Base class for entropy-minimzation MR bias correction functional. More...

#include <cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h>

Inheritance diagram for cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase:

Collaboration diagram for cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase:

Classes
class	UpdateOutputImageThreadParameters
	Class for output image update thread parameters. More...
Public Types
typedef EntropyMinimizationIntensityCorrectionFunctionalBase	Self
	This class type.
typedef SmartPointer< Self >	SmartPtr
	Pointer to this class.
typedef Functional	Superclass
	Superclass type.
Public Member Functions
	EntropyMinimizationIntensityCorrectionFunctionalBase ()
	Constructor.
virtual	~EntropyMinimizationIntensityCorrectionFunctionalBase ()
	Virtual destructor.
virtual size_t	GetNumberOfMonomialsAdd () const =0
	Get number of additive monomials.
virtual size_t	GetNumberOfMonomialsMul () const =0
	Get number of multiplicative monomials.
virtual void	SetInputImage (UniformVolume::SmartConstPtr &inputImage)
	Set input image.
virtual void	SetForegroundMask (const UniformVolume &foregroundMask)
	Set foreground mask.
virtual void	SetSamplingDensity (const float samplingDensity)
	Set sampling density.
virtual void	SetNumberOfHistogramBins (const size_t numberOfHistogramBins)
	Set number of histogram bins.
void	SetUseLogIntensities (const bool flag)
	Set flag for use of log intensities for entropy estimation.
virtual UniformVolume::SmartPtr &	GetOutputImage (const bool update=false)
	Get corrected output image.
virtual UniformVolume::SmartPtr &	GetOutputImage (CoordinateVector &v, const bool foregroundOnly=false)
	Update and return corrected output image.
virtual UniformVolume::SmartPtr	GetBiasFieldAdd (const bool updateCompleteImage=false)
	Get additive bias field.
virtual void	SetBiasFieldAdd (const UniformVolume &biasFieldAdd)
	Set additive bias field.
virtual UniformVolume::SmartPtr	GetBiasFieldMul (const bool updateCompleteImage=false)
	Get multiplicative bias field.
virtual void	SetBiasFieldMul (const UniformVolume &biasFieldMul)
	Set multiplicative bias field.
virtual Self::ReturnType	Evaluate ()
	Evaluate functional.
virtual Self::ReturnType	EvaluateAt (CoordinateVector &v)
	Evaluate functional for given parameter vector.
Protected Types
typedef Histogram< unsigned int >	HistogramType
	Type for histogram.
typedef LogHistogram< unsigned int >	LogHistogramType
	Type for histogram using log-intensities.
Protected Member Functions
virtual void	UpdateCorrectionFactors ()=0
	Update polynomial correction factors from input image.
virtual void	UpdateOutputImage (const bool foregroundOnly=true)
	Update output image estimate based on current bias field parameters.
virtual void	UpdateBiasFields (const bool foregroundOnly=true)=0
	Jointly update both bias images.
virtual void	UpdateBiasFieldAdd (const bool foregroundOnly=true)=0
	Update additive bias image.
virtual void	UpdateBiasFieldMul (const bool foregroundOnly=true)=0
	Update additive bias image.
Protected Attributes
UniformVolume::SmartConstPtr	m_InputImage
	Original input image.
Types::DataItem	m_InputImageRange
	Input intensity image range.
UniformVolume::SmartPtr	m_OutputImage
	Evolving corrected output image.
HistogramType::SmartPtr	m_EntropyHistogram
	Histogram for entropy evaluation.
std::vector< bool >	m_ForegroundMask
	Binary foreground mask.
FloatArray::SmartPtr	m_BiasFieldAdd
	Additive bias field.
FloatArray::SmartPtr	m_BiasFieldMul
	Multiplicative bias field.
size_t	m_NumberOfPixels
	Number of input image pixels.
float	m_SamplingDensity
	Sampling density.
size_t	m_NumberOfHistogramBins
	Number of histogram bins for entropy estimation.
bool	m_UseLogIntensities
	Flag for using log-intensities for entropy estimation.
Static Private Member Functions
static void	UpdateOutputImageThreadFunc (void *args, const size_t taskIdx, const size_t taskCnt, const size_t, const size_t)
	Thread function: update output image.

Detailed Description

Base class for entropy-minimzation MR bias correction functional.

Definition at line 57 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

Member Typedef Documentation

typedef Histogram<unsigned int> cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::HistogramType [protected]

Type for histogram.

Definition at line 185 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

typedef LogHistogram<unsigned int> cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::LogHistogramType [protected]

Type for histogram using log-intensities.

Definition at line 188 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

typedef EntropyMinimizationIntensityCorrectionFunctionalBase cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::Self

This class type.

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::EntropyMinimizationIntensityCorrectionFunctionalDevice< NOrderAdd, NOrderMul >, and cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

Definition at line 62 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

typedef SmartPointer<Self> cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr

Pointer to this class.

Reimplemented from cmtk::Functional.

Reimplemented in cmtk::EntropyMinimizationIntensityCorrectionFunctionalDevice< NOrderAdd, NOrderMul >, and cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

Definition at line 65 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

typedef Functional cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::Superclass

Superclass type.

Reimplemented in cmtk::EntropyMinimizationIntensityCorrectionFunctionalDevice< NOrderAdd, NOrderMul >, and cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

Definition at line 68 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

Constructor & Destructor Documentation

cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::EntropyMinimizationIntensityCorrectionFunctionalBase ( ) [inline]

Constructor.

Definition at line 71 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::~EntropyMinimizationIntensityCorrectionFunctionalBase ( ) [inline, virtual]

Virtual destructor.

Definition at line 78 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

Member Function Documentation

virtual Self::ReturnType cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::Evaluate ( ) [inline, virtual]

Evaluate functional.

Reimplemented from cmtk::Functional.

Definition at line 161 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual UniformVolume::SmartPtr cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetBiasFieldAdd ( const bool updateCompleteImage = false ) [inline, virtual]

Get additive bias field.

Definition at line 127 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual UniformVolume::SmartPtr cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetBiasFieldMul ( const bool updateCompleteImage = false ) [inline, virtual]

Get multiplicative bias field.

Definition at line 144 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual size_t cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetNumberOfMonomialsAdd ( ) const [pure virtual]

Get number of additive monomials.

Implemented in cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

virtual size_t cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetNumberOfMonomialsMul ( ) const [pure virtual]

Get number of multiplicative monomials.

Implemented in cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

virtual UniformVolume::SmartPtr& cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetOutputImage ( const bool update = false ) [inline, virtual]

Get corrected output image.

Definition at line 115 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetBiasFieldAdd ( const UniformVolume & biasFieldAdd ) [inline, virtual]

Set additive bias field.

Definition at line 138 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetBiasFieldMul ( const UniformVolume & biasFieldMul ) [inline, virtual]

Set multiplicative bias field.

Definition at line 155 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetNumberOfHistogramBins ( const size_t numberOfHistogramBins ) [inline, virtual]

Set number of histogram bins.

Definition at line 99 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetSamplingDensity ( const float samplingDensity ) [inline, virtual]

Set sampling density.

Definition at line 93 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetUseLogIntensities ( const bool flag ) [inline]

Set flag for use of log intensities for entropy estimation.

Using log intensities compensates for the entropy increase otherwise caused by spreading distributions of values in brightened areas. This can help make bias field estimation more robust, potentially without any masking.

Definition at line 109 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateBiasFieldAdd ( const bool foregroundOnly = true ) [protected, pure virtual]

Update additive bias image.

Parameters:

foregroundOnly If this flag is set and an image foreground mask is set, then only image pixels are updated for which the mask is nonzero.

Implemented in cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateBiasFieldMul ( const bool foregroundOnly = true ) [protected, pure virtual]

Update additive bias image.

Parameters:

foregroundOnly If this flag is set and an image foreground mask is set, then only image pixels are updated for which the mask is nonzero.

Implemented in cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateBiasFields ( const bool foregroundOnly = true ) [protected, pure virtual]

Jointly update both bias images.

Parameters:

foregroundOnly If this flag is set and an image foreground mask is set, then only image pixels are updated for which the mask is nonzero.

Implemented in cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.

virtual void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateCorrectionFactors ( ) [protected, pure virtual]

Update polynomial correction factors from input image.

Implemented in cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >.