diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-09-27 08:53:57 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-09-27 08:53:57 +0000 |
commit | 7a701f8a2326268b2aadb369fbc0848b227078a1 (patch) | |
tree | f5d17d492a5e5e1a61c6eae785beee08506e0637 | |
parent | 2f0d4a7a06f8fde904b75b27c3836e362f549707 (diff) |
Fix naming conventions and cpplint
Add Bottleneck_distance to GUDHI_MODULES in GUDHI_user_version_target.txt
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1569 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: b96a2be25477ddf227e43d9941989f93a0f626bb
12 files changed, 74 insertions, 43 deletions
diff --git a/src/Bottleneck_distance/concept/Persistence_diagram.h b/src/Bottleneck_distance/concept/Persistence_diagram.h index bd90cc11..4c69343c 100644 --- a/src/Bottleneck_distance/concept/Persistence_diagram.h +++ b/src/Bottleneck_distance/concept/Persistence_diagram.h @@ -1,6 +1,31 @@ +/* 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): François Godi + * + * Copyright (C) 2016 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#ifndef CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ +#define CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ + namespace Gudhi { -namespace Bottleneck_distance { -namespace Concept { + +namespace bottleneck_distance { /** \brief Concept of persistence diagram point. The double first is the birth of the component and the double second is the death of the component. * @@ -21,6 +46,8 @@ struct Persistence_Diagram const_iterator<Diagram_point> cend() const; }; -} //namespace Concept -} //namespace Bottleneck_distance -} //namespace Gudhi +} // namespace bottleneck_distance + +} // namespace Gudhi + +#endif // CONCEPT_BOTTLENECK_DISTANCE_PERSISTENCE_DIAGRAM_H_ diff --git a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h index 2cf10975..9a792048 100644 --- a/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h +++ b/src/Bottleneck_distance/doc/Intro_bottleneck_distance.h @@ -26,15 +26,20 @@ // needs namespace for Doxygen to link on classes namespace Gudhi { // needs namespace for Doxygen to link on classes -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \defgroup bottleneck_distance Bottleneck distance * * \author François Godi + * @{ * + * \section bottleneckdefinition Definition + * + * Bottleneck distance is blablabla... */ +/** @} */ // end defgroup bottleneck_distance -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi diff --git a/src/Bottleneck_distance/example/bottleneck_example.cpp b/src/Bottleneck_distance/example/bottleneck_example.cpp index 472c5c84..0bec9746 100644 --- a/src/Bottleneck_distance/example/bottleneck_example.cpp +++ b/src/Bottleneck_distance/example/bottleneck_example.cpp @@ -28,12 +28,9 @@ #include <sstream> #include <string> -using namespace std; - -//PD: I am using this type of procedures a lot in Gudhi stat. We should make one for all at some point. std::vector< std::pair<double, double> > read_diagram_from_file( const char* filename ) { - ifstream in; + std::ifstream in; in.open( filename ); std::vector< std::pair<double, double> > result; if ( !in.is_open() ) @@ -58,13 +55,15 @@ std::vector< std::pair<double, double> > read_diagram_from_file( const char* fil } in.close(); return result; -}//read_diagram_from_file +} //read_diagram_from_file int main( int argc , char** argv ) { if ( argc < 3 ) { - std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck distance (set by default to zero). The program will now terminate \n"; + std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " << + "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" << + " distance (set by default to zero). The program will now terminate \n"; } std::vector< std::pair< double , double > > diag1 = read_diagram_from_file( argv[1] ); std::vector< std::pair< double , double > > diag2 = read_diagram_from_file( argv[2] ); @@ -73,6 +72,6 @@ int main( int argc , char** argv ) { tolerance = atof( argv[3] ); } - double b = Gudhi::Bottleneck_distance::compute(diag1, diag2, tolerance); + double b = Gudhi::bottleneck_distance::compute(diag1, diag2, tolerance); std::cout << "The distance between the diagrams is : " << b << ". The tolerace is : " << tolerance << std::endl; } diff --git a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h index 21be0bc7..91632149 100644 --- a/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h +++ b/src/Bottleneck_distance/include/gudhi/CGAL/Miscellaneous.h @@ -27,7 +27,7 @@ namespace CGAL { -typedef Gudhi::Bottleneck_distance::Internal_point Internal_point; +typedef Gudhi::bottleneck_distance::Internal_point Internal_point; template <> struct Kernel_traits<Internal_point> { diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h index 7a8c8ee0..5f579a0c 100644 --- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h +++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#ifndef GRAPH_MATCHING_H_ +#define GRAPH_MATCHING_H_ #include <deque> @@ -29,7 +29,7 @@ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams. You get an additive e-approximation. * @@ -238,11 +238,11 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_ +#endif // GRAPH_MATCHING_H_ /* Dichotomic version template<typename Persistence_diagram1, typename Persistence_diagram2> diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h index 2080900d..f05d5fc9 100644 --- a/src/Bottleneck_distance/include/gudhi/Internal_point.h +++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h @@ -20,12 +20,12 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ +#ifndef INTERNAL_POINT_H_ +#define INTERNAL_POINT_H_ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \internal \brief Returns the used index for encoding none of the points */ int null_point_index(); @@ -67,8 +67,8 @@ inline int null_point_index() { return -1; } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_INTERNAL_POINT_H_ +#endif // INTERNAL_POINT_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h index 7ad79126..1bd5879c 100644 --- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h @@ -20,15 +20,15 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#ifndef NEIGHBORS_FINDER_H_ +#define NEIGHBORS_FINDER_H_ #include <unordered_set> #include <gudhi/Planar_neighbors_finder.h> namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U * (which can be a projection). @@ -147,8 +147,8 @@ inline int Layered_neighbors_finder::vlayers_number() const { return static_cast<int>(neighbors_finder.size()); } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_ +#endif // NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h index e31b2dae..1f6d6683 100644 --- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h +++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#ifndef PERSISTENCE_DIAGRAMS_GRAPH_H_ +#define PERSISTENCE_DIAGRAMS_GRAPH_H_ #include <vector> #include <set> @@ -34,7 +34,7 @@ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \internal \brief Structure representing an euclidean bipartite graph containing @@ -162,8 +162,8 @@ inline double G::diameter() { return max; } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_ +#endif // PERSISTENCE_DIAGRAMS_GRAPH_H_ diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h index 30f7dc3c..bf70ed0b 100644 --- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h +++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h @@ -20,8 +20,8 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ -#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ +#ifndef PLANAR_NEIGHBORS_FINDER_H_ +#define PLANAR_NEIGHBORS_FINDER_H_ #include <list> #include <map> @@ -40,7 +40,7 @@ namespace Gudhi { -namespace Bottleneck_distance { +namespace bottleneck_distance { /** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U. * @@ -217,8 +217,8 @@ inline std::shared_ptr< std::list<int> > Cgal_pnf::pull_all_near(int u_point_ind } -} // namespace Bottleneck_distance +} // namespace bottleneck_distance } // namespace Gudhi -#endif // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_ +#endif // PLANAR_NEIGHBORS_FINDER_H_ diff --git a/src/Bottleneck_distance/test/bottleneck_chrono.cpp b/src/Bottleneck_distance/test/bottleneck_chrono.cpp index 8b49b6be..8b143b18 100644 --- a/src/Bottleneck_distance/test/bottleneck_chrono.cpp +++ b/src/Bottleneck_distance/test/bottleneck_chrono.cpp @@ -24,7 +24,7 @@ #include <chrono> #include <fstream> -using namespace Gudhi::Bottleneck_distance; +using namespace Gudhi::bottleneck_distance; double upper_bound = 400.; // any real >0 diff --git a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp index d5b71156..d2331c5d 100644 --- a/src/Bottleneck_distance/test/bottleneck_unit_test.cpp +++ b/src/Bottleneck_distance/test/bottleneck_unit_test.cpp @@ -27,7 +27,7 @@ #include <random> #include <gudhi/Graph_matching.h> -using namespace Gudhi::Bottleneck_distance; +using namespace Gudhi::bottleneck_distance; int n1 = 81; // a natural number >0 int n2 = 180; // a natural number >0 diff --git a/src/cmake/modules/GUDHI_user_version_target.txt b/src/cmake/modules/GUDHI_user_version_target.txt index 805f0a83..de16ef4c 100644 --- a/src/cmake/modules/GUDHI_user_version_target.txt +++ b/src/cmake/modules/GUDHI_user_version_target.txt @@ -48,7 +48,7 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11) add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI) - set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex") + set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Simplex_tree;Skeleton_blocker;Witness_complex") foreach(GUDHI_MODULE ${GUDHI_MODULES}) # doc files |