vtkEMSegmentMRMLManager Class Reference

#include <vtkEMSegmentMRMLManager.h>

Inheritance diagram for vtkEMSegmentMRMLManager:

Public Types
enum	{ DistributionSpecificationManual, DistributionSpecificationManuallySample, DistributionSpecificationAutoSample }
enum	{ StoppingConditionIterations = 0, StoppingConditionLabelMapMeasure = 1, StoppingConditionWeightsMeasure = 2 }
enum	{ RegistrationTest = -1, RegistrationOff = 0, RegistrationFast = 1, RegistrationSlow = 2 }
enum	{ InterpolationLinear = 0, InterpolationNearestNeighbor = 1, InterpolationCubic = 2 }
enum	{ CMTK = 0, BRAINS = 1 }
Public Member Functions
virtual void	AddTargetSelectedVolume (vtkIdType volumeID)
virtual void	AddTargetSelectedVolumeByMRMLID (char *mrmlID)
virtual vtkIdType	AddTreeNode (vtkIdType parentNodeID)
virtual int	AddTreeNodeDistributionSamplePoint (vtkIdType nodeID, double xyz[3])
virtual void	ChangeTreeNodeDistributionsFromManualSamplingToManual ()
virtual int	CheckEMSTemplateVolumeNodes (vtkMRMLEMSTemplateNode *emsTemplateNode)
virtual int	CheckMRMLNodeStructureForProcessing ()
virtual int	CheckTemplateMRMLStructure (vtkMRMLEMSTemplateNode *emsTemp, int guiFlag)
virtual vtkMRMLEMSAtlasNode *	CloneAtlasNode (vtkMRMLEMSAtlasNode target, const char name)
virtual vtkMRMLEMSVolumeCollectionNode *	CloneSubParcellationNode (vtkMRMLEMSVolumeCollectionNode target, const char name)
virtual vtkMRMLEMSVolumeCollectionNode *	CloneTargetNode (vtkMRMLEMSVolumeCollectionNode target, const char name)
virtual void	CompleteTemplateMRMLStructureForGUI (vtkMRMLEMSTemplateNode *emsTemp)
virtual void	ComputeAtlasNumberOfTrainingSamples ()
virtual void	CopyEMRelatedNodesToMRMLScene (vtkMRMLScene *newScene)
virtual void	CreateAndObserveNewParameterSet ()
int	CreateTemplateFile ()
virtual bool	DoTargetAndAtlasDataTypesMatch (vtkMRMLEMSVolumeCollectionNode targetNode, vtkMRMLEMSAtlasNode atlasNode)
virtual bool	ExistRegistrationAtlasVolumeKey (vtkIdType inputID)
vtkMRMLVolumeNode *	GetAlignedSpatialPriorFromTreeNodeID (vtkIdType nodeID)
vtkMRMLVolumeNode *	GetAlignedSubParcellationFromTreeNodeID (vtkIdType nodeID)
virtual vtkMRMLEMSAtlasNode *	GetAtlasAlignedNode ()
virtual vtkMRMLEMSAtlasNode *	GetAtlasInputNode ()
virtual int	GetAtlasNumberOfTrainingSamples ()
virtual const char *	GetColorNodeID ()
virtual int	GetEnableMultithreading ()
virtual int	GetEnableSubParcellation ()
virtual int	GetEnableTargetToTargetRegistration ()
virtual vtkMRMLEMSGlobalParametersNode *	GetGlobalParametersNode ()
int	GetInterpolationTypeFromString (const char *type)
virtual void	GetListOfTreeNodeIDs (vtkIdType rootNodeID, vtkstd::vector< vtkIdType > &list)
virtual int	GetMinimumIslandSize ()
virtual const char *	GetNthParameterSetName (int n)
virtual int	GetNumberOfParameterSets ()
virtual const char *	GetOutputVolumeMRMLID ()
virtual vtkMRMLScalarVolumeNode *	GetOutputVolumeNode ()
int	GetPackageTypeFromString (const char *type)
virtual int	GetRegistrationAffineType ()
virtual vtkIdType	GetRegistrationAtlasVolumeID (vtkIdType inputID)
virtual vtkIdType	GetRegistrationAtlasVolumeID ()
virtual int	GetRegistrationDeformableType ()
virtual int	GetRegistrationInterpolationType ()
virtual int	GetRegistrationPackageType ()
int	GetRegistrationTypeFromString (const char *type)
virtual int	GetSaveIntermediateResults ()
virtual int	GetSaveSurfaceModels ()
virtual int	GetSaveTemplateAfterSegmentation ()
virtual const char *	GetSaveTemplateFilename ()
virtual const char *	GetSaveWorkingDirectory ()
virtual void	GetSegmentationBoundaryMax (int maxPoint[3])
virtual void	GetSegmentationBoundaryMin (int minPoint[3])
virtual vtkMRMLEMSVolumeCollectionNode *	GetSubParcellationInputNode ()
virtual vtkMRMLEMSVolumeCollectionNode *	GetTargetInputNode ()
virtual int	GetTargetNumberOfSelectedVolumes ()
virtual vtkIdType	GetTargetSelectedVolumeNthID (int n)
virtual const char *	GetTargetSelectedVolumeNthMRMLID (int n)
virtual const char *	GetTclTaskFilename ()
virtual vtkMRMLEMSTreeNode *	GetTreeNode (vtkIdType)
virtual double	GetTreeNodeAlpha (vtkIdType nodeID)
virtual int	GetTreeNodeBiasCalculationMaxIterations (vtkIdType nodeID)
virtual vtkIdType	GetTreeNodeChildNodeID (vtkIdType parentNodeID, int childIndex)
virtual double	GetTreeNodeChildrenSumClassProbability (vtkIdType nodeID)
virtual double	GetTreeNodeClassProbability (vtkIdType nodeID)
virtual void	GetTreeNodeColor (vtkIdType nodeID, double rgb[3])
virtual double	GetTreeNodeDistributionLogCovarianceWithCorrection (vtkIdType nodeID, int rowIndex, int columnIndex)
virtual double	GetTreeNodeDistributionLogMeanWithCorrection (vtkIdType nodeID, int volumeNumber)
virtual double	GetTreeNodeDistributionMeanWithCorrection (vtkIdType nodeID, int volumeNumber)
virtual int	GetTreeNodeDistributionNumberOfSamples (vtkIdType nodeID)
virtual double	GetTreeNodeDistributionSampleIntensityValue (vtkIdType nodeID, int tupleNumber, vtkIdType volumeID)
virtual void	GetTreeNodeDistributionSamplePoint (vtkIdType nodeID, int tupleNumber, double xyz[3])
virtual int	GetTreeNodeDistributionSpecificationMethod (vtkIdType nodeID)
virtual int	GetTreeNodeExcludeFromIncompleteEStep (vtkIdType nodeID)
virtual vtkIdType	GetTreeNodeFirstIDWithChildProbabilityError ()
virtual int	GetTreeNodeGenerateBackgroundProbability (vtkIdType nodeID)
virtual double	GetTreeNodeInputChannelWeight (vtkIdType nodeID, int volumeNumber)
int	GetTreeNodeIntensityLabel (vtkIdType nodeID)
virtual int	GetTreeNodeIsLeaf (vtkIdType nodeID)
virtual const char *	GetTreeNodeName (vtkIdType id)
virtual int	GetTreeNodeNumberOfChildren (vtkIdType nodeID)
virtual vtkIdType	GetTreeNodeParentNodeID (vtkIdType childNodeID)
virtual int	GetTreeNodePrintBias (vtkIdType nodeID)
virtual int	GetTreeNodePrintEMLabelMapConvergence (vtkIdType nodeID)
virtual int	GetTreeNodePrintEMWeightsConvergence (vtkIdType nodeID)
virtual int	GetTreeNodePrintFrequency (vtkIdType nodeID)
virtual int	GetTreeNodePrintLabelMap (vtkIdType nodeID)
virtual int	GetTreeNodePrintMFALabelMapConvergence (vtkIdType nodeID)
virtual int	GetTreeNodePrintMFAWeightsConvergence (vtkIdType nodeID)
virtual int	GetTreeNodePrintQuality (vtkIdType nodeID)
virtual int	GetTreeNodePrintWeight (vtkIdType nodeID)
virtual double	GetTreeNodeSmoothingKernelSigma (vtkIdType nodeID)
virtual int	GetTreeNodeSmoothingKernelWidth (vtkIdType nodeID)
virtual vtkIdType	GetTreeNodeSpatialPriorVolumeID (vtkIdType nodeID)
virtual double	GetTreeNodeSpatialPriorWeight (vtkIdType nodeID)
virtual int	GetTreeNodeStoppingConditionEMIterations (vtkIdType nodeID)
virtual int	GetTreeNodeStoppingConditionEMType (vtkIdType nodeID)
virtual double	GetTreeNodeStoppingConditionEMValue (vtkIdType nodeID)
virtual int	GetTreeNodeStoppingConditionMFAIterations (vtkIdType nodeID)
virtual int	GetTreeNodeStoppingConditionMFAType (vtkIdType nodeID)
virtual double	GetTreeNodeStoppingConditionMFAValue (vtkIdType nodeID)
virtual vtkIdType	GetTreeNodeSubParcellationVolumeID (vtkIdType nodeID)
virtual vtkMRMLEMSTreeParametersLeafNode *	GetTreeParametersLeafNode (vtkIdType)
virtual vtkMRMLEMSTreeNode *	GetTreeRootNode ()
virtual vtkIdType	GetTreeRootNodeID ()
virtual int	GetUpdateIntermediateData ()
virtual const char *	GetVolumeName (vtkIdType volumeID)
virtual vtkMRMLVolumeNode *	GetVolumeNode (vtkIdType)
virtual vtkIdType	GetVolumeNthID (int n)
virtual int	GetVolumeNumberOfChoices ()
virtual vtkMRMLEMSWorkingDataNode *	GetWorkingDataNode ()
virtual int	HasGlobalParametersNode ()
virtual int	IDMapContainsMRMLNodeID (const char *MRMLNodeID)
virtual int	IDMapContainsVTKNodeID (vtkIdType id)
void	ImportMRMLFile (const char *mrmlFile, vtksys_stl::string errMSG)
virtual bool	IsTreeNodeDistributionLogCovarianceWithCorrectionInvertableAndSemiDefinite (vtkIdType nodeID)
virtual vtkIdType	MapMRMLNodeIDToVTKNodeID (const char *MRMLNodeID)
virtual void	MoveNthTargetSelectedVolume (int fromIndex, int toIndex)
virtual void	MoveTargetSelectedVolume (vtkIdType volumeID, int toIndex)
void	PrintInfo ()
void	PrintInfo (ostream &os)
void	PrintSelf (ostream &os, vtkIndent indent)
virtual void	PrintTree (vtkIdType rootID, vtkIndent indent)
virtual void	PrintTree ()
virtual void	PrintVolumeInfo (vtkMRMLScene *mrmlScene)
virtual void	ProcessMRMLEvents (vtkObject caller, unsigned long event, void callData)
virtual void	RegisterMRMLNodesWithScene ()
virtual void	RemoveAllTreeNodeDistributionSamplePoints (vtkIdType nodeID)
virtual void	RemoveLegacyNodes ()
virtual void	RemoveTargetSelectedVolume (vtkIdType volumeID)
virtual void	RemoveTargetSelectedVolumeIndex (vtkIdType imageIndex)
virtual void	RemoveTreeNode (vtkIdType removedNodeID)
virtual void	RemoveTreeNodeDistributionSamplePoint (vtkIdType nodeID, int samplePointNumber)
void	ResetLogCovarianceCorrectionOfAllNodes ()
virtual void	ResetTargetSelectedVolumes (const std::vector< vtkIdType > &volumeID)
void	ResetTreeNodeDistributionLogCovarianceCorrection (vtkIdType nodeID)
virtual void	ResetTreeNodeDistributionLogMeanCorrection (vtkIdType nodeID)
virtual void	SetColorNodeID (const char *colormap)
virtual void	SetEnableMultithreading (int isEnabled)
virtual void	SetEnableSubParcellation (int state)
virtual void	SetEnableTargetToTargetRegistration (int enable)
virtual int	SetLoadedParameterSetIndex (int i)
virtual void	SetMinimumIslandSize (int value)
virtual int	SetNodeWithCheck (vtkMRMLEMSTemplateNode *)
virtual void	SetNthParameterName (int n, const char *newName)
virtual void	SetOutputVolumeMRMLID (const char *mrmlID)
virtual void	SetRegistrationAffineType (int affineType)
virtual void	SetRegistrationAtlasVolumeID (vtkIdType inputID, vtkIdType volumeID)
virtual void	SetRegistrationAtlasVolumeID (vtkIdType volumeID)
virtual void	SetRegistrationDeformableType (int deformableType)
virtual void	SetRegistrationInterpolationType (int interpolationType)
virtual void	SetRegistrationPackageType (int packageType)
virtual void	SetSaveIntermediateResults (int shouldSaveResults)
virtual void	SetSaveSurfaceModels (int shouldSaveModels)
virtual void	SetSaveTemplateAfterSegmentation (int shouldSave)
virtual void	SetSaveTemplateFilename (const char *file)
virtual void	SetSaveWorkingDirectory (const char *directory)
virtual void	SetSegmentationBoundaryMax (int maxPoint[3])
virtual void	SetSegmentationBoundaryMin (int minPoint[3])
virtual void	SetTargetSelectedVolumeNthID (int n, vtkIdType newVolumeID)
virtual void	SetTargetSelectedVolumeNthMRMLID (int n, const char *mrmlID)
virtual void	SetTclTaskFilename (const char *fileName)
virtual void	SetTreeNodeAlpha (vtkIdType nodeID, double value)
virtual void	SetTreeNodeBiasCalculationMaxIterations (vtkIdType nodeID, int value)
virtual void	SetTreeNodeClassProbability (vtkIdType nodeID, double value)
virtual void	SetTreeNodeColor (vtkIdType nodeID, double rgb[3])
virtual void	SetTreeNodeDistributionLogCovariance (vtkIdType nodeID, int rowIndex, int columnIndex, double value)
void	SetTreeNodeDistributionLogCovarianceOffDiagonal (vtkIdType nodeID, double value)
void	SetTreeNodeDistributionLogCovarianceWithCorrection (vtkIdType nodeID, int rowIndex, int columnIndex, double value)
virtual void	SetTreeNodeDistributionLogMean (vtkIdType nodeID, int volumeNumber, double value)
virtual void	SetTreeNodeDistributionMeanWithCorrection (vtkIdType nodeID, int volumeNumber, double value)
virtual void	SetTreeNodeDistributionSpecificationMethod (vtkIdType nodeID, int method)
virtual void	SetTreeNodeExcludeFromIncompleteEStep (vtkIdType nodeID, int shouldExclude)
virtual void	SetTreeNodeGenerateBackgroundProbability (vtkIdType nodeID, int value)
virtual void	SetTreeNodeInputChannelWeight (vtkIdType nodeID, int volumeNumber, double value)
virtual void	SetTreeNodeIntensityLabel (vtkIdType nodeID, int label)
virtual void	SetTreeNodeName (vtkIdType id, const char *label)
virtual void	SetTreeNodeParentNodeID (vtkIdType childNodeID, vtkIdType newParentNodeID)
virtual void	SetTreeNodePrintBias (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintEMLabelMapConvergence (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintEMWeightsConvergence (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintFrequency (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintLabelMap (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintMFALabelMapConvergence (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintMFAWeightsConvergence (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintQuality (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodePrintWeight (vtkIdType nodeID, int shouldPrint)
virtual void	SetTreeNodeSmoothingKernelSigma (vtkIdType nodeID, double value)
virtual void	SetTreeNodeSmoothingKernelWidth (vtkIdType nodeID, int value)
virtual void	SetTreeNodeSpatialPriorVolumeID (vtkIdType nodeID, vtkIdType volumeID)
virtual void	SetTreeNodeSpatialPriorWeight (vtkIdType nodeID, double value)
virtual void	SetTreeNodeStoppingConditionEMIterations (vtkIdType nodeID, int iterations)
virtual void	SetTreeNodeStoppingConditionEMType (vtkIdType nodeID, int conditionType)
virtual void	SetTreeNodeStoppingConditionEMValue (vtkIdType nodeID, double value)
virtual void	SetTreeNodeStoppingConditionMFAIterations (vtkIdType nodeID, int iterations)
virtual void	SetTreeNodeStoppingConditionMFAType (vtkIdType nodeID, int conditionType)
virtual void	SetTreeNodeStoppingConditionMFAValue (vtkIdType nodeID, double value)
virtual void	SetTreeNodeSubParcellationVolumeID (vtkIdType nodeID, vtkIdType volumeID)
virtual void	SetUpdateIntermediateData (int shouldUpdate)
virtual void	SynchronizeAtlasNode (vtkMRMLEMSAtlasNode templateNode, vtkMRMLEMSAtlasNode changingNode, const char *name)
virtual void	SynchronizeSubParcellationNode (vtkMRMLEMSVolumeCollectionNode templateNode, vtkMRMLEMSVolumeCollectionNode changingNode, const char *name)
virtual void	SynchronizeTargetNode (vtkMRMLEMSVolumeCollectionNode templateNode, vtkMRMLEMSVolumeCollectionNode changingNode, const char *name)
vtksys_stl::string	TurnDefaultMRMLFileIntoTaskName (const char *fileName)
vtksys_stl::string	TurnDefaultTclFileIntoPreprocessingName (const char *fileName)
virtual void	UpdateIntensityDistributions ()
	vtkGetObjectMacro (Node, vtkMRMLEMSTemplateNode)
	vtkGetObjectMacro (MRMLScene, vtkMRMLScene)
	vtkSetObjectMacro (MRMLScene, vtkMRMLScene)
	vtkTypeMacro (vtkEMSegmentMRMLManager, vtkObject)
Static Public Member Functions
static vtkEMSegmentMRMLManager *	New ()
Private Types
typedef vtksys_stl::map < vtksys_stl::string, vtkIdType >	MRMLToVTKMapType
typedef vtksys_stl::map < vtkIdType, vtksys_stl::string >	VTKToMRMLMapType
Private Member Functions
virtual vtkIdType	AddNewTreeNode ()
virtual vtkMRMLEMSVolumeCollectionNode *	CloneVolumeCollectionNode (vtkMRMLEMSVolumeCollectionNode target, const char name)
virtual vtkIdType	GetNewVTKNodeID ()
virtual int	GetTargetVolumeIndex (vtkIdType vtkID)
virtual double	GetTreeNodeDistributionLogCovariance (vtkIdType nodeID, int rowIndex, int columnIndex)
vtkstd::vector< vtkstd::vector < double > >	GetTreeNodeDistributionLogCovariance (vtkIdType nodeID)
virtual double	GetTreeNodeDistributionLogCovarianceCorrection (vtkIdType nodeID, int rowIndex, int columnIndex)
vtkstd::vector< vtkstd::vector < double > >	GetTreeNodeDistributionLogCovarianceCorrection (vtkIdType nodeID)
virtual double	GetTreeNodeDistributionLogMean (vtkIdType nodeID, int volumeNumber)
virtual double	GetTreeNodeDistributionLogMeanCorrection (vtkIdType nodeID, int volumeNumber)
virtual void	IDMapInsertPair (vtkIdType vtkID, const char *MRMLNodeID)
virtual void	IDMapRemovePair (const char *MRMLNodeID)
virtual void	IDMapRemovePair (vtkIdType vtkID)
virtual const char *	MapVTKNodeIDToMRMLNodeID (vtkIdType vtkID)
void	operator= (const vtkEMSegmentMRMLManager &)
virtual void	PropogateAdditionOfSelectedTargetImage ()
virtual void	PropogateMovementOfSelectedTargetImage (int fromIndex, int toIndex)
virtual void	PropogateRemovalOfSelectedTargetImage (int index)
virtual void	RemoveTreeNodeParametersNodes (vtkIdType nodeID)
void	ResetLogCovarianceCorrectionsOfAllNodes (vtkIdType rootID)
virtual void	SetNode (vtkMRMLEMSTemplateNode *)
virtual void	SetOutputVolumeID (vtkIdType volumeID)
virtual void	SetTreeNodeDistributionLogMeanCorrection (vtkIdType nodeID, int volumeNumber, double value)
virtual void	SynchronizeVolumeCollectionNode (vtkMRMLEMSVolumeCollectionNode templateNode, vtkMRMLEMSVolumeCollectionNode changingNode, const char *name)
int	TreeNodeDistributionLogCovarianceCorrectionEnabled (vtkIdType nodeID)
vtksys_stl::string	TurnDefaultFileIntoName (vtksys_stl::string taskName)
void	TurnFromParentToLeafNode (vtkMRMLEMSTreeNode *treeNode)
virtual void	UpdateIntensityDistributionFromSample (vtkIdType nodeID)
virtual void	UpdateMapsFromMRML ()
	vtkEMSegmentMRMLManager (const vtkEMSegmentMRMLManager &)
	vtkEMSegmentMRMLManager ()
	~vtkEMSegmentMRMLManager ()
Private Attributes
bool	HideNodesFromEditors
MRMLToVTKMapType	MRMLNodeIDToVTKNodeIDMap
vtkMRMLScene *	MRMLScene
vtkIdType	NextVTKNodeID
vtkMRMLEMSTemplateNode *	Node
VTKToMRMLMapType	VTKNodeIDToMRMLNodeIDMap

Member Typedef Documentation

typedef vtksys_stl::map<vtksys_stl::string, vtkIdType> vtkEMSegmentMRMLManager::MRMLToVTKMapType [private]

typedef vtksys_stl::map<vtkIdType, vtksys_stl::string> vtkEMSegmentMRMLManager::VTKToMRMLMapType [private]

Member Enumeration Documentation

anonymous enum

Enumerator:

DistributionSpecificationManual
DistributionSpecificationManuallySample
DistributionSpecificationAutoSample

anonymous enum

Enumerator:

StoppingConditionIterations
StoppingConditionLabelMapMeasure
StoppingConditionWeightsMeasure

anonymous enum

Enumerator:

RegistrationTest
RegistrationOff
RegistrationFast
RegistrationSlow

anonymous enum

Enumerator:

InterpolationLinear
InterpolationNearestNeighbor
InterpolationCubic

anonymous enum

Enumerator:

CMTK
BRAINS

Constructor & Destructor Documentation

vtkEMSegmentMRMLManager::vtkEMSegmentMRMLManager ( ) [private]

References HideNodesFromEditors, MRMLScene, and NextVTKNodeID.

vtkEMSegmentMRMLManager::~vtkEMSegmentMRMLManager ( ) [private]

References SetNode().

vtkEMSegmentMRMLManager::vtkEMSegmentMRMLManager ( const vtkEMSegmentMRMLManager & ) [private]

Member Function Documentation

vtkIdType vtkEMSegmentMRMLManager::AddNewTreeNode ( ) [private, virtual]

References GetTargetInputNode(), HideNodesFromEditors, MapMRMLNodeIDToVTKNodeID(), New(), vtkMRMLEMSTreeNode::SetNumberOfTargetInputChannels(), and SetTreeNodeIntensityLabel().

Referenced by AddTreeNode().

void vtkEMSegmentMRMLManager::AddTargetSelectedVolume ( vtkIdType volumeID ) [virtual]

References vtkMRMLEMSVolumeCollectionNode::AddVolume(), GetTargetInputNode(), GetVolumeNode(), GetWorkingDataNode(), MapVTKNodeIDToMRMLNodeID(), slicerget::name, PropogateAdditionOfSelectedTargetImage(), and UpdateIntensityDistributions().

Referenced by AddTargetSelectedVolumeByMRMLID(), and main().

void vtkEMSegmentMRMLManager::AddTargetSelectedVolumeByMRMLID ( char * mrmlID ) [virtual]

References AddTargetSelectedVolume(), and MapMRMLNodeIDToVTKNodeID().

Referenced by vtkEMSegmentInputChannelsStep::Validate().

vtkIdType vtkEMSegmentMRMLManager::AddTreeNode ( vtkIdType parentNodeID ) [virtual]

References AddNewTreeNode(), and SetTreeNodeParentNodeID().

Referenced by vtkEMSegmentAnatomicalStructureStep::AddChildNodeCallback(), and main().

int vtkEMSegmentMRMLManager::AddTreeNodeDistributionSamplePoint	(	vtkIdType	nodeID,
		double	xyz[3]
	)			`[virtual]`

References vtkMRMLEMSTreeParametersLeafNode::AddSamplePoint(), DistributionSpecificationManuallySample, GetTreeParametersLeafNode(), and UpdateIntensityDistributionFromSample().

Referenced by vtkEMSegmentIntensityDistributionsStep::AddIntensityDistributionSamplePoint(), and main().

void vtkEMSegmentMRMLManager::ChangeTreeNodeDistributionsFromManualSamplingToManual ( ) [virtual]

References DistributionSpecificationManual, vtkMRMLEMSTreeParametersLeafNode::DistributionSpecificationManuallySample, GetListOfTreeNodeIDs(), GetTreeParametersLeafNode(), GetTreeRootNodeID(), and SetTreeNodeDistributionSpecificationMethod().

Referenced by main().

int vtkEMSegmentMRMLManager::CheckEMSTemplateVolumeNodes ( vtkMRMLEMSTemplateNode * emsTemplateNode ) [virtual]

References vtkMRMLScene::GetNextNodeByClass(), vtkMRMLScene::GetReferencedSubScene(), vtkMRMLScene::InitTraversal(), and New().

Referenced by SetLoadedParameterSetIndex().

virtual int vtkEMSegmentMRMLManager::CheckMRMLNodeStructureForProcessing ( ) [inline, virtual]

Referenced by main().

int vtkEMSegmentMRMLManager::CheckTemplateMRMLStructure	(	vtkMRMLEMSTemplateNode *	emsTemp,
		int	guiFlag
	)			`[virtual]`

References vtkMRMLEMSTemplateNode::GetEMSWorkingDataNode(), vtkMRMLEMSTemplateNode::GetGlobalParametersNode(), vtkMRMLEMSWorkingDataNode::GetInputTargetNode(), vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes(), vtkMRMLEMSWorkingDataNode::GetOutputSegmentationNode(), vtkMRMLEMSTemplateNode::GetSpatialAtlasNode(), vtkMRMLEMSTemplateNode::GetSubParcellationNode(), and vtkMRMLEMSTemplateNode::GetTreeNode().

Referenced by SetNodeWithCheck().

vtkMRMLEMSAtlasNode * vtkEMSegmentMRMLManager::CloneAtlasNode	(	vtkMRMLEMSAtlasNode *	target,
		const char *	name
	)			`[virtual]`

References vtkMRMLScene::AddNode(), vtkMRMLEMSVolumeCollectionNode::CloneVolumes(), vtkMRMLNode::CopyWithScene(), MRMLScene, and New().

virtual vtkMRMLEMSVolumeCollectionNode* vtkEMSegmentMRMLManager::CloneSubParcellationNode	(	vtkMRMLEMSVolumeCollectionNode *	target,
		const char *	name
	)			`[inline, virtual]`

virtual vtkMRMLEMSVolumeCollectionNode* vtkEMSegmentMRMLManager::CloneTargetNode	(	vtkMRMLEMSVolumeCollectionNode *	target,
		const char *	name
	)			`[inline, virtual]`

vtkMRMLEMSVolumeCollectionNode * vtkEMSegmentMRMLManager::CloneVolumeCollectionNode	(	vtkMRMLEMSVolumeCollectionNode *	target,
		const char *	name
	)			`[private, virtual]`

References vtkMRMLScene::AddNode(), vtkMRMLEMSVolumeCollectionNode::CloneVolumes(), vtkMRMLNode::CopyWithScene(), MRMLScene, and New().

void vtkEMSegmentMRMLManager::CompleteTemplateMRMLStructureForGUI ( vtkMRMLEMSTemplateNode * emsTemp ) [virtual]

References vtkMRMLEMSCollectionNode::AddNode(), vtkMRMLEMSTemplateNode::GetEMSWorkingDataNode(), vtkMRMLEMSWorkingDataNode::GetInputTargetNode(), vtkMRMLEMSTemplateNode::GetSpatialAtlasNode(), vtkMRMLEMSTemplateNode::GetSubParcellationNode(), HideNodesFromEditors, and New().

Referenced by CreateAndObserveNewParameterSet(), and SetLoadedParameterSetIndex().

void vtkEMSegmentMRMLManager::ComputeAtlasNumberOfTrainingSamples ( ) [virtual]

References GetAtlasInputNode(), vtkMRMLEMSCollectionNode::GetIndexByKey(), GetListOfTreeNodeIDs(), vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), GetTreeNode(), GetTreeNodeIsLeaf(), GetTreeRootNodeID(), and GetWorkingDataNode().

void vtkEMSegmentMRMLManager::CopyEMRelatedNodesToMRMLScene ( vtkMRMLScene * newScene ) [virtual]

References vtkMRMLScene::GetReferencedSubScene().

Referenced by CreateTemplateFile().

void vtkEMSegmentMRMLManager::CreateAndObserveNewParameterSet ( ) [virtual]

References CompleteTemplateMRMLStructureForGUI(), GetTreeRootNodeID(), HideNodesFromEditors, New(), SetNodeWithCheck(), SetTreeNodeIntensityLabel(), and SetTreeNodeName().

Referenced by vtkEMSegmentParametersSetStep::SelectedDefaultTaskChangedCallback().

int vtkEMSegmentMRMLManager::CreateTemplateFile ( )

References vtkMRMLScene::Commit(), CopyEMRelatedNodesToMRMLScene(), fileName, GetGlobalParametersNode(), GetSaveTemplateFilename(), vtkMRMLScene::GetURL(), GetWorkingDataNode(), MRMLScene, New(), vtkMRMLScene::SetRootDirectory(), SetSaveTemplateFilename(), SetSegmentationBoundaryMax(), vtkMRMLScene::SetURL(), TurnDefaultMRMLFileIntoTaskName(), and vtkMRMLScene::Undo().

Referenced by main(), and vtkEMSegmentRunSegmentationStep::SelectTemplateFileCallback().

bool vtkEMSegmentMRMLManager::DoTargetAndAtlasDataTypesMatch	(	vtkMRMLEMSVolumeCollectionNode *	targetNode,
		vtkMRMLEMSAtlasNode *	atlasNode
	)			`[virtual]`

References vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), and vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes().

Referenced by vtkEMSegmentRunSegmentationStep::StartSegmentationCallback().

bool vtkEMSegmentMRMLManager::ExistRegistrationAtlasVolumeKey ( vtkIdType inputID ) [virtual]

References GetGlobalParametersNode(), and vtkMRMLEMSGlobalParametersNode::GetRegistrationAtlasVolumeKey().

Referenced by vtkEMSegmentRegistrationParametersStep::AssignAtlasScansToInputChannels().

vtkMRMLVolumeNode * vtkEMSegmentMRMLManager::GetAlignedSpatialPriorFromTreeNodeID ( vtkIdType nodeID )

References vtkMRMLEMSWorkingDataNode::GetAlignedAtlasNode(), vtkMRMLEMSCollectionNode::GetIndexByKey(), vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), GetTreeNode(), and GetWorkingDataNode().

Referenced by vtkEMSegmentLogic::AutoCorrectSpatialPriorWeight(), and vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter().

vtkMRMLVolumeNode * vtkEMSegmentMRMLManager::GetAlignedSubParcellationFromTreeNodeID ( vtkIdType nodeID )

References vtkMRMLEMSWorkingDataNode::GetAlignedSubParcellationNode(), vtkMRMLEMSCollectionNode::GetIndexByKey(), vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), GetTreeNodeIsLeaf(), GetTreeParametersLeafNode(), and GetWorkingDataNode().

Referenced by vtkEMSegmentLogic::SubParcelateSegmentation().

vtkMRMLEMSAtlasNode * vtkEMSegmentMRMLManager::GetAtlasAlignedNode ( ) [virtual]

References vtkMRMLEMSWorkingDataNode::GetAlignedAtlasNode(), and GetWorkingDataNode().

vtkMRMLEMSAtlasNode * vtkEMSegmentMRMLManager::GetAtlasInputNode ( ) [virtual]

Referenced by ComputeAtlasNumberOfTrainingSamples(), GetAtlasNumberOfTrainingSamples(), GetRegistrationAtlasVolumeID(), GetTreeNodeSpatialPriorVolumeID(), LoadUserDefinedAtlas(), PrintInfo(), SetRegistrationAtlasVolumeID(), and SetTreeNodeSpatialPriorVolumeID().

int vtkEMSegmentMRMLManager::GetAtlasNumberOfTrainingSamples ( ) [virtual]

References GetAtlasInputNode().

const char * vtkEMSegmentMRMLManager::GetColorNodeID ( ) [virtual]

References vtkSlicerColorLogic::GetDefaultLabelMapColorNodeID(), GetGlobalParametersNode(), vtkMRMLScene::GetNodeByID(), MRMLScene, and New().

Referenced by vtkEMSegmentLogic::CreateOutputVolumeNode(), and vtkEMSegmentAnatomicalStructureStep::ShowUserInterface().

int vtkEMSegmentMRMLManager::GetEnableMultithreading ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentLogic::CopyGlobalDataToSegmenter(), and vtkEMSegmentRunSegmentationStep::ShowUserInterface().

int vtkEMSegmentMRMLManager::GetEnableSubParcellation ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::ShowUserInterface().

int vtkEMSegmentMRMLManager::GetEnableTargetToTargetRegistration ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentIntensityImagesStep::ShowUserInterface(), and vtkEMSegmentInputChannelsStep::ShowUserInterface().

vtkMRMLEMSGlobalParametersNode * vtkEMSegmentMRMLManager::GetGlobalParametersNode ( ) [virtual]

Referenced by vtkEMSegmentRegistrationParametersStep::AssignAtlasScansToInputChannels(), CreateTemplateFile(), vtkEMSegmentNodeParametersStep::DefineInputChannelWeightOverviewWindow(), DefineTargetVolume(), ExistRegistrationAtlasVolumeKey(), GetColorNodeID(), GetEnableMultithreading(), GetEnableSubParcellation(), GetEnableTargetToTargetRegistration(), GetMinimumIslandSize(), GetRegistrationAffineType(), GetRegistrationAtlasVolumeID(), GetRegistrationDeformableType(), GetRegistrationInterpolationType(), GetRegistrationPackageType(), GetSaveIntermediateResults(), GetSaveSurfaceModels(), GetSaveTemplateAfterSegmentation(), GetSaveTemplateFilename(), GetSaveWorkingDirectory(), GetSegmentationBoundaryMax(), GetSegmentationBoundaryMin(), GetUpdateIntermediateData(), HasGlobalParametersNode(), main(), PrintInfo(), PropogateAdditionOfSelectedTargetImage(), PropogateMovementOfSelectedTargetImage(), PropogateRemovalOfSelectedTargetImage(), vtkEMSegmentKWDynamicFrame::SaveSettingToMRML(), vtkEMSegmentKWDynamicFrame::SetButtonsFromMRML(), SetColorNodeID(), SetEnableMultithreading(), SetEnableSubParcellation(), SetEnableTargetToTargetRegistration(), SetMinimumIslandSize(), SetRegistrationAffineType(), SetRegistrationAtlasVolumeID(), SetRegistrationDeformableType(), SetRegistrationInterpolationType(), SetRegistrationPackageType(), SetSaveIntermediateResults(), SetSaveSurfaceModels(), SetSaveTemplateAfterSegmentation(), SetSaveTemplateFilename(), SetSaveWorkingDirectory(), SetSegmentationBoundaryMax(), SetSegmentationBoundaryMin(), SetUpdateIntermediateData(), vtkEMSegmentInputChannelsStep::UpdateInputChannelsfromMRML(), and vtkEMSegmentInputChannelsStep::Validate().

int vtkEMSegmentMRMLManager::GetInterpolationTypeFromString ( const char * type )

References InterpolationCubic, InterpolationLinear, and InterpolationNearestNeighbor.

void vtkEMSegmentMRMLManager::GetListOfTreeNodeIDs	(	vtkIdType	rootNodeID,
		vtkstd::vector< vtkIdType > &	list
	)			`[virtual]`

References GetTreeNodeChildNodeID(), and GetTreeNodeNumberOfChildren().

Referenced by ChangeTreeNodeDistributionsFromManualSamplingToManual(), ComputeAtlasNumberOfTrainingSamples(), GetTreeNodeFirstIDWithChildProbabilityError(), PropogateAdditionOfSelectedTargetImage(), PropogateMovementOfSelectedTargetImage(), PropogateRemovalOfSelectedTargetImage(), and UpdateIntensityDistributions().

int vtkEMSegmentMRMLManager::GetMinimumIslandSize ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::ShowUserInterface().

vtkIdType vtkEMSegmentMRMLManager::GetNewVTKNodeID ( ) [private, virtual]

References NextVTKNodeID, and VTKNodeIDToMRMLNodeIDMap.

Referenced by ProcessMRMLEvents(), and UpdateMapsFromMRML().

const char * vtkEMSegmentMRMLManager::GetNthParameterSetName ( int n ) [virtual]

Referenced by DefineEMSTemplate(), vtkEMSegmentParametersSetStep::LoadDefaultTask(), main(), vtkEMSegmentParametersSetStep::PopulateLoadedParameterSets(), and vtkEMSegmentParametersSetStep::UpdateTaskListIndex().

int vtkEMSegmentMRMLManager::GetNumberOfParameterSets ( ) [virtual]

References RemoveLegacyNodes().

Referenced by DefineEMSTemplate(), vtkEMSegmentParametersSetStep::LoadDefaultTask(), LoadMRMLScene(), main(), vtkEMSegmentParametersSetStep::PopulateLoadedParameterSets(), and vtkEMSegmentParametersSetStep::SelectedDefaultTaskChangedCallback().

const char * vtkEMSegmentMRMLManager::GetOutputVolumeMRMLID ( ) [virtual]

References GetWorkingDataNode().

Referenced by CompareResultsToStandard().

vtkMRMLScalarVolumeNode * vtkEMSegmentMRMLManager::GetOutputVolumeNode ( ) [virtual]

References vtkMRMLEMSWorkingDataNode::GetOutputSegmentationNode(), and GetWorkingDataNode().

Referenced by DefineFinalOutput(), and WriteResultsToFile().

int vtkEMSegmentMRMLManager::GetPackageTypeFromString ( const char * type )

References BRAINS, and CMTK.

Referenced by vtkEMSegmentPreProcessingStep::Validate().

int vtkEMSegmentMRMLManager::GetRegistrationAffineType ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRegistrationParametersStep::ShowUserInterface().

vtkIdType vtkEMSegmentMRMLManager::GetRegistrationAtlasVolumeID ( vtkIdType inputID ) [virtual]

References ERROR_NODE_VTKID, GetAtlasInputNode(), GetGlobalParametersNode(), vtkMRMLEMSGlobalParametersNode::GetRegistrationAtlasVolumeKey(), vtkMRMLEMSVolumeCollectionNode::GetVolumeNodeIDByKey(), and MapMRMLNodeIDToVTKNodeID().

vtkIdType vtkEMSegmentMRMLManager::GetRegistrationAtlasVolumeID ( ) [virtual]

References ERROR_NODE_VTKID, GetAtlasInputNode(), GetGlobalParametersNode(), vtkMRMLEMSGlobalParametersNode::GetRegistrationAtlasVolumeKey(), and MapMRMLNodeIDToVTKNodeID().

Referenced by vtkEMSegmentRegistrationParametersStep::AssignAtlasScansToInputChannels().

int vtkEMSegmentMRMLManager::GetRegistrationDeformableType ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRegistrationParametersStep::ShowUserInterface().

int vtkEMSegmentMRMLManager::GetRegistrationInterpolationType ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentLogic::CopyGlobalDataToSegmenter(), and vtkEMSegmentRegistrationParametersStep::ShowUserInterface().

int vtkEMSegmentMRMLManager::GetRegistrationPackageType ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRegistrationParametersStep::ShowUserInterface(), and vtkEMSegmentPreProcessingStep::Validate().

int vtkEMSegmentMRMLManager::GetRegistrationTypeFromString ( const char * type )

References RegistrationFast, RegistrationOff, and RegistrationSlow.

int vtkEMSegmentMRMLManager::GetSaveIntermediateResults ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::ShowUserInterface(), and vtkEMSegmentRunSegmentationStep::StartSegmentationCallback().

int vtkEMSegmentMRMLManager::GetSaveSurfaceModels ( ) [virtual]

References GetGlobalParametersNode().

int vtkEMSegmentMRMLManager::GetSaveTemplateAfterSegmentation ( ) [virtual]

References GetGlobalParametersNode().

const char * vtkEMSegmentMRMLManager::GetSaveTemplateFilename ( ) [virtual]

References GetGlobalParametersNode().

Referenced by CreateTemplateFile(), and vtkEMSegmentRunSegmentationStep::ShowUserInterface().

const char * vtkEMSegmentMRMLManager::GetSaveWorkingDirectory ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentLogic::CopyGlobalDataToSegmenter(), vtkEMSegmentRunSegmentationStep::ShowUserInterface(), and vtkEMSegmentRunSegmentationStep::StartSegmentationCallback().

void vtkEMSegmentMRMLManager::GetSegmentationBoundaryMax ( int maxPoint[3] ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter(), vtkEMSegmentLogic::DefineValidSegmentationBoundary(), main(), vtkEMSegmentRunSegmentationStep::MRMLUpdateROINodeFromROI(), vtkEMSegmentRunSegmentationStep::ROICheck(), vtkEMSegmentRunSegmentationStep::ROIIntensityMinMaxUpdate(), and vtkEMSegmentRunSegmentationStep::ROIMapUpdate().

void vtkEMSegmentMRMLManager::GetSegmentationBoundaryMin ( int minPoint[3] ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter(), vtkEMSegmentLogic::DefineValidSegmentationBoundary(), main(), vtkEMSegmentRunSegmentationStep::MRMLUpdateROINodeFromROI(), vtkEMSegmentRunSegmentationStep::ROICheck(), vtkEMSegmentRunSegmentationStep::ROIIntensityMinMaxUpdate(), vtkEMSegmentRunSegmentationStep::ROIMapUpdate(), and vtkEMSegmentRunSegmentationStep::ROIReset().

vtkMRMLEMSVolumeCollectionNode * vtkEMSegmentMRMLManager::GetSubParcellationInputNode ( ) [virtual]

Referenced by GetTreeNodeSubParcellationVolumeID(), and SetTreeNodeSubParcellationVolumeID().

vtkMRMLEMSVolumeCollectionNode * vtkEMSegmentMRMLManager::GetTargetInputNode ( ) [virtual]

References vtkMRMLEMSWorkingDataNode::GetInputTargetNode(), and GetWorkingDataNode().

Referenced by AddNewTreeNode(), AddTargetSelectedVolume(), vtkEMSegmentRegistrationParametersStep::AssignAtlasScansToInputChannels(), vtkEMSegmentNodeParametersStep::DefineInputChannelWeightOverviewWindow(), DefineTargetVolume(), vtkEMSegmentLogic::DefineValidSegmentationBoundary(), GetTargetNumberOfSelectedVolumes(), GetTargetSelectedVolumeNthID(), GetTargetSelectedVolumeNthMRMLID(), GetTargetVolumeIndex(), MoveNthTargetSelectedVolume(), PropogateAdditionOfSelectedTargetImage(), RemoveTargetSelectedVolumeIndex(), ResetTargetSelectedVolumes(), SetTargetSelectedVolumeNthID(), vtkEMSegmentInputChannelsStep::UpdateInputChannelsfromMRML(), vtkEMSegmentIntensityImagesStep::Validate(), and vtkEMSegmentInputChannelsStep::Validate().

int vtkEMSegmentMRMLManager::GetTargetNumberOfSelectedVolumes ( ) [virtual]

References vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes(), and GetTargetInputNode().

Referenced by vtkEMSegmentRegistrationParametersStep::AssignAtlasScansToInputChannels(), vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter(), vtkEMSegmentLogic::CopyTreeLeafDataToSegmenter(), vtkEMSegmentNodeParametersStep::DefineInputChannelWeightOverviewWindow(), vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), IsTreeNodeDistributionLogCovarianceWithCorrectionInvertableAndSemiDefinite(), main(), MoveNthTargetSelectedVolume(), vtkEMSegmentIntensityImagesStep::PopulateIntensityImagesTargetVolumeSelector(), vtkEMSegmentStep::PopulateMenuWithTargetVolumes(), SetTreeNodeDistributionLogCovarianceOffDiagonal(), vtkEMSegmentIntensityImagesStep::Validate(), and vtkEMSegmentInputChannelsStep::Validate().

vtkIdType vtkEMSegmentMRMLManager::GetTargetSelectedVolumeNthID ( int n ) [virtual]

References ERROR_NODE_VTKID, vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNodeID(), GetTargetInputNode(), IDMapContainsMRMLNodeID(), and MapMRMLNodeIDToVTKNodeID().

Referenced by vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), main(), vtkEMSegmentIntensityImagesStep::PopulateIntensityImagesTargetVolumeSelector(), vtkEMSegmentStep::PopulateMenuWithTargetVolumes(), and SetTargetSelectedVolumeNthID().

const char * vtkEMSegmentMRMLManager::GetTargetSelectedVolumeNthMRMLID ( int n ) [virtual]

References vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNodeID(), and GetTargetInputNode().

int vtkEMSegmentMRMLManager::GetTargetVolumeIndex ( vtkIdType vtkID ) [private, virtual]

References vtkMRMLEMSVolumeCollectionNode::GetIndexByVolumeNodeID(), GetTargetInputNode(), and MapVTKNodeIDToMRMLNodeID().

Referenced by MoveTargetSelectedVolume(), and RemoveTargetSelectedVolume().

const char * vtkEMSegmentMRMLManager::GetTclTaskFilename ( ) [virtual]

Referenced by vtkEMSegmentParametersSetStep::SelectedParameterSetChangedCallback().

vtkMRMLEMSTreeNode * vtkEMSegmentMRMLManager::GetTreeNode ( vtkIdType nodeID ) [virtual]

References MapVTKNodeIDToMRMLNodeID().

double vtkEMSegmentMRMLManager::GetTreeNodeAlpha ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeBiasCalculationMaxIterations ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

vtkIdType vtkEMSegmentMRMLManager::GetTreeNodeChildNodeID	(	vtkIdType	parentNodeID,
		int	childIndex
	)			`[virtual]`

References ERROR_NODE_VTKID, vtkMRMLEMSTreeNode::GetNthChildNode(), GetTreeNode(), and MapMRMLNodeIDToVTKNodeID().

Referenced by vtkEMSegmentLogic::AutoCorrectSpatialPriorWeight(), vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), vtkEMSegmentLogic::CopyTreeDataToSegmenter(), vtkEMSegmentNodeParametersStep::DefineClassOverviewWeightWindow(), GetListOfTreeNodeIDs(), GetTreeNodeChildrenSumClassProbability(), main(), vtkEMSegmentAnatomicalStructureStep::PopulateAnatomicalStructureTree(), PrintTree(), RemoveTreeNode(), ResetLogCovarianceCorrectionsOfAllNodes(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeLeafNodeSelectableState(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeParentNodeSelectableState(), and vtkEMSegmentLogic::SubParcelateSegmentation().

double vtkEMSegmentMRMLManager::GetTreeNodeChildrenSumClassProbability ( vtkIdType nodeID ) [virtual]

References GetTreeNode(), GetTreeNodeChildNodeID(), GetTreeNodeClassProbability(), GetTreeNodeNumberOfChildren(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), GetTreeNodeFirstIDWithChildProbabilityError(), and vtkEMSegmentNodeParametersStep::Validate().

double vtkEMSegmentMRMLManager::GetTreeNodeClassProbability ( vtkIdType nodeID ) [virtual]

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), vtkEMSegmentLogic::CopyTreeDataToSegmenter(), vtkEMSegmentNodeParametersStep::DefineClassOverviewWeightWindow(), vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and GetTreeNodeChildrenSumClassProbability().

void vtkEMSegmentMRMLManager::GetTreeNodeColor	(	vtkIdType	nodeID,
		double	rgb[3]
	)			`[virtual]`

References GetTreeNode(), and mathExample::n.

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogCovariance	(	vtkIdType	nodeID,
		int	rowIndex,
		int	columnIndex
	)			`[private, virtual]`

References GetTreeParametersLeafNode().

vtkstd::vector< vtkstd::vector< double > > vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogCovariance ( vtkIdType nodeID ) [private]

References vtkMRMLEMSTreeParametersLeafNode::GetLogCovariance(), and GetTreeParametersLeafNode().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogCovarianceCorrection	(	vtkIdType	nodeID,
		int	rowIndex,
		int	columnIndex
	)			`[private, virtual]`

References vtkMRMLEMSTreeParametersLeafNode::GetLogCovarianceCorrection(), and GetTreeParametersLeafNode().

vtkstd::vector< vtkstd::vector< double > > vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogCovarianceCorrection ( vtkIdType nodeID ) [private]

References vtkMRMLEMSTreeParametersLeafNode::GetLogCovarianceCorrection(), and GetTreeParametersLeafNode().

Referenced by TreeNodeDistributionLogCovarianceCorrectionEnabled().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogCovarianceWithCorrection	(	vtkIdType	nodeID,
		int	rowIndex,
		int	columnIndex
	)			`[virtual]`

References vtkMRMLEMSTreeParametersLeafNode::GetLogCovariance(), vtkMRMLEMSTreeParametersLeafNode::GetLogCovarianceCorrection(), GetTreeParametersLeafNode(), mathExample::n, and TreeNodeDistributionLogCovarianceCorrectionEnabled().

Referenced by vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), and main().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogMean	(	vtkIdType	nodeID,
		int	volumeNumber
	)			`[private, virtual]`

References vtkMRMLEMSTreeParametersLeafNode::GetLogMean(), and GetTreeParametersLeafNode().

Referenced by GetTreeNodeDistributionLogMeanWithCorrection(), and SetTreeNodeDistributionMeanWithCorrection().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogMeanCorrection	(	vtkIdType	nodeID,
		int	volumeNumber
	)			`[private, virtual]`

References vtkMRMLEMSTreeParametersLeafNode::GetLogMeanCorrection(), and GetTreeParametersLeafNode().

Referenced by GetTreeNodeDistributionLogMeanWithCorrection().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogMeanWithCorrection	(	vtkIdType	nodeID,
		int	volumeNumber
	)			`[virtual]`

References GetTreeNodeDistributionLogMean(), GetTreeNodeDistributionLogMeanCorrection(), and GetTreeParametersLeafNode().

Referenced by GetTreeNodeDistributionMeanWithCorrection(), and main().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionMeanWithCorrection	(	vtkIdType	nodeID,
		int	volumeNumber
	)			`[virtual]`

References GetTreeNodeDistributionLogMeanWithCorrection(), and LogToNormalIntensities().

Referenced by vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeDistributionNumberOfSamples ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeParametersLeafNode::GetNumberOfSamplePoints(), and GetTreeParametersLeafNode().

Referenced by vtkEMSegmentIntensityDistributionsStep::AddIntensityDistributionSamplePoint(), vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), main(), and UpdateIntensityDistributionFromSample().

double vtkEMSegmentMRMLManager::GetTreeNodeDistributionSampleIntensityValue	(	vtkIdType	nodeID,
		int	tupleNumber,
		vtkIdType	volumeID
	)			`[virtual]`

References vtkMRMLVolumeNode::GetRASToIJKMatrix(), GetTreeNodeDistributionSamplePoint(), GetVolumeNode(), New(), and rasToijk.

Referenced by vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), and UpdateIntensityDistributionFromSample().

void vtkEMSegmentMRMLManager::GetTreeNodeDistributionSamplePoint	(	vtkIdType	nodeID,
		int	tupleNumber,
		double	xyz[3]
	)			`[virtual]`

References vtkMRMLEMSTreeParametersLeafNode::GetNthSamplePoint(), and GetTreeParametersLeafNode().

Referenced by GetTreeNodeDistributionSampleIntensityValue(), and main().

int vtkEMSegmentMRMLManager::GetTreeNodeDistributionSpecificationMethod ( vtkIdType nodeID ) [virtual]

References GetTreeParametersLeafNode().

Referenced by vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), and vtkEMSegmentIntensityDistributionsStep::IntensityDistributionSpecificationCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeExcludeFromIncompleteEStep ( vtkIdType nodeID ) [virtual]

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

vtkIdType vtkEMSegmentMRMLManager::GetTreeNodeFirstIDWithChildProbabilityError ( ) [virtual]

References GetListOfTreeNodeIDs(), GetTreeNodeChildrenSumClassProbability(), GetTreeNodeIsLeaf(), and GetTreeRootNodeID().

Referenced by vtkEMSegmentNodeParametersStep::Validate().

int vtkEMSegmentMRMLManager::GetTreeNodeGenerateBackgroundProbability ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

double vtkEMSegmentMRMLManager::GetTreeNodeInputChannelWeight	(	vtkIdType	nodeID,
		int	volumeNumber
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetInputChannelWeight(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and main().

int vtkEMSegmentMRMLManager::GetTreeNodeIntensityLabel ( vtkIdType nodeID )

References vtkMRMLEMSTreeNode::GetLeafParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeLeafDataToSegmenter(), main(), vtkEMSegmentAnatomicalStructureStep::SelectedAnatomicalNodeChangedCallback(), and vtkEMSegmentLogic::SubParcelateSegmentation().

int vtkEMSegmentMRMLManager::GetTreeNodeIsLeaf ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetNumberOfChildNodes(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::AutoCorrectSpatialPriorWeight(), ComputeAtlasNumberOfTrainingSamples(), vtkEMSegmentLogic::CopyTreeDataToSegmenter(), vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), vtkEMSegmentSpatialPriorsStep::DisplaySelectedNodeSpatialPriorsCallback(), GetAlignedSubParcellationFromTreeNodeID(), GetTreeNodeFirstIDWithChildProbabilityError(), main(), PrintTree(), vtkEMSegmentIntensityDistributionsStep::ResetDistributionCallback(), vtkEMSegmentAnatomicalStructureStep::SelectedAnatomicalNodeChangedCallback(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeLeafNodeSelectableState(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeParentNodeSelectableState(), and vtkEMSegmentLogic::SubParcelateSegmentation().

const char * vtkEMSegmentMRMLManager::GetTreeNodeName ( vtkIdType id ) [virtual]

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeDataToSegmenter(), vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter(), vtkEMSegmentNodeParametersStep::DefineClassOverviewWeightWindow(), vtkEMSegmentAnatomicalStructureStep::PopulateAnatomicalStructureTree(), PrintTree(), vtkEMSegmentAnatomicalStructureStep::SelectedNodeNameChangedCallback(), and vtkEMSegmentNodeParametersStep::Validate().

int vtkEMSegmentMRMLManager::GetTreeNodeNumberOfChildren ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetNumberOfChildNodes(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::AutoCorrectSpatialPriorWeight(), vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), vtkEMSegmentLogic::CopyTreeDataToSegmenter(), vtkEMSegmentNodeParametersStep::DefineClassOverviewWeightWindow(), GetListOfTreeNodeIDs(), GetTreeNodeChildrenSumClassProbability(), main(), vtkEMSegmentAnatomicalStructureStep::PopulateAnatomicalStructureTree(), PrintTree(), RemoveTreeNode(), ResetLogCovarianceCorrectionsOfAllNodes(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeLeafNodeSelectableState(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeParentNodeSelectableState(), and vtkEMSegmentLogic::SubParcelateSegmentation().

vtkIdType vtkEMSegmentMRMLManager::GetTreeNodeParentNodeID ( vtkIdType childNodeID ) [virtual]

References ERROR_NODE_VTKID, vtkMRMLEMSTreeNode::GetParentNode(), GetTreeNode(), and MapMRMLNodeIDToVTKNodeID().

Referenced by vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), and vtkEMSegmentNodeParametersStep::DefineClassOverviewWeightWindow().

int vtkEMSegmentMRMLManager::GetTreeNodePrintBias ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintEMLabelMapConvergence ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintEMWeightsConvergence ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintFrequency ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintLabelMap ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintMFALabelMapConvergence ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintMFAWeightsConvergence ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintQuality ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetLeafParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeLeafDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodePrintWeight ( vtkIdType nodeID ) [virtual]

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeGenericDataToSegmenter(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

double vtkEMSegmentMRMLManager::GetTreeNodeSmoothingKernelSigma ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

int vtkEMSegmentMRMLManager::GetTreeNodeSmoothingKernelWidth ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

vtkIdType vtkEMSegmentMRMLManager::GetTreeNodeSpatialPriorVolumeID ( vtkIdType nodeID ) [virtual]

References ERROR_NODE_VTKID, GetAtlasInputNode(), GetTreeNode(), vtkMRMLEMSVolumeCollectionNode::GetVolumeNodeIDByKey(), IDMapContainsMRMLNodeID(), MapMRMLNodeIDToVTKNodeID(), and mathExample::n.

Referenced by vtkEMSegmentSpatialPriorsStep::DisplaySelectedNodeSpatialPriorsCallback().

double vtkEMSegmentMRMLManager::GetTreeNodeSpatialPriorWeight ( vtkIdType nodeID ) [virtual]

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::AutoCorrectSpatialPriorWeight(), and vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeStoppingConditionEMIterations ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and vtkEMSegmentNodeParametersStep::StoppingConditionsEMIterationsCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeStoppingConditionEMType ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and vtkEMSegmentNodeParametersStep::StoppingConditionsEMCallback().

double vtkEMSegmentMRMLManager::GetTreeNodeStoppingConditionEMValue ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and vtkEMSegmentNodeParametersStep::StoppingConditionsEMValueCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeStoppingConditionMFAIterations ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::CopyTreeParentDataToSegmenter(), vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and vtkEMSegmentNodeParametersStep::StoppingConditionsMFAIterationsCallback().

int vtkEMSegmentMRMLManager::GetTreeNodeStoppingConditionMFAType ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and vtkEMSegmentNodeParametersStep::StoppingConditionsMFACallback().

double vtkEMSegmentMRMLManager::GetTreeNodeStoppingConditionMFAValue ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::DisplaySelectedNodeParametersCallback(), and vtkEMSegmentNodeParametersStep::StoppingConditionsMFAValueCallback().

vtkIdType vtkEMSegmentMRMLManager::GetTreeNodeSubParcellationVolumeID ( vtkIdType nodeID ) [virtual]

References ERROR_NODE_VTKID, GetSubParcellationInputNode(), GetTreeParametersLeafNode(), vtkMRMLEMSVolumeCollectionNode::GetVolumeNodeIDByKey(), IDMapContainsMRMLNodeID(), MapMRMLNodeIDToVTKNodeID(), and mathExample::n.

Referenced by vtkEMSegmentSpatialPriorsStep::DisplaySelectedNodeSpatialPriorsCallback().

vtkMRMLEMSTreeParametersLeafNode * vtkEMSegmentMRMLManager::GetTreeParametersLeafNode ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeNode::GetLeafParametersNode(), and GetTreeNode().

vtkMRMLEMSTreeNode * vtkEMSegmentMRMLManager::GetTreeRootNode ( ) [virtual]

Referenced by GetTreeRootNodeID(), and vtkEMSegmentNodeParametersStep::Validate().

vtkIdType vtkEMSegmentMRMLManager::GetTreeRootNodeID ( ) [virtual]

References ERROR_NODE_VTKID, GetTreeRootNode(), and MapMRMLNodeIDToVTKNodeID().

Referenced by ChangeTreeNodeDistributionsFromManualSamplingToManual(), vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback(), ComputeAtlasNumberOfTrainingSamples(), vtkEMSegmentLogic::CopyDataToSegmenter(), vtkEMSegmentLogic::CopyGlobalDataToSegmenter(), CreateAndObserveNewParameterSet(), vtkEMSegmentNodeParametersStep::DefineClassOverviewWeightWindow(), GetTreeNodeFirstIDWithChildProbabilityError(), main(), PrintTree(), PropogateAdditionOfSelectedTargetImage(), PropogateMovementOfSelectedTargetImage(), PropogateRemovalOfSelectedTargetImage(), ResetLogCovarianceCorrectionOfAllNodes(), vtkEMSegmentAnatomicalStructureStep::SetAnatomicalTreeNodesSelectableOn(), vtkEMSegmentAnatomicalStructureStep::ShowAnatomicalStructureTree(), vtkEMSegmentSpatialPriorsStep::ShowUserInterface(), vtkEMSegmentIntensityDistributionsStep::ShowUserInterface(), UpdateIntensityDistributions(), and vtkEMSegmentNodeParametersStep::Validate().

int vtkEMSegmentMRMLManager::GetUpdateIntermediateData ( ) [virtual]

References GetGlobalParametersNode().

const char * vtkEMSegmentMRMLManager::GetVolumeName ( vtkIdType volumeID ) [virtual]

References GetVolumeNode().

Referenced by vtkEMSegmentKWDynamicFrame::DefineVolumeMenuButton(), vtkEMSegmentIntensityDistributionsStep::DisplaySelectedNodeIntensityDistributionsCallback(), vtkEMSegmentIntensityImagesStep::PopulateIntensityImagesTargetVolumeSelector(), vtkEMSegmentGUI::PopulateMenuWithLoadedVolumes(), vtkEMSegmentStep::PopulateMenuWithTargetVolumes(), and vtkEMSegmentKWDynamicFrame::SetButtonsFromMRML().

vtkMRMLVolumeNode * vtkEMSegmentMRMLManager::GetVolumeNode ( vtkIdType volumeID ) [virtual]

References MapVTKNodeIDToMRMLNodeID().

Referenced by AddTargetSelectedVolume(), GetTreeNodeDistributionSampleIntensityValue(), GetVolumeName(), ResetTargetSelectedVolumes(), vtkEMSegmentKWDynamicFrame::SaveSettingToMRML(), SetOutputVolumeID(), SetTargetSelectedVolumeNthID(), and vtkEMSegmentIntensityImagesStep::Validate().

vtkIdType vtkEMSegmentMRMLManager::GetVolumeNthID ( int n ) [virtual]

References ERROR_NODE_VTKID, IDMapContainsMRMLNodeID(), and MapMRMLNodeIDToVTKNodeID().

Referenced by main(), vtkEMSegmentIntensityImagesStep::PopulateIntensityImagesTargetVolumeSelector(), and vtkEMSegmentGUI::PopulateMenuWithLoadedVolumes().

int vtkEMSegmentMRMLManager::GetVolumeNumberOfChoices ( ) [virtual]

Referenced by vtkEMSegmentRegistrationParametersStep::AssignAtlasScansToInputChannels(), vtkEMSegmentIntensityImagesStep::PopulateIntensityImagesTargetVolumeSelector(), and vtkEMSegmentGUI::PopulateMenuWithLoadedVolumes().

vtkMRMLEMSWorkingDataNode * vtkEMSegmentMRMLManager::GetWorkingDataNode ( ) [virtual]

int vtkEMSegmentMRMLManager::HasGlobalParametersNode ( ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::ShowUserInterface(), vtkEMSegmentRegistrationParametersStep::ShowUserInterface(), vtkEMSegmentIntensityImagesStep::ShowUserInterface(), and vtkEMSegmentInputChannelsStep::ShowUserInterface().

int vtkEMSegmentMRMLManager::IDMapContainsMRMLNodeID ( const char * MRMLNodeID ) [virtual]

References MRMLNodeIDToVTKNodeIDMap.

Referenced by GetTargetSelectedVolumeNthID(), GetTreeNodeSpatialPriorVolumeID(), GetTreeNodeSubParcellationVolumeID(), and GetVolumeNthID().

int vtkEMSegmentMRMLManager::IDMapContainsVTKNodeID ( vtkIdType id ) [virtual]

References VTKNodeIDToMRMLNodeIDMap.

Referenced by vtkEMSegmentRegistrationParametersStep::RegistrationAtlasImageCallback().

void vtkEMSegmentMRMLManager::IDMapInsertPair	(	vtkIdType	vtkID,
		const char *	MRMLNodeID
	)			`[private, virtual]`

References MRMLNodeIDToVTKNodeIDMap, and VTKNodeIDToMRMLNodeIDMap.

Referenced by ProcessMRMLEvents().

void vtkEMSegmentMRMLManager::IDMapRemovePair ( const char * MRMLNodeID ) [private, virtual]

References MRMLNodeIDToVTKNodeIDMap, and VTKNodeIDToMRMLNodeIDMap.

void vtkEMSegmentMRMLManager::IDMapRemovePair ( vtkIdType vtkID ) [private, virtual]

References MRMLNodeIDToVTKNodeIDMap, and VTKNodeIDToMRMLNodeIDMap.

Referenced by ProcessMRMLEvents().

void vtkEMSegmentMRMLManager::ImportMRMLFile	(	const char *	mrmlFile,
		vtksys_stl::string	errMSG
	)

References vtkMRMLScene::GetErrorMessage(), vtkMRMLScene::GetURL(), vtkMRMLScene::Import(), MRMLScene, and vtkMRMLScene::SetURL().

bool vtkEMSegmentMRMLManager::IsTreeNodeDistributionLogCovarianceWithCorrectionInvertableAndSemiDefinite ( vtkIdType nodeID ) [virtual]

References determinant(), vtkMRMLEMSTreeParametersLeafNode::GetLogCovariance(), vtkMRMLEMSTreeParametersLeafNode::GetLogCovarianceCorrection(), GetTargetNumberOfSelectedVolumes(), GetTreeParametersLeafNode(), InvertMatrix(), j, mathExample::n, and TreeNodeDistributionLogCovarianceCorrectionEnabled().

vtkIdType vtkEMSegmentMRMLManager::MapMRMLNodeIDToVTKNodeID ( const char * MRMLNodeID ) [virtual]

References ERROR_NODE_VTKID, and MRMLNodeIDToVTKNodeIDMap.

Referenced by AddNewTreeNode(), AddTargetSelectedVolumeByMRMLID(), GetRegistrationAtlasVolumeID(), GetTargetSelectedVolumeNthID(), GetTreeNodeChildNodeID(), GetTreeNodeParentNodeID(), GetTreeNodeSpatialPriorVolumeID(), GetTreeNodeSubParcellationVolumeID(), GetTreeRootNodeID(), GetVolumeNthID(), RemoveTreeNode(), vtkEMSegmentKWDynamicFrame::SetButtonsFromMRML(), SetTargetSelectedVolumeNthMRMLID(), and UpdateIntensityDistributionFromSample().

const char * vtkEMSegmentMRMLManager::MapVTKNodeIDToMRMLNodeID ( vtkIdType vtkID ) [private, virtual]

References VTKNodeIDToMRMLNodeIDMap.

Referenced by AddTargetSelectedVolume(), GetTargetVolumeIndex(), GetTreeNode(), GetVolumeNode(), PrintTree(), SetOutputVolumeID(), SetRegistrationAtlasVolumeID(), SetTargetSelectedVolumeNthID(), SetTreeNodeSpatialPriorVolumeID(), and SetTreeNodeSubParcellationVolumeID().

void vtkEMSegmentMRMLManager::MoveNthTargetSelectedVolume	(	int	fromIndex,
		int	toIndex
	)			`[virtual]`

References GetTargetInputNode(), GetTargetNumberOfSelectedVolumes(), GetWorkingDataNode(), vtkMRMLEMSVolumeCollectionNode::MoveNthVolume(), and PropogateMovementOfSelectedTargetImage().

Referenced by MoveTargetSelectedVolume().

void vtkEMSegmentMRMLManager::MoveTargetSelectedVolume	(	vtkIdType	volumeID,
		int	toIndex
	)			`[virtual]`

References GetTargetVolumeIndex(), and MoveNthTargetSelectedVolume().

Referenced by main().

vtkEMSegmentMRMLManager * vtkEMSegmentMRMLManager::New ( ) [static]

References autoSlicerTracto2regions::ret.

Referenced by AddNewTreeNode(), CheckEMSTemplateVolumeNodes(), CloneAtlasNode(), CloneVolumeCollectionNode(), CompleteTemplateMRMLStructureForGUI(), CreateAndObserveNewParameterSet(), CreateTemplateFile(), GetColorNodeID(), GetTreeNodeDistributionSampleIntensityValue(), RegisterMRMLNodesWithScene(), RemoveLegacyNodes(), SetTreeNodeParentNodeID(), and TurnFromParentToLeafNode().

void vtkEMSegmentMRMLManager::operator= ( const vtkEMSegmentMRMLManager & ) [private]

void vtkEMSegmentMRMLManager::PrintInfo ( )

void vtkEMSegmentMRMLManager::PrintInfo ( ostream & os )

References GetAtlasInputNode(), GetGlobalParametersNode(), vtkMRMLScene::GetURL(), GetWorkingDataNode(), MRMLScene, vtkMRMLEMSAtlasNode::PrintSelf(), vtkMRMLEMSWorkingDataNode::PrintSelf(), and vtkMRMLEMSGlobalParametersNode::PrintSelf().

Referenced by main().

void vtkEMSegmentMRMLManager::PrintSelf	(	ostream &	os,
		vtkIndent	indent
	)

References vtkMRMLScene::GetURL(), MRMLNodeIDToVTKNodeIDMap, MRMLScene, NextVTKNodeID, and VTKNodeIDToMRMLNodeIDMap.

void vtkEMSegmentMRMLManager::PrintTree	(	vtkIdType	rootID,
		vtkIndent	indent
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetNthChildNode(), vtkMRMLEMSTreeNode::GetNthChildNodeID(), GetTreeNode(), GetTreeNodeChildNodeID(), GetTreeNodeIsLeaf(), GetTreeNodeName(), GetTreeNodeNumberOfChildren(), MapVTKNodeIDToMRMLNodeID(), slicerget::name, and PrintTree().

void vtkEMSegmentMRMLManager::PrintTree ( ) [virtual]

References GetTreeRootNodeID().

Referenced by main(), and PrintTree().

void vtkEMSegmentMRMLManager::PrintVolumeInfo ( vtkMRMLScene * mrmlScene ) [virtual]

References vtkMRMLDisplayableNode::GetDisplayNode(), vtkMRMLScene::GetNthNodeByClass(), vtkMRMLScene::GetNumberOfNodesByClass(), and vtkMRMLStorableNode::GetStorageNode().

Referenced by LoadMRMLScene().

void vtkEMSegmentMRMLManager::ProcessMRMLEvents	(	vtkObject *	caller,
		unsigned long	event,
		void *	callData
	)			`[virtual]`

References GetNewVTKNodeID(), IDMapInsertPair(), IDMapRemovePair(), MRMLScene, vtkMRMLScene::NodeAddedEvent, and vtkMRMLScene::NodeRemovedEvent.

void vtkEMSegmentMRMLManager::PropogateAdditionOfSelectedTargetImage ( ) [private, virtual]

References vtkMRMLEMSTreeNode::AddTargetInputChannel(), vtkMRMLEMSGlobalParametersNode::AddTargetInputChannel(), GetGlobalParametersNode(), GetListOfTreeNodeIDs(), vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes(), GetTargetInputNode(), GetTreeNode(), and GetTreeRootNodeID().

Referenced by AddTargetSelectedVolume(), ResetTargetSelectedVolumes(), and SetTargetSelectedVolumeNthID().

void vtkEMSegmentMRMLManager::PropogateMovementOfSelectedTargetImage	(	int	fromIndex,
		int	toIndex
	)			`[private, virtual]`

References GetGlobalParametersNode(), GetListOfTreeNodeIDs(), GetTreeNode(), and GetTreeRootNodeID().

Referenced by MoveNthTargetSelectedVolume().

void vtkEMSegmentMRMLManager::PropogateRemovalOfSelectedTargetImage ( int index ) [private, virtual]

References GetGlobalParametersNode(), GetListOfTreeNodeIDs(), GetTreeNode(), GetTreeRootNodeID(), and vtkMRMLEMSGlobalParametersNode::RemoveNthTargetInputChannel().

Referenced by RemoveTargetSelectedVolumeIndex(), and ResetTargetSelectedVolumes().

void vtkEMSegmentMRMLManager::RegisterMRMLNodesWithScene ( ) [virtual]

References New().

void vtkEMSegmentMRMLManager::RemoveAllTreeNodeDistributionSamplePoints ( vtkIdType nodeID ) [virtual]

References vtkMRMLEMSTreeParametersLeafNode::ClearSamplePoints(), DistributionSpecificationManuallySample, GetTreeParametersLeafNode(), and UpdateIntensityDistributionFromSample().

Referenced by vtkEMSegmentIntensityDistributionsStep::DeleteAllManualIntensitySampleCallback(), and main().

void vtkEMSegmentMRMLManager::RemoveLegacyNodes ( ) [virtual]

cout << "vtkEMSegmentMRMLManager::RemoveLegacyNodes Start " << endl;

References vtkMRMLEMSCollectionNode::Copy(), vtkMRMLEMSWorkingDataNode::GetAlignedTargetNode(), vtkMRMLEMSTemplateNode::GetGlobalParametersNode(), vtkMRMLEMSTreeParametersNode::GetInputChannelWeight(), vtkMRMLEMSWorkingDataNode::GetInputTargetNode(), vtkMRMLEMSTreeParametersNode::GetLeafParametersNode(), vtkMRMLScene::GetNodesByClass(), vtkMRMLEMSTreeNode::GetNumberOfChildNodes(), vtkMRMLScene::GetNumberOfNodesByClass(), vtkMRMLEMSSegmenterNode::GetOutputVolumeNode(), vtkMRMLEMSTreeParametersNode::GetParentParametersNode(), vtkMRMLEMSNode::GetSegmenterNode(), vtkMRMLEMSSegmenterNode::GetTemplateNode(), vtkMRMLEMSTreeNode::GetTreeParametersNode(), vtkMRMLEMSSegmenterNode::GetWorkingDataNode(), MRMLScene, mathExample::n, New(), vtkMRMLEMSWorkingDataNode::RemoveInputAtlasNodeID(), vtkMRMLEMSWorkingDataNode::RemoveInputSubParcellationNodeID(), vtkMRMLScene::RemoveNode(), vtkMRMLEMSTreeNode::SetInputChannelWeight(), and vtkMRMLEMSTreeNode::SetNumberOfTargetInputChannels().

Referenced by GetNumberOfParameterSets().

void vtkEMSegmentMRMLManager::RemoveTargetSelectedVolume ( vtkIdType volumeID ) [virtual]

References GetTargetVolumeIndex(), and RemoveTargetSelectedVolumeIndex().

Referenced by main().

void vtkEMSegmentMRMLManager::RemoveTargetSelectedVolumeIndex ( vtkIdType imageIndex ) [virtual]

References GetTargetInputNode(), GetWorkingDataNode(), PropogateRemovalOfSelectedTargetImage(), and vtkMRMLEMSVolumeCollectionNode::RemoveNthVolume().

Referenced by RemoveTargetSelectedVolume(), and vtkEMSegmentInputChannelsStep::Validate().

void vtkEMSegmentMRMLManager::RemoveTreeNode ( vtkIdType removedNodeID ) [virtual]

References ERROR_NODE_VTKID, vtkMRMLEMSTreeNode::GetChildIndexByMRMLID(), vtkMRMLEMSTreeNode::GetParentNode(), GetTreeNode(), GetTreeNodeChildNodeID(), GetTreeNodeNumberOfChildren(), MapMRMLNodeIDToVTKNodeID(), vtkMRMLEMSTreeNode::RemoveNthChildNode(), RemoveTreeNodeParametersNodes(), and TurnFromParentToLeafNode().

Referenced by vtkEMSegmentAnatomicalStructureStep::DeleteNodeCallback(), and main().

void vtkEMSegmentMRMLManager::RemoveTreeNodeDistributionSamplePoint	(	vtkIdType	nodeID,
		int	samplePointNumber
	)			`[virtual]`

References DistributionSpecificationManuallySample, GetTreeParametersLeafNode(), vtkMRMLEMSTreeParametersLeafNode::RemoveNthSamplePoint(), and UpdateIntensityDistributionFromSample().

Referenced by vtkEMSegmentIntensityDistributionsStep::DeleteManualIntensitySampleCallback(), and main().

void vtkEMSegmentMRMLManager::RemoveTreeNodeParametersNodes ( vtkIdType nodeID ) [private, virtual]

References vtkMRMLEMSTreeNode::GetLeafParametersNode(), vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by RemoveTreeNode().

void vtkEMSegmentMRMLManager::ResetLogCovarianceCorrectionOfAllNodes ( )

References GetTreeRootNodeID(), and ResetLogCovarianceCorrectionsOfAllNodes().

Referenced by vtkEMSegmentInputChannelsStep::Validate().

void vtkEMSegmentMRMLManager::ResetLogCovarianceCorrectionsOfAllNodes ( vtkIdType rootID ) [private]

References GetTreeNodeChildNodeID(), GetTreeNodeNumberOfChildren(), GetTreeParametersLeafNode(), and ResetTreeNodeDistributionLogCovarianceCorrection().

Referenced by ResetLogCovarianceCorrectionOfAllNodes().

void vtkEMSegmentMRMLManager::ResetTargetSelectedVolumes ( const std::vector< vtkIdType > & volumeID ) [virtual]

References vtkMRMLEMSVolumeCollectionNode::AddVolume(), vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes(), GetTargetInputNode(), GetVolumeNode(), GetWorkingDataNode(), slicerget::name, PropogateAdditionOfSelectedTargetImage(), PropogateRemovalOfSelectedTargetImage(), vtkMRMLEMSVolumeCollectionNode::RemoveAllVolumes(), and UpdateIntensityDistributions().

Referenced by vtkEMSegmentIntensityImagesStep::Validate().

void vtkEMSegmentMRMLManager::ResetTreeNodeDistributionLogCovarianceCorrection ( vtkIdType nodeID )

References GetTreeParametersLeafNode(), j, mathExample::n, and vtkMRMLEMSTreeParametersLeafNode::SetLogCovarianceCorrection().

Referenced by vtkEMSegmentIntensityDistributionsStep::ResetDistributionCallback(), and ResetLogCovarianceCorrectionsOfAllNodes().

void vtkEMSegmentMRMLManager::ResetTreeNodeDistributionLogMeanCorrection ( vtkIdType nodeID ) [virtual]

References GetTreeParametersLeafNode(), mathExample::n, and vtkMRMLEMSTreeParametersLeafNode::SetLogMeanCorrection().

Referenced by vtkEMSegmentIntensityDistributionsStep::ResetDistributionCallback().

void vtkEMSegmentMRMLManager::SetColorNodeID ( const char * colormap ) [virtual]

References GetGlobalParametersNode().

void vtkEMSegmentMRMLManager::SetEnableMultithreading ( int isEnabled ) [virtual]

References GetGlobalParametersNode().

Referenced by main(), and vtkEMSegmentRunSegmentationStep::MultiThreadingCallback().

void vtkEMSegmentMRMLManager::SetEnableSubParcellation ( int state ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::PostprocessingSubparcellationCallback().

void vtkEMSegmentMRMLManager::SetEnableTargetToTargetRegistration ( int enable ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentIntensityImagesStep::AlignTargetImagesCallback(), and vtkEMSegmentInputChannelsStep::AlignTargetImagesCallback().

int vtkEMSegmentMRMLManager::SetLoadedParameterSetIndex ( int i ) [virtual]

References CheckEMSTemplateVolumeNodes(), CompleteTemplateMRMLStructureForGUI(), and SetNodeWithCheck().

Referenced by DefineEMSTemplate(), main(), and vtkEMSegmentParametersSetStep::SelectedParameterSetChangedCallback().

void vtkEMSegmentMRMLManager::SetMinimumIslandSize ( int value ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::PostprocessingMinimumIslandSizeCallback().

void vtkEMSegmentMRMLManager::SetNode ( vtkMRMLEMSTemplateNode * n ) [private, virtual]

References UpdateMapsFromMRML().

Referenced by SetNodeWithCheck(), and ~vtkEMSegmentMRMLManager().

int vtkEMSegmentMRMLManager::SetNodeWithCheck ( vtkMRMLEMSTemplateNode * n ) [virtual]

References CheckTemplateMRMLStructure(), and SetNode().

Referenced by CreateAndObserveNewParameterSet(), and SetLoadedParameterSetIndex().

void vtkEMSegmentMRMLManager::SetNthParameterName	(	int	n,
		const char *	newName
	)			`[virtual]`

Referenced by vtkEMSegmentParametersSetStep::RenameApplyCallback().

void vtkEMSegmentMRMLManager::SetOutputVolumeID ( vtkIdType volumeID ) [private, virtual]

References GetVolumeNode(), MapVTKNodeIDToMRMLNodeID(), and SetOutputVolumeMRMLID().

void vtkEMSegmentMRMLManager::SetOutputVolumeMRMLID ( const char * mrmlID ) [virtual]

References GetWorkingDataNode().

Referenced by vtkEMSegmentLogic::CreateOutputVolumeNode(), DefineFinalOutput(), and SetOutputVolumeID().

void vtkEMSegmentMRMLManager::SetRegistrationAffineType ( int affineType ) [virtual]

References GetGlobalParametersNode().

Referenced by main(), and vtkEMSegmentRegistrationParametersStep::RegistrationAffineCallback().

void vtkEMSegmentMRMLManager::SetRegistrationAtlasVolumeID	(	vtkIdType	inputID,
		vtkIdType	volumeID
	)			`[virtual]`

References vtkMRMLEMSVolumeCollectionNode::AddVolume(), GetAtlasInputNode(), GetGlobalParametersNode(), MapVTKNodeIDToMRMLNodeID(), and vtkMRMLEMSGlobalParametersNode::SetRegistrationAtlasVolumeKey().

void vtkEMSegmentMRMLManager::SetRegistrationAtlasVolumeID ( vtkIdType volumeID ) [virtual]

References vtkMRMLEMSVolumeCollectionNode::AddVolume(), GetAtlasInputNode(), GetGlobalParametersNode(), and MapVTKNodeIDToMRMLNodeID().

Referenced by vtkEMSegmentRegistrationParametersStep::RegistrationAtlasImageCallback().

void vtkEMSegmentMRMLManager::SetRegistrationDeformableType ( int deformableType ) [virtual]

References GetGlobalParametersNode().

Referenced by main(), and vtkEMSegmentRegistrationParametersStep::RegistrationDeformableCallback().

void vtkEMSegmentMRMLManager::SetRegistrationInterpolationType ( int interpolationType ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRegistrationParametersStep::RegistrationInterpolationCallback().

void vtkEMSegmentMRMLManager::SetRegistrationPackageType ( int packageType ) [virtual]

References GetGlobalParametersNode().

Referenced by main(), and vtkEMSegmentRegistrationParametersStep::RegistrationPackageCallback().

void vtkEMSegmentMRMLManager::SetSaveIntermediateResults ( int shouldSaveResults ) [virtual]

References GetGlobalParametersNode().

Referenced by main(), and vtkEMSegmentRunSegmentationStep::SaveIntermediateCallback().

void vtkEMSegmentMRMLManager::SetSaveSurfaceModels ( int shouldSaveModels ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::GenerateSurfaceModelsCallback().

void vtkEMSegmentMRMLManager::SetSaveTemplateAfterSegmentation ( int shouldSave ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::SaveAfterSegmentationCallback().

void vtkEMSegmentMRMLManager::SetSaveTemplateFilename ( const char * file ) [virtual]

References GetGlobalParametersNode().

Referenced by CreateTemplateFile(), main(), and vtkEMSegmentRunSegmentationStep::SelectTemplateFileCallback().

void vtkEMSegmentMRMLManager::SetSaveWorkingDirectory ( const char * directory ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentRunSegmentationStep::SelectDirectoryCallback().

void vtkEMSegmentMRMLManager::SetSegmentationBoundaryMax ( int maxPoint[3] ) [virtual]

References GetGlobalParametersNode().

Referenced by CreateTemplateFile(), vtkEMSegmentLogic::DefineValidSegmentationBoundary(), and vtkEMSegmentRunSegmentationStep::MRMLUpdateROIFromROINode().

void vtkEMSegmentMRMLManager::SetSegmentationBoundaryMin ( int minPoint[3] ) [virtual]

References GetGlobalParametersNode().

Referenced by vtkEMSegmentLogic::DefineValidSegmentationBoundary(), and vtkEMSegmentRunSegmentationStep::MRMLUpdateROIFromROINode().

void vtkEMSegmentMRMLManager::SetTargetSelectedVolumeNthID	(	int	n,
		vtkIdType	newVolumeID
	)			`[virtual]`

References ERROR_NODE_VTKID, GetTargetInputNode(), GetTargetSelectedVolumeNthID(), GetVolumeNode(), GetWorkingDataNode(), MapVTKNodeIDToMRMLNodeID(), PropogateAdditionOfSelectedTargetImage(), return, vtkMRMLEMSVolumeCollectionNode::SetNthVolumeNodeID(), and UpdateIntensityDistributions().

Referenced by SetTargetSelectedVolumeNthMRMLID().

void vtkEMSegmentMRMLManager::SetTargetSelectedVolumeNthMRMLID	(	int	n,
		const char *	mrmlID
	)			`[virtual]`

References MapMRMLNodeIDToVTKNodeID(), and SetTargetSelectedVolumeNthID().

Referenced by vtkEMSegmentInputChannelsStep::Validate().

void vtkEMSegmentMRMLManager::SetTclTaskFilename ( const char * fileName ) [virtual]

Referenced by vtkEMSegmentParametersSetStep::SelectedPreprocessingChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeAlpha	(	vtkIdType	nodeID,
		double	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersAlphaChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeBiasCalculationMaxIterations	(	vtkIdType	nodeID,
		int	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsBiasIterationsCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeClassProbability	(	vtkIdType	nodeID,
		double	value
	)			`[virtual]`

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::ClassWeightChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeColor	(	vtkIdType	nodeID,
		double	rgb[3]
	)			`[virtual]`

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentAnatomicalStructureStep::SelectedNodeColorChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogCovariance	(	vtkIdType	nodeID,
		int	rowIndex,
		int	columnIndex,
		double	value
	)			`[virtual]`

References GetTreeParametersLeafNode().

Referenced by main().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogCovarianceOffDiagonal	(	vtkIdType	nodeID,
		double	value
	)

References GetTargetNumberOfSelectedVolumes(), GetTreeParametersLeafNode(), j, mathExample::n, return, vtkMRMLEMSTreeParametersLeafNode::SetLogCovariance(), vtkMRMLEMSTreeParametersLeafNode::SetLogCovarianceCorrection(), and TreeNodeDistributionLogCovarianceCorrectionEnabled().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogCovarianceWithCorrection	(	vtkIdType	nodeID,
		int	rowIndex,
		int	columnIndex,
		double	value
	)

References vtkMRMLEMSTreeParametersLeafNode::GetLogCovariance(), GetTreeParametersLeafNode(), j, mathExample::n, return, vtkMRMLEMSTreeParametersLeafNode::SetLogCovarianceCorrection(), and TreeNodeDistributionLogCovarianceCorrectionEnabled().

Referenced by vtkEMSegmentIntensityDistributionsStep::IntensityDistributionCovarianceChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogMean	(	vtkIdType	nodeID,
		int	volumeNumber,
		double	value
	)			`[virtual]`

References GetTreeParametersLeafNode(), and vtkMRMLEMSTreeParametersLeafNode::SetLogMean().

Referenced by main().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionLogMeanCorrection	(	vtkIdType	nodeID,
		int	volumeNumber,
		double	value
	)			`[private, virtual]`

References GetTreeParametersLeafNode(), and vtkMRMLEMSTreeParametersLeafNode::SetLogMeanCorrection().

Referenced by SetTreeNodeDistributionMeanWithCorrection().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionMeanWithCorrection	(	vtkIdType	nodeID,
		int	volumeNumber,
		double	value
	)			`[virtual]`

References GetTreeNodeDistributionLogMean(), GetTreeParametersLeafNode(), NormalToLogIntensities(), and SetTreeNodeDistributionLogMeanCorrection().

void vtkEMSegmentMRMLManager::SetTreeNodeDistributionSpecificationMethod	(	vtkIdType	nodeID,
		int	method
	)			`[virtual]`

References DistributionSpecificationManuallySample, GetTreeParametersLeafNode(), and UpdateIntensityDistributionFromSample().

Referenced by ChangeTreeNodeDistributionsFromManualSamplingToManual(), and vtkEMSegmentIntensityDistributionsStep::IntensityDistributionSpecificationCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeExcludeFromIncompleteEStep	(	vtkIdType	nodeID,
		int	shouldExclude
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::ExcludeIncompleteEStepCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeGenerateBackgroundProbability	(	vtkIdType	nodeID,
		int	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::GenerateBackgroundProbabilityCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeInputChannelWeight	(	vtkIdType	nodeID,
		int	volumeNumber,
		double	value
	)			`[virtual]`

References GetTreeNode(), mathExample::n, and vtkMRMLEMSTreeNode::SetInputChannelWeight().

Referenced by main(), and vtkEMSegmentNodeParametersStep::NodeParametersInputChannelWeightChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeIntensityLabel	(	vtkIdType	nodeID,
		int	label
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetLeafParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by AddNewTreeNode(), CreateAndObserveNewParameterSet(), main(), and vtkEMSegmentAnatomicalStructureStep::SelectedNodeIntensityLabelChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeName	(	vtkIdType	id,
		const char *	label
	)			`[virtual]`

References GetTreeNode(), and mathExample::n.

Referenced by CreateAndObserveNewParameterSet(), and vtkEMSegmentAnatomicalStructureStep::SelectedNodeNameChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeParentNodeID	(	vtkIdType	childNodeID,
		vtkIdType	newParentNodeID
	)			`[virtual]`

References vtkMRMLEMSTreeNode::AddChildNode(), vtkMRMLScene::AddNode(), vtkMRMLEMSTreeNode::GetChildIndexByMRMLID(), vtkMRMLEMSTreeNode::GetLeafParametersNode(), vtkMRMLEMSTreeNode::GetParentNode(), vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), HideNodesFromEditors, MRMLScene, New(), vtkMRMLScene::RemoveNode(), vtkMRMLEMSTreeNode::RemoveNthChildNode(), and TurnFromParentToLeafNode().

Referenced by AddTreeNode(), main(), and vtkEMSegmentAnatomicalStructureStep::NodeParentChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintBias	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintBiasCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintEMLabelMapConvergence	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintEMLabelMapCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintEMWeightsConvergence	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintEMWeightsCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintFrequency	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintFrequencyChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintLabelMap	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintLabelMapCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintMFALabelMapConvergence	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintMFALabelMapCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintMFAWeightsConvergence	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintMFAWeightsCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintQuality	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetLeafParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintQualityCallback().

void vtkEMSegmentMRMLManager::SetTreeNodePrintWeight	(	vtkIdType	nodeID,
		int	shouldPrint
	)			`[virtual]`

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::NodeParametersPrintWeightCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeSmoothingKernelSigma	(	vtkIdType	nodeID,
		double	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

void vtkEMSegmentMRMLManager::SetTreeNodeSmoothingKernelWidth	(	vtkIdType	nodeID,
		int	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

void vtkEMSegmentMRMLManager::SetTreeNodeSpatialPriorVolumeID	(	vtkIdType	nodeID,
		vtkIdType	volumeID
	)			`[virtual]`

References vtkMRMLEMSVolumeCollectionNode::AddVolume(), GetAtlasInputNode(), GetTreeNode(), GetWorkingDataNode(), MapVTKNodeIDToMRMLNodeID(), and mathExample::n.

Referenced by vtkEMSegmentSpatialPriorsStep::SpatialPriorsVolumeCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeSpatialPriorWeight	(	vtkIdType	nodeID,
		double	value
	)			`[virtual]`

References GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentLogic::AutoCorrectSpatialPriorWeight(), and vtkEMSegmentNodeParametersStep::NodeParametersSpatialPriorWeightChangedCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeStoppingConditionEMIterations	(	vtkIdType	nodeID,
		int	iterations
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsEMIterationsCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeStoppingConditionEMType	(	vtkIdType	nodeID,
		int	conditionType
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsEMCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeStoppingConditionEMValue	(	vtkIdType	nodeID,
		double	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsEMValueCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeStoppingConditionMFAIterations	(	vtkIdType	nodeID,
		int	iterations
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsMFAIterationsCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeStoppingConditionMFAType	(	vtkIdType	nodeID,
		int	conditionType
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsMFACallback().

void vtkEMSegmentMRMLManager::SetTreeNodeStoppingConditionMFAValue	(	vtkIdType	nodeID,
		double	value
	)			`[virtual]`

References vtkMRMLEMSTreeNode::GetParentParametersNode(), GetTreeNode(), and mathExample::n.

Referenced by vtkEMSegmentNodeParametersStep::StoppingConditionsMFAValueCallback().

void vtkEMSegmentMRMLManager::SetTreeNodeSubParcellationVolumeID	(	vtkIdType	nodeID,
		vtkIdType	volumeID
	)			`[virtual]`

References vtkMRMLEMSVolumeCollectionNode::AddVolume(), GetSubParcellationInputNode(), GetTreeParametersLeafNode(), GetWorkingDataNode(), MapVTKNodeIDToMRMLNodeID(), and mathExample::n.

Referenced by vtkEMSegmentSpatialPriorsStep::ParcellationVolumeCallback().

void vtkEMSegmentMRMLManager::SetUpdateIntermediateData ( int shouldUpdate ) [virtual]

References GetGlobalParametersNode().

Referenced by main().

void vtkEMSegmentMRMLManager::SynchronizeAtlasNode	(	vtkMRMLEMSAtlasNode *	templateNode,
		vtkMRMLEMSAtlasNode *	changingNode,
		const char *	name
	)			`[virtual]`

References vtkMRMLEMSVolumeCollectionNode::CloneVolumes(), vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), and vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes().

virtual void vtkEMSegmentMRMLManager::SynchronizeSubParcellationNode	(	vtkMRMLEMSVolumeCollectionNode *	templateNode,
		vtkMRMLEMSVolumeCollectionNode *	changingNode,
		const char *	name
	)			`[inline, virtual]`

virtual void vtkEMSegmentMRMLManager::SynchronizeTargetNode	(	vtkMRMLEMSVolumeCollectionNode *	templateNode,
		vtkMRMLEMSVolumeCollectionNode *	changingNode,
		const char *	name
	)			`[inline, virtual]`

void vtkEMSegmentMRMLManager::SynchronizeVolumeCollectionNode	(	vtkMRMLEMSVolumeCollectionNode *	templateNode,
		vtkMRMLEMSVolumeCollectionNode *	changingNode,
		const char *	name
	)			`[private, virtual]`

References vtkMRMLEMSVolumeCollectionNode::CloneVolumes(), vtkMRMLEMSVolumeCollectionNode::GetNthVolumeNode(), and vtkMRMLEMSVolumeCollectionNode::GetNumberOfVolumes().

int vtkEMSegmentMRMLManager::TreeNodeDistributionLogCovarianceCorrectionEnabled ( vtkIdType nodeID ) [private]

References GetTreeNodeDistributionLogCovarianceCorrection(), and GetTreeParametersLeafNode().

Referenced by GetTreeNodeDistributionLogCovarianceWithCorrection(), IsTreeNodeDistributionLogCovarianceWithCorrectionInvertableAndSemiDefinite(), SetTreeNodeDistributionLogCovarianceOffDiagonal(), and SetTreeNodeDistributionLogCovarianceWithCorrection().

vtksys_stl::string vtkEMSegmentMRMLManager::TurnDefaultFileIntoName ( vtksys_stl::string taskName ) [private]

Referenced by TurnDefaultMRMLFileIntoTaskName(), and TurnDefaultTclFileIntoPreprocessingName().

vtksys_stl::string vtkEMSegmentMRMLManager::TurnDefaultMRMLFileIntoTaskName ( const char * fileName )

References TurnDefaultFileIntoName().

Referenced by vtkEMSegmentLogic::AddDefaultTasksToList(), and CreateTemplateFile().

vtksys_stl::string vtkEMSegmentMRMLManager::TurnDefaultTclFileIntoPreprocessingName ( const char * fileName )

References TurnDefaultFileIntoName().

Referenced by vtkEMSegmentLogic::AddDefaultTasksToList().

void vtkEMSegmentMRMLManager::TurnFromParentToLeafNode ( vtkMRMLEMSTreeNode * treeNode ) [private]

References vtkMRMLScene::AddNode(), vtkMRMLEMSTreeNode::GetLeafParametersNode(), vtkMRMLEMSTreeNode::GetNumberOfChildNodes(), vtkMRMLEMSTreeNode::GetParentParametersNode(), HideNodesFromEditors, MRMLScene, New(), and vtkMRMLScene::RemoveNode().

Referenced by RemoveTreeNode(), and SetTreeNodeParentNodeID().

void vtkEMSegmentMRMLManager::UpdateIntensityDistributionFromSample ( vtkIdType nodeID ) [private, virtual]

void vtkEMSegmentMRMLManager::UpdateIntensityDistributions ( ) [virtual]

References vtkMRMLEMSTreeParametersLeafNode::DistributionSpecificationManuallySample, GetListOfTreeNodeIDs(), GetTreeParametersLeafNode(), GetTreeRootNodeID(), and UpdateIntensityDistributionFromSample().

Referenced by AddTargetSelectedVolume(), ResetTargetSelectedVolumes(), and SetTargetSelectedVolumeNthID().

void vtkEMSegmentMRMLManager::UpdateMapsFromMRML ( ) [private, virtual]

References GetNewVTKNodeID(), MRMLNodeIDToVTKNodeIDMap, and VTKNodeIDToMRMLNodeIDMap.

Referenced by SetNode().

vtkEMSegmentMRMLManager::vtkGetObjectMacro	(	Node	,
		vtkMRMLEMSTemplateNode
	)

vtkEMSegmentMRMLManager::vtkGetObjectMacro	(	MRMLScene	,
		vtkMRMLScene
	)

vtkEMSegmentMRMLManager::vtkSetObjectMacro	(	MRMLScene	,
		vtkMRMLScene
	)

vtkEMSegmentMRMLManager::vtkTypeMacro	(	vtkEMSegmentMRMLManager	,
		vtkObject
	)

Member Data Documentation

bool vtkEMSegmentMRMLManager::HideNodesFromEditors [private]

Referenced by AddNewTreeNode(), CompleteTemplateMRMLStructureForGUI(), CreateAndObserveNewParameterSet(), SetTreeNodeParentNodeID(), TurnFromParentToLeafNode(), and vtkEMSegmentMRMLManager().

MRMLToVTKMapType vtkEMSegmentMRMLManager::MRMLNodeIDToVTKNodeIDMap [private]

Referenced by IDMapContainsMRMLNodeID(), IDMapInsertPair(), IDMapRemovePair(), MapMRMLNodeIDToVTKNodeID(), PrintSelf(), and UpdateMapsFromMRML().

vtkMRMLScene* vtkEMSegmentMRMLManager::MRMLScene [private]

Referenced by CloneAtlasNode(), CloneVolumeCollectionNode(), CreateTemplateFile(), GetColorNodeID(), ImportMRMLFile(), PrintInfo(), PrintSelf(), ProcessMRMLEvents(), RemoveLegacyNodes(), SetTreeNodeParentNodeID(), TurnFromParentToLeafNode(), and vtkEMSegmentMRMLManager().

vtkIdType vtkEMSegmentMRMLManager::NextVTKNodeID [private]

Referenced by GetNewVTKNodeID(), PrintSelf(), and vtkEMSegmentMRMLManager().

vtkMRMLEMSTemplateNode* vtkEMSegmentMRMLManager::Node [private]

VTKToMRMLMapType vtkEMSegmentMRMLManager::VTKNodeIDToMRMLNodeIDMap [private]

Referenced by GetNewVTKNodeID(), IDMapContainsVTKNodeID(), IDMapInsertPair(), IDMapRemovePair(), MapVTKNodeIDToMRMLNodeID(), PrintSelf(), and UpdateMapsFromMRML().

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

Modules/EMSegment/vtkEMSegmentMRMLManager.h
Modules/EMSegment/vtkEMSegmentMRMLManager.cxx

vtkEMSegmentMRMLManager Class Reference

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation