Inheritance diagram for itk::MammographicTumourDistribution< InputPixelType, InputDimension >:

Collaboration diagram for itk::MammographicTumourDistribution< InputPixelType, InputDimension >:

Public Types
typedef MammographicTumourDistribution	Self

typedef MammogramAnalysis < InputPixelType, InputDimension >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::ImageType	ImageType

typedef Superclass::OutputImageType	OutputImageType

typedef Superclass::LabelImageType	LabelImageType

typedef Superclass::ImageTypeUCHAR	ImageTypeUCHAR

typedef Superclass::ReaderType	ReaderType

typedef Superclass::PolygonType	PolygonType

typedef Superclass::LeftOrRightSideCalculatorType	LeftOrRightSideCalculatorType

Public Types inherited from itk::MammogramAnalysis< InputPixelType, InputDimension >
enum	MammogramType { UNKNOWN_MAMMO_TYPE, DIAGNOSTIC_MAMMO, PREDIAGNOSTIC_MAMMO, CONTROL_MAMMO }

enum	LocusType { UNKNOWN_LOCUS_TYPE, BREAST_EDGE, PECTORAL }

typedef MammogramAnalysis	Self

typedef Object	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef itk::Image < InputPixelType, InputDimension >	ImageType

typedef itk::ImageFileReader < ImageType >	ReaderType

typedef itk::ImageRegionIterator < ImageType >	IteratorType

typedef itk::ImageRegionIteratorWithIndex < ImageType >	IteratorWithIndexType

typedef unsigned int	LabelPixelType

typedef Image< LabelPixelType, InputDimension >	LabelImageType

typedef short int	OutputPixelType

typedef itk::Image < OutputPixelType, InputDimension >	OutputImageType

typedef itk::MetaDataDictionary	DictionaryType

typedef itk::MetaDataObject < std::string >	MetaDataStringType

typedef float	RealType

typedef itk::Vector< RealType, DataDimension >	VectorType

typedef itk::Image< VectorType, ParametricDimension >	VectorImageType

typedef itk::PointSet < VectorType, ParametricDimension >	PointSetType

typedef itk::Image< RealType, InputDimension >	RealImageType

typedef itk::Image< unsigned char, InputDimension >	ImageTypeUCHAR

typedef PointSetType::PointsContainer	PointsContainer

typedef PointsContainer::Iterator	PointsIterator

typedef PointSetType::PointDataContainer	PointDataContainer

typedef PointDataContainer::Iterator	PointDataIterator

typedef itk::PolygonSpatialObject < InputDimension >	PolygonType

typedef itk::MammogramLeftOrRightSideCalculator < ImageType >	LeftOrRightSideCalculatorType

typedef LeftOrRightSideCalculatorType::BreastSideType	BreastSideType

typedef itk::ImageMomentsCalculator < ImageType >	ImageMomentCalculatorType

typedef itk::SignedMaurerDistanceMapImageFilter < ImageType, RealImageType >	DistanceTransformType

typedef itk::MammogramRegistrationFilter < ImageType, ImageType >	RegistrationFilterType

typedef RegistrationFilterType::enumRegistrationImagesType	enumRegistrationImagesType

Public Member Functions
virtual const char *	GetClassName () const

	itkStaticConstMacro (ParametricDimension, unsigned int, 2)

	itkStaticConstMacro (DataDimension, unsigned int, 1)

void	SetOutputCSV (std::ofstream *foutOutputCSV)

void	WriteDataToCSVFile (std::ofstream *foutCSV)

bool	Compute (void)

Public Member Functions inherited from itk::MammogramAnalysis< InputPixelType, InputDimension >
	itkStaticConstMacro (ParametricDimension, unsigned int, 2)

	itkStaticConstMacro (DataDimension, unsigned int, 1)

void	SetTypeOfInputImagesToRegister (enumRegistrationImagesType regImagesType)
	Set the registration image type. More...

void	SetPatientID (std::string idPatient)

void	SetInputDirectory (std::string dirIn)

void	SetOutputDirectory (std::string dirOut)

void	SetIDDiagnosticImage (std::string idDiagImage)

void	SetIDPreDiagnosticImage (std::string idPreDiagImage)

void	SetIDControlImage (std::string idControlImage)

void	SetFileDiagnostic (std::string fileDiag)

void	SetFilePreDiagnostic (std::string filePreDiag)

void	SetFileControl (std::string fileControl)

void	SetTumourID (std::string strTumID)

void	SetTumourImageID (std::string strTumImageID)

void	SetSetNumberDiagnostic (int thrDiag)

void	SetSetNumberPreDiagnostic (int thrPreDiag)

void	SetSetNumberControl (int thrControl)

void	SetThresholdDiagnostic (int thrDiag)

void	SetThresholdPreDiagnostic (int thrPreDiag)

void	SetThresholdControl (int thrControl)

void	SetBreastAreaDiagnostic (int thrDiag)

void	SetBreastAreaPreDiagnostic (int thrPreDiag)

void	SetBreastAreaControl (int thrControl)

void	SetTumourLeft (int tumLeft)

void	SetTumourRight (int tumRight)

void	SetTumourTop (int tumTop)

void	SetTumourBottom (int tumBottom)

void	SetTumourDiameter (float diameter)

void	SetRegionSizeInMM (float roiSize)

void	SetRegisterOn (void)

void	SetRegisterOff (void)

void	SetVerboseOn (void)

void	SetVerboseOff (void)

void	SetOverwriteOn (void)

void	SetOverwriteOff (void)

void	SetDebugOn (void)

void	SetDebugOff (void)

void	SetRegisterNonRigidOn (void)
	Specify whether to perform a non-rigid registration. More...

void	SetRegisterNonRigidOff (void)

std::string	GetPatientID (void)

std::string	GetIDDiagnosticImage (void)

std::string	GetIDPreDiagnosticImage (void)

std::string	GetIDControlImage (void)

std::string	GetFileDiagnostic (void)

std::string	GetFilePreDiagnostic (void)

std::string	GetFileControl (void)

std::string	GetStrTumourID (void)

std::string	GetStrTumourImageID (void)

int	GetSetNumberDiagnostic (void)

int	GetSetNumberPreDiagnostic (void)

int	GetSetNumberControl (void)

int	GetThresholdDiagnostic (void)

int	GetThresholdPreDiagnostic (void)

int	GetThresholdControl (void)

int	GetBreastAreaDiagnostic (void)

int	GetBreastAreaPreDiagnostic (void)

int	GetBreastAreaControl (void)

int	GetTumourLeft (void)

int	GetTumourRight (void)

int	GetTumourTop (void)

int	GetTumourBottom (void)

float	GetTumourDiameter (void)

void	LoadImages (void)

void	UnloadImages (void)

void	Print (bool flgVerbose=false)

std::vector< PointOnBoundary > *	GetBreastEdgeCoords (std::string strBreastEdgeImageID)

void	SetBreastEdgeCoords (std::string strBreastEdgeImageID, std::vector< PointOnBoundary > *edgeCoords)

void	PushBackBreastEdgeCoord (std::string strBreastEdgeImageID, int id, int x, int y)

std::vector< PointOnBoundary > *	GetPectoralCoords (std::string strPectoralImageID)

void	SetPectoralCoords (std::string strPectoralImageID, std::vector< PointOnBoundary > *pecCoords)

void	PushBackPectoralCoord (std::string strPectoralImageID, int id, int x, int y)

void	WriteDataToCSVFile (std::ofstream *foutOutputDensityCSV)

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::MammogramAnalysis< InputPixelType, InputDimension >
static Pointer	New ()

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

virtual	~MammographicTumourDistribution ()
	Destructor. More...

void	AddPointToTumourPolygon (typename PolygonType::Pointer &polygon, int i, int j)
	Add a point to a polygon of the transformed tumour region. More...

ImageType::Pointer	DrawTumourOnReferenceImage ()
	Draw the tranformed tumour region on the reference image. More...

void	RunRegistration ()
	Register the images. More...

Protected Member Functions inherited from itk::MammogramAnalysis< InputPixelType, InputDimension >
	MammogramAnalysis ()
	Constructor. More...

virtual	~MammogramAnalysis ()
	Destructor. More...

void	CreateDirectoryAndParents (std::string filename)

void	PrintDictionary (DictionaryType &dictionary)

ImageType::SpacingType	GetImageResolutionFromDictionary (DictionaryType &dictionary)

bool	ReadImage (MammogramType mammoType)

std::string	BuildOutputFilename (std::string fileInput, std::string suffix)

template<typename TOutputImageType >
std::string	CastImageAndWriteToFile (std::string fileOutput, const char *description, typename ImageType::Pointer image, DictionaryType &dictionary)

template<typename TOutputImageType >
std::string	CastImageAndWriteToFile (std::string fileInput, std::string suffix, const char *description, typename ImageType::Pointer image, DictionaryType &dictionary)

template<typename TOutputImageType >
std::string	WriteImageFile (std::string fileInput, std::string suffix, const char *description, typename TOutputImageType::Pointer image, DictionaryType &dictionary)

void	WriteLabelImageFile (std::string fileInput, std::string suffix, const char *description, typename LabelImageType::Pointer image, typename LabelImageType::RegionType &tumourRegion, DictionaryType &dictionary)

void	WriteRegistrationDifferenceImage (std::string fileInput, std::string suffix, const char *description, typename ImageType::Pointer image, DictionaryType &dictionary)

void	AddPointToPolygon (typename PolygonType::Pointer &polygon, typename ImageType::Pointer &image, typename ImageType::SizeType &polySize, int x, int y)

ImageType::Pointer	MaskWithPolygon (MammogramType mammoType, LocusType locusType)

ImageType::Pointer	MaskWithPolygon (MammogramType mammoType)

void	RemoveTumourFromRegnMask (void)

template<typename ScalesType >
ScalesType	SetRegistrationParameterScales (typename itk::TransformTypeEnum transformType, unsigned int nParameters)

RegistrationFilterType::Pointer	RegisterTheImages (typename ImageType::Pointer imSource, std::string fileInputSource, typename ImageType::Pointer maskSource, std::string fileOutputAffineTransformation, std::string fileOutputAffineRegistered, std::string fileOutputNonRigidTransformation, std::string fileOutputNonRigidRegistered, std::string *dirOutput=0)

LabelImageType::IndexType	TransformTumourPositionIntoImage (typename LabelImageType::IndexType &idxTumourCenter, typename ImageType::Pointer &image, typename RegistrationFilterType::Pointer registration)

LabelImageType::Pointer	GenerateRegionLabels (BreastSideType breastSide, typename LabelImageType::IndexType &idxTumourCenter, typename LabelImageType::RegionType &tumourRegion, LabelPixelType &tumourRegionValue, typename ImageType::Pointer &image, typename ImageType::Pointer &imMask, typename std::map< LabelPixelType, Patch > &listOfPatches, int threshold)

void	GenerateRandomTumourPositionInImage (MammogramType mammoType)

ImageType::Pointer	DrawTumourRegion (typename ImageType::Pointer image)

Protected Attributes
std::ofstream *	m_foutOutputCSV
	The output CSV file stream. More...

Protected Attributes inherited from itk::MammogramAnalysis< InputPixelType, InputDimension >
bool	m_FlgVerbose

bool	m_FlgDebug

bool	m_FlgOverwrite

bool	m_FlgRegister

bool	m_FlgRegisterNonRigid
	Specify whether to perform a non-rigid registration. More...

enumRegistrationImagesType	m_TypeOfInputImagesToRegister
	Specify the input images to register. More...

std::string	m_Id

std::string	m_DirInput

std::string	m_DirOutput

std::string	m_IdDiagnosticImage

std::string	m_FileDiagnostic

std::string	m_FileDiagnosticRegn

std::string	m_FileDiagnosticRegnMask

int	m_SetNumberDiagnostic

int	m_ThresholdDiagnostic

int	m_BreastAreaDiagnostic

BreastSideType	m_BreastSideDiagnostic

std::string	m_IdPreDiagnosticImage

std::string	m_FilePreDiagnostic

std::string	m_FilePreDiagnosticRegn

int	m_SetNumberPreDiagnostic

int	m_ThresholdPreDiagnostic

int	m_BreastAreaPreDiagnostic

BreastSideType	m_BreastSidePreDiagnostic

std::string	m_IdControlImage

std::string	m_FileControl

std::string	m_FileControlRegn

int	m_SetNumberControl

int	m_ThresholdControl

int	m_BreastAreaControl

BreastSideType	m_BreastSideControl

std::string	m_StrTumourID

std::string	m_StrTumourImageID

int	m_TumourLeft

int	m_TumourRight

int	m_TumourTop

int	m_TumourBottom

float	m_TumourDiameter

LabelPixelType	m_DiagTumourRegionValue

LabelImageType::IndexType	m_DiagTumourCenterIndex

LabelImageType::RegionType	m_DiagTumourRegion

LabelPixelType	m_PreDiagTumourRegionValue

LabelImageType::IndexType	m_PreDiagCenterIndex

LabelImageType::RegionType	m_PreDiagTumourRegion

LabelPixelType	m_ControlTumourRegionValue

LabelImageType::IndexType	m_ControlCenterIndex

LabelImageType::RegionType	m_ControlTumourRegion

float	m_RegionSizeInMM

DictionaryType	m_DiagDictionary

DictionaryType	m_PreDiagDictionary

DictionaryType	m_ControlDictionary

ImageType::Pointer	m_ImDiagnostic

ImageType::Pointer	m_ImPreDiagnostic

ImageType::Pointer	m_ImControl

ImageType::Pointer	m_ImDiagnosticMask

ImageType::Pointer	m_ImPreDiagnosticMask

ImageType::Pointer	m_ImControlMask

LabelImageType::Pointer	m_ImDiagnosticLabels

LabelImageType::Pointer	m_ImPreDiagnosticLabels

LabelImageType::Pointer	m_ImControlLabels

ImageType::Pointer	m_ImDiagnosticRegnMask

ImageType::Pointer	m_ImPreDiagnosticRegnMask

ImageType::Pointer	m_ImControlRegnMask

std::vector< PointOnBoundary >	m_DiagBreastEdgePoints

std::vector< PointOnBoundary >	m_PreDiagBreastEdgePoints

std::vector< PointOnBoundary >	m_ControlBreastEdgePoints

std::vector< PointOnBoundary >	m_DiagPectoralPoints

std::vector< PointOnBoundary >	m_PreDiagPectoralPoints

std::vector< PointOnBoundary >	m_ControlPectoralPoints

std::map< LabelPixelType, Patch >	m_DiagPatches

std::map< LabelPixelType, Patch >	m_PreDiagPatches

std::map< LabelPixelType, Patch >	m_ControlPatches

RegistrationFilterType::Pointer	m_RegistrationPreDiag

RegistrationFilterType::Pointer	m_RegistrationControl

Additional Inherited Members
Static Public Attributes inherited from itk::MammogramAnalysis< InputPixelType, InputDimension >
static const char *	MammogramTypeNames []