A class for thresholding connectomics networks. More...

#include <mitkConnectomicsNetworkThresholder.h>

Inheritance diagram for mitk::ConnectomicsNetworkThresholder:

Collaboration diagram for mitk::ConnectomicsNetworkThresholder:

Public Types
enum	ThresholdingSchemes { RandomRemovalOfWeakest, LargestLowerThanDensity, ThresholdBased }
	Possible schemes for thresholding the network. More...

typedef mitk::ConnectomicsNetwork::NetworkType	NetworkType

typedef mitk::ConnectomicsNetwork::VertexDescriptorType	VertexDescriptorType

typedef mitk::ConnectomicsNetwork::EdgeDescriptorType	EdgeDescriptorType

typedef boost::graph_traits< NetworkType >::vertex_iterator	VertexIteratorType

typedef boost::graph_traits< NetworkType >::edge_iterator	EdgeIteratorType

typedef boost::graph_traits< NetworkType >::adjacency_iterator	AdjacencyIteratorType

typedef std::map< EdgeDescriptorType, int >	EdgeIndexStdMapType

typedef boost::associative_property_map< EdgeIndexStdMapType >	EdgeIndexMapType

typedef std::map< VertexDescriptorType, int >	VertexIndexStdMapType

typedef boost::associative_property_map< VertexIndexStdMapType >	VertexIndexMapType

Public Member Functions
	mitkClassMacroItkParent (ConnectomicsNetworkThresholder, itk::Object)

Pointer	Clone () const

virtual void	SetNetwork (mitk::ConnectomicsNetwork *_arg)

virtual void	SetThresholdingScheme (ThresholdingSchemes _arg)

virtual void	SetTargetThreshold (double _arg)

virtual void	SetTargetDensity (double _arg)

virtual mitk::ConnectomicsNetwork *	GetNetwork ()

virtual ThresholdingSchemes	GetThresholdingScheme ()

virtual double	GetTargetThreshold ()

virtual double	GetTargetDensity ()

mitk::ConnectomicsNetwork::Pointer	GetThresholdedNetwork ()
	Apply thresholding scheme and get resulting network. More...

Static Public Member Functions
static Pointer	New ()

Protected Member Functions
	ConnectomicsNetworkThresholder ()

	~ConnectomicsNetworkThresholder ()

mitk::ConnectomicsNetwork::Pointer	ThresholdByRandomRemoval (mitk::ConnectomicsNetwork::Pointer input, double targetDensity)

mitk::ConnectomicsNetwork::Pointer	ThresholdBelowDensity (mitk::ConnectomicsNetwork::Pointer input, double targetDensity)

mitk::ConnectomicsNetwork::Pointer	Threshold (mitk::ConnectomicsNetwork::Pointer input, double targetThreshold)

bool	CheckValidity ()

Protected Attributes
mitk::ConnectomicsNetwork::Pointer	m_Network

ThresholdingSchemes	m_ThresholdingScheme

double	m_TargetThreshold

double	m_TargetDensity

Detailed Description

A class for thresholding connectomics networks.

Definition at line 34 of file mitkConnectomicsNetworkThresholder.h.

Member Typedef Documentation

typedef boost::graph_traits<NetworkType>::adjacency_iterator mitk::ConnectomicsNetworkThresholder::AdjacencyIteratorType

Definition at line 51 of file mitkConnectomicsNetworkThresholder.h.

typedef mitk::ConnectomicsNetwork::EdgeDescriptorType mitk::ConnectomicsNetworkThresholder::EdgeDescriptorType

Definition at line 48 of file mitkConnectomicsNetworkThresholder.h.

typedef boost::associative_property_map< EdgeIndexStdMapType > mitk::ConnectomicsNetworkThresholder::EdgeIndexMapType

Definition at line 53 of file mitkConnectomicsNetworkThresholder.h.

typedef std::map<EdgeDescriptorType, int> mitk::ConnectomicsNetworkThresholder::EdgeIndexStdMapType

Definition at line 52 of file mitkConnectomicsNetworkThresholder.h.

typedef boost::graph_traits<NetworkType>::edge_iterator mitk::ConnectomicsNetworkThresholder::EdgeIteratorType

Definition at line 50 of file mitkConnectomicsNetworkThresholder.h.

typedef mitk::ConnectomicsNetwork::NetworkType mitk::ConnectomicsNetworkThresholder::NetworkType

Definition at line 46 of file mitkConnectomicsNetworkThresholder.h.

typedef mitk::ConnectomicsNetwork::VertexDescriptorType mitk::ConnectomicsNetworkThresholder::VertexDescriptorType

Definition at line 47 of file mitkConnectomicsNetworkThresholder.h.

typedef boost::associative_property_map< VertexIndexStdMapType > mitk::ConnectomicsNetworkThresholder::VertexIndexMapType

Definition at line 55 of file mitkConnectomicsNetworkThresholder.h.

typedef std::map<VertexDescriptorType, int> mitk::ConnectomicsNetworkThresholder::VertexIndexStdMapType

Definition at line 54 of file mitkConnectomicsNetworkThresholder.h.

typedef boost::graph_traits<NetworkType>::vertex_iterator mitk::ConnectomicsNetworkThresholder::VertexIteratorType

Definition at line 49 of file mitkConnectomicsNetworkThresholder.h.

Member Enumeration Documentation

enum mitk::ConnectomicsNetworkThresholder::ThresholdingSchemes

Possible schemes for thresholding the network.

RandomRemovalOfWeakest: Randomly remove one of the weakest edges until a given density is reached
LargestLowerThanDensity: Remove all edges of the lowest weight, repeat until below the specified density
ThresholdBased: Remove all edges with a weight of threshold and lower. This will not take density information into account.

Enumerator
RandomRemovalOfWeakest
LargestLowerThanDensity
ThresholdBased

Definition at line 63 of file mitkConnectomicsNetworkThresholder.h.

Constructor & Destructor Documentation

mitk::ConnectomicsNetworkThresholder::ConnectomicsNetworkThresholder ( )

protected

Definition at line 21 of file mitkConnectomicsNetworkThresholder.cpp.

mitk::ConnectomicsNetworkThresholder::~ConnectomicsNetworkThresholder ( )

protected

Definition at line 29 of file mitkConnectomicsNetworkThresholder.cpp.

Member Function Documentation

bool mitk::ConnectomicsNetworkThresholder::CheckValidity ( )

protected

Definition at line 70 of file mitkConnectomicsNetworkThresholder.cpp.

References MITK_ERROR.

Pointer mitk::ConnectomicsNetworkThresholder::Clone ( ) const

virtual mitk::ConnectomicsNetwork* mitk::ConnectomicsNetworkThresholder::GetNetwork ( )

virtual

virtual double mitk::ConnectomicsNetworkThresholder::GetTargetDensity ( )

virtual

virtual double mitk::ConnectomicsNetworkThresholder::GetTargetThreshold ( )

virtual

mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::GetThresholdedNetwork ( )

Apply thresholding scheme and get resulting network.

Definition at line 33 of file mitkConnectomicsNetworkThresholder.cpp.

References MITK_ERROR.

virtual ThresholdingSchemes mitk::ConnectomicsNetworkThresholder::GetThresholdingScheme ( )

virtual

mitk::ConnectomicsNetworkThresholder::mitkClassMacroItkParent	(	ConnectomicsNetworkThresholder	,
		itk::Object
	)

Standard class typedefs. Method for creation through the object factory.

static Pointer mitk::ConnectomicsNetworkThresholder::New ( )

static

Referenced by main().

virtual void mitk::ConnectomicsNetworkThresholder::SetNetwork ( mitk::ConnectomicsNetwork * _arg )

virtual

virtual void mitk::ConnectomicsNetworkThresholder::SetTargetDensity ( double _arg )

virtual

virtual void mitk::ConnectomicsNetworkThresholder::SetTargetThreshold ( double _arg )

virtual

virtual void mitk::ConnectomicsNetworkThresholder::SetThresholdingScheme ( ThresholdingSchemes _arg )

virtual

mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::Threshold	(	mitk::ConnectomicsNetwork::Pointer	input,
		double	targetThreshold
	)

protected

Definition at line 205 of file mitkConnectomicsNetworkThresholder.cpp.

References mitk::ConnectomicsNetwork::New().

mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::ThresholdBelowDensity	(	mitk::ConnectomicsNetwork::Pointer	input,
		double	targetDensity
	)

protected

Definition at line 182 of file mitkConnectomicsNetworkThresholder.cpp.

References mitk::ConnectomicsStatisticsCalculator::New(), and mitk::ConnectomicsNetwork::New().

mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::ThresholdByRandomRemoval	(	mitk::ConnectomicsNetwork::Pointer	input,
		double	targetDensity
	)