Helper class for mitk::Images containing diffusion weighted data. More...

#include <mitkDiffusionPropertyHelper.h>

Collaboration diagram for mitk::DiffusionPropertyHelper:

Public Types
typedef short	DiffusionPixelType

typedef mitk::BValueMapProperty::BValueMap	BValueMapType

typedef GradientDirectionsProperty::GradientDirectionType	GradientDirectionType

typedef GradientDirectionsProperty::GradientDirectionsContainerType	GradientDirectionsContainerType

typedef mitk::MeasurementFrameProperty::MeasurementFrameType	MeasurementFrameType

typedef itk::VectorImage< DiffusionPixelType, 3 >	ImageType

Public Member Functions
	DiffusionPropertyHelper (mitk::Image *inputImage)
	Public constructor, takes a mitk::Image pointer as argument. More...

	~DiffusionPropertyHelper ()

const BValueMapType &	GetBValueMap () const

float	GetReferenceBValue () const

const MeasurementFrameType &	GetMeasurementFrame () const

GradientDirectionsContainerType::Pointer	GetOriginalGradientContainer () const

GradientDirectionsContainerType::Pointer	GetGradientContainer () const

bool	IsDiffusionWeightedImage () const

void	AverageRedundantGradients (double precision)

void	InitializeImage ()
	Make certain the owned image is up to date with all necessary properties. More...

GradientDirectionsContainerType::Pointer	CalcAveragedDirectionSet (double precision, GradientDirectionsContainerType::Pointer directions)

Static Public Member Functions
static bool	IsDiffusionWeightedImage (const mitk::Image *)
	Decide whether a provided image is a valid diffusion weighted image. More...

static bool	IsDiffusionWeightedImage (const mitk::DataNode *node)

static ImageType::Pointer	GetItkVectorImage (Image *image)

static const BValueMapType &	GetBValueMap (const mitk::Image *)
	Convenience method to get the BValueMap. More...

static float	GetReferenceBValue (const mitk::Image *)
	Convenience method to get the BValue. More...

static const MeasurementFrameType &	GetMeasurementFrame (const mitk::Image *)
	Convenience method to get the measurement frame. More...

static GradientDirectionsContainerType::Pointer	GetOriginalGradientContainer (const mitk::Image *)
	Convenience method to get the original gradient directions. More...

static GradientDirectionsContainerType::Pointer	GetGradientContainer (const mitk::Image *)
	Convenience method to get the gradient directions. More...

Static Public Attributes
static const std::string	GRADIENTCONTAINERPROPERTYNAME

static const std::string	ORIGINALGRADIENTCONTAINERPROPERTYNAME

static const std::string	MEASUREMENTFRAMEPROPERTYNAME

static const std::string	REFERENCEBVALUEPROPERTYNAME

static const std::string	BVALUEMAPPROPERTYNAME

static const std::string	MODALITY

Protected Member Functions
	DiffusionPropertyHelper ()

void	ApplyMeasurementFrame ()
	Apply the previouse set MeasurementFrame to all gradients in the GradientsDirectionContainer (m_Directions) More...

void	UpdateBValueMap ()
	Update the BValueMap (m_B_ValueMap) using the current gradient directions (m_Directions) More...

bool	AreAlike (GradientDirectionType g1, GradientDirectionType g2, double precision)
	Determines whether gradients can be considered to be equal. More...

float	GetB_Value (unsigned int i)
	Get the b value belonging to an index. More...

Protected Attributes
mitk::Image *	m_Image

Detailed Description

Helper class for mitk::Images containing diffusion weighted data.

This class takes a pointer to a mitk::Image containing diffusion weighted information and provides functions to manipulate the diffusion meta-data. Will log an error if required information is missing.

Definition at line 37 of file mitkDiffusionPropertyHelper.h.

Member Typedef Documentation

typedef mitk::BValueMapProperty::BValueMap mitk::DiffusionPropertyHelper::BValueMapType

Definition at line 43 of file mitkDiffusionPropertyHelper.h.

typedef short mitk::DiffusionPropertyHelper::DiffusionPixelType

Definition at line 41 of file mitkDiffusionPropertyHelper.h.

typedef GradientDirectionsProperty::GradientDirectionsContainerType mitk::DiffusionPropertyHelper::GradientDirectionsContainerType

Definition at line 45 of file mitkDiffusionPropertyHelper.h.

typedef GradientDirectionsProperty::GradientDirectionType mitk::DiffusionPropertyHelper::GradientDirectionType

Definition at line 44 of file mitkDiffusionPropertyHelper.h.

typedef itk::VectorImage< DiffusionPixelType, 3> mitk::DiffusionPropertyHelper::ImageType

Definition at line 47 of file mitkDiffusionPropertyHelper.h.

typedef mitk::MeasurementFrameProperty::MeasurementFrameType mitk::DiffusionPropertyHelper::MeasurementFrameType

Definition at line 46 of file mitkDiffusionPropertyHelper.h.

Constructor & Destructor Documentation

mitk::DiffusionPropertyHelper::DiffusionPropertyHelper ( mitk::Image * inputImage )

Public constructor, takes a mitk::Image pointer as argument.

Definition at line 34 of file mitkDiffusionPropertyHelper.cpp.

mitk::DiffusionPropertyHelper::~DiffusionPropertyHelper ( )

Definition at line 40 of file mitkDiffusionPropertyHelper.cpp.

mitk::DiffusionPropertyHelper::DiffusionPropertyHelper ( )

protected

Definition at line 30 of file mitkDiffusionPropertyHelper.cpp.

Member Function Documentation

void mitk::DiffusionPropertyHelper::ApplyMeasurementFrame ( )

protected

Apply the previouse set MeasurementFrame to all gradients in the GradientsDirectionContainer (m_Directions)

Warning: first set the MeasurementFrame

Definition at line 185 of file mitkDiffusionPropertyHelper.cpp.

References GRADIENTCONTAINERPROPERTYNAME, mitk::New(), and ORIGINALGRADIENTCONTAINERPROPERTYNAME.

bool mitk::DiffusionPropertyHelper::AreAlike	(	GradientDirectionType	g1,
		GradientDirectionType	g2,
		double	precision
	)

protected

Determines whether gradients can be considered to be equal.

Definition at line 249 of file mitkDiffusionPropertyHelper.cpp.

void mitk::DiffusionPropertyHelper::AverageRedundantGradients ( double precision )

Definition at line 84 of file mitkDiffusionPropertyHelper.cpp.

References mitk::CastToItkImage(), mitk::GradientDirectionsProperty::GetGradientDirectionsContainer(), mitk::GrabItkImageMemory(), GRADIENTCONTAINERPROPERTYNAME, MITK_ERROR, mitk::New(), and ORIGINALGRADIENTCONTAINERPROPERTYNAME.

Referenced by main().

mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::CalcAveragedDirectionSet	(	double	precision,
		GradientDirectionsContainerType::Pointer	directions
	)

Definition at line 53 of file mitkDiffusionPropertyHelper.cpp.

References mitk::New().

float mitk::DiffusionPropertyHelper::GetB_Value ( unsigned int i )

protected

Get the b value belonging to an index.

Definition at line 258 of file mitkDiffusionPropertyHelper.cpp.

References GRADIENTCONTAINERPROPERTYNAME, and REFERENCEBVALUEPROPERTYNAME.

const mitk::DiffusionPropertyHelper::BValueMapType & mitk::DiffusionPropertyHelper::GetBValueMap ( const mitk::Image * image )

static

Convenience method to get the BValueMap.

Definition at line 359 of file mitkDiffusionPropertyHelper.cpp.

References mitk::BaseData::GetProperty().

const mitk::DiffusionPropertyHelper::BValueMapType & mitk::DiffusionPropertyHelper::GetBValueMap ( ) const

Definition at line 398 of file mitkDiffusionPropertyHelper.cpp.

Referenced by mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GetTransformedHeaderInformation(), and main().

mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetGradientContainer ( const mitk::Image * image )

static

Convenience method to get the gradient directions.

Definition at line 388 of file mitkDiffusionPropertyHelper.cpp.

References mitk::BaseData::GetProperty().

mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetGradientContainer ( ) const

Definition at line 418 of file mitkDiffusionPropertyHelper.cpp.

Referenced by mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GenerateData(), mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GetTransformedHeaderInformation(), mitk::TrackingForestHandler< ShOrder, NumberOfSignalFeatures >::InitForTracking(), mitk::DiffusionImageCreationFilter::InternalGetGradientDirections(), KurtosisMapComputation(), main(), mitk::TrackingForestHandler< ShOrder, NumberOfSignalFeatures >::PreprocessInputDataForTraining(), ResampleDWIbySpacing(), mitk::DiffusionImageNiftiWriterService::Write(), and mitk::DiffusionImageNrrdWriterService::Write().

mitk::DiffusionPropertyHelper::ImageType::Pointer mitk::DiffusionPropertyHelper::GetItkVectorImage ( mitk::Image * image )

static

Definition at line 45 of file mitkDiffusionPropertyHelper.cpp.

References mitk::CastToItkImage(), and mitk::New().

Referenced by mitk::TrackingForestHandler< ShOrder, NumberOfSignalFeatures >::InitForTracking(), main(), and mitk::TrackingForestHandler< ShOrder, NumberOfSignalFeatures >::PreprocessInputDataForTraining().

const mitk::DiffusionPropertyHelper::MeasurementFrameType & mitk::DiffusionPropertyHelper::GetMeasurementFrame ( const mitk::Image * image )

static

Convenience method to get the measurement frame.

This method will return the measurement frame of the image.

Note: If the image has no associated measurement frame the identity will be returned.

Definition at line 369 of file mitkDiffusionPropertyHelper.cpp.

References mitk::BaseData::GetProperty(), and mitk::New().

const mitk::DiffusionPropertyHelper::MeasurementFrameType & mitk::DiffusionPropertyHelper::GetMeasurementFrame ( ) const

Definition at line 408 of file mitkDiffusionPropertyHelper.cpp.

Referenced by mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GenerateData(), mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GetTransformedHeaderInformation(), mitk::DiffusionImageCreationFilter::InternalGetMeasurementFrame(), mitk::DiffusionImageNrrdWriterService::Write(), and mitk::DiffusionImageNiftiWriterService::Write().

mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetOriginalGradientContainer ( const mitk::Image * image )

static

Convenience method to get the original gradient directions.

Definition at line 383 of file mitkDiffusionPropertyHelper.cpp.

References mitk::BaseData::GetProperty().

mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetOriginalGradientContainer ( ) const

Definition at line 413 of file mitkDiffusionPropertyHelper.cpp.

float mitk::DiffusionPropertyHelper::GetReferenceBValue ( const mitk::Image * image )

static

Convenience method to get the BValue.

Definition at line 364 of file mitkDiffusionPropertyHelper.cpp.

References mitk::BaseData::GetProperty().

float mitk::DiffusionPropertyHelper::GetReferenceBValue ( ) const

Definition at line 403 of file mitkDiffusionPropertyHelper.cpp.

Referenced by mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GenerateData(), mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GetTransformedHeaderInformation(), mitk::TrackingForestHandler< ShOrder, NumberOfSignalFeatures >::InitForTracking(), mitk::DiffusionImageCreationFilter::InternalGetBValue(), KurtosisMapComputation(), main(), mitk::TrackingForestHandler< ShOrder, NumberOfSignalFeatures >::PreprocessInputDataForTraining(), ResampleDWIbySpacing(), mitk::DiffusionImageNiftiWriterService::Write(), and mitk::DiffusionImageNrrdWriterService::Write().

void mitk::DiffusionPropertyHelper::InitializeImage ( )

Make certain the owned image is up to date with all necessary properties.

This function will generate the B Value map and copy all properties to the owned image.

Definition at line 285 of file mitkDiffusionPropertyHelper.cpp.

References MEASUREMENTFRAMEPROPERTYNAME, and mitk::New().

Referenced by mitk::RegistrationWrapper::ApplyTransformationToImage(), mitk::DiffusionImageTransformedCreationFilter< TTransformType >::GenerateData(), mitk::DWIHeadMotionCorrectionFilter::GenerateData(), mitk::DiffusionDICOMFileReader::LoadSingleOutputImage(), main(), and ResampleDWIbySpacing().

bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage ( const mitk::Image * image )

static

Decide whether a provided image is a valid diffusion weighted image.

An image will be considered a valid diffusion weighted image if the following are true

It has a reference b value
It has a gradient directions property
The number of gradients directions matches the number of components of the image

This does not guarantee that the data is sensible or accurate, it just verfies that it meets the formal requirements to possibly be a valid diffusion weighted image.

Definition at line 311 of file mitkDiffusionPropertyHelper.cpp.

References mitk::PixelType::GetNumberOfComponents(), mitk::Image::GetPixelType(), and mitk::BaseData::GetProperty().

bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage ( const mitk::DataNode * node )

static

Definition at line 301 of file mitkDiffusionPropertyHelper.cpp.

References mitk::DataNode::GetData().

bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage ( ) const

Definition at line 393 of file mitkDiffusionPropertyHelper.cpp.

Referenced by mitk::RegistrationWrapper::ApplyTransformationToImage(), mitk::NodePredicateIsDWI::CheckNode(), mitk::DiffusionImageNiftiWriterService::GetConfidenceLevel(), mitk::DiffusionImageNrrdWriterService::GetConfidenceLevel(), mitk::RegistrationWrapper::GetTransformation(), main(), and mitk::DiffusionImageCreationFilter::SetReferenceImage().

void mitk::DiffusionPropertyHelper::UpdateBValueMap ( )

protected

Update the BValueMap (m_B_ValueMap) using the current gradient directions (m_Directions)

Warning: Have to be called after each manipulation on the GradientDirectionContainer !especially after manipulation of the m_Directions (GetDirections()) container via pointer access!

Definition at line 218 of file mitkDiffusionPropertyHelper.cpp.

References BVALUEMAPPROPERTYNAME, GRADIENTCONTAINERPROPERTYNAME, and mitk::New().