ITK  4.6.0
Insight Segmentation and Registration Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
itk::MRASlabIdentifier< TInputImage > Class Template Reference

#include <itkMRASlabIdentifier.h>

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

Detailed Description

template<typename 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.

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
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 (void) const
 
void GenerateSlabRegions (void)
 
virtual const char * GetNameOfClass () const
 
SlabRegionVectorType GetSlabRegionVector (void)
 
virtual void SetImage (const ImageType *_arg)
 
virtual const ImageTypeGetImage () const
 
virtual void SetNumberOfSamples (unsigned int _arg)
 
virtual const unsigned int & GetNumberOfSamples () const
 
virtual void SetBackgroundMinimumThreshold (ImagePixelType _arg)
 
virtual const ImagePixelTypeGetBackgroundMinimumThreshold () const
 
virtual void SetTolerance (double _arg)
 
virtual const double & GetTolerance () const
 
virtual void SetSlicingDirection (int _arg)
 
virtual const int & GetSlicingDirection () 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 (void)
 
const MetaDataDictionaryGetMetaDataDictionary (void) 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 ITK_OVERRIDE
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
virtual void SetReferenceCount (int) ITK_OVERRIDE
 
virtual void UnRegister () const ITK_OVERRIDE
 
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 ()
 

Protected Member Functions

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

Additional Inherited Members

- Protected Types inherited from itk::LightObject
typedef int InternalReferenceCountType
 
- Protected Attributes inherited from itk::LightObject
InternalReferenceCountType m_ReferenceCount
 
SimpleFastMutexLock m_ReferenceCountLock
 

Member Typedef Documentation

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

Definition at line 72 of file itkMRASlabIdentifier.h.

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

Const Pointer type for the image.

Definition at line 87 of file itkMRASlabIdentifier.h.

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

Definition at line 91 of file itkMRASlabIdentifier.h.

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

Pointer type for the image.

Definition at line 84 of file itkMRASlabIdentifier.h.

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

Definition at line 93 of file itkMRASlabIdentifier.h.

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

Definition at line 92 of file itkMRASlabIdentifier.h.

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

Type definition for the input image.

Definition at line 78 of file itkMRASlabIdentifier.h.

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

Definition at line 71 of file itkMRASlabIdentifier.h.

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

Standard class typedefs.

Definition at line 69 of file itkMRASlabIdentifier.h.

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

Definition at line 94 of file itkMRASlabIdentifier.h.

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

Definition at line 70 of file itkMRASlabIdentifier.h.

Constructor & Destructor Documentation

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

Definition at line 131 of file itkMRASlabIdentifier.h.

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

Member Function Documentation

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

Set/Get the minimum threshold value for the background pixels

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

Set/Get the input image.

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

Run-time type information (and related methods).

Reimplemented from itk::Object.

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

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

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

Get slab regions.

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

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

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

Set/Get the tolerance value.

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

Method for creation through the object factory.

template<typename TInputImage >
void itk::MRASlabIdentifier< TInputImage >::operator= ( const Self )
private
template<typename TInputImage >
virtual 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<typename TInputImage >
virtual void itk::MRASlabIdentifier< TInputImage >::SetBackgroundMinimumThreshold ( ImagePixelType  _arg)
virtual

Set/Get the minimum threshold value for the background pixels

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

Set/Get the input image.

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

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

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

Set/Get the tolerance value.

Member Data Documentation

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

Definition at line 146 of file itkMRASlabIdentifier.h.

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

Target image pointer that MRASlabIdentifier will use.

Definition at line 139 of file itkMRASlabIdentifier.h.

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

Definition at line 148 of file itkMRASlabIdentifier.h.

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

Definition at line 145 of file itkMRASlabIdentifier.h.

template<typename 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: