Normalization filter for CEST images using M0 reference images. More...

#include <mitkCESTImageNormalizationFilter.h>

Inheritance diagram for mitk::CESTImageNormalizationFilter:

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Collaboration diagram for mitk::CESTImageNormalizationFilter:

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Public Member Functions
	mitkClassMacro (CESTImageNormalizationFilter, ImageToImageFilter)

Pointer	Clone () const

Public Member Functions inherited from mitk::ImageToImageFilter
	mitkClassMacro (ImageToImageFilter, ImageSource)

Pointer	Clone () const

virtual void	SetInput (const InputImageType *image)
	Set the image input of this process object. More...

virtual void	SetInput (unsigned int idx, const InputImageType *image)
	Set the image input at the specified index. More...

InputImageType *	GetInput (void)
	Get the input image (non-const). More...

InputImageType *	GetInput (unsigned int idx)
	Get the input image at the specified index (non-const). More...

const InputImageType *	GetInput (void) const
	Get the input image (const). More...

const InputImageType *	GetInput (unsigned int idx) const
	Get the input image at the specified index (const). More...

Public Member Functions inherited from mitk::ImageSource
	mitkClassMacro (ImageSource, BaseDataSource)

Pointer	Clone () const

mitkBaseDataSourceGetOutputDeclarations itk::DataObject::Pointer	MakeOutput (DataObjectPointerArraySizeType idx) override
	Get the output data of this image source object. More...

itk::DataObject::Pointer	MakeOutput (const DataObjectIdentifierType &name) override

virtual vtkImageData *	GetVtkImageData ()
	Get the output as VTK image data (non-const version). More...

virtual const vtkImageData *	GetVtkImageData () const
	Get the output as VTK image data (const version). More...

Public Member Functions inherited from mitk::BaseDataSource
	mitkClassMacroItkParent (BaseDataSource, itk::ProcessObject)

OutputType *	GetOutput ()

const OutputType *	GetOutput () const

OutputType *	GetOutput (DataObjectPointerArraySizeType idx)

const OutputType *	GetOutput (DataObjectPointerArraySizeType idx) const

virtual void	GraftOutput (OutputType *output)
	Graft the specified BaseData onto this BaseDataSource's output. More...

virtual void	GraftOutput (const DataObjectIdentifierType &key, OutputType *output)
	Graft the specified base data object onto a named output. More...

virtual void	GraftNthOutput (unsigned int idx, OutputType *output)
	Graft the specified base data object onto this BaseDataSource's idx'th output. More...

bool	Updating () const
	Check whether the pipeline is currently executing. More...

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from mitk::ImageToImageFilter
static Pointer	New ()
	Method for creation through the object factory. More...

Static Public Member Functions inherited from mitk::ImageSource
static Pointer	New ()
	Method for creation through the object factory. More...

Protected Member Functions
	CESTImageNormalizationFilter ()
	Standard constructor. More...

	~CESTImageNormalizationFilter () override
	Standard destructor. More...

void	GenerateOutputInformation () override
	Generate the output information of this filter (e.g. image dimension, image type, etc.). The interface ImageToImageFilter requires this implementation. Everything is taken from the input image. More...

void	GenerateData () override
	Generate the normalized output image. More...

template<typename TPixel , unsigned int VImageDimension>
void	NormalizeTimeSteps (const itk::Image< TPixel, VImageDimension > *image)

Protected Member Functions inherited from mitk::ImageToImageFilter
	ImageToImageFilter ()

	~ImageToImageFilter () override

void	PrintSelf (std::ostream &os, itk::Indent indent) const override
	Print self information to the given stream. More...

void	GenerateInputRequestedRegion () override
	Determine the input requested region to produce the output requested region. More...

Protected Member Functions inherited from mitk::ImageSource
	ImageSource ()

	~ImageSource () override

void	GenerateData () override
	A version of GenerateData() specific for image processing filters. More...

virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, itk::ThreadIdType threadId)
	If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). More...

void	PrepareOutputs () override
	This method is intentionally left blank. More...

virtual void	AllocateOutputs ()
	The GenerateData method normally allocates the buffers for all of the outputs of a filter. More...

virtual void	BeforeThreadedGenerateData ()
	If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can provide an implementation for BeforeThreadedGenerateData(). More...

virtual void	AfterThreadedGenerateData ()
	If an imaging filter needs to perform processing after all processing threads have completed, the filter can provide an implementation for AfterThreadedGenerateData(). More...

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
	Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". More...

Protected Member Functions inherited from mitk::BaseDataSource
	BaseDataSource ()
	Constructor. More...

	~BaseDataSource () override
	Destructor. More...

Protected Attributes
std::string	m_RealOffsets
	Offsets without M0s, space-separated, stored after normalization. More...

std::vector< unsigned int >	m_NonM0Indices
	Indices of non-M0 timesteps in the original input image. More...

Additional Inherited Members
Public Types inherited from mitk::ImageToImageFilter
typedef Superclass::OutputImageRegionType	OutputImageRegionType
	Superclass typedefs. More...

typedef mitk::Image	InputImageType
	Some convenient typedefs. More...

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef SlicedData::RegionType	InputImageRegionType

Public Types inherited from mitk::ImageSource
typedef mitk::Image	OutputImageType
	Some convenient typedefs. More...

typedef OutputImageType	OutputType

typedef OutputImageType::Pointer	OutputImagePointer

typedef SlicedData::RegionType	OutputImageRegionType

Public Types inherited from mitk::BaseDataSource
typedef BaseData	OutputType
	Output data type. More...

typedef itk::DataObject::DataObjectIdentifierType	DataObjectIdentifierType
	Identifier type for named data objects. More...

Static Protected Member Functions inherited from mitk::ImageSource
static itk::ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
	Static function used as a "callback" by the MultiThreader. More...

Static Protected Member Functions inherited from mitk::BaseDataSource
static Pointer	New ()

Detailed Description

Normalization filter for CEST images using M0 reference images.

This filter normalizes CEST images by dividing each voxel value by the corresponding M0 (normalization) reference voxel value. It only works with 4D images and assumes that the input mitk::Image has a property called "CEST.Offsets" (mitk::CEST_PROPERTY_NAME_OFFSETS), with offsets separated by spaces. The number of offsets must match the number of timesteps.

Each timestep with a corresponding offset greater than 299 or less than -299 will be interpreted as a normalization (M0) image. If only one M0 image is present, normalization is done by dividing the voxel value by the corresponding M0 voxel value. If multiple M0 images are present, normalization between any two M0 images is done by dividing by a linear interpolation between them. The M0 images themselves are removed from the result.

The output image will have:

The same 3D geometry as the input image
A time geometry consisting only of non-M0 timesteps
Double pixel type
Updated "CEST.Offsets" property without M0 offset values
Removed DICOM UIDs (series, study, SOP instance)

Precondition: The input image must be a 4D image.; The input image must have a "CEST.Offsets" property with space-separated offset values.; The number of offsets must match the number of timesteps.; At least one offset must be an M0 indicator (absolute value > 299).

See also: CustomTagParser, ExtractCESTOffset, IsNotNormalizedCESTImage, ImageToImageFilter

Definition at line 50 of file mitkCESTImageNormalizationFilter.h.

Constructor & Destructor Documentation

◆ CESTImageNormalizationFilter()

mitk::CESTImageNormalizationFilter::CESTImageNormalizationFilter ( )

protected

Standard constructor.

◆ ~CESTImageNormalizationFilter()

mitk::CESTImageNormalizationFilter::~CESTImageNormalizationFilter ( )

overrideprotected

Standard destructor.

Member Function Documentation

◆ Clone()

Pointer mitk::CESTImageNormalizationFilter::Clone ( ) const

◆ GenerateData()

void mitk::CESTImageNormalizationFilter::GenerateData ( )

overrideprotected

Generate the normalized output image.

Performs the actual M0 normalization across all timesteps. M0 timesteps are identified, linear interpolation weights are computed between adjacent M0 images, and each non-M0 timestep is divided by the interpolated M0 value. The time geometry is updated to exclude M0 timesteps.

Exceptions

mitk::Exception if the input image is not 4D.

◆ GenerateOutputInformation()

void mitk::CESTImageNormalizationFilter::GenerateOutputInformation ( )

overrideprotected

Generate the output information of this filter (e.g. image dimension, image type, etc.). The interface ImageToImageFilter requires this implementation. Everything is taken from the input image.

◆ mitkClassMacro()

mitk::CESTImageNormalizationFilter::mitkClassMacro	(	CESTImageNormalizationFilter	,
		ImageToImageFilter
	)

◆ New()

static Pointer mitk::CESTImageNormalizationFilter::New ( )

static

◆ NormalizeTimeSteps()

template<typename TPixel , unsigned int VImageDimension>

void mitk::CESTImageNormalizationFilter::NormalizeTimeSteps ( const itk::Image< TPixel, VImageDimension > * image )

protected

Internal templated method that normalizes across timesteps.

Template Parameters

TPixel	The pixel type of the input image.
VImageDimension	The dimensionality of the input image (must be 4).

Parameters

[in] image The ITK image to normalize.

Member Data Documentation

◆ m_NonM0Indices

std::vector< unsigned int > mitk::CESTImageNormalizationFilter::m_NonM0Indices

protected

Indices of non-M0 timesteps in the original input image.

Definition at line 95 of file mitkCESTImageNormalizationFilter.h.

◆ m_RealOffsets

std::string mitk::CESTImageNormalizationFilter::m_RealOffsets

protected

Offsets without M0s, space-separated, stored after normalization.

Definition at line 92 of file mitkCESTImageNormalizationFilter.h.

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

mitkCESTImageNormalizationFilter.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CESTImageNormalizationFilter()

◆ ~CESTImageNormalizationFilter()

Member Function Documentation

◆ Clone()

◆ GenerateData()

◆ GenerateOutputInformation()

◆ mitkClassMacro()

◆ New()

◆ NormalizeTimeSteps()

Member Data Documentation

◆ m_NonM0Indices

◆ m_RealOffsets