf 100644 --- a/src/Witness_complex/doc/COPYRIGHT +++ b/src/Witness_complex/doc/COPYRIGHT @@ -4,7 +4,7 @@ computational topology. Author(s): Siargey Kachanovich -Copyright (C) 2015 INRIA +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 diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index a8231392..3d838c0d 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_examples) add_executable ( Witness_complex_example_nearest_landmark_table example_nearest_landmark_table.cpp ) diff --git a/src/Witness_complex/example/example_nearest_landmark_table.cpp b/src/Witness_complex/example/example_nearest_landmark_table.cpp index b8594212..acaf7c54 100644 --- a/src/Witness_complex/example/example_nearest_landmark_table.cpp +++ b/src/Witness_complex/example/example_nearest_landmark_table.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_PARAMETER_MAX_ARITY 12 #include <gudhi/Simplex_tree.h> 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 346bef6d..19f73836 100644 --- a/src/Witness_complex/example/example_strong_witness_complex_off.cpp +++ b/src/Witness_complex/example/example_strong_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) 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/Euclidean_strong_witness_complex.h> #include <gudhi/pick_n_random_points.h> diff --git a/src/Witness_complex/example/example_witness_complex_sphere.cpp b/src/Witness_complex/example/example_witness_complex_sphere.cpp index a6e9b11a..9e3c972d 100644 --- a/src/Witness_complex/example/example_witness_complex_sphere.cpp +++ b/src/Witness_complex/example/example_witness_complex_sphere.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_PARAMETER_MAX_ARITY 12 #include <gudhi/Simplex_tree.h> diff --git a/src/Witness_complex/example/generators.h b/src/Witness_complex/example/generators.h index 7df43db5..81566824 100644 --- a/src/Witness_complex/example/generators.h +++ b/src/Witness_complex/example/generators.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA Sophia Antipolis-Méditerranée (France) + * 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 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 d41a6811..8cb8662b 100644 --- a/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h +++ b/src/Witness_complex/include/gudhi/Active_witness/Active_witness.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * 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 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 0a05173a..10d2ec52 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 @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * 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 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 4f3cef4f..ea97cd3f 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * 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 diff --git a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h index ff8bb139..1dacefa5 100644 --- a/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Euclidean_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * 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 diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h index b3d00b11..fd6b3f38 100644 --- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h +++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * 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 diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h index 53c38520..67885258 100644 --- a/src/Witness_complex/include/gudhi/Witness_complex.h +++ b/src/Witness_complex/include/gudhi/Witness_complex.h @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * 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 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 b68d75a1..c7b732b9 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 @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2015 INRIA (France) + * 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 diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt index 0b523eaf..58ac60c5 100644 --- a/src/Witness_complex/test/CMakeLists.txt +++ b/src/Witness_complex/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_tests) include(GUDHI_test_coverage) diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt index 125a41ff..ce5e29f2 100644 --- a/src/Witness_complex/utilities/CMakeLists.txt +++ b/src/Witness_complex/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Witness_complex_utilities) # CGAL and Eigen3 are required for Euclidean version of Witness diff --git a/src/Witness_complex/utilities/strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp index 2fba631b..9d23df74 100644 --- a/src/Witness_complex/utilities/strong_witness_persistence.cpp +++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/Witness_complex/utilities/weak_witness_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp index 23fa93aa..1315d2ba 100644 --- a/src/Witness_complex/utilities/weak_witness_persistence.cpp +++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp @@ -4,7 +4,7 @@ * * Author(s): Siargey Kachanovich * - * Copyright (C) 2016 INRIA (France) + * 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 diff --git a/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake new file mode 100644 index 00000000..394f1f42 --- /dev/null +++ b/src/cmake/modules/GUDHI_compilation_flags.cmake @@ -0,0 +1,35 @@ +# This files manage compilation flags required by GUDHI + +include(TestCXXAcceptsFlag) + +# add a compiler flag only if it is accepted +macro(add_cxx_compiler_flag _flag) + string(REPLACE "-" "_" _flag_var ${_flag}) + check_cxx_accepts_flag("${_flag}" CXX_COMPILER_${_flag_var}_OK) + if(CXX_COMPILER_${_flag_var}_OK) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_flag}") + endif() +endmacro() + +set (CMAKE_CXX_STANDARD 11) + +enable_testing() + +if(MSVC) + # Turn off some VC++ warnings + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018") +endif() + +add_cxx_compiler_flag("-Wall") + +if(CMAKE_BUILD_TYPE MATCHES Debug) + message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}") +else() + message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}") +endif() + +if (DEBUG_TRACES) + # For programs to be more verbose + message(STATUS "DEBUG_TRACES are activated") + add_definitions(-DDEBUG_TRACES) +endif() diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake index a008dd0a..7433f2f3 100644 --- a/src/cmake/modules/GUDHI_third_party_libraries.cmake +++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake @@ -54,12 +54,12 @@ if(CGAL_FOUND) endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS}) endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0) - if (NOT CGAL_VERSION VERSION_GREATER 4.11.0) + if (CGAL_VERSION VERSION_LESS 4.11.0) # For dev version include_directories(BEFORE "src/common/include/gudhi_patches") # For user version include_directories(BEFORE "include/gudhi_patches") - endif (NOT CGAL_VERSION VERSION_GREATER 4.11.0) + endif () endif() endif() diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake index 4abc2574..1205966a 100644 --- a/src/cmake/modules/GUDHI_user_version_target.cmake +++ b/src/cmake/modules/GUDHI_user_version_target.cmake @@ -48,10 +48,10 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) set(GUDHI_DIRECTORIES "doc;example;concept;utilities") - if (NOT CGAL_VERSION VERSION_GREATER 4.11.0) - set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches") + if (CGAL_VERSION VERSION_LESS 4.11.0) + set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/Miniball;include/gudhi_patches") else () - set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi") + set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/Miniball") endif () foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST}) diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h index c60ed15a..523153b8 100644 --- a/src/common/doc/file_formats.h +++ b/src/common/doc/file_formats.h @@ -4,7 +4,7 @@ * * Author(s): Clément Jamin * -* Copyright (C) 2017 INRIA +* Copyright (C) 2017 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 diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 25675cc5..12407c18 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -5,8 +5,9 @@ * Examples of GUDHI headers inclusion can be found in \ref demos. * * \section compiling Compiling - * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or - * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. + * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> ≥ 1.48.0 + * and <a target="_blank" href="https://www.cmake.org/">CMake</a> ≥ 3.1. + * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015. * * \subsection demos Demos and examples * To build the demos and examples, run the following commands in a terminal: diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h index b3e9ea03..30d4e71b 100644 --- a/src/common/doc/main_page.h +++ b/src/common/doc/main_page.h @@ -42,6 +42,22 @@ </td> </tr> </table> + \subsection CechComplexDataStructure Čech complex + \image html "cech_complex_representation.png" "Čech complex representation" +<table border="0"> + <tr> + <td width="25%"> + <b>Author:</b> Vincent Rouvreau<br> + <b>Introduced in:</b> GUDHI 2.2.0<br> + <b>Copyright:</b> GPL v3<br> + </td> + <td width="75%"> + The Čech complex is a simplicial complex constructed from a proximity graph.<br> + The set of all simplices is filtered by the radius of their minimal enclosing ball.<br> + <b>User manual:</b> \ref cech_complex - <b>Reference manual:</b> Gudhi::cech_complex::Cech_complex + </td> + </tr> +</table> \subsection CubicalComplexDataStructure Cubical complex \image html "Cubical_complex_representation.png" "Cubical complex representation" <table border="0"> @@ -57,6 +73,7 @@ <b>User manual:</b> \ref cubical_complex - <b>Reference manual:</b> Gudhi::cubical_complex::Bitmap_cubical_complex </td> </tr> +</table> \subsection RipsComplexDataStructure Rips complex \image html "rips_complex_representation.png" "Rips complex representation" <table border="0"> @@ -75,7 +92,6 @@ </td> </tr> </table> -</table> \subsection SimplexTreeDataStructure Simplex tree \image html "Simplex_tree_representation.png" "Simplex tree representation" <table border="0"> diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt index 1273c699..04015cdc 100644 --- a/src/common/example/CMakeLists.txt +++ b/src/common/example/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Common_examples) add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp ) diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h index b83de2f5..cdf18cb2 100644 --- a/src/common/include/gudhi/Clock.h +++ b/src/common/include/gudhi/Clock.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/common/include/gudhi/Debug_utils.h b/src/common/include/gudhi/Debug_utils.h index 90d3cf47..3f5cb04f 100644 --- a/src/common/include/gudhi/Debug_utils.h +++ b/src/common/include/gudhi/Debug_utils.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/common/include/gudhi/Null_output_iterator.h b/src/common/include/gudhi/Null_output_iterator.h index 42e6e449..c700af5f 100644 --- a/src/common/include/gudhi/Null_output_iterator.h +++ b/src/common/include/gudhi/Null_output_iterator.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h index 32320e4d..024f0568 100644 --- a/src/common/include/gudhi/Off_reader.h +++ b/src/common/include/gudhi/Off_reader.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/common/include/gudhi/Point.h b/src/common/include/gudhi/Point.h index 0479e71e..345a8465 100644 --- a/src/common/include/gudhi/Point.h +++ b/src/common/include/gudhi/Point.h @@ -4,7 +4,7 @@ * * Author(s): David Salinas * - * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France) + * Copyright (C) 2014 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 diff --git a/src/common/include/gudhi/Points_3D_off_io.h b/src/common/include/gudhi/Points_3D_off_io.h index b0d24998..704f73a7 100644 --- a/src/common/include/gudhi/Points_3D_off_io.h +++ b/src/common/include/gudhi/Points_3D_off_io.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA Saclay (France) + * 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 diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h index 08f324c6..38029658 100644 --- a/src/common/include/gudhi/Points_off_io.h +++ b/src/common/include/gudhi/Points_off_io.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 INRIA Saclay (France) + * 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 diff --git a/src/common/include/gudhi/Simple_object_pool.h b/src/common/include/gudhi/Simple_object_pool.h index fb9c8e23..47283521 100644 --- a/src/common/include/gudhi/Simple_object_pool.h +++ b/src/common/include/gudhi/Simple_object_pool.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile de France + * 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 diff --git a/src/common/include/gudhi/Unitary_tests_utils.h b/src/common/include/gudhi/Unitary_tests_utils.h index 8394a062..e07c8d42 100644 --- a/src/common/include/gudhi/Unitary_tests_utils.h +++ b/src/common/include/gudhi/Unitary_tests_utils.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/common/include/gudhi/allocator.h b/src/common/include/gudhi/allocator.h index 4ede14e4..3de16a49 100644 --- a/src/common/include/gudhi/allocator.h +++ b/src/common/include/gudhi/allocator.h @@ -4,7 +4,7 @@ * * Author(s): Marc Glisse * - * Copyright (C) 2015 INRIA Saclay - Ile de France + * 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 diff --git a/src/common/include/gudhi/console_color.h b/src/common/include/gudhi/console_color.h index c4671da3..a493e0d0 100644 --- a/src/common/include/gudhi/console_color.h +++ b/src/common/include/gudhi/console_color.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA Sophia-Antipolis (France) + * 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 diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h index 3a5d1fd5..4dfba1bf 100644 --- a/src/common/include/gudhi/distance_functions.h +++ b/src/common/include/gudhi/distance_functions.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -25,7 +25,10 @@ #include <gudhi/Debug_utils.h> +#include <gudhi/Miniball.hpp> + #include <boost/range/metafunctions.hpp> +#include <boost/range/size.hpp> #include <cmath> // for std::sqrt #include <type_traits> // for std::decay @@ -68,6 +71,53 @@ class Euclidean_distance { } }; +/** @brief Compute the radius of the minimal enclosing ball between Points given by a range of coordinates. + * The points are assumed to have the same dimension. */ +class Minimal_enclosing_ball_radius { + public: + /** \brief Minimal_enclosing_ball_radius from two points. + * + * @param[in] point_1 First point. + * @param[in] point_2 second point. + * @return The minimal enclosing ball radius for the two points (aka. Euclidean distance / 2.). + * + * \tparam Point must be a range of Cartesian coordinates. + * + */ + template< typename Point > + typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type + operator()(const Point& point_1, const Point& point_2) const { + return Euclidean_distance()(point_1, point_2) / 2.; + } + /** \brief Minimal_enclosing_ball_radius from a point cloud. + * + * @param[in] point_cloud The points. + * @return The minimal enclosing ball radius for the points. + * + * \tparam Point_cloud must be a range of points with Cartesian coordinates. + * Point_cloud is a range over a range of Coordinate. + * + */ + template< typename Point_cloud, + typename Point_iterator = typename boost::range_const_iterator<Point_cloud>::type, + typename Point= typename std::iterator_traits<Point_iterator>::value_type, + typename Coordinate_iterator = typename boost::range_const_iterator<Point>::type, + typename Coordinate = typename std::iterator_traits<Coordinate_iterator>::value_type> + Coordinate + operator()(const Point_cloud& point_cloud) const { + using Min_sphere = Miniball::Miniball<Miniball::CoordAccessor<Point_iterator, Coordinate_iterator>>; + + Min_sphere ms(boost::size(*point_cloud.begin()), point_cloud.begin(),point_cloud.end()); +#ifdef DEBUG_TRACES + std::cout << "Minimal_enclosing_ball_radius = " << std::sqrt(ms.squared_radius()) << " | nb points = " + << boost::size(point_cloud) << " | dimension = " + << boost::size(*point_cloud.begin()) << std::endl; +#endif // DEBUG_TRACES + + return std::sqrt(ms.squared_radius()); + } +}; + } // namespace Gudhi #endif // DISTANCE_FUNCTIONS_H_ diff --git a/src/common/include/gudhi/graph_simplicial_complex.h b/src/common/include/gudhi/graph_simplicial_complex.h index d84421b2..49fe56cc 100644 --- a/src/common/include/gudhi/graph_simplicial_complex.h +++ b/src/common/include/gudhi/graph_simplicial_complex.h @@ -4,7 +4,7 @@ * * Author(s): Clément Maria * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 @@ -42,6 +42,12 @@ struct vertex_filtration_t { typedef boost::vertex_property_tag kind; }; +/** \brief Proximity_graph contains the vertices and edges with their filtration values in order to store the result + * of `Gudhi::compute_proximity_graph` function. + * + * \tparam SimplicialComplexForProximityGraph furnishes `Filtration_value` type definition. + * + */ template <typename SimplicialComplexForProximityGraph> using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS , boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > diff --git a/src/common/include/gudhi/random_point_generators.h b/src/common/include/gudhi/random_point_generators.h index 9df77760..1f8f2cd8 100644 --- a/src/common/include/gudhi/random_point_generators.h +++ b/src/common/include/gudhi/random_point_generators.h @@ -4,7 +4,7 @@ * * Author(s): Clement Jamin * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h index 90be4fc7..26eeb76d 100644 --- a/src/common/include/gudhi/reader_utils.h +++ b/src/common/include/gudhi/reader_utils.h @@ -4,7 +4,7 @@ * * Author(s): Clement Maria, Pawel Dlotko, Clement Jamin * - * Copyright (C) 2014 INRIA + * Copyright (C) 2014 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 diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt index de3e765a..0b49fa1e 100644 --- a/src/common/test/CMakeLists.txt +++ b/src/common/test/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(Common_tests) include(GUDHI_test_coverage) diff --git a/src/common/test/test_distance_matrix_reader.cpp b/src/common/test/test_distance_matrix_reader.cpp index 656e6f2e..6fee86e2 100644 --- a/src/common/test/test_distance_matrix_reader.cpp +++ b/src/common/test/test_distance_matrix_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/common/test/test_persistence_intervals_reader.cpp b/src/common/test/test_persistence_intervals_reader.cpp index be299376..b7ece9bd 100644 --- a/src/common/test/test_persistence_intervals_reader.cpp +++ b/src/common/test/test_persistence_intervals_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp index 0a78d190..ba3bab71 100644 --- a/src/common/test/test_points_off_reader.cpp +++ b/src/common/test/test_points_off_reader.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2015 + * 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 diff --git a/src/common/utilities/CMakeLists.txt b/src/common/utilities/CMakeLists.txt index b3e4b436..7f1d1cd7 100644 --- a/src/common/utilities/CMakeLists.txt +++ b/src/common/utilities/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.6) project(off_file_from_shape_generator) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/common/utilities/off_file_from_shape_generator.cpp b/src/common/utilities/off_file_from_shape_generator.cpp index afcd558c..5e3da7f7 100644 --- a/src/common/utilities/off_file_from_shape_generator.cpp +++ b/src/common/utilities/off_file_from_shape_generator.cpp @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2014 INRIA Saclay (France) + * Copyright (C) 2014 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 diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt index f9721b46..158c7561 100644 --- a/src/cython/CMakeLists.txt +++ b/src/cython/CMakeLists.txt @@ -1,4 +1,3 @@ -cmake_minimum_required(VERSION 2.8) project(Cython) include(CheckCXXSourceCompiles) @@ -100,12 +99,11 @@ if(CYTHON_FOUND) add_gudhi_cython_lib(${Boost_THREAD_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ") endif() - # Add CGAL compilation args if(CGAL_HEADER_ONLY) set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ") else(CGAL_HEADER_ONLY) - add_gudhi_cython_lib(${CGAL_LIBRARIES}) + add_gudhi_cython_lib(${CGAL_LIBRARY}) set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ") # If CGAL is not header only, CGAL library may link with boost system, add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY}) diff --git a/src/cython/cython/alpha_complex.pyx b/src/cython/cython/alpha_complex.pyx index a0e8f9b7..4f772e31 100644 --- a/src/cython/cython/alpha_complex.pyx +++ b/src/cython/cython/alpha_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Alpha_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/bottleneck_distance.pyx b/src/cython/cython/bottleneck_distance.pyx index 9fb377ff..76ef81f4 100644 --- a/src/cython/cython/bottleneck_distance.pyx +++ b/src/cython/cython/bottleneck_distance.pyx @@ -9,7 +9,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Bottleneck_distance_interface.h" namespace "Gudhi::persistence_diagram": diff --git a/src/cython/cython/cubical_complex.pyx b/src/cython/cython/cubical_complex.pyx index ffc85130..a98a3ec3 100644 --- a/src/cython/cython/cubical_complex.pyx +++ b/src/cython/cython/cubical_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/euclidean_strong_witness_complex.pyx b/src/cython/cython/euclidean_strong_witness_complex.pyx index c1523892..62b7cf71 100644 --- a/src/cython/cython/euclidean_strong_witness_complex.pyx +++ b/src/cython/cython/euclidean_strong_witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Euclidean_strong_witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/euclidean_witness_complex.pyx b/src/cython/cython/euclidean_witness_complex.pyx index 7c443b6b..c10ca73d 100644 --- a/src/cython/cython/euclidean_witness_complex.pyx +++ b/src/cython/cython/euclidean_witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Euclidean_witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/off_reader.pyx b/src/cython/cython/off_reader.pyx index 266dae2c..b939013f 100644 --- a/src/cython/cython/off_reader.pyx +++ b/src/cython/cython/off_reader.pyx @@ -9,7 +9,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Off_reader_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/periodic_cubical_complex.pyx b/src/cython/cython/periodic_cubical_complex.pyx index 3025f125..c25b83e9 100644 --- a/src/cython/cython/periodic_cubical_complex.pyx +++ b/src/cython/cython/periodic_cubical_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Cubical_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 4629018c..216ab8d6 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -9,7 +9,7 @@ import os Author(s): Vincent Rouvreau, Bertrand Michel - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import os """ __author__ = "Vincent Rouvreau, Bertrand Michel" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" def __min_birth_max_death(persistence, band=0.): diff --git a/src/cython/cython/reader_utils.pyx b/src/cython/cython/reader_utils.pyx index 3a17c5a0..e4572db0 100644 --- a/src/cython/cython/reader_utils.pyx +++ b/src/cython/cython/reader_utils.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2017 INRIA + Copyright (C) 2017 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 @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" cdef extern from "Reader_utils_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/rips_complex.pyx b/src/cython/cython/rips_complex.pyx index 73b154b8..59c16bff 100644 --- a/src/cython/cython/rips_complex.pyx +++ b/src/cython/cython/rips_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Rips_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx index 667fd40b..e302486b 100644 --- a/src/cython/cython/simplex_tree.pyx +++ b/src/cython/cython/simplex_tree.pyx @@ -10,7 +10,7 @@ from libcpp.string cimport string Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -27,7 +27,7 @@ from libcpp.string cimport string """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Simplex_tree_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/strong_witness_complex.pyx b/src/cython/cython/strong_witness_complex.pyx index 770b46f5..74c5cb05 100644 --- a/src/cython/cython/strong_witness_complex.pyx +++ b/src/cython/cython/strong_witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Strong_witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/subsampling.pyx b/src/cython/cython/subsampling.pyx index 894a4fbe..ac09b7a3 100644 --- a/src/cython/cython/subsampling.pyx +++ b/src/cython/cython/subsampling.pyx @@ -10,7 +10,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -27,7 +27,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Subsampling_interface.h" namespace "Gudhi::subsampling": diff --git a/src/cython/cython/tangential_complex.pyx b/src/cython/cython/tangential_complex.pyx index 44a3a96a..4bb07076 100644 --- a/src/cython/cython/tangential_complex.pyx +++ b/src/cython/cython/tangential_complex.pyx @@ -11,7 +11,7 @@ import os Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -28,7 +28,7 @@ import os """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Tangential_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/cython/witness_complex.pyx b/src/cython/cython/witness_complex.pyx index 96d122bb..8591465a 100644 --- a/src/cython/cython/witness_complex.pyx +++ b/src/cython/cython/witness_complex.pyx @@ -8,7 +8,7 @@ from libcpp.utility cimport pair Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ from libcpp.utility cimport pair """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" cdef extern from "Witness_complex_interface.h" namespace "Gudhi": diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst index 28d9dba2..b0bc5f38 100644 --- a/src/cython/doc/installation.rst +++ b/src/cython/doc/installation.rst @@ -3,10 +3,10 @@ Installation Compiling ********* - -The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with -version 1.48.0 or more recent. It is a multi-platform library and compiles on -Linux, Mac OSX and Visual Studio 2015. +The library uses c++11 and requires `Boost <https://www.boost.org/>`_ ≥ 1.48.0 +and `CMake <https://www.cmake.org/>`_ ≥ 3.1. +It is a multi-platform library and compiles on Linux, Mac OSX and Visual +Studio 2015. It also requires cmake to generate makefiles, and cython to compile the library. diff --git a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py index 10d4867a..4abe22d4 100755 --- a/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/alpha_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='AlphaComplex creation from ' diff --git a/src/cython/example/alpha_complex_from_points_example.py b/src/cython/example/alpha_complex_from_points_example.py index 7d6278ce..ad73c744 100755 --- a/src/cython/example/alpha_complex_from_points_example.py +++ b/src/cython/example/alpha_complex_from_points_example.py @@ -8,7 +8,7 @@ from gudhi import AlphaComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ from gudhi import AlphaComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py index 386f8457..b51fa7a8 100755 --- a/src/cython/example/alpha_rips_persistence_bottleneck_distance.py +++ b/src/cython/example/alpha_rips_persistence_bottleneck_distance.py @@ -10,7 +10,7 @@ import math Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -27,7 +27,7 @@ import math """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='AlphaComplex and RipsComplex ' diff --git a/src/cython/example/bottleneck_basic_example.py b/src/cython/example/bottleneck_basic_example.py index a7fa01c1..287956e7 100755 --- a/src/cython/example/bottleneck_basic_example.py +++ b/src/cython/example/bottleneck_basic_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Francois Godi, Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Francois Godi, Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]] diff --git a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py index 28a8599c..3b29781f 100755 --- a/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='EuclideanStrongWitnessComplex creation from ' diff --git a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py index b19d7d8c..db34962d 100755 --- a/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='EuclideanWitnessComplex creation from ' diff --git a/src/cython/example/gudhi_graphical_tools_example.py b/src/cython/example/gudhi_graphical_tools_example.py index d21d44c2..ac3d146c 100755 --- a/src/cython/example/gudhi_graphical_tools_example.py +++ b/src/cython/example/gudhi_graphical_tools_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py index 00334121..5f968bf1 100755 --- a/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py +++ b/src/cython/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" def is_file_perseus(file): diff --git a/src/cython/example/random_cubical_complex_persistence_example.py b/src/cython/example/random_cubical_complex_persistence_example.py index c832d6bf..80ff2452 100755 --- a/src/cython/example/random_cubical_complex_persistence_example.py +++ b/src/cython/example/random_cubical_complex_persistence_example.py @@ -13,7 +13,7 @@ import operator Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -30,7 +30,7 @@ import operator """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='Random cubical complex.', diff --git a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py index 0af4397a..0c9dfc43 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_correlation_matrix_file_example.py @@ -10,7 +10,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2017 INRIA + Copyright (C) 2017 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 @@ -27,7 +27,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py index 266c09ca..4d2ed577 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' diff --git a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py index fede920c..d15d5eb0 100755 --- a/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py +++ b/src/cython/example/rips_complex_diagram_persistence_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='RipsComplex creation from ' diff --git a/src/cython/example/rips_complex_from_points_example.py b/src/cython/example/rips_complex_from_points_example.py index 5d411b1a..ffa9d91f 100755 --- a/src/cython/example/rips_complex_from_points_example.py +++ b/src/cython/example/rips_complex_from_points_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/rips_persistence_diagram.py b/src/cython/example/rips_persistence_diagram.py index 9bfea41c..7a6a9f46 100755 --- a/src/cython/example/rips_persistence_diagram.py +++ b/src/cython/example/rips_persistence_diagram.py @@ -8,7 +8,7 @@ import gudhi Author(s): Marc Glisse - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Marc Glisse" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py index 51a60e73..28679015 100755 --- a/src/cython/example/simplex_tree_example.py +++ b/src/cython/example/simplex_tree_example.py @@ -8,7 +8,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py index 1f562b5c..0f8f5e80 100755 --- a/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py +++ b/src/cython/example/tangential_complex_plain_homology_from_off_file_example.py @@ -9,7 +9,7 @@ import argparse Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -26,7 +26,7 @@ import argparse """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" parser = argparse.ArgumentParser(description='TangentialComplex creation from ' diff --git a/src/cython/example/witness_complex_from_nearest_landmark_table.py b/src/cython/example/witness_complex_from_nearest_landmark_table.py index 92ed970b..e6b295ee 100755 --- a/src/cython/example/witness_complex_from_nearest_landmark_table.py +++ b/src/cython/example/witness_complex_from_nearest_landmark_table.py @@ -8,7 +8,7 @@ from gudhi import StrongWitnessComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -25,7 +25,7 @@ from gudhi import StrongWitnessComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" print("#####################################################################") diff --git a/src/cython/gudhi.pyx.in b/src/cython/gudhi.pyx.in index a8dd9f80..b94f2251 100644 --- a/src/cython/gudhi.pyx.in +++ b/src/cython/gudhi.pyx.in @@ -4,7 +4,7 @@ Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -21,7 +21,7 @@ """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" __version__ = "@GUDHI_VERSION@" # This variable is used by doctest to find files diff --git a/src/cython/include/Alpha_complex_interface.h b/src/cython/include/Alpha_complex_interface.h index d47db71f..8cf527fc 100644 --- a/src/cython/include/Alpha_complex_interface.h +++ b/src/cython/include/Alpha_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Bottleneck_distance_interface.h b/src/cython/include/Bottleneck_distance_interface.h index d5fbf6ea..5ad9d77d 100644 --- a/src/cython/include/Bottleneck_distance_interface.h +++ b/src/cython/include/Bottleneck_distance_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Cubical_complex_interface.h b/src/cython/include/Cubical_complex_interface.h index fad92c2c..85b717b3 100644 --- a/src/cython/include/Cubical_complex_interface.h +++ b/src/cython/include/Cubical_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Euclidean_strong_witness_complex_interface.h b/src/cython/include/Euclidean_strong_witness_complex_interface.h index b9dd8177..d86355d6 100644 --- a/src/cython/include/Euclidean_strong_witness_complex_interface.h +++ b/src/cython/include/Euclidean_strong_witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Euclidean_witness_complex_interface.h b/src/cython/include/Euclidean_witness_complex_interface.h index 2a09b3b5..dc303533 100644 --- a/src/cython/include/Euclidean_witness_complex_interface.h +++ b/src/cython/include/Euclidean_witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Off_reader_interface.h b/src/cython/include/Off_reader_interface.h index 0ca55500..f6b14f38 100644 --- a/src/cython/include/Off_reader_interface.h +++ b/src/cython/include/Off_reader_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Persistent_cohomology_interface.h b/src/cython/include/Persistent_cohomology_interface.h index e8889444..dee5e487 100644 --- a/src/cython/include/Persistent_cohomology_interface.h +++ b/src/cython/include/Persistent_cohomology_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Reader_utils_interface.h b/src/cython/include/Reader_utils_interface.h index 8ec34f61..5f7527d9 100644 --- a/src/cython/include/Reader_utils_interface.h +++ b/src/cython/include/Reader_utils_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2017 INRIA + * Copyright (C) 2017 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 diff --git a/src/cython/include/Rips_complex_interface.h b/src/cython/include/Rips_complex_interface.h index f26befbc..8b6c9c35 100644 --- a/src/cython/include/Rips_complex_interface.h +++ b/src/cython/include/Rips_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Simplex_tree_interface.h b/src/cython/include/Simplex_tree_interface.h index 54a4f824..3481eeff 100644 --- a/src/cython/include/Simplex_tree_interface.h +++ b/src/cython/include/Simplex_tree_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Strong_witness_complex_interface.h b/src/cython/include/Strong_witness_complex_interface.h index d05eaac5..3c72c916 100644 --- a/src/cython/include/Strong_witness_complex_interface.h +++ b/src/cython/include/Strong_witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Subsampling_interface.h b/src/cython/include/Subsampling_interface.h index b0f4a50a..f990da0c 100644 --- a/src/cython/include/Subsampling_interface.h +++ b/src/cython/include/Subsampling_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h index aef50424..71418886 100644 --- a/src/cython/include/Tangential_complex_interface.h +++ b/src/cython/include/Tangential_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/include/Witness_complex_interface.h b/src/cython/include/Witness_complex_interface.h index 6501cc35..01b372e7 100644 --- a/src/cython/include/Witness_complex_interface.h +++ b/src/cython/include/Witness_complex_interface.h @@ -4,7 +4,7 @@ * * Author(s): Vincent Rouvreau * - * Copyright (C) 2016 INRIA + * 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 diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in index eda1ee04..a798717d 100644 --- a/src/cython/setup.py.in +++ b/src/cython/setup.py.in @@ -7,7 +7,7 @@ from Cython.Build import cythonize Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -24,7 +24,7 @@ from Cython.Build import cythonize """ __author__ = "GUDHI Editorial Board" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" gudhi = Extension( diff --git a/src/cython/test/test_alpha_complex.py b/src/cython/test/test_alpha_complex.py index 2c76d9d7..e97f2530 100755 --- a/src/cython/test/test_alpha_complex.py +++ b/src/cython/test/test_alpha_complex.py @@ -6,7 +6,7 @@ from gudhi import AlphaComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ from gudhi import AlphaComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_bottleneck_distance.py b/src/cython/test/test_bottleneck_distance.py index 3d982d34..4eb5848f 100755 --- a/src/cython/test/test_bottleneck_distance.py +++ b/src/cython/test/test_bottleneck_distance.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py index 0e81554d..92e591e9 100755 --- a/src/cython/test/test_cubical_complex.py +++ b/src/cython/test/test_cubical_complex.py @@ -6,7 +6,7 @@ from gudhi import CubicalComplex Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ from gudhi import CubicalComplex """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" @@ -72,6 +72,17 @@ def test_dimension_simple_constructor(): assert cub.betti_numbers() == [1, 0, 0] assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0] +def test_user_case_simple_constructor(): + cub = CubicalComplex(dimensions=[3, 3], + top_dimensional_cells = [float('inf'), 0.,0.,0.,1.,0.,0.,0.,0.]) + assert cub.__is_defined() == True + assert cub.__is_persistence_defined() == False + assert cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))] + assert cub.__is_persistence_defined() == True + other_cub = CubicalComplex(dimensions=[3, 3], + top_dimensional_cells = [1000., 0.,0.,0.,1.,0.,0.,0.,0.]) + assert other_cub.persistence() == [(1, (0.0, 1.0)), (0, (0.0, float('inf')))] + def test_dimension_file_constructor(): # Create test file test_file = open('CubicalOneSphere.txt', 'w') diff --git a/src/cython/test/test_euclidean_witness_complex.py b/src/cython/test/test_euclidean_witness_complex.py index 737f1ef4..2f77210a 100755 --- a/src/cython/test/test_euclidean_witness_complex.py +++ b/src/cython/test/test_euclidean_witness_complex.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_reader_utils.py b/src/cython/test/test_reader_utils.py index 25591fb3..b240c84f 100755 --- a/src/cython/test/test_reader_utils.py +++ b/src/cython/test/test_reader_utils.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2017 INRIA + Copyright (C) 2017 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 @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2017 INRIA" +__copyright__ = "Copyright (C) 2017 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_rips_complex.py b/src/cython/test/test_rips_complex.py index c7d2ead4..c37b5400 100755 --- a/src/cython/test/test_rips_complex.py +++ b/src/cython/test/test_rips_complex.py @@ -7,7 +7,7 @@ from math import sqrt Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -24,7 +24,7 @@ from math import sqrt """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py index bc16183a..cb701c9a 100755 --- a/src/cython/test/test_simplex_tree.py +++ b/src/cython/test/test_simplex_tree.py @@ -6,7 +6,7 @@ from gudhi import SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ from gudhi import SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_subsampling.py b/src/cython/test/test_subsampling.py index 2caf4ddb..96906a6f 100755 --- a/src/cython/test/test_subsampling.py +++ b/src/cython/test/test_subsampling.py @@ -6,7 +6,7 @@ import gudhi Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ import gudhi """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_tangential_complex.py b/src/cython/test/test_tangential_complex.py index ca9d936d..5385a0d3 100755 --- a/src/cython/test/test_tangential_complex.py +++ b/src/cython/test/test_tangential_complex.py @@ -6,7 +6,7 @@ from gudhi import TangentialComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ from gudhi import TangentialComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" diff --git a/src/cython/test/test_witness_complex.py b/src/cython/test/test_witness_complex.py index 7d1fb6be..bcbc521b 100755 --- a/src/cython/test/test_witness_complex.py +++ b/src/cython/test/test_witness_complex.py @@ -6,7 +6,7 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree Author(s): Vincent Rouvreau - Copyright (C) 2016 INRIA + 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 @@ -23,7 +23,7 @@ from gudhi import WitnessComplex, StrongWitnessComplex, SimplexTree """ __author__ = "Vincent Rouvreau" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" |
