Connectomics Network Class. More...

#include <mitkConnectomicsNetwork.h>

Inheritance diagram for mitk::ConnectomicsNetwork:

Collaboration diagram for mitk::ConnectomicsNetwork:

Classes
struct	NetworkEdge

struct	NetworkNode

Public Types
typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, NetworkNode, NetworkEdge >	NetworkType

typedef boost::graph_traits< NetworkType >::vertex_descriptor	VertexDescriptorType

typedef boost::graph_traits< NetworkType >::edge_descriptor	EdgeDescriptorType

Public Types inherited from mitk::BaseData
typedef BaseData	Self

typedef itk::DataObject	Superclass

typedef itk::SmartPointer< Self >	Pointer

typedef itk::SmartPointer< const Self >	ConstPointer

Public Member Functions
virtual void	UpdateOutputInformation () override

virtual void	SetRequestedRegionToLargestPossibleRegion () override
	Set the RequestedRegion to the LargestPossibleRegion. More...

virtual bool	RequestedRegionIsOutsideOfTheBufferedRegion () override
	Determine whether the RequestedRegion is outside of the BufferedRegion. More...

virtual bool	VerifyRequestedRegion () override
	Verify that the RequestedRegion is within the LargestPossibleRegion. More...

virtual void	SetRequestedRegion (const itk::DataObject *) override
	Set the requested region from this data object to match the requested region of the data object passed in as a parameter. More...

	mitkClassMacro (ConnectomicsNetwork, BaseData)

Pointer	Clone () const

bool	EdgeExists (VertexDescriptorType vertexA, VertexDescriptorType vertexB) const

void	IncreaseEdgeWeight (VertexDescriptorType vertexA, VertexDescriptorType vertexB)

void	AddEdge (VertexDescriptorType vertexA, VertexDescriptorType vertexB)

void	AddEdge (VertexDescriptorType vertexA, VertexDescriptorType vertexB, int sourceID, int targetID, int weight=1, double edge_weight=1.0)

VertexDescriptorType	AddVertex (int id)

void	SetLabel (VertexDescriptorType vertex, std::string inLabel)

void	SetCoordinates (VertexDescriptorType vertex, std::vector< float > inCoordinates)

void	clear ()

NetworkNode	GetNode (VertexDescriptorType vertex) const

NetworkEdge	GetEdge (VertexDescriptorType vertexA, VertexDescriptorType vertexB) const

std::vector< NetworkNode >	GetVectorOfAllNodes () const

std::vector< VertexDescriptorType >	GetVectorOfAllVertexDescriptors () const

std::vector< VertexDescriptorType >	GetVectorOfAdjacentNodes (VertexDescriptorType vertex) const

std::vector< std::pair< std::pair< NetworkNode, NetworkNode >, NetworkEdge > >	GetVectorOfAllEdges () const

int	GetNumberOfVertices () const

int	GetNumberOfEdges () const

int	GetNumberOfSelfLoops ()

double	GetAverageDegree ()

double	GetConnectionDensity ()

int	GetMaximumWeight () const

std::vector< int >	GetDegreeOfNodes () const

int	GetMaximumDegree () const

std::vector< double >	GetLocalClusteringCoefficients () const

std::vector< double >	GetClusteringCoefficientsByDegree ()

double	GetGlobalClusteringCoefficient ()

std::vector< double >	GetNodeBetweennessVector () const

std::vector< double >	GetEdgeBetweennessVector () const

bool	CheckForLabel (std::string targetLabel) const

std::vector< double >	GetShortestDistanceVectorFromLabel (std::string targetLabel) const

NetworkType *	GetBoostGraph ()

void	SetBoostGraph (NetworkType *newGraph)

void	ImportNetwort (mitk::ConnectomicsNetwork::Pointer source)

bool	GetIsModified () const

void	SetIsModified (bool)

void	UpdateBounds ()

void	PruneUnconnectedSingleNodes ()

void	UpdateIDs ()

Public Member Functions inherited from mitk::BaseData
virtual std::vector< std::string >	GetClassHierarchy () const

virtual const char *	GetClassName () const

const mitk::TimeGeometry *	GetTimeGeometry () const
	Return the TimeGeometry of the data as const pointer. More...

const mitk::TimeGeometry *	GetTimeSlicedGeometry () const
	Return the TimeGeometry of the data as const pointer. More...

mitk::TimeGeometry *	GetTimeGeometry ()
	Return the TimeGeometry of the data as pointer. More...

const mitk::TimeGeometry *	GetUpdatedTimeGeometry ()
	Return the TimeGeometry of the data. More...

const mitk::TimeGeometry *	GetUpdatedTimeSliceGeometry ()
	Return the TimeGeometry of the data. More...

virtual void	Expand (unsigned int timeSteps)
	Expands the TimeGeometry to a number of TimeSteps. More...

const mitk::BaseGeometry *	GetUpdatedGeometry (int t=0)
	Return the BaseGeometry of the data at time t. More...

mitk::BaseGeometry *	GetGeometry (int t=0) const
	Return the geometry, which is a TimeGeometry, of the data as non-const pointer. More...

void	UpdateOutputInformation () override
	Update the information for this BaseData (the geometry in particular) so that it can be used as an output of a BaseProcess. More...

void	CopyInformation (const itk::DataObject *data) override
	Copy information from the specified data set. More...

virtual bool	IsInitialized () const
	Check whether the data has been initialized, i.e., at least the Geometry and other header data has been set. More...

virtual void	Clear ()
	Calls ClearData() and InitializeEmpty();. More...

virtual bool	IsEmptyTimeStep (unsigned int t) const
	Check whether object contains data (at a specified time), e.g., a set of points may be empty. More...

virtual bool	IsEmpty () const
	Check whether object contains data (at least at one point in time), e.g., a set of points may be empty. More...

void	ExecuteOperation (Operation *operation) override
	overwrite if the Data can be called by an Interactor (StateMachine). More...

virtual void	SetGeometry (BaseGeometry *aGeometry3D)
	Set the BaseGeometry of the data, which will be referenced (not copied!). Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry which saves the given BaseGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...

virtual void	SetTimeGeometry (TimeGeometry *geometry)
	Set the TimeGeometry of the data, which will be referenced (not copied!). More...

virtual void	SetClonedGeometry (const BaseGeometry *aGeometry3D)
	Set a clone of the provided TimeGeometry as TimeGeometry of the data. Assumes the data object has only 1 time step ( is a 3D object ) and creates a new TimeGeometry. If an TimeGeometry has already been set for the object, it will be replaced after calling this function. More...

virtual void	SetClonedTimeGeometry (const TimeGeometry *geometry)
	Set a clone of the provided TimeGeometry as TimeGeometry of the data. More...

virtual void	SetClonedGeometry (const BaseGeometry *aGeometry3D, unsigned int time)
	Set a clone of the provided geometry as BaseGeometry of a given time step. More...

mitk::PropertyList::Pointer	GetPropertyList () const
	Get the data's property list. More...

void	SetPropertyList (PropertyList *propertyList)
	Set the data's property list. More...

mitk::BaseProperty::Pointer	GetProperty (const char *propertyKey) const
	Get the property (instance of BaseProperty) with key propertyKey from the PropertyList, and set it to this, respectively;. More...

void	SetProperty (const char propertyKey, BaseProperty property)

virtual void	SetOrigin (const Point3D &origin)
	Convenience method for setting the origin of the BaseGeometry instances of all time steps. More...

itk::SmartPointer< mitk::BaseDataSource >	GetSource () const
	Get the process object that generated this data object. More...

unsigned int	GetTimeSteps () const
	Get the number of time steps from the TimeGeometry As the base data has not a data vector given by itself, the number of time steps is defined over the time sliced geometry. In sub classes, a better implementation could be over the length of the data vector. More...

virtual unsigned long	GetMTime () const override
	Get the modified time of the last change of the contents this data object or its geometry. More...

virtual void	Graft (const DataObject *) override

Public Member Functions inherited from mitk::OperationActor
	itkTypeMacroNoParent (OperationActor) virtual ~OperationActor()

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::BaseData
static const char *	GetStaticNameOfClass ()

Protected Member Functions
	ConnectomicsNetwork ()

virtual	~ConnectomicsNetwork ()

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

	BaseData (const BaseData &other)

	~BaseData ()

virtual void	InitializeTimeGeometry (unsigned int timeSteps=1)
	Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...

virtual void	InitializeTimeSlicedGeometry (unsigned int timeSteps=1)
	Initialize the TimeGeometry for a number of time steps. The TimeGeometry is initialized empty and evenly timed. In many cases it will be necessary to overwrite this in sub-classes. More...

virtual void	ClearData ()
	reset to non-initialized state, release memory More...

virtual void	InitializeEmpty ()
	Pure virtual; Must be used in subclasses to get a data object to a valid state. Should at least create one empty object and call Superclass::InitializeTimeGeometry() to ensure an existing valid geometry. More...

virtual void	PrintSelf (std::ostream &os, itk::Indent indent) const override

Protected Attributes
NetworkType	m_Network

bool	m_IsModified

Protected Attributes inherited from mitk::BaseData
bool	m_LastRequestedRegionWasOutsideOfTheBufferedRegion

unsigned int	m_SourceOutputIndexDuplicate

bool	m_Initialized

Detailed Description

Connectomics Network Class.

This class is designed to represent a connectomics network (brain network). It encapsulates a boost adjacency list and provides additional capabilities. The information contained in the nodes and edges is:

Network Node:

int ID - The id of the node
string label - The label of the node, this can be any string, such as an anatomical label
vector<float> coordinates - The coordinates the node should be displayed at

Network Edge:

int sourceId - The Id of the source node
int targetId - The Id of the target node
int weight - Weight of the edge as int (used for counting fibers)
double edge_weight - Used for boost and algorithms, should be between 0 and 1

Definition at line 53 of file mitkConnectomicsNetwork.h.

Member Typedef Documentation

typedef boost::graph_traits<NetworkType>::edge_descriptor mitk::ConnectomicsNetwork::EdgeDescriptorType

Definition at line 79 of file mitkConnectomicsNetwork.h.

typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, NetworkNode, NetworkEdge > mitk::ConnectomicsNetwork::NetworkType

Typedefs

Definition at line 77 of file mitkConnectomicsNetwork.h.

typedef boost::graph_traits<NetworkType>::vertex_descriptor mitk::ConnectomicsNetwork::VertexDescriptorType

Definition at line 78 of file mitkConnectomicsNetwork.h.

Constructor & Destructor Documentation

mitk::ConnectomicsNetwork::ConnectomicsNetwork ( )

protected

Definition at line 24 of file mitkConnectomicsNetwork.cpp.

mitk::ConnectomicsNetwork::~ConnectomicsNetwork ( )

protectedvirtual

Definition at line 29 of file mitkConnectomicsNetwork.cpp.

Member Function Documentation

void mitk::ConnectomicsNetwork::AddEdge	(	VertexDescriptorType	vertexA,
		VertexDescriptorType	vertexB
	)

add an edge between two given vertices

Definition at line 49 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::AddEdge	(	VertexDescriptorType	vertexA,
		VertexDescriptorType	vertexB,
		int	sourceID,
		int	targetID,
		int	weight = `1`,
		double	edge_weight = `1.0`
	)

add an edge between two given vertices ( with a specific weight )

Definition at line 57 of file mitkConnectomicsNetwork.cpp.

mitk::ConnectomicsNetwork::VertexDescriptorType mitk::ConnectomicsNetwork::AddVertex ( int id )

add a vertex with a specified id

Definition at line 71 of file mitkConnectomicsNetwork.cpp.

bool mitk::ConnectomicsNetwork::CheckForLabel ( std::string targetLabel ) const

Check whether a vertex with the specified label exists

Definition at line 703 of file mitkConnectomicsNetwork.cpp.

Referenced by main().

void mitk::ConnectomicsNetwork::clear ( )

clear the graph

Definition at line 97 of file mitkConnectomicsNetwork.cpp.

Pointer mitk::ConnectomicsNetwork::Clone ( ) const

bool mitk::ConnectomicsNetwork::EdgeExists	(	VertexDescriptorType	vertexA,
		VertexDescriptorType	vertexB
	)		const

return whether an edge exists between the two given vertices

Definition at line 35 of file mitkConnectomicsNetwork.cpp.

double mitk::ConnectomicsNetwork::GetAverageDegree ( )

get number of vertices, that are connected to themselves

Definition at line 274 of file mitkConnectomicsNetwork.cpp.

mitk::ConnectomicsNetwork::NetworkType * mitk::ConnectomicsNetwork::GetBoostGraph ( )

Access boost graph directly

Definition at line 436 of file mitkConnectomicsNetwork.cpp.

Referenced by mitk::ConnectomicsBetweennessHistogram::ComputeFromConnectomicsNetwork(), and mitk::ConnectomicsShortestPathHistogram::ComputeFromConnectomicsNetwork().

std::vector< double > mitk::ConnectomicsNetwork::GetClusteringCoefficientsByDegree ( )

Get a vector in the format vector[ degree ] = average clustering coefficient

Definition at line 373 of file mitkConnectomicsNetwork.cpp.

double mitk::ConnectomicsNetwork::GetConnectionDensity ( )

get number of edges divided by number of possible edges

Definition at line 282 of file mitkConnectomicsNetwork.cpp.

std::vector< int > mitk::ConnectomicsNetwork::GetDegreeOfNodes ( ) const

Get a vector in the format vector[ vertexID ] = degree

Definition at line 291 of file mitkConnectomicsNetwork.cpp.

Referenced by mitk::ConnectomicsDegreeHistogram::ComputeFromConnectomicsNetwork().

mitk::ConnectomicsNetwork::NetworkEdge mitk::ConnectomicsNetwork::GetEdge	(	VertexDescriptorType	vertexA,
		VertexDescriptorType	vertexB
	)		const

return the edge struct for two given node descriptors

Definition at line 504 of file mitkConnectomicsNetwork.cpp.

References mitkThrow.

std::vector< double > mitk::ConnectomicsNetwork::GetEdgeBetweennessVector ( ) const

Get the betweenness centrality for each edge in form of a vector of length (number edges)

Definition at line 637 of file mitkConnectomicsNetwork.cpp.

double mitk::ConnectomicsNetwork::GetGlobalClusteringCoefficient ( )

Get the global clustering coefficient

Definition at line 407 of file mitkConnectomicsNetwork.cpp.

bool mitk::ConnectomicsNetwork::GetIsModified ( ) const

Get the modified flag

Definition at line 486 of file mitkConnectomicsNetwork.cpp.

std::vector< double > mitk::ConnectomicsNetwork::GetLocalClusteringCoefficients ( ) const

Get a vector in the format vector[ vertexID ] = clustering coefficient

Definition at line 344 of file mitkConnectomicsNetwork.cpp.

References MITK_ERROR.

int mitk::ConnectomicsNetwork::GetMaximumDegree ( ) const

Get the maximum degree of all nodes

Definition at line 327 of file mitkConnectomicsNetwork.cpp.

int mitk::ConnectomicsNetwork::GetMaximumWeight ( ) const

Get the maximum weight of all edges

Definition at line 214 of file mitkConnectomicsNetwork.cpp.

mitk::ConnectomicsNetwork::NetworkNode mitk::ConnectomicsNetwork::GetNode ( VertexDescriptorType vertex ) const

return the node struct for a given node descriptor

Definition at line 498 of file mitkConnectomicsNetwork.cpp.

std::vector< double > mitk::ConnectomicsNetwork::GetNodeBetweennessVector ( ) const

Get the betweenness centrality for each vertex in form of a vector of length (number vertices)

Definition at line 620 of file mitkConnectomicsNetwork.cpp.

int mitk::ConnectomicsNetwork::GetNumberOfEdges ( ) const

get overall number of edges in the network

Definition at line 209 of file mitkConnectomicsNetwork.cpp.

int mitk::ConnectomicsNetwork::GetNumberOfSelfLoops ( )

get number of vertices, that are connected to themselves

Definition at line 239 of file mitkConnectomicsNetwork.cpp.

int mitk::ConnectomicsNetwork::GetNumberOfVertices ( ) const

get overall number of vertices in the network

Definition at line 204 of file mitkConnectomicsNetwork.cpp.

Referenced by mitk::ConnectomicsBetweennessHistogram::ComputeFromConnectomicsNetwork().

std::vector< double > mitk::ConnectomicsNetwork::GetShortestDistanceVectorFromLabel ( std::string targetLabel ) const

Get the shortest distance from a specified vertex to all other vertices in form of a vector of length (number vertices)

Definition at line 676 of file mitkConnectomicsNetwork.cpp.

References MITK_WARN.

std::vector< mitk::ConnectomicsNetwork::VertexDescriptorType > mitk::ConnectomicsNetwork::GetVectorOfAdjacentNodes ( VertexDescriptorType vertex ) const

get vector containing the descriptors of nodes adjacent to the vertex denoted by the given descriptor

Definition at line 311 of file mitkConnectomicsNetwork.cpp.

std::vector< std::pair< std::pair< mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode >, mitk::ConnectomicsNetwork::NetworkEdge > > mitk::ConnectomicsNetwork::GetVectorOfAllEdges ( ) const

get vector containing all the edges of the network and the connected nodes

Definition at line 172 of file mitkConnectomicsNetwork.cpp.

std::vector< mitk::ConnectomicsNetwork::NetworkNode > mitk::ConnectomicsNetwork::GetVectorOfAllNodes ( ) const

get vector containing all the nodes of the network

Definition at line 129 of file mitkConnectomicsNetwork.cpp.

std::vector< mitk::ConnectomicsNetwork::VertexDescriptorType > mitk::ConnectomicsNetwork::GetVectorOfAllVertexDescriptors ( ) const

get vector containing all the vertex descriptors of the network

Definition at line 152 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::ImportNetwort ( mitk::ConnectomicsNetwork::Pointer source )

Definition at line 449 of file mitkConnectomicsNetwork.cpp.

References MITK_ERROR.

void mitk::ConnectomicsNetwork::IncreaseEdgeWeight	(	VertexDescriptorType	vertexA,
		VertexDescriptorType	vertexB
	)

increase the weight of an edge between the two given vertices

Definition at line 41 of file mitkConnectomicsNetwork.cpp.

mitk::ConnectomicsNetwork::mitkClassMacro	(	ConnectomicsNetwork	,
		BaseData
	)

static Pointer mitk::ConnectomicsNetwork::New ( )

static

Referenced by mitk::ConnectomicsNetworkCreator::CreateNetworkFromFibersAndSegmentation(), mitk::ConnectomicsSyntheticNetworkGenerator::CreateSyntheticNetwork(), mitk::ConnectomicsNetworkReader::Read(), mitk::ConnectomicsSimulatedAnnealingPermutationModularity::splitModule(), mitk::ConnectomicsNetworkThresholder::Threshold(), mitk::ConnectomicsNetworkThresholder::ThresholdBelowDensity(), and mitk::ConnectomicsNetworkThresholder::ThresholdByRandomRemoval().

void mitk::ConnectomicsNetwork::PruneUnconnectedSingleNodes ( )

Remove nodes not connected to any other node

Definition at line 567 of file mitkConnectomicsNetwork.cpp.

bool mitk::ConnectomicsNetwork::RequestedRegionIsOutsideOfTheBufferedRegion ( )

overridevirtual

Determine whether the RequestedRegion is outside of the BufferedRegion.

This method returns true if the RequestedRegion is outside the BufferedRegion (true if at least one pixel is outside). This is used by the pipeline mechanism to determine whether a filter needs to re-execute in order to satisfy the current request. If the current RequestedRegion is already inside the BufferedRegion from the previous execution (and the current filter is up to date), then a given filter does not need to re-execute

Implements mitk::BaseData.

Definition at line 113 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::SetBoostGraph ( NetworkType * newGraph )

Set the boost graph directly

Definition at line 441 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::SetCoordinates	(	VertexDescriptorType	vertex,
		std::vector< float >	inCoordinates
	)

set the coordinates of a vertex

Definition at line 89 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::SetIsModified ( bool value )

Set the modified flag

Definition at line 492 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::SetLabel	(	VertexDescriptorType	vertex,
		std::string	inLabel
	)

set the label of a vertex

Definition at line 81 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::SetRequestedRegion ( const itk::DataObject * data )

overridevirtual

Set the requested region from this data object to match the requested region of the data object passed in as a parameter.

This method is implemented in the concrete subclasses of BaseData.

Implements mitk::BaseData.

Definition at line 121 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::SetRequestedRegionToLargestPossibleRegion ( )

overridevirtual

Set the RequestedRegion to the LargestPossibleRegion.

This forces a filter to produce all of the output in one execution (i.e. not streaming) on the next call to Update().

Implements mitk::BaseData.

Definition at line 109 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::UpdateBounds ( )

Update the bounds of the geometry to fit the network

Definition at line 516 of file mitkConnectomicsNetwork.cpp.

References max(), and min().

void mitk::ConnectomicsNetwork::UpdateIDs ( )

This function will relabel all vertices and edges in a continuous manner

Mainly important after removing vertices, to make sure that the ids run continuously from 0 to number of vertices - 1 and edge target and source ids match the corresponding node.

Definition at line 596 of file mitkConnectomicsNetwork.cpp.

void mitk::ConnectomicsNetwork::UpdateOutputInformation ( )

overridevirtual

Definition at line 105 of file mitkConnectomicsNetwork.cpp.

bool mitk::ConnectomicsNetwork::VerifyRequestedRegion ( )

overridevirtual

Verify that the RequestedRegion is within the LargestPossibleRegion.

If the RequestedRegion is not within the LargestPossibleRegion, then the filter cannot possibly satisfy the request. This method returns true if the request can be satisfied (even if it will be necessary to process the entire LargestPossibleRegion) and returns false otherwise. This method is used by PropagateRequestedRegion(). PropagateRequestedRegion() throws a InvalidRequestedRegionError exception if the requested region is not within the LargestPossibleRegion.

Implements mitk::BaseData.

Definition at line 117 of file mitkConnectomicsNetwork.cpp.

Member Data Documentation

bool mitk::ConnectomicsNetwork::m_IsModified

protected

Flag which indicates whether the network has been modified since the last check

mainly for rendering purposes

Definition at line 219 of file mitkConnectomicsNetwork.h.

NetworkType mitk::ConnectomicsNetwork::m_Network

protected

Definition at line 213 of file mitkConnectomicsNetwork.h.

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

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation