Dendrogram< MarkerLabelT, NodeT, ValGraphT > Class Template Reference

Dendrogram. More...

Detailed Description

template<class MarkerLabelT = size_t, class NodeT = size_t, class ValGraphT = size_t>
class smil::Dendrogram< MarkerLabelT, NodeT, ValGraphT >

Dendrogram.

#include <Dendrogram.hpp>

Collaboration diagram for Dendrogram< MarkerLabelT, NodeT, ValGraphT >:

Public Types
typedef Dendrogram< MarkerLabelT, NodeT, ValGraphT >	DendrogramType
typedef DendroNode< MarkerLabelT >	DendroNodeType
typedef std::map< NodeT, ValGraphT >	NodeValuesType
typedef std::vector< Edge< NodeT, ValGraphT > >	EdgeListType

Public Member Functions
	Dendrogram ()
	Default constructor.
	Dendrogram (const Dendrogram &dendrogramToCopy)
	Copy constructor.
	Dendrogram (Graph< NodeT, ValGraphT > &mst)
	Dendrogram constructor from a MST graph. More...
	Dendrogram (Graph< NodeT, ValGraphT > &mst, smil::Image< MarkerLabelT > &imLabels, smil::Image< MarkerLabelT > &imIn, const size_t nbOfMoments=5)
	Constructor from a MST graph and labels/image to compute the moments. More...
virtual	~Dendrogram ()
	Destructor.
Dendrogram	clone ()
	Clone Dendrogram.
void	sortNodes (bool reverse=false)
	Reorganizes dendroNodes...
void	sortReverseNodes ()
	Reorganizes dendroNodes by decreasing valuationInitial.
void	addDendroNodes (DendroNodeType *dendroNode)
DendroNodeType *	researchLabel (MarkerLabelT researchedLabel) const
void	setMomentsContours (Image< MarkerLabelT > &imLabels, Image< MarkerLabelT > &imIn, const size_t nbOfMoments)
void	reorganize ()
void	normalize (const std::string typeOfNormalization="reg")
	Dendrogram ultrametric values normalization. More...
void	putValuationsFinalInInitial ()
	Put the internalNodeValuationFinal in internalNodeValuationInitial and then set internalNodeValuationFinal = 0.
void	setValuationsToZero ()
void	removeMSTEdgesDendrogram (Graph< NodeT, ValGraphT > &associated_mst, double lbd)
	Given an internal node index lambda of the dendrogram, remove corresponding edge in the associated MST.
void	HierarchicalConstruction (const std::string typeOfHierarchy, const int nParam=50, const smil::Image< MarkerLabelT > &imMosa=smil::Image< MarkerLabelT >(), const std::string typeOfTransform="erode", const StrElt &se=DEFAULT_SE)
	Computes a new hierarchy from a given dendrogram hierarchy. More...
void	EnergyConstruction (const std::string typeOfHierarchy)
	Computes a new hierarchy from a given dendrogram hierarchy.
std::vector< DendroNodeType * > &	getDendroNodes ()
	Setters and Getters.
void	setNbrNodes (size_t nNbrNodes)
size_t	getNbrNodes ()
void	setNbrMarkers (size_t nNbrMarkers)
size_t	getNbrMarkers ()
double	getNodeValue (size_t nodeIndex, string nameOfValueWanted)
	Access a value of a node in the dendrogram. More...
void	setNodeValue (size_t nodeIndex, string nameOfValueWanted, double value)
	Manually modify a value of a node in the dendrogram. More...
std::vector< MarkerLabelT >	getLookupProgeny (size_t nodeIndex, string nameOfValueWanted)
	Get the lookup of the progeny of a node. More...
std::vector< MarkerLabelT >	getThreshLookupProgeny (double thresh, string nameOfValueWanted)
	Get the lookup of the progeny below a certain ultrametric threshold. More...
std::vector< std::vector< double > >	getPersistences (string typeOfMatrix="sparse", string momentOfLife="death")
	Compute persistences matrix (persistence measures only the order of fusion) More...
std::vector< std::vector< double > >	getSaliences (string typeOfMatrix="sparse", string momentOfLife="death")
	Compute saliences matrix (salience expresses ultrametric values) More...
double	computeDasguptaCF (Graph< NodeT, ValGraphT > completeGraph)
	Compute dasgupta score (paper "A cost function for similarity-based hierarchical clustering") More...
double	computeScoreInteractiveSeg ()

Protected Attributes
size_t	nbrNodes
size_t	nbrMarkers
std::vector< DendroNode< MarkerLabelT > * >	dendroNodes

Constructor & Destructor Documentation

Dendrogram() [1/2]

Dendrogram ( Graph< NodeT, ValGraphT > &  mst )

inline

Dendrogram constructor from a MST graph.

Parameters

[in]

mst

Input mst (graph)

Dendrogram() [2/2]

Dendrogram ( Graph< NodeT, ValGraphT > &  mst, smil::Image< MarkerLabelT > &  imLabels, smil::Image< MarkerLabelT > &  imIn, const size_t  nbOfMoments = 5  )

inline

Constructor from a MST graph and labels/image to compute the moments.

Parameters

[in]	mst	Input mst (graph)
[in]	imLabels	Labels image
[in]	imIn	Original image
[in]	nbOfMoments	(optional) Number of moments to compute (default = 5)

Member Function Documentation

normalize()

void normalize ( const std::string  typeOfNormalization = "reg" )

inline

Dendrogram ultrametric values normalization.

Parameters

[in]

typeOfNormalization

Desired type of normalization: "reg" (according to the number of regions), "maxnorm" (according to the maximum value)

HierarchicalConstruction()

void HierarchicalConstruction ( const std::string  typeOfHierarchy, const int  nParam = 50, const smil::Image< MarkerLabelT > &  imMosa = smil::Image<MarkerLabelT>(), const std::string  typeOfTransform = "erode", const StrElt &  se = DEFAULT_SE  )

inline

Computes a new hierarchy from a given dendrogram hierarchy.

Parameters

[in]	typeOfHierarchy	Desired type of hierarchy: "none", "surfacic", "volumic", "stochasticSurfacic", "stochasticVolumic" etc.
[in]	nParam	:
[in]	imMosa	(optional) Mosaic image - necessary for hierarchies implying labels image deformations
[in]	typeOfTransform	(optional) Type of transform (deformation) applied to each mosaic image region
[in]	se	(optional) Structuring element

getNodeValue()

double getNodeValue ( size_t  nodeIndex, string  nameOfValueWanted  )

inline

Access a value of a node in the dendrogram.

Parameters

[in]	nodeIndex	Index of the node to access
[in]	nameOfValueWanted	Name of the value to access ("valuation", "internalNodeValuationInitial", "label" etc.)

setNodeValue()

void setNodeValue ( size_t  nodeIndex, string  nameOfValueWanted, double  value  )

inline

Manually modify a value of a node in the dendrogram.

Parameters

[in]	nodeIndex	Index of the node to modify
[in]	nameOfValueWanted	Name of the value to modify ("valuation", "internalNodeValuationInitial", "label" etc.)
[in]	value	New value

getLookupProgeny()

std::vector<MarkerLabelT> getLookupProgeny ( size_t  nodeIndex, string  nameOfValueWanted  )

inline

Get the lookup of the progeny of a node.

Parameters

[in]	nodeIndex	Index of the node to access
[in]	nameOfValueWanted	Name of the exact node ("current", "childLeft", "childRight")

getThreshLookupProgeny()

std::vector<MarkerLabelT> getThreshLookupProgeny ( double  thresh, string  nameOfValueWanted  )

inline

Get the lookup of the progeny below a certain ultrametric threshold.

Parameters

[in]	thresh	Ultrametric value threshold
[in]	nameOfValueWanted	Name of the exact node ("current", "childLeft", "childRight")

getPersistences()

std::vector<std::vector<double> > getPersistences ( string  typeOfMatrix = "sparse", string  momentOfLife = "death"  )

inline

Compute persistences matrix (persistence measures only the order of fusion)

Parameters

[in]	typeOfMatrix	"sparse" (only between adjacent regions) or "full"
[in]	momentOfLife	"death" (when regions fuse) or "life" (when regions appear)

getSaliences()

std::vector<std::vector<double> > getSaliences ( string  typeOfMatrix = "sparse", string  momentOfLife = "death"  )

inline

Compute saliences matrix (salience expresses ultrametric values)

Parameters

[in]	typeOfMatrix	"sparse" (only between adjacent regions) or "full"
[in]	momentOfLife	"death" (when regions fuse) or "life" (when regions appear)

computeDasguptaCF()

double computeDasguptaCF ( Graph< NodeT, ValGraphT >  completeGraph )

inline

Compute dasgupta score (paper "A cost function for similarity-based hierarchical clustering")

Parameters

[in]

completeGraph

complete graph (with all adjacent regions connected)

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

• Addons/Dendrogram/include/private/Dendrogram.hpp