#include <BayesTree.h>

Public Types
typedef CLIQUE::BayesNetType	BayesNetType

typedef CLIQUE	Clique
	The clique type, normally BayesTreeClique. More...

typedef FastList< sharedClique >	Cliques

typedef CLIQUE::ConditionalType	ConditionalType

typedef FactorGraphType::Eliminate	Eliminate

typedef CLIQUE::EliminationTraitsType	EliminationTraitsType

typedef CLIQUE::FactorGraphType	FactorGraphType

typedef CLIQUE::FactorType	FactorType

typedef Clique	Node
	Synonym for Clique (TODO: remove) More...

typedef ConcurrentMap< Key, sharedClique >	Nodes

typedef FastVector< sharedClique >	Roots

typedef std::shared_ptr< BayesNetType >	sharedBayesNet

typedef std::shared_ptr< Clique >	sharedClique
	Shared pointer to a clique. More...

typedef std::shared_ptr< ConditionalType >	sharedConditional

typedef std::shared_ptr< FactorType >	sharedFactor

typedef std::shared_ptr< FactorGraphType >	sharedFactorGraph

typedef sharedClique	sharedNode
	Synonym for sharedClique (TODO: remove) More...

Protected Types
typedef std::shared_ptr< This >	shared_ptr

typedef BayesTree< CLIQUE >	This

Protected Member Functions
This &	operator= (const This &other)

	~BayesTree ()

Protected Attributes
Nodes	nodes_

Roots	roots_

Standard Constructors
	BayesTree ()

	BayesTree (const This &other)

Testable
bool	equals (const This &other, double tol=1e-9) const

void	print (const std::string &s="", const KeyFormatter &keyFormatter=DefaultKeyFormatter) const

Standard Interface
size_t	size () const

bool	empty () const

const Nodes &	nodes () const

sharedClique	operator[] (Key j) const

const Roots &	roots () const

const sharedClique &	clique (Key j) const

BayesTreeCliqueData	getCliqueData () const

size_t	numCachedSeparatorMarginals () const

sharedConditional	marginalFactor (Key j, const Eliminate &function=EliminationTraitsType::DefaultEliminate) const

sharedFactorGraph	joint (Key j1, Key j2, const Eliminate &function=EliminationTraitsType::DefaultEliminate) const

sharedBayesNet	jointBayesNet (Key j1, Key j2, const Eliminate &function=EliminationTraitsType::DefaultEliminate) const

Graph Display
void	dot (std::ostream &os, const KeyFormatter &keyFormatter=DefaultKeyFormatter) const
	Output to graphviz format, stream version. More...

std::string	dot (const KeyFormatter &keyFormatter=DefaultKeyFormatter) const
	Output to graphviz format string. More...

void	saveGraph (const std::string &filename, const KeyFormatter &keyFormatter=DefaultKeyFormatter) const
	output to file with graphviz format. More...

Advanced Interface
template<class BAYESTREE , class GRAPH >
class	EliminatableClusterTree

void	dot (std::ostream &s, sharedClique clique, const KeyFormatter &keyFormatter, int parentnum=0) const

void	getCliqueData (sharedClique clique, BayesTreeCliqueData *stats) const

void	removeClique (sharedClique clique)

void	fillNodesIndex (const sharedClique &subtree)

template<class CONTAINER >
Key	findParentClique (const CONTAINER &parents) const

void	clear ()

void	deleteCachedShortcuts ()

void	removePath (sharedClique clique, BayesNetType bn, Cliques orphans)

void	removeTop (const KeyVector &keys, BayesNetType bn, Cliques orphans)

Cliques	removeSubtree (const sharedClique &subtree)

void	insertRoot (const sharedClique &subtree)

void	addClique (const sharedClique &clique, const sharedClique &parent_clique=sharedClique())

void	addFactorsToGraph (FactorGraph< FactorType > *graph) const

Detailed Description

template<class CLIQUE>
class gtsam::BayesTree< CLIQUE >

Bayes tree

Template Parameters

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.
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.

Definition at line 66 of file BayesTree.h.

Member Typedef Documentation

◆ BayesNetType

template<class CLIQUE>

typedef CLIQUE::BayesNetType gtsam::BayesTree< CLIQUE >::BayesNetType

Definition at line 79 of file BayesTree.h.

◆ Clique

template<class CLIQUE>

typedef CLIQUE gtsam::BayesTree< CLIQUE >::Clique

The clique type, normally BayesTreeClique.

Definition at line 73 of file BayesTree.h.

◆ Cliques

template<class CLIQUE>

typedef FastList<sharedClique> gtsam::BayesTree< CLIQUE >::Cliques

A convenience class for a list of shared cliques

Definition at line 89 of file BayesTree.h.

◆ ConditionalType

template<class CLIQUE>

typedef CLIQUE::ConditionalType gtsam::BayesTree< CLIQUE >::ConditionalType

Definition at line 77 of file BayesTree.h.

◆ Eliminate

template<class CLIQUE>

typedef FactorGraphType::Eliminate gtsam::BayesTree< CLIQUE >::Eliminate

Definition at line 85 of file BayesTree.h.

◆ EliminationTraitsType

template<class CLIQUE>

typedef CLIQUE::EliminationTraitsType gtsam::BayesTree< CLIQUE >::EliminationTraitsType

Definition at line 86 of file BayesTree.h.

◆ FactorGraphType

template<class CLIQUE>

typedef CLIQUE::FactorGraphType gtsam::BayesTree< CLIQUE >::FactorGraphType

Definition at line 83 of file BayesTree.h.

◆ FactorType

template<class CLIQUE>

typedef CLIQUE::FactorType gtsam::BayesTree< CLIQUE >::FactorType

Definition at line 81 of file BayesTree.h.

◆ Node

template<class CLIQUE>

typedef Clique gtsam::BayesTree< CLIQUE >::Node

Synonym for Clique (TODO: remove)

Definition at line 75 of file BayesTree.h.

◆ Nodes

template<class CLIQUE>

typedef ConcurrentMap<Key, sharedClique> gtsam::BayesTree< CLIQUE >::Nodes

Map from keys to Clique

Definition at line 92 of file BayesTree.h.

◆ Roots

template<class CLIQUE>

typedef FastVector<sharedClique> gtsam::BayesTree< CLIQUE >::Roots

Root cliques

Definition at line 95 of file BayesTree.h.

◆ shared_ptr

template<class CLIQUE>

typedef std::shared_ptr<This> gtsam::BayesTree< CLIQUE >::shared_ptr

protected

Definition at line 70 of file BayesTree.h.

◆ sharedBayesNet

template<class CLIQUE>

typedef std::shared_ptr<BayesNetType> gtsam::BayesTree< CLIQUE >::sharedBayesNet

Definition at line 80 of file BayesTree.h.

◆ sharedClique

template<class CLIQUE>

typedef std::shared_ptr<Clique> gtsam::BayesTree< CLIQUE >::sharedClique

Shared pointer to a clique.

Definition at line 74 of file BayesTree.h.

◆ sharedConditional

template<class CLIQUE>

typedef std::shared_ptr<ConditionalType> gtsam::BayesTree< CLIQUE >::sharedConditional

Definition at line 78 of file BayesTree.h.

◆ sharedFactor

template<class CLIQUE>

typedef std::shared_ptr<FactorType> gtsam::BayesTree< CLIQUE >::sharedFactor

Definition at line 82 of file BayesTree.h.

◆ sharedFactorGraph

template<class CLIQUE>

typedef std::shared_ptr<FactorGraphType> gtsam::BayesTree< CLIQUE >::sharedFactorGraph

Definition at line 84 of file BayesTree.h.

◆ sharedNode

template<class CLIQUE>

typedef sharedClique gtsam::BayesTree< CLIQUE >::sharedNode

Synonym for sharedClique (TODO: remove)

Definition at line 76 of file BayesTree.h.

◆ This

template<class CLIQUE>

typedef BayesTree<CLIQUE> gtsam::BayesTree< CLIQUE >::This

protected

Definition at line 69 of file BayesTree.h.

Constructor & Destructor Documentation

◆ BayesTree() [1/2]

template<class CLIQUE>

gtsam::BayesTree< CLIQUE >::BayesTree ( )

inlineprotected

Create an empty Bayes Tree

Definition at line 109 of file BayesTree.h.

◆ BayesTree() [2/2]

template<class CLIQUE >

gtsam::BayesTree< CLIQUE >::BayesTree ( const This & other )

protected

Copy constructor

Definition at line 178 of file BayesTree-inst.h.

◆ ~BayesTree()

template<class CLIQUE >

gtsam::BayesTree< CLIQUE >::~BayesTree ( )

protected

Destructor

Destructor Using default destructor causes stack overflow for large trees due to recursive destruction of nodes; so we manually decrease the reference count of each node in the tree through a BFS, and the nodes with reference count 0 will be deleted. Please see PR-1441 for more details.

Definition at line 190 of file BayesTree-inst.h.

Member Function Documentation

◆ addClique()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::addClique	(	const sharedClique &	clique,
		const sharedClique &	parent_clique = `sharedClique()`
	)

add a clique (top down)

Definition at line 142 of file BayesTree-inst.h.

◆ addFactorsToGraph()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::addFactorsToGraph ( FactorGraph< FactorType > * graph ) const

Add all cliques in this BayesTree to the specified factor graph

Definition at line 168 of file BayesTree-inst.h.

◆ clear()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::clear ( void )

Remove all nodes

Definition at line 449 of file BayesTree-inst.h.

◆ clique()

template<class CLIQUE>

const sharedClique& gtsam::BayesTree< CLIQUE >::clique ( Key j ) const

inline

alternate syntax for matlab: find the clique that contains the variable with Key j

Definition at line 155 of file BayesTree.h.

◆ deleteCachedShortcuts()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::deleteCachedShortcuts ( )

Clear all shortcut caches - use before timing on marginal calculation to avoid residual cache data

Definition at line 457 of file BayesTree-inst.h.

◆ dot() [1/3]

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::dot	(	std::ostream &	os,
		const KeyFormatter &	keyFormatter = `DefaultKeyFormatter`
	)		const

Output to graphviz format, stream version.

Definition at line 64 of file BayesTree-inst.h.

◆ dot() [2/3]

template<class CLIQUE >

std::string gtsam::BayesTree< CLIQUE >::dot ( const KeyFormatter & keyFormatter = DefaultKeyFormatter ) const

Output to graphviz format string.

Definition at line 77 of file BayesTree-inst.h.

◆ dot() [3/3]

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::dot	(	std::ostream &	s,
		sharedClique	clique,
		const KeyFormatter &	keyFormatter,
		int	parentnum = `0`
	)		const

protected

private helper method for saving the Tree to a text file in GraphViz format

Definition at line 94 of file BayesTree-inst.h.

◆ empty()

template<class CLIQUE>

bool gtsam::BayesTree< CLIQUE >::empty ( ) const

inline

Check if there are any cliques in the tree

Definition at line 141 of file BayesTree.h.

◆ equals()

template<class CLIQUE >

bool gtsam::BayesTree< CLIQUE >::equals	(	const This &	other,
		double	tol = `1e-9`
	)		const

protected

check equality

Definition at line 269 of file BayesTree-inst.h.

◆ fillNodesIndex()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::fillNodesIndex ( const sharedClique & subtree )

protected

Fill the nodes index for a subtree

Definition at line 285 of file BayesTree-inst.h.

◆ findParentClique()

template<class CLIQUE >

template<class CONTAINER >

Key gtsam::BayesTree< CLIQUE >::findParentClique ( const CONTAINER & parents ) const

Find parent clique of a conditional. It will look at all parents and return the one with the lowest index in the ordering.

Definition at line 277 of file BayesTree-inst.h.

◆ getCliqueData() [1/2]

template<class CLIQUE >

BayesTreeCliqueData gtsam::BayesTree< CLIQUE >::getCliqueData ( ) const

Gather data on all cliques

Definition at line 35 of file BayesTree-inst.h.

◆ getCliqueData() [2/2]

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::getCliqueData	(	sharedClique	clique,
		BayesTreeCliqueData *	stats
	)		const

protected

Gather data on a single clique

Definition at line 43 of file BayesTree-inst.h.

◆ insertRoot()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::insertRoot ( const sharedClique & subtree )

Insert a new subtree with known parent clique. This function does not check that the specified parent is the correct parent. This function updates all of the internal data structures associated with adding a subtree, such as populating the nodes index.

Definition at line 299 of file BayesTree-inst.h.

◆ joint()

template<class CLIQUE >

BayesTree< CLIQUE >::sharedFactorGraph gtsam::BayesTree< CLIQUE >::joint	(	Key	j1,
		Key	j2,
		const Eliminate &	function = `EliminationTraitsType::DefaultEliminate`
	)		const

return joint on two variables Limitation: can only calculate joint if cliques are disjoint or one of them is root

Definition at line 332 of file BayesTree-inst.h.

◆ jointBayesNet()

template<class CLIQUE >

BayesTree< CLIQUE >::sharedBayesNet gtsam::BayesTree< CLIQUE >::jointBayesNet	(	Key	j1,
		Key	j2,
		const Eliminate &	function = `EliminationTraitsType::DefaultEliminate`
	)		const

return joint on two variables as a BayesNet Limitation: can only calculate joint if cliques are disjoint or one of them is root

Definition at line 341 of file BayesTree-inst.h.

◆ marginalFactor()

template<class CLIQUE >

BayesTree< CLIQUE >::sharedConditional gtsam::BayesTree< CLIQUE >::marginalFactor	(	Key	j,
		const Eliminate &	function = `EliminationTraitsType::DefaultEliminate`
	)		const

Return marginal on any variable. Note that this actually returns a conditional, for which a solution may be directly obtained by calling .solve() on the returned object. Alternatively, it may be directly used as its factor base class. For example, for Gaussian systems, this returns a GaussianConditional, which inherits from JacobianFactor and GaussianFactor.

Definition at line 309 of file BayesTree-inst.h.

◆ nodes()

template<class CLIQUE>

const Nodes& gtsam::BayesTree< CLIQUE >::nodes ( ) const

inline

Return nodes. Each node is a clique of variables obtained after elimination.

Definition at line 146 of file BayesTree.h.

◆ numCachedSeparatorMarginals()

template<class CLIQUE >

size_t gtsam::BayesTree< CLIQUE >::numCachedSeparatorMarginals ( ) const

Collect number of cliques with cached separator marginals

Definition at line 55 of file BayesTree-inst.h.

◆ operator=()

template<class CLIQUE >

BayesTree< CLIQUE > & gtsam::BayesTree< CLIQUE >::operator= ( const This & other )

protected

Assignment operator

Definition at line 238 of file BayesTree-inst.h.

◆ operator[]()

template<class CLIQUE>

sharedClique gtsam::BayesTree< CLIQUE >::operator[] ( Key j ) const

inline

Access node by variable

Definition at line 149 of file BayesTree.h.

◆ print()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::print	(	const std::string &	s = `""`,
		const KeyFormatter &	keyFormatter = `DefaultKeyFormatter`
	)		const

print

Definition at line 251 of file BayesTree-inst.h.

◆ removeClique()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::removeClique ( sharedClique clique )

protected

remove a clique: warning, can result in a forest

Definition at line 465 of file BayesTree-inst.h.

◆ removePath()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::removePath	(	sharedClique	clique,
		BayesNetType *	bn,
		Cliques *	orphans
	)

Remove path from clique to root and return that path as factors plus a list of orphaned subtree roots. Used in removeTop below.

Definition at line 489 of file BayesTree-inst.h.

◆ removeSubtree()

template<class CLIQUE >

BayesTree< CLIQUE >::Cliques gtsam::BayesTree< CLIQUE >::removeSubtree ( const sharedClique & subtree )

Remove the requested subtree.

Definition at line 537 of file BayesTree-inst.h.

◆ removeTop()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::removeTop	(	const KeyVector &	keys,
		BayesNetType *	bn,
		Cliques *	orphans
	)

Given a list of indices, turn "contaminated" part of the tree back into a factor graph. Factors and orphans are added to the in/out arguments.

Definition at line 516 of file BayesTree-inst.h.

◆ roots()

template<class CLIQUE>

const Roots& gtsam::BayesTree< CLIQUE >::roots ( ) const

inline

return root cliques

Definition at line 152 of file BayesTree.h.

◆ saveGraph()

template<class CLIQUE >

void gtsam::BayesTree< CLIQUE >::saveGraph	(	const std::string &	filename,
		const KeyFormatter &	keyFormatter = `DefaultKeyFormatter`
	)		const

output to file with graphviz format.

Definition at line 85 of file BayesTree-inst.h.

◆ size()

template<class CLIQUE >

size_t gtsam::BayesTree< CLIQUE >::size ( ) const

number of cliques

Definition at line 133 of file BayesTree-inst.h.

Friends And Related Function Documentation

◆ EliminatableClusterTree

template<class CLIQUE>

template<class BAYESTREE , class GRAPH >

friend class EliminatableClusterTree

friend

Definition at line 262 of file BayesTree.h.

Member Data Documentation

◆ nodes_

template<class CLIQUE>

Nodes gtsam::BayesTree< CLIQUE >::nodes_

protected

Map from indices to Clique

Definition at line 100 of file BayesTree.h.

◆ roots_

template<class CLIQUE>

Roots gtsam::BayesTree< CLIQUE >::roots_

protected

Root cliques

Definition at line 103 of file BayesTree.h.

The documentation for this class was generated from the following files:

Public Types

Protected Types

Protected Member Functions

Protected Attributes

Standard Constructors

Testable

Standard Interface

Graph Display

Advanced Interface

Detailed Description

template<class CLIQUE> class gtsam::BayesTree< CLIQUE >

Member Typedef Documentation

◆ BayesNetType

◆ Clique

◆ Cliques

◆ ConditionalType

◆ Eliminate

◆ EliminationTraitsType

◆ FactorGraphType

◆ FactorType

◆ Node

◆ Nodes

◆ Roots

◆ shared_ptr

◆ sharedBayesNet

◆ sharedClique

◆ sharedConditional

◆ sharedFactor

◆ sharedFactorGraph

◆ sharedNode

◆ This

Constructor & Destructor Documentation

◆ BayesTree() [1/2]

◆ BayesTree() [2/2]

◆ ~BayesTree()

Member Function Documentation

◆ addClique()

◆ addFactorsToGraph()

◆ clear()

◆ clique()

◆ deleteCachedShortcuts()

◆ dot() [1/3]

◆ dot() [2/3]

◆ dot() [3/3]

◆ empty()

◆ equals()

◆ fillNodesIndex()

◆ findParentClique()

◆ getCliqueData() [1/2]

◆ getCliqueData() [2/2]

◆ insertRoot()

◆ joint()

◆ jointBayesNet()

◆ marginalFactor()

◆ nodes()

◆ numCachedSeparatorMarginals()

◆ operator=()

◆ operator[]()

◆ print()

◆ removeClique()

◆ removePath()

◆ removeSubtree()

◆ removeTop()

◆ roots()

◆ saveGraph()

◆ size()

Friends And Related Function Documentation

◆ EliminatableClusterTree

Member Data Documentation

◆ nodes_

◆ roots_

template<class CLIQUE>
class gtsam::BayesTree< CLIQUE >