370 lines
12 KiB
C++
370 lines
12 KiB
C++
/* ----------------------------------------------------------------------------
|
|
|
|
* 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 BayesTree
|
|
* @brief Bayes Tree is a tree of cliques of a Bayes Chain
|
|
* @author Frank Dellaert
|
|
*/
|
|
|
|
// \callgraph
|
|
|
|
#pragma once
|
|
|
|
#include <vector>
|
|
#include <stdexcept>
|
|
#include <deque>
|
|
#include <boost/function.hpp>
|
|
#include <boost/shared_ptr.hpp>
|
|
#include <boost/make_shared.hpp>
|
|
|
|
#include <gtsam/base/types.h>
|
|
#include <gtsam/base/FastVector.h>
|
|
#include <gtsam/inference/FactorGraph.h>
|
|
#include <gtsam/inference/BayesNet.h>
|
|
#include <gtsam/inference/BayesTreeCliqueBase.h>
|
|
#include <gtsam/inference/IndexConditional.h>
|
|
#include <gtsam/linear/VectorValues.h>
|
|
|
|
namespace gtsam {
|
|
|
|
// Forward declaration of BayesTreeClique which is defined below BayesTree in this file
|
|
template<class CONDITIONAL> struct BayesTreeClique;
|
|
|
|
/**
|
|
* Bayes tree
|
|
* @tparam CONDITIONAL The type of the conditional densities, i.e. the type of node in the underlying Bayes chain,
|
|
* which could be a ConditionalProbabilityTable, a GaussianConditional, or a SymbolicConditional.
|
|
* @tparam CLIQUE The type of the clique data structure, defaults to BayesTreeClique, normally do not change this
|
|
* as it is only used when developing special versions of BayesTree, e.g. for ISAM2.
|
|
*
|
|
* \ingroup Multifrontal
|
|
* \nosubgrouping
|
|
*/
|
|
template<class CONDITIONAL, class CLIQUE=BayesTreeClique<CONDITIONAL> >
|
|
class BayesTree {
|
|
|
|
public:
|
|
|
|
typedef BayesTree<CONDITIONAL, CLIQUE> This;
|
|
typedef boost::shared_ptr<BayesTree<CONDITIONAL, CLIQUE> > shared_ptr;
|
|
typedef boost::shared_ptr<CONDITIONAL> sharedConditional;
|
|
typedef boost::shared_ptr<BayesNet<CONDITIONAL> > sharedBayesNet;
|
|
typedef CONDITIONAL ConditionalType;
|
|
typedef typename CONDITIONAL::FactorType FactorType;
|
|
typedef typename FactorGraph<FactorType>::Eliminate Eliminate;
|
|
|
|
typedef CLIQUE Clique; ///< The clique type, normally BayesTreeClique
|
|
|
|
// typedef for shared pointers to cliques
|
|
typedef boost::shared_ptr<Clique> sharedClique;
|
|
|
|
// A convenience class for a list of shared cliques
|
|
struct Cliques : public std::list<sharedClique> {
|
|
void print(const std::string& s = "Cliques") const;
|
|
bool equals(const Cliques& other, double tol = 1e-9) const;
|
|
};
|
|
|
|
/** clique statistics */
|
|
struct CliqueStats {
|
|
double avgConditionalSize;
|
|
std::size_t maxConditionalSize;
|
|
double avgSeparatorSize;
|
|
std::size_t maxSeparatorSize;
|
|
};
|
|
|
|
/** store all the sizes */
|
|
struct CliqueData {
|
|
std::vector<std::size_t> conditionalSizes;
|
|
std::vector<std::size_t> separatorSizes;
|
|
CliqueStats getStats() const;
|
|
};
|
|
|
|
/** Map from keys to Clique */
|
|
typedef std::deque<sharedClique> Nodes;
|
|
|
|
protected:
|
|
|
|
/** Map from keys to Clique */
|
|
Nodes nodes_;
|
|
|
|
/** private helper method for saving the Tree to a text file in GraphViz format */
|
|
void saveGraph(std::ostream &s, sharedClique clique,
|
|
int parentnum = 0) const;
|
|
|
|
/** Gather data on a single clique */
|
|
void getCliqueData(CliqueData& stats, sharedClique clique) const;
|
|
|
|
/** Root clique */
|
|
sharedClique root_;
|
|
|
|
/** remove a clique: warning, can result in a forest */
|
|
void removeClique(sharedClique clique);
|
|
|
|
/** add a clique (top down) */
|
|
sharedClique addClique(const sharedConditional& conditional, const sharedClique& parent_clique = sharedClique());
|
|
|
|
/** add a clique (top down) */
|
|
void addClique(const sharedClique& clique, const sharedClique& parent_clique = sharedClique());
|
|
|
|
/** add a clique (bottom up) */
|
|
sharedClique addClique(const sharedConditional& conditional, std::list<sharedClique>& child_cliques);
|
|
|
|
/**
|
|
* Add a conditional to the front of a clique, i.e. a conditional whose
|
|
* parents are already in the clique or its separators. This function does
|
|
* not check for this condition, it just updates the data structures.
|
|
*/
|
|
static void addToCliqueFront(BayesTree<CONDITIONAL,CLIQUE>& bayesTree,
|
|
const sharedConditional& conditional, const sharedClique& clique);
|
|
|
|
/** Fill the nodes index for a subtree */
|
|
void fillNodesIndex(const sharedClique& subtree);
|
|
|
|
/** Helper function to build a non-symbolic tree (e.g. Gaussian) using a
|
|
* symbolic tree, used in the BT(BN) constructor.
|
|
*/
|
|
void recursiveTreeBuild(const boost::shared_ptr<BayesTreeClique<IndexConditional> >& symbolic,
|
|
const std::vector<boost::shared_ptr<CONDITIONAL> >& conditionals,
|
|
const typename BayesTree<CONDITIONAL,CLIQUE>::sharedClique& parent);
|
|
|
|
public:
|
|
|
|
/// @name Standard Constructors
|
|
/// @{
|
|
|
|
/** Create an empty Bayes Tree */
|
|
BayesTree() {}
|
|
|
|
/** Create a Bayes Tree from a Bayes Net (requires CONDITIONAL is IndexConditional *or* CONDITIONAL::Combine) */
|
|
BayesTree(const BayesNet<CONDITIONAL>& bayesNet);
|
|
|
|
/** Copy constructor */
|
|
BayesTree(const This& other);
|
|
|
|
/** Assignment operator */
|
|
This& operator=(const This& other);
|
|
|
|
/// @}
|
|
/// @name Advanced Constructors
|
|
/// @{
|
|
|
|
/**
|
|
* Create a Bayes Tree from a Bayes Net and some subtrees. The Bayes net corresponds to the
|
|
* new root clique and the subtrees are connected to the root clique.
|
|
*/
|
|
BayesTree(const BayesNet<CONDITIONAL>& bayesNet, std::list<BayesTree<CONDITIONAL,CLIQUE> > subtrees);
|
|
|
|
/** Destructor */
|
|
virtual ~BayesTree() {}
|
|
|
|
/// @}
|
|
/// @name Testable
|
|
/// @{
|
|
|
|
/** check equality */
|
|
bool equals(const BayesTree<CONDITIONAL,CLIQUE>& other, double tol = 1e-9) const;
|
|
|
|
/** print */
|
|
void print(const std::string& s = "") const;
|
|
|
|
/// @}
|
|
/// @name Standard Interface
|
|
/// @{
|
|
|
|
public:
|
|
|
|
/**
|
|
* Find parent clique of a conditional. It will look at all parents and
|
|
* return the one with the lowest index in the ordering.
|
|
*/
|
|
template<class CONTAINER>
|
|
Index findParentClique(const CONTAINER& parents) const;
|
|
|
|
/** number of cliques */
|
|
inline size_t size() const {
|
|
if(root_)
|
|
return root_->treeSize();
|
|
else
|
|
return 0;
|
|
}
|
|
|
|
/** return nodes */
|
|
Nodes nodes() const { return nodes_; }
|
|
|
|
/** return root clique */
|
|
const sharedClique& root() const { return root_; }
|
|
|
|
/** find the clique to which key belongs */
|
|
sharedClique operator[](Index key) const {
|
|
return nodes_.at(key);
|
|
}
|
|
|
|
/** Gather data on all cliques */
|
|
CliqueData getCliqueData() const;
|
|
|
|
/** return marginal on any variable */
|
|
typename FactorType::shared_ptr marginalFactor(Index key, Eliminate function) const;
|
|
|
|
/**
|
|
* return marginal on any variable, as a Bayes Net
|
|
* NOTE: this function calls marginal, and then eliminates it into a Bayes Net
|
|
* This is more expensive than the above function
|
|
*/
|
|
typename BayesNet<CONDITIONAL>::shared_ptr marginalBayesNet(Index key, Eliminate function) const;
|
|
|
|
/** return joint on two variables */
|
|
typename FactorGraph<FactorType>::shared_ptr joint(Index key1, Index key2, Eliminate function) const;
|
|
|
|
/** return joint on two variables as a BayesNet */
|
|
typename BayesNet<CONDITIONAL>::shared_ptr jointBayesNet(Index key1, Index key2, Eliminate function) const;
|
|
|
|
/**
|
|
* Read only with side effects
|
|
*/
|
|
|
|
/** saves the Tree to a text file in GraphViz format */
|
|
void saveGraph(const std::string& s) const;
|
|
|
|
/// @}
|
|
/// @name Advanced Interface
|
|
/// @{
|
|
|
|
/** Access the root clique (non-const version) */
|
|
sharedClique& root() { return root_; }
|
|
|
|
/** Remove all nodes */
|
|
void clear();
|
|
|
|
/**
|
|
* Remove path from clique to root and return that path as factors
|
|
* plus a list of orphaned subtree roots. Used in removeTop below.
|
|
*/
|
|
void removePath(sharedClique clique, BayesNet<CONDITIONAL>& bn, Cliques& orphans);
|
|
|
|
/**
|
|
* Given a list of keys, turn "contaminated" part of the tree back into a factor graph.
|
|
* Factors and orphans are added to the in/out arguments.
|
|
*/
|
|
template<class CONTAINER>
|
|
void removeTop(const CONTAINER& keys, BayesNet<CONDITIONAL>& bn, Cliques& orphans);
|
|
|
|
/**
|
|
* Hang a new subtree off of the existing tree. This finds the appropriate
|
|
* parent clique for the subtree (which may be the root), and updates the
|
|
* nodes index with the new cliques in the subtree. None of the frontal
|
|
* variables in the subtree may appear in the separators of the existing
|
|
* BayesTree.
|
|
*/
|
|
void insert(const sharedClique& subtree);
|
|
|
|
/** Insert a new conditional
|
|
* This function only applies for Symbolic case with IndexCondtional,
|
|
* We make it static so that it won't be compiled in GaussianConditional case.
|
|
* */
|
|
static void insert(BayesTree<CONDITIONAL,CLIQUE>& bayesTree, const sharedConditional& conditional);
|
|
|
|
/**
|
|
* Insert a new clique corresponding to the given Bayes net.
|
|
* It is the caller's responsibility to decide whether the given Bayes net is a valid clique,
|
|
* i.e. all the variables (frontal and separator) are connected
|
|
*/
|
|
sharedClique insert(const sharedConditional& clique,
|
|
std::list<sharedClique>& children, bool isRootClique = false);
|
|
|
|
private:
|
|
|
|
/** deep copy to another tree */
|
|
void cloneTo(This& newTree) const;
|
|
|
|
/** deep copy to another tree */
|
|
void cloneTo(This& newTree, const sharedClique& subtree, const sharedClique& parent) const;
|
|
|
|
/** Serialization function */
|
|
friend class boost::serialization::access;
|
|
template<class ARCHIVE>
|
|
void serialize(ARCHIVE & ar, const unsigned int version) {
|
|
ar & BOOST_SERIALIZATION_NVP(nodes_);
|
|
ar & BOOST_SERIALIZATION_NVP(root_);
|
|
}
|
|
|
|
/// @}
|
|
|
|
}; // BayesTree
|
|
|
|
|
|
/* ************************************************************************* */
|
|
template<class CONDITIONAL, class CLIQUE>
|
|
void _BayesTree_dim_adder(
|
|
std::vector<size_t>& dims,
|
|
const typename BayesTree<CONDITIONAL,CLIQUE>::sharedClique& clique) {
|
|
|
|
if(clique) {
|
|
// Add dims from this clique
|
|
for(typename CONDITIONAL::const_iterator it = (*clique)->beginFrontals(); it != (*clique)->endFrontals(); ++it)
|
|
dims[*it] = (*clique)->dim(it);
|
|
|
|
// Traverse children
|
|
typedef typename BayesTree<CONDITIONAL,CLIQUE>::sharedClique sharedClique;
|
|
BOOST_FOREACH(const sharedClique& child, clique->children()) {
|
|
_BayesTree_dim_adder<CONDITIONAL,CLIQUE>(dims, child);
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ************************************************************************* */
|
|
template<class CONDITIONAL,class CLIQUE>
|
|
boost::shared_ptr<VectorValues> allocateVectorValues(const BayesTree<CONDITIONAL,CLIQUE>& bt) {
|
|
std::vector<size_t> dimensions(bt.nodes().size(), 0);
|
|
_BayesTree_dim_adder<CONDITIONAL,CLIQUE>(dimensions, bt.root());
|
|
return boost::shared_ptr<VectorValues>(new VectorValues(dimensions));
|
|
}
|
|
|
|
|
|
/* ************************************************************************* */
|
|
/**
|
|
* A Clique in the tree is an incomplete Bayes net: the variables
|
|
* in the Bayes net are the frontal nodes, and the variables conditioned
|
|
* on are the separator. We also have pointers up and down the tree.
|
|
*
|
|
* Since our Conditional class already handles multiple frontal variables,
|
|
* this Clique contains exactly 1 conditional.
|
|
*
|
|
* This is the default clique type in a BayesTree, but some algorithms, like
|
|
* iSAM2 (see ISAM2Clique), use a different clique type in order to store
|
|
* extra data along with the clique.
|
|
*/
|
|
template<class CONDITIONAL>
|
|
struct BayesTreeClique : public BayesTreeCliqueBase<BayesTreeClique<CONDITIONAL>, CONDITIONAL> {
|
|
public:
|
|
typedef CONDITIONAL ConditionalType;
|
|
typedef BayesTreeClique<CONDITIONAL> This;
|
|
typedef BayesTreeCliqueBase<This, CONDITIONAL> Base;
|
|
typedef boost::shared_ptr<This> shared_ptr;
|
|
typedef boost::weak_ptr<This> weak_ptr;
|
|
BayesTreeClique() {}
|
|
BayesTreeClique(const typename ConditionalType::shared_ptr& conditional) : Base(conditional) {}
|
|
BayesTreeClique(const std::pair<typename ConditionalType::shared_ptr, typename ConditionalType::FactorType::shared_ptr>& result) : Base(result) {}
|
|
|
|
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);
|
|
}
|
|
};
|
|
|
|
} /// namespace gtsam
|
|
|
|
#include <gtsam/inference/BayesTree-inl.h>
|
|
#include <gtsam/inference/BayesTreeCliqueBase-inl.h>
|