Watershed implementation as described in Cousty et al - Watershed cuts: minimum spanning forests and the drop of water principle (2007) The computation is done in linear time. More...

#include <bioprocessing/watershed/coustywatershed.h>

Collaboration diagram for bio::CoustyWatershed< T, L >:

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Public Types
typedef Point4dl	Point
	Point type.

typedef VolumeGraphRef< T, Point >	Graph
	Graph type.

typedef Graph::Vertex	Vertex
	Vertex type.

typedef Graph::Edge	Edge
	Edge type.

typedef CoustyStreamRef< Vertex >	Stream
	Stream type (a set of vertices)

typedef CoustyFlowMapRef< Vertex, L >	FlowMap
	FlowMap type (the labelled image)

Public Member Functions
	CoustyWatershed ()

	~CoustyWatershed ()

void	setVerbose (int verbose=1)

void	setQuiet ()

void	set3D ()
	When 3D mode is active, a 3D connectivity is used (6XYZ)

void	set2D ()
	When 2D mode is active, a 2D connectivity is used (4XY)

carto::VolumeRef< L >	execute (carto::VolumeRef< T > in)
	Allocate and return the watershed segmentation of the input image.

void	execute (carto::VolumeRef< T > in, carto::VolumeRef< L > out)
	Return the watershed segmentation of the input image into an already allocated volume.

carto::VolumeRef< L >	getMinima ()

Protected Member Functions
void	computeWatershed ()
	Iterates on the vertices of the image, and for each one follows a descent stream until it encounters a labelled vertex or a local minima.

L	computeStream (Vertex x)
	Follows the descent stream from vertex `v`.

bool	findEdge (Vertex y, Vertex &z)
	Finds an edge of minimum altitude for y.

void	setLabel (L lab)
	Sets the label `lab` for all vertices in the stream _s.

Protected Attributes
Graph	_g

Stream	_s

FlowMap	_psi

int	_verbose

bool	_3d

Detailed Description

template<typename T, typename L>
class bio::CoustyWatershed< T, L >

Watershed implementation as described in Cousty et al - Watershed cuts: minimum spanning forests and the drop of water principle (2007) The computation is done in linear time.

In order to save memory, this implementations uses a volume and not a classic graph.

Definition at line 39 of file coustywatershed.h.

Member Typedef Documentation

◆ Edge

template<typename T, typename L>

typedef Graph::Edge bio::CoustyWatershed< T, L >::Edge

Edge type.

Definition at line 46 of file coustywatershed.h.

◆ FlowMap

template<typename T, typename L>

typedef CoustyFlowMapRef<Vertex,L> bio::CoustyWatershed< T, L >::FlowMap

FlowMap type (the labelled image)

Definition at line 48 of file coustywatershed.h.

◆ Graph

template<typename T, typename L>

typedef VolumeGraphRef<T,Point> bio::CoustyWatershed< T, L >::Graph

Graph type.

Definition at line 44 of file coustywatershed.h.

◆ Point

template<typename T, typename L>

typedef Point4dl bio::CoustyWatershed< T, L >::Point

Point type.

Definition at line 43 of file coustywatershed.h.

◆ Stream

template<typename T, typename L>

typedef CoustyStreamRef<Vertex> bio::CoustyWatershed< T, L >::Stream

Stream type (a set of vertices)

Definition at line 47 of file coustywatershed.h.

◆ Vertex

template<typename T, typename L>

typedef Graph::Vertex bio::CoustyWatershed< T, L >::Vertex

Vertex type.

Definition at line 45 of file coustywatershed.h.

Constructor & Destructor Documentation

◆ CoustyWatershed()

template<typename T, typename L>

bio::CoustyWatershed< T, L >::CoustyWatershed ( )

inline

Definition at line 52 of file coustywatershed.h.

References _3d, _g, _psi, _s, and _verbose.

◆ ~CoustyWatershed()

template<typename T, typename L>

bio::CoustyWatershed< T, L >::~CoustyWatershed ( )

inline

Definition at line 53 of file coustywatershed.h.

Member Function Documentation

◆ computeStream()

template<typename T, typename L>

L bio::CoustyWatershed< T, L >::computeStream ( Vertex x )

protected

Follows the descent stream from vertex v.

Definition at line 167 of file coustywatershed.h.

References _g, _psi, _s, bio::CoustyStreamRef< V >::begin(), bio::CoustyStreamRef< V >::empty(), bio::CoustyStreamRef< V >::erase(), findEdge(), bio::CoustyStreamRef< V >::insert(), and bio::CoustyStreamRef< V >::reset().

Referenced by computeWatershed().

◆ computeWatershed()

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::computeWatershed ( )

protected

Iterates on the vertices of the image, and for each one follows a descent stream until it encounters a labelled vertex or a local minima.

This label (or new label if it's a new local minima) is set to all the vertices of the stream.

Definition at line 125 of file coustywatershed.h.

References _psi, _verbose, computeStream(), and setLabel().

Referenced by execute().

◆ execute() [1/2]

template<typename T, typename L>

carto::VolumeRef< L > bio::CoustyWatershed< T, L >::execute ( carto::VolumeRef< T > in )

Allocate and return the watershed segmentation of the input image.

Definition at line 101 of file coustywatershed.h.

References execute().

Referenced by execute(), and bio::Watershed< T, L >::execute().

◆ execute() [2/2]

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::execute	(	carto::VolumeRef< T >	in,
		carto::VolumeRef< L >	out )

Return the watershed segmentation of the input image into an already allocated volume.

Definition at line 111 of file coustywatershed.h.

References _3d, _g, _psi, _s, and computeWatershed().

◆ findEdge()

template<typename T, typename L>

bool bio::CoustyWatershed< T, L >::findEdge	(	Vertex	y,
		Vertex &	z )

protected

Finds an edge of minimum altitude for y.

Definition at line 203 of file coustywatershed.h.

References _g, and _s.

Referenced by computeStream().

◆ getMinima()

template<typename T, typename L>

carto::VolumeRef< L > bio::CoustyWatershed< T, L >::getMinima ( )

inline

Definition at line 71 of file coustywatershed.h.

References _psi.

Referenced by bio::Watershed< T, L >::execute().

◆ set2D()

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::set2D ( )

inline

When 2D mode is active, a 2D connectivity is used (4XY)

Definition at line 62 of file coustywatershed.h.

References _3d.

Referenced by bio::Watershed< T, L >::execute().

◆ set3D()

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::set3D ( )

inline

When 3D mode is active, a 3D connectivity is used (6XYZ)

Definition at line 60 of file coustywatershed.h.

References _3d.

◆ setLabel()

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::setLabel ( L lab )

protected

Sets the label lab for all vertices in the stream _s.

Definition at line 157 of file coustywatershed.h.

References _psi, and _s.

Referenced by computeWatershed().

◆ setQuiet()

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::setQuiet ( )

inline

Definition at line 58 of file coustywatershed.h.

References setVerbose().

◆ setVerbose()

template<typename T, typename L>

void bio::CoustyWatershed< T, L >::setVerbose ( int verbose = 1 )

inline

Definition at line 57 of file coustywatershed.h.

References _verbose.

Referenced by bio::Watershed< T, L >::execute(), and setQuiet().

Member Data Documentation

◆ _3d

template<typename T, typename L>

bool bio::CoustyWatershed< T, L >::_3d

protected

Definition at line 93 of file coustywatershed.h.

Referenced by CoustyWatershed(), execute(), set2D(), and set3D().

◆ _g

template<typename T, typename L>

Graph bio::CoustyWatershed< T, L >::_g

protected

Definition at line 89 of file coustywatershed.h.

Referenced by computeStream(), CoustyWatershed(), execute(), and findEdge().

◆ _psi

template<typename T, typename L>

FlowMap bio::CoustyWatershed< T, L >::_psi

protected

Definition at line 91 of file coustywatershed.h.

Referenced by computeStream(), computeWatershed(), CoustyWatershed(), execute(), getMinima(), and setLabel().

◆ _s

template<typename T, typename L>

Stream bio::CoustyWatershed< T, L >::_s

protected

Definition at line 90 of file coustywatershed.h.

Referenced by computeStream(), CoustyWatershed(), execute(), findEdge(), and setLabel().

◆ _verbose

template<typename T, typename L>

int bio::CoustyWatershed< T, L >::_verbose

protected

Definition at line 92 of file coustywatershed.h.

Referenced by computeWatershed(), CoustyWatershed(), and setVerbose().

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

bioprocessing/watershed/coustywatershed.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ Edge

◆ FlowMap

◆ Graph

◆ Point

◆ Stream

◆ Vertex

Constructor & Destructor Documentation

◆ CoustyWatershed()

◆ ~CoustyWatershed()

Member Function Documentation

◆ computeStream()

◆ computeWatershed()

◆ execute() [1/2]

◆ execute() [2/2]

◆ findEdge()

◆ getMinima()

◆ set2D()

◆ set3D()

◆ setLabel()

◆ setQuiet()

◆ setVerbose()

Member Data Documentation

◆ _3d

◆ _g

◆ _psi

◆ _s

◆ _verbose