Base class for breast mask MRI segmentation methods. More...

Inheritance diagram for itk::BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType >:

Collaboration diagram for itk::BreastMaskSegmentationFromMRI< ImageDimension, InputPixelType >:

Classes
class	BIFIntensityAccessor

struct	larger_second

Public Types
enum	enumBreastSideType { BOTH_BREASTS, LEFT_BREAST, RIGHT_BREAST }
	Breast side. More...

typedef BreastMaskSegmentationFromMRI	Self

typedef Object	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef float	RealType

typedef itk::Image < InputPixelType, ImageDimension >	InternalImageType

typedef itk::Image< RealType, SliceDimension >	AxialImageType

typedef itk::Vector< RealType, DataDimension >	VectorType

typedef itk::Image< VectorType, ParametricDimension >	VectorImageType

typedef itk::PointSet < VectorType, ParametricDimension >	PointSetType

typedef PointSetType::PointsContainer	PointsContainer

typedef PointsContainer::Iterator	PointsIterator

typedef PointSetType::PointDataContainer	PointDataContainer

typedef PointDataContainer::Iterator	PointDataIterator

typedef itk::ImageRegionIterator < InternalImageType >	IteratorType

typedef itk::ImageRegionIteratorWithIndex < InternalImageType >	IteratorWithIndexType

typedef itk::ImageSliceIteratorWithIndex < InternalImageType >	SliceIteratorType

typedef itk::ImageLinearIteratorWithIndex < InternalImageType >	LineIteratorType

typedef itk::ImageDuplicator < InternalImageType >	DuplicatorType

typedef itk::Image < InputPixelType, SliceDimension >	InputSliceType

typedef itk::BasicImageFeaturesImageFilter < InputSliceType, InputSliceType >	BasicImageFeaturesFilterType

typedef itk::SliceBySliceImageFilter < InternalImageType, InternalImageType >	SliceBySliceImageFilterType

typedef itk::RegionGrowSurfacePoints < InternalImageType, InternalImageType >	ConnectedSurfaceVoxelFilterType

typedef itk::CurvatureAnisotropicDiffusionImageFilter < InternalImageType, InternalImageType >	SmoothingFilterType

typedef itk::GradientMagnitudeRecursiveGaussianImageFilter < InternalImageType, InternalImageType >	GradientFilterType

typedef itk::SigmoidImageFilter < InternalImageType, InternalImageType >	SigmoidFilterType

typedef itk::FastMarchingImageFilter < InternalImageType, InternalImageType >	FastMarchingFilterType

typedef itk::BinaryThresholdImageFilter < InternalImageType, InternalImageType >	ThresholdingFilterType

typedef itk::LewisGriffinRecursiveGaussianImageFilter < InternalImageType, InternalImageType >	DerivativeFilterType

typedef DerivativeFilterType::Pointer	DerivativeFilterPointer

typedef itk::MaximumImageFilter < InternalImageType, InternalImageType >	MaxImageFilterType

typedef itk::ConnectedThresholdImageFilter < InternalImageType, InternalImageType >	ConnectedFilterType

Public Member Functions
virtual const char *	GetClassName () const

	itkStaticConstMacro (SliceDimension, unsigned int, 2)

	itkStaticConstMacro (ParametricDimension, unsigned int, 2)

	itkStaticConstMacro (DataDimension, unsigned int, 1)

void	SetVerbose (bool flag)

void	SetSmooth (bool flag)

void	SetLeftBreast (bool flag)

void	SetRightBreast (bool flag)

void	SetExtInitialPect (bool flag)

void	SetRegionGrowX (int coord)

void	SetRegionGrowY (int coord)

void	SetRegionGrowZ (int coord)

void	SetBackgroundThreshold (float threshold)

void	SetFinalSegmThreshold (float threshold)

void	SetSigmaInMM (float sigma)

void	SetMarchingK1 (float k1)

void	SetMarchingK2 (float k2)

void	SetMarchingTime (float t)

void	SetCoilCropDistance (float cropDist)

void	SetCropDistancePosteriorToMidSternum (float fDistIn)

void	SetOutputBIFS (std::string fn)

void	SetSigmaBIF (float sig)

void	SetOutputSmoothedStructural (std::string fn)

void	SetOutputSmoothedFatSat (std::string fn)

void	SetOutputClosedStructural (std::string fn)

void	SetOutputHistogram (std::string fn)

void	SetOutputFit (std::string fn)

void	SetOutputCDF (std::string fn)

void	SetOutputImageMax (std::string fn)

void	SetOutputImageMaxClosed (std::string fn)

void	SetOutputBackground (std::string fn)

void	SetOutputChestPoints (std::string fn)

void	SetPectoralControlPointSpacing (float d)

void	SetOutputPectoralMask (std::string fn)

void	SetOutputPecSurfaceMask (std::string fn)

void	SetOutputGradientMagImage (std::string fn)

void	SetOutputSpeedImage (std::string fn)

void	SetOutputFastMarchingImage (std::string fn)

void	SetOutputPectoralSurf (std::string fn)

void	SetExcludeAxilla (bool flag)

void	SetCropFit (bool flag)

void	SetOutputBreastFittedSurfMask (std::string fn)

void	SetOutputVTKSurface (std::string fn)

void	SetOutputSkinElevationMap (std::string fn)

void	SetOutputSkinSurfaceNoBreasts (std::string fn)

void	SetStructuralImage (typename InternalImageType::Pointer image)

void	SetFatSatImage (typename InternalImageType::Pointer image)

void	SetBIFImage (typename InternalImageType::Pointer image)

InternalImageType::IndexType	GetLeftNippleIndex (void)

InternalImageType::IndexType	GetRightNippleIndex (void)

InternalImageType::IndexType	GetMidSternumIndex (void)

virtual void	Execute (void)=0
	Execute the segmentation - must be implemented in derived class. More...

InternalImageType::Pointer	GetSegmentedImage (void)

void	WriteSegmentationToAFile (std::string fileOutput)
	Write the segmented image to a file. More...

Protected Member Functions
	BreastMaskSegmentationFromMRI ()
	Constructor. More...

virtual	~BreastMaskSegmentationFromMRI ()
	Destructor. More...

virtual void	Initialise (void)
	Initialise the segmentor. More...

virtual void	CreateBIFs (void)
	Create the BIF Image. More...

void	SmoothTheInputImages (void)
	Smooth the structural and FatSat images. More...

InternalImageType::Pointer	ScanLineMaxima (typename InternalImageType::Pointer image, typename InternalImageType::RegionType region, unsigned int direction, bool flgForward)
	Scan an image in a particular direction and replace voxels with scanned maximum intensity. More...

InternalImageType::Pointer	GreyScaleCloseImage (typename InternalImageType::Pointer image, typename InternalImageType::RegionType region, unsigned int direction, const std::string label)
	Scan an image in a particular direction and replace voxels with closed intensities. More...

InternalImageType::Pointer	GreyScaleCloseImage (typename InternalImageType::Pointer image, typename InternalImageType::RegionType region, const char *strSide)
	Scan an image in all directions and replace voxels with closed intensities. More...

void	GreyScaleClosing (void)
	Scan rows and columns in the image to fill in the center of the breast. More...

void	CalculateTheMaximumImage (void)
	Calculate the maximum image. More...

void	EnsureMaxImageHasOnlyPositiveIntensities (void)
	Ensure the maximum image contains only positive intensities. More...

void	SmoothMaxImageToIncreaseSeparationOfTheBackground (void)
	Smooth the image to increase separation of the background. More...

void	SegmentForegroundFromBackground (void)
	Segment the backgound using itkForegroundFromBackgroundImageThresholdCalculator. More...

void	SegmentBackground (void)
	Segment the backgound using the maximum image histogram. More...

void	ComputeElevationOfAnteriorSurface (bool flgCoilCrop=false)
	Compute a 2D map of the height of the patient's anterior skin surface. More...

InternalImageType::IndexType	FindSurfacePoint (typename InternalImageType::IndexType idxNipple, float deltaXinMM, float deltaZinMM)
	Find a point in the surface offset from the nipple. More...

void	FindBreastLandmarks (void)
	Find the nipple and mid-sternum landmarks. More...

PointSetType::Pointer	SegmentThePectoralMuscle (RealType rYHeightOffset, unsigned long &iPointPec, bool flgIncludeNippleSeeds=false)
	Segment the Pectoral Muscle. More...

void	CropTheMaskAccordingToEstimateOfCoilExtentInCoronalPlane (void)
	Discard anything not within the skin elevation mask. More...

void	MaskWithBSplineBreastSurface (RealType rYHeightOffset)
	Discard anything not within a B-Spline fitted to the breast skin surface. More...

void	MaskBreastWithSphere (void)
	Mask with a sphere centered on each breast. More...

void	SmoothMask (void)
	Smooth the mask and threshold to round corners etc. More...

void	ExtractLargestObject (enumBreastSideType breastSide)
	Extract the largest object. More...

double	DistanceBetweenVoxels (typename InternalImageType::IndexType p, typename InternalImageType::IndexType q)

std::string	ModifySuffix (std::string filename, std::string strInsertBeforeSuffix)

std::string	GetBreastSide (std::string &fileOutput, enumBreastSideType breastSide)

InternalImageType::Pointer	GetBreastSide (typename InternalImageType::Pointer inImage, enumBreastSideType breastSide)

bool	WriteImageToFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, enumBreastSideType breastSide)

bool	WriteImageToFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, bool flgLeft=false, bool flgRight=false)

bool	WriteBinaryImageToUCharFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, enumBreastSideType breastSide)

bool	WriteBinaryImageToUCharFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, bool flgLeft, bool flgRight)

bool	WriteBinaryImageToUCharFileOrVTKSurfaceFile (std::string &fileOutput, const char *description, typename InternalImageType::Pointer image, bool flgLeft, bool flgRight)
	Based on the file extension it will be decided wheter a vtk surface is written or an image is saved. More...

void	WriteHistogramToFile (std::string fileOutput, vnl_vector< double > &xHistIntensity, vnl_vector< double > &yHistFrequency, unsigned int nBins)

void	polyDataInfo (vtkPolyData *polyData)

void	WriteImageToVTKSurfaceFile (typename InternalImageType::Pointer image, std::string &fileOutput, enumBreastSideType breastSide, bool flgVerbose, float finalSegmThreshold)

InternalImageType::Pointer	MaskImageFromBSplineFittedSurface (const typename PointSetType::Pointer &pointSet, const typename InternalImageType::RegionType &region, const typename InternalImageType::PointType &origin, const typename InternalImageType::SpacingType &spacing, const typename InternalImageType::DirectionType &direction, const RealType rYHeightOffset, const int splineOrder, const RealType controlPointSpacingInMM, const int numOfLevels, bool correctSurfaceOffest)

Protected Attributes
bool	flgVerbose

bool	flgXML

bool	flgSmooth

bool	flgLeft

bool	flgRight

bool	flgExtInitialPect

bool	flgRegGrowXcoord

bool	flgRegGrowYcoord

bool	flgRegGrowZcoord

bool	flgCropWithFittedSurface

bool	flgExcludeAxilla

unsigned int	i

int	regGrowXcoord

int	regGrowYcoord

int	regGrowZcoord

float	maxIntensity

float	minIntensity

float	bgndThresholdProb

float	finalSegmThreshold

float	sigmaInMM

float	fMarchingK1

float	fMarchingK2

float	fMarchingTime

float	sigmaBIF

float	coilCropDistance

float	cropDistPosteriorToMidSternum

float	pecControlPointSpacing

std::string	fileOutputBIFs

std::string	fileOutputSmoothedStructural

std::string	fileOutputSmoothedFatSat

std::string	fileOutputClosedStructural

std::string	fileOutputCombinedHistogram

std::string	fileOutputRayleigh

std::string	fileOutputFreqLessBgndCDF

std::string	fileOutputMaxImage

std::string	fileOutputMaxClosedImage

std::string	fileOutputBackground

std::string	fileOutputPectoralSurfaceMask

std::string	fileOutputChestPoints

std::string	fileOutputPectoral

std::string	fileOutputGradientMagImage

std::string	fileOutputSpeedImage

std::string	fileOutputFastMarchingImage

std::string	fileOutputPectoralSurfaceVoxels

std::string	fileOutputFittedBreastMask

std::string	fileOutputVTKSurface

std::string	fileOutputSkinElevationMap

std::string	fileOutputSkinSurfaceNoBreasts

InternalImageType::Pointer	imStructural

InternalImageType::Pointer	imFatSat

InternalImageType::Pointer	imBIFs

InternalImageType::Pointer	imSpeedFuncInputImage

InternalImageType::Pointer	imMaximum

InternalImageType::Pointer	imMaxClosed

InternalImageType::Pointer	imPectoralVoxels

InternalImageType::Pointer	imPectoralSurfaceVoxels

InternalImageType::Pointer	imChestSurfaceVoxels

InternalImageType::Pointer	imSegmented

InternalImageType::Pointer	imTmp

AxialImageType::Pointer	imSkinElevationMap

InternalImageType::RegionType	m_LeftLateralRegion
	The left side of the image. More...

InternalImageType::RegionType	m_RightLateralRegion

InternalImageType::IndexType	idxMidSternum
	Breast Landmarks. More...

InternalImageType::IndexType	idxNippleRight

InternalImageType::IndexType	idxNippleLeft

InternalImageType::IndexType	idxLeftBreastMidPoint
	Landmarks used by the segmentation. More...

InternalImageType::IndexType	idxRightBreastMidPoint

InternalImageType::IndexType	idxLeftPosterior

InternalImageType::IndexType	idxRightPosterior

InternalImageType::IndexType	idxAreolarRight [4]

InternalImageType::IndexType	idxAreolarLeft [4]

Detailed Description