doc + problem test

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@356 636b058d-ea47-450e-bf9e-a15bfbe3eedb

9 files changed, 24 insertions, 214 deletions

diff --git a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h
index eddfec44..60ef3b5f 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Cost_policy.h
@@ -29,6 +29,9 @@ namespace Gudhi{
 
 namespace contraction {
 
+/**
+*@brief Policy to specify the cost of contracting an edge.
+*/ 
 template< typename EdgeProfile> class Cost_policy{
 public:
 	typedef typename EdgeProfile::Point Point;
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 a3cbbd2e..de473944 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Dummy_valid_contraction.h
@@ -31,7 +31,9 @@ namespace contraction {
 
 
 
-
+  /**
+  *@brief Policy that accept all edge contraction.
+  */
 template< typename EdgeProfile> class Dummy_valid_contraction : public Valid_contraction_policy<EdgeProfile>{
 public:
 	typedef typename EdgeProfile::Point Point;
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 d1e0b7db..31c02e43 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
@@ -32,7 +32,9 @@ namespace Gudhi{
 namespace contraction {
 
 
-
+  /**
+  *@brief Policy that only accept edges verifying the link condition (and therefore whose contraction preserving homotopy type). 
+  */
 template< typename EdgeProfile> class Link_condition_valid_contraction : public Valid_contraction_policy<EdgeProfile>{
 public:
 	typedef typename EdgeProfile::Edge_handle Edge_handle;
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h
index 3d7a72e8..30f0a570 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Middle_placement.h
@@ -30,6 +30,8 @@ namespace Gudhi{
 
 namespace contraction {
 
+
+  
 template< typename EdgeProfile> class Middle_placement : public Placement_policy<EdgeProfile>{
 
 public:
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h
index b4ff6301..37b36dfe 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Placement_policy.h
@@ -28,6 +28,10 @@
 namespace Gudhi {
 namespace contraction {
 
+
+  /**
+  *@brief Policy to specify where the merged point had to be placed after an edge contraction. 
+  */
 template< typename EdgeProfile> class Placement_policy{
 public:
 	typedef typename EdgeProfile::Point Point;
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 b8e7d6d7..a053042b 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Valid_contraction_policy.h
@@ -25,6 +25,10 @@
 
 namespace Gudhi {
 namespace contraction {
+
+  /**
+  *@brief Policy to specify if an edge contraction is valid or not. 
+  */
 template< typename EdgeProfile> class Valid_contraction_policy{
 public:
 	typedef typename EdgeProfile::Point Point;
diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
index f8037897..56f4891f 100644
--- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
+++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
@@ -28,7 +28,6 @@
 
 // todo remove the queue to be independent from cgald
 #include "gudhi/Contraction/CGAL_queue/Modifiable_priority_queue.h"
-//#include <CGAL/Modifiable_priority_queue.h>
 
 
 #include <list>
@@ -68,7 +67,9 @@ Valid_contraction_policy<Profile>* make_link_valid_contraction(){
 }
 
 
-// visitor that remove popable blockers after an edge contraction
+/**
+*@brief Visitor to remove popable blockers after an edge contraction.
+*/
 template <class Profile>
 class Contraction_visitor_remove_popable : public Contraction_visitor<Profile>{
 public:
@@ -116,9 +117,9 @@ Contraction_visitor<Profile>* make_remove_popable_blockers_visitor(){
  *@class Skeleton_blocker_contractor
  *@brief Class that allows to contract iteratively edges of a simplicial complex.
  *
- * @details Basically, the simplification algorithm consists in iteratively picking the
+ * @details The simplification algorithm consists in iteratively picking the
  * edge with lowest cost and performing an edge contraction if the contraction is valid.
- * This class is policy based (and much inspired from the edge collapse package of CGAL).
+ * This class is policy based (and much inspired from the edge collapse package of CGAL http://doc.cgal.org/latest/Surface_mesh_simplification/index.html).
  *
  * Policies that can be changed are :
  *  - the cost policy : how much cost an edge contraction
@@ -126,7 +127,6 @@ Contraction_visitor<Profile>* make_remove_popable_blockers_visitor(){
  *  - the valid contraction policy : is the contraction valid. For instance, it can be
  *  a topological condition (link condition) or a geometrical condition (normals messed up).
  *
- * TODO expliquer la pile
  */
 template<
 class GeometricSimplifiableComplex,
diff --git a/src/Contraction/test/CMakeLists.txt b/src/Contraction/test/CMakeLists.txt
deleted file mode 100644
index 049b4ea1..00000000
--- a/src/Contraction/test/CMakeLists.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIskbl)
-
-add_executable ( TestContraction            TestContraction.cpp )
-
-
diff --git a/src/Contraction/test/TestContraction.cpp b/src/Contraction/test/TestContraction.cpp
deleted file mode 100644
index 42bf7d82..00000000
--- a/src/Contraction/test/TestContraction.cpp
+++ /dev/null
@@ -1,201 +0,0 @@
- /*    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 <ctime>
-#include <list>
-
-#include "combinatorics/Skeleton_blocker/Skeleton_blocker_simple_traits.h"
-#include "geometry/Skeleton_blocker_simple_geometric_traits.h"
-//#include "Skeleton_blocker/Simplex.h"
-#include "contraction/Skeleton_blocker_contractor.h"
-#include "Utils.h"
-#include "iofile.h"
-#include "Test.h"
-#include "Skeleton_blocker_geometric_complex.h"
-//#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
-
-
-#include "contraction/Edge_profile.h"
-
-#include "contraction/policies/Cost_policy.h"
-#include "contraction/policies/Edge_length_cost.h"
-#include "contraction/policies/Placement_policy.h"
-#include "contraction/policies/Middle_placement.h"
-
-#include "contraction/policies/Valid_contraction_policy.h"
-#include "contraction/policies/Dummy_valid_contraction.h"
-#include "contraction/policies/Link_condition_valid_contraction.h"
-
-
-using namespace std;
-
-using namespace Gudhi;
-
-using namespace skbl;
-
-struct Geometry_trait{
-	typedef std::vector<double> Point;
-};
-
-typedef Geometry_trait::Point Point;
-
-
-typedef Skeleton_blocker_complex<Skeleton_blocker_simple_traits> AbstractComplex;
-typedef Skeleton_blocker_simple_geometric_traits<Geometry_trait> Complex_geometric_traits;
-
-
-typedef Skeleton_blocker_geometric_complex< Complex_geometric_traits > Complex;
-
-typedef Complex::Vertex_handle Vertex_handle;
-typedef Complex::Simplex_handle Simplex_handle;
-
-typedef Complex::Root_vertex_handle Root_vertex_handle;
-
-using namespace contraction;
-
-typedef Skeleton_blocker_contractor<Complex> Complex_contractor;
-
-typedef Edge_profile<Complex> Profile;
-
-// compute the distance todo utiliser Euclidean_geometry a la place
-template<typename Point>
-double eucl_distance(const Point& a,const Point& b){
-	double res = 0;
-	auto a_coord = a.begin();
-	auto b_coord = b.begin();
-	for(; a_coord != a.end(); a_coord++, b_coord++){
-		res += (*a_coord - *b_coord) * (*a_coord - *b_coord);
-	}
-	return sqrt(res);
-}
-
-// build the Rips complex todo utiliser Euclidean_geometry a la place
-template<typename ComplexType>
-void build_rips(ComplexType& complex, double offset){
-	if (offset<=0) return;
-	auto vertices = complex.vertex_range();
-	for (auto p = vertices.begin(); p != vertices.end(); ++p)
-		for (auto q = p; ++q != vertices.end(); /**/)
-		if (eucl_distance(complex.point(*p), complex.point(*q)) < 2 * offset){
-				complex.add_edge(*p,*q);
-			}
-}
-
-
-
-
-void test_contraction_rips(string name_file, double offset){
-	Complex complex;
-	// load the points
-	if (!read_off_file<Complex>(name_file,complex,true)){
-		std::cerr << "Unable to read file:"<<name_file<<std::endl;
-		std::cerr << "current path : ";
-		system("pwd");
-		std::cerr<<endl;
-		return;
-	}
-
-	clock_t time = clock();
-
-	TEST("build the Rips complex");
-
-	build_rips(complex,offset);
-
-	std::cerr << "Rips contruction took "<< ( (float)(clock()-time))/CLOCKS_PER_SEC << " seconds\n";
-
-	TESTMSG("Initial number of vertices :",complex.num_vertices());
-	TESTMSG("Initial number of edges :",complex.num_edges());
-	TESTMSG("Initial number of blockers:",complex.num_blockers());
-
-	time = clock();
-
-	Complex_contractor contractor(complex,
-			new Edge_length_cost<Profile>,
-			contraction::make_first_vertex_placement<Profile>(),
-			contraction::make_link_valid_contraction<Profile>(),
-			contraction::make_remove_popable_blockers_visitor<Profile>());
-	contractor.contract_edges();
-
-	TESTVALUE(complex.to_string());
-
-	TESTVALUE(complex.num_vertices());
-	TESTVALUE(complex.num_edges());
-	TESTVALUE(complex.num_blockers());
-
-	std::cerr << "Edge contractions took "<< ( (float)(clock()-time))/CLOCKS_PER_SEC << " seconds\n";
-
-}
-
-
-void test_geometric_link(){
-
-	Complex complex;
-	std::vector<double> p0(2,0);
-	std::vector<double> p1(2,0); p1[0] = 1.;
-	std::vector<double> p2(2,1);
-	complex.add_vertex(p0);
-	complex.add_vertex(p1);
-	complex.add_vertex(p2);
-
-	complex.add_edge(Vertex_handle(0),Vertex_handle(1));
-	complex.add_edge(Vertex_handle(1),Vertex_handle(2));
-	complex.add_edge(Vertex_handle(2),Vertex_handle(0));
-
-
-
-	cerr << "complex points:" <<endl;
-	for(auto v : complex.vertex_range()){
-		cerr <<v <<" -> ";
-		DBGCONT(complex.point(v));
-	}
-
-	cerr << "complex : "<<complex.to_string()<<endl;
-
-
-
-
-	auto link = complex.link(Vertex_handle(0));
-
-
-	cerr << "link of 0 points:" <<endl;
-	for(auto v : link.vertex_range()){
-		cerr <<v <<" -> ";
-		DBGCONT(link.point(v));
-	}
-
-	cerr << "link : "<<link.to_string()<<endl;
-}
-
-
-
-
-int main (int argc, char *argv[])
-{
-	if (argc!=3){
-		std::cerr << "Usage "<<argv[0]<<" GUDHIPATH/src/data/sphere3D.off 0.1 to load the file GUDHIPATH/src/data/sphere3D.off and contract the Rips complex built with paremeter 0.2.\n";
-		return -1;
-	}
-
-	std::string name_file(argv[1]);
-	test_contraction_rips(name_file,atof(argv[2]));
-}
-
-