this class implements methods for dendrogram processing, such as pruning, node collapsing and decimation it operates over the class WHtree. More...

#include <WHtreeProcesser.h>

Collaboration diagram for WHtreeProcesser:

Public Member Functions
	WHtreeProcesser (WHtree *const tree)
	Constructor. More...

	~WHtreeProcesser ()
	Destructor. More...

std::pair< size_t, size_t >	pruneTree (float condition, size_t safeSize, const HTPROC_MODE pruneType)
	Prunes the tree according to the options specified. More...

std::pair< size_t, size_t >	pruneRandom (const size_t numberPruned, unsigned int seed=0)
	Prunes the tree from randomly chosen leaves. More...

size_t	collapseTree (const dist_t flatGap, const dist_t distLevelLimit, const bool keepBaseNodes)
	Collapses the nodes of the tree that have branch lenghts equal or lower to the one indicated. More...

size_t	collapseTreeLinear (const dist_t coefficient, const bool keepBaseNodes)
	Collapses the nodes of the tree that have branch lenghts smoller than the distance level multiplied by the coefficient indicated. More...

size_t	collapseTreeSquare (const dist_t coefficient, const bool keepBaseNodes)
	Collapses the nodes of the tree that have branch lenghts smoller than the squared distance level multiplied by the coefficient indicated. More...

size_t	collapseBranch (const dist_t flatGap, const dist_t distLevelLimit, size_t root, const bool keepBaseNodes)
	Collapses the nodes of the subtree that have branch lenghts equal or lower to the one indicated. More...

size_t	flattenSelection (const std::list< size_t > selection, const bool keepBaseNodes)
	Collapses all the nodes of the subtrees indicated (using only non-leaf node ID) More...

size_t	flattenSelection (const std::vector< size_t > &selection, const bool keepBaseNodes)
	Collapses all the nodes of the subtrees indicated (using only non-leaf node ID) More...

size_t	flattenSelection (const std::vector< nodeID_t > &selection, const bool keepBaseNodes)
	Collapses all the nodes of the subtrees indicated (using full boolean-integer node ID) More...

std::pair< size_t, size_t >	pruneSelection (const std::vector< size_t > &selection)
	Prunes all of the subtrees indicated (using only non-leaf node ID) More...

std::pair< size_t, size_t >	pruneSelection (const std::vector< nodeID_t > &selection)
	Prunes all of the subtrees indicated (using full boolean-integer node ID) More...

void	flagSelection (const std::vector< size_t > &selection)
	set flags for pruning all of the subtrees indicated (using only non-leaf node ID) More...

void	flagSelection (const std::vector< nodeID_t > &selection)
	set flags for pruning all of the subtrees indicated (using full boolean-integer node ID) More...

void	flagLeaves (const std::vector< size_t > &selection)
	set flags for pruning all of the leaves indicated More...

void	coarseTree (const unsigned int coarseRatio)
	Reduces the tree grid size by the ratio specified (as if it had been obtained from an image of lower resolution) More...

size_t	baseNodes2Leaves ()
	converts the base nodes into leaves, pruning out all excess leaves and information More...

void	forceMonotonicity (double errorMult=1)
	calls on private WHtree member to eliminate non monotonic steps in the tree while keeping as much information as possible. More...

void	forceMonotonicityUp ()
	calls on private WHtree member to eliminate non monotonic steps in the tree bottom-up, lowering the level of children involved in the non-monotonic steps to the parent level More...

void	forceMonotonicityDown ()
	calls on private WHtree member to eliminate non monotonic steps in the tree top-down, raising the level of parents involved in the non-monotonic steps to the children level More...

size_t	debinarize (const bool keepBaseNodes)
	calls on private WHtree member to merge nodes joining binary at the same level into non-binary structures More...

Private Member Functions
size_t	flattenBranch (size_t root, const bool keepBaseNodes)
	Collapses all the nodes of the subtree. More...

void	collapseNode (const size_t thisNodeID, const dist_t coefficient, HTPROC_COLLAPSE collapseMode=HTPR_C_CONSTANT)
	eliminates branchings in the tree, raising them to the parent level More...

void	collapseNode (const nodeID_t &thisNodeID, const dist_t coefficient, HTPROC_COLLAPSE collapseMode=HTPR_C_CONSTANT)
	eliminates non monotonic steps in the tree, raising them to the parent level More...

Private Attributes
WHtree &	m_tree
	tree object More...

Detailed Description

this class implements methods for dendrogram processing, such as pruning, node collapsing and decimation it operates over the class WHtree.

As a result of its operations the tree structure is changed and previous structure cannot be recovered unless a class copy is previously made.

Definition at line 83 of file WHtreeProcesser.h.

Constructor & Destructor Documentation

◆ WHtreeProcesser()

WHtreeProcesser::WHtreeProcesser ( WHtree *const tree )

explicit

Constructor.

Parameters

tree	a pointer to the tree to be processed

Definition at line 60 of file WHtreeProcesser.cpp.

◆ ~WHtreeProcesser()

WHtreeProcesser::~WHtreeProcesser ( )

Destructor.

Definition at line 64 of file WHtreeProcesser.cpp.

Member Function Documentation

◆ baseNodes2Leaves()

size_t WHtreeProcesser::baseNodes2Leaves ( )

converts the base nodes into leaves, pruning out all excess leaves and information

Returns: new number of leaves of the tree

Definition at line 505 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), WHtree::fetchLeaf(), WHtree::getLeaves4node(), WHtree::getNumLeaves(), WHtree::getRootBaseNodes(), m_tree, WHtree::m_treeName, WHnode::setFlag(), and WHtree::testRootBaseNodes().

Here is the call graph for this function:

◆ coarseTree()

void WHtreeProcesser::coarseTree ( const unsigned int coarseRatio )

Reduces the tree grid size by the ratio specified (as if it had been obtained from an image of lower resolution)

Parameters

coarseRatio coarsing ratio

Definition at line 410 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), WHtree::debinarize(), WHtree::fetchLeaf(), WHtree::m_coordinates, WHtree::m_datasetSize, WHtree::m_discarded, m_tree, WHtree::m_treeName, WHcoord::m_x, WHcoord::m_y, WHcoord::m_z, WHnode::setFlag(), and string_utils::toString().

Here is the call graph for this function:

◆ collapseBranch()

size_t WHtreeProcesser::collapseBranch	(	const dist_t	flatGap,
		const dist_t	distLevelLimit,
		size_t	root,
		const bool	keepBaseNodes
	)

Collapses the nodes of the subtree that have branch lenghts equal or lower to the one indicated.

Parameters

flatGap	branch lenght limit to be collapsed
distLevelLimit	distance level under which no collapsing will take place
root	root node of the subtree
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 350 of file WHtreeProcesser.cpp.

References collapseNode(), WHtree::debinarize(), WHtree::getBranchNodes(), WHnode::getDistLevel(), WHtree::getNode(), and m_tree.

Here is the call graph for this function:

◆ collapseNode() [1/2]

void WHtreeProcesser::collapseNode	(	const nodeID_t &	thisNodeID,
		const dist_t	coefficient,
		HTPROC_COLLAPSE	collapseMode = `HTPR_C_CONSTANT`
	)

private

eliminates non monotonic steps in the tree, raising them to the parent level

Parameters

thisNodeID	id of the sub-branch node where to start the flatteing
coefficient	coefficient for collapsing depending on distance level
collapseMode	collapsing mode

Definition at line 661 of file WHtreeProcesser.cpp.

References collapseNode().

Here is the call graph for this function:

◆ collapseNode() [2/2]

void WHtreeProcesser::collapseNode	(	const size_t	thisNodeID,
		const dist_t	coefficient,
		HTPROC_COLLAPSE	collapseMode = `HTPR_C_CONSTANT`
	)

private

eliminates branchings in the tree, raising them to the parent level

Parameters

thisNodeID	id of the sub-branch node where to start the flatteing
coefficient	coefficient for collapsing depending on distance level
collapseMode	collapsing mode

Definition at line 674 of file WHtreeProcesser.cpp.

References WHtree::fetchNode(), WHnode::getChildren(), WHnode::getDistLevel(), WHnode::getFullID(), WHnode::getID(), WHtree::getNode(), WHtree::getRoot(), WHnode::isNode(), m_tree, and WHnode::setDistLevel().

Referenced by collapseBranch(), collapseNode(), collapseTree(), collapseTreeLinear(), collapseTreeSquare(), and flattenBranch().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ collapseTree()

size_t WHtreeProcesser::collapseTree	(	const dist_t	flatGap,
		const dist_t	distLevelLimit,
		const bool	keepBaseNodes
	)

Collapses the nodes of the tree that have branch lenghts equal or lower to the one indicated.

Parameters

flatGap	branch lenght limit to be collapsed
distLevelLimit	distance level under which no collapsing will take place
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 273 of file WHtreeProcesser.cpp.

References collapseNode(), WHtree::debinarize(), WHtree::forceMonotonicityDown(), WHnode::getDistLevel(), WHnode::getID(), WHtree::getNode(), WHtree::getRoot(), m_tree, and WHtree::m_treeName.

Here is the call graph for this function:

◆ collapseTreeLinear()

size_t WHtreeProcesser::collapseTreeLinear	(	const dist_t	coefficient,
		const bool	keepBaseNodes
	)

Collapses the nodes of the tree that have branch lenghts smoller than the distance level multiplied by the coefficient indicated.

Parameters

coefficient	coefficient for collapsing depending on distance level
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 303 of file WHtreeProcesser.cpp.

References collapseNode(), WHtree::debinarize(), WHnode::getID(), WHtree::getRoot(), m_tree, and WHtree::m_treeName.

Referenced by WMHierchClustDisplay::moduleMain().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ collapseTreeSquare()

size_t WHtreeProcesser::collapseTreeSquare	(	const dist_t	coefficient,
		const bool	keepBaseNodes
	)

Collapses the nodes of the tree that have branch lenghts smoller than the squared distance level multiplied by the coefficient indicated.

Parameters

coefficient	coefficient for collapsing depending on distance level
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 326 of file WHtreeProcesser.cpp.

References collapseNode(), WHtree::debinarize(), WHnode::getID(), WHtree::getRoot(), m_tree, and WHtree::m_treeName.

Here is the call graph for this function:

◆ debinarize()

size_t WHtreeProcesser::debinarize ( const bool keepBaseNodes )

calls on private WHtree member to merge nodes joining binary at the same level into non-binary structures

Parameters

keepBaseNodes if set base nodes ( nodes with only single leaves as children) will not be merged

Returns: number of nodes collapsed

Definition at line 549 of file WHtreeProcesser.cpp.

References WHtree::debinarize(), and m_tree.

Here is the call graph for this function:

◆ flagLeaves()

void WHtreeProcesser::flagLeaves ( const std::vector< size_t > & selection )

set flags for pruning all of the leaves indicated

Parameters

selection vector with the leaves to be pruned

Definition at line 650 of file WHtreeProcesser.cpp.

References WHtree::fetchLeaf(), m_tree, and WHnode::setFlag().

Referenced by flagSelection().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ flagSelection() [1/2]

void WHtreeProcesser::flagSelection ( const std::vector< nodeID_t > & selection )

set flags for pruning all of the subtrees indicated (using full boolean-integer node ID)

Parameters

selection vector with the nodes to be pruned

Definition at line 641 of file WHtreeProcesser.cpp.

References flagLeaves(), WHtree::getLeaves4node(), and m_tree.

Here is the call graph for this function:

◆ flagSelection() [2/2]

void WHtreeProcesser::flagSelection ( const std::vector< size_t > & selection )

set flags for pruning all of the subtrees indicated (using only non-leaf node ID)

Parameters

selection vector with the nodes to be pruned

Definition at line 632 of file WHtreeProcesser.cpp.

References flagLeaves(), WHtree::getLeaves4node(), and m_tree.

Referenced by pruneSelection().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ flattenBranch()

size_t WHtreeProcesser::flattenBranch	(	size_t	root,
		const bool	keepBaseNodes
	)

private

Collapses all the nodes of the subtree.

Parameters

root	root node of the subtree
keepBaseNodes	if set base nodes ( nodes with only single leaves as children) will not be merged

Returns: number of nodes eliminated

Definition at line 557 of file WHtreeProcesser.cpp.

References collapseNode(), WHtree::debinarize(), and m_tree.

Here is the call graph for this function:

◆ flattenSelection() [1/3]

size_t WHtreeProcesser::flattenSelection	(	const std::list< size_t >	selection,
		const bool	keepBaseNodes
	)

Collapses all the nodes of the subtrees indicated (using only non-leaf node ID)

Parameters

selection	list with the root nodes of the subtree
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 567 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), WHtree::fetchNode(), WHnode::getChildren(), WHnode::getHLevel(), WHtree::getNode(), m_tree, WHnode::setFlag(), and WHtree::testRootBaseNodes().

Referenced by flattenSelection(), and WMHierchClustDisplay::moduleMain().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ flattenSelection() [2/3]

size_t WHtreeProcesser::flattenSelection	(	const std::vector< nodeID_t > &	selection,
		const bool	keepBaseNodes
	)

Collapses all the nodes of the subtrees indicated (using full boolean-integer node ID)

Parameters

selection	vector with the root nodes of the subtree
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 605 of file WHtreeProcesser.cpp.

References flattenSelection().

Here is the call graph for this function:

◆ flattenSelection() [3/3]

size_t WHtreeProcesser::flattenSelection	(	const std::vector< size_t > &	selection,
		const bool	keepBaseNodes
	)

Collapses all the nodes of the subtrees indicated (using only non-leaf node ID)

Parameters

selection	vector with the root nodes of the subtree
keepBaseNodes	flag to avoid collapsing base nodes (those that have only single-leaf children)

Returns: number of nodes eliminated

Definition at line 600 of file WHtreeProcesser.cpp.

References flattenSelection().

Here is the call graph for this function:

◆ forceMonotonicity()

void WHtreeProcesser::forceMonotonicity ( double errorMult = 1 )

calls on private WHtree member to eliminate non monotonic steps in the tree while keeping as much information as possible.

it searches bottom-up for non-monotonic steps. When detected a corrected value for the parent node is computed this value consists of a average between the non-monotonic children levels weighted by their sizes in number of leaves and the parent level weighted by the sizes of the remaining monotonic children in orther to avoid infinite loops an error tolerance is included. default value is 1*E-5

Parameters

errorMult multiplier to increase the base error tolerance (default value is 1 makign the tolerance 1*E-5, maximum value is 100 making the tolerance 1*E-3)

Definition at line 543 of file WHtreeProcesser.cpp.

References WHtree::forceMonotonicity(), and m_tree.

Here is the call graph for this function:

◆ forceMonotonicityDown()

void WHtreeProcesser::forceMonotonicityDown ( )

calls on private WHtree member to eliminate non monotonic steps in the tree top-down, raising the level of parents involved in the non-monotonic steps to the children level

Definition at line 537 of file WHtreeProcesser.cpp.

References WHtree::forceMonotonicityDown(), and m_tree.

Here is the call graph for this function:

◆ forceMonotonicityUp()

void WHtreeProcesser::forceMonotonicityUp ( )

calls on private WHtree member to eliminate non monotonic steps in the tree bottom-up, lowering the level of children involved in the non-monotonic steps to the parent level

Definition at line 531 of file WHtreeProcesser.cpp.

References WHtree::forceMonotonicityUp(), and m_tree.

Here is the call graph for this function:

◆ pruneRandom()

std::pair< size_t, size_t > WHtreeProcesser::pruneRandom	(	const size_t	numberPruned,
		unsigned int	seed = `0`
	)

Prunes the tree from randomly chosen leaves.

Parameters

numberPruned	number of leaves to be pruned
seed	seed for the random number generator to choose the leaves to be pruned

Returns: pair with the number of nodes and leaves eliminated

Definition at line 235 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), WHtree::debinarize(), WHtree::fetchLeaf(), WHtree::getNumLeaves(), WHnode::isFlagged(), m_tree, WHtree::m_treeName, WHnode::setFlag(), and string_utils::toString().

Referenced by WMHierchClustDisplay::moduleMain().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ pruneSelection() [1/2]

std::pair< size_t, size_t > WHtreeProcesser::pruneSelection ( const std::vector< nodeID_t > & selection )

Prunes all of the subtrees indicated (using full boolean-integer node ID)

Parameters

selection vector with the nodes to be pruned

Returns: pair with the number of nodes and leaves eliminated

Definition at line 625 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), flagSelection(), and m_tree.

Here is the call graph for this function:

◆ pruneSelection() [2/2]

std::pair< size_t, size_t > WHtreeProcesser::pruneSelection ( const std::vector< size_t > & selection )

Prunes all of the subtrees indicated (using only non-leaf node ID)

Parameters

selection vector with the nodes to be pruned

Returns: pair with the number of nodes and leaves eliminated

Definition at line 619 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), flagSelection(), and m_tree.

Referenced by WMHierchClustDisplay::moduleMain().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ pruneTree()

std::pair< size_t, size_t > WHtreeProcesser::pruneTree	(	float	condition,
		size_t	safeSize,
		const HTPROC_MODE	pruneType
	)

Prunes the tree according to the options specified.

Parameters

condition	value of the condition to choose when pruning (size of joining cluster, size ratio or joining level)
safeSize	maximum size that a cluster can have in order to be pruned, bigger clusters wont be prune regardless of the condition
pruneType	type of pruning method (max size, maxlevel, sizeratio)

Returns: pair with the number of nodes and leaves eliminated

Definition at line 72 of file WHtreeProcesser.cpp.

References WHtree::cleanup(), WHtree::debinarize(), WHtree::fetchNode(), WHnode::getChildren(), WHnode::getDistLevel(), WHtree::getNode(), WHtree::getNumLeaves(), WHnode::getSize(), WHnode::isFlagged(), WHtree::m_leaves, WHtree::m_nodes, m_tree, WHtree::m_treeName, WHnode::setFlag(), and string_utils::toString().

Referenced by WMHierchClustDisplay::moduleMain().

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

◆ m_tree

WHtree& WHtreeProcesser::m_tree

private

tree object

Definition at line 255 of file WHtreeProcesser.h.

Referenced by baseNodes2Leaves(), coarseTree(), collapseBranch(), collapseNode(), collapseTree(), collapseTreeLinear(), collapseTreeSquare(), debinarize(), flagLeaves(), flagSelection(), flattenBranch(), flattenSelection(), forceMonotonicity(), forceMonotonicityDown(), forceMonotonicityUp(), pruneRandom(), pruneSelection(), and pruneTree().

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ WHtreeProcesser()

◆ ~WHtreeProcesser()

Member Function Documentation

◆ baseNodes2Leaves()

◆ coarseTree()

◆ collapseBranch()

◆ collapseNode() [1/2]

◆ collapseNode() [2/2]

◆ collapseTree()

◆ collapseTreeLinear()

◆ collapseTreeSquare()

◆ debinarize()

◆ flagLeaves()

◆ flagSelection() [1/2]

◆ flagSelection() [2/2]

◆ flattenBranch()

◆ flattenSelection() [1/3]

◆ flattenSelection() [2/3]

◆ flattenSelection() [3/3]

◆ forceMonotonicity()

◆ forceMonotonicityDown()

◆ forceMonotonicityUp()

◆ pruneRandom()

◆ pruneSelection() [1/2]

◆ pruneSelection() [2/2]

◆ pruneTree()

Member Data Documentation

◆ m_tree