ITK  4.9.0
Insight Segmentation and Registration Toolkit
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itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage > Class Template Reference

#include <itkN4BiasFieldCorrectionImageFilter.h>

+ Inheritance diagram for itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >:
+ Collaboration diagram for itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >:

Detailed Description

template<typename TInputImage, typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
class itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >

Implementation of the N4 bias field correction algorithm.

The nonparametric nonuniform intensity normalization (N3) algorithm, as introduced by Sled et al. in 1998 is a method for correcting nonuniformity associated with MR images. The algorithm assumes a simple parametric model (Gaussian) for the bias field and does not require tissue class segmentation. In addition, there are only a couple of parameters to tune with the default values performing quite well. N3 has been publicly available as a set of perl scripts (http://www.bic.mni.mcgill.ca/ServicesSoftwareAdvancedImageProcessingTools/HomePage)

The N4 algorithm, encapsulated with this class, is a variation of the original N3 algorithm with the additional benefits of an improved B-spline fitting routine which allows for multiple resolutions to be used during the correction process. We also modify the iterative update component of algorithm such that the residual bias field is continually updated

Notes for the user:

  1. Since much of the image manipulation is done in the log space of the intensities, input images with negative and small values (< 1) can produce poor results.
  2. The original authors recommend performing the bias field correction on a downsampled version of the original image.
  3. A binary mask or a weighted image can be supplied. If a binary mask is specified, those voxels in the input image which correspond to the voxels in the mask image with a value equal to m_MaskLabel, are used to estimate the bias field. If a confidence image is specified, the input voxels are weighted in the b-spline fitting routine according to the confidence voxel values.
  4. The filter returns the corrected image. If the bias field is wanted, one can reconstruct it using the class itkBSplineControlPointImageFilter. See the IJ article and the test file for an example.
  5. The 'Z' parameter in Sled's 1998 paper is the square root of the class variable 'm_WienerFilterNoise'.

The basic algorithm iterates between sharpening the intensity histogram of the corrected input image and spatially smoothing those results with a B-spline scalar field estimate of the bias field.

Author
Nicholas J. Tustison

Contributed by Nicholas J. Tustison, James C. Gee in the Insight Journal paper: http://hdl.handle.net/10380/3053

REFERENCE

J.G. Sled, A.P. Zijdenbos and A.C. Evans. "A Nonparametric Method for Automatic Correction of Intensity Nonuniformity in Data" IEEE Transactions on Medical Imaging, Vol 17, No 1. Feb 1998.

N.J. Tustison, B.B. Avants, P.A. Cook, Y. Zheng, A. Egan, P.A. Yushkevich, and J.C. Gee. "N4ITK: Improved N3 Bias Correction" IEEE Transactions on Medical Imaging, 29(6):1310-1320, June 2010.

Definition at line 93 of file itkN4BiasFieldCorrectionImageFilter.h.

Public Types

typedef
BSplineFilterType::ArrayType 
ArrayType
 
typedef
BSplineFilterType::PointDataImageType 
BiasFieldControlPointLatticeType
 
typedef
BSplineScatteredDataPointSetToImageFilter
< PointSetType,
ScalarImageType
BSplineFilterType
 
typedef SmartPointer< const SelfConstPointer
 
typedef TInputImage InputImageType
 
typedef TMaskImage MaskImageType
 
typedef MaskImageType::PixelType MaskPixelType
 
typedef TOutputImage OutputImageType
 
typedef SmartPointer< SelfPointer
 
typedef RealImageType::Pointer RealImagePointer
 
typedef Image< RealType,
ImageDimension
RealImageType
 
typedef float RealType
 
typedef
N4BiasFieldCorrectionImageFilter 
Self
 
typedef ImageToImageFilter
< TInputImage, TOutputImage > 
Superclass
 
typedef Array< unsigned int > VariableSizeArrayType
 
typedef Vector< RealType, 1 > ScalarType
 
typedef PointSet< ScalarType,
itkGetStaticConstMacro(ImageDimension)> 
PointSetType
 
typedef Image< ScalarType,
itkGetStaticConstMacro(ImageDimension)> 
ScalarImageType
 
typedef PointSetType::Pointer PointSetPointer
 
typedef PointSetType::PointType PointType
 
- Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef SmartPointer< const SelfConstPointer
 
typedef
InputImageType::ConstPointer 
InputImageConstPointer
 
typedef InputImageType::PixelType InputImagePixelType
 
typedef InputImageType::Pointer InputImagePointer
 
typedef InputImageType::RegionType InputImageRegionType
 
typedef TInputImage InputImageType
 
typedef
Superclass::OutputImagePixelType 
OutputImagePixelType
 
typedef
Superclass::OutputImageRegionType 
OutputImageRegionType
 
typedef SmartPointer< SelfPointer
 
typedef ImageToImageFilter Self
 
typedef ImageSource< TOutputImage > Superclass
 
- Public Types inherited from itk::ImageSource< TOutputImage >
typedef SmartPointer< const SelfConstPointer
 
typedef
Superclass::DataObjectIdentifierType 
DataObjectIdentifierType
 
typedef DataObject::Pointer DataObjectPointer
 
typedef
Superclass::DataObjectPointerArraySizeType 
DataObjectPointerArraySizeType
 
typedef OutputImageType::PixelType OutputImagePixelType
 
typedef OutputImageType::Pointer OutputImagePointer
 
typedef OutputImageType::RegionType OutputImageRegionType
 
typedef TOutputImage OutputImageType
 
typedef SmartPointer< SelfPointer
 
typedef ImageSource Self
 
typedef ProcessObject Superclass
 
- Public Types inherited from itk::ProcessObject
typedef SmartPointer< const SelfConstPointer
 
typedef
DataObject::DataObjectIdentifierType 
DataObjectIdentifierType
 
typedef DataObject::Pointer DataObjectPointer
 
typedef std::vector
< DataObjectPointer
DataObjectPointerArray
 
typedef
DataObjectPointerArray::size_type 
DataObjectPointerArraySizeType
 
typedef std::vector
< DataObjectIdentifierType
NameArray
 
typedef SmartPointer< SelfPointer
 
typedef ProcessObject Self
 
typedef Object Superclass
 
- Public Types inherited from itk::Object
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef Object Self
 
typedef LightObject Superclass
 
- Public Types inherited from itk::LightObject
typedef SmartPointer< const SelfConstPointer
 
typedef SmartPointer< SelfPointer
 
typedef LightObject Self
 

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother () const
 
virtual RealType GetBiasFieldFullWidthAtHalfMaximum () const
 
const RealImageTypeGetConfidenceImage () const
 
virtual RealType GetConvergenceThreshold () const
 
virtual RealType GetCurrentConvergenceMeasurement () const
 
virtual unsigned int GetCurrentLevel () const
 
virtual unsigned int GetElapsedIterations () const
 
virtual
BiasFieldControlPointLatticeType::Pointer 
GetLogBiasFieldControlPointLattice () const
 
const MaskImageTypeGetMaskImage () const
 
virtual MaskPixelType GetMaskLabel () const
 
virtual VariableSizeArrayType GetMaximumNumberOfIterations () const
 
virtual const char * GetNameOfClass () const
 
virtual ArrayType GetNumberOfControlPoints () const
 
virtual ArrayType GetNumberOfFittingLevels () const
 
virtual unsigned int GetNumberOfHistogramBins () const
 
virtual unsigned int GetSplineOrder () const
 
virtual RealType GetWienerFilterNoise () const
 
virtual void SetBiasFieldFullWidthAtHalfMaximum (RealType _arg)
 
virtual void SetConvergenceThreshold (RealType _arg)
 
void SetInput1 (const InputImageType *image)
 
virtual void SetMaskLabel (MaskPixelType _arg)
 
virtual void SetMaximumNumberOfIterations (VariableSizeArrayType _arg)
 
virtual void SetNumberOfControlPoints (ArrayType _arg)
 
virtual void SetNumberOfFittingLevels (ArrayType _arg)
 
void SetNumberOfFittingLevels (unsigned int n)
 
virtual void SetNumberOfHistogramBins (unsigned int _arg)
 
virtual void SetSplineOrder (unsigned int _arg)
 
virtual void SetWienerFilterNoise (RealType _arg)
 
void SetMaskImage (const MaskImageType *mask)
 
void SetInput2 (const MaskImageType *mask)
 
void SetConfidenceImage (const RealImageType *image)
 
void SetInput3 (const RealImageType *image)
 
- Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
const InputImageTypeGetInput () const
 
const InputImageTypeGetInput (unsigned int idx) const
 
virtual void PopBackInput () override
 
virtual void PopFrontInput () override
 
virtual void PushBackInput (const InputImageType *image)
 
virtual void PushFrontInput (const InputImageType *image)
 
virtual void SetInput (const InputImageType *image)
 
virtual void SetInput (unsigned int, const TInputImage *image)
 
virtual void SetCoordinateTolerance (double _arg)
 
virtual double GetCoordinateTolerance () const
 
virtual void SetDirectionTolerance (double _arg)
 
virtual double GetDirectionTolerance () const
 
- Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageTypeGetOutput (unsigned int idx)
 
virtual void GraftNthOutput (unsigned int idx, DataObject *output)
 
virtual void GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
 
OutputImageTypeGetOutput ()
 
const OutputImageTypeGetOutput () const
 
virtual void GraftOutput (DataObject *output)
 
virtual
ProcessObject::DataObjectPointer 
MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
 
virtual
ProcessObject::DataObjectPointer 
MakeOutput (const ProcessObject::DataObjectIdentifierType &) override
 
- Public Member Functions inherited from itk::ProcessObject
virtual void AbortGenerateDataOff ()
 
virtual void AbortGenerateDataOn ()
 
virtual void EnlargeOutputRequestedRegion (DataObject *)
 
virtual const bool & GetAbortGenerateData () const
 
DataObjectPointerArray GetIndexedInputs ()
 
DataObjectPointerArray GetIndexedOutputs ()
 
NameArray GetInputNames () const
 
DataObjectPointerArray GetInputs ()
 
MultiThreader * GetMultiThreader () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedInputs () const
 
DataObjectPointerArraySizeType GetNumberOfIndexedOutputs () const
 
DataObjectPointerArraySizeType GetNumberOfInputs () const
 
DataObjectPointerArraySizeType GetNumberOfOutputs () const
 
virtual
DataObjectPointerArraySizeType 
GetNumberOfValidRequiredInputs () const
 
NameArray GetOutputNames () const
 
DataObjectPointerArray GetOutputs ()
 
virtual const float & GetProgress () const
 
NameArray GetRequiredInputNames () const
 
bool HasInput (const DataObjectIdentifierType &key) const
 
bool HasOutput (const DataObjectIdentifierType &key) const
 
virtual void PrepareOutputs ()
 
virtual void PropagateRequestedRegion (DataObject *output)
 
virtual void ResetPipeline ()
 
virtual void SetAbortGenerateData (bool _arg)
 
virtual void Update ()
 
virtual void UpdateLargestPossibleRegion ()
 
virtual void UpdateOutputData (DataObject *output)
 
virtual void UpdateOutputInformation ()
 
void UpdateProgress (float progress)
 
void SetProgress (float progress)
 
virtual void SetReleaseDataFlag (bool flag)
 
virtual bool GetReleaseDataFlag () const
 
void ReleaseDataFlagOn ()
 
void ReleaseDataFlagOff ()
 
virtual void SetReleaseDataBeforeUpdateFlag (bool _arg)
 
virtual const bool & GetReleaseDataBeforeUpdateFlag () const
 
virtual void ReleaseDataBeforeUpdateFlagOn ()
 
virtual void ReleaseDataBeforeUpdateFlagOff ()
 
virtual void SetNumberOfThreads (ThreadIdType _arg)
 
virtual const ThreadIdTypeGetNumberOfThreads () const
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *)
 
unsigned long AddObserver (const EventObject &event, Command *) const
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
CommandGetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionaryGetMetaDataDictionary ()
 
const MetaDataDictionaryGetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStampGetTimeStamp () const
 
bool HasObserver (const EventObject &event) const
 
void InvokeEvent (const EventObject &)
 
void InvokeEvent (const EventObject &) const
 
virtual void Modified () const
 
virtual void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
virtual void SetReferenceCount (int) override
 
virtual void UnRegister () const noexceptoverride
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkCloneMacro (Self)
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool flag)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Static Public Attributes

static const unsigned int ImageDimension = TInputImage::ImageDimension
 
- Static Public Attributes inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
static const unsigned int InputImageDimension = TInputImage::ImageDimension
 
static const unsigned int OutputImageDimension = TOutputImage::ImageDimension
 
- Static Public Attributes inherited from itk::ImageSource< TOutputImage >
static const unsigned int OutputImageDimension = TOutputImage::ImageDimension
 

Protected Member Functions

void GenerateData () override
 
 N4BiasFieldCorrectionImageFilter ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
 ~N4BiasFieldCorrectionImageFilter ()
 
- Protected Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual void CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
 
virtual void CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
 
virtual void GenerateInputRequestedRegion () override
 
 ImageToImageFilter ()
 
virtual void VerifyInputInformation () override
 
 ~ImageToImageFilter ()
 
void PushBackInput (const DataObject *input) override
 
void PushFrontInput (const DataObject *input) override
 
- Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void AfterThreadedGenerateData ()
 
virtual void AllocateOutputs ()
 
virtual void BeforeThreadedGenerateData ()
 
virtual const
ImageRegionSplitterBase
GetImageRegionSplitter () const
 
 ImageSource ()
 
virtual unsigned int SplitRequestedRegion (unsigned int i, unsigned int pieces, OutputImageRegionType &splitRegion)
 
virtual void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
 
virtual ~ImageSource ()
 
- Protected Member Functions inherited from itk::ProcessObject
virtual void AddInput (DataObject *input)
 
virtual void AddOutput (DataObject *output)
 
bool AddRequiredInputName (const DataObjectIdentifierType &)
 
bool AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)
 
virtual void CacheInputReleaseDataFlags ()
 
virtual void GenerateOutputInformation ()
 
virtual void GenerateOutputRequestedRegion (DataObject *output)
 
DataObjectGetInput (const DataObjectIdentifierType &key)
 
const DataObjectGetInput (const DataObjectIdentifierType &key) const
 
virtual const
DataObjectPointerArraySizeType
GetNumberOfRequiredInputs () const
 
virtual const
DataObjectPointerArraySizeType
GetNumberOfRequiredOutputs () const
 
bool IsIndexedInputName (const DataObjectIdentifierType &) const
 
bool IsIndexedOutputName (const DataObjectIdentifierType &) const
 
bool IsRequiredInputName (const DataObjectIdentifierType &) const
 
 itkLegacyMacro (virtual void RemoveOutput(DataObject *output))
 
 itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))
 
 itkLegacyMacro (virtual void RemoveInput(DataObject *input))
 
 itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))
 
DataObjectPointerArraySizeType MakeIndexFromInputName (const DataObjectIdentifierType &name) const
 
DataObjectPointerArraySizeType MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
 
DataObjectIdentifierType MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
 
DataObjectIdentifierType MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
 
 ProcessObject ()
 
virtual void PropagateResetPipeline ()
 
virtual void ReleaseInputs ()
 
virtual void RemoveInput (const DataObjectIdentifierType &key)
 
virtual void RemoveInput (DataObjectPointerArraySizeType)
 
virtual void RemoveOutput (const DataObjectIdentifierType &key)
 
virtual void RemoveOutput (DataObjectPointerArraySizeType idx)
 
bool RemoveRequiredInputName (const DataObjectIdentifierType &)
 
virtual void RestoreInputReleaseDataFlags ()
 
virtual void SetInput (const DataObjectIdentifierType &key, DataObject *input)
 
virtual void SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
 
virtual void SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
 
void SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
 
void SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
 
virtual void SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
 
virtual void SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
 
virtual void SetOutput (const DataObjectIdentifierType &key, DataObject *output)
 
virtual void SetPrimaryInput (DataObject *input)
 
virtual void SetPrimaryOutput (DataObject *output)
 
void SetRequiredInputNames (const NameArray &)
 
virtual void VerifyPreconditions ()
 
 ~ProcessObject ()
 
DataObjectGetInput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetInput (DataObjectPointerArraySizeType idx) const
 
DataObjectGetPrimaryInput ()
 
const DataObjectGetPrimaryInput () const
 
virtual void SetPrimaryInputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryInputName (void) const
 
DataObjectGetOutput (const DataObjectIdentifierType &key)
 
const DataObjectGetOutput (const DataObjectIdentifierType &key) const
 
virtual void SetPrimaryOutputName (const DataObjectIdentifierType &key)
 
virtual const char * GetPrimaryOutputName (void) const
 
DataObjectGetOutput (DataObjectPointerArraySizeType idx)
 
const DataObjectGetOutput (DataObjectPointerArraySizeType idx) const
 
DataObjectGetPrimaryOutput ()
 
const DataObjectGetPrimaryOutput () const
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &time)
 
virtual ~Object ()
 
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 
 LightObject ()
 
virtual void PrintHeader (std::ostream &os, Indent indent) const
 
virtual void PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 

Private Member Functions

RealType CalculateConvergenceMeasurement (const RealImageType *, const RealImageType *) const
 
 N4BiasFieldCorrectionImageFilter (const Self &) ITK_DELETE_FUNCTION
 
void operator= (const Self &) ITK_DELETE_FUNCTION
 
RealImagePointer ReconstructBiasField (BiasFieldControlPointLatticeType *)
 
RealImagePointer SharpenImage (const RealImageType *) const
 
RealImagePointer UpdateBiasFieldEstimate (RealImageType *)
 

Private Attributes

RealType m_BiasFieldFullWidthAtHalfMaximum
 
RealType m_ConvergenceThreshold
 
RealType m_CurrentConvergenceMeasurement
 
unsigned int m_CurrentLevel
 
unsigned int m_ElapsedIterations
 
BiasFieldControlPointLatticeType::Pointer m_LogBiasFieldControlPointLattice
 
MaskPixelType m_MaskLabel
 
VariableSizeArrayType m_MaximumNumberOfIterations
 
ArrayType m_NumberOfControlPoints
 
ArrayType m_NumberOfFittingLevels
 
unsigned int m_NumberOfHistogramBins
 
unsigned int m_SplineOrder
 
RealType m_WienerFilterNoise
 

Additional Inherited Members

- Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(OutputImageDimension),
itkGetStaticConstMacro(InputImageDimension) > 
InputToOutputRegionCopierType
 
typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(InputImageDimension),
itkGetStaticConstMacro(OutputImageDimension) > 
OutputToInputRegionCopierType
 
- Static Protected Member Functions inherited from itk::ImageSource< TOutputImage >
static const
ImageRegionSplitterBase
GetGlobalDefaultSplitter ()
 
static ITK_THREAD_RETURN_TYPE ThreaderCallback (void *arg)
 
- Protected Attributes inherited from itk::ProcessObject
TimeStamp m_OutputInformationMTime
 
bool m_Updating
 
- Protected Attributes inherited from itk::LightObject
AtomicInt< int > m_ReferenceCount
 

Member Typedef Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef BSplineFilterType::ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ArrayType

Definition at line 136 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef BSplineFilterType::PointDataImageType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BiasFieldControlPointLatticeType

Definition at line 135 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef BSplineScatteredDataPointSetToImageFilter< PointSetType, ScalarImageType> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BSplineFilterType

B-sline filter typedefs

Definition at line 134 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef SmartPointer<const Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ConstPointer

Definition at line 101 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef TInputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::InputImageType

Some convenient typedefs.

Definition at line 114 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef TMaskImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskImageType

Definition at line 116 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef MaskImageType::PixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskPixelType

Definition at line 117 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef TOutputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::OutputImageType

Definition at line 115 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef SmartPointer<Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Pointer

Definition at line 100 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef PointSetType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetPointer

B-spline smoothing filter argument typedefs

Definition at line 128 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef PointSet<ScalarType, itkGetStaticConstMacro( ImageDimension )> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetType

B-spline smoothing filter argument typedefs

Definition at line 126 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef PointSetType::PointType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointType

B-spline smoothing filter argument typedefs

Definition at line 129 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef RealImageType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImagePointer

Definition at line 121 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef Image<RealType, ImageDimension> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImageType

Definition at line 120 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef float itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealType

Definition at line 119 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef Image<ScalarType, itkGetStaticConstMacro( ImageDimension )> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarImageType

B-spline smoothing filter argument typedefs

Definition at line 127 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef Vector<RealType, 1> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarType

B-spline smoothing filter argument typedefs

Definition at line 125 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef N4BiasFieldCorrectionImageFilter itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Self

Standard class typedefs.

Definition at line 98 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef ImageToImageFilter<TInputImage, TOutputImage> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Superclass

Definition at line 99 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
typedef Array<unsigned int> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::VariableSizeArrayType

Definition at line 122 of file itkN4BiasFieldCorrectionImageFilter.h.

Constructor & Destructor Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( )
protected
template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::~N4BiasFieldCorrectionImageFilter ( )
inlineprotected

Definition at line 373 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( const Self )
private

Member Function Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CalculateConvergenceMeasurement ( const RealImageType ,
const RealImageType  
) const
private

Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual::itk::LightObject::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CreateAnother ( ) const
virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GenerateData ( )
overrideprotectedvirtual

A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See Also
ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetBiasFieldFullWidthAtHalfMaximum ( ) const
virtual

Get the full width at half maximum parameter characterizing the width of the Gaussian deconvolution. Default = 0.15.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
const RealImageType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetConfidenceImage ( ) const
inline

Get confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 193 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetConvergenceThreshold ( ) const
virtual

Get the convergence threshold. Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate. If this value is less than the specified threshold, the algorithm proceeds to the next fitting level or terminates if it is at the last level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetCurrentConvergenceMeasurement ( ) const
virtual

Get the current convergence measurement. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetCurrentLevel ( ) const
virtual

Get the current fitting level. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetElapsedIterations ( ) const
virtual

Get the number of elapsed iterations. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual BiasFieldControlPointLatticeType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetLogBiasFieldControlPointLattice ( ) const
virtual

Typically, a reduced size image is used as input to the N4 filter using something like itkShrinkImageFilter. Since the output is a corrected version of the input, the user will probably want to apply the bias field correction to the full resolution image. This can be done by using the LogBiasFieldControlPointLattice to reconstruct the bias field at the full image resolution (using the class BSplineControlPointImageFilter).

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
const MaskImageType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskImage ( ) const
inline

Get mask image function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 161 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskLabel ( ) const
virtual

Get mask label function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field. Default = 1.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaximumNumberOfIterations ( ) const
virtual

Get the maximum number of iterations specified at each fitting level. Default = 50.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual const char* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNameOfClass ( ) const
virtual

Runtime information support.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfControlPoints ( ) const
virtual

Get the control point grid size defining the B-spline estimate of the scalar bias field. In each dimension, the B-spline mesh size is equal to the number of control points in that dimension minus the spline order. Default = 4 control points in each dimension for a mesh size of 1 in each dimension.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfFittingLevels ( ) const
virtual

Get the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfHistogramBins ( ) const
virtual

Get number of bins defining the log input intensity histogram. Default = 200.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetSplineOrder ( ) const
virtual

Get the spline order defining the bias field estimate. Default = 3.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetWienerFilterNoise ( ) const
virtual

Get the noise estimate defining the Wiener filter. Default = 0.01.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
static Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::New ( )
static

Standard New method.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::operator= ( const Self )
private
template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
overrideprotectedvirtual

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ReconstructBiasField ( BiasFieldControlPointLatticeType )
private

Reconstruct bias field given the control point lattice.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetBiasFieldFullWidthAtHalfMaximum ( RealType  _arg)
virtual

Set the full width at half maximum parameter characterizing the width of the Gaussian deconvolution. Default = 0.15.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConfidenceImage ( const RealImageType image)
inline

Set confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 176 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::SetNthInput().

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput3().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConvergenceThreshold ( RealType  _arg)
virtual

Set the convergence threshold. Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate. If this value is less than the specified threshold, the algorithm proceeds to the next fitting level or terminates if it is at the last level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput1 ( const InputImageType image)
inline

The image expected for input for bias correction.

Definition at line 141 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ImageToImageFilter< TInputImage, TOutputImage >::SetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput2 ( const MaskImageType mask)
inline

Set mask image function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 153 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskImage().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput3 ( const RealImageType image)
inline

Set confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 180 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConfidenceImage().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskImage ( const MaskImageType mask)
inline

Set mask image function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 149 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::SetNthInput().

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput2().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskLabel ( MaskPixelType  _arg)
virtual

Set mask label function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field. Default = 1.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaximumNumberOfIterations ( VariableSizeArrayType  _arg)
virtual

Set the maximum number of iterations specified at each fitting level. Default = 50.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfControlPoints ( ArrayType  _arg)
virtual

Set the control point grid size defining the B-spline estimate of the scalar bias field. In each dimension, the B-spline mesh size is equal to the number of control points in that dimension minus the spline order. Default = 4 control points in each dimension for a mesh size of 1 in each dimension.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels ( ArrayType  _arg)
virtual

Set the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels ( unsigned int  n)
inline

Set the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

Definition at line 295 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::FixedArray< TValue, VLength >::Fill(), and itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfHistogramBins ( unsigned int  _arg)
virtual

Set number of bins defining the log input intensity histogram. Default = 200.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetSplineOrder ( unsigned int  _arg)
virtual

Set the spline order defining the bias field estimate. Default = 3.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetWienerFilterNoise ( RealType  _arg)
virtual

Set the noise estimate defining the Wiener filter. Default = 0.01.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SharpenImage ( const RealImageType ) const
private

Sharpen the intensity histogram of the current estimate of the corrected image and map those results to a new estimate of the unsmoothed corrected image.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::UpdateBiasFieldEstimate ( RealImageType )
private

Given the unsmoothed estimate of the bias field, this function smooths the estimate and adds the resulting control point values to the total bias field estimate.

Member Data Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
const unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ImageDimension = TInputImage::ImageDimension
static

ImageDimension constants

Definition at line 111 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_BiasFieldFullWidthAtHalfMaximum
private

Definition at line 421 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ConvergenceThreshold
private

Definition at line 427 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentConvergenceMeasurement
private

Definition at line 428 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentLevel
private

Definition at line 429 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ElapsedIterations
private

Definition at line 426 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
BiasFieldControlPointLatticeType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_LogBiasFieldControlPointLattice
private

Definition at line 434 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaskLabel
private

Definition at line 415 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaximumNumberOfIterations
private

Definition at line 425 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfControlPoints
private

Definition at line 437 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfFittingLevels
private

Definition at line 438 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfHistogramBins
private

Definition at line 419 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_SplineOrder
private

Definition at line 436 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_WienerFilterNoise
private

Definition at line 420 of file itkN4BiasFieldCorrectionImageFilter.h.


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