BIG: eliminate and eliminateOne now doubly templated functions, not methods.

Minor: Standardized on new shared_ptr naming convention:
shared_factor -> sharedFactor
conditional_ptr -> sharedConditional
node_ptr -> sharedClique

.cproject

@@ -300,7 +300,6 @@
 <buildTargets>
 <target name="install" path="wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>install</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -308,7 +307,6 @@
 </target>
 <target name="check" path="wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>check</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -316,7 +314,7 @@
 </target>
 <target name="check" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments>-k</buildArguments>
+<buildArguments/>
 <buildTarget>check</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -324,7 +322,6 @@
 </target>
 <target name="testSimpleCamera.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testSimpleCamera.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -340,6 +337,7 @@
 </target>
 <target name="testVSLAMFactor.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testVSLAMFactor.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -347,7 +345,6 @@
 </target>
 <target name="testCalibratedCamera.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testCalibratedCamera.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -355,6 +352,7 @@
 </target>
 <target name="testConditionalGaussian.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testConditionalGaussian.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -362,7 +360,6 @@
 </target>
 <target name="testPose2.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testPose2.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -378,7 +375,6 @@
 </target>
 <target name="testRot3.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testRot3.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -386,6 +382,7 @@
 </target>
 <target name="testNonlinearOptimizer.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testNonlinearOptimizer.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -393,7 +390,6 @@
 </target>
 <target name="testLinearFactor.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testLinearFactor.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -401,7 +397,6 @@
 </target>
 <target name="testConstrainedNonlinearFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testConstrainedNonlinearFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -409,7 +404,6 @@
 </target>
 <target name="testLinearFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testLinearFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -417,6 +411,7 @@
 </target>
 <target name="testNonlinearFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testNonlinearFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -424,7 +419,6 @@
 </target>
 <target name="testPose3.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testPose3.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -432,6 +426,7 @@
 </target>
 <target name="testConstrainedLinearFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testConstrainedLinearFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -439,6 +434,7 @@
 </target>
 <target name="testVectorConfig.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testVectorConfig.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -446,6 +442,7 @@
 </target>
 <target name="testPoint2.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testPoint2.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -453,7 +450,6 @@
 </target>
 <target name="testNonlinearFactor.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testNonlinearFactor.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -461,7 +457,6 @@
 </target>
 <target name="timeLinearFactor.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>timeLinearFactor.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -469,7 +464,6 @@
 </target>
 <target name="timeLinearFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>timeLinearFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -477,7 +471,6 @@
 </target>
 <target name="testGaussianBayesNet.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testGaussianBayesNet.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -485,6 +478,7 @@
 </target>
 <target name="testBayesTree.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testBayesTree.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -492,7 +486,6 @@
 </target>
 <target name="testSymbolicBayesNet.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testSymbolicBayesNet.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -500,6 +493,7 @@
 </target>
 <target name="testSymbolicFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>testSymbolicFactorGraph.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -507,7 +501,6 @@
 </target>
 <target name="testVector.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testVector.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -515,7 +508,6 @@
 </target>
 <target name="testMatrix.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testMatrix.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -523,6 +515,7 @@
 </target>
 <target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>install</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -530,6 +523,7 @@
 </target>
 <target name="clean" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>clean</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -537,6 +531,7 @@
 </target>
 <target name="check" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
+<buildArguments/>
 <buildTarget>check</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>

cpp/BayesNet-inl.h

@@ -23,7 +23,7 @@ namespace gtsam {
 	void BayesNet<Conditional>::print(const string& s) const {
 		cout << s << ":\n";
 		std::string key;
-		BOOST_FOREACH(conditional_ptr conditional,conditionals_)
+		BOOST_FOREACH(sharedConditional conditional,conditionals_)
 			conditional->print("Node[" + conditional->key() + "]");
 	}
 
@@ -38,26 +38,17 @@ namespace gtsam {
 	template<class Conditional>
 	Ordering BayesNet<Conditional>::ordering() const {
 		Ordering ord;
-		BOOST_FOREACH(conditional_ptr conditional,conditionals_)
+		BOOST_FOREACH(sharedConditional conditional,conditionals_)
 		   ord.push_back(conditional->key());
 		return ord;
 	}
 
 	/* ************************************************************************* */
-	// predicate to check whether a conditional has the sought key
-	template<class Conditional>
-	class HasKey {
-		const string& key_;
-	public:
-		HasKey(const std::string& key):key_(key) {}
-		bool operator()(const boost::shared_ptr<Conditional>& conditional) {
-			return (conditional->key()==key_);
-		}
-	};
 
 	template<class Conditional>
-	boost::shared_ptr<Conditional> BayesNet<Conditional>::operator[](const std::string& key) const {
+	typename BayesNet<Conditional>::sharedConditional
-		const_iterator it = find_if(conditionals_.begin(),conditionals_.end(),HasKey<Conditional>(key));
+	BayesNet<Conditional>::operator[](const std::string& key) const {
+		const_iterator it = find_if(conditionals_.begin(),conditionals_.end(),onKey<Conditional>(key));
 		if (it == conditionals_.end()) throw(invalid_argument(
 						"BayesNet::operator['"+key+"']: not found"));
 		return *it;

cpp/BayesNet.h

@@ -31,8 +31,8 @@ namespace gtsam {
 	public:
 
 		/** We store shared pointers to Conditional densities */
-		typedef typename boost::shared_ptr<Conditional> conditional_ptr;
+		typedef typename boost::shared_ptr<Conditional> sharedConditional;
-		typedef typename std::list<conditional_ptr> Conditionals;
+		typedef typename std::list<sharedConditional> Conditionals;
 
 		typedef typename Conditionals::const_iterator const_iterator;
 		typedef typename Conditionals::const_reverse_iterator const_reverse_iterator;
@@ -55,12 +55,12 @@ namespace gtsam {
 		bool equals(const BayesNet& other, double tol = 1e-9) const;
 
 		/** push_back: use reverse topological sort (i.e. parents last / elimination order) */
-		inline void push_back(const boost::shared_ptr<Conditional>& conditional) {
+		inline void push_back(const sharedConditional& conditional) {
 			conditionals_.push_back(conditional);
 		}
 
 		/** push_front: use topological sort (i.e. parents first / reverse elimination order) */
-		inline void push_front(const boost::shared_ptr<Conditional>& conditional) {
+		inline void push_front(const sharedConditional& conditional) {
 			conditionals_.push_front(conditional);
 		}
 
@@ -73,9 +73,9 @@ namespace gtsam {
 		Ordering ordering() const;
 
 		/** SLOW O(n) random access to Conditional by key */
-		conditional_ptr operator[](const std::string& key) const;
+		sharedConditional operator[](const std::string& key) const;
 
-		inline conditional_ptr back() { return conditionals_.back(); }
+		inline sharedConditional back() { return conditionals_.back(); }
 
 		/** return iterators. FD: breaks encapsulation? */
 		inline const_iterator const begin() const {return conditionals_.begin();}

cpp/BayesTree-inl.h

@@ -14,7 +14,7 @@ namespace gtsam {
 
 	/* ************************************************************************* */
 	template<class Conditional>
-	BayesTree<Conditional>::Clique::Clique(const boost::shared_ptr<Conditional>& conditional) {
+	BayesTree<Conditional>::Clique::Clique(const sharedConditional& conditional) {
 			separator_ = conditional->parents();
 			this->push_back(conditional);
 		}
@@ -91,8 +91,7 @@ namespace gtsam {
 
 	/* ************************************************************************* */
 	template<class Conditional>
-	void BayesTree<Conditional>::insert
+	void BayesTree<Conditional>::insert(const sharedConditional& conditional)
-	(const boost::shared_ptr<Conditional>& conditional)
 	{
 		// get key and parents
 		string key = conditional->key();
@@ -129,7 +128,8 @@ namespace gtsam {
 	/* ************************************************************************* */
 	template<class Conditional>
 	template<class Factor>
-	boost::shared_ptr<Conditional> BayesTree<Conditional>::marginal(const string& key) const {
+	typename BayesTree<Conditional>::sharedConditional
+	BayesTree<Conditional>::marginal(const string& key) const {
 
 		// get clique containing key, and remove all factors below key
 		sharedClique clique = (*this)[key];
@@ -160,9 +160,7 @@ namespace gtsam {
 		ordering.reverse();
 
 		// eliminate to get marginal
-		boost::shared_ptr<BayesNet<Conditional> > bayesNet;
+		sharedBayesNet chordalBayesNet = eliminate<Factor,Conditional>(graph,ordering);
-		typename boost::shared_ptr<BayesNet<Conditional> > chordalBayesNet =
-				graph.eliminate(bayesNet,ordering);
 
 		return chordalBayesNet->back(); // the root is the marginal
 	}

cpp/Conditional.h

@@ -49,4 +49,17 @@ namespace gtsam {
     /** return the number of parents */
     virtual std::size_t nrParents() const = 0;
   };
+
+	// predicate to check whether a conditional has the sought key
+	template<class Conditional>
+	class onKey {
+		const std::string& key_;
+	public:
+		onKey(const std::string& key):key_(key) {}
+		bool operator()(const typename Conditional::shared_ptr& conditional) {
+			return (conditional->key()==key_);
+		}
+	};
+
+
 }

cpp/ConstrainedLinearFactorGraph.cpp

@@ -83,7 +83,8 @@ GaussianBayesNet::shared_ptr ConstrainedLinearFactorGraph::eliminate(const Order
 		}
 		else
 		{
-			ConditionalGaussian::shared_ptr cg = eliminateOne<ConditionalGaussian>(key);
+			ConditionalGaussian::shared_ptr cg =
+					eliminateOne<LinearFactor,ConditionalGaussian>(*this,key);
 			cbn->push_back(cg);
 		}
 	}

cpp/FactorGraph-inl.h

@@ -29,7 +29,7 @@ FactorGraph<Factor>::FactorGraph(const BayesNet<Conditional>& bayesNet)
 {
 	typename BayesNet<Conditional>::const_iterator it = bayesNet.begin();
 	for(; it != bayesNet.end(); it++) {
-		typename boost::shared_ptr<Factor>::shared_ptr factor(new Factor(*it));
+		sharedFactor factor(new Factor(*it));
 		push_back(factor);
 	}
 }
@@ -56,7 +56,7 @@ bool FactorGraph<Factor>::equals
 	/** check whether the factors_ are the same */
 	for (size_t i = 0; i < factors_.size(); i++) {
 		// TODO: Doesn't this force order of factor insertion?
-		shared_factor f1 = factors_[i], f2 = fg.factors_[i];
+		sharedFactor f1 = factors_[i], f2 = fg.factors_[i];
 		if (f1 == NULL && f2 == NULL) continue;
 		if (f1 == NULL || f2 == NULL) return false;
 		if (!f1->equals(*f2, tol)) return false;
@@ -75,7 +75,7 @@ size_t FactorGraph<Factor>::nrFactors() const {
 
 /* ************************************************************************* */
 template<class Factor>
-void FactorGraph<Factor>::push_back(shared_factor factor) {
+void FactorGraph<Factor>::push_back(sharedFactor factor) {
 	factors_.push_back(factor);                  // add the actual factor
 	if (factor==NULL) return;
 
@@ -184,11 +184,11 @@ list<int> FactorGraph<Factor>::factors(const string& key) const {
 template<class Factor>
 vector<boost::shared_ptr<Factor> >
 FactorGraph<Factor>::findAndRemoveFactors(const string& key) {
-	vector<boost::shared_ptr<Factor> > found;
+	vector<sharedFactor> found;
 
 	Indices::iterator it = indices_.find(key);
 	if (it == indices_.end())
-		throw(std::invalid_argument
+		throw(invalid_argument
 				("FactorGraph::findAndRemoveFactors invalid key: " + key));
 
 	list<int> *indices_ptr; // pointer to indices list in indices_ map
@@ -206,14 +206,13 @@ FactorGraph<Factor>::findAndRemoveFactors(const string& key) {
 /* find factors and remove them from the factor graph: O(n)                  */
 /* ************************************************************************* */
 template<class Factor>
-boost::shared_ptr<Factor>
+typename FactorGraph<Factor>::sharedFactor
 FactorGraph<Factor>::removeAndCombineFactors(const string& key)
 {
 	bool verbose = false;
 	if (verbose) cout << "FactorGraph::removeAndCombineFactors" << endl;
-	typedef typename boost::shared_ptr<Factor> shared_factor;
+	vector<sharedFactor> found = findAndRemoveFactors(key);
-	vector<shared_factor> found = findAndRemoveFactors(key);
+	sharedFactor new_factor(new Factor(found));
-	shared_factor new_factor(new Factor(found));
 	if (verbose) cout << "FactorGraph::removeAndCombineFactors done" << endl;
 	return new_factor;
 }
@@ -221,21 +220,20 @@ FactorGraph<Factor>::removeAndCombineFactors(const string& key)
 /* ************************************************************************* */
 /* eliminate one node from the factor graph                           */
 /* ************************************************************************* */
-template<class Factor>
+template<class Factor,class Conditional>
-template<class Conditional>
+boost::shared_ptr<Conditional> eliminateOne(FactorGraph<Factor>& graph, const string& key) {
-boost::shared_ptr<Conditional> FactorGraph<Factor>::eliminateOne(const std::string& key) {
 
 	// combine the factors of all nodes connected to the variable to be eliminated
 	// if no factors are connected to key, returns an empty factor
-	shared_factor joint_factor = removeAndCombineFactors(key);
+	boost::shared_ptr<Factor> joint_factor = graph.removeAndCombineFactors(key);
 
 	// eliminate that joint factor
-	shared_factor factor;
+	boost::shared_ptr<Factor> factor;
 	boost::shared_ptr<Conditional> conditional;
 	boost::tie(conditional, factor) = joint_factor->eliminate(key);
 
 	// add new factor on separator back into the graph
-	if (!factor->empty()) push_back(factor);
+	if (!factor->empty()) graph.push_back(factor);
 
 	// return the conditional Gaussian
 	return conditional;
@@ -245,16 +243,16 @@ boost::shared_ptr<Conditional> FactorGraph<Factor>::eliminateOne(const std::stri
 // This doubly templated function is generic. There is a LinearFactorGraph
 // version that returns a more specific GaussianBayesNet.
 // Note, you will need to include this file to instantiate the function.
+// TODO: get rid of summy argument
 /* ************************************************************************* */
-template<class Factor>
+template<class Factor,class Conditional>
-template<class Conditional>
 boost::shared_ptr<BayesNet<Conditional> >
-FactorGraph<Factor>::eliminate(boost::shared_ptr<BayesNet<Conditional> > xxx, const Ordering& ordering)
+eliminate(FactorGraph<Factor>& factorGraph, const Ordering& ordering)
 {
 	boost::shared_ptr<BayesNet<Conditional> > bayesNet (new BayesNet<Conditional>()); // empty
 
 	BOOST_FOREACH(string key, ordering) {
-		boost::shared_ptr<Conditional> cg = eliminateOne<Conditional>(key);
+		boost::shared_ptr<Conditional> cg = eliminateOne<Factor,Conditional>(factorGraph,key);
 		bayesNet->push_back(cg);
 	}
 

cpp/FactorGraph.h

@@ -30,13 +30,13 @@ namespace gtsam {
 	 */
 	template<class Factor> class FactorGraph: public Testable<FactorGraph<Factor> > {
 	public:
-		typedef typename boost::shared_ptr<Factor> shared_factor;
+		typedef typename boost::shared_ptr<Factor> sharedFactor;
-		typedef typename std::vector<shared_factor>::iterator iterator;
+		typedef typename std::vector<sharedFactor>::iterator iterator;
-		typedef typename std::vector<shared_factor>::const_iterator const_iterator;
+		typedef typename std::vector<sharedFactor>::const_iterator const_iterator;
 
 	protected:
 		/** Collection of factors */
-		std::vector<shared_factor> factors_;
+		std::vector<sharedFactor> factors_;
 
 		/** For each variable a list of factor indices connected to it  */
 		typedef std::map<std::string, std::list<int> > Indices;
@@ -73,7 +73,7 @@ namespace gtsam {
 		}
 
 		/** Get a specific factor by index */
-		inline shared_factor operator[](size_t i) const {
+		inline sharedFactor operator[](size_t i) const {
 			return factors_[i];
 		}
 
@@ -84,7 +84,7 @@ namespace gtsam {
 	  size_t nrFactors() const;
 
 		/** Add a factor */
-		void push_back(shared_factor factor);
+		void push_back(sharedFactor factor);
 
 		/**
 		 * Compute colamd ordering
@@ -102,29 +102,14 @@ namespace gtsam {
      * from the factor graph
      * @param key the key for the given node
      */
-		std::vector<shared_factor> findAndRemoveFactors(const std::string& key);
+		std::vector<sharedFactor> findAndRemoveFactors(const std::string& key);
 
     /**
      * extract and combine all the factors that involve a given node
      * @param key the key for the given node
      * @return the combined linear factor
      */
-    shared_factor removeAndCombineFactors(const std::string& key);
+    sharedFactor removeAndCombineFactors(const std::string& key);
-
-    /**
-     * Eliminate a single node yielding a Conditional
-     * Eliminates the factors from the factor graph through findAndRemoveFactors
-     * and adds a new factor on the separator to the factor graph
-     */
-		template<class Conditional>
-		boost::shared_ptr<Conditional> eliminateOne(const std::string& key);
-
-		/**
-		 * eliminate factor graph using the given (not necessarily complete)
-		 * ordering, yielding a chordal Bayes net and (partially eliminated) FG
-		 */
-		template<class Conditional>
-		boost::shared_ptr<BayesNet<Conditional> > eliminate(boost::shared_ptr<BayesNet<Conditional> > bayesNet, const Ordering& ordering);
 
 	private:
 
@@ -136,5 +121,24 @@ namespace gtsam {
 			ar & BOOST_SERIALIZATION_NVP(indices_);
 		}
 	}; // FactorGraph
+
+	/** doubly templated functions */
+
+	/**
+   * Eliminate a single node yielding a Conditional
+   * Eliminates the factors from the factor graph through findAndRemoveFactors
+   * and adds a new factor on the separator to the factor graph
+   */
+	template<class Factor, class Conditional>
+	boost::shared_ptr<Conditional> eliminateOne(FactorGraph<Factor>& factorGraph, const std::string& key);
+
+	/**
+	 * eliminate factor graph using the given (not necessarily complete)
+	 * ordering, yielding a chordal Bayes net and (partially eliminated) FG
+	 */
+	template<class Factor, class Conditional>
+	boost::shared_ptr<BayesNet<Conditional> >
+	eliminate(FactorGraph<Factor>& factorGraph, const Ordering& ordering);
+
 } // namespace gtsam
 

cpp/LinearFactorGraph.cpp

@@ -34,7 +34,7 @@ LinearFactorGraph::LinearFactorGraph(const GaussianBayesNet& CBN) :
 set<string> LinearFactorGraph::find_separator(const string& key) const
 {
 	set<string> separator;
-	BOOST_FOREACH(shared_factor factor,factors_)
+	BOOST_FOREACH(sharedFactor factor,factors_)
 		factor->tally_separator(key,separator);
 
 	return separator;
@@ -46,7 +46,8 @@ LinearFactorGraph::eliminate(const Ordering& ordering)
 {
 	GaussianBayesNet::shared_ptr chordalBayesNet (new GaussianBayesNet()); // empty
 	BOOST_FOREACH(string key, ordering) {
-		ConditionalGaussian::shared_ptr cg = eliminateOne<ConditionalGaussian>(key);
+		ConditionalGaussian::shared_ptr cg =
+				eliminateOne<LinearFactor,ConditionalGaussian>(*this, key);
 		chordalBayesNet->push_back(cg);
 	}
 	return chordalBayesNet;
@@ -90,7 +91,7 @@ LinearFactorGraph LinearFactorGraph::combine2(const LinearFactorGraph& lfg1,
 /* ************************************************************************* */  
 Dimensions LinearFactorGraph::dimensions() const {
 	Dimensions result;
-	BOOST_FOREACH(shared_factor factor,factors_) {
+	BOOST_FOREACH(sharedFactor factor,factors_) {
 		Dimensions vs = factor->dimensions();
 		string key; int dim;
 		FOREACH_PAIR(key,dim,vs) result.insert(make_pair(key,dim));
@@ -112,7 +113,7 @@ LinearFactorGraph LinearFactorGraph::add_priors(double sigma) const {
 	FOREACH_PAIR(key,dim,vs) {
 		Matrix A = eye(dim);
 		Vector b = zero(dim);
-		shared_factor prior(new LinearFactor(key,A,b, sigma));
+		sharedFactor prior(new LinearFactor(key,A,b, sigma));
 		result.push_back(prior);
 	}
 	return result;
@@ -123,7 +124,7 @@ pair<Matrix,Vector> LinearFactorGraph::matrix(const Ordering& ordering) const {
 
 	// get all factors
 	LinearFactorSet found;
-	BOOST_FOREACH(shared_factor factor,factors_)
+	BOOST_FOREACH(sharedFactor factor,factors_)
 		found.push_back(factor);
 
 	// combine them
@@ -145,7 +146,7 @@ Matrix LinearFactorGraph::sparse(const Ordering& ordering) const {
 
 	// Collect the I,J,S lists for all factors
 	int row_index = 0;
-	BOOST_FOREACH(shared_factor factor,factors_) {
+	BOOST_FOREACH(sharedFactor factor,factors_) {
 
 		// get sparse lists for the factor
 		list<int> i1,j1;

cpp/SymbolicFactorGraph.cpp

@@ -25,7 +25,8 @@ namespace gtsam {
 		SymbolicBayesNet::shared_ptr bayesNet (new SymbolicBayesNet());
 
 		BOOST_FOREACH(string key, ordering) {
-			SymbolicConditional::shared_ptr conditional = eliminateOne<SymbolicConditional>(key);
+			SymbolicConditional::shared_ptr conditional =
+					eliminateOne<SymbolicFactor,SymbolicConditional>(*this,key);
 			bayesNet->push_back(conditional);
 		}
 

cpp/testConstrainedLinearFactorGraph.cpp

@@ -256,7 +256,8 @@ TEST( ConstrainedLinearFactorGraph, eliminate_multi_constraint )
 	CHECK(fg.nrFactors() == 0);
 
 	// eliminate the linear factor
-	ConditionalGaussian::shared_ptr cg3 = fg.eliminateOne<ConditionalGaussian>("z");
+	ConditionalGaussian::shared_ptr cg3 =
+			eliminateOne<LinearFactor,ConditionalGaussian>(fg,"z");
 	CHECK(cg3->nrParents() == 0);
 	CHECK(fg.size() == 0);
 

cpp/testLinearFactorGraph.cpp

@@ -191,7 +191,7 @@ TEST( LinearFactorGraph, eliminateOne_x1 )
 {
   LinearFactorGraph fg = createLinearFactorGraph();
   ConditionalGaussian::shared_ptr actual =
-  		fg.eliminateOne<ConditionalGaussian>("x1");
+  		eliminateOne<LinearFactor,ConditionalGaussian>(fg,"x1");
 
   // create expected Conditional Gaussian
   Matrix R11 = Matrix_(2,2,
@@ -220,7 +220,7 @@ TEST( LinearFactorGraph, eliminateOne_x2 )
 {
   LinearFactorGraph fg = createLinearFactorGraph();
   ConditionalGaussian::shared_ptr actual =
-  		fg.eliminateOne<ConditionalGaussian>("x2");
+  		eliminateOne<LinearFactor,ConditionalGaussian>(fg,"x2");
 
   // create expected Conditional Gaussian
   Matrix R11 = Matrix_(2,2,
@@ -248,7 +248,7 @@ TEST( LinearFactorGraph, eliminateOne_l1 )
 {
   LinearFactorGraph fg = createLinearFactorGraph();
   ConditionalGaussian::shared_ptr actual =
-  		fg.eliminateOne<ConditionalGaussian>("l1");
+  		eliminateOne<LinearFactor,ConditionalGaussian>(fg,"l1");
 
   // create expected Conditional Gaussian
   Matrix R11 = Matrix_(2,2,
@@ -383,8 +383,8 @@ TEST( LinearFactorGraph, matrix )
     );
   Vector b1 = Vector_(8,-1., -1., 2., -1., 0., 1., -1., 1.5);
 
-  EQUALITY(A,A1); // currently fails
+  EQUALITY(A,A1);
-  CHECK(b==b1); // currently fails
+  CHECK(b==b1);
 }
 
 /* ************************************************************************* */
@@ -400,9 +400,10 @@ TEST( LinearFactorGraph, sparse )
 	Matrix ijs = fg.sparse(ord);
 
 	EQUALITY(ijs, Matrix_(3, 14,
-		+1., 2.,  3., 4.,  3.,  4., 5.,6., 5., 6.,  7., 8.,7.,8.,
+		// f(x1)   f(x2,x1)            f(l1,x1)         f(x2,l1)
-		+5., 6.,  1., 2.,  5.,  6., 3.,4., 5., 6.,  1., 2.,3.,4.,
+		+1., 2.,   3., 4.,  3.,  4.,   5.,6., 5., 6.,   7., 8.,7.,8.,
-		10.,10., 10.,10.,-10.,-10., 5.,5.,-5.,-5., -5.,-5.,5.,5.));
+		+5., 6.,   1., 2.,  5.,  6.,   3.,4., 5., 6.,   1., 2.,3.,4.,
+		10.,10.,  10.,10.,-10.,-10.,   5.,5.,-5.,-5.,  -5.,-5.,5.,5.));
 }
 
 /* ************************************************************************* */
@@ -422,9 +423,8 @@ TEST( LinearFactorGraph, CONSTRUCTOR_GaussianBayesNet )
 
   // Base FactorGraph only
   FactorGraph<LinearFactor> fg3(*CBN);
-  boost::shared_ptr<BayesNet<ConditionalGaussian> > dummy;
   boost::shared_ptr<BayesNet<ConditionalGaussian> > CBN3 =
-  		fg3.eliminate<ConditionalGaussian>(dummy,ord);
+  		eliminate<LinearFactor,ConditionalGaussian>(fg3,ord);
   CHECK(CBN->equals(*CBN3));
 }
 

cpp/testSymbolicFactorGraph.cpp

@@ -112,7 +112,7 @@ TEST( LinearFactorGraph, eliminateOne )
 
 	// eliminate
 	SymbolicConditional::shared_ptr actual =
-  		fg.eliminateOne<SymbolicConditional>("x1");
+  		eliminateOne<SymbolicFactor,SymbolicConditional>(fg,"x1");
 
   // create expected symbolic Conditional
   SymbolicConditional expected("x1","l1","x2");