ITK  4.2.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes
itk::MRASlabIdentifier< TInputImage > Class Template Reference

#include <itkMRASlabIdentifier.h>

+ Inheritance diagram for itk::MRASlabIdentifier< TInputImage >:
+ Collaboration diagram for itk::MRASlabIdentifier< TInputImage >:

List of all members.

Public Types

typedef SmartPointer< const SelfConstPointer
typedef TInputImage::ConstPointer ImageConstPointer
typedef TInputImage::IndexType ImageIndexType
typedef TInputImage::PixelType ImagePixelType
typedef TInputImage::Pointer ImagePointer
typedef TInputImage::RegionType ImageRegionType
typedef TInputImage::SizeType ImageSizeType
typedef TInputImage ImageType
typedef SmartPointer< SelfPointer
typedef MRASlabIdentifier Self
typedef std::vector
< ImageRegionType
SlabRegionVectorType
typedef Object Superclass
- Public Types inherited from itk::Object
- Public Types inherited from itk::LightObject

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
void GenerateSlabRegions (void)
virtual const char * GetNameOfClass () const
SlabRegionVectorType GetSlabRegionVector (void)
virtual void SetImage (const ImageType *_arg)
virtual const ImageTypeGetImage ()
virtual void SetNumberOfSamples (unsigned int _arg)
virtual const unsigned int & GetNumberOfSamples ()
virtual void SetBackgroundMinimumThreshold (ImagePixelType _arg)
virtual const ImagePixelTypeGetBackgroundMinimumThreshold ()
virtual void SetTolerance (double _arg)
virtual const double & GetTolerance ()
virtual void SetSlicingDirection (int _arg)
virtual const int & GetSlicingDirection ()
- 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 (void)
const MetaDataDictionaryGetMetaDataDictionary (void) const
virtual unsigned long 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
void RemoveAllObservers ()
void RemoveObserver (unsigned long tag)
void SetDebug (bool debugFlag) const
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void SetReferenceCount (int)
virtual void UnRegister () 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 void SetGlobalWarningDisplay (bool flag)
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()

Protected Member Functions

 MRASlabIdentifier ()
void PrintSelf (std::ostream &os, Indent indent) const
virtual ~MRASlabIdentifier ()
- 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

 MRASlabIdentifier (const Self &)
void operator= (const Self &)

Private Attributes

ImagePixelType m_BackgroundMinimumThreshold
ImageConstPointer m_Image
unsigned int m_NumberOfSamples
SlabRegionVectorType m_Slabs
int m_SlicingDirection
double m_Tolerance

Detailed Description

template<class TInputImage>
class itk::MRASlabIdentifier< TInputImage >

identifies slab in MR images comparing minimum intensity averages

This class is templated over the type of image. In many cases, a 3D MR image is constructed by merging smaller 3D blocks (slabs) which were acquired with different settings such as magnetic settings and patient positions. Therefore, stripe like patterns with slabs can be present in the resulting image. Such artifacts are called "slab boundary" artifacts or "venetian blind" artifacts.

With the slab boundary artifacts in an image, even a same tissue class's intensity values might vary significantly along the borders of slabs. Such rough value changes are not appropriate for some image processing methods. For example, MRIBiasFieldCorrectionFilter assumes a smooth bias field. However, with the slab boundary artifacts, the bias field estimation scheme that MRIBiasFieldCorrectionFilter uses might not adopt well. So, the MRIBiasFieldCorrectionFilter creates regions for slabs using the MRASlabIdentifier and then apply its bias correction scheme to each slab.

For this identifier, a slice means 2D image data which is extracted from the input image along one of three axes (x, y, z). Users can specify the slicing axis using the SetSlicingDirection(int dimension) member. (0 - x, 1 - y, 2 - z).

The identification scheme used here is very simple. 1) Users should specify how many pixels per slice the identifier will sample. 2) For each slice, the identifier searches the specified number of pixels of which intensity values are greater than 0 and less than those of the other pixels in the slice 3) The identifier calculates the average for each slice and the overall average using the search results. 4) For each slice, it subtracts the overall average from the slice average. If the sign of the subtraction result changes, then it assumes that a slab ends and another slab begins.

Definition at line 65 of file itkMRASlabIdentifier.h.


Member Typedef Documentation

template<class TInputImage >
typedef SmartPointer< const Self > itk::MRASlabIdentifier< TInputImage >::ConstPointer

Reimplemented from itk::Object.

Definition at line 72 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage::ConstPointer itk::MRASlabIdentifier< TInputImage >::ImageConstPointer

Const Pointer type for the image.

Definition at line 87 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage::IndexType itk::MRASlabIdentifier< TInputImage >::ImageIndexType

Definition at line 91 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage::PixelType itk::MRASlabIdentifier< TInputImage >::ImagePixelType

Type definition for the input image pixel type.

Definition at line 90 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage::Pointer itk::MRASlabIdentifier< TInputImage >::ImagePointer

Pointer type for the image.

Definition at line 84 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage::RegionType itk::MRASlabIdentifier< TInputImage >::ImageRegionType

Definition at line 93 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage::SizeType itk::MRASlabIdentifier< TInputImage >::ImageSizeType

Definition at line 92 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef TInputImage itk::MRASlabIdentifier< TInputImage >::ImageType

Type definition for the input image.

Definition at line 78 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef SmartPointer< Self > itk::MRASlabIdentifier< TInputImage >::Pointer

Reimplemented from itk::Object.

Definition at line 71 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef MRASlabIdentifier itk::MRASlabIdentifier< TInputImage >::Self

Standard class typedefs.

Reimplemented from itk::Object.

Definition at line 69 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef std::vector< ImageRegionType > itk::MRASlabIdentifier< TInputImage >::SlabRegionVectorType

Definition at line 94 of file itkMRASlabIdentifier.h.

template<class TInputImage >
typedef Object itk::MRASlabIdentifier< TInputImage >::Superclass

Reimplemented from itk::Object.

Definition at line 70 of file itkMRASlabIdentifier.h.


Constructor & Destructor Documentation

template<class TInputImage >
itk::MRASlabIdentifier< TInputImage >::MRASlabIdentifier ( )
protected
template<class TInputImage >
virtual itk::MRASlabIdentifier< TInputImage >::~MRASlabIdentifier ( )
inlineprotectedvirtual

Definition at line 131 of file itkMRASlabIdentifier.h.

template<class TInputImage >
itk::MRASlabIdentifier< TInputImage >::MRASlabIdentifier ( const Self )
private

Member Function Documentation

template<class TInputImage >
virtual::itk::LightObject::Pointer itk::MRASlabIdentifier< TInputImage >::CreateAnother ( void  ) 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<class TInputImage >
void itk::MRASlabIdentifier< TInputImage >::GenerateSlabRegions ( void  )

Compute the average values of miminum intensity pixels for each slice and compare the average values with overall averages.

template<class TInputImage >
virtual const ImagePixelType& itk::MRASlabIdentifier< TInputImage >::GetBackgroundMinimumThreshold ( )
virtual

Set/Get the minimum threshold value for the background pixels

template<class TInputImage >
virtual const ImageType* itk::MRASlabIdentifier< TInputImage >::GetImage ( )
virtual

Set/Get the input image.

template<class TInputImage >
virtual const char* itk::MRASlabIdentifier< TInputImage >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::Object.

template<class TInputImage >
virtual const unsigned int& itk::MRASlabIdentifier< TInputImage >::GetNumberOfSamples ( )
virtual

Set/Get the number of minimum intensity pixels per slice.

template<class TInputImage >
SlabRegionVectorType itk::MRASlabIdentifier< TInputImage >::GetSlabRegionVector ( void  )

Get slab regions.

template<class TInputImage >
virtual const int& itk::MRASlabIdentifier< TInputImage >::GetSlicingDirection ( )
virtual

Set/Get the direction of slicing/ 0 - x axis, 1 - y axis, 2 - z axis

template<class TInputImage >
virtual const double& itk::MRASlabIdentifier< TInputImage >::GetTolerance ( )
virtual

Set/Get the tolerance value.

template<class TInputImage >
static Pointer itk::MRASlabIdentifier< TInputImage >::New ( )
static

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TInputImage >
void itk::MRASlabIdentifier< TInputImage >::operator= ( const Self )
private

Mutex lock to protect modification to the reference count

Reimplemented from itk::Object.

template<class TInputImage >
void itk::MRASlabIdentifier< TInputImage >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
protectedvirtual

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::Object.

template<class TInputImage >
virtual void itk::MRASlabIdentifier< TInputImage >::SetBackgroundMinimumThreshold ( ImagePixelType  _arg)
virtual

Set/Get the minimum threshold value for the background pixels

template<class TInputImage >
virtual void itk::MRASlabIdentifier< TInputImage >::SetImage ( const ImageType _arg)
virtual

Set/Get the input image.

template<class TInputImage >
virtual void itk::MRASlabIdentifier< TInputImage >::SetNumberOfSamples ( unsigned int  _arg)
virtual

Set/Get the number of minimum intensity pixels per slice.

template<class TInputImage >
virtual void itk::MRASlabIdentifier< TInputImage >::SetSlicingDirection ( int  _arg)
virtual

Set/Get the direction of slicing/ 0 - x axis, 1 - y axis, 2 - z axis

template<class TInputImage >
virtual void itk::MRASlabIdentifier< TInputImage >::SetTolerance ( double  _arg)
virtual

Set/Get the tolerance value.


Member Data Documentation

template<class TInputImage >
ImagePixelType itk::MRASlabIdentifier< TInputImage >::m_BackgroundMinimumThreshold
private

Definition at line 146 of file itkMRASlabIdentifier.h.

template<class TInputImage >
ImageConstPointer itk::MRASlabIdentifier< TInputImage >::m_Image
private

Target image pointer that MRASlabIdentifier will use.

Definition at line 139 of file itkMRASlabIdentifier.h.

template<class TInputImage >
unsigned int itk::MRASlabIdentifier< TInputImage >::m_NumberOfSamples
private

The number of pixels per slice which will be included for average calculation. In a sense, it's sampling size per slice.

Definition at line 143 of file itkMRASlabIdentifier.h.

template<class TInputImage >
SlabRegionVectorType itk::MRASlabIdentifier< TInputImage >::m_Slabs
private

Definition at line 148 of file itkMRASlabIdentifier.h.

template<class TInputImage >
int itk::MRASlabIdentifier< TInputImage >::m_SlicingDirection
private

Definition at line 145 of file itkMRASlabIdentifier.h.

template<class TInputImage >
double itk::MRASlabIdentifier< TInputImage >::m_Tolerance
private

Definition at line 147 of file itkMRASlabIdentifier.h.


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