Renamed BayesNet::insert -> push_back. BayesTree now uses Bayes nets as nodes.

.cproject

@@ -300,6 +300,7 @@
 <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>
@@ -307,6 +308,7 @@
 </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>
@@ -314,14 +316,15 @@
 </target>
 <target name="check" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
+<buildArguments>-k</buildArguments>
 <buildTarget>check</buildTarget>
 <stopOnError>true</stopOnError>
-<useDefaultCommand>true</useDefaultCommand>
+<useDefaultCommand>false</useDefaultCommand>
 <runAllBuilders>true</runAllBuilders>
 </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>
@@ -337,7 +340,6 @@
 </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>
@@ -345,6 +347,7 @@
 </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>
@@ -352,7 +355,6 @@
 </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>
@@ -360,6 +362,7 @@
 </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>
@@ -375,6 +378,7 @@
 </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>
@@ -382,7 +386,6 @@
 </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>
@@ -390,6 +393,7 @@
 </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>
@@ -397,6 +401,7 @@
 </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>
@@ -404,6 +409,7 @@
 </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>
@@ -411,7 +417,6 @@
 </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>
@@ -419,6 +424,7 @@
 </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>
@@ -426,7 +432,6 @@
 </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>
@@ -434,7 +439,6 @@
 </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>
@@ -442,7 +446,6 @@
 </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>
@@ -450,6 +453,7 @@
 </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>
@@ -457,6 +461,7 @@
 </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>
@@ -464,6 +469,7 @@
 </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>
@@ -471,6 +477,7 @@
 </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>
@@ -478,7 +485,6 @@
 </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>
@@ -486,7 +492,6 @@
 </target>
 <target name="testSymbolicBayesChain.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>testSymbolicBayesChain.run</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>false</useDefaultCommand>
@@ -494,7 +499,6 @@
 </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>
@@ -502,6 +506,7 @@
 </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>
@@ -509,6 +514,7 @@
 </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>
@@ -516,7 +522,6 @@
 </target>
 <target name="install" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>install</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -524,7 +529,6 @@
 </target>
 <target name="clean" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
 <buildCommand>make</buildCommand>
-<buildArguments/>
 <buildTarget>clean</buildTarget>
 <stopOnError>true</stopOnError>
 <useDefaultCommand>true</useDefaultCommand>
@@ -532,7 +536,6 @@
 </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

@@ -37,7 +37,7 @@ namespace gtsam {
 
 	/* ************************************************************************* */
 	template<class Conditional>
-	void BayesNet<Conditional>::insert
+	void BayesNet<Conditional>::push_back
 		(const boost::shared_ptr<Conditional>& conditional) {
 		indices_.insert(make_pair(conditional->key(),conditionals_.size()));
 		conditionals_.push_back(conditional);

cpp/BayesNet.h

@@ -67,8 +67,8 @@ namespace gtsam {
 		/** check equality */
 		bool equals(const BayesNet& other, double tol = 1e-9) const;
 
-		/** insert: use reverse topological sort (i.e. parents last / elimination order) */
+		/** push_back: use reverse topological sort (i.e. parents last / elimination order) */
-		void insert(const boost::shared_ptr<Conditional>& conditional);
+		void push_back(const boost::shared_ptr<Conditional>& conditional);
 
 		/** size is the number of nodes */
 		inline size_t size() const {

cpp/BayesTree-inl.h

@@ -13,16 +13,16 @@ namespace gtsam {
 
 	/* ************************************************************************* */
 	template<class Conditional>
-	Front<Conditional>::Front(const conditional_ptr& conditional) {
+	BayesTree<Conditional>::Node::Node(const boost::shared_ptr<Conditional>& conditional) {
-		add(conditional);
 			separator_ = conditional->parents();
+			this->push_back(conditional);
 		}
 
 	/* ************************************************************************* */
 	template<class Conditional>
-	void Front<Conditional>::print(const string& s) const {
+	void BayesTree<Conditional>::Node::print(const string& s) const {
 			cout << s;
-		BOOST_FOREACH(const conditional_ptr& conditional, conditionals_)
+			BOOST_REVERSE_FOREACH(const conditional_ptr& conditional, this->conditionals_)
 				cout << " " << conditional->key();
 			if (!separator_.empty()) {
 				cout << " :";
@@ -34,14 +34,10 @@ namespace gtsam {
 
 	/* ************************************************************************* */
 	template<class Conditional>
-	bool Front<Conditional>::equals(const Front<Conditional>& other, double tol) const {
+	void BayesTree<Conditional>::Node::printTree(const string& indent) const {
-		return equal(conditionals_.begin(),conditionals_.end(),other.conditionals_.begin(),equals_star<Conditional>);
+			print(indent);
-	}
+			BOOST_FOREACH(shared_ptr child, children_)
-
+				child->printTree(indent+"  ");
-	/* ************************************************************************* */
-	template<class Conditional>
-	void Front<Conditional>::add(const conditional_ptr& conditional) {
-		conditionals_.push_front(conditional);
 		}
 
 	/* ************************************************************************* */
@@ -104,12 +100,13 @@ namespace gtsam {
 						"BayesTree::insert('"+key+"'): parent '" + parent + "' was not yet inserted"));
 		int index = it->second;
 		node_ptr parent_clique = nodes_[index];
+		if (verbose) cout << "Parent clique " << index << " of size " << parent_clique->size() << endl;
 
 		// if the parents and parent clique have the same size, add to parent clique
 		if (parent_clique->size() == parents.size()) {
 			if (verbose) cout << "Adding to clique " << index << endl;
 			nodeMap_.insert(make_pair(key, index));
-			parent_clique->add(conditional);
+			parent_clique->push_back(conditional);
 			return;
 		}
 

cpp/BayesTree.h

@@ -13,36 +13,12 @@
 #include <vector>
 #include <boost/serialization/map.hpp>
 #include <boost/serialization/list.hpp>
+
 #include "Testable.h"
 #include "BayesNet.h"
 
 namespace gtsam {
 
-	/** A clique in a Bayes tree consisting of frontal nodes and conditionals */
-	template<class Conditional>
-	class Front: Testable<Front<Conditional> > {
-	private:
-		typedef boost::shared_ptr<Conditional> conditional_ptr;
-		std::list<conditional_ptr> conditionals_; /** conditionals */
-		std::list<std::string> separator_; /** separator keys */
-	public:
-
-		/** constructor */
-		Front(const conditional_ptr& conditional);
-
-		/** print */
-		void print(const std::string& s = "") const;
-
-		/** check equality */
-		bool equals(const Front<Conditional>& other, double tol = 1e-9) const;
-
-		/** add a frontal node */
-		void add(const conditional_ptr& conditional);
-
-		/** return size of the clique */
-		inline size_t size() const {return conditionals_.size() + separator_.size();}
-	};
-
 	/**
 	 * Bayes tree
 	 * Templated on the Conditional class, the type of node in the underlying Bayes chain.
@@ -58,20 +34,27 @@ namespace gtsam {
 
 	private:
 
-		/** A Node in the tree is a Front with tree connectivity */
+		/** A Node in the tree is an incomplete Bayes net: the variables
-		struct Node : public Front<Conditional> {
+		 * in the Bayes net are the frontal nodes, and the variables conditioned
+		 * on is the separator. We also have pointers up and down the tree.
+		 */
+		struct Node : public BayesNet<Conditional> {
 			typedef boost::shared_ptr<Node> shared_ptr;
 			shared_ptr parent_;
+			std::list<std::string> separator_; /** separator keys */
 			std::list<shared_ptr> children_;
 
-			Node(const boost::shared_ptr<Conditional>& conditional):Front<Conditional>(conditional) {}
+			//* Constructor */
+			Node(const boost::shared_ptr<Conditional>& conditional);
+
+			/** The size *includes* the separator */
+			size_t size() const { return this->conditionals_.size() + separator_.size(); }
+
+			/** print this node */
+			void print(const std::string& s="Bayes tree node") const;
 
 			/** print this node and entire subtree below it*/
-			void printTree(const std::string& indent) const {
+			void printTree(const std::string& indent) const;
-				print(indent);
-				BOOST_FOREACH(shared_ptr child, children_)
-					child->printTree(indent+"  ");
-			}
 		};
 
 		/** vector of Nodes */
@@ -107,7 +90,7 @@ namespace gtsam {
 		inline size_t size() const { return nodes_.size();}
 
 		/** return root clique */
-		const Front<Conditional>& root() const {return *(nodes_[0]);}
+		const BayesNet<Conditional>& root() const {return *(nodes_[0]);}
 
 	}; // BayesTree
 

cpp/ConstrainedLinearFactorGraph.cpp

@@ -79,12 +79,12 @@ GaussianBayesNet::shared_ptr ConstrainedLinearFactorGraph::eliminate(const Order
 		if (is_constrained(key))
 		{
 			ConditionalGaussian::shared_ptr ccg = eliminate_constraint(key);
-			cbn->insert(ccg);
+			cbn->push_back(ccg);
 		}
 		else
 		{
 			ConditionalGaussian::shared_ptr cg = eliminateOne<ConditionalGaussian>(key);
-			cbn->insert(cg);
+			cbn->push_back(cg);
 		}
 	}
 

cpp/LinearFactorGraph.cpp

@@ -63,7 +63,7 @@ LinearFactorGraph::eliminate_partially(const Ordering& ordering)
 
 	BOOST_FOREACH(string key, ordering) {
 		ConditionalGaussian::shared_ptr cg = eliminateOne<ConditionalGaussian>(key);
-		chordalBayesNet->insert(cg);
+		chordalBayesNet->push_back(cg);
 	}
 
 	return chordalBayesNet;

cpp/SymbolicFactorGraph.cpp

@@ -26,7 +26,7 @@ namespace gtsam {
 
 		BOOST_FOREACH(string key, ordering) {
 			SymbolicConditional::shared_ptr conditional = eliminateOne<SymbolicConditional>(key);
-			bayesNet->insert(conditional);
+			bayesNet->push_back(conditional);
 		}
 
 		return bayesNet;

cpp/smallExample.cpp

@@ -203,8 +203,8 @@ GaussianBayesNet createSmallGaussianBayesNet()
     Px_y(new ConditionalGaussian("x",d1,R11,"y",S12)),
     Py(new ConditionalGaussian("y",d2,R22));
   GaussianBayesNet cbn;
-  cbn.insert(Px_y);
+  cbn.push_back(Px_y);
-  cbn.insert(Py);
+  cbn.push_back(Py);
 
   return cbn;
 }

cpp/testBayesTree.cpp

@@ -27,10 +27,12 @@ SymbolicConditional::shared_ptr B(new SymbolicConditional("B")), L(
 /* ************************************************************************* */
 TEST( BayesTree, Front )
 {
-	Front<SymbolicConditional> f1(B);
+	BayesNet<SymbolicConditional> f1;
-	f1.add(L);
+	f1.push_back(B);
-	Front<SymbolicConditional> f2(L);
+	f1.push_back(L);
-	f2.add(B);
+	BayesNet<SymbolicConditional> f2;
+	f2.push_back(L);
+	f2.push_back(B);
 	CHECK(f1.equals(f1));
 	CHECK(!f1.equals(f2));
 }
@@ -51,21 +53,24 @@ TEST( BayesTree, constructor )
 	LONGS_EQUAL(4,bayesTree.size());
 
 	// Check root
-	Front<SymbolicConditional> expected_root(B);
+	BayesNet<SymbolicConditional> expected_root;
-	expected_root.add(L);
+	expected_root.push_back(B);
-	expected_root.add(E);
+	expected_root.push_back(L);
-	Front<SymbolicConditional> actual_root = bayesTree.root();
+	expected_root.push_back(E);
+	BayesNet<SymbolicConditional> actual_root = bayesTree.root();
 	CHECK(assert_equal(expected_root,actual_root));
 
 	// Create from symbolic Bayes chain in which we want to discover cliques
 	SymbolicBayesNet ASIA;
-	ASIA.insert(X);
+	ASIA.push_back(X);
-	ASIA.insert(T);
+	ASIA.push_back(T);
-	ASIA.insert(S);
+	ASIA.push_back(S);
-	ASIA.insert(E);
+	ASIA.push_back(E);
-	ASIA.insert(L);
+	ASIA.push_back(L);
-	ASIA.insert(B);
+	ASIA.push_back(B);
-	BayesTree<SymbolicConditional> bayesTree2(ASIA);
+	bool verbose = true;
+	BayesTree<SymbolicConditional> bayesTree2(ASIA,verbose);
+	if (verbose) bayesTree2.print("bayesTree2");
 
 	// Check whether the same
 	CHECK(assert_equal(bayesTree,bayesTree2));

cpp/testLinearFactorGraph.cpp

@@ -276,9 +276,9 @@ TEST( LinearFactorGraph, eliminateAll )
   ConditionalGaussian::shared_ptr cg3(new ConditionalGaussian("x2",d3, R3, "l1", A21, "x1", A22));
   
   GaussianBayesNet expected;
-  expected.insert(cg3);
+  expected.push_back(cg3);
-  expected.insert(cg2);
+  expected.push_back(cg2);
-  expected.insert(cg1);
+  expected.push_back(cg1);
   
   // Check one ordering
   LinearFactorGraph fg1 = createLinearFactorGraph();

cpp/testSymbolicBayesNet.cpp

@@ -27,9 +27,9 @@ TEST( SymbolicBayesNet, constructor )
 		l1(new SymbolicConditional("l1","x1")),
 		x1(new SymbolicConditional("x1"));
 	SymbolicBayesNet expected;
-	expected.insert(x2);
+	expected.push_back(x2);
-	expected.insert(l1);
+	expected.push_back(l1);
-	expected.insert(x1);
+	expected.push_back(x1);
 
 	// Create from a factor graph
 	LinearFactorGraph factorGraph = createLinearFactorGraph();

cpp/testSymbolicFactorGraph.cpp

@@ -129,9 +129,9 @@ TEST( LinearFactorGraph, eliminate )
   SymbolicConditional::shared_ptr x1(new SymbolicConditional("x1"));
 
   SymbolicBayesNet expected;
-  expected.insert(x2);
+  expected.push_back(x2);
-  expected.insert(l1);
+  expected.push_back(l1);
-  expected.insert(x1);
+  expected.push_back(x1);
 
   // create a test graph
 	LinearFactorGraph factorGraph = createLinearFactorGraph();