Merge pull request #1286 from borglab/hybrid/serialization

Hybrid Serialization

gtsam/discrete/DiscreteKey.cpp

@@ -48,4 +48,25 @@ namespace gtsam {
     return keys & key2;
   }
 
+  void DiscreteKeys::print(const std::string& s,
+                           const KeyFormatter& keyFormatter) const {
+    for (auto&& dkey : *this) {
+      std::cout << DefaultKeyFormatter(dkey.first) << " " << dkey.second
+                << std::endl;
+    }
+  }
+
+  bool DiscreteKeys::equals(const DiscreteKeys& other, double tol) const {
+    if (this->size() != other.size()) {
+      return false;
+    }
+
+    for (size_t i = 0; i < this->size(); i++) {
+      if (this->at(i).first != other.at(i).first ||
+          this->at(i).second != other.at(i).second) {
+        return false;
+      }
+    }
+    return true;
+  }
 }

gtsam/discrete/DiscreteKey.h

@@ -21,6 +21,7 @@
 #include <gtsam/global_includes.h>
 #include <gtsam/inference/Key.h>
 
+#include <boost/serialization/vector.hpp>
 #include <map>
 #include <string>
 #include <vector>
@@ -72,15 +73,27 @@ namespace gtsam {
 
     /// Print the keys and cardinalities.
     void print(const std::string& s = "",
-               const KeyFormatter& keyFormatter = DefaultKeyFormatter) const {
+               const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
-      for (auto&& dkey : *this) {
+
-        std::cout << DefaultKeyFormatter(dkey.first) << " " << dkey.second
+    /// Check equality to another DiscreteKeys object.
-                  << std::endl;
+    bool equals(const DiscreteKeys& other, double tol = 0) const;
-      }
+
+    /** Serialization function */
+    friend class boost::serialization::access;
+    template <class ARCHIVE>
+    void serialize(ARCHIVE& ar, const unsigned int /*version*/) {
+      ar& boost::serialization::make_nvp(
+          "DiscreteKeys",
+          boost::serialization::base_object<std::vector<DiscreteKey>>(*this));
     }
 
   }; // DiscreteKeys
 
   /// Create a list from two keys
   GTSAM_EXPORT DiscreteKeys operator&(const DiscreteKey& key1, const DiscreteKey& key2);
-}
+
+  // traits
+  template <>
+  struct traits<DiscreteKeys> : public Testable<DiscreteKeys> {};
+
+  }  // namespace gtsam

gtsam/discrete/tests/testDiscreteFactor.cpp

@@ -16,14 +16,29 @@
  *  @author Duy-Nguyen Ta
  */
 
-#include <gtsam/base/Testable.h>
-#include <gtsam/discrete/DiscreteFactor.h>
 #include <CppUnitLite/TestHarness.h>
+#include <gtsam/base/Testable.h>
+#include <gtsam/base/serializationTestHelpers.h>
+#include <gtsam/discrete/DiscreteFactor.h>
+
 #include <boost/assign/std/map.hpp>
 using namespace boost::assign;
 
 using namespace std;
 using namespace gtsam;
+using namespace gtsam::serializationTestHelpers;
+
+/* ************************************************************************* */
+TEST(DisreteKeys, Serialization) {
+  DiscreteKeys keys;
+  keys& DiscreteKey(0, 2);
+  keys& DiscreteKey(1, 3);
+  keys& DiscreteKey(2, 4);
+
+  EXPECT(equalsObj<DiscreteKeys>(keys));
+  EXPECT(equalsXML<DiscreteKeys>(keys));
+  EXPECT(equalsBinary<DiscreteKeys>(keys));
+}
 
 /* ************************************************************************* */
 int main() {
@@ -31,4 +46,3 @@ int main() {
   return TestRegistry::runAllTests(tr);
 }
 /* ************************************************************************* */
-

gtsam/hybrid/HybridBayesNet.h

@@ -18,6 +18,7 @@
 #pragma once
 
 #include <gtsam/discrete/DecisionTreeFactor.h>
+#include <gtsam/global_includes.h>
 #include <gtsam/hybrid/HybridConditional.h>
 #include <gtsam/hybrid/HybridValues.h>
 #include <gtsam/inference/BayesNet.h>
@@ -37,12 +38,31 @@ class GTSAM_EXPORT HybridBayesNet : public BayesNet<HybridConditional> {
   using shared_ptr = boost::shared_ptr<HybridBayesNet>;
   using sharedConditional = boost::shared_ptr<ConditionalType>;
 
+  /// @name Standard Constructors
+  /// @{
+
   /** Construct empty bayes net */
   HybridBayesNet() = default;
 
-  /// Prune the Hybrid Bayes Net given the discrete decision tree.
+  /// @}
-  HybridBayesNet prune(
+  /// @name Testable
-      const DecisionTreeFactor::shared_ptr &discreteFactor) const;
+  /// @{
+
+  /** Check equality */
+  bool equals(const This &bn, double tol = 1e-9) const {
+    return Base::equals(bn, tol);
+  }
+
+  /// print graph
+  void print(
+      const std::string &s = "",
+      const KeyFormatter &formatter = DefaultKeyFormatter) const override {
+    Base::print(s, formatter);
+  }
+
+  /// @}
+  /// @name Standard Interface
+  /// @{
 
   /// Add HybridConditional to Bayes Net
   using Base::add;
@@ -71,9 +91,13 @@ class GTSAM_EXPORT HybridBayesNet : public BayesNet<HybridConditional> {
    */
   GaussianBayesNet choose(const DiscreteValues &assignment) const;
 
-  /// Solve the HybridBayesNet by back-substitution.
+  /**
-  /// TODO(Shangjie) do we need to create a HybridGaussianBayesNet class, and
+   * @brief Solve the HybridBayesNet by first computing the MPE of all the
-  /// put this method there?
+   * discrete variables and then optimizing the continuous variables based on
+   * the MPE assignment.
+   *
+   * @return HybridValues
+   */
   HybridValues optimize() const;
 
   /**
@@ -84,6 +108,24 @@ class GTSAM_EXPORT HybridBayesNet : public BayesNet<HybridConditional> {
    * @return Values
    */
   VectorValues optimize(const DiscreteValues &assignment) const;
+
+  /// Prune the Hybrid Bayes Net given the discrete decision tree.
+  HybridBayesNet prune(
+      const DecisionTreeFactor::shared_ptr &discreteFactor) const;
+
+  /// @}
+
+ private:
+  /** Serialization function */
+  friend class boost::serialization::access;
+  template <class ARCHIVE>
+  void serialize(ARCHIVE &ar, const unsigned int /*version*/) {
+    ar &BOOST_SERIALIZATION_BASE_OBJECT_NVP(Base);
+  }
 };
 
+/// traits
+template <>
+struct traits<HybridBayesNet> : public Testable<HybridBayesNet> {};
+
 }  // namespace gtsam

gtsam/hybrid/HybridBayesTree.h

@@ -89,8 +89,20 @@ class GTSAM_EXPORT HybridBayesTree : public BayesTree<HybridBayesTreeClique> {
   VectorValues optimize(const DiscreteValues& assignment) const;
 
   /// @}
+
+ private:
+  /** Serialization function */
+  friend class boost::serialization::access;
+  template <class ARCHIVE>
+  void serialize(ARCHIVE& ar, const unsigned int /*version*/) {
+    ar& BOOST_SERIALIZATION_BASE_OBJECT_NVP(Base);
+  }
 };
 
+/// traits
+template <>
+struct traits<HybridBayesTree> : public Testable<HybridBayesTree> {};
+
 /**
  * @brief Class for Hybrid Bayes tree orphan subtrees.
  *

gtsam/hybrid/HybridConditional.h

@@ -178,6 +178,15 @@ class GTSAM_EXPORT HybridConditional
   /// Get the type-erased pointer to the inner type
   boost::shared_ptr<Factor> inner() { return inner_; }
 
+ private:
+  /** Serialization function */
+  friend class boost::serialization::access;
+  template <class Archive>
+  void serialize(Archive& ar, const unsigned int /*version*/) {
+    ar& BOOST_SERIALIZATION_BASE_OBJECT_NVP(BaseFactor);
+    ar& BOOST_SERIALIZATION_BASE_OBJECT_NVP(BaseConditional);
+  }
+
 };  // HybridConditional
 
 // traits

gtsam/hybrid/HybridFactor.h

@@ -47,6 +47,7 @@ class GTSAM_EXPORT HybridFactor : public Factor {
   bool isContinuous_ = false;
   bool isHybrid_ = false;
 
+  // TODO(Varun) remove
   size_t nrContinuous_ = 0;
 
  protected:
@@ -129,6 +130,19 @@ class GTSAM_EXPORT HybridFactor : public Factor {
   const KeyVector &continuousKeys() const { return continuousKeys_; }
 
   /// @}
+
+ private:
+  /** Serialization function */
+  friend class boost::serialization::access;
+  template <class ARCHIVE>
+  void serialize(ARCHIVE &ar, const unsigned int /*version*/) {
+    ar &BOOST_SERIALIZATION_BASE_OBJECT_NVP(Base);
+    ar &BOOST_SERIALIZATION_NVP(isDiscrete_);
+    ar &BOOST_SERIALIZATION_NVP(isContinuous_);
+    ar &BOOST_SERIALIZATION_NVP(isHybrid_);
+    ar &BOOST_SERIALIZATION_NVP(discreteKeys_);
+    ar &BOOST_SERIALIZATION_NVP(continuousKeys_);
+  }
 };
 // HybridFactor
 

gtsam/hybrid/tests/testHybridBayesNet.cpp

@@ -18,6 +18,7 @@
  * @date    December 2021
  */
 
+#include <gtsam/base/serializationTestHelpers.h>
 #include <gtsam/hybrid/HybridBayesNet.h>
 #include <gtsam/nonlinear/NonlinearFactorGraph.h>
 
@@ -28,6 +29,8 @@
 
 using namespace std;
 using namespace gtsam;
+using namespace gtsam::serializationTestHelpers;
+
 using noiseModel::Isotropic;
 using symbol_shorthand::M;
 using symbol_shorthand::X;
@@ -146,6 +149,18 @@ TEST(HybridBayesNet, Optimize) {
   EXPECT(assert_equal(expectedValues, delta.continuous(), 1e-5));
 }
 
+/* ****************************************************************************/
+// Test HybridBayesNet serialization.
+TEST(HybridBayesNet, Serialization) {
+  Switching s(4);
+  Ordering ordering = s.linearizedFactorGraph.getHybridOrdering();
+  HybridBayesNet hbn = *(s.linearizedFactorGraph.eliminateSequential(ordering));
+
+  EXPECT(equalsObj<HybridBayesNet>(hbn));
+  EXPECT(equalsXML<HybridBayesNet>(hbn));
+  EXPECT(equalsBinary<HybridBayesNet>(hbn));
+}
+
 /* ************************************************************************* */
 int main() {
   TestResult tr;

gtsam/hybrid/tests/testHybridBayesTree.cpp

@@ -16,6 +16,7 @@
  * @date    August 2022
  */
 
+#include <gtsam/base/serializationTestHelpers.h>
 #include <gtsam/discrete/DiscreteFactorGraph.h>
 #include <gtsam/hybrid/HybridBayesTree.h>
 #include <gtsam/hybrid/HybridGaussianISAM.h>
@@ -143,6 +144,20 @@ TEST(HybridBayesTree, Optimize) {
   EXPECT(assert_equal(expectedValues, delta.continuous()));
 }
 
+/* ****************************************************************************/
+// Test HybridBayesTree serialization.
+TEST(HybridBayesTree, Serialization) {
+  Switching s(4);
+  Ordering ordering = s.linearizedFactorGraph.getHybridOrdering();
+  HybridBayesTree hbt =
+      *(s.linearizedFactorGraph.eliminateMultifrontal(ordering));
+
+  using namespace gtsam::serializationTestHelpers;
+  EXPECT(equalsObj<HybridBayesTree>(hbt));
+  EXPECT(equalsXML<HybridBayesTree>(hbt));
+  EXPECT(equalsBinary<HybridBayesTree>(hbt));
+}
+
 /* ************************************************************************* */
 int main() {
   TestResult tr;

gtsam/linear/tests/testSerializationLinear.cpp

@@ -198,6 +198,33 @@ TEST (Serialization, gaussian_factor_graph) {
   EXPECT(equalsBinary(graph));
 }
 
+/* ****************************************************************************/
+TEST(Serialization, gaussian_bayes_net) {
+  // Create an arbitrary Bayes Net
+  GaussianBayesNet gbn;
+  gbn += GaussianConditional::shared_ptr(new GaussianConditional(
+      0, Vector2(1.0, 2.0), (Matrix2() << 3.0, 4.0, 0.0, 6.0).finished(), 3,
+      (Matrix2() << 7.0, 8.0, 9.0, 10.0).finished(), 4,
+      (Matrix2() << 11.0, 12.0, 13.0, 14.0).finished()));
+  gbn += GaussianConditional::shared_ptr(new GaussianConditional(
+      1, Vector2(15.0, 16.0), (Matrix2() << 17.0, 18.0, 0.0, 20.0).finished(),
+      2, (Matrix2() << 21.0, 22.0, 23.0, 24.0).finished(), 4,
+      (Matrix2() << 25.0, 26.0, 27.0, 28.0).finished()));
+  gbn += GaussianConditional::shared_ptr(new GaussianConditional(
+      2, Vector2(29.0, 30.0), (Matrix2() << 31.0, 32.0, 0.0, 34.0).finished(),
+      3, (Matrix2() << 35.0, 36.0, 37.0, 38.0).finished()));
+  gbn += GaussianConditional::shared_ptr(new GaussianConditional(
+      3, Vector2(39.0, 40.0), (Matrix2() << 41.0, 42.0, 0.0, 44.0).finished(),
+      4, (Matrix2() << 45.0, 46.0, 47.0, 48.0).finished()));
+  gbn += GaussianConditional::shared_ptr(new GaussianConditional(
+      4, Vector2(49.0, 50.0), (Matrix2() << 51.0, 52.0, 0.0, 54.0).finished()));
+
+  std::string serialized = serialize(gbn);
+  GaussianBayesNet actual;
+  deserialize(serialized, actual);
+  EXPECT(assert_equal(gbn, actual));
+}
+
 /* ************************************************************************* */
 TEST (Serialization, gaussian_bayes_tree) {
   const Key x1=1, x2=2, x3=3, x4=4;