ITK  5.4.0
Insight Toolkit
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
itk::MRASlabIdentifier< TInputImage > Class Template Reference

#include <itkMRASlabIdentifier.h>

Detailed Description

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

Identifies slabs 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.

Due to the slab boundary artifacts in an image, even same tissue class' 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 adapt well. The MRIBiasFieldCorrectionFilter creates regions for slabs using the MRASlabIdentifier and then applies 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, where the dimension variable follows the convention \({X, Y, Z} : {0, 1, 2}\).

The identification scheme used works according to the following steps:

  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 67 of file itkMRASlabIdentifier.h.

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

Public Types

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

Public Member Functions

void GenerateSlabRegions ()
 
SlabRegionVectorType GetSlabRegionVector ()
 
 itkOverrideGetNameOfClassMacro (MRASlabIdentifier)
 
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
 
unsigned long AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
 
LightObject::Pointer CreateAnother () const override
 
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
 
 itkOverrideGetNameOfClassMacro (Object)
 
virtual void Modified () const
 
void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag)
 
void SetDebug (bool debugFlag) const
 
void SetReferenceCount (int) override
 
void UnRegister () const noexcept override
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
void SetMetaDataDictionary (MetaDataDictionary &&rrhs)
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
Pointer Clone () const
 
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
 itkVirtualGetNameOfClassMacro (LightObject)
 
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 val)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Protected Member Functions

 MRASlabIdentifier ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
 ~MRASlabIdentifier () override=default
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &timeStamp)
 
 ~Object () override
 
- 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 Attributes

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

Additional Inherited Members

- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount {}
 

Member Typedef Documentation

◆ ConstPointer

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

Definition at line 76 of file itkMRASlabIdentifier.h.

◆ ImageConstPointer

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImageConstPointer = typename TInputImage::ConstPointer

Const Pointer type for the image.

Definition at line 91 of file itkMRASlabIdentifier.h.

◆ ImageIndexType

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImageIndexType = typename TInputImage::IndexType

Definition at line 95 of file itkMRASlabIdentifier.h.

◆ ImagePixelType

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImagePixelType = typename TInputImage::PixelType

Type definition for the input image pixel type.

Definition at line 94 of file itkMRASlabIdentifier.h.

◆ ImagePointer

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImagePointer = typename TInputImage::Pointer

Pointer type for the image.

Definition at line 88 of file itkMRASlabIdentifier.h.

◆ ImageRegionType

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImageRegionType = typename TInputImage::RegionType

Definition at line 97 of file itkMRASlabIdentifier.h.

◆ ImageSizeType

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImageSizeType = typename TInputImage::SizeType

Definition at line 96 of file itkMRASlabIdentifier.h.

◆ ImageType

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::ImageType = TInputImage

Type definition for the input image.

Definition at line 85 of file itkMRASlabIdentifier.h.

◆ Pointer

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::Pointer = SmartPointer<Self>

Definition at line 75 of file itkMRASlabIdentifier.h.

◆ Self

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::Self = MRASlabIdentifier

Standard class type aliases.

Definition at line 73 of file itkMRASlabIdentifier.h.

◆ SlabRegionVectorType

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

Definition at line 98 of file itkMRASlabIdentifier.h.

◆ Superclass

template<typename TInputImage >
using itk::MRASlabIdentifier< TInputImage >::Superclass = Object

Definition at line 74 of file itkMRASlabIdentifier.h.

Constructor & Destructor Documentation

◆ MRASlabIdentifier()

template<typename TInputImage >
itk::MRASlabIdentifier< TInputImage >::MRASlabIdentifier ( )
protected

◆ ~MRASlabIdentifier()

template<typename TInputImage >
itk::MRASlabIdentifier< TInputImage >::~MRASlabIdentifier ( )
overrideprotecteddefault

Member Function Documentation

◆ GenerateSlabRegions()

template<typename TInputImage >
void itk::MRASlabIdentifier< TInputImage >::GenerateSlabRegions ( )

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

◆ GetBackgroundMinimumThreshold()

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

Set/Get the minimum threshold value for the background pixels

◆ GetImage()

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

Set/Get the input image.

◆ GetNumberOfSamples()

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

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

◆ GetSlabRegionVector()

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

Get slab regions.

◆ GetSlicingDirection()

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

◆ GetTolerance()

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

Set/Get the tolerance value.

◆ itkOverrideGetNameOfClassMacro()

template<typename TInputImage >
itk::MRASlabIdentifier< TInputImage >::itkOverrideGetNameOfClassMacro ( MRASlabIdentifier< TInputImage >  )

Run-time type information (and related methods).

◆ New()

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

Method for creation through the object factory.

◆ PrintSelf()

template<typename TInputImage >
void itk::MRASlabIdentifier< TInputImage >::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::Object.

◆ SetBackgroundMinimumThreshold()

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

Set/Get the minimum threshold value for the background pixels

◆ SetImage()

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

Set/Get the input image.

◆ SetNumberOfSamples()

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

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

◆ SetSlicingDirection()

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

◆ SetTolerance()

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

Set/Get the tolerance value.

Member Data Documentation

◆ m_BackgroundMinimumThreshold

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

Definition at line 150 of file itkMRASlabIdentifier.h.

◆ m_Image

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

Target image pointer that MRASlabIdentifier will use.

Definition at line 143 of file itkMRASlabIdentifier.h.

◆ m_NumberOfSamples

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 147 of file itkMRASlabIdentifier.h.

◆ m_Slabs

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

Definition at line 152 of file itkMRASlabIdentifier.h.

◆ m_SlicingDirection

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

Definition at line 149 of file itkMRASlabIdentifier.h.

◆ m_Tolerance

template<typename TInputImage >
double itk::MRASlabIdentifier< TInputImage >::m_Tolerance {}
private

Definition at line 151 of file itkMRASlabIdentifier.h.


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