From 58362579bb6d22ca9b94d4c0a3daf63bda0508a2 Mon Sep 17 00:00:00 2001
From: Frank dellaert <dellaert@gmail.com>
Date: Sun, 12 Jul 2020 12:27:10 -0400
Subject: [PATCH 1/9] Resurrecting DiscreteBayesTree tests

---
 gtsam/discrete/DiscreteBayesNet.h             |   3 +-
 gtsam/discrete/DiscreteBayesTree.cpp          |  13 +-
 gtsam/discrete/DiscreteBayesTree.h            |   3 +
 .../discrete/tests/testDiscreteBayesTree.cpp  | 499 +++++++++---------
 4 files changed, 257 insertions(+), 261 deletions(-)

diff --git a/gtsam/discrete/DiscreteBayesNet.h b/gtsam/discrete/DiscreteBayesNet.h
index dcc336f89..237caf745 100644
--- a/gtsam/discrete/DiscreteBayesNet.h
+++ b/gtsam/discrete/DiscreteBayesNet.h
@@ -20,13 +20,14 @@
 #include <vector>
 #include <map>
 #include <boost/shared_ptr.hpp>
+#include <gtsam/inference/BayesNet.h>
 #include <gtsam/inference/FactorGraph.h>
 #include <gtsam/discrete/DiscreteConditional.h>
 
 namespace gtsam {
 
 /** A Bayes net made from linear-Discrete densities */
-  class GTSAM_EXPORT DiscreteBayesNet: public FactorGraph<DiscreteConditional>
+  class GTSAM_EXPORT DiscreteBayesNet: public BayesNet<DiscreteConditional>
   {
   public:
 
diff --git a/gtsam/discrete/DiscreteBayesTree.cpp b/gtsam/discrete/DiscreteBayesTree.cpp
index bed50a470..8fcc34e25 100644
--- a/gtsam/discrete/DiscreteBayesTree.cpp
+++ b/gtsam/discrete/DiscreteBayesTree.cpp
@@ -29,10 +29,19 @@ namespace gtsam {
   template class BayesTreeCliqueBase<DiscreteBayesTreeClique, DiscreteFactorGraph>;
   template class BayesTree<DiscreteBayesTreeClique>;
 
+  /* ************************************************************************* */
+  double DiscreteBayesTreeClique::evaluate(
+      const DiscreteConditional::Values& values) const {
+    // evaluate all conditionals and multiply
+    double result = (*conditional_)(values);
+    for (const auto& child : children) {
+      result *= child->evaluate(values);
+    }
+    return result;
+  }
 
   /* ************************************************************************* */
-  bool DiscreteBayesTree::equals(const This& other, double tol) const
-  {
+  bool DiscreteBayesTree::equals(const This& other, double tol) const {
     return Base::equals(other, tol);
   }
 
diff --git a/gtsam/discrete/DiscreteBayesTree.h b/gtsam/discrete/DiscreteBayesTree.h
index 0df6ab476..aa8f4657c 100644
--- a/gtsam/discrete/DiscreteBayesTree.h
+++ b/gtsam/discrete/DiscreteBayesTree.h
@@ -42,6 +42,9 @@ namespace gtsam {
     typedef boost::weak_ptr<This> weak_ptr;
     DiscreteBayesTreeClique() {}
     DiscreteBayesTreeClique(const boost::shared_ptr<DiscreteConditional>& conditional) : Base(conditional) {}
+
+    //** evaluate conditional probability of subtree for given Values */
+    double evaluate(const DiscreteConditional::Values & values) const;
   };
 
   /* ************************************************************************* */
diff --git a/gtsam/discrete/tests/testDiscreteBayesTree.cpp b/gtsam/discrete/tests/testDiscreteBayesTree.cpp
index 93126f642..f58fd2b19 100644
--- a/gtsam/discrete/tests/testDiscreteBayesTree.cpp
+++ b/gtsam/discrete/tests/testDiscreteBayesTree.cpp
@@ -1,261 +1,245 @@
-///* ----------------------------------------------------------------------------
-//
-// * GTSAM Copyright 2010, Georgia Tech Research Corporation,
-// * Atlanta, Georgia 30332-0415
-// * All Rights Reserved
-// * Authors: Frank Dellaert, et al. (see THANKS for the full author list)
-//
-// * See LICENSE for the license information
-//
-// * -------------------------------------------------------------------------- */
-//
-///*
-// * @file testDiscreteBayesTree.cpp
-// * @date sept 15, 2012
-// * @author Frank Dellaert
-// */
-//
-//#include <gtsam/discrete/DiscreteBayesNet.h>
-//#include <gtsam/discrete/DiscreteBayesTree.h>
-//#include <gtsam/discrete/DiscreteFactorGraph.h>
-//
-//#include <boost/assign/std/vector.hpp>
-//using namespace boost::assign;
-//
+/* ----------------------------------------------------------------------------
+
+* GTSAM Copyright 2010-2020, Georgia Tech Research Corporation,
+* Atlanta, Georgia 30332-0415
+* All Rights Reserved
+* Authors: Frank Dellaert, et al. (see THANKS for the full author list)
+
+* See LICENSE for the license information
+
+* -------------------------------------------------------------------------- */
+
+/*
+ * @file testDiscreteBayesTree.cpp
+ * @date sept 15, 2012
+ * @author Frank Dellaert
+ */
+
+#include <gtsam/base/Vector.h>
+#include <gtsam/discrete/DiscreteBayesNet.h>
+#include <gtsam/discrete/DiscreteBayesTree.h>
+#include <gtsam/discrete/DiscreteFactorGraph.h>
+#include <gtsam/inference/BayesNet-inst.h>
+
+#include <boost/assign/std/vector.hpp>
+using namespace boost::assign;
+
 #include <CppUnitLite/TestHarness.h>
-//
-//using namespace std;
-//using namespace gtsam;
-//
-//static bool debug = false;
-//
-///**
-// * Custom clique class to debug shortcuts
-// */
-////class Clique: public BayesTreeCliqueBaseOrdered<Clique, DiscreteConditional> {
-////
-////protected:
-////
-////public:
-////
-////  typedef BayesTreeCliqueBaseOrdered<Clique, DiscreteConditional> Base;
-////  typedef boost::shared_ptr<Clique> shared_ptr;
-////
-////  // Constructors
-////  Clique() {
-////  }
-////  Clique(const DiscreteConditional::shared_ptr& conditional) :
-////      Base(conditional) {
-////  }
-////  Clique(
-////      const std::pair<DiscreteConditional::shared_ptr,
-////          DiscreteConditional::FactorType::shared_ptr>& result) :
-////      Base(result) {
-////  }
-////
-////  /// print index signature only
-////  void printSignature(const std::string& s = "Clique: ",
-////      const KeyFormatter& indexFormatter = DefaultKeyFormatter) const {
-////    ((IndexConditionalOrdered::shared_ptr) conditional_)->print(s, indexFormatter);
-////  }
-////
-////  /// evaluate value of sub-tree
-////  double evaluate(const DiscreteConditional::Values & values) {
-////    double result = (*(this->conditional_))(values);
-////    // evaluate all children and multiply into result
-////    for(boost::shared_ptr<Clique> c: children_)
-////      result *= c->evaluate(values);
-////    return result;
-////  }
-////
-////};
-//
-////typedef BayesTreeOrdered<DiscreteConditional, Clique> DiscreteBayesTree;
-////
-/////* ************************************************************************* */
-////double evaluate(const DiscreteBayesTree& tree,
-////    const DiscreteConditional::Values & values) {
-////  return tree.root()->evaluate(values);
-////}
-//
-///* ************************************************************************* */
-//
-//TEST_UNSAFE( DiscreteBayesTree, thinTree ) {
-//
-//  const int nrNodes = 15;
-//  const size_t nrStates = 2;
-//
-//  // define variables
-//  vector<DiscreteKey> key;
-//  for (int i = 0; i < nrNodes; i++) {
-//    DiscreteKey key_i(i, nrStates);
-//    key.push_back(key_i);
-//  }
-//
-//  // create a thin-tree Bayesnet, a la Jean-Guillaume
-//  DiscreteBayesNet bayesNet;
-//  bayesNet.add(key[14] % "1/3");
-//
-//  bayesNet.add(key[13] | key[14] = "1/3 3/1");
-//  bayesNet.add(key[12] | key[14] = "3/1 3/1");
-//
-//  bayesNet.add((key[11] | key[13], key[14]) = "1/4 2/3 3/2 4/1");
-//  bayesNet.add((key[10] | key[13], key[14]) = "1/4 3/2 2/3 4/1");
-//  bayesNet.add((key[9] | key[12], key[14]) = "4/1 2/3 F 1/4");
-//  bayesNet.add((key[8] | key[12], key[14]) = "T 1/4 3/2 4/1");
-//
-//  bayesNet.add((key[7] | key[11], key[13]) = "1/4 2/3 3/2 4/1");
-//  bayesNet.add((key[6] | key[11], key[13]) = "1/4 3/2 2/3 4/1");
-//  bayesNet.add((key[5] | key[10], key[13]) = "4/1 2/3 3/2 1/4");
-//  bayesNet.add((key[4] | key[10], key[13]) = "2/3 1/4 3/2 4/1");
-//
-//  bayesNet.add((key[3] | key[9], key[12]) = "1/4 2/3 3/2 4/1");
-//  bayesNet.add((key[2] | key[9], key[12]) = "1/4 8/2 2/3 4/1");
-//  bayesNet.add((key[1] | key[8], key[12]) = "4/1 2/3 3/2 1/4");
-//  bayesNet.add((key[0] | key[8], key[12]) = "2/3 1/4 3/2 4/1");
-//
-////  if (debug) {
-////    GTSAM_PRINT(bayesNet);
-////    bayesNet.saveGraph("/tmp/discreteBayesNet.dot");
-////  }
-//
-//  // create a BayesTree out of a Bayes net
-//  DiscreteBayesTree bayesTree(bayesNet);
-//  if (debug) {
-//    GTSAM_PRINT(bayesTree);
-//    bayesTree.saveGraph("/tmp/discreteBayesTree.dot");
-//  }
-//
-//  // Check whether BN and BT give the same answer on all configurations
-//  // Also calculate all some marginals
-//  Vector marginals = zero(15);
-//  double joint_12_14 = 0, joint_9_12_14 = 0, joint_8_12_14 = 0, joint_8_12 = 0,
-//      joint82 = 0, joint12 = 0, joint24 = 0, joint45 = 0, joint46 = 0,
-//      joint_4_11 = 0;
-//  vector<DiscreteFactor::Values> allPosbValues = cartesianProduct(
-//      key[0] & key[1] & key[2] & key[3] & key[4] & key[5] & key[6] & key[7]
-//          & key[8] & key[9] & key[10] & key[11] & key[12] & key[13] & key[14]);
-//  for (size_t i = 0; i < allPosbValues.size(); ++i) {
-//    DiscreteFactor::Values x = allPosbValues[i];
-//    double expected = evaluate(bayesNet, x);
-//    double actual = evaluate(bayesTree, x);
-//    DOUBLES_EQUAL(expected, actual, 1e-9);
-//    // collect marginals
-//    for (size_t i = 0; i < 15; i++)
-//      if (x[i])
-//        marginals[i] += actual;
-//    // calculate shortcut 8 and 0
-//    if (x[12] && x[14])
-//      joint_12_14 += actual;
-//    if (x[9] && x[12] & x[14])
-//      joint_9_12_14 += actual;
-//    if (x[8] && x[12] & x[14])
-//      joint_8_12_14 += actual;
-//    if (x[8] && x[12])
-//      joint_8_12 += actual;
-//    if (x[8] && x[2])
-//      joint82 += actual;
-//    if (x[1] && x[2])
-//      joint12 += actual;
-//    if (x[2] && x[4])
-//      joint24 += actual;
-//    if (x[4] && x[5])
-//      joint45 += actual;
-//    if (x[4] && x[6])
-//      joint46 += actual;
-//    if (x[4] && x[11])
-//      joint_4_11 += actual;
-//  }
-//  DiscreteFactor::Values all1 = allPosbValues.back();
-//
-//  Clique::shared_ptr R = bayesTree.root();
-//
-//  // check separator marginal P(S0)
-//  Clique::shared_ptr c = bayesTree[0];
-//  DiscreteFactorGraph separatorMarginal0 = c->separatorMarginal(R,
-//      EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(joint_8_12, separatorMarginal0(all1), 1e-9);
-//
-//  // check separator marginal P(S9), should be P(14)
-//  c = bayesTree[9];
-//  DiscreteFactorGraph separatorMarginal9 = c->separatorMarginal(R,
-//      EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(marginals[14], separatorMarginal9(all1), 1e-9);
-//
-//  // check separator marginal of root, should be empty
-//  c = bayesTree[11];
-//  DiscreteFactorGraph separatorMarginal11 = c->separatorMarginal(R,
-//      EliminateDiscrete);
-//  EXPECT_LONGS_EQUAL(0, separatorMarginal11.size());
-//
-//  // check shortcut P(S9||R) to root
-//  c = bayesTree[9];
-//  DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
-//  EXPECT_LONGS_EQUAL(0, shortcut.size());
-//
-//  // check shortcut P(S8||R) to root
-//  c = bayesTree[8];
-//  shortcut = c->shortcut(R, EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(joint_12_14/marginals[14], evaluate(shortcut,all1),
-//      1e-9);
-//
-//  // check shortcut P(S2||R) to root
-//  c = bayesTree[2];
-//  shortcut = c->shortcut(R, EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(joint_9_12_14/marginals[14], evaluate(shortcut,all1),
-//      1e-9);
-//
-//  // check shortcut P(S0||R) to root
-//  c = bayesTree[0];
-//  shortcut = c->shortcut(R, EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(joint_8_12_14/marginals[14], evaluate(shortcut,all1),
-//      1e-9);
-//
-//  // calculate all shortcuts to root
-//  DiscreteBayesTree::Nodes cliques = bayesTree.nodes();
-//  for(Clique::shared_ptr c: cliques) {
-//    DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
-//    if (debug) {
-//      c->printSignature();
-//      shortcut.print("shortcut:");
-//    }
-//  }
-//
-//  // Check all marginals
-//  DiscreteFactor::shared_ptr marginalFactor;
-//  for (size_t i = 0; i < 15; i++) {
-//    marginalFactor = bayesTree.marginalFactor(i, EliminateDiscrete);
-//    double actual = (*marginalFactor)(all1);
-//    EXPECT_DOUBLES_EQUAL(marginals[i], actual, 1e-9);
-//  }
-//
-//  DiscreteBayesNet::shared_ptr actualJoint;
-//
-//  // Check joint P(8,2) TODO: not disjoint !
-////  actualJoint = bayesTree.jointBayesNet(8, 2, EliminateDiscrete);
-////  EXPECT_DOUBLES_EQUAL(joint82, evaluate(*actualJoint,all1), 1e-9);
-//
-//  // Check joint P(1,2) TODO: not disjoint !
-////  actualJoint = bayesTree.jointBayesNet(1, 2, EliminateDiscrete);
-////  EXPECT_DOUBLES_EQUAL(joint12, evaluate(*actualJoint,all1), 1e-9);
-//
-//  // Check joint P(2,4)
-//  actualJoint = bayesTree.jointBayesNet(2, 4, EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(joint24, evaluate(*actualJoint,all1), 1e-9);
-//
-//  // Check joint P(4,5) TODO: not disjoint !
-////  actualJoint = bayesTree.jointBayesNet(4, 5, EliminateDiscrete);
-////  EXPECT_DOUBLES_EQUAL(joint46, evaluate(*actualJoint,all1), 1e-9);
-//
-//  // Check joint P(4,6) TODO: not disjoint !
-////  actualJoint = bayesTree.jointBayesNet(4, 6, EliminateDiscrete);
-////  EXPECT_DOUBLES_EQUAL(joint46, evaluate(*actualJoint,all1), 1e-9);
-//
-//  // Check joint P(4,11)
-//  actualJoint = bayesTree.jointBayesNet(4, 11, EliminateDiscrete);
-//  EXPECT_DOUBLES_EQUAL(joint_4_11, evaluate(*actualJoint,all1), 1e-9);
-//
-//}
+
+#include <vector>
+
+using namespace std;
+using namespace gtsam;
+
+static bool debug = false;
+
+// /**
+//  * Custom clique class to debug shortcuts
+//  */
+// struct Clique : public BayesTreeCliqueBase<Clique, DiscreteConditional> {
+//   typedef BayesTreeCliqueBase<Clique, DiscreteConditional> Base;
+//   typedef boost::shared_ptr<Clique> shared_ptr;
+
+//   // Constructors
+//   Clique() {}
+//   explicit Clique(const DiscreteConditional::shared_ptr& conditional)
+//       : Base(conditional) {}
+//   Clique(const std::pair<DiscreteConditional::shared_ptr,
+//                          DiscreteConditional::FactorType::shared_ptr>&
+//                          result)
+//       : Base(result) {}
+
+//   /// print index signature only
+//   void printSignature(
+//       const std::string& s = "Clique: ",
+//       const KeyFormatter& indexFormatter = DefaultKeyFormatter) const {
+//     ((IndexConditionalOrdered::shared_ptr)conditional_)
+//         ->print(s, indexFormatter);
+//   }
+
+//   /// evaluate value of sub-tree
+//   double evaluate(const DiscreteConditional::Values& values) {
+//     double result = (*(this->conditional_))(values);
+//     // evaluate all children and multiply into result
+//     for (boost::shared_ptr<Clique> c : children_) result *=
+//     c->evaluate(values); return result;
+//   }
+// };
+
+// typedef BayesTreeOrdered<DiscreteConditional, Clique> DiscreteBayesTree;
+
+/* ************************************************************************* */
+
+TEST_UNSAFE(DiscreteBayesTree, thinTree) {
+  const int nrNodes = 15;
+  const size_t nrStates = 2;
+
+  // define variables
+  vector<DiscreteKey> key;
+  for (int i = 0; i < nrNodes; i++) {
+    DiscreteKey key_i(i, nrStates);
+    key.push_back(key_i);
+  }
+
+  // create a thin-tree Bayesnet, a la Jean-Guillaume
+  DiscreteBayesNet bayesNet;
+  bayesNet.add(key[14] % "1/3");
+
+  bayesNet.add(key[13] | key[14] = "1/3 3/1");
+  bayesNet.add(key[12] | key[14] = "3/1 3/1");
+
+  bayesNet.add((key[11] | key[13], key[14]) = "1/4 2/3 3/2 4/1");
+  bayesNet.add((key[10] | key[13], key[14]) = "1/4 3/2 2/3 4/1");
+  bayesNet.add((key[9] | key[12], key[14]) = "4/1 2/3 F 1/4");
+  bayesNet.add((key[8] | key[12], key[14]) = "T 1/4 3/2 4/1");
+
+  bayesNet.add((key[7] | key[11], key[13]) = "1/4 2/3 3/2 4/1");
+  bayesNet.add((key[6] | key[11], key[13]) = "1/4 3/2 2/3 4/1");
+  bayesNet.add((key[5] | key[10], key[13]) = "4/1 2/3 3/2 1/4");
+  bayesNet.add((key[4] | key[10], key[13]) = "2/3 1/4 3/2 4/1");
+
+  bayesNet.add((key[3] | key[9], key[12]) = "1/4 2/3 3/2 4/1");
+  bayesNet.add((key[2] | key[9], key[12]) = "1/4 8/2 2/3 4/1");
+  bayesNet.add((key[1] | key[8], key[12]) = "4/1 2/3 3/2 1/4");
+  bayesNet.add((key[0] | key[8], key[12]) = "2/3 1/4 3/2 4/1");
+
+  if (debug) {
+    GTSAM_PRINT(bayesNet);
+    bayesNet.saveGraph("/tmp/discreteBayesNet.dot");
+  }
+
+  // create a BayesTree out of a Bayes net
+  auto bayesTree = DiscreteFactorGraph(bayesNet).eliminateMultifrontal();
+  if (debug) {
+    GTSAM_PRINT(*bayesTree);
+    bayesTree->saveGraph("/tmp/discreteBayesTree.dot");
+  }
+
+  auto R = bayesTree->roots().front();
+
+  // Check whether BN and BT give the same answer on all configurations
+  vector<DiscreteFactor::Values> allPosbValues = cartesianProduct(
+      key[0] & key[1] & key[2] & key[3] & key[4] & key[5] & key[6] & key[7] &
+      key[8] & key[9] & key[10] & key[11] & key[12] & key[13] & key[14]);
+  for (size_t i = 0; i < allPosbValues.size(); ++i) {
+    DiscreteFactor::Values x = allPosbValues[i];
+    double expected = bayesNet.evaluate(x);
+    double actual = R->evaluate(x);
+    DOUBLES_EQUAL(expected, actual, 1e-9);
+  }
+
+  // Calculate all some marginals
+  Vector marginals = zero(15);
+  double joint_12_14 = 0, joint_9_12_14 = 0, joint_8_12_14 = 0, joint_8_12 = 0,
+         joint82 = 0, joint12 = 0, joint24 = 0, joint45 = 0, joint46 = 0,
+         joint_4_11 = 0;
+  for (size_t i = 0; i < allPosbValues.size(); ++i) {
+    DiscreteFactor::Values x = allPosbValues[i];
+    double px = R->evaluate(x);
+    for (size_t i = 0; i < 15; i++)
+      if (x[i]) marginals[i] += px;
+    // calculate shortcut 8 and 0
+    if (x[12] && x[14]) joint_12_14 += px;
+    if (x[9] && x[12] & x[14]) joint_9_12_14 += px;
+    if (x[8] && x[12] & x[14]) joint_8_12_14 += px;
+    if (x[8] && x[12]) joint_8_12 += px;
+    if (x[8] && x[2]) joint82 += px;
+    if (x[1] && x[2]) joint12 += px;
+    if (x[2] && x[4]) joint24 += px;
+    if (x[4] && x[5]) joint45 += px;
+    if (x[4] && x[6]) joint46 += px;
+    if (x[4] && x[11]) joint_4_11 += px;
+  }
+  DiscreteFactor::Values all1 = allPosbValues.back();
+
+
+  // check separator marginal P(S0)
+  auto c = (*bayesTree)[0];
+  DiscreteFactorGraph separatorMarginal0 =
+      c->separatorMarginal(EliminateDiscrete);
+  EXPECT_DOUBLES_EQUAL(joint_8_12, separatorMarginal0(all1), 1e-9);
+
+  // // check separator marginal P(S9), should be P(14)
+  // c = (*bayesTree)[9];
+  // DiscreteFactorGraph separatorMarginal9 =
+  //     c->separatorMarginal(EliminateDiscrete);
+  // EXPECT_DOUBLES_EQUAL(marginals[14], separatorMarginal9(all1), 1e-9);
+
+  // // check separator marginal of root, should be empty
+  // c = (*bayesTree)[11];
+  // DiscreteFactorGraph separatorMarginal11 =
+  //     c->separatorMarginal(EliminateDiscrete);
+  // EXPECT_LONGS_EQUAL(0, separatorMarginal11.size());
+
+  // // check shortcut P(S9||R) to root
+  // c = (*bayesTree)[9];
+  // DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
+  // EXPECT_LONGS_EQUAL(0, shortcut.size());
+
+  // // check shortcut P(S8||R) to root
+  // c = (*bayesTree)[8];
+  // shortcut = c->shortcut(R, EliminateDiscrete);
+  // EXPECT_DOUBLES_EQUAL(joint_12_14 / marginals[14], evaluate(shortcut, all1),
+  //                      1e-9);
+
+  // // check shortcut P(S2||R) to root
+  // c = (*bayesTree)[2];
+  // shortcut = c->shortcut(R, EliminateDiscrete);
+  // EXPECT_DOUBLES_EQUAL(joint_9_12_14 / marginals[14], evaluate(shortcut,
+  // all1),
+  //                      1e-9);
+
+  // // check shortcut P(S0||R) to root
+  // c = (*bayesTree)[0];
+  // shortcut = c->shortcut(R, EliminateDiscrete);
+  // EXPECT_DOUBLES_EQUAL(joint_8_12_14 / marginals[14], evaluate(shortcut,
+  // all1),
+  //                      1e-9);
+
+  // // calculate all shortcuts to root
+  // DiscreteBayesTree::Nodes cliques = bayesTree->nodes();
+  // for (auto c : cliques) {
+  //   DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
+  //   if (debug) {
+  //     c->printSignature();
+  //     shortcut.print("shortcut:");
+  //   }
+  // }
+
+  // // Check all marginals
+  // DiscreteFactor::shared_ptr marginalFactor;
+  // for (size_t i = 0; i < 15; i++) {
+  //   marginalFactor = bayesTree->marginalFactor(i, EliminateDiscrete);
+  //   double actual = (*marginalFactor)(all1);
+  //   EXPECT_DOUBLES_EQUAL(marginals[i], actual, 1e-9);
+  // }
+
+  // DiscreteBayesNet::shared_ptr actualJoint;
+
+  // Check joint P(8,2) TODO: not disjoint !
+  //  actualJoint = bayesTree->jointBayesNet(8, 2, EliminateDiscrete);
+  //  EXPECT_DOUBLES_EQUAL(joint82, evaluate(*actualJoint,all1), 1e-9);
+
+  // Check joint P(1,2) TODO: not disjoint !
+  //  actualJoint = bayesTree->jointBayesNet(1, 2, EliminateDiscrete);
+  //  EXPECT_DOUBLES_EQUAL(joint12, evaluate(*actualJoint,all1), 1e-9);
+
+  // Check joint P(2,4)
+  // actualJoint = bayesTree->jointBayesNet(2, 4, EliminateDiscrete);
+  // EXPECT_DOUBLES_EQUAL(joint24, evaluate(*actualJoint, all1), 1e-9);
+
+  // Check joint P(4,5) TODO: not disjoint !
+  //  actualJoint = bayesTree->jointBayesNet(4, 5, EliminateDiscrete);
+  //  EXPECT_DOUBLES_EQUAL(joint46, evaluate(*actualJoint,all1), 1e-9);
+
+  // Check joint P(4,6) TODO: not disjoint !
+  //  actualJoint = bayesTree->jointBayesNet(4, 6, EliminateDiscrete);
+  //  EXPECT_DOUBLES_EQUAL(joint46, evaluate(*actualJoint,all1), 1e-9);
+
+  // Check joint P(4,11)
+  // actualJoint = bayesTree->jointBayesNet(4, 11, EliminateDiscrete);
+  // EXPECT_DOUBLES_EQUAL(joint_4_11, evaluate(*actualJoint, all1), 1e-9);
+}
 
 /* ************************************************************************* */
 int main() {
@@ -263,4 +247,3 @@ int main() {
   return TestRegistry::runAllTests(tr);
 }
 /* ************************************************************************* */
-

From 3f4bf163e73a5f04cb8291e40fc1892ab80bb83e Mon Sep 17 00:00:00 2001
From: Frank dellaert <dellaert@gmail.com>
Date: Sun, 12 Jul 2020 14:59:17 -0400
Subject: [PATCH 2/9] Checked in pdf for easy reference

---
 gtsam/discrete/tests/testDiscreteBayesTree.pdf | Bin 0 -> 10622 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 gtsam/discrete/tests/testDiscreteBayesTree.pdf

diff --git a/gtsam/discrete/tests/testDiscreteBayesTree.pdf b/gtsam/discrete/tests/testDiscreteBayesTree.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..e8167d455477f97aadb2101d26120a6c145891f5
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HcmV?d00001


From 968b207135bede702bcedd1f6398642fcc7547f6 Mon Sep 17 00:00:00 2001
From: Frank dellaert <dellaert@gmail.com>
Date: Sun, 12 Jul 2020 14:59:43 -0400
Subject: [PATCH 3/9] added printSignature and evaluate

---
 gtsam/discrete/DiscreteBayesTree.cpp | 10 ++++
 gtsam/discrete/DiscreteBayesTree.h   | 85 ++++++++++++++++------------
 gtsam/discrete/DiscreteConditional.h |  9 +++
 gtsam/inference/Conditional.h        |  3 +-
 4 files changed, 71 insertions(+), 36 deletions(-)

diff --git a/gtsam/discrete/DiscreteBayesTree.cpp b/gtsam/discrete/DiscreteBayesTree.cpp
index 8fcc34e25..990d10dbe 100644
--- a/gtsam/discrete/DiscreteBayesTree.cpp
+++ b/gtsam/discrete/DiscreteBayesTree.cpp
@@ -45,6 +45,16 @@ namespace gtsam {
     return Base::equals(other, tol);
   }
 
+  /* ************************************************************************* */
+  double DiscreteBayesTree::evaluate(
+      const DiscreteConditional::Values& values) const {
+    double result = 1.0;
+    for (const auto& root : roots_) {
+      result *= root->evaluate(values);
+    }
+    return result;
+  }
+
 } // \namespace gtsam
 
 
diff --git a/gtsam/discrete/DiscreteBayesTree.h b/gtsam/discrete/DiscreteBayesTree.h
index aa8f4657c..3d6e016fd 100644
--- a/gtsam/discrete/DiscreteBayesTree.h
+++ b/gtsam/discrete/DiscreteBayesTree.h
@@ -11,7 +11,8 @@
 
 /**
  * @file    DiscreteBayesTree.h
- * @brief   Discrete Bayes Tree, the result of eliminating a DiscreteJunctionTree
+ * @brief   Discrete Bayes Tree, the result of eliminating a
+ * DiscreteJunctionTree
  * @brief   DiscreteBayesTree
  * @author  Frank Dellaert
  * @author  Richard Roberts
@@ -22,48 +23,62 @@
 #include <gtsam/discrete/DiscreteBayesNet.h>
 #include <gtsam/discrete/DiscreteFactorGraph.h>
 #include <gtsam/inference/BayesTree.h>
+#include <gtsam/inference/Conditional.h>
 #include <gtsam/inference/BayesTreeCliqueBase.h>
 
+#include <string>
+
 namespace gtsam {
 
-  // Forward declarations
-  class DiscreteConditional;
-  class VectorValues;
+// Forward declarations
+class DiscreteConditional;
+class VectorValues;
 
-  /* ************************************************************************* */
-  /** A clique in a DiscreteBayesTree */
-  class GTSAM_EXPORT DiscreteBayesTreeClique :
-    public BayesTreeCliqueBase<DiscreteBayesTreeClique, DiscreteFactorGraph>
-  {
-  public:
-    typedef DiscreteBayesTreeClique This;
-    typedef BayesTreeCliqueBase<DiscreteBayesTreeClique, DiscreteFactorGraph> Base;
-    typedef boost::shared_ptr<This> shared_ptr;
-    typedef boost::weak_ptr<This> weak_ptr;
-    DiscreteBayesTreeClique() {}
-    DiscreteBayesTreeClique(const boost::shared_ptr<DiscreteConditional>& conditional) : Base(conditional) {}
+/* ************************************************************************* */
+/** A clique in a DiscreteBayesTree */
+class GTSAM_EXPORT DiscreteBayesTreeClique
+    : public BayesTreeCliqueBase<DiscreteBayesTreeClique, DiscreteFactorGraph> {
+ public:
+  typedef DiscreteBayesTreeClique This;
+  typedef BayesTreeCliqueBase<DiscreteBayesTreeClique, DiscreteFactorGraph>
+      Base;
+  typedef boost::shared_ptr<This> shared_ptr;
+  typedef boost::weak_ptr<This> weak_ptr;
+  DiscreteBayesTreeClique() {}
+  DiscreteBayesTreeClique(
+      const boost::shared_ptr<DiscreteConditional>& conditional)
+      : Base(conditional) {}
 
-    //** evaluate conditional probability of subtree for given Values */
-    double evaluate(const DiscreteConditional::Values & values) const;
-  };
+  /// print index signature only
+  void printSignature(
+      const std::string& s = "Clique: ",
+      const KeyFormatter& formatter = DefaultKeyFormatter) const {
+    conditional_->printSignature(s, formatter);
+  }
 
-  /* ************************************************************************* */
-  /** A Bayes tree representing a Discrete density */
-  class GTSAM_EXPORT DiscreteBayesTree :
-    public BayesTree<DiscreteBayesTreeClique>
-  {
-  private:
-    typedef BayesTree<DiscreteBayesTreeClique> Base;
+  //** evaluate conditional probability of subtree for given Values */
+  double evaluate(const DiscreteConditional::Values& values) const;
+};
 
-  public:
-    typedef DiscreteBayesTree This;
-    typedef boost::shared_ptr<This> shared_ptr;
+/* ************************************************************************* */
+/** A Bayes tree representing a Discrete density */
+class GTSAM_EXPORT DiscreteBayesTree
+    : public BayesTree<DiscreteBayesTreeClique> {
+ private:
+  typedef BayesTree<DiscreteBayesTreeClique> Base;
 
-    /** Default constructor, creates an empty Bayes tree */
-    DiscreteBayesTree() {}
+ public:
+  typedef DiscreteBayesTree This;
+  typedef boost::shared_ptr<This> shared_ptr;
 
-    /** Check equality */
-    bool equals(const This& other, double tol = 1e-9) const;
-  };
+  /** Default constructor, creates an empty Bayes tree */
+  DiscreteBayesTree() {}
 
-}
+  /** Check equality */
+  bool equals(const This& other, double tol = 1e-9) const;
+
+  //** evaluate probability for given Values */
+  double evaluate(const DiscreteConditional::Values& values) const;
+};
+
+}  // namespace gtsam
diff --git a/gtsam/discrete/DiscreteConditional.h b/gtsam/discrete/DiscreteConditional.h
index 3da8d0a82..225e6e1d3 100644
--- a/gtsam/discrete/DiscreteConditional.h
+++ b/gtsam/discrete/DiscreteConditional.h
@@ -24,6 +24,8 @@
 #include <boost/shared_ptr.hpp>
 #include <boost/make_shared.hpp>
 
+#include <string>
+
 namespace gtsam {
 
 /**
@@ -92,6 +94,13 @@ public:
   /// @name Standard Interface
   /// @{
 
+  /// print index signature only
+  void printSignature(
+      const std::string& s = "Discrete Conditional: ",
+      const KeyFormatter& formatter = DefaultKeyFormatter) const {
+    static_cast<const BaseConditional*>(this)->print(s, formatter);
+  }
+
   /// Evaluate, just look up in AlgebraicDecisonTree
   virtual double operator()(const Values& values) const {
     return Potentials::operator()(values);
diff --git a/gtsam/inference/Conditional.h b/gtsam/inference/Conditional.h
index 1d486030c..295122879 100644
--- a/gtsam/inference/Conditional.h
+++ b/gtsam/inference/Conditional.h
@@ -65,6 +65,8 @@ namespace gtsam {
     Conditional(size_t nrFrontals) : nrFrontals_(nrFrontals) {}
 
     /// @}
+
+  public:
     /// @name Testable
     /// @{
 
@@ -76,7 +78,6 @@ namespace gtsam {
 
     /// @}
 
-  public:
     /// @name Standard Interface
     /// @{
 

From ae808d039cda45df8334d1857773c9c06c2943a0 Mon Sep 17 00:00:00 2001
From: Frank dellaert <dellaert@gmail.com>
Date: Sun, 12 Jul 2020 15:00:34 -0400
Subject: [PATCH 4/9] Fixed link issue

---
 gtsam/discrete/tests/testDiscreteFactorGraph.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gtsam/discrete/tests/testDiscreteFactorGraph.cpp b/gtsam/discrete/tests/testDiscreteFactorGraph.cpp
index 0fbf44097..7a0e1eaf7 100644
--- a/gtsam/discrete/tests/testDiscreteFactorGraph.cpp
+++ b/gtsam/discrete/tests/testDiscreteFactorGraph.cpp
@@ -19,6 +19,7 @@
 #include <gtsam/discrete/DiscreteFactorGraph.h>
 #include <gtsam/discrete/DiscreteEliminationTree.h>
 #include <gtsam/discrete/DiscreteBayesTree.h>
+#include <gtsam/inference/BayesNet-inst.h>
 
 #include <CppUnitLite/TestHarness.h>
 

From d456dddc6f1860f76b3ff8a7be555d55a430fb6d Mon Sep 17 00:00:00 2001
From: Frank dellaert <dellaert@gmail.com>
Date: Sun, 12 Jul 2020 15:00:54 -0400
Subject: [PATCH 5/9] Cleaned up formatting

---
 gtsam/inference/BayesTreeCliqueBase-inst.h | 54 ++++++++++++----------
 1 file changed, 29 insertions(+), 25 deletions(-)

diff --git a/gtsam/inference/BayesTreeCliqueBase-inst.h b/gtsam/inference/BayesTreeCliqueBase-inst.h
index e762786f5..a02fe274e 100644
--- a/gtsam/inference/BayesTreeCliqueBase-inst.h
+++ b/gtsam/inference/BayesTreeCliqueBase-inst.h
@@ -136,57 +136,61 @@ namespace gtsam {
     }
   }
 
-  /* ************************************************************************* */
+  /* *********************************************************************** */
   // separator marginal, uses separator marginal of parent recursively
   // P(C) = P(F|S) P(S)
-  /* ************************************************************************* */
-  template<class DERIVED, class FACTORGRAPH>
+  /* *********************************************************************** */
+  template <class DERIVED, class FACTORGRAPH>
   typename BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::FactorGraphType
-    BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::separatorMarginal(Eliminate function) const
-  {
+  BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::separatorMarginal(
+      Eliminate function) const {
     gttic(BayesTreeCliqueBase_separatorMarginal);
     // Check if the Separator marginal was already calculated
-    if (!cachedSeparatorMarginal_)
-    {
+    if (!cachedSeparatorMarginal_) {
       gttic(BayesTreeCliqueBase_separatorMarginal_cachemiss);
+
       // If this is the root, there is no separator
-      if (parent_.expired() /*(if we're the root)*/)
-      {
+      if (parent_.expired() /*(if we're the root)*/) {
         // we are root, return empty
         FactorGraphType empty;
         cachedSeparatorMarginal_ = empty;
-      }
-      else
-      {
+      } else {
+        // Flatten recursion in timing outline
+        gttoc(BayesTreeCliqueBase_separatorMarginal_cachemiss);
+        gttoc(BayesTreeCliqueBase_separatorMarginal);
+
         // Obtain P(S) = \int P(Cp) = \int P(Fp|Sp) P(Sp)
         // initialize P(Cp) with the parent separator marginal
         derived_ptr parent(parent_.lock());
-        gttoc(BayesTreeCliqueBase_separatorMarginal_cachemiss); // Flatten recursion in timing outline
-        gttoc(BayesTreeCliqueBase_separatorMarginal);
-        FactorGraphType p_Cp(parent->separatorMarginal(function)); // P(Sp)
+        FactorGraphType p_Cp(parent->separatorMarginal(function));  // P(Sp)
+
         gttic(BayesTreeCliqueBase_separatorMarginal);
         gttic(BayesTreeCliqueBase_separatorMarginal_cachemiss);
+
         // now add the parent conditional
-        p_Cp += parent->conditional_; // P(Fp|Sp)
+        p_Cp += parent->conditional_;  // P(Fp|Sp)
 
         // The variables we want to keepSet are exactly the ones in S
-        KeyVector indicesS(this->conditional()->beginParents(), this->conditional()->endParents());
-        cachedSeparatorMarginal_ = *p_Cp.marginalMultifrontalBayesNet(Ordering(indicesS), function);
+        KeyVector indicesS(this->conditional()->beginParents(),
+                           this->conditional()->endParents());
+        auto separatorMarginal =
+            p_Cp.marginalMultifrontalBayesNet(Ordering(indicesS), function);
+        cachedSeparatorMarginal_.reset(*separatorMarginal);
       }
     }
 
     // return the shortcut P(S||B)
-    return *cachedSeparatorMarginal_; // return the cached version
+    return *cachedSeparatorMarginal_;  // return the cached version
   }
 
-  /* ************************************************************************* */
-  // marginal2, uses separator marginal of parent recursively
+  /* *********************************************************************** */
+  // marginal2, uses separator marginal of parent
   // P(C) = P(F|S) P(S)
-  /* ************************************************************************* */
-  template<class DERIVED, class FACTORGRAPH>
+  /* *********************************************************************** */
+  template <class DERIVED, class FACTORGRAPH>
   typename BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::FactorGraphType
-    BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::marginal2(Eliminate function) const
-  {
+  BayesTreeCliqueBase<DERIVED, FACTORGRAPH>::marginal2(
+      Eliminate function) const {
     gttic(BayesTreeCliqueBase_marginal2);
     // initialize with separator marginal P(S)
     FactorGraphType p_C = this->separatorMarginal(function);

From 468c7aee0cd9b5933178b7304a6acce34eeb8692 Mon Sep 17 00:00:00 2001
From: Frank dellaert <dellaert@gmail.com>
Date: Sun, 12 Jul 2020 15:01:00 -0400
Subject: [PATCH 6/9] Fixed tests

---
 .../discrete/tests/testDiscreteBayesTree.cpp  | 191 ++++++++----------
 1 file changed, 81 insertions(+), 110 deletions(-)

diff --git a/gtsam/discrete/tests/testDiscreteBayesTree.cpp b/gtsam/discrete/tests/testDiscreteBayesTree.cpp
index f58fd2b19..150a41c24 100644
--- a/gtsam/discrete/tests/testDiscreteBayesTree.cpp
+++ b/gtsam/discrete/tests/testDiscreteBayesTree.cpp
@@ -33,41 +33,6 @@ using namespace gtsam;
 
 static bool debug = false;
 
-// /**
-//  * Custom clique class to debug shortcuts
-//  */
-// struct Clique : public BayesTreeCliqueBase<Clique, DiscreteConditional> {
-//   typedef BayesTreeCliqueBase<Clique, DiscreteConditional> Base;
-//   typedef boost::shared_ptr<Clique> shared_ptr;
-
-//   // Constructors
-//   Clique() {}
-//   explicit Clique(const DiscreteConditional::shared_ptr& conditional)
-//       : Base(conditional) {}
-//   Clique(const std::pair<DiscreteConditional::shared_ptr,
-//                          DiscreteConditional::FactorType::shared_ptr>&
-//                          result)
-//       : Base(result) {}
-
-//   /// print index signature only
-//   void printSignature(
-//       const std::string& s = "Clique: ",
-//       const KeyFormatter& indexFormatter = DefaultKeyFormatter) const {
-//     ((IndexConditionalOrdered::shared_ptr)conditional_)
-//         ->print(s, indexFormatter);
-//   }
-
-//   /// evaluate value of sub-tree
-//   double evaluate(const DiscreteConditional::Values& values) {
-//     double result = (*(this->conditional_))(values);
-//     // evaluate all children and multiply into result
-//     for (boost::shared_ptr<Clique> c : children_) result *=
-//     c->evaluate(values); return result;
-//   }
-// };
-
-// typedef BayesTreeOrdered<DiscreteConditional, Clique> DiscreteBayesTree;
-
 /* ************************************************************************* */
 
 TEST_UNSAFE(DiscreteBayesTree, thinTree) {
@@ -124,24 +89,24 @@ TEST_UNSAFE(DiscreteBayesTree, thinTree) {
   for (size_t i = 0; i < allPosbValues.size(); ++i) {
     DiscreteFactor::Values x = allPosbValues[i];
     double expected = bayesNet.evaluate(x);
-    double actual = R->evaluate(x);
+    double actual = bayesTree->evaluate(x);
     DOUBLES_EQUAL(expected, actual, 1e-9);
   }
 
-  // Calculate all some marginals
+  // Calculate all some marginals for Values==all1
   Vector marginals = zero(15);
   double joint_12_14 = 0, joint_9_12_14 = 0, joint_8_12_14 = 0, joint_8_12 = 0,
          joint82 = 0, joint12 = 0, joint24 = 0, joint45 = 0, joint46 = 0,
-         joint_4_11 = 0;
+         joint_4_11 = 0, joint_11_13 = 0, joint_11_13_14 = 0,
+         joint_11_12_13_14 = 0, joint_9_11_12_13 = 0, joint_8_11_12_13 = 0;
   for (size_t i = 0; i < allPosbValues.size(); ++i) {
     DiscreteFactor::Values x = allPosbValues[i];
-    double px = R->evaluate(x);
+    double px = bayesTree->evaluate(x);
     for (size_t i = 0; i < 15; i++)
       if (x[i]) marginals[i] += px;
-    // calculate shortcut 8 and 0
     if (x[12] && x[14]) joint_12_14 += px;
-    if (x[9] && x[12] & x[14]) joint_9_12_14 += px;
-    if (x[8] && x[12] & x[14]) joint_8_12_14 += px;
+    if (x[9] && x[12] && x[14]) joint_9_12_14 += px;
+    if (x[8] && x[12] && x[14]) joint_8_12_14 += px;
     if (x[8] && x[12]) joint_8_12 += px;
     if (x[8] && x[2]) joint82 += px;
     if (x[1] && x[2]) joint12 += px;
@@ -149,96 +114,102 @@ TEST_UNSAFE(DiscreteBayesTree, thinTree) {
     if (x[4] && x[5]) joint45 += px;
     if (x[4] && x[6]) joint46 += px;
     if (x[4] && x[11]) joint_4_11 += px;
+    if (x[11] && x[13]) {
+      joint_11_13 += px;
+      if (x[8] && x[12]) joint_8_11_12_13 += px;
+      if (x[9] && x[12]) joint_9_11_12_13 += px;
+      if (x[14]) {
+        joint_11_13_14 += px;
+        if (x[12]) {
+          joint_11_12_13_14 += px;
+        }
+      }
+    }
   }
   DiscreteFactor::Values all1 = allPosbValues.back();
 
-
   // check separator marginal P(S0)
   auto c = (*bayesTree)[0];
   DiscreteFactorGraph separatorMarginal0 =
       c->separatorMarginal(EliminateDiscrete);
-  EXPECT_DOUBLES_EQUAL(joint_8_12, separatorMarginal0(all1), 1e-9);
+  DOUBLES_EQUAL(joint_8_12, separatorMarginal0(all1), 1e-9);
 
-  // // check separator marginal P(S9), should be P(14)
-  // c = (*bayesTree)[9];
-  // DiscreteFactorGraph separatorMarginal9 =
-  //     c->separatorMarginal(EliminateDiscrete);
-  // EXPECT_DOUBLES_EQUAL(marginals[14], separatorMarginal9(all1), 1e-9);
+  // check separator marginal P(S9), should be P(14)
+  c = (*bayesTree)[9];
+  DiscreteFactorGraph separatorMarginal9 =
+      c->separatorMarginal(EliminateDiscrete);
+  DOUBLES_EQUAL(marginals[14], separatorMarginal9(all1), 1e-9);
 
-  // // check separator marginal of root, should be empty
-  // c = (*bayesTree)[11];
-  // DiscreteFactorGraph separatorMarginal11 =
-  //     c->separatorMarginal(EliminateDiscrete);
-  // EXPECT_LONGS_EQUAL(0, separatorMarginal11.size());
+  // check separator marginal of root, should be empty
+  c = (*bayesTree)[11];
+  DiscreteFactorGraph separatorMarginal11 =
+      c->separatorMarginal(EliminateDiscrete);
+  LONGS_EQUAL(0, separatorMarginal11.size());
 
-  // // check shortcut P(S9||R) to root
-  // c = (*bayesTree)[9];
-  // DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
-  // EXPECT_LONGS_EQUAL(0, shortcut.size());
+  // check shortcut P(S9||R) to root
+  c = (*bayesTree)[9];
+  DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
+  LONGS_EQUAL(1, shortcut.size());
+  DOUBLES_EQUAL(joint_11_13_14 / joint_11_13, shortcut.evaluate(all1), 1e-9);
 
-  // // check shortcut P(S8||R) to root
-  // c = (*bayesTree)[8];
-  // shortcut = c->shortcut(R, EliminateDiscrete);
-  // EXPECT_DOUBLES_EQUAL(joint_12_14 / marginals[14], evaluate(shortcut, all1),
-  //                      1e-9);
+  // check shortcut P(S8||R) to root
+  c = (*bayesTree)[8];
+  shortcut = c->shortcut(R, EliminateDiscrete);
+  DOUBLES_EQUAL(joint_11_12_13_14 / joint_11_13, shortcut.evaluate(all1), 1e-9);
 
-  // // check shortcut P(S2||R) to root
-  // c = (*bayesTree)[2];
-  // shortcut = c->shortcut(R, EliminateDiscrete);
-  // EXPECT_DOUBLES_EQUAL(joint_9_12_14 / marginals[14], evaluate(shortcut,
-  // all1),
-  //                      1e-9);
+  // check shortcut P(S2||R) to root
+  c = (*bayesTree)[2];
+  shortcut = c->shortcut(R, EliminateDiscrete);
+  DOUBLES_EQUAL(joint_9_11_12_13 / joint_11_13, shortcut.evaluate(all1), 1e-9);
 
-  // // check shortcut P(S0||R) to root
-  // c = (*bayesTree)[0];
-  // shortcut = c->shortcut(R, EliminateDiscrete);
-  // EXPECT_DOUBLES_EQUAL(joint_8_12_14 / marginals[14], evaluate(shortcut,
-  // all1),
-  //                      1e-9);
+  // check shortcut P(S0||R) to root
+  c = (*bayesTree)[0];
+  shortcut = c->shortcut(R, EliminateDiscrete);
+  DOUBLES_EQUAL(joint_8_11_12_13 / joint_11_13, shortcut.evaluate(all1), 1e-9);
 
-  // // calculate all shortcuts to root
-  // DiscreteBayesTree::Nodes cliques = bayesTree->nodes();
-  // for (auto c : cliques) {
-  //   DiscreteBayesNet shortcut = c->shortcut(R, EliminateDiscrete);
-  //   if (debug) {
-  //     c->printSignature();
-  //     shortcut.print("shortcut:");
-  //   }
-  // }
+  // calculate all shortcuts to root
+  DiscreteBayesTree::Nodes cliques = bayesTree->nodes();
+  for (auto c : cliques) {
+    DiscreteBayesNet shortcut = c.second->shortcut(R, EliminateDiscrete);
+    if (debug) {
+      c.second->conditional_->printSignature();
+      shortcut.print("shortcut:");
+    }
+  }
 
-  // // Check all marginals
-  // DiscreteFactor::shared_ptr marginalFactor;
-  // for (size_t i = 0; i < 15; i++) {
-  //   marginalFactor = bayesTree->marginalFactor(i, EliminateDiscrete);
-  //   double actual = (*marginalFactor)(all1);
-  //   EXPECT_DOUBLES_EQUAL(marginals[i], actual, 1e-9);
-  // }
+  // Check all marginals
+  DiscreteFactor::shared_ptr marginalFactor;
+  for (size_t i = 0; i < 15; i++) {
+    marginalFactor = bayesTree->marginalFactor(i, EliminateDiscrete);
+    double actual = (*marginalFactor)(all1);
+    DOUBLES_EQUAL(marginals[i], actual, 1e-9);
+  }
 
-  // DiscreteBayesNet::shared_ptr actualJoint;
+  DiscreteBayesNet::shared_ptr actualJoint;
 
-  // Check joint P(8,2) TODO: not disjoint !
-  //  actualJoint = bayesTree->jointBayesNet(8, 2, EliminateDiscrete);
-  //  EXPECT_DOUBLES_EQUAL(joint82, evaluate(*actualJoint,all1), 1e-9);
+  // Check joint P(8, 2)
+  actualJoint = bayesTree->jointBayesNet(8, 2, EliminateDiscrete);
+  DOUBLES_EQUAL(joint82, actualJoint->evaluate(all1), 1e-9);
 
-  // Check joint P(1,2) TODO: not disjoint !
-  //  actualJoint = bayesTree->jointBayesNet(1, 2, EliminateDiscrete);
-  //  EXPECT_DOUBLES_EQUAL(joint12, evaluate(*actualJoint,all1), 1e-9);
+  // Check joint P(1, 2)
+  actualJoint = bayesTree->jointBayesNet(1, 2, EliminateDiscrete);
+  DOUBLES_EQUAL(joint12, actualJoint->evaluate(all1), 1e-9);
 
-  // Check joint P(2,4)
-  // actualJoint = bayesTree->jointBayesNet(2, 4, EliminateDiscrete);
-  // EXPECT_DOUBLES_EQUAL(joint24, evaluate(*actualJoint, all1), 1e-9);
+  // Check joint P(2, 4)
+  actualJoint = bayesTree->jointBayesNet(2, 4, EliminateDiscrete);
+  DOUBLES_EQUAL(joint24, actualJoint->evaluate(all1), 1e-9);
 
-  // Check joint P(4,5) TODO: not disjoint !
-  //  actualJoint = bayesTree->jointBayesNet(4, 5, EliminateDiscrete);
-  //  EXPECT_DOUBLES_EQUAL(joint46, evaluate(*actualJoint,all1), 1e-9);
+  // Check joint P(4, 5)
+  actualJoint = bayesTree->jointBayesNet(4, 5, EliminateDiscrete);
+  DOUBLES_EQUAL(joint45, actualJoint->evaluate(all1), 1e-9);
 
-  // Check joint P(4,6) TODO: not disjoint !
-  //  actualJoint = bayesTree->jointBayesNet(4, 6, EliminateDiscrete);
-  //  EXPECT_DOUBLES_EQUAL(joint46, evaluate(*actualJoint,all1), 1e-9);
+  // Check joint P(4, 6)
+  actualJoint = bayesTree->jointBayesNet(4, 6, EliminateDiscrete);
+  DOUBLES_EQUAL(joint46, actualJoint->evaluate(all1), 1e-9);
 
-  // Check joint P(4,11)
-  // actualJoint = bayesTree->jointBayesNet(4, 11, EliminateDiscrete);
-  // EXPECT_DOUBLES_EQUAL(joint_4_11, evaluate(*actualJoint, all1), 1e-9);
+  // Check joint P(4, 11)
+  actualJoint = bayesTree->jointBayesNet(4, 11, EliminateDiscrete);
+  DOUBLES_EQUAL(joint_4_11, actualJoint->evaluate(all1), 1e-9);
 }
 
 /* ************************************************************************* */

From c68ab6b3bedf9576416b816089482c1a2e14ce50 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Sun, 12 Jul 2020 19:54:23 -0400
Subject: [PATCH 7/9] correct vector init

---
 gtsam/discrete/tests/testDiscreteBayesTree.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gtsam/discrete/tests/testDiscreteBayesTree.cpp b/gtsam/discrete/tests/testDiscreteBayesTree.cpp
index 150a41c24..9950c014e 100644
--- a/gtsam/discrete/tests/testDiscreteBayesTree.cpp
+++ b/gtsam/discrete/tests/testDiscreteBayesTree.cpp
@@ -35,7 +35,7 @@ static bool debug = false;
 
 /* ************************************************************************* */
 
-TEST_UNSAFE(DiscreteBayesTree, thinTree) {
+TEST_UNSAFE(DiscreteBayesTree, ThinTree) {
   const int nrNodes = 15;
   const size_t nrStates = 2;
 
@@ -94,7 +94,7 @@ TEST_UNSAFE(DiscreteBayesTree, thinTree) {
   }
 
   // Calculate all some marginals for Values==all1
-  Vector marginals = zero(15);
+  Vector marginals = Vector::Zero(15);
   double joint_12_14 = 0, joint_9_12_14 = 0, joint_8_12_14 = 0, joint_8_12 = 0,
          joint82 = 0, joint12 = 0, joint24 = 0, joint45 = 0, joint46 = 0,
          joint_4_11 = 0, joint_11_13 = 0, joint_11_13_14 = 0,

From c67779fdce5f0897ce36c85b1b2ea65896513862 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Sun, 12 Jul 2020 19:54:42 -0400
Subject: [PATCH 8/9] delete extra pdf file

---
 gtsam/discrete/tests/testDiscreteBayesTree.pdf | Bin 10622 -> 0 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 gtsam/discrete/tests/testDiscreteBayesTree.pdf

diff --git a/gtsam/discrete/tests/testDiscreteBayesTree.pdf b/gtsam/discrete/tests/testDiscreteBayesTree.pdf
deleted file mode 100644
index e8167d455477f97aadb2101d26120a6c145891f5..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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From 80b42dcbefeae96b53a5598b3a470734c5e5df68 Mon Sep 17 00:00:00 2001
From: Varun Agrawal <varagrawal@gmail.com>
Date: Sun, 12 Jul 2020 20:55:13 -0400
Subject: [PATCH 9/9] Revert "delete extra pdf file"

This reverts commit c67779fdce5f0897ce36c85b1b2ea65896513862.
---
 gtsam/discrete/tests/testDiscreteBayesTree.pdf | Bin 0 -> 10622 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 gtsam/discrete/tests/testDiscreteBayesTree.pdf

diff --git a/gtsam/discrete/tests/testDiscreteBayesTree.pdf b/gtsam/discrete/tests/testDiscreteBayesTree.pdf
new file mode 100644
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