A class providing permutations for the calculation of modularity using simulated annealing. More...

#include <mitkConnectomicsSimulatedAnnealingPermutationModularity.h>

Inheritance diagram for mitk::ConnectomicsSimulatedAnnealingPermutationModularity:

Collaboration diagram for mitk::ConnectomicsSimulatedAnnealingPermutationModularity:

Public Types
typedef mitk::ConnectomicsNetwork::VertexDescriptorType	VertexDescriptorType

typedef std::map< VertexDescriptorType, int >	ToModuleMapType

typedef std::map< VertexDescriptorType, VertexDescriptorType >	VertexToVertexMapType

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

Pointer	Clone () const

virtual void	Initialize () override

virtual void	Permutate (double temperature) override

virtual void	CleanUp () override

void	SetNetwork (mitk::ConnectomicsNetwork::Pointer theNetwork)

int	getNumberOfModules (ToModuleMapType *vertexToModuleMap) const

int	getNumberOfVerticesInModule (ToModuleMapType *vertexToModuleMap, int module) const

void	SetMapping (ToModuleMapType mapping)

ToModuleMapType	GetMapping ()

void	SetDepth (int depth)

void	SetStepSize (double size)

Public Member Functions inherited from mitk::ConnectomicsSimulatedAnnealingPermutationBase
	mitkClassMacroItkParent (ConnectomicsSimulatedAnnealingPermutationBase, itk::Object)

Pointer	Clone () const

void	SetCostFunction (mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::Pointer costFunction)

bool	HasCostFunction ()

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ConnectomicsSimulatedAnnealingPermutationBase
static Pointer	New ()

Protected Member Functions
	ConnectomicsSimulatedAnnealingPermutationModularity ()

	~ConnectomicsSimulatedAnnealingPermutationModularity ()

void	permutateMappingSingleNodeShift (ToModuleMapType *vertexToModuleMap, mitk::ConnectomicsNetwork::Pointer network)

void	permutateMappingModuleChange (ToModuleMapType *vertexToModuleMap, double currentTemperature, mitk::ConnectomicsNetwork::Pointer network)

void	joinTwoModules (ToModuleMapType *vertexToModuleMap, int moduleA, int moduleB)

void	splitModule (ToModuleMapType *vertexToModuleMap, double currentTemperature, mitk::ConnectomicsNetwork::Pointer network, int moduleToSplit)

void	extractModuleSubgraph (ToModuleMapType vertexToModuleMap, mitk::ConnectomicsNetwork::Pointer network, int moduleToSplit, mitk::ConnectomicsNetwork::Pointer subNetwork, VertexToVertexMapType graphToSubgraphVertexMap, VertexToVertexMapType *subgraphToGraphVertexMap)

void	removeModule (ToModuleMapType *vertexToModuleMap, int module)

void	randomlyAssignNodesToModules (ToModuleMapType *vertexToModuleMap, int numberOfIntendedModules)

double	Evaluate (ToModuleMapType *mapping) const

bool	AcceptChange (double costBefore, double costAfter, double temperature) const

Protected Member Functions inherited from mitk::ConnectomicsSimulatedAnnealingPermutationBase
	ConnectomicsSimulatedAnnealingPermutationBase ()

	~ConnectomicsSimulatedAnnealingPermutationBase ()

Protected Attributes
ToModuleMapType	m_BestSolution

mitk::ConnectomicsNetwork::Pointer	m_Network

int	m_Depth

double	m_StepSize

Protected Attributes inherited from mitk::ConnectomicsSimulatedAnnealingPermutationBase
mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::Pointer	m_CostFunction

Detailed Description

A class providing permutations for the calculation of modularity using simulated annealing.

Definition at line 28 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.h.

Member Typedef Documentation

typedef std::map< VertexDescriptorType, int > mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ToModuleMapType

Definition at line 33 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.h.

typedef mitk::ConnectomicsNetwork::VertexDescriptorType mitk::ConnectomicsSimulatedAnnealingPermutationModularity::VertexDescriptorType

Definition at line 32 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.h.

typedef std::map< VertexDescriptorType, VertexDescriptorType > mitk::ConnectomicsSimulatedAnnealingPermutationModularity::VertexToVertexMapType

Definition at line 34 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.h.

Constructor & Destructor Documentation

mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ConnectomicsSimulatedAnnealingPermutationModularity ( )

protected

Definition at line 25 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

mitk::ConnectomicsSimulatedAnnealingPermutationModularity::~ConnectomicsSimulatedAnnealingPermutationModularity ( )

protected

Definition at line 29 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

Member Function Documentation

bool mitk::ConnectomicsSimulatedAnnealingPermutationModularity::AcceptChange	(	double	costBefore,
		double	costAfter,
		double	temperature
	)		const

protected

Definition at line 507 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::CleanUp ( )

overridevirtual

Reimplemented from mitk::ConnectomicsSimulatedAnnealingPermutationBase.

Definition at line 94 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

Pointer mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Clone ( ) const

double mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Evaluate ( ToModuleMapType * mapping ) const

protected

Definition at line 493 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

References mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Evaluate().

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::extractModuleSubgraph	(	ToModuleMapType *	vertexToModuleMap,
		mitk::ConnectomicsNetwork::Pointer	network,
		int	moduleToSplit,
		mitk::ConnectomicsNetwork::Pointer	subNetwork,
		VertexToVertexMapType *	graphToSubgraphVertexMap,
		VertexToVertexMapType *	subgraphToGraphVertexMap
	)

protected

Definition at line 291 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ToModuleMapType mitk::ConnectomicsSimulatedAnnealingPermutationModularity::GetMapping ( )

Definition at line 488 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

int mitk::ConnectomicsSimulatedAnnealingPermutationModularity::getNumberOfModules ( ToModuleMapType * vertexToModuleMap ) const

Definition at line 355 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

int mitk::ConnectomicsSimulatedAnnealingPermutationModularity::getNumberOfVerticesInModule	(	ToModuleMapType *	vertexToModuleMap,
		int	module
	)		const

Definition at line 374 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Initialize ( )

overridevirtual

Reimplemented from mitk::ConnectomicsSimulatedAnnealingPermutationBase.

Definition at line 39 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::joinTwoModules	(	ToModuleMapType *	vertexToModuleMap,
		int	moduleA,
		int	moduleB
	)

protected

Definition at line 192 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

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

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

static Pointer mitk::ConnectomicsSimulatedAnnealingPermutationModularity::New ( )

static

Referenced by splitModule().

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Permutate ( double temperature )

overridevirtual

Reimplemented from mitk::ConnectomicsSimulatedAnnealingPermutationBase.

Definition at line 56 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::permutateMappingModuleChange	(	ToModuleMapType *	vertexToModuleMap,
		double	currentTemperature,
		mitk::ConnectomicsNetwork::Pointer	network
	)

protected

Definition at line 148 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::permutateMappingSingleNodeShift	(	ToModuleMapType *	vertexToModuleMap,
		mitk::ConnectomicsNetwork::Pointer	network
	)

protected

Definition at line 106 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::randomlyAssignNodesToModules	(	ToModuleMapType *	vertexToModuleMap,
		int	numberOfIntendedModules
	)

protected

Definition at line 423 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

References MBI_ERROR.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::removeModule	(	ToModuleMapType *	vertexToModuleMap,
		int	module
	)

protected

Definition at line 393 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

References MBI_WARN.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetDepth ( int depth )

Definition at line 532 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetMapping ( ToModuleMapType mapping )

Definition at line 482 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetNetwork ( mitk::ConnectomicsNetwork::Pointer theNetwork )

Definition at line 33 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetStepSize ( double size )

Definition at line 537 of file mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp.

void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::splitModule	(	ToModuleMapType *	vertexToModuleMap,
		double	currentTemperature,
		mitk::ConnectomicsNetwork::Pointer	network,
		int	moduleToSplit
	)