DMRITool  v0.1.1-139-g860d86b4
Diffusion MRI Tool
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage > Class Template Reference

#include <itkDWISingleVoxelGenerator.h>

+ Inheritance diagram for itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >:
+ Collaboration diagram for itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >:

Detailed Description

template<class TOutputImage, class TScalarImage = Image<float,3>>
class itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >

Generate DWI data with the same diffusion parameter set for all voxels. If random mode is used, the diffusion parameters are randomly rotated.

Author
Jian Cheng (jian..nosp@m.chen.nosp@m.g.198.nosp@m.3@gm.nosp@m.ail.c.nosp@m.om)

Definition at line 35 of file itkDWISingleVoxelGenerator.h.

Public Types

typedef Superclass::DiffusionParameterContainerType DiffusionParameterContainerType
 
typedef Superclass::DiffusionParameterValuesType DiffusionParameterValuesType
 
typedef Superclass::MatrixPointer MatrixPointer
 
typedef Superclass::MatrixType MatrixType
 
typedef Superclass::OutputImageDirectionType OutputImageDirectionType
 
typedef Superclass::OutputImageIndexType OutputImageIndexType
 
typedef Superclass::OutputImageInternalPixelType OutputImageInternalPixelType
 
typedef Superclass::OutputImagePixelType OutputImagePixelType
 
typedef Superclass::OutputImagePointer OutputImagePointer
 
typedef Superclass::OutputImagePointType OutputImagePointType
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef Superclass::OutputImageSizeType OutputImageSizeType
 
typedef Superclass::OutputImageSpacingType OutputImageSpacingType
 
typedef Superclass::OutputImageType OutputImageType
 
typedef SmartPointer< SelfPointer
 
typedef Superclass::PrecisionType PrecisionType
 
enum  RandomType {
  FIXED =0,
  UNIFORM
}
 
typedef Superclass::ScalarImagePointer ScalarImagePointer
 
typedef Superclass::ScalarImageType ScalarImageType
 
typedef DWISingleVoxelGenerator Self
 
typedef Superclass::STDVectorPointer STDVectorPointer
 
typedef Superclass::STDVectorType STDVectorType
 
typedef DWIGeneratorBase< TOutputImage, TScalarImage > Superclass
 
- Public Types inherited from itk::DWIGeneratorBase< TOutputImage, TScalarImage >
typedef CylinderModelType::Pointer CylinderModelPointer
 
typedef CylinderModelGenerator< double > CylinderModelType
 
typedef std::vector< DiffusionParameterValuesTypeDiffusionParameterContainerType
 
typedef std::vector< double > DiffusionParameterValuesType
 
typedef utl_shared_ptr< MatrixTypeMatrixPointer
 
typedef utl::NDArray< PrecisionType, 2 > MatrixType
 
enum  ModelType {
  SYMMETRICAL_TENSOR_IN_CARTESIAN_COORDS =0,
  SYMMETRICAL_TENSOR_IN_SPHERICAL_COORDS,
  TENSOR_IN_EULER_ANGLES,
  CYLINDER_SPHERICAL_MODEL
}
 
typedef OutputImageType::DirectionType OutputImageDirectionType
 
typedef OutputImageType::IndexType OutputImageIndexType
 
typedef OutputImageType::InternalPixelType OutputImageInternalPixelType
 
typedef OutputImageType::PixelType OutputImagePixelType
 
typedef OutputImageType::Pointer OutputImagePointer
 
typedef OutputImageType::PointType OutputImagePointType
 
typedef OutputImageType::RegionType OutputImageRegionType
 
typedef OutputImageType::SizeType OutputImageSizeType
 
typedef OutputImageType::SpacingType OutputImageSpacingType
 
typedef TOutputImage OutputImageType
 
typedef SmartPointer< SelfPointer
 
typedef double PrecisionType
 
typedef SamplingSchemeQSpaceType::Pointer SamplingSchemeQSpacePointer
 
typedef SamplingSchemeQSpace< double > SamplingSchemeQSpaceType
 
typedef SamplingSchemeRSpaceType::Pointer SamplingSchemeRSpacePointer
 
typedef SamplingScheme3D< double > SamplingSchemeRSpaceType
 
typedef ScalarImageType::Pointer ScalarImagePointer
 
typedef TScalarImage ScalarImageType
 
typedef DWIGeneratorBase Self
 
typedef utl_shared_ptr< STDVectorTypeSTDVectorPointer
 
typedef std::vector< PrecisionTypeSTDVectorType
 
typedef ImageSource< TOutputImage > Superclass
 
typedef utl::NDArray< PrecisionType, 1 > VectorType
 

Public Member Functions

virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual DiffusionParameterValuesType GetDiffusionParameterValues ()
 
virtual const char * GetNameOfClass () const
 
virtual RandomType GetRandomType ()
 
virtual MatrixPointer GetStoredOrientationMatrix ()
 
virtual void SetDiffusionParameterValues (DiffusionParameterValuesType _arg)
 
virtual void SetRandomType (RandomType _arg)
 
virtual void SetStoredOrientationMatrix (MatrixPointer _arg)
 
void SetUniformFromElectrostaticEnergy (const int num)
 
void SetUniformFromTessellation (const int num)
 
- Public Member Functions inherited from itk::DWIGeneratorBase< TOutputImage, TScalarImage >
ScalarImageTypeGetB0Image ()
 
virtual double GetB0Scale ()
 
OutputImageTypeGetDWIImage ()
 
OutputImageTypeGetEAPImage ()
 
virtual int GetMaxNumberOfPeaks ()
 
virtual ModelType GetModelType () const
 
ScalarImageTypeGetMSDImage ()
 
virtual double GetNoiseSigma ()
 
unsigned int GetNumberOfQSpaceSamples () const
 
unsigned int GetNumberOfRSpaceSamples () const
 
OutputImageTypeGetODFImage ()
 
virtual unsigned int GetODFOrder ()
 
virtual OutputImageSizeType GetOutputSize ()
 
OutputImageTypeGetPeakImage ()
 
virtual PeakType GetPeakType ()
 
ScalarImageTypeGetRTOImage ()
 
virtual double GetSNR ()
 
 itkGetObjectMacro (SamplingSchemeQSpace, SamplingSchemeQSpaceType)
 
 itkGetObjectMacro (SamplingSchemeRSpace, SamplingSchemeRSpaceType)
 
 itkGetObjectMacro (CylinderModel, CylinderModelType)
 
 itkSetGetBooleanMacro (IsOutputDWI)
 
 itkSetGetBooleanMacro (IsOutputEAP)
 
 itkSetGetBooleanMacro (IsOutputODF)
 
 itkSetGetBooleanMacro (IsOutputRTO)
 
 itkSetGetBooleanMacro (IsOutputMSD)
 
virtual void SetB0Scale (double _arg)
 
virtual void SetCylinderModel (CylinderModelType *_arg)
 
virtual void SetMaxNumberOfPeaks (int _arg)
 
virtual void SetModelType (const ModelType _arg)
 
virtual void SetNoiseSigma (double _arg)
 
virtual void SetODFOrder (unsigned int _arg)
 
virtual void SetOutputSize (OutputImageSizeType _arg)
 
virtual void SetPeakType (PeakType _arg)
 
virtual void SetSamplingSchemeQSpace (SamplingSchemeQSpaceType *_arg)
 
virtual void SetSamplingSchemeRSpace (SamplingSchemeRSpaceType *_arg)
 
virtual void SetSNR (double _arg)
 

Static Public Member Functions

static Pointer New ()
 

Static Public Attributes

static const unsigned int OutputImageDimension = OutputImageType::ImageDimension
 
- Static Public Attributes inherited from itk::DWIGeneratorBase< TOutputImage, TScalarImage >
static const unsigned int OutputImageDimension = OutputImageType::ImageDimension
 

Protected Member Functions

 DWISingleVoxelGenerator ()
 
void GenerateData ()
 
void Initialization ()
 
LightObject::Pointer InternalClone () const
 
void PrintSelf (std::ostream &os, Indent indent) const
 
 ~DWISingleVoxelGenerator ()
 
- Protected Member Functions inherited from itk::DWIGeneratorBase< TOutputImage, TScalarImage >
virtual void AllocateOutputs () ITK_OVERRIDE
 
 DWIGeneratorBase ()
 
LightObject::Pointer InternalClone () const ITK_OVERRIDE
 
void PrintSelf (std::ostream &os, Indent indent) const ITK_OVERRIDE
 
 ~DWIGeneratorBase ()
 

Protected Attributes

DiffusionParameterValuesType m_DiffusionParameterValues
 
RandomType m_RandomType
 
MatrixPointer m_StoredOrientationMatrix
 
- Protected Attributes inherited from itk::DWIGeneratorBase< TOutputImage, TScalarImage >
double m_B0Scale
 
CylinderModelPointer m_CylinderModel
 
bool m_IsOutputDWI
 
bool m_IsOutputEAP
 
bool m_IsOutputMSD
 
bool m_IsOutputODF
 
bool m_IsOutputRTO
 
int m_MaxNumberOfPeaks
 
ModelType m_ModelType
 
double m_NoiseSigma
 
unsigned int m_ODFOrder
 
OutputImageDirectionType m_OutputDirection
 
OutputImagePointType m_OutputOrigin
 
OutputImageSizeType m_OutputSize
 
OutputImageSpacingType m_OutputSpacing
 
PeakType m_PeakType
 
SamplingSchemeQSpacePointer m_SamplingSchemeQSpace
 
SamplingSchemeRSpacePointer m_SamplingSchemeRSpace
 
double m_SNR
 

Private Member Functions

 DWISingleVoxelGenerator (const Self &)
 
void operator= (const Self &)
 

Member Typedef Documentation

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::DiffusionParameterContainerType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::DiffusionParameterContainerType

Definition at line 77 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::DiffusionParameterValuesType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::DiffusionParameterValuesType

Some convenient typedefs for diffusion parameters.

Definition at line 76 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::MatrixPointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::MatrixPointer

Definition at line 71 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::MatrixType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::MatrixType

Definition at line 70 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageDirectionType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageDirectionType

Definition at line 56 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageIndexType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageIndexType

Definition at line 54 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageInternalPixelType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageInternalPixelType

Definition at line 59 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImagePixelType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImagePixelType

Definition at line 58 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImagePointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImagePointer

Definition at line 51 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImagePointType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImagePointType

Definition at line 55 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageRegionType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageRegionType

Definition at line 57 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageSizeType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageSizeType

Definition at line 52 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageSpacingType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageSpacingType

Definition at line 53 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::OutputImageType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageType

Some convenient typedefs.

Definition at line 47 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef SmartPointer<Self> itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::Pointer

Definition at line 41 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::PrecisionType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::PrecisionType

Orientation Matrice Type

Definition at line 69 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::ScalarImagePointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::ScalarImagePointer

Definition at line 66 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::ScalarImageType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::ScalarImageType

B0 Image

Definition at line 65 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef DWISingleVoxelGenerator itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::Self

Standard class typedefs.

Definition at line 39 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::STDVectorPointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::STDVectorPointer

Definition at line 73 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef Superclass::STDVectorType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::STDVectorType

Definition at line 72 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
typedef DWIGeneratorBase<TOutputImage, TScalarImage> itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::Superclass

Definition at line 40 of file itkDWISingleVoxelGenerator.h.

Member Enumeration Documentation

template<class TOutputImage , class TScalarImage = Image<float,3>>
enum itk::DWISingleVoxelGenerator::RandomType
Parameters
FIXEDfixed fiber configuration for all voxels.
UNIFORMIf m_StoredOrientationMatrix is not set, then rotate the fiber configruation using a uniformly random rotation matrix. Otherwise, rotate the fiber configruation using the stored m_StoredOrientationMatrix, and m_OutputSize is overridden by the number of stored orienrations.
GAUSSIANrotate the fiber configruation using a random rotation matrix generated by a Riemannian Gaussian distribution.
Enumerator
FIXED 
UNIFORM 

Definition at line 84 of file itkDWISingleVoxelGenerator.h.

Constructor & Destructor Documentation

template<class TOutputImage , class TScalarImage >
itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::DWISingleVoxelGenerator ( )
protected

Definition at line 30 of file itkDWISingleVoxelGenerator.hxx.

References itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::PrintSelf().

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template<class TOutputImage , class TScalarImage = Image<float,3>>
itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::~DWISingleVoxelGenerator ( )
inlineprotected

Definition at line 115 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::DWISingleVoxelGenerator ( const Self )
private

Member Function Documentation

template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual::itk::LightObject::Pointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::CreateAnother ( void  ) const
template<class TOutputImage , class TScalarImage >
void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::GenerateData ( void  )
protectedvirtual
template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual DiffusionParameterValuesType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::GetDiffusionParameterValues ( )
virtual
template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual const char* itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::DWIGeneratorBase< TOutputImage, TScalarImage >.

template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual RandomType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::GetRandomType ( )
virtual
template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual MatrixPointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::GetStoredOrientationMatrix ( )
virtual
template<class TOutputImage , class TScalarImage >
void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::Initialization ( )
protectedvirtual

initialization, test

Reimplemented from itk::DWIGeneratorBase< TOutputImage, TScalarImage >.

Definition at line 68 of file itkDWISingleVoxelGenerator.hxx.

References itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::GenerateData().

Referenced by itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::InternalClone().

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template<class TOutputImage , class TScalarImage >
LightObject::Pointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::InternalClone ( ) const
protected

Definition at line 50 of file itkDWISingleVoxelGenerator.hxx.

References itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::Initialization().

Referenced by itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::PrintSelf().

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template<class TOutputImage , class TScalarImage = Image<float,3>>
static Pointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::New ( )
static

Method for creation through the object factory.

template<class TOutputImage , class TScalarImage = Image<float,3>>
void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::operator= ( const Self )
private
template<class TOutputImage , class TScalarImage >
void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
protected

Definition at line 39 of file itkDWISingleVoxelGenerator.hxx.

References itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::InternalClone(), utl::PrintUtlMatrix(), and PrintVar1.

Referenced by itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::DWISingleVoxelGenerator().

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template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::SetDiffusionParameterValues ( DiffusionParameterValuesType  _arg)
virtual

diffusion parameters for all voxels

template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::SetRandomType ( RandomType  _arg)
virtual
template<class TOutputImage , class TScalarImage = Image<float,3>>
virtual void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::SetStoredOrientationMatrix ( MatrixPointer  _arg)
virtual
template<class TOutputImage , class TScalarImage = Image<float,3>>
void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::SetUniformFromElectrostaticEnergy ( const int  num)
inline
template<class TOutputImage , class TScalarImage = Image<float,3>>
void itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::SetUniformFromTessellation ( const int  num)
inline

Member Data Documentation

template<class TOutputImage , class TScalarImage = Image<float,3>>
DiffusionParameterValuesType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::m_DiffusionParameterValues
protected

Definition at line 125 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
RandomType itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::m_RandomType
protected

Definition at line 127 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
MatrixPointer itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::m_StoredOrientationMatrix
protected

Definition at line 129 of file itkDWISingleVoxelGenerator.h.

template<class TOutputImage , class TScalarImage = Image<float,3>>
const unsigned int itk::DWISingleVoxelGenerator< TOutputImage, TScalarImage >::OutputImageDimension = OutputImageType::ImageDimension
static

Output image dimension

Definition at line 62 of file itkDWISingleVoxelGenerator.h.


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