diff options
4 files changed, 152 insertions, 13 deletions
diff --git a/src/Skeleton_blocker/example/CMakeLists.txt b/src/Skeleton_blocker/example/CMakeLists.txt index c8e976cd..d9eab4e1 100644 --- a/src/Skeleton_blocker/example/CMakeLists.txt +++ b/src/Skeleton_blocker/example/CMakeLists.txt @@ -1,7 +1,8 @@ cmake_minimum_required(VERSION 2.6) project(GUDHIskbl) + +add_executable(SkeletonBlockerFromSimplices Skeleton_blocker_from_simplices.cpp) + add_executable(SkeletonBlockerIteration Skeleton_blocker_iteration.cpp) target_link_libraries(SkeletonBlockerIteration ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY}) - -add_test(SkeletonBlockerIteration ${CMAKE_CURRENT_BINARY_DIR}/SkeletonBlockerIteration) diff --git a/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp new file mode 100644 index 00000000..db3a759c --- /dev/null +++ b/src/Skeleton_blocker/example/Skeleton_blocker_from_simplices.cpp @@ -0,0 +1,83 @@ + /* 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 Sophia Antipolis-Mediterranee (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 <stdio.h> +#include <stdlib.h> +#include <string> +#include <fstream> +#include <sstream> + + +#include "gudhi/Skeleton_blocker.h" + +using namespace std; +using namespace Gudhi; +using namespace skbl; + +typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> Complex; +typedef Complex::Vertex_handle Vertex_handle; +typedef Complex::Simplex_handle Simplex_handle; +typedef Complex::Simplex_handle Simplex; + +int main (int argc, char *argv[]){ + std::vector<Simplex_handle> simplices; + + //add 4 triangles of a tetrahedron 0123 + simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3))); + simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1))); + + Complex complex; + //get complex from top faces + make_complex_from_top_faces(complex,simplices.begin(),simplices.end()); + + std::cout << "Simplices:"<<std::endl; + for(const Simplex & s : complex.simplex_range()) + std::cout << s << " "; + std::cout << std::endl; + + //One blocker as simplex 0123 is not in the complex but all its proper faces are. + std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl; + + //now build a complex from its full list of simplices + simplices.clear(); + simplices.push_back(Simplex_handle(Vertex_handle(0))); + simplices.push_back(Simplex_handle(Vertex_handle(1))); + simplices.push_back(Simplex_handle(Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1))); + simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(2),Vertex_handle(0))); + complex = Complex(simplices.begin(),simplices.end()); + + std::cout << "Simplices:"<<std::endl; + for(const Simplex & s : complex.simplex_range()) + std::cout << s << " "; + std::cout << std::endl; + + //One blocker as simplex 012 is not in the complex but all its proper faces are. + std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl; + + return EXIT_SUCCESS; +} + diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h index 1d1a9bba..7057437c 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h @@ -116,7 +116,7 @@ You may want to use this visitor to compute statistics or to update another data \section Example -\subsection s Iterating through vertices, edges, blockers and simplices +\subsection Iterating Iterating through vertices, edges, blockers and simplices Iteration through vertices, edges, simplices or blockers is straightforward with c++11 for range loops. Note that simplex iteration with this implicit data-structure just takes @@ -177,8 +177,60 @@ The Euler Characteristic is 1 \endverbatim +\subsection s Constructing a skeleton-blockers from a list of maximal faces or from a list of faces -\subsection Acknowledgements + \code{.cpp} + std::vector<Simplex_handle> simplices; + + //add 4 triangles of a tetrahedron 0123 + simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1),Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2),Vertex_handle(3))); + simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(3),Vertex_handle(0),Vertex_handle(1))); + + Complex complex; + //get complex from top faces + make_complex_from_top_faces(complex,simplices.begin(),simplices.end()); + + std::cout << "Simplices:"<<std::endl; + for(const Simplex & s : complex.simplex_range()) + std::cout << s << " "; + std::cout << std::endl; + + //One blocker as simplex 0123 is not in the complex but all its proper faces are. + std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl; + + //now build a complex from its full list of simplices + simplices.clear(); + simplices.push_back(Simplex_handle(Vertex_handle(0))); + simplices.push_back(Simplex_handle(Vertex_handle(1))); + simplices.push_back(Simplex_handle(Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(0),Vertex_handle(1))); + simplices.push_back(Simplex_handle(Vertex_handle(1),Vertex_handle(2))); + simplices.push_back(Simplex_handle(Vertex_handle(2),Vertex_handle(0))); + complex = Complex(simplices.begin(),simplices.end()); + + std::cout << "Simplices:"<<std::endl; + for(const Simplex & s : complex.simplex_range()) + std::cout << s << " "; + std::cout << std::endl; + + //One blocker as simplex 012 is not in the complex but all its proper faces are. + std::cout << "Blockers: "<<complex.blockers_to_string()<<std::endl; + \endcode +\verbatim +./SkeletonBlockerFromSimplices +Simplices: +{0} {0,1} {0,2} {0,3} {0,1,2} {0,1,3} {0,2,3} {1} {1,2} {1,3} {1,2,3} {2} {2,3} {3} +Blockers: {0,1,2,3} + +Simplices: +{0} {0,1} {0,2} {1} {1,2} {2} +Blockers: {0,1,2} +\endverbatim + + +\section Acknowledgements The author wishes to thank Dominique Attali and André Lieutier for their collaboration to write the two initial papers \cite socg_blockers_2011,\cite blockers2012 diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h index a013ba52..865ff55a 100644 --- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h +++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h @@ -198,11 +198,14 @@ public: visitor(visitor_){ std::vector<std::pair<Vertex_handle,Vertex_handle>> edges; - //first pass add vertices and store edges + //first pass count vertices and store edges + int num_vertex = -1; for(auto s_it = simplex_begin; s_it != simplex_end; ++s_it){ - if(s_it->dimension()==0) add_vertex(); + if(s_it->dimension()==0) num_vertex = (std::max)(num_vertex,s_it->first_vertex().vertex); if(s_it->dimension()==1) edges.emplace_back(s_it->first_vertex(),s_it->last_vertex()); } + while(num_vertex-->=0) add_vertex(); + for(const auto& e : edges) add_edge(e.first,e.second); @@ -1213,7 +1216,7 @@ public: std::string vertices_to_string() const { std::ostringstream stream; for (auto vertex : vertex_range()) { - stream << "(" << (*this)[vertex].get_id() << "),"; + stream << "{" << (*this)[vertex].get_id() << "} "; } stream << std::endl; return stream.str(); @@ -1221,18 +1224,17 @@ public: std::string edges_to_string() const { std::ostringstream stream; - for (auto edge : edge_range()) { - stream << "(" << (*this)[edge].first() << "," << (*this)[edge].second() << ")" << " id = " << (*this)[edge].index() << std::endl; - } + for (auto edge : edge_range()) + stream << "{" << (*this)[edge].first() << "," << (*this)[edge].second() << "} "; stream << std::endl; return stream.str(); } std::string blockers_to_string() const { std::ostringstream stream; - for (auto bl : blocker_map_) { - stream << bl.first << " => " << bl.second << ":" << *bl.second << std::endl; - } + + for(auto b : const_blocker_range()) + stream<<*b<<std::endl; return stream.str(); } @@ -1254,6 +1256,7 @@ unsigned make_complex_from_top_faces(Complex& complex,SimplexHandleIterator begi auto subfaces_topface = subfaces(*top_face); simplices.insert(simplices.end(),subfaces_topface.begin(),subfaces_topface.end()); } + complex = Complex(simplices.begin(),simplices.end()); return simplices.size(); } |