ANIMA  4.0
Classes | Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Protected Member Functions | List of all members
anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType > Class Template Reference

#include <animaDTIEstimationImageFilter.h>

+ Inheritance diagram for anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >:
+ Collaboration diagram for anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >:

Classes

struct  OptimizationDataStructure
 

Public Types

typedef itk::SmartPointer< const SelfConstPointer
 
typedef OutputImageType DTIImageType
 
typedef itk::Image< InputPixelScalarType, 4 > Image4DType
 
typedef InputImageType::Pointer InputImagePointer
 
typedef Superclass::InputImageRegionType InputImageRegionType
 
typedef itk::Image< InputPixelScalarType, 3 > InputImageType
 
typedef Superclass::MaskImageType MaskImageType
 
typedef itk::Image< OutputPixelScalarType, 3 > OutputB0ImageType
 
typedef OutputImageType::Pointer OutputImagePointer
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef itk::VectorImage< OutputPixelScalarType, 3 > OutputImageType
 
typedef itk::SmartPointer< SelfPointer
 
typedef DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType > Self
 
typedef anima::MaskedImageToImageFilter< InputImageType, OutputImageTypeSuperclass
 
- Public Types inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
typedef itk::SmartPointer< const SelfConstPointer
 
typedef Superclass::InputImageRegionType InputImageRegionType
 
typedef MaskImageType::Pointer MaskImagePointer
 
typedef itk::Image< unsigned char, itk::Image< InputPixelScalarType, 3 > ::ImageDimension > MaskImageType
 
typedef MaskImageType::IndexType MaskIndexType
 
typedef MaskImageType::RegionType MaskRegionType
 
typedef MaskImageType::SizeType MaskSizeType
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef itk::SmartPointer< SelfPointer
 
typedef MaskedImageToImageFilter Self
 
typedef anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > > Superclass
 
typedef itk::ImageSource< itk::VectorImage< OutputPixelScalarType, 3 > >::ThreadStruct ThreadStruct
 
- Public Types inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
typedef itk::SmartPointer< const SelfConstPointer
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef itk::SmartPointer< SelfPointer
 
typedef NumberedThreadImageToImageFilter Self
 
typedef itk::ImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > > Superclass
 
typedef itk::ImageSource< itk::VectorImage< OutputPixelScalarType, 3 > >::ThreadStruct ThreadStruct
 

Public Member Functions

void AddGradientDirection (unsigned int i, vnl_vector_fixed< double, 3 > &grad)
 
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual double GetB0Threshold ()
 
virtual OutputB0ImageTypeGetEstimatedB0Image ()
 
virtual OutputB0ImageTypeGetEstimatedVarianceImage ()
 
virtual const char * GetNameOfClass () const
 
virtual void SetB0Threshold (double _arg)
 
void SetBValuesList (std::vector< double > bValuesList)
 
- Public Member Functions inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual MaskImageTypeGetComputationMask ()
 
virtual void SetComputationMask (MaskImagePointer _arg)
 
- Public Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual OutputImageRegionType GetComputationRegion ()
 
virtual void SetComputationRegion (OutputImageRegionType _arg)
 
virtual void SetNumberOfPointsToProcess (unsigned int _arg)
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
static Pointer New ()
 
- Static Public Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
static Pointer New ()
 

Protected Member Functions

void BeforeThreadedGenerateData () ITK_OVERRIDE
 
void CheckComputationMask () ITK_OVERRIDE
 
double ComputeB0AndVarianceFromTensorVector (const vnl_matrix< double > &tensorValue, const std::vector< double > &dwiSignal, double &outVarianceValue)
 
double ComputeCostAtPosition (const std::vector< double > &x, const std::vector< double > &observedData, std::vector< double > &predictedValues, vnl_matrix< double > &rotationMatrix, vnl_matrix< double > &workTensor, vnl_diag_matrix< double > &workEigenValues)
 
 DTIEstimationImageFilter ()
 
void DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread) ITK_OVERRIDE
 
void GenerateOutputInformation () ITK_OVERRIDE
 
virtual ~DTIEstimationImageFilter ()
 
- Protected Member Functions inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
void InitializeComputationRegionFromMask ()
 
 MaskedImageToImageFilter ()
 
virtual ~MaskedImageToImageFilter ()
 
- Protected Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
virtual void GenerateData () ITK_OVERRIDE
 
unsigned int GetSafeThreadId ()
 
void IncrementNumberOfProcessedPoints ()
 
void InitializeZeroPixel (itk::VectorImage< OutputPixelScalarType, 3 > *image, itk::VariableLengthVector< ScalarRealType > &zeroPixel)
 Utility function to initialize output images pixel to zero for vector images. More...
 
void InitializeZeroPixel (itk::VectorImage< OutputPixelScalarType, 3 > *, PixelType &zeroPixel)
 Utility function to initialize output images pixel to zero for all images except vector images. More...
 
 NumberedThreadImageToImageFilter ()
 
void SafeReleaseThreadId (unsigned int threadId)
 
virtual void ThreadProcessSlices ()
 
virtual ~NumberedThreadImageToImageFilter ()
 

Static Protected Member Functions

static double OptimizationFunction (const std::vector< double > &x, std::vector< double > &grad, void *func_data)
 
- Static Protected Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION ThreaderMultiSplitCallback (void *arg)
 

Additional Inherited Members

- Static Public Attributes inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelScalarType, 3 >, itk::VectorImage< OutputPixelScalarType, 3 > >
static constexpr unsigned int OutputImageDimension
 

Detailed Description

template<class InputPixelScalarType, class OutputPixelScalarType>
class anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >

Definition at line 11 of file animaDTIEstimationImageFilter.h.

Member Typedef Documentation

◆ ConstPointer

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef itk::SmartPointer<const Self> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::ConstPointer

Definition at line 24 of file animaDTIEstimationImageFilter.h.

◆ DTIImageType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef OutputImageType anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DTIImageType

Definition at line 20 of file animaDTIEstimationImageFilter.h.

◆ Image4DType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef itk::Image<InputPixelScalarType,4> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::Image4DType

Definition at line 21 of file animaDTIEstimationImageFilter.h.

◆ InputImagePointer

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef InputImageType::Pointer anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::InputImagePointer

Image typedef support

Definition at line 33 of file animaDTIEstimationImageFilter.h.

◆ InputImageRegionType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef Superclass::InputImageRegionType anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::InputImageRegionType

Definition at line 38 of file animaDTIEstimationImageFilter.h.

◆ InputImageType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef itk::Image<InputPixelScalarType,3> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::InputImageType

Definition at line 17 of file animaDTIEstimationImageFilter.h.

◆ MaskImageType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef Superclass::MaskImageType anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::MaskImageType

Superclass typedefs.

Definition at line 37 of file animaDTIEstimationImageFilter.h.

◆ OutputB0ImageType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef itk::Image<OutputPixelScalarType,3> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::OutputB0ImageType

Definition at line 19 of file animaDTIEstimationImageFilter.h.

◆ OutputImagePointer

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef OutputImageType::Pointer anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::OutputImagePointer

Definition at line 34 of file animaDTIEstimationImageFilter.h.

◆ OutputImageRegionType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef Superclass::OutputImageRegionType anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::OutputImageRegionType

Definition at line 39 of file animaDTIEstimationImageFilter.h.

◆ OutputImageType

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef itk::VectorImage<OutputPixelScalarType,3> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::OutputImageType

Definition at line 18 of file animaDTIEstimationImageFilter.h.

◆ Pointer

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef itk::SmartPointer<Self> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::Pointer

Definition at line 23 of file animaDTIEstimationImageFilter.h.

◆ Self

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef DTIEstimationImageFilter<InputPixelScalarType, OutputPixelScalarType> anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::Self

Standard class typedefs.

Definition at line 16 of file animaDTIEstimationImageFilter.h.

◆ Superclass

template<class InputPixelScalarType , class OutputPixelScalarType >
typedef anima::MaskedImageToImageFilter< InputImageType, OutputImageType > anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::Superclass

Definition at line 22 of file animaDTIEstimationImageFilter.h.

Constructor & Destructor Documentation

◆ DTIEstimationImageFilter()

template<class InputPixelScalarType , class OutputPixelScalarType >
anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DTIEstimationImageFilter ( )
inlineprotected

Definition at line 60 of file animaDTIEstimationImageFilter.h.

◆ ~DTIEstimationImageFilter()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::~DTIEstimationImageFilter ( )
inlineprotectedvirtual

Member Function Documentation

◆ AddGradientDirection()

template<class InputPixelScalarType , class OutputPixelScalarType >
void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::AddGradientDirection ( unsigned int  i,
vnl_vector_fixed< double, 3 > &  grad 
)

◆ BeforeThreadedGenerateData()

template<class InputPixelScalarType , class OutputPixelScalarType >
void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::BeforeThreadedGenerateData ( )
protectedvirtual

◆ CheckComputationMask()

template<class InputPixelScalarType , class OutputPixelScalarType >
void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::CheckComputationMask ( )
protectedvirtual

◆ ComputeB0AndVarianceFromTensorVector()

template<class InputPixelScalarType , class OutputPixelScalarType >
double anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::ComputeB0AndVarianceFromTensorVector ( const vnl_matrix< double > &  tensorValue,
const std::vector< double > &  dwiSignal,
double &  outVarianceValue 
)
protected

◆ ComputeCostAtPosition()

template<class InputPixelScalarType , class OutputPixelScalarType >
double anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::ComputeCostAtPosition ( const std::vector< double > &  x,
const std::vector< double > &  observedData,
std::vector< double > &  predictedValues,
vnl_matrix< double > &  rotationMatrix,
vnl_matrix< double > &  workTensor,
vnl_diag_matrix< double > &  workEigenValues 
)
protected

◆ CreateAnother()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual::itk::LightObject::Pointer anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::CreateAnother ( void  ) const

◆ DynamicThreadedGenerateData()

template<class InputPixelScalarType , class OutputPixelScalarType >
void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DynamicThreadedGenerateData ( const OutputImageRegionType outputRegionForThread)
protected

◆ GenerateOutputInformation()

template<class InputPixelScalarType , class OutputPixelScalarType >
void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::GenerateOutputInformation ( )
protected

◆ GetB0Threshold()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual double anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::GetB0Threshold ( )
virtual

◆ GetEstimatedB0Image()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual OutputB0ImageType* anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::GetEstimatedB0Image ( )
virtual

◆ GetEstimatedVarianceImage()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual OutputB0ImageType* anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::GetEstimatedVarianceImage ( )
virtual

◆ GetNameOfClass()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual const char* anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::GetNameOfClass ( ) const
virtual

◆ New()

template<class InputPixelScalarType , class OutputPixelScalarType >
static Pointer anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::New ( )
static

Method for creation through the object factory.

◆ OptimizationFunction()

template<class InputPixelScalarType , class OutputPixelScalarType >
double anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::OptimizationFunction ( const std::vector< double > &  x,
std::vector< double > &  grad,
void *  func_data 
)
staticprotected

◆ SetB0Threshold()

template<class InputPixelScalarType , class OutputPixelScalarType >
virtual void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::SetB0Threshold ( double  _arg)
virtual

◆ SetBValuesList()

template<class InputPixelScalarType , class OutputPixelScalarType >
void anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::SetBValuesList ( std::vector< double >  bValuesList)
inline

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