#include <SeansVesselReg.hxx>

Classes
struct	Context

Public Types
typedef boost::shared_ptr < Context >	ContextPtr

Public Member Functions
	SeansVesselReg ()

	~SeansVesselReg ()

bool	initialize (DataPtr source, DataPtr target, QString logPath)

bool	isValid () const

bool	execute ()

bool	performOneRegistration ()

Transform3D	getLinearResult (ContextPtr context=ContextPtr())

double	getResultMetric (ContextPtr context=ContextPtr())

double	getResultLtsRatio (ContextPtr context=ContextPtr())

Transform3D	getNonLinearTransform ()

void	checkQuality (Transform3D linearTransform)

void	setDebugOutput (bool on)

vtkPolyDataPtr	getDifferenceLines ()
	Lines connecting the moving and fixed data, according to LTS. More...

void	notifyPreRegistrationWarnings ()

ContextPtr	createContext (DataPtr source, DataPtr target)

void	performOneRegistration (ContextPtr context, bool linear)
	Register the source points to the target point in a single ste. More...

void	computeDistances (ContextPtr context=ContextPtr())
	Compute distances between the two datasets. More...

Static Public Member Functions
static vtkPolyDataPtr	convertToPolyData (vtkPointsPtr input)

static vtkPolyDataPtr	extractPolyData (ImagePtr image, int p_neighborhoodFilterThreshold, double p_BoundingBox[6])

Public Attributes
bool	mt_auto_lts

int	mt_ltsRatio

double	mt_distanceDeltaStopThreshold

double	mt_lambda

double	mt_sigma

bool	mt_doOnlyLinear

int	mt_sampleRatio

int	mt_singlePointThreshold

int	mt_maximumNumberOfIterations

bool	mt_verbose

double	mt_maximumDurationSeconds

double	margin

QString	m_logPath

Protected Member Functions
bool	runAlgorithm (ContextPtr context, vtkGeneralTransformPtr myConcatenation, int largeSteps, double fraction)

void	printOutResults (QString fileNamePrefix, vtkGeneralTransformPtr myConcatenation)

vtkAbstractTransformPtr	linearRegistration (vtkPointsPtr sortedSourcePoints, vtkPointsPtr sortedTargetPoints)

vtkAbstractTransformPtr	nonLinearRegistration (vtkPointsPtr sortedSourcePoints, vtkPointsPtr sortedTargetPoints)

vtkPolyDataPtr	convertToPolyData (DataPtr data, QString id)

vtkPointsPtr	transformPoints (vtkPointsPtr input, vtkAbstractTransformPtr transform)

vtkPointsPtr	createSortedPoints (vtkIdListPtr sortedIDList, vtkPointsPtr unsortedPoints, int numPoints)

vtkPolyDataPtr	crop (vtkPolyDataPtr input, vtkPolyDataPtr fixed, double margin)

ContextPtr	linearRefineAllLTS (ContextPtr context)

void	linearRefine (ContextPtr context)

SeansVesselReg::ContextPtr	splitContext (ContextPtr context)

void	print (vtkPointsPtr points)

void	print (vtkPolyDataPtr data)

Protected Attributes
ContextPtr	mLastRun
	result from last run of execute() More...

Detailed Description

Vessel - vessel registration algorithm.

Input is two centerline representations of vessel trees. Output is either a linear transform or a nonlinear transform (nonlinear not used yet).

Basic usage: Run execute(), then get result with getLinearTransform()

Date: Feb 4, 2011

Author: Christian Askeland, SINTEF

Original authors: Ingerid Reinertsen - algorithm. Sean (get full name) - refactored code.

Definition at line 30 of file SeansVesselReg.hxx.

Member Typedef Documentation

typedef boost::shared_ptr<Context> cx::SeansVesselReg::ContextPtr

Definition at line 60 of file SeansVesselReg.hxx.

Constructor & Destructor Documentation

cx::SeansVesselReg::SeansVesselReg ( )

Definition at line 39 of file SeansVesselReg.cxx.

cx::SeansVesselReg::~SeansVesselReg ( )

Definition at line 55 of file SeansVesselReg.cxx.

Member Function Documentation

void cx::SeansVesselReg::checkQuality ( Transform3D linearTransform )

Analyze 'size' of transform. Warn if too far away from an identity matrix.

Definition at line 954 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::computeDistances ( ContextPtr context = ContextPtr() )

Compute distances between the two datasets.

The results will be added into the context: sorted source and target points, and the metric.

Definition at line 310 of file SeansVesselReg.cxx.

vtkPolyDataPtr cx::SeansVesselReg::convertToPolyData ( vtkPointsPtr input )

static

Definition at line 581 of file SeansVesselReg.cxx.

vtkPolyDataPtr cx::SeansVesselReg::convertToPolyData	(	DataPtr	data,
		QString	id
	)

protected

Definition at line 501 of file SeansVesselReg.cxx.

SeansVesselReg::ContextPtr cx::SeansVesselReg::createContext	(	DataPtr	source,
		DataPtr	target
	)

Create a context containing data to use during iteration

< local copy of the lts ratio, can be changed for current iteration.

Definition at line 243 of file SeansVesselReg.cxx.

vtkPointsPtr cx::SeansVesselReg::createSortedPoints	(	vtkIdListPtr	sortedIDList,
		vtkPointsPtr	unsortedPoints,
		int	numPoints
	)

protected

Using the already sorted list of point ID's, create a sorted list of points based on the numPoint first of unsortedPoints.

Definition at line 417 of file SeansVesselReg.cxx.

vtkPolyDataPtr cx::SeansVesselReg::crop	(	vtkPolyDataPtr	input,
		vtkPolyDataPtr	fixed,
		double	margin
	)

protected

Crop the input data using a bounding box generated from the fixed data. The margin is used to enlarge the bounding box.

Definition at line 617 of file SeansVesselReg.cxx.

bool cx::SeansVesselReg::execute ( )

Execute the vessel to vessel registration. The result is available via the getLinearResult().

source is moving and target is fixed

Definition at line 82 of file SeansVesselReg.cxx.

vtkPolyDataPtr cx::SeansVesselReg::extractPolyData	(	ImagePtr	image,
		int	p_neighborhoodFilterThreshold,
		double	p_BoundingBox[6]
	)

static

Extract polydata from a image.

Parameters

image
p_neighborhoodFilterThreshold
p_BoundingBox

Returns

Input an image representation of centerlines. Transform to polydata, reject all data outside bounding box, unknown parameter: p_neighborhoodFilterThreshold

Definition at line 813 of file SeansVesselReg.cxx.

vtkPolyDataPtr cx::SeansVesselReg::getDifferenceLines ( )

Lines connecting the moving and fixed data, according to LTS.

Definition at line 978 of file SeansVesselReg.cxx.

Transform3D cx::SeansVesselReg::getLinearResult ( ContextPtr context = ContextPtr() )

Definition at line 659 of file SeansVesselReg.cxx.

Transform3D cx::SeansVesselReg::getNonLinearTransform ( )

double cx::SeansVesselReg::getResultLtsRatio ( ContextPtr context = ContextPtr() )

Definition at line 680 of file SeansVesselReg.cxx.

double cx::SeansVesselReg::getResultMetric ( ContextPtr context = ContextPtr() )

Definition at line 671 of file SeansVesselReg.cxx.

bool cx::SeansVesselReg::initialize	(	DataPtr	source,
		DataPtr	target,
		QString	logPath
	)

Execute the vessel to vessel registration. The result is available via the getLinearResult().

source is moving and target is fixed

Definition at line 64 of file SeansVesselReg.cxx.

bool cx::SeansVesselReg::isValid ( ) const

Definition at line 137 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::linearRefine ( ContextPtr context )

protected

iteratetively register linearly on the input context until it converges.

Definition at line 189 of file SeansVesselReg.cxx.

SeansVesselReg::ContextPtr cx::SeansVesselReg::linearRefineAllLTS ( ContextPtr seed )

protected

Search along several LTS for the best solution. Return the completed (linear) registration with the lowest metric.

Definition at line 146 of file SeansVesselReg.cxx.

vtkAbstractTransformPtr cx::SeansVesselReg::linearRegistration	(	vtkPointsPtr	sortedSourcePoints,
		vtkPointsPtr	sortedTargetPoints
	)

protected

Definition at line 457 of file SeansVesselReg.cxx.

vtkAbstractTransformPtr cx::SeansVesselReg::nonLinearRegistration	(	vtkPointsPtr	sortedSourcePoints,
		vtkPointsPtr	sortedTargetPoints
	)

protected

Definition at line 472 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::notifyPreRegistrationWarnings ( )

Definition at line 986 of file SeansVesselReg.cxx.

bool cx::SeansVesselReg::performOneRegistration ( )

Definition at line 127 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::performOneRegistration	(	ContextPtr	context,
		bool	linear
	)

Register the source points to the target point in a single ste.

Use the source to find the closest points on the target set, then register using either a landmark transform or a thinplatetransform. The context source points will be updated with the new transformation.

If sorted points are available in the context, they are used instead of computing new ones. The sorted data will always be cleared at the end of this method, This is because we want to call it iteratively.

Definition at line 382 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::print ( vtkPointsPtr points )

protected

Definition at line 599 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::print ( vtkPolyDataPtr data )

protected

Definition at line 608 of file SeansVesselReg.cxx.

void cx::SeansVesselReg::printOutResults	(	QString	fileNamePrefix,
		vtkGeneralTransformPtr	myConcatenation
	)

protected

Definition at line 705 of file SeansVesselReg.cxx.

bool cx::SeansVesselReg::runAlgorithm	(	ContextPtr	context,
		vtkGeneralTransformPtr	myConcatenation,
		int	largeSteps,
		double	fraction
	)

protected

void cx::SeansVesselReg::setDebugOutput ( bool on )

inline

Definition at line 76 of file SeansVesselReg.hxx.

SeansVesselReg::ContextPtr cx::SeansVesselReg::splitContext ( ContextPtr context )

protected

Create a copy of context that can be used to start a new iteration.

Definition at line 217 of file SeansVesselReg.cxx.

vtkPointsPtr cx::SeansVesselReg::transformPoints	(	vtkPointsPtr	input,
		vtkAbstractTransformPtr	transform
	)

protected

Transform input using the transform

Definition at line 437 of file SeansVesselReg.cxx.

Member Data Documentation

QString cx::SeansVesselReg::m_logPath

Definition at line 97 of file SeansVesselReg.hxx.

double cx::SeansVesselReg::margin

Definition at line 96 of file SeansVesselReg.hxx.

ContextPtr cx::SeansVesselReg::mLastRun

protected

result from last run of execute()

Definition at line 136 of file SeansVesselReg.hxx.

bool cx::SeansVesselReg::mt_auto_lts

Definition at line 84 of file SeansVesselReg.hxx.

double cx::SeansVesselReg::mt_distanceDeltaStopThreshold

Definition at line 86 of file SeansVesselReg.hxx.

bool cx::SeansVesselReg::mt_doOnlyLinear

Definition at line 89 of file SeansVesselReg.hxx.

double cx::SeansVesselReg::mt_lambda

Definition at line 87 of file SeansVesselReg.hxx.

int cx::SeansVesselReg::mt_ltsRatio

Definition at line 85 of file SeansVesselReg.hxx.

double cx::SeansVesselReg::mt_maximumDurationSeconds

Definition at line 95 of file SeansVesselReg.hxx.

int cx::SeansVesselReg::mt_maximumNumberOfIterations

Definition at line 93 of file SeansVesselReg.hxx.

int cx::SeansVesselReg::mt_sampleRatio

Definition at line 91 of file SeansVesselReg.hxx.

double cx::SeansVesselReg::mt_sigma

Definition at line 88 of file SeansVesselReg.hxx.

int cx::SeansVesselReg::mt_singlePointThreshold

Definition at line 92 of file SeansVesselReg.hxx.

bool cx::SeansVesselReg::mt_verbose

Definition at line 94 of file SeansVesselReg.hxx.

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

/media/jenkins/bamboo/buildagent/xml-data/build-dir/NN-RE-JOB1/CX/CX/source/resource/core/vesselReg/SeansVesselReg.hxx
/media/jenkins/bamboo/buildagent/xml-data/build-dir/NN-RE-JOB1/CX/CX/source/resource/core/vesselReg/SeansVesselReg.cxx

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation