Merge of cpplint branch

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@357 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8b6af51684401f4c45c953142aae90d6f45e6778

3 files changed, 221 insertions, 2 deletions

diff --git a/src/Contraction/example/CMakeLists.txt b/src/Contraction/example/CMakeLists.txt
index 717830da..13eb5537 100644
--- a/src/Contraction/example/CMakeLists.txt
+++ b/src/Contraction/example/CMakeLists.txt
@@ -1,6 +1,7 @@
 cmake_minimum_required(VERSION 2.6)
 project(GUDHIskbl)
-add_executable ( RipsContraction Rips_contraction.cpp)
-target_link_libraries( RipsContraction ${Boost_TIMER_LIBRARY})	
 
+add_executable(RipsContraction Rips_contraction.cpp)
+target_link_libraries(RipsContraction ${Boost_TIMER_LIBRARY} ${Boost_SYSTEM_LIBRARY})	
 
+add_test(RipsContraction ${CMAKE_CURRENT_BINARY_DIR}/RipsContraction ${CMAKE_SOURCE_DIR}/data/meshes/sphere3D_2646.off 0.2)
diff --git a/src/Contraction/test/CMakeLists.txt b/src/Contraction/test/CMakeLists.txt
new file mode 100644
index 00000000..6dddff1b
--- /dev/null
+++ b/src/Contraction/test/CMakeLists.txt
@@ -0,0 +1,20 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIskbl)
+
+if(NOT MSVC)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} --coverage")	
+  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} --coverage")
+endif()
+
+add_executable(TestContraction TestContraction.cpp)
+
+# Unitary tests
+add_test(TestContraction ${CMAKE_CURRENT_BINARY_DIR}/TestContraction ${CMAKE_SOURCE_DIR}/data/meshes/SO3_50000.off 0.2)
+
+if (LCOV_PATH)
+  # Lcov code coverage of unitary test
+  add_test(src/Contraction/lcov/coverage.log ${CMAKE_SOURCE_DIR}/scripts/check_code_coverage.sh ${CMAKE_SOURCE_DIR}/src/Contraction)
+endif()
+
+cpplint_add_tests("${CMAKE_SOURCE_DIR}/src/Contraction/include/gudhi")
diff --git a/src/Contraction/test/TestContraction.cpp b/src/Contraction/test/TestContraction.cpp
new file mode 100644
index 00000000..872f24a0
--- /dev/null
+++ b/src/Contraction/test/TestContraction.cpp
@@ -0,0 +1,198 @@
+ /*    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 "gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h"
+#include "gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h"
+//#include "Skeleton_blocker/Simplex.h"
+#include "gudhi/Skeleton_blocker_contractor.h"
+#include "gudhi/Utils.h"
+#include "gudhi/Test.h"
+#include "gudhi/Skeleton_blocker_geometric_complex.h"
+//#include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+
+
+#include "gudhi/Contraction/Edge_profile.h"
+#include "gudhi/Contraction/policies/Cost_policy.h"
+#include "gudhi/Contraction/policies/Edge_length_cost.h"
+#include "gudhi/Contraction/policies/Placement_policy.h"
+#include "gudhi/Contraction/policies/Middle_placement.h"
+#include "gudhi/Contraction/policies/Valid_contraction_policy.h"
+#include "gudhi/Contraction/policies/Dummy_valid_contraction.h"
+#include "gudhi/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]));
+}
+
+