skbl add an example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@450 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1a0efe7084ccff068823a4ab33bd3ec8522349ed

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();
 }