mark helper methods as protected and add docstrings

gtsam/hybrid/HybridEliminationTree.h

@@ -73,6 +73,7 @@ class GTSAM_EXPORT HybridEliminationTree
   /** Test whether the tree is equal to another */
   bool equals(const This& other, double tol = 1e-9) const;
 
+ protected:
   /**
    * @brief Helper method to eliminate continuous variables.
    *
@@ -87,6 +88,22 @@ class GTSAM_EXPORT HybridEliminationTree
             boost::shared_ptr<HybridGaussianFactorGraph>>
   eliminateContinuous(Eliminate function) const;
 
+  /**
+   * @brief Compute the unnormalized probability P'(X | M, Z)
+   * for the factor graph in each leaf of the discrete tree.
+   * The discrete decision tree formed as a result is added to the
+   * `discreteGraph` for discrete elimination.
+   *
+   * @param continuousBayesNet The bayes nets corresponding to
+   * the eliminated continuous variables.
+   * @param discreteGraph Factor graph consisting of factors
+   * on discrete variables only.
+   * @return boost::shared_ptr<HybridGaussianFactorGraph>
+   */
+  boost::shared_ptr<HybridGaussianFactorGraph> addProbPrimes(
+      const HybridBayesNet::shared_ptr& continuousBayesNet,
+      const HybridGaussianFactorGraph::shared_ptr& discreteGraph) const;
+
   /**
    * @brief Helper method to eliminate the discrete variables after the
    * continuous variables have been eliminated.
@@ -105,6 +122,7 @@ class GTSAM_EXPORT HybridEliminationTree
       Eliminate function,
       const HybridGaussianFactorGraph::shared_ptr& discreteGraph) const;
 
+ public:
   /**
    * @brief Override the EliminationTree eliminate method
    * so we can perform hybrid elimination correctly.

gtsam/hybrid/HybridJunctionTree.cpp

@@ -252,11 +252,11 @@ HybridJunctionTree::eliminateDiscrete(
 
 /* ************************************************************************* */
 boost::shared_ptr<HybridGaussianFactorGraph> HybridJunctionTree::addProbPrimes(
-    const HybridGaussianFactorGraph& graph,
     const HybridBayesTree::shared_ptr& continuousBayesTree,
-    const HybridGaussianFactorGraph::shared_ptr& discreteGraph,
+    const HybridGaussianFactorGraph::shared_ptr& discreteGraph) const {
-    const Ordering& continuous_ordering,
+  Ordering continuous_ordering = etree_.continuousOrdering();
-    const Ordering& discrete_ordering) const {
+  Ordering discrete_ordering = etree_.discreteOrdering();
+
   // If we have eliminated continuous variables
   // and have discrete variables to eliminate,
   // then compute P(X | M, Z)
@@ -272,6 +272,8 @@ boost::shared_ptr<HybridGaussianFactorGraph> HybridJunctionTree::addProbPrimes(
     std::set<DiscreteKey> dkeys_set(discrete_keys.begin(), discrete_keys.end());
     discrete_keys = DiscreteKeys(dkeys_set.begin(), dkeys_set.end());
 
+    FactorGraphType graph = etree_.graph();
+
     // DecisionTree for P'(X|M, Z) for all mode sequences M
     const AlgebraicDecisionTree<Key> probPrimeTree =
         graph.continuousProbPrimes(discrete_keys, continuousBayesTree);
@@ -298,8 +300,7 @@ HybridJunctionTree::eliminate(const Eliminate& function) const {
       this->eliminateContinuous(function, graph, continuous_ordering);
 
   FactorGraphType::shared_ptr updatedDiscreteGraph =
-      this->addProbPrimes(graph, continuousBayesTree, discreteGraph,
+      this->addProbPrimes(continuousBayesTree, discreteGraph);
-                          continuous_ordering, discrete_ordering);
 
   // Eliminate discrete variables to get the discrete bayes tree.
   return this->eliminateDiscrete(function, continuousBayesTree,

gtsam/hybrid/HybridJunctionTree.h

@@ -73,14 +73,15 @@ class GTSAM_EXPORT HybridJunctionTree
    */
   HybridJunctionTree(const HybridEliminationTree& eliminationTree);
 
+ protected:
   /**
-   * @brief 
+   * @brief Eliminate all the continuous variables from the factor graph.
-   * 
+   *
-   * @param function 
+   * @param function The hybrid elimination function.
-   * @param graph 
+   * @param graph The factor graph to eliminate.
-   * @param continuous_ordering 
+   * @param continuous_ordering The ordering of continuous variables.
    * @return std::pair<boost::shared_ptr<HybridBayesTree>,
-   * boost::shared_ptr<HybridGaussianFactorGraph>> 
+   * boost::shared_ptr<HybridGaussianFactorGraph>>
    */
   std::pair<boost::shared_ptr<HybridBayesTree>,
             boost::shared_ptr<HybridGaussianFactorGraph>>
@@ -89,14 +90,17 @@ class GTSAM_EXPORT HybridJunctionTree
                       const Ordering& continuous_ordering) const;
 
   /**
-   * @brief 
+   * @brief Eliminate all the discrete variables in the hybrid factor graph.
-   * 
+   *
-   * @param function 
+   * @param function The hybrid elimination function.
-   * @param continuousBayesTree 
+   * @param continuousBayesTree The bayes tree corresponding to
-   * @param discreteGraph 
+   * the eliminated continuous variables.
-   * @param discrete_ordering 
+   * @param discreteGraph Factor graph of factors containing
+   * only discrete variables.
+   * @param discrete_ordering The elimination ordering for
+   * the discrete variables.
    * @return std::pair<boost::shared_ptr<HybridBayesTree>,
-   * boost::shared_ptr<HybridGaussianFactorGraph>> 
+   * boost::shared_ptr<HybridGaussianFactorGraph>>
    */
   std::pair<boost::shared_ptr<HybridBayesTree>,
             boost::shared_ptr<HybridGaussianFactorGraph>>
@@ -106,28 +110,29 @@ class GTSAM_EXPORT HybridJunctionTree
                     const Ordering& discrete_ordering) const;
 
   /**
-   * @brief 
+   * @brief Compute the unnormalized probability P'(X | M, Z)
-   * 
+   * for the factor graph in each leaf of the discrete tree.
-   * @param graph 
+   * The discrete decision tree formed as a result is added to the
-   * @param continuousBayesTree 
+   * `discreteGraph` for discrete elimination.
-   * @param discreteGraph 
+   *
-   * @param continuous_ordering 
+   * @param continuousBayesTree The bayes tree corresponding to
-   * @param discrete_ordering 
+   * the eliminated continuous variables.
-   * @return boost::shared_ptr<HybridGaussianFactorGraph> 
+   * @param discreteGraph Factor graph consisting of factors
+   * on discrete variables only.
+   * @return boost::shared_ptr<HybridGaussianFactorGraph>
    */
   boost::shared_ptr<HybridGaussianFactorGraph> addProbPrimes(
-      const HybridGaussianFactorGraph& graph,
       const HybridBayesTree::shared_ptr& continuousBayesTree,
-      const HybridGaussianFactorGraph::shared_ptr& discreteGraph,
+      const HybridGaussianFactorGraph::shared_ptr& discreteGraph) const;
-      const Ordering& continuous_ordering,
-      const Ordering& discrete_ordering) const;
 
+ public:
   /**
-   * @brief 
+   * @brief Override the eliminate method so we can
-   * 
+   * perform hybrid elimination correctly.
-   * @param function 
+   *
+   * @param function The hybrid elimination function.
    * @return std::pair<boost::shared_ptr<HybridBayesTree>,
-   * boost::shared_ptr<HybridGaussianFactorGraph>> 
+   * boost::shared_ptr<HybridGaussianFactorGraph>>
    */
   std::pair<boost::shared_ptr<HybridBayesTree>,
             boost::shared_ptr<HybridGaussianFactorGraph>>