Merge pull request #1041 from borglab/release/4.2a3

.github/workflows/build-linux.yml

@@ -15,7 +15,7 @@ jobs:
       BOOST_VERSION: 1.67.0
 
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         # Github Actions requires a single row to be added to the build matrix.
         # See https://help.github.com/en/articles/workflow-syntax-for-github-actions.

CMakeLists.txt

@@ -11,7 +11,7 @@ endif()
 set (GTSAM_VERSION_MAJOR 4)
 set (GTSAM_VERSION_MINOR 2)
 set (GTSAM_VERSION_PATCH 0)
-set (GTSAM_PRERELEASE_VERSION "a2")
+set (GTSAM_PRERELEASE_VERSION "a3")
 math (EXPR GTSAM_VERSION_NUMERIC "10000 * ${GTSAM_VERSION_MAJOR} + 100 * ${GTSAM_VERSION_MINOR} + ${GTSAM_VERSION_PATCH}")
 
 if (${GTSAM_VERSION_PATCH} EQUAL 0)

gtsam/discrete/DecisionTreeFactor.h

@@ -57,7 +57,7 @@ namespace gtsam {
     /** Default constructor for I/O */
     DecisionTreeFactor();
 
-    /** Constructor from Indices, Ordering, and AlgebraicDecisionDiagram */
+    /** Constructor from DiscreteKeys and AlgebraicDecisionTree */
     DecisionTreeFactor(const DiscreteKeys& keys, const ADT& potentials);
 
     /** Constructor from doubles */
@@ -139,22 +139,22 @@ namespace gtsam {
     /**
      * Apply binary operator (*this) "op" f
      * @param f the second argument for op
-     * @param op a binary operator that operates on AlgebraicDecisionDiagram potentials
+     * @param op a binary operator that operates on AlgebraicDecisionTree
      */
     DecisionTreeFactor apply(const DecisionTreeFactor& f, ADT::Binary op) const;
 
     /**
      * Combine frontal variables using binary operator "op"
      * @param nrFrontals nr. of frontal to combine variables in this factor
-     * @param op a binary operator that operates on AlgebraicDecisionDiagram potentials
+     * @param op a binary operator that operates on AlgebraicDecisionTree
      * @return shared pointer to newly created DecisionTreeFactor
      */
     shared_ptr combine(size_t nrFrontals, ADT::Binary op) const;
 
     /**
      * Combine frontal variables in an Ordering using binary operator "op"
      * @param nrFrontals nr. of frontal to combine variables in this factor
-     * @param op a binary operator that operates on AlgebraicDecisionDiagram potentials
+     * @param op a binary operator that operates on AlgebraicDecisionTree
      * @return shared pointer to newly created DecisionTreeFactor
      */
     shared_ptr combine(const Ordering& keys, ADT::Binary op) const;

gtsam/discrete/DiscreteBayesNet.h

@@ -19,7 +19,7 @@
 #pragma once
 
 #include <gtsam/discrete/DiscreteConditional.h>
-#include <gtsam/discrete/DiscretePrior.h>
+#include <gtsam/discrete/DiscreteDistribution.h>
 #include <gtsam/inference/BayesNet.h>
 #include <gtsam/inference/FactorGraph.h>
 
@@ -79,9 +79,9 @@ namespace gtsam {
     // Add inherited versions of add.
     using Base::add;
 
-    /** Add a DiscretePrior using a table or a string */
+    /** Add a DiscreteDistribution using a table or a string */
     void add(const DiscreteKey& key, const std::string& spec) {
-      emplace_shared<DiscretePrior>(key, spec);
+      emplace_shared<DiscreteDistribution>(key, spec);
     }
 
     /** Add a DiscreteCondtional */

gtsam/discrete/DiscreteConditional.cpp

@@ -30,6 +30,7 @@
 #include <string>
 #include <vector>
 #include <utility>
+#include <set>
 
 using namespace std;
 using std::stringstream;
@@ -38,38 +39,97 @@ using std::pair;
 namespace gtsam {
 
 // Instantiate base class
-template class GTSAM_EXPORT Conditional<DecisionTreeFactor, DiscreteConditional> ;
+template class GTSAM_EXPORT
+    Conditional<DecisionTreeFactor, DiscreteConditional>;
 
-/* ******************************************************************************** */
+/* ************************************************************************** */
 DiscreteConditional::DiscreteConditional(const size_t nrFrontals,
-    const DecisionTreeFactor& f) :
-    BaseFactor(f / (*f.sum(nrFrontals))), BaseConditional(nrFrontals) {
-}
+                                         const DecisionTreeFactor& f)
+    : BaseFactor(f / (*f.sum(nrFrontals))), BaseConditional(nrFrontals) {}
 
-/* ******************************************************************************** */
+/* ************************************************************************** */
+DiscreteConditional::DiscreteConditional(size_t nrFrontals,
+                                         const DiscreteKeys& keys,
+                                         const ADT& potentials)
+    : BaseFactor(keys, potentials), BaseConditional(nrFrontals) {}
+
+/* ************************************************************************** */
 DiscreteConditional::DiscreteConditional(const DecisionTreeFactor& joint,
-    const DecisionTreeFactor& marginal) :
-    BaseFactor(
-        ISDEBUG("DiscreteConditional::COUNT") ? joint : joint / marginal), BaseConditional(
-            joint.size()-marginal.size()) {
-  if (ISDEBUG("DiscreteConditional::DiscreteConditional"))
-    cout << (firstFrontalKey()) << endl; //TODO Print all keys
-}
+                                         const DecisionTreeFactor& marginal)
+    : BaseFactor(joint / marginal),
+      BaseConditional(joint.size() - marginal.size()) {}
 
-/* ******************************************************************************** */
+/* ************************************************************************** */
 DiscreteConditional::DiscreteConditional(const DecisionTreeFactor& joint,
-    const DecisionTreeFactor& marginal, const Ordering& orderedKeys) :
-    DiscreteConditional(joint, marginal) {
+                                         const DecisionTreeFactor& marginal,
+                                         const Ordering& orderedKeys)
+    : DiscreteConditional(joint, marginal) {
   keys_.clear();
   keys_.insert(keys_.end(), orderedKeys.begin(), orderedKeys.end());
 }
 
-/* ******************************************************************************** */
+/* ************************************************************************** */
 DiscreteConditional::DiscreteConditional(const Signature& signature)
     : BaseFactor(signature.discreteKeys(), signature.cpt()),
       BaseConditional(1) {}
 
-/* ******************************************************************************** */
+/* ************************************************************************** */
+DiscreteConditional DiscreteConditional::operator*(
+    const DiscreteConditional& other) const {
+  // Take union of frontal keys
+  std::set<Key> newFrontals;
+  for (auto&& key : this->frontals()) newFrontals.insert(key);
+  for (auto&& key : other.frontals()) newFrontals.insert(key);
+
+  // Check if frontals overlapped
+  if (nrFrontals() + other.nrFrontals() > newFrontals.size())
+    throw std::invalid_argument(
+        "DiscreteConditional::operator* called with overlapping frontal keys.");
+
+  // Now, add cardinalities.
+  DiscreteKeys discreteKeys;
+  for (auto&& key : frontals())
+    discreteKeys.emplace_back(key, cardinality(key));
+  for (auto&& key : other.frontals())
+    discreteKeys.emplace_back(key, other.cardinality(key));
+
+  // Sort
+  std::sort(discreteKeys.begin(), discreteKeys.end());
+
+  // Add parents to set, to make them unique
+  std::set<DiscreteKey> parents;
+  for (auto&& key : this->parents())
+    if (!newFrontals.count(key)) parents.emplace(key, cardinality(key));
+  for (auto&& key : other.parents())
+    if (!newFrontals.count(key)) parents.emplace(key, other.cardinality(key));
+
+  // Finally, add parents to keys, in order
+  for (auto&& dk : parents) discreteKeys.push_back(dk);
+
+  ADT product = ADT::apply(other, ADT::Ring::mul);
+  return DiscreteConditional(newFrontals.size(), discreteKeys, product);
+}
+
+/* ************************************************************************** */
+DiscreteConditional DiscreteConditional::marginal(Key key) const {
+  if (nrParents() > 0)
+    throw std::invalid_argument(
+        "DiscreteConditional::marginal: single argument version only valid for "
+        "fully specified joint distributions (i.e., no parents).");
+
+  // Calculate the keys as the frontal keys without the given key.
+  DiscreteKeys discreteKeys{{key, cardinality(key)}};
+
+  // Calculate sum
+  ADT adt(*this);
+  for (auto&& k : frontals())
+    if (k != key) adt = adt.sum(k, cardinality(k));
+
+  // Return new factor
+  return DiscreteConditional(1, discreteKeys, adt);
+}
+
+/* ************************************************************************** */
 void DiscreteConditional::print(const string& s,
                                 const KeyFormatter& formatter) const {
   cout << s << " P( ";
@@ -82,7 +142,7 @@ void DiscreteConditional::print(const string& s,
       cout << formatter(*it) << " ";
     }
   }
-  cout << ")";
+  cout << "):\n";
   ADT::print("");
   cout << endl;
 }

gtsam/discrete/DiscreteConditional.h

@@ -49,14 +49,21 @@ class GTSAM_EXPORT DiscreteConditional
   /// @name Standard Constructors
   /// @{
 
-  /** default constructor needed for serialization */
+  /// Default constructor needed for serialization.
   DiscreteConditional() {}
 
-  /** constructor from factor */
+  /// Construct from factor, taking the first `nFrontals` keys as frontals.
   DiscreteConditional(size_t nFrontals, const DecisionTreeFactor& f);
 
+  /**
+   * Construct from DiscreteKeys and AlgebraicDecisionTree, taking the first
+   * `nFrontals` keys as frontals, in the order given.
+   */
+  DiscreteConditional(size_t nFrontals, const DiscreteKeys& keys,
+                      const ADT& potentials);
+
   /** Construct from signature */
-  DiscreteConditional(const Signature& signature);
+  explicit DiscreteConditional(const Signature& signature);
 
   /**
    * Construct from key, parents, and a Signature::Table specifying the
@@ -82,31 +89,45 @@ class GTSAM_EXPORT DiscreteConditional
                       const std::string& spec)
       : DiscreteConditional(Signature(key, parents, spec)) {}
 
-  /// No-parent specialization; can also use DiscretePrior.
+  /// No-parent specialization; can also use DiscreteDistribution.
   DiscreteConditional(const DiscreteKey& key, const std::string& spec)
       : DiscreteConditional(Signature(key, {}, spec)) {}
 
-  /** construct P(X|Y)=P(X,Y)/P(Y) from P(X,Y) and P(Y) */
+  /** 
+   * @brief construct P(X|Y) = f(X,Y)/f(Y) from f(X,Y) and f(Y)
+   * Assumes but *does not check* that f(Y)=sum_X f(X,Y). 
+   */
   DiscreteConditional(const DecisionTreeFactor& joint,
                       const DecisionTreeFactor& marginal);
 
-  /** construct P(X|Y)=P(X,Y)/P(Y) from P(X,Y) and P(Y) */
+  /** 
+   * @brief construct P(X|Y) = f(X,Y)/f(Y) from f(X,Y) and f(Y)
+   * Assumes but *does not check* that f(Y)=sum_X f(X,Y).
+   * Makes sure the keys are ordered as given. Does not check orderedKeys.
+   */
   DiscreteConditional(const DecisionTreeFactor& joint,
                       const DecisionTreeFactor& marginal,
                       const Ordering& orderedKeys);
 
   /**
-   * Combine several conditional into a single one.
-   * The conditionals must be given in increasing order, meaning that the
-   * parents of any conditional may not include a conditional coming before it.
-   * @param firstConditional Iterator to the first conditional to combine, must
-   * dereference to a shared_ptr<DiscreteConditional>.
-   * @param lastConditional Iterator to after the last conditional to combine,
-   * must dereference to a shared_ptr<DiscreteConditional>.
-   * */
-  template <typename ITERATOR>
-  static shared_ptr Combine(ITERATOR firstConditional,
-                            ITERATOR lastConditional);
+   * @brief Combine two conditionals, yielding a new conditional with the union
+   * of the frontal keys, ordered by gtsam::Key.
+   *
+   * The two conditionals must make a valid Bayes net fragment, i.e.,
+   * the frontal variables cannot overlap, and must be acyclic:
+   * Example of correct use:
+   *   P(A,B) = P(A|B) * P(B)
+   *   P(A,B|C) = P(A|B) * P(B|C)
+   *   P(A,B,C) = P(A,B|C) * P(C)
+   * Example of incorrect use:
+   *   P(A|B) * P(A|C) = ?
+   *   P(A|B) * P(B|A) = ?
+   * We check for overlapping frontals, but do *not* check for cyclic.
+   */
+  DiscreteConditional operator*(const DiscreteConditional& other) const;
+
+  /** Calculate marginal on given key, no parent case. */
+  DiscreteConditional marginal(Key key) const;
 
   /// @}
   /// @name Testable
@@ -136,11 +157,6 @@ class GTSAM_EXPORT DiscreteConditional
     return ADT::operator()(values);
   }
 
-  /** Convert to a factor */
-  DecisionTreeFactor::shared_ptr toFactor() const {
-    return DecisionTreeFactor::shared_ptr(new DecisionTreeFactor(*this));
-  }
-
   /** Restrict to given parent values, returns DecisionTreeFactor */
   DecisionTreeFactor::shared_ptr choose(
       const DiscreteValues& parentsValues) const;
@@ -208,23 +224,4 @@ class GTSAM_EXPORT DiscreteConditional
 template <>
 struct traits<DiscreteConditional> : public Testable<DiscreteConditional> {};
 
-/* ************************************************************************* */
-template <typename ITERATOR>
-DiscreteConditional::shared_ptr DiscreteConditional::Combine(
-    ITERATOR firstConditional, ITERATOR lastConditional) {
-  // TODO:  check for being a clique
-
-  // multiply all the potentials of the given conditionals
-  size_t nrFrontals = 0;
-  DecisionTreeFactor product;
-  for (ITERATOR it = firstConditional; it != lastConditional;
-       ++it, ++nrFrontals) {
-    DiscreteConditional::shared_ptr c = *it;
-    DecisionTreeFactor::shared_ptr factor = c->toFactor();
-    product = (*factor) * product;
-  }
-  // and then create a new multi-frontal conditional
-  return boost::make_shared<DiscreteConditional>(nrFrontals, product);
-}
-
 }  // namespace gtsam

gtsam/discrete/DiscretePrior.cpp → gtsam/discrete/DiscreteDistribution.cpp

@@ -10,21 +10,23 @@
  * -------------------------------------------------------------------------- */
 
 /**
- *  @file DiscretePrior.cpp
+ *  @file DiscreteDistribution.cpp
  *  @date December 2021
  *  @author Frank Dellaert
  */
 
-#include <gtsam/discrete/DiscretePrior.h>
+#include <gtsam/discrete/DiscreteDistribution.h>
+
+#include <vector>
 
 namespace gtsam {
 
-void DiscretePrior::print(const std::string& s,
-                          const KeyFormatter& formatter) const {
+void DiscreteDistribution::print(const std::string& s,
+                                 const KeyFormatter& formatter) const {
   Base::print(s, formatter);
 }
 
-double DiscretePrior::operator()(size_t value) const {
+double DiscreteDistribution::operator()(size_t value) const {
   if (nrFrontals() != 1)
     throw std::invalid_argument(
         "Single value operator can only be invoked on single-variable "
@@ -34,10 +36,10 @@ double DiscretePrior::operator()(size_t value) const {
   return Base::operator()(values);
 }
 
-std::vector<double> DiscretePrior::pmf() const {
+std::vector<double> DiscreteDistribution::pmf() const {
   if (nrFrontals() != 1)
     throw std::invalid_argument(
-        "DiscretePrior::pmf only defined for single-variable priors");
+        "DiscreteDistribution::pmf only defined for single-variable priors");
   const size_t nrValues = cardinalities_.at(keys_[0]);
   std::vector<double> array;
   array.reserve(nrValues);