test is manifold

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@437 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: a515b3216d21c8a5736744842fdcf09644f5c7b1

7 files changed, 316 insertions, 11 deletions

diff --git a/src/GudhUI/gui/MainWindow.cpp b/src/GudhUI/gui/MainWindow.cpp
index f5abfffc..e41b15ba 100644
--- a/src/GudhUI/gui/MainWindow.cpp
+++ b/src/GudhUI/gui/MainWindow.cpp
@@ -98,6 +98,9 @@ MainWindow::connectActions(){
 				SLOT(persistence_menu()));
 	QObject::connect(this->actionEstimate_topological_changes, SIGNAL(triggered()), this,
 				SLOT(critical_points_menu()));
+	QObject::connect(this->actionIs_manifold, SIGNAL(triggered()), this,
+				SLOT(is_manifold_menu()));
+
 
 	QObject::connect(this, SIGNAL(sceneChanged()), this->viewer_instructor_,
 			SLOT(sceneChanged()));
@@ -223,8 +226,7 @@ MainWindow::contract_edges(unsigned num_collapses){
 
 void
 MainWindow::collapse_edges(){
-	std::cerr <<"Collapse "<<100<< " edges\n";
-	model_.collapse_edges(100);
+	model_.collapse_edges(model_.num_edges());
 	update_view();
 }
 
@@ -287,5 +289,10 @@ MainWindow::critical_points_menu(){
 		model_.show_critical_points(max_length);
 }
 
+void
+MainWindow::is_manifold_menu(){
+	model_.show_is_manifold();
+}
+
 
 #include "MainWindow.moc"
diff --git a/src/GudhUI/gui/MainWindow.h b/src/GudhUI/gui/MainWindow.h
index 506a1f3a..587f1c6f 100644
--- a/src/GudhUI/gui/MainWindow.h
+++ b/src/GudhUI/gui/MainWindow.h
@@ -84,6 +84,7 @@ public:
 	void persistence_menu();
 	void compute_persistence(int p,double threshold,int max_dim,double min_pers);
 	void critical_points_menu();
+	void is_manifold_menu();
 
 
 public:
diff --git a/src/GudhUI/gui/main_window.ui b/src/GudhUI/gui/main_window.ui
index 8a7ad7da..312480b6 100644
--- a/src/GudhUI/gui/main_window.ui
+++ b/src/GudhUI/gui/main_window.ui
@@ -90,6 +90,7 @@
     <addaction name="actionShow_homology_group"/>
     <addaction name="actionPersistence"/>
     <addaction name="actionEstimate_topological_changes"/>
+    <addaction name="actionIs_manifold"/>
    </widget>
    <addaction name="menuFile"/>
    <addaction name="menuPoints"/>
@@ -236,6 +237,11 @@
     <bool>false</bool>
    </property>
   </action>
+  <action name="actionIs_manifold">
+   <property name="text">
+    <string>Is manifold</string>
+   </property>
+  </action>
  </widget>
  <customwidgets>
   <customwidget>
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 39bbd9d8..6ac971d0 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -20,6 +20,7 @@
 #include "utils/Edge_contractor.h"
 #include "utils/Persistence_compute.h"
 #include "utils/Critical_points.h"
+#include "utils/Is_manifold.h"
 
 #include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h"
 #include "gudhi/Skeleton_blocker_geometric_complex.h"
@@ -56,8 +57,9 @@ public:
 
 	void maximal_face(std::vector<int> vertices){
 		if (!load_only_points_){
-			for (int i = 0; i<vertices.size()-1 ; ++i)
-				for (int j = i+1; j<vertices.size()-1 ; ++j)
+			std::cout<<"size:"<<vertices.size()<<std::endl;
+			for (int i = 0; i<vertices.size() ; ++i)
+				for (int j = i+1; j<vertices.size() ; ++j)
 					complex_.add_edge(Vertex_handle(vertices[i]),Vertex_handle(vertices[j]));
 		}
 	}
@@ -80,23 +82,54 @@ public:
 	void off_file_open(const std::string& name_file){
 		UIDBGMSG("load off file",name_file);
 		complex_.clear();
-		CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_);
+		CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_,false);
 		Gudhi::read_off(name_file,read_wraper);
 	}
 
 	void off_points_open(const std::string& name_file){
 		UIDBGMSG("load off points",name_file);
 		complex_.clear();
-		CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_);
+		CGAL_geometric_flag_complex_wrapper<Complex> read_wraper(complex_,true);
 		Gudhi::read_off(name_file,read_wraper);
 	}
 
 	void off_file_save(const std::string& name_file){
 		UIDBG("save off file");
+		UIDBG("save off off_points_save");
+		std::ofstream file(name_file);
+		if(file.is_open()){
+			file<<"OFF\n";
+			file<<complex_.num_vertices()<<" "<<complex_.num_edges()<<" 0\n";
+			for(auto v : complex_.vertex_range()){
+				const auto& pt(complex_.point(v));
+				for(auto it = pt.cartesian_begin();it!=pt.cartesian_end();++it)
+					file<<*it<<" ";
+				file<<std::endl;
+			}
+			for(auto e : complex_.edge_range())
+				file<<"2 "<<complex_.first_vertex(e)<<" "<<complex_.second_vertex(e)<<"\n";
+			file.close();
+		}
+		else std::cerr << "Could not open file "<<name_file<<std::endl;
+
 	}
 
 	void off_points_save(const std::string& name_file){
 		UIDBG("save off off_points_save");
+		std::ofstream file(name_file);
+		if(file.is_open()){
+			file<<"OFF\n";
+			file<<complex_.num_vertices()<<" 0 0\n";
+			for(auto v : complex_.vertex_range()){
+				const auto& pt(complex_.point(v));
+				for(auto it = pt.cartesian_begin();it!=pt.cartesian_end();++it)
+					file<<*it<<" ";
+				file<<std::endl;
+			}
+			file.close();
+		}
+		else std::cerr << "Could not open file "<<name_file<<std::endl;
+
 	}
 
 	// point sets operations
@@ -160,7 +193,7 @@ public:
 	}
 
 	void collapse_edges(unsigned num_collapses){
-		Edge_collapsor<Complex> collapsor(complex_,complex_.num_edges());
+		Edge_collapsor<Complex> collapsor(complex_,num_collapses);
 	}
 
 
@@ -268,6 +301,17 @@ public:
 		Critical_points<Complex> critical_points(complex_,std::cout,max_distance);
 	}
 
+	void show_is_manifold(){
+		unsigned dim;
+		bool is_manifold;
+		Is_manifold<Complex> test_manifold(complex_,dim,is_manifold);
+
+		if(is_manifold) std::cout << "The complex is a "<<dim<<"-manifold\n";
+		else
+			if(dim<4) std::cout << "The complex has dimension greater than "<<dim<<" and is not a manifold\n";
+			else std::cout << "The complex has dimension>=4 and may or may not be a manifold\n";
+	}
+
 
 private:
 	void run_chomp(){
@@ -296,6 +340,11 @@ public:
 	unsigned num_vertices() const{
 		return  complex_.num_vertices();
 	}
+
+	unsigned num_edges() const{
+		return  complex_.num_edges();
+	}
+
 };
 
 #endif /* MODEL_H_ */
diff --git a/src/GudhUI/utils/Critical_points.h b/src/GudhUI/utils/Critical_points.h
new file mode 100644
index 00000000..92392d4a
--- /dev/null
+++ b/src/GudhUI/utils/Critical_points.h
@@ -0,0 +1,137 @@
+/*
+ * Critical_points.h
+ *  Created on: Jan 27, 2015
+ * 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-Méditerranée (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/>.
+ * 
+ */
+
+
+#ifndef CRITICAL_POINTS_H_
+#define CRITICAL_POINTS_H_
+
+#include <deque>
+#include "utils/Edge_contractor.h"
+
+/**
+ * Iteratively tries to anticollapse smallest edge non added so far.
+ * If its link is contractible then no topological change and else possible topological change.
+ *
+ * todo do a sparsification with some parameter eps while growing
+ */
+template<typename SkBlComplex> class Critical_points{
+private:
+	SkBlComplex filled_complex_;
+	const SkBlComplex& input_complex_;
+	double max_length_;
+	std::ostream& stream_;
+public:
+	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+	typedef typename SkBlComplex::Edge_handle Edge_handle;
+	typedef typename std::pair<Vertex_handle,Vertex_handle> Edge;
+
+	/**
+	 * @brief check all pair of points with length smaller than max_length
+	 */
+	Critical_points(const SkBlComplex& input_complex,std::ostream& stream,double max_length):
+		input_complex_(input_complex),max_length_(max_length),stream_(stream)
+	{
+
+		std::deque<Edge> edges;
+		auto vertices = input_complex.vertex_range();
+		for(auto p = vertices.begin(); p!= vertices.end(); ++p){
+			filled_complex_.add_vertex(input_complex.point(*p));
+			for (auto q = p; ++q != vertices.end(); /**/)
+				if (squared_eucl_distance(input_complex.point(*p),input_complex.point(*q)) < max_length_*max_length_)
+					edges.emplace_back(*p,*q);
+		}
+
+		std::sort(edges.begin(),edges.end(),
+				[&](Edge e1,Edge e2){
+			return squared_edge_length(e1) < squared_edge_length(e2);
+		});
+
+		anti_collapse_edges(edges);
+
+	}
+
+private:
+	double squared_eucl_distance(const Point& p1,const Point& p2) const{
+		return Geometry_trait::Squared_distance_d()(p1,p2);
+	}
+
+
+	void anti_collapse_edges(const std::deque<Edge>& edges){
+		unsigned pos = 0;
+		for(Edge e : edges){
+			std::cout<<"edge "<<pos++<<"/"<<edges.size()<<"\n";
+			auto eh = filled_complex_.add_edge(e.first,e.second);
+			int is_contractible(is_link_reducible(eh));
+
+			switch (is_contractible) {
+				case 0:
+					stream_<<"alpha="<<std::sqrt(squared_edge_length(e))<< " topological change"<<std::endl;
+					break;
+				case 2:
+					stream_<<"alpha="<<std::sqrt(squared_edge_length(e))<< " maybe a topological change"<<std::endl;
+					break;
+				default:
+					break;
+			}
+		}
+
+	}
+
+
+	//0 -> not
+	//1 -> yes
+	//2 -> maybe
+	int is_link_reducible(Edge_handle e){
+		auto link = filled_complex_.link(e);
+
+		if(link.empty()) return 0;
+
+		Edge_contractor<Complex> contractor(link,link.num_vertices()-1);
+
+		if(link.num_connected_components()>1) return 0; //one than more CC -> not contractible
+
+		if (link.num_vertices()==1) return 1; //reduced to one point -> contractible
+		else return 2; //we dont know
+	}
+
+
+	double squared_edge_length(Edge_handle e) const{
+		return squared_eucl_distance(input_complex_.point(input_complex_.first_vertex(e)),input_complex_.point(input_complex_.second_vertex(e)));
+	}
+
+	double squared_edge_length(Edge e) const{
+		return squared_eucl_distance(input_complex_.point(e.first),input_complex_.point(e.second));
+	}
+
+
+
+};
+
+
+
+
+
+#endif /* CRITICAL_POINTS_H_ */
diff --git a/src/GudhUI/utils/Edge_collapsor.h b/src/GudhUI/utils/Edge_collapsor.h
index 9cf880e0..4dcd18ac 100644
--- a/src/GudhUI/utils/Edge_collapsor.h
+++ b/src/GudhUI/utils/Edge_collapsor.h
@@ -10,6 +10,7 @@
 
 #include <list>
 #include "utils/Edge_contractor.h"
+#include "utils/UI_utils.h"
 
 /**
  * Iteratively puts every vertex at the center of its neighbors
@@ -23,8 +24,9 @@ public:
 	typedef typename SkBlComplex::Edge_handle Edge_handle;
 
 	/**
-	 * @brief Modify complex to be the expansion of the k-nearest neighbor
-	 * symetric graph.
+	 * @brief Collapse num_collapses edges. If num_collapses<0 then it collapses all possible edges.
+	 * Largest edges are collapsed first.
+	 *
 	 */
 	Edge_collapsor(SkBlComplex& complex,unsigned num_collapses):
 		complex_(complex),num_collapses_(num_collapses)
@@ -43,7 +45,6 @@ public:
 
 private:
 
-
 	void collapse_edges(std::list<Edge_handle>& edges){
 		while(!edges.empty() && num_collapses_--){
 			Edge_handle current_edge = edges.front();
@@ -63,7 +64,7 @@ private:
 
 		if(link.num_connected_components()>1) return false;
 
-		Edge_contractor<Complex> contractor(link,link.num_vertices()-1);
+		Edge_contractor<SkBlComplex> contractor(link,link.num_vertices()-1);
 
 		return (link.num_vertices()==1);
 	}
diff --git a/src/GudhUI/utils/Is_manifold.h b/src/GudhUI/utils/Is_manifold.h
new file mode 100644
index 00000000..e708a6a4
--- /dev/null
+++ b/src/GudhUI/utils/Is_manifold.h
@@ -0,0 +1,104 @@
+/*
+ * Is_manifold.h
+ *  Created on: Jan 28, 2015
+ * 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-Méditerranée (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/>.
+ * 
+ */
+
+
+#ifndef IS_MANIFOLD_H_
+#define IS_MANIFOLD_H_
+
+#include "utils/UI_utils.h"
+
+#include "utils/Edge_contractor.h"
+
+/**
+ * Iteratively tries to anticollapse smallest edge non added so far.
+ * If its link is contractible then no topological change and else possible topological change.
+ *
+ * todo do a sparsification with some parameter eps while growing
+ */
+template<typename SkBlComplex> class Is_manifold{
+private:
+	const SkBlComplex& input_complex_;
+	typedef typename SkBlComplex::Vertex_handle Vertex_handle;
+
+
+public:
+	/*
+	 * return dim the maximum dimension around one simplex and res which is true if the complex is a manifold.
+	 * If the complex has dimension <= 3 then if res is false, the complex is not a manifold.
+	 * For d-manifold with d>=4, res may be false while the complex is a manifold.
+	 */
+	Is_manifold(const SkBlComplex& input_complex,unsigned& dim,bool & res):input_complex_(input_complex){
+		res = true;
+		dim = -1;
+		if(!input_complex_.empty()){
+			for(auto v : input_complex_.vertex_range()){
+				dim = local_dimension(v);
+				break;
+			}
+			//check that the link of every vertex is a dim-1 sphere
+			for(auto v : input_complex_.vertex_range()){
+				if(!is_k_sphere(v,dim-1)) {
+					res = false;
+					break;
+				}
+			}
+		}
+	}
+
+private:
+	unsigned local_dimension(Vertex_handle v){
+		unsigned dim = 0;
+		for(const auto& s: input_complex_.simplex_range(v))
+			dim = (std::max)(dim,(unsigned)s.dimension());
+		return dim;
+	}
+
+	bool is_k_sphere(Vertex_handle v,int k){
+		auto link = input_complex_.link(v);
+		Edge_contractor<Complex> contractor(link,link.num_vertices()-1);
+		return (is_sphere_simplex(link)==k);
+	}
+
+	// A minimal sphere is a complex that contains vertices v1...vn and all faces
+	// made upon this set except the face {v1,...,vn}
+	// return -2 if not a minimal sphere
+	// and d otherwise if complex is a d minimal sphere
+	template<typename SubComplex>
+	int is_sphere_simplex(const SubComplex& complex){
+		if(complex.empty()) return -1;
+		if(complex.num_blockers()!=1) return -2;
+
+		//necessary and sufficient condition : there exists a unique blocker that passes through all vertices
+		auto first_blocker = *(complex.const_blocker_range().begin());
+
+		if (first_blocker->dimension()+1 != complex.num_vertices())
+			return -2;
+		else
+			return (first_blocker->dimension()-1);
+	}
+};
+
+#endif /* IS_MANIFOLD_H_ */