cmtkSegmentation Library

This library provides classes for atlas-based image segmentation and correction of MR intensity bias field artifacts. More...

Classes
class	cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >
	Functional to correct MR intensity bias by miniming image entropy. More...
class	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase
	Base class for entropy-minimzation MR bias correction functional. More...
class	cmtk::LabelCombinationMultiClassSTAPLE
	Multi-class STAPLE label combination. More...
class	cmtk::LabelCombinationSTAPLE
	Binary STAPLE label combination. More...
class	cmtk::LabelCombinationVoting
	Label voting image combination. More...
class	cmtk::OverlapMeasures
	Class for overlap measures between multiple segmentations. More...
class	cmtk::SimpleLevelset
	Class for computing a simple two-phase levelset evolution. More...
class	cmtk::SimpleLevelsetCommandLine< TImpl >
	Command line interface class template for simple levelset segmentation with a particular implementation (CPU or GPU). More...
class	cmtk::SimpleLevelsetCommandLineBase
	Command line interface base class for simple levelset segmentation. More...
Typedefs
typedef float	cmtk::LabelCombinationMultiClassSTAPLE::RealValueType
	Real value type for internal computations.
typedef Matrix2D< RealValueType >	cmtk::LabelCombinationMultiClassSTAPLE::ConfusionMatrixType
	Confusion matrix type.
typedef TImpl	cmtk::SimpleLevelsetCommandLine::SimpleLevelsetImplementation
	The actual levelset implementation.
Functions
template<unsigned int NDegreeMul>
EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional (const unsigned int polynomialDegreeAdd)
	Create functional templated over polynomial degrees.
EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul)
	Create functional templated over polynomial degrees.
EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul, EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr oldFunctional)
	Create functional templated over polynomial degrees with initialization from old functional.
	cmtk::LabelCombinationMultiClassSTAPLE::LabelCombinationMultiClassSTAPLE (const std::vector< TypedArray::SmartPtr > &data, const int maxIterations)
	Constructor: compute label combination.
TypedArray::SmartPtr &	cmtk::LabelCombinationMultiClassSTAPLE::GetResult ()
	Get result.
TypedArray::SmartPtr &	cmtk::LabelCombinationSTAPLE::GetResult ()
	Get result.
float	cmtk::LabelCombinationSTAPLE::GetPValue (const size_t i) const
	Get one p value.
float	cmtk::LabelCombinationSTAPLE::GetQValue (const size_t i) const
	Get one q value.
TypedArray::SmartPtr &	cmtk::LabelCombinationVoting::GetResult ()
	Get result.
void	cmtk::SimpleLevelset::SetScaleInitialSphere (const Types::Coordinate scale)
	Set initial sphere scale factor.
void	cmtk::SimpleLevelset::SetFilterSigma (const Units::GaussianSigma filterSigma)
	Set filter sigma parameter.
void	cmtk::SimpleLevelset::SetTimeDelta (const Types::Coordinate timeDelta)
	Set evolution time delta.
void	cmtk::SimpleLevelset::SetLevelsetThreshold (const Types::Coordinate levelsetThreshold)
	Set levelset threshold.
void	cmtk::SimpleLevelset::InitializeCenteredSphere ()
	Initialize levelset with a centered sphere.
virtual void	cmtk::SimpleLevelset::Evolve (const int numberOfIterations, const bool forceIterations=false, const bool verbose=false)
	Levelset evolution.
UniformVolume::SmartPtr &	cmtk::SimpleLevelset::GetLevelset (const bool binarize=false, const float threshold=0.5)
	Return levelset, optionally converting to a binarized byte pixel representation.
void	cmtk::SimpleLevelsetCommandLine::Execute ()
	Execute levelset segmentation.
	cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase ()
	Default constructor.
int	cmtk::SimpleLevelsetCommandLineBase::Init (const int argc, const char *argv[])
	Initialize from command line arguments.
CommandLine &	cmtk::SimpleLevelsetCommandLineBase::GetCommandLine ()
	Reference to command line object.
virtual void	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetInputImage (UniformVolume::SmartConstPtr &inputImage)
	Set input image.
virtual void	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetForegroundMask (const UniformVolume &foregroundMask)
	Set foreground mask.
virtual UniformVolume::SmartPtr &	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetOutputImage (CoordinateVector &v, const bool foregroundOnly=false)
	Update and return corrected output image.
virtual Self::ReturnType	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::EvaluateAt (CoordinateVector &v)
	Evaluate functional for given parameter vector.
virtual void	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImage (const bool foregroundOnly=true)
	Update output image estimate based on current bias field parameters.
static void	cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImageThreadFunc (void *args, const size_t taskIdx, const size_t taskCnt, const size_t, const size_t)
	Thread function: update output image.
	cmtk::LabelCombinationSTAPLE::LabelCombinationSTAPLE (const std::vector< TypedArray::SmartPtr > &data, const int maxIterations, const ScalarDataType resultType=TYPE_FLOAT)
	Constructor: compute label combination.
	cmtk::LabelCombinationVoting::LabelCombinationVoting (const std::vector< TypedArray::SmartPtr > &data)
	Constructor: compute label combination.
	cmtk::OverlapMeasures::OverlapMeasures (const std::vector< TypedArray::SmartPtr > &dataArrays)
	Constructor: allocate local data structures and do precomputations (e.g., count labels, etc).
size_t	cmtk::OverlapMeasures::ComputeGroupwiseOverlap (const int firstLabel, const int numberOfLabels, double &overlapEqualWeighted, double &overlapVolumeWeighted, double &overlapInverseWeighted) const
	Compute groupwise overlap with advanced options.
double	cmtk::OverlapMeasures::ComputePairwiseOverlapMinMax (double &overlap_min, double &overlap_max, const TypedArray::SmartPtr &data0, const TypedArray::SmartPtr &data1, const int label) const
	Compute pairwise overlap minimum.
Variables
TypedArray::SmartPtr	cmtk::LabelCombinationMultiClassSTAPLE::m_Result
	Resulting data array.
std::vector< RealValueType >	cmtk::LabelCombinationMultiClassSTAPLE::m_Priors
	Array of prior probabilities per class.
std::vector < Self::ConfusionMatrixType >	cmtk::LabelCombinationMultiClassSTAPLE::m_Confusion
	Array of confusion matrices.
std::vector < Self::ConfusionMatrixType >	cmtk::LabelCombinationMultiClassSTAPLE::m_ConfusionNew
	Array of updated confusion matrices.
TypedArray::SmartPtr	cmtk::LabelCombinationSTAPLE::m_Result
	Resulting data array.
std::vector< float >	cmtk::LabelCombinationSTAPLE::m_VecP
	p-Values.
std::vector< float >	cmtk::LabelCombinationSTAPLE::m_VecQ
	q-Values.
TypedArray::SmartPtr	cmtk::LabelCombinationVoting::m_Result
	Resulting data array.
UniformVolume::SmartConstPtr	cmtk::SimpleLevelset::m_Volume
	The volume to compute a levelset segmentation for.
UniformVolume::SmartPtr	cmtk::SimpleLevelset::m_Levelset
	The evolving levelset.
Types::Coordinate	cmtk::SimpleLevelset::m_ScaleInitialSphere
	Initial sphere scale factor.
Units::GaussianSigma	cmtk::SimpleLevelset::m_FilterSigma
	Sigma parameter of the Gaussian filter kernel.
Types::Coordinate	cmtk::SimpleLevelset::m_TimeDelta
	Delta time constant.
Types::Coordinate	cmtk::SimpleLevelset::m_LevelsetThreshold
	Levelset threshold.
bool	cmtk::SimpleLevelsetCommandLineBase::m_Verbose
	Verbose mode.
Types::Coordinate	cmtk::SimpleLevelsetCommandLineBase::m_ScaleInitialSphere
	Initial sphere scale factor.
Types::Coordinate	cmtk::SimpleLevelsetCommandLineBase::m_FilterSigma
	Gaussian smoothing kernel sigma in mm.
Types::Coordinate	cmtk::SimpleLevelsetCommandLineBase::m_TimeDelta
	Levelset evolution time constant.
Types::Coordinate	cmtk::SimpleLevelsetCommandLineBase::m_LevelsetThreshold
	Levelset threshold: the levelset function is truncated to plus/minus this value at each iteration.
int	cmtk::SimpleLevelsetCommandLineBase::m_NumberOfIterations
	Number of levelset evolution iterations.
bool	cmtk::SimpleLevelsetCommandLineBase::m_ForceIterations
	Flag to force given number of iterations even when premature (discrete) convergence is detected.
bool	cmtk::SimpleLevelsetCommandLineBase::m_Binarize
	Binarize levelset before output.
const char *	cmtk::SimpleLevelsetCommandLineBase::m_InFile
	Input image path.
const char *	cmtk::SimpleLevelsetCommandLineBase::m_OutFile
	Output image path.
UniformVolume::SmartConstPtr	cmtk::SimpleLevelsetCommandLineBase::m_Volume
	The input image volume.
cmtk::CommandLine	cmtk::SimpleLevelsetCommandLineBase::m_CommandLine
	The command line parser object.

---

Detailed Description

This library provides classes for atlas-based image segmentation and correction of MR intensity bias field artifacts.

---

Typedef Documentation

typedef Matrix2D<RealValueType> cmtk::LabelCombinationMultiClassSTAPLE::ConfusionMatrixType [inherited]

Confusion matrix type.

Definition at line 66 of file cmtkLabelCombinationMultiClassSTAPLE.h.

typedef float cmtk::LabelCombinationMultiClassSTAPLE::RealValueType [inherited]

Real value type for internal computations.

Definition at line 63 of file cmtkLabelCombinationMultiClassSTAPLE.h.

template<class TImpl >

typedef TImpl cmtk::SimpleLevelsetCommandLine< TImpl >::SimpleLevelsetImplementation [inherited]

The actual levelset implementation.

Definition at line 67 of file cmtkSimpleLevelsetCommandLine.h.

---

Function Documentation

size_t cmtk::OverlapMeasures::ComputeGroupwiseOverlap	(	const int	firstLabel,
		const int	numberOfLabels,
		double &	overlapEqualWeighted,
		double &	overlapVolumeWeighted,
		double &	overlapInverseWeighted
	)		const [inherited]

Compute groupwise overlap with advanced options.

Returns:

Number of labels included in computation. If this is zero, the resulting overlap values are invalid.

Parameters:

firstLabel	Analysis starts with this label.
numberOfLabels	Analysis covers these labels
overlapEqualWeighted	Equal-weighted overlap score is returned herein.
overlapVolumeWeighted	Volume-weighted overlap score is returned herein.
overlapInverseWeighted	Inverse volume-weighted overlap score is returned herein.

Definition at line 70 of file cmtkOverlapMeasures.cxx.

double cmtk::OverlapMeasures::ComputePairwiseOverlapMinMax	(	double &	overlap_min,
		double &	overlap_max,
		const TypedArray::SmartPtr &	data0,
		const TypedArray::SmartPtr &	data1,
		const int	label
	)		const [private, inherited]

Compute pairwise overlap minimum.

Definition at line 233 of file cmtkOverlapMeasures.cxx.

EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional	(	const unsigned int	polynomialDegreeAdd,
		const unsigned int	polynomialDegreeMul
	)

Create functional templated over polynomial degrees.

Definition at line 78 of file cmtkEntropyMinimizationIntensityCorrectionFunctional.cxx.

References cmtk::Console::printf(), and cmtk::StdErr.

template<unsigned int NDegreeMul>

EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional

(

const unsigned int

polynomialDegreeAdd )

Create functional templated over polynomial degrees.

Definition at line 46 of file cmtkEntropyMinimizationIntensityCorrectionFunctional.cxx.

References cmtk::Console::printf(), and cmtk::StdErr.

Referenced by cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional().

EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional	(	const unsigned int	polynomialDegreeAdd,
		const unsigned int	polynomialDegreeMul,
		EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr	oldFunctional
	)

Create functional templated over polynomial degrees with initialization from old functional.

This function creates a new functional and copies the polynomial coefficients from an existing functional of equal or lower polynomial degrees into the correct locations of the new functional's parameter vector. This is for incremental computation.

Definition at line 110 of file cmtkEntropyMinimizationIntensityCorrectionFunctional.cxx.

References cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional(), and cmtk::Vector< T >::SetAll().

EntropyMinimizationIntensityCorrectionFunctionalBase::ReturnType cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::EvaluateAt

(

CoordinateVector &

v )

[virtual, inherited]

Evaluate functional for given parameter vector.

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

Definition at line 125 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.cxx.

void cmtk::SimpleLevelset::Evolve	(	const int	numberOfIterations,
		const bool	forceIterations = false,
		const bool	verbose = false
	)		[virtual, inherited]

Levelset evolution.

Parameters:

numberOfIterations	Number of iterations
forceIterations	If this is set, evolution continues until maximum iteration count is reached, even when convergence is detected
verbose	Verbose flag

Definition at line 62 of file cmtkSimpleLevelset.cxx.

References cmtk::AXIS_Z.

template<class TImpl >

void cmtk::SimpleLevelsetCommandLine< TImpl >::Execute

(

)

[inline, inherited]

Execute levelset segmentation.

Definition at line 70 of file cmtkSimpleLevelsetCommandLine.h.

References cmtk::ImageXformDB::AddImage(), and cmtk::VolumeIO::Write().

CommandLine& cmtk::SimpleLevelsetCommandLineBase::GetCommandLine

(

)

[inline, inherited]

Reference to command line object.

Definition at line 64 of file cmtkSimpleLevelsetCommandLineBase.h.

cmtk::UniformVolume::SmartPtr & cmtk::SimpleLevelset::GetLevelset	(	const bool	binarize = false,
		const float	threshold = 0.5
	)		[inherited]

Return levelset, optionally converting to a binarized byte pixel representation.

Warning:

If the levelset is retrieved with the "binarize" flag set, then the levelset stored in this object will remain binarized after the call and should be re-initialized before calling "Evolve" again.

Parameters:

binarize	If set, levelset is binarized and converted to byte data
threshold	Threshold for optional binarization

Definition at line 130 of file cmtkSimpleLevelset.cxx.

References cmtk::TYPE_BYTE.

UniformVolume::SmartPtr & cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::GetOutputImage	(	CoordinateVector &	v,
		const bool	foregroundOnly = false
	)		[virtual, inherited]

Update and return corrected output image.

Definition at line 115 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.cxx.

float cmtk::LabelCombinationSTAPLE::GetPValue

(

const size_t

i )

const [inline, inherited]

Get one p value.

Definition at line 72 of file cmtkLabelCombinationSTAPLE.h.

float cmtk::LabelCombinationSTAPLE::GetQValue

(

const size_t

i )

const [inline, inherited]

Get one q value.

Definition at line 78 of file cmtkLabelCombinationSTAPLE.h.

TypedArray::SmartPtr& cmtk::LabelCombinationVoting::GetResult

(

)

[inline, inherited]

Get result.

Definition at line 66 of file cmtkLabelCombinationVoting.h.

Referenced by cmtk::LabelCombinationMultiClassSTAPLE::LabelCombinationMultiClassSTAPLE().

TypedArray::SmartPtr& cmtk::LabelCombinationMultiClassSTAPLE::GetResult

(

)

[inline, inherited]

Get result.

Definition at line 74 of file cmtkLabelCombinationMultiClassSTAPLE.h.

TypedArray::SmartPtr& cmtk::LabelCombinationSTAPLE::GetResult

(

)

[inline, inherited]

Get result.

Definition at line 66 of file cmtkLabelCombinationSTAPLE.h.

int cmtk::SimpleLevelsetCommandLineBase::Init	(	const int	argc,
		const char *	argv[]
	)		[inherited]

Initialize from command line arguments.

Definition at line 89 of file cmtkSimpleLevelsetCommandLineBase.cxx.

References cmtk::VolumeIO::ReadOriented(), and cmtk::StdErr.

void cmtk::SimpleLevelset::InitializeCenteredSphere

(

)

[inherited]

Initialize levelset with a centered sphere.

Definition at line 47 of file cmtkSimpleLevelset.cxx.

References cmtk::UniformVolumePainter::DrawSphere(), and cmtk::TYPE_FLOAT.

cmtk::LabelCombinationMultiClassSTAPLE::LabelCombinationMultiClassSTAPLE	(	const std::vector< TypedArray::SmartPtr > &	data,
		const int	maxIterations
	)		[inherited]

Constructor: compute label combination.

Parameters:

data	Array of typed arrays with input data.
maxIterations	Maximum number of STAPLE iterations.

Definition at line 47 of file cmtkLabelCombinationMultiClassSTAPLE.cxx.

References cmtk::LabelCombinationVoting::GetResult(), and cmtk::Types::Range< T >::m_UpperBound.

cmtk::LabelCombinationSTAPLE::LabelCombinationSTAPLE	(	const std::vector< TypedArray::SmartPtr > &	data,
		const int	maxIterations,
		const ScalarDataType	resultType = TYPE_FLOAT
	)		[inherited]

Constructor: compute label combination.

Parameters:

data	Array of typed arrays with input data.
maxIterations	Maximum number of STAPLE iterations.
resultType	Primitive data type for results.

Definition at line 42 of file cmtkLabelCombinationSTAPLE.cxx.

cmtk::LabelCombinationVoting::LabelCombinationVoting

(

const std::vector< TypedArray::SmartPtr > &

data )

[inherited]

Constructor: compute label combination.

Definition at line 41 of file cmtkLabelCombinationVoting.cxx.

References cmtk::TYPE_SHORT.

cmtk::OverlapMeasures::OverlapMeasures

(

const std::vector< TypedArray::SmartPtr > &

dataArrays )

[inherited]

Constructor: allocate local data structures and do precomputations (e.g., count labels, etc).

Definition at line 48 of file cmtkOverlapMeasures.cxx.

References cmtk::Types::Range< T >::m_UpperBound.

void cmtk::SimpleLevelset::SetFilterSigma

(

const Units::GaussianSigma

filterSigma )

[inline, inherited]

Set filter sigma parameter.

Definition at line 61 of file cmtkSimpleLevelset.h.

void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetForegroundMask

(

const UniformVolume &

foregroundMask )

[virtual, inherited]

Set foreground mask.

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

Definition at line 84 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.cxx.

References cmtk::DataGrid::GetDataAt(), cmtk::DataGrid::GetNumberOfPixels(), and cmtk::MathUtil::UniformRandom().

void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::SetInputImage

(

UniformVolume::SmartConstPtr &

inputImage )

[virtual, inherited]

Set input image.

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

Definition at line 51 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.cxx.

References cmtk::TemplateArray< T >::Create(), cmtk::Types::Range< T >::m_LowerBound, cmtk::Types::Range< T >::m_UpperBound, cmtk::TYPE_FLOAT, and cmtk::Types::Range< T >::Width().

void cmtk::SimpleLevelset::SetLevelsetThreshold

(

const Types::Coordinate

levelsetThreshold )

[inline, inherited]

Set levelset threshold.

Definition at line 73 of file cmtkSimpleLevelset.h.

void cmtk::SimpleLevelset::SetScaleInitialSphere

(

const Types::Coordinate

scale )

[inline, inherited]

Set initial sphere scale factor.

Definition at line 55 of file cmtkSimpleLevelset.h.

void cmtk::SimpleLevelset::SetTimeDelta

(

const Types::Coordinate

timeDelta )

[inline, inherited]

Set evolution time delta.

Definition at line 67 of file cmtkSimpleLevelset.h.

cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase

(

)

[inherited]

Default constructor.

Definition at line 39 of file cmtkSimpleLevelsetCommandLineBase.cxx.

References cmtk::CommandLine::AddOption(), cmtk::CommandLine::AddParameter(), cmtk::CommandLine::AddSwitch(), cmtk::CommandLine::BeginGroup(), cmtk::CommandLine::EndGroup(), cmtk::SimpleLevelsetCommandLineBase::m_Binarize, cmtk::SimpleLevelsetCommandLineBase::m_CommandLine, cmtk::SimpleLevelsetCommandLineBase::m_FilterSigma, cmtk::SimpleLevelsetCommandLineBase::m_ForceIterations, cmtk::SimpleLevelsetCommandLineBase::m_InFile, cmtk::SimpleLevelsetCommandLineBase::m_LevelsetThreshold, cmtk::SimpleLevelsetCommandLineBase::m_NumberOfIterations, cmtk::SimpleLevelsetCommandLineBase::m_OutFile, cmtk::SimpleLevelsetCommandLineBase::m_ScaleInitialSphere, cmtk::SimpleLevelsetCommandLineBase::m_TimeDelta, cmtk::SimpleLevelsetCommandLineBase::m_Verbose, NULL, cmtk::CommandLine::PRG_CATEG, cmtk::CommandLine::PRG_DESCR, cmtk::CommandLine::PRG_TITLE, cmtk::CommandLine::PROPS_ADVANCED, cmtk::CommandLine::PROPS_IMAGE, cmtk::CommandLine::PROPS_LABELS, cmtk::CommandLine::PROPS_NOXML, cmtk::CommandLine::PROPS_OUTPUT, and cmtk::CommandLine::SetProgramInfo().

void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImage

(

const bool

foregroundOnly = true )

[protected, virtual, inherited]

Update output image estimate based on current bias field parameters.

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.

Definition at line 154 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.cxx.

References cmtk::ThreadPool::GetGlobalThreadPool(), cmtk::ThreadPool::GetNumberOfThreads(), and cmtk::ThreadPool::Run().

void cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImageThreadFunc	(	void *	args,
		const size_t	taskIdx,
		const size_t	taskCnt,
		const	size_t,
		const	size_t
	)		[static, private, inherited]

Thread function: update output image.

Definition at line 170 of file cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.cxx.

References cmtk::DataGrid::GetDataAt(), cmtk::DataGrid::GetNumberOfPixels(), cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImageThreadParameters::m_ForegroundOnly, and cmtk::ThreadParameters< T >::thisObject.

---

Variable Documentation

bool cmtk::SimpleLevelsetCommandLineBase::m_Binarize [protected, inherited]

Binarize levelset before output.

Definition at line 92 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

cmtk::CommandLine cmtk::SimpleLevelsetCommandLineBase::m_CommandLine [private, inherited]

The command line parser object.

Definition at line 110 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

std::vector<Self::ConfusionMatrixType> cmtk::LabelCombinationMultiClassSTAPLE::m_Confusion [private, inherited]

Array of confusion matrices.

Definition at line 87 of file cmtkLabelCombinationMultiClassSTAPLE.h.

std::vector<Self::ConfusionMatrixType> cmtk::LabelCombinationMultiClassSTAPLE::m_ConfusionNew [private, inherited]

Array of updated confusion matrices.

Definition at line 90 of file cmtkLabelCombinationMultiClassSTAPLE.h.

Types::Coordinate cmtk::SimpleLevelsetCommandLineBase::m_FilterSigma [protected, inherited]

Gaussian smoothing kernel sigma in mm.

Definition at line 77 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

Units::GaussianSigma cmtk::SimpleLevelset::m_FilterSigma [protected, inherited]

Sigma parameter of the Gaussian filter kernel.

Definition at line 104 of file cmtkSimpleLevelset.h.

bool cmtk::SimpleLevelsetCommandLineBase::m_ForceIterations [protected, inherited]

Flag to force given number of iterations even when premature (discrete) convergence is detected.

Definition at line 89 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

const char* cmtk::SimpleLevelsetCommandLineBase::m_InFile [protected, inherited]

Input image path.

Definition at line 95 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

UniformVolume::SmartPtr cmtk::SimpleLevelset::m_Levelset [protected, inherited]

The evolving levelset.

Definition at line 98 of file cmtkSimpleLevelset.h.

Types::Coordinate cmtk::SimpleLevelsetCommandLineBase::m_LevelsetThreshold [protected, inherited]

Levelset threshold: the levelset function is truncated to plus/minus this value at each iteration.

Definition at line 83 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

Types::Coordinate cmtk::SimpleLevelset::m_LevelsetThreshold [protected, inherited]

Levelset threshold.

Definition at line 110 of file cmtkSimpleLevelset.h.

int cmtk::SimpleLevelsetCommandLineBase::m_NumberOfIterations [protected, inherited]

Number of levelset evolution iterations.

Definition at line 86 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

const char* cmtk::SimpleLevelsetCommandLineBase::m_OutFile [protected, inherited]

Output image path.

Definition at line 98 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

std::vector<RealValueType> cmtk::LabelCombinationMultiClassSTAPLE::m_Priors [private, inherited]

Array of prior probabilities per class.

Definition at line 84 of file cmtkLabelCombinationMultiClassSTAPLE.h.

TypedArray::SmartPtr cmtk::LabelCombinationMultiClassSTAPLE::m_Result [private, inherited]

Resulting data array.

Definition at line 81 of file cmtkLabelCombinationMultiClassSTAPLE.h.

TypedArray::SmartPtr cmtk::LabelCombinationVoting::m_Result [private, inherited]

Resulting data array.

Definition at line 73 of file cmtkLabelCombinationVoting.h.

TypedArray::SmartPtr cmtk::LabelCombinationSTAPLE::m_Result [private, inherited]

Resulting data array.

Definition at line 85 of file cmtkLabelCombinationSTAPLE.h.

Types::Coordinate cmtk::SimpleLevelsetCommandLineBase::m_ScaleInitialSphere [protected, inherited]

Initial sphere scale factor.

Definition at line 74 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

Types::Coordinate cmtk::SimpleLevelset::m_ScaleInitialSphere [protected, inherited]

Initial sphere scale factor.

Definition at line 101 of file cmtkSimpleLevelset.h.

Types::Coordinate cmtk::SimpleLevelsetCommandLineBase::m_TimeDelta [protected, inherited]

Levelset evolution time constant.

Definition at line 80 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

Types::Coordinate cmtk::SimpleLevelset::m_TimeDelta [protected, inherited]

Delta time constant.

Definition at line 107 of file cmtkSimpleLevelset.h.

std::vector<float> cmtk::LabelCombinationSTAPLE::m_VecP [private, inherited]

p-Values.

Definition at line 88 of file cmtkLabelCombinationSTAPLE.h.

std::vector<float> cmtk::LabelCombinationSTAPLE::m_VecQ [private, inherited]

q-Values.

Definition at line 91 of file cmtkLabelCombinationSTAPLE.h.

bool cmtk::SimpleLevelsetCommandLineBase::m_Verbose [protected, inherited]

Verbose mode.

Definition at line 71 of file cmtkSimpleLevelsetCommandLineBase.h.

Referenced by cmtk::SimpleLevelsetCommandLineBase::SimpleLevelsetCommandLineBase().

UniformVolume::SmartConstPtr cmtk::SimpleLevelset::m_Volume [protected, inherited]

The volume to compute a levelset segmentation for.

Definition at line 95 of file cmtkSimpleLevelset.h.

UniformVolume::SmartConstPtr cmtk::SimpleLevelsetCommandLineBase::m_Volume [protected, inherited]

The input image volume.

Definition at line 101 of file cmtkSimpleLevelsetCommandLineBase.h.