ANIMA  4.0
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | List of all members
anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType > Class Template Reference

#include <animaMCMEstimatorImageFilter.h>

+ Inheritance diagram for anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >:
+ Collaboration diagram for anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >:

Public Types

typedef anima::BaseCompartment BaseCompartmentType
 
typedef anima::MultiCompartmentModelCreator::CompartmentType CompartmentType
 
typedef itk::SmartPointer< const Self > ConstPointer
 
typedef CostFunctionBaseType::Pointer CostFunctionBasePointer
 
typedef itk::CostFunction CostFunctionBaseType
 
typedef vnl_vector_fixed< double, 3 > GradientType
 
typedef itk::Image< InputPixelType, 4 > Image4DType
 
typedef InputImageType::Pointer InputImagePointer
 
typedef Superclass::InputImageRegionType InputImageRegionType
 
typedef TInputImage InputImageType
 
typedef Superclass::MaskImageType MaskImageType
 
enum  MaximumLikelihoodEstimationMode {
  Marginal = 0,
  Profile,
  VariableProjection
}
 
typedef anima::MultiCompartmentModelCreator MCMCreatorType
 
typedef MCMCreatorType::MCMPointer MCMPointer
 
typedef MCMCreatorType::MCMType MCMType
 
typedef MCMType::ListType MCMVectorType
 
typedef anima::MCMImage< OutputPixelType, 3 > ModelImageType
 
typedef MoseImageType::Pointer MoseImagePointer
 
typedef itk::Image< unsigned char, 3 > MoseImageType
 
typedef OptimizerType::Pointer OptimizerPointer
 
typedef itk::NonLinearOptimizer OptimizerType
 
typedef OutputImageType::Pointer OutputImagePointer
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef TOutputImage OutputImageType
 
typedef OutputScalarImageType::Pointer OutputScalarImagePointer
 
typedef itk::Image< OutputPixelType, 3 > OutputScalarImageType
 
typedef OptimizerType::ParametersType ParametersType
 
typedef itk::SmartPointer< Self > Pointer
 
typedef MCMEstimatorImageFilter< InputPixelType, OutputPixelType > Self
 
enum  SignalNoiseType {
  Gaussian = 0,
  NCC
}
 Denotes noise type on input signal. Based on this, a different cost function should be created. More...
 
typedef anima::MaskedImageToImageFilter< TInputImage, TOutputImage > Superclass
 
typedef itk::Image< InputPixelType, 3 > TInputImage
 
typedef anima::MCMImage< OutputPixelType, 3 > TOutputImage
 
typedef OutputImageType::PixelType VariableLengthVectorType
 
typedef VectorImageType::Pointer VectorImagePointer
 
typedef itk::VectorImage< OutputPixelType, 3 > VectorImageType
 
- Public Types inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
typedef itk::SmartPointer< const Self > ConstPointer
 
typedef Superclass::InputImageRegionType InputImageRegionType
 
typedef MaskImageType::Pointer MaskImagePointer
 
typedef itk::Image< unsigned char, itk::Image< InputPixelType, 3 > ::ImageDimension > MaskImageType
 
typedef MaskImageType::IndexType MaskIndexType
 
typedef MaskImageType::RegionType MaskRegionType
 
typedef MaskImageType::SizeType MaskSizeType
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef itk::SmartPointer< Self > Pointer
 
typedef MaskedImageToImageFilter Self
 
typedef anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > > Superclass
 
typedef itk::ImageSource< anima::MCMImage< OutputPixelType, 3 > >::ThreadStruct ThreadStruct
 
- Public Types inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
typedef itk::SmartPointer< const Self > ConstPointer
 
typedef Superclass::OutputImageRegionType OutputImageRegionType
 
typedef itk::SmartPointer< Self > Pointer
 
typedef NumberedThreadImageToImageFilter Self
 
typedef itk::ImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > > Superclass
 
typedef itk::ImageSource< anima::MCMImage< OutputPixelType, 3 > >::ThreadStruct ThreadStruct
 

Public Member Functions

void AddGradientDirection (unsigned int i, GradientType &grad)
 
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
OutputScalarImageType * GetAICcVolume ()
 
OutputScalarImageType * GetB0Volume ()
 
virtual double GetBigDelta ()
 
std::vector< GradientType > & GetGradientDirections ()
 
std::vector< double > & GetGradientStrengths ()
 
MCMCreatorType * GetMCMCreator (unsigned int i)
 
virtual MaximumLikelihoodEstimationMode GetMLEstimationStrategy ()
 
MoseImageType * GetMoseVolume ()
 
virtual const char * GetNameOfClass () const
 
virtual MCMCreatorType * GetNewMCMCreatorInstance ()
 
virtual SignalNoiseType GetNoiseType ()
 
virtual unsigned int GetNumberOfCoils ()
 
std::string GetOptimizer ()
 
OutputScalarImageType * GetSigmaSquareVolume ()
 
virtual double GetSmallDelta ()
 
virtual void SetAbsoluteCostChange (double _arg)
 
virtual void SetAxialDiffusivityValue (double _arg)
 
virtual void SetB0Threshold (double _arg)
 
virtual void SetBigDelta (double _arg)
 
virtual void SetCompartmentType (CompartmentType _arg)
 
virtual void SetFindOptimalNumberOfCompartments (bool _arg)
 
virtual void SetFTolerance (double _arg)
 
void SetGradientStrengths (std::vector< double > &mb)
 
virtual void SetIRWDiffusivityValue (double _arg)
 
virtual void SetMaxEval (unsigned int _arg)
 
virtual void SetMLEstimationStrategy (MaximumLikelihoodEstimationMode _arg)
 
virtual void SetModelWithFreeWaterComponent (bool _arg)
 
virtual void SetModelWithRestrictedWaterComponent (bool _arg)
 
virtual void SetModelWithStaniszComponent (bool _arg)
 
virtual void SetModelWithStationaryWaterComponent (bool _arg)
 
void SetMoseVolume (MoseImageType *img)
 
virtual void SetNoiseType (SignalNoiseType _arg)
 
virtual void SetNumberOfCoils (unsigned int _arg)
 
virtual void SetNumberOfCompartments (unsigned int _arg)
 
void SetOptimizer (std::string &opt)
 
virtual void SetRadialDiffusivity1Value (double _arg)
 
virtual void SetRadialDiffusivity2Value (double _arg)
 
virtual void SetSmallDelta (double _arg)
 
virtual void SetStaniszDiffusivityValue (double _arg)
 
virtual void SetUseCommonConcentrations (bool _arg)
 
virtual void SetUseCommonDiffusivities (bool _arg)
 
virtual void SetUseCommonExtraAxonalFractions (bool _arg)
 
virtual void SetUseConstrainedDiffusivity (bool _arg)
 
virtual void SetUseConstrainedExtraAxonalFraction (bool _arg)
 
virtual void SetUseConstrainedFreeWaterDiffusivity (bool _arg)
 
virtual void SetUseConstrainedIRWDiffusivity (bool _arg)
 
virtual void SetUseConstrainedOrientationConcentration (bool _arg)
 
virtual void SetUseConstrainedStaniszDiffusivity (bool _arg)
 
virtual void SetUseConstrainedStaniszRadius (bool _arg)
 
virtual void SetXTolerance (double _arg)
 
void WriteMCMOutput (std::string fileName)
 
- Public Member Functions inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
virtual MaskImageType * GetComputationMask ()
 
virtual void SetComputationMask (MaskImagePointer _arg)
 
- Public Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 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< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
static Pointer New ()
 
- Static Public Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
static Pointer New ()
 

Protected Member Functions

virtual void BeforeThreadedGenerateData () ITK_OVERRIDE
 
void CheckComputationMask () ITK_OVERRIDE
 
double ComputeAICcValue (MCMPointer &mcmValue, double costValue)
 Compute AICc value from a cost function value and model. More...
 
void ComputeExtraAxonalAndKappaCoarseGrids ()
 Computes extra axonal and kappa coarse grids (used for NODDI and DDI initialization) More...
 
void ComputeTensorRadialDiffsAndAzimuthCoarseGrids ()
 Computes extra axonal and kappa coarse grids (used for tensor final initaialization) More...
 
virtual CostFunctionBasePointer CreateCostFunction (std::vector< double > &observedSignals, MCMPointer &mcmModel)
 Create a cost function following the noise type and estimation mode. More...
 
OptimizerPointer CreateOptimizer (CostFunctionBasePointer &cost, itk::Array< double > &lowerBounds, itk::Array< double > &upperBounds)
 Create an optimizer following the optimizer type and estimation mode. More...
 
void DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread) ITK_OVERRIDE
 
void EstimateFreeWaterModel (MCMPointer &mcmValue, std::vector< double > &observedSignals, itk::ThreadIdType threadId, double &aiccValue, double &b0Value, double &sigmaSqValue)
 Specific method for N=0 compartments estimation (only free water) More...
 
void ExtraAxonalAndKappaCoarseGridInitialization (MCMPointer &mcmUpdateValue, CostFunctionBasePointer &cost, MCMType::ListType &workVec, ParametersType &p)
 Coarse grid initialization of NODDI and DDI models. More...
 
void GenerateOutputInformation () ITK_OVERRIDE
 
double GetCostValue (CostFunctionBasePointer &cost, ParametersType &p)
 Utility function to get a value from a cost function. More...
 
void GetProfiledInformation (CostFunctionBasePointer &cost, MCMPointer &mcm, double &b0Value, double &sigmaSqValue)
 Utility function to get profiled data from the cost function into an MCM model. More...
 
virtual void InitializeModelFromSimplifiedOne (MCMPointer &simplifiedModel, MCMPointer &complexModel)
 Performs initialization from simplified model with the same number of compartments. More...
 
void InitialOrientationsEstimation (MCMPointer &mcmValue, bool authorizedNegativeB0Value, unsigned int currentNumberOfCompartments, std::vector< double > &observedSignals, itk::ThreadIdType threadId, double &aiccValue, double &b0Value, double &sigmaSqValue)
 Doing estimation only of multiple orientations. More...
 
 MCMEstimatorImageFilter ()
 
void ModelEstimation (MCMPointer &mcmValue, bool authorizedNegativeB0Value, std::vector< double > &observedSignals, itk::ThreadIdType threadId, double &aiccValue, double &b0Value, double &sigmaSqValue)
 Doing estimation, calling initialization procedure until ball and zeppelin, returns AICc value. More...
 
void OptimizeNonIsotropicCompartments (MCMPointer &mcmValue, unsigned int currentNumberOfCompartments, std::vector< double > &observedSignals, itk::ThreadIdType threadId, double &aiccValue, double &b0Value, double &sigmaSqValue)
 Doing estimation of non isotropic compartments (for a given number of anisotropic compartments) More...
 
double PerformSingleOptimization (ParametersType &p, CostFunctionBasePointer &cost, itk::Array< double > &lowerBounds, itk::Array< double > &upperBounds)
 Performs an optimization of the supplied cost function and parameters using the specified optimizer(s). Returns the optimized parameters. More...
 
virtual void SparseInitializeSticks (MCMPointer &complexModel, bool authorizeNegativeB0Value, std::vector< double > &observedSignals, itk::ThreadIdType threadId)
 Performs initialization from single DTI. More...
 
void TensorCoarseGridInitialization (MCMPointer &mcmUpdateValue, CostFunctionBasePointer &cost, MCMType::ListType &workVec, ParametersType &p)
 Coarse grid initialization of tensor model. More...
 
virtual ~MCMEstimatorImageFilter ()
 
- Protected Member Functions inherited from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
void InitializeComputationRegionFromMask ()
 
 MaskedImageToImageFilter ()
 
virtual ~MaskedImageToImageFilter ()
 
- Protected Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
virtual void GenerateData () ITK_OVERRIDE
 
unsigned int GetSafeThreadId ()
 
void IncrementNumberOfProcessedPoints ()
 
void InitializeZeroPixel (anima::MCMImage< OutputPixelType, 3 > *image, itk::VariableLengthVector< ScalarRealType > &zeroPixel)
 Utility function to initialize output images pixel to zero for vector images. More...
 
void InitializeZeroPixel (anima::MCMImage< OutputPixelType, 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 ()
 

Additional Inherited Members

- Static Public Attributes inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
static constexpr unsigned int OutputImageDimension
 
- Static Protected Member Functions inherited from anima::NumberedThreadImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >
static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION ThreaderMultiSplitCallback (void *arg)
 

Detailed Description

template<class InputPixelType, class OutputPixelType>
class anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >

Definition at line 21 of file animaMCMEstimatorImageFilter.h.

Member Typedef Documentation

◆ BaseCompartmentType

template<class InputPixelType, class OutputPixelType>
typedef anima::BaseCompartment anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BaseCompartmentType

Definition at line 45 of file animaMCMEstimatorImageFilter.h.

◆ CompartmentType

template<class InputPixelType, class OutputPixelType>
typedef anima::MultiCompartmentModelCreator::CompartmentType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CompartmentType

Definition at line 44 of file animaMCMEstimatorImageFilter.h.

◆ ConstPointer

template<class InputPixelType, class OutputPixelType>
typedef itk::SmartPointer<const Self> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ConstPointer

Definition at line 35 of file animaMCMEstimatorImageFilter.h.

◆ CostFunctionBasePointer

template<class InputPixelType, class OutputPixelType>
typedef CostFunctionBaseType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CostFunctionBasePointer

Definition at line 54 of file animaMCMEstimatorImageFilter.h.

◆ CostFunctionBaseType

template<class InputPixelType, class OutputPixelType>
typedef itk::CostFunction anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CostFunctionBaseType

Definition at line 53 of file animaMCMEstimatorImageFilter.h.

◆ GradientType

template<class InputPixelType, class OutputPixelType>
typedef vnl_vector_fixed<double,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GradientType

Definition at line 88 of file animaMCMEstimatorImageFilter.h.

◆ Image4DType

template<class InputPixelType, class OutputPixelType>
typedef itk::Image<InputPixelType,4> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Image4DType

Definition at line 29 of file animaMCMEstimatorImageFilter.h.

◆ InputImagePointer

template<class InputPixelType, class OutputPixelType>
typedef InputImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InputImagePointer

Definition at line 79 of file animaMCMEstimatorImageFilter.h.

◆ InputImageRegionType

template<class InputPixelType, class OutputPixelType>
typedef Superclass::InputImageRegionType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InputImageRegionType

Definition at line 85 of file animaMCMEstimatorImageFilter.h.

◆ InputImageType

template<class InputPixelType, class OutputPixelType>
typedef TInputImage anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InputImageType

Image typedef support

Definition at line 77 of file animaMCMEstimatorImageFilter.h.

◆ MaskImageType

template<class InputPixelType, class OutputPixelType>
typedef Superclass::MaskImageType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MaskImageType

Superclass typedefs.

Definition at line 84 of file animaMCMEstimatorImageFilter.h.

◆ MCMCreatorType

template<class InputPixelType, class OutputPixelType>
typedef anima::MultiCompartmentModelCreator anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMCreatorType

Definition at line 43 of file animaMCMEstimatorImageFilter.h.

◆ MCMPointer

template<class InputPixelType, class OutputPixelType>
typedef MCMCreatorType::MCMPointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMPointer

Definition at line 47 of file animaMCMEstimatorImageFilter.h.

◆ MCMType

template<class InputPixelType, class OutputPixelType>
typedef MCMCreatorType::MCMType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMType

Definition at line 46 of file animaMCMEstimatorImageFilter.h.

◆ MCMVectorType

template<class InputPixelType, class OutputPixelType>
typedef MCMType::ListType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMVectorType

Definition at line 48 of file animaMCMEstimatorImageFilter.h.

◆ ModelImageType

template<class InputPixelType, class OutputPixelType>
typedef anima::MCMImage<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ModelImageType

Definition at line 28 of file animaMCMEstimatorImageFilter.h.

◆ MoseImagePointer

template<class InputPixelType, class OutputPixelType>
typedef MoseImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MoseImagePointer

Definition at line 38 of file animaMCMEstimatorImageFilter.h.

◆ MoseImageType

template<class InputPixelType, class OutputPixelType>
typedef itk::Image<unsigned char,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MoseImageType

Definition at line 37 of file animaMCMEstimatorImageFilter.h.

◆ OptimizerPointer

template<class InputPixelType, class OutputPixelType>
typedef OptimizerType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizerPointer

Definition at line 51 of file animaMCMEstimatorImageFilter.h.

◆ OptimizerType

template<class InputPixelType, class OutputPixelType>
typedef itk::NonLinearOptimizer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizerType

Definition at line 50 of file animaMCMEstimatorImageFilter.h.

◆ OutputImagePointer

template<class InputPixelType, class OutputPixelType>
typedef OutputImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputImagePointer

Definition at line 81 of file animaMCMEstimatorImageFilter.h.

◆ OutputImageRegionType

template<class InputPixelType, class OutputPixelType>
typedef Superclass::OutputImageRegionType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputImageRegionType

Definition at line 86 of file animaMCMEstimatorImageFilter.h.

◆ OutputImageType

template<class InputPixelType, class OutputPixelType>
typedef TOutputImage anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputImageType

Definition at line 78 of file animaMCMEstimatorImageFilter.h.

◆ OutputScalarImagePointer

template<class InputPixelType, class OutputPixelType>
typedef OutputScalarImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputScalarImagePointer

Definition at line 32 of file animaMCMEstimatorImageFilter.h.

◆ OutputScalarImageType

template<class InputPixelType, class OutputPixelType>
typedef itk::Image<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputScalarImageType

Definition at line 31 of file animaMCMEstimatorImageFilter.h.

◆ ParametersType

template<class InputPixelType, class OutputPixelType>
typedef OptimizerType::ParametersType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ParametersType

Definition at line 52 of file animaMCMEstimatorImageFilter.h.

◆ Pointer

template<class InputPixelType, class OutputPixelType>
typedef itk::SmartPointer<Self> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Pointer

Definition at line 34 of file animaMCMEstimatorImageFilter.h.

◆ Self

template<class InputPixelType, class OutputPixelType>
typedef MCMEstimatorImageFilter<InputPixelType, OutputPixelType> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Self

Standard class typedefs.

Definition at line 26 of file animaMCMEstimatorImageFilter.h.

◆ Superclass

template<class InputPixelType, class OutputPixelType>
typedef anima::MaskedImageToImageFilter< TInputImage, TOutputImage > anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Superclass

Definition at line 33 of file animaMCMEstimatorImageFilter.h.

◆ TInputImage

template<class InputPixelType, class OutputPixelType>
typedef itk::Image<InputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TInputImage

Definition at line 27 of file animaMCMEstimatorImageFilter.h.

◆ TOutputImage

template<class InputPixelType, class OutputPixelType>
typedef anima::MCMImage<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TOutputImage

Definition at line 30 of file animaMCMEstimatorImageFilter.h.

◆ VariableLengthVectorType

template<class InputPixelType, class OutputPixelType>
typedef OutputImageType::PixelType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::VariableLengthVectorType

Definition at line 80 of file animaMCMEstimatorImageFilter.h.

◆ VectorImagePointer

template<class InputPixelType, class OutputPixelType>
typedef VectorImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::VectorImagePointer

Definition at line 41 of file animaMCMEstimatorImageFilter.h.

◆ VectorImageType

template<class InputPixelType, class OutputPixelType>
typedef itk::VectorImage<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::VectorImageType

Definition at line 40 of file animaMCMEstimatorImageFilter.h.

Member Enumeration Documentation

◆ MaximumLikelihoodEstimationMode

template<class InputPixelType, class OutputPixelType>
enum anima::MCMEstimatorImageFilter::MaximumLikelihoodEstimationMode
Enumerator
Marginal 
Profile 
VariableProjection 

Definition at line 63 of file animaMCMEstimatorImageFilter.h.

◆ SignalNoiseType

template<class InputPixelType, class OutputPixelType>
enum anima::MCMEstimatorImageFilter::SignalNoiseType

Denotes noise type on input signal. Based on this, a different cost function should be created.

Enumerator
Gaussian 
NCC 

Definition at line 57 of file animaMCMEstimatorImageFilter.h.

Constructor & Destructor Documentation

◆ MCMEstimatorImageFilter()

template<class InputPixelType, class OutputPixelType>
anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMEstimatorImageFilter ( )
inlineprotected

Definition at line 163 of file animaMCMEstimatorImageFilter.h.

References anima::DiffusionBigDelta, anima::DiffusionSmallDelta, anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Gaussian, anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Marginal, and anima::Tensor.

◆ ~MCMEstimatorImageFilter()

template<class InputPixelType, class OutputPixelType>
virtual anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter ( )
inlineprotectedvirtual

Definition at line 220 of file animaMCMEstimatorImageFilter.h.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CheckComputationMask(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeAICcValue(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeExtraAxonalAndKappaCoarseGrids(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeTensorRadialDiffsAndAzimuthCoarseGrids(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateCostFunction(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateOptimizer(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::DynamicThreadedGenerateData(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::EstimateFreeWaterModel(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ExtraAxonalAndKappaCoarseGridInitialization(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GenerateOutputInformation(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetCostValue(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetProfiledInformation(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitializeModelFromSimplifiedOne(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitialOrientationsEstimation(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ModelEstimation(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizeNonIsotropicCompartments(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::PerformSingleOptimization(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TensorCoarseGridInitialization().

Member Function Documentation

◆ AddGradientDirection()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::AddGradientDirection ( unsigned int  i,
GradientType &  grad 
)

Definition at line 33 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNewMCMCreatorInstance().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetGradientStrengths().

◆ BeforeThreadedGenerateData()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData ( )
protectedvirtual

Reimplemented from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >.

Definition at line 135 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeExtraAxonalAndKappaCoarseGrids(), anima::DDI, anima::MultiCompartmentModelCreator::GetNewMultiCompartmentModel(), anima::GetSphereEvenSampling(), anima::NODDI, anima::MultiCompartmentModelCreator::SetCompartmentType(), anima::MultiCompartmentModelCreator::SetModelWithFreeWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithRestrictedWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithStaniszComponent(), anima::MultiCompartmentModelCreator::SetModelWithStationaryWaterComponent(), anima::MultiCompartmentModelCreator::SetNumberOfCompartments(), anima::Stick, anima::Tensor, anima::TransformCartesianToSphericalCoordinates(), and anima::TransformSphericalToCartesianCoordinates().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CheckComputationMask(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ CheckComputationMask()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CheckComputationMask ( )
protectedvirtual

Reimplemented from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >.

Definition at line 99 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData(), and anima::GetBValueFromAcquisitionParameters().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::WriteMCMOutput(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ ComputeAICcValue()

template<class InputPixelType , class OutputPixelType >
double anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeAICcValue ( MCMPointer &  mcmValue,
double  costValue 
)
protected

Compute AICc value from a cost function value and model.

Definition at line 1312 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetProfiledInformation(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ ComputeExtraAxonalAndKappaCoarseGrids()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeExtraAxonalAndKappaCoarseGrids ( )
protected

Computes extra axonal and kappa coarse grids (used for NODDI and DDI initialization)

Definition at line 374 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeTensorRadialDiffsAndAzimuthCoarseGrids().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ ComputeTensorRadialDiffsAndAzimuthCoarseGrids()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeTensorRadialDiffsAndAzimuthCoarseGrids ( )
protected

Computes extra axonal and kappa coarse grids (used for tensor final initaialization)

Definition at line 402 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::DynamicThreadedGenerateData().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeExtraAxonalAndKappaCoarseGrids(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ CreateAnother()

template<class InputPixelType, class OutputPixelType>
virtual::itk::LightObject::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateAnother ( void  ) const

◆ CreateCostFunction()

template<class InputPixelType , class OutputPixelType >
MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CostFunctionBasePointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateCostFunction ( std::vector< double > &  observedSignals,
MCMPointer &  mcmModel 
)
protectedvirtual

Create a cost function following the noise type and estimation mode.

Definition at line 717 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitialOrientationsEstimation(), anima::MCMSingleValuedCostFunction::New(), anima::MCMMultipleValuedCostFunction::New(), anima::GaussianMCMCost::New(), and anima::GaussianMCMVariableProjectionCost::New().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ CreateOptimizer()

template<class InputPixelType , class OutputPixelType >
MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizerPointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateOptimizer ( CostFunctionBasePointer &  cost,
itk::Array< double > &  lowerBounds,
itk::Array< double > &  upperBounds 
)
protected

Create an optimizer following the optimizer type and estimation mode.

Definition at line 1148 of file animaMCMEstimatorImageFilter.hxx.

References anima::NLOPTOptimizers::New(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::PerformSingleOptimization().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TensorCoarseGridInitialization(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ DynamicThreadedGenerateData()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::DynamicThreadedGenerateData ( const OutputImageRegionType &  outputRegionForThread)
protected

Definition at line 424 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizeNonIsotropicCompartments().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeTensorRadialDiffsAndAzimuthCoarseGrids(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ EstimateFreeWaterModel()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::EstimateFreeWaterModel ( MCMPointer &  mcmValue,
std::vector< double > &  observedSignals,
itk::ThreadIdType  threadId,
double &  aiccValue,
double &  b0Value,
double &  sigmaSqValue 
)
protected

Specific method for N=0 compartments estimation (only free water)

Definition at line 615 of file animaMCMEstimatorImageFilter.hxx.

References anima::MultiCompartmentModelCreator::GetNewMultiCompartmentModel(), anima::MultiCompartmentModelCreator::SetModelWithFreeWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithRestrictedWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithStaniszComponent(), anima::MultiCompartmentModelCreator::SetModelWithStationaryWaterComponent(), anima::MultiCompartmentModelCreator::SetNumberOfCompartments(), anima::MultiCompartmentModelCreator::SetUseConstrainedFreeWaterDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedIRWDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedStaniszDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedStaniszRadius(), and anima::MultiCompartmentModelCreator::SetVariableProjectionEstimationMode().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizeNonIsotropicCompartments(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ ExtraAxonalAndKappaCoarseGridInitialization()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ExtraAxonalAndKappaCoarseGridInitialization ( MCMPointer &  mcmUpdateValue,
CostFunctionBasePointer &  cost,
MCMType::ListType &  workVec,
ParametersType &  p 
)
protected

Coarse grid initialization of NODDI and DDI models.

Definition at line 999 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TensorCoarseGridInitialization().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ModelEstimation(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ GenerateOutputInformation()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GenerateOutputInformation ( )
protected

Definition at line 54 of file animaMCMEstimatorImageFilter.hxx.

References anima::MultiCompartmentModelCreator::GetNewMultiCompartmentModel(), anima::MultiCompartmentModelCreator::SetCompartmentType(), anima::MCMImage< TPixel, VImageDimension >::SetDescriptionModel(), anima::MultiCompartmentModelCreator::SetModelWithFreeWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithRestrictedWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithStaniszComponent(), anima::MultiCompartmentModelCreator::SetModelWithStationaryWaterComponent(), anima::MultiCompartmentModelCreator::SetNumberOfCompartments(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::WriteMCMOutput().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNewMCMCreatorInstance(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ GetAICcVolume()

template<class InputPixelType, class OutputPixelType>
OutputScalarImageType* anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetAICcVolume ( )
inline

Definition at line 143 of file animaMCMEstimatorImageFilter.h.

◆ GetB0Volume()

template<class InputPixelType, class OutputPixelType>
OutputScalarImageType* anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetB0Volume ( )
inline

Definition at line 144 of file animaMCMEstimatorImageFilter.h.

◆ GetBigDelta()

template<class InputPixelType, class OutputPixelType>
virtual double anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetBigDelta ( )
virtual

◆ GetCostValue()

template<class InputPixelType , class OutputPixelType >
double anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetCostValue ( CostFunctionBasePointer &  cost,
ParametersType &  p 
)
protected

Utility function to get a value from a cost function.

Definition at line 1259 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMMultipleValuedCostFunction::GetInternalCost(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetProfiledInformation(), and anima::MCMSingleValuedCostFunction::GetValue().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::PerformSingleOptimization(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ GetGradientDirections()

template<class InputPixelType, class OutputPixelType>
std::vector< GradientType >& anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetGradientDirections ( )
inline

Definition at line 137 of file animaMCMEstimatorImageFilter.h.

◆ GetGradientStrengths()

template<class InputPixelType, class OutputPixelType>
std::vector<double>& anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetGradientStrengths ( )
inline

Definition at line 134 of file animaMCMEstimatorImageFilter.h.

◆ GetMCMCreator()

template<class InputPixelType, class OutputPixelType>
MCMCreatorType* anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetMCMCreator ( unsigned int  i)
inline

Definition at line 139 of file animaMCMEstimatorImageFilter.h.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNewMCMCreatorInstance().

◆ GetMLEstimationStrategy()

template<class InputPixelType, class OutputPixelType>
virtual MaximumLikelihoodEstimationMode anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetMLEstimationStrategy ( )
virtual

◆ GetMoseVolume()

template<class InputPixelType, class OutputPixelType>
MoseImageType* anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetMoseVolume ( )
inline

Definition at line 148 of file animaMCMEstimatorImageFilter.h.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::WriteMCMOutput().

◆ GetNameOfClass()

template<class InputPixelType, class OutputPixelType>
virtual const char* anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods)

Reimplemented from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >.

◆ GetNewMCMCreatorInstance()

template<class InputPixelType , class OutputPixelType >
MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMCreatorType * anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNewMCMCreatorInstance ( )
virtual

Definition at line 46 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GenerateOutputInformation().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::AddGradientDirection(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetMCMCreator().

◆ GetNoiseType()

template<class InputPixelType, class OutputPixelType>
virtual SignalNoiseType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNoiseType ( )
virtual

◆ GetNumberOfCoils()

template<class InputPixelType, class OutputPixelType>
virtual unsigned int anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNumberOfCoils ( )
virtual

◆ GetOptimizer()

template<class InputPixelType, class OutputPixelType>
std::string anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetOptimizer ( )
inline

Definition at line 132 of file animaMCMEstimatorImageFilter.h.

◆ GetProfiledInformation()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetProfiledInformation ( CostFunctionBasePointer &  cost,
MCMPointer &  mcm,
double &  b0Value,
double &  sigmaSqValue 
)
protected

Utility function to get profiled data from the cost function into an MCM model.

Definition at line 1279 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeAICcValue(), anima::MCMSingleValuedCostFunction::GetMCMStructure(), anima::MCMMultipleValuedCostFunction::GetMCMStructure(), anima::MCMSingleValuedCostFunction::GetSigmaSquare(), and anima::MCMMultipleValuedCostFunction::GetSigmaSquare().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetCostValue(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ GetSigmaSquareVolume()

template<class InputPixelType, class OutputPixelType>
OutputScalarImageType* anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetSigmaSquareVolume ( )
inline

Definition at line 145 of file animaMCMEstimatorImageFilter.h.

◆ GetSmallDelta()

template<class InputPixelType, class OutputPixelType>
virtual double anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetSmallDelta ( )
virtual

◆ InitializeModelFromSimplifiedOne()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitializeModelFromSimplifiedOne ( MCMPointer &  simplifiedModel,
MCMPointer &  complexModel 
)
protectedvirtual

Performs initialization from simplified model with the same number of compartments.

Definition at line 1530 of file animaMCMEstimatorImageFilter.hxx.

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ InitialOrientationsEstimation()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitialOrientationsEstimation ( MCMPointer &  mcmValue,
bool  authorizedNegativeB0Value,
unsigned int  currentNumberOfCompartments,
std::vector< double > &  observedSignals,
itk::ThreadIdType  threadId,
double &  aiccValue,
double &  b0Value,
double &  sigmaSqValue 
)
protected

Doing estimation only of multiple orientations.

Definition at line 769 of file animaMCMEstimatorImageFilter.hxx.

References anima::MultiCompartmentModelCreator::GetNewMultiCompartmentModel(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ModelEstimation(), anima::MultiCompartmentModelCreator::SetCompartmentType(), anima::MultiCompartmentModelCreator::SetModelWithFreeWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithRestrictedWaterComponent(), anima::MultiCompartmentModelCreator::SetModelWithStaniszComponent(), anima::MultiCompartmentModelCreator::SetModelWithStationaryWaterComponent(), anima::MultiCompartmentModelCreator::SetNumberOfCompartments(), anima::MultiCompartmentModelCreator::SetUseCommonDiffusivities(), anima::MultiCompartmentModelCreator::SetUseConstrainedDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedFreeWaterDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedIRWDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedStaniszDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedStaniszRadius(), anima::MultiCompartmentModelCreator::SetVariableProjectionEstimationMode(), and anima::Stick.

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateCostFunction(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ ModelEstimation()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ModelEstimation ( MCMPointer &  mcmValue,
bool  authorizedNegativeB0Value,
std::vector< double > &  observedSignals,
itk::ThreadIdType  threadId,
double &  aiccValue,
double &  b0Value,
double &  sigmaSqValue 
)
protected

Doing estimation, calling initialization procedure until ball and zeppelin, returns AICc value.

Definition at line 839 of file animaMCMEstimatorImageFilter.hxx.

References anima::DDI, anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ExtraAxonalAndKappaCoarseGridInitialization(), anima::MultiCompartmentModelCreator::GetNewMultiCompartmentModel(), anima::NODDI, anima::MultiCompartmentModelCreator::SetCompartmentType(), anima::MultiCompartmentModelCreator::SetNumberOfCompartments(), anima::MultiCompartmentModelCreator::SetUseCommonConcentrations(), anima::MultiCompartmentModelCreator::SetUseCommonExtraAxonalFractions(), anima::MultiCompartmentModelCreator::SetUseConstrainedDiffusivity(), anima::MultiCompartmentModelCreator::SetUseConstrainedExtraAxonalFraction(), anima::MultiCompartmentModelCreator::SetUseConstrainedOrientationConcentration(), anima::Stick, anima::Tensor, and anima::Zeppelin.

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitialOrientationsEstimation(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ New()

template<class InputPixelType, class OutputPixelType>
static Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::New ( )
static

Method for creation through the object factory.

◆ OptimizeNonIsotropicCompartments()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizeNonIsotropicCompartments ( MCMPointer &  mcmValue,
unsigned int  currentNumberOfCompartments,
std::vector< double > &  observedSignals,
itk::ThreadIdType  threadId,
double &  aiccValue,
double &  b0Value,
double &  sigmaSqValue 
)
protected

Doing estimation of non isotropic compartments (for a given number of anisotropic compartments)

Definition at line 580 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::EstimateFreeWaterModel().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::DynamicThreadedGenerateData(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ PerformSingleOptimization()

template<class InputPixelType , class OutputPixelType >
double anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::PerformSingleOptimization ( ParametersType &  p,
CostFunctionBasePointer &  cost,
itk::Array< double > &  lowerBounds,
itk::Array< double > &  upperBounds 
)
protected

Performs an optimization of the supplied cost function and parameters using the specified optimizer(s). Returns the optimized parameters.

Definition at line 1229 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetCostValue().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateOptimizer(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ SetAbsoluteCostChange()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetAbsoluteCostChange ( double  _arg)
virtual

◆ SetAxialDiffusivityValue()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetAxialDiffusivityValue ( double  _arg)
virtual

◆ SetB0Threshold()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetB0Threshold ( double  _arg)
virtual

◆ SetBigDelta()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetBigDelta ( double  _arg)
virtual

◆ SetCompartmentType()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetCompartmentType ( CompartmentType  _arg)
virtual

◆ SetFindOptimalNumberOfCompartments()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetFindOptimalNumberOfCompartments ( bool  _arg)
virtual

◆ SetFTolerance()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetFTolerance ( double  _arg)
virtual

◆ SetGradientStrengths()

template<class InputPixelType, class OutputPixelType>
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetGradientStrengths ( std::vector< double > &  mb)
inline

Definition at line 91 of file animaMCMEstimatorImageFilter.h.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::AddGradientDirection().

◆ SetIRWDiffusivityValue()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetIRWDiffusivityValue ( double  _arg)
virtual

◆ SetMaxEval()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetMaxEval ( unsigned int  _arg)
virtual

◆ SetMLEstimationStrategy()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetMLEstimationStrategy ( MaximumLikelihoodEstimationMode  _arg)
virtual

◆ SetModelWithFreeWaterComponent()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetModelWithFreeWaterComponent ( bool  _arg)
virtual

◆ SetModelWithRestrictedWaterComponent()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetModelWithRestrictedWaterComponent ( bool  _arg)
virtual

◆ SetModelWithStaniszComponent()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetModelWithStaniszComponent ( bool  _arg)
virtual

◆ SetModelWithStationaryWaterComponent()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetModelWithStationaryWaterComponent ( bool  _arg)
virtual

◆ SetMoseVolume()

template<class InputPixelType, class OutputPixelType>
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetMoseVolume ( MoseImageType *  img)
inline

Definition at line 147 of file animaMCMEstimatorImageFilter.h.

◆ SetNoiseType()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetNoiseType ( SignalNoiseType  _arg)
virtual

◆ SetNumberOfCoils()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetNumberOfCoils ( unsigned int  _arg)
virtual

◆ SetNumberOfCompartments()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetNumberOfCompartments ( unsigned int  _arg)
virtual

◆ SetOptimizer()

template<class InputPixelType, class OutputPixelType>
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetOptimizer ( std::string &  opt)
inline

Definition at line 98 of file animaMCMEstimatorImageFilter.h.

◆ SetRadialDiffusivity1Value()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetRadialDiffusivity1Value ( double  _arg)
virtual

◆ SetRadialDiffusivity2Value()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetRadialDiffusivity2Value ( double  _arg)
virtual

◆ SetSmallDelta()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetSmallDelta ( double  _arg)
virtual

◆ SetStaniszDiffusivityValue()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetStaniszDiffusivityValue ( double  _arg)
virtual

◆ SetUseCommonConcentrations()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseCommonConcentrations ( bool  _arg)
virtual

◆ SetUseCommonDiffusivities()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseCommonDiffusivities ( bool  _arg)
virtual

◆ SetUseCommonExtraAxonalFractions()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseCommonExtraAxonalFractions ( bool  _arg)
virtual

◆ SetUseConstrainedDiffusivity()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedDiffusivity ( bool  _arg)
virtual

◆ SetUseConstrainedExtraAxonalFraction()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedExtraAxonalFraction ( bool  _arg)
virtual

◆ SetUseConstrainedFreeWaterDiffusivity()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedFreeWaterDiffusivity ( bool  _arg)
virtual

◆ SetUseConstrainedIRWDiffusivity()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedIRWDiffusivity ( bool  _arg)
virtual

◆ SetUseConstrainedOrientationConcentration()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedOrientationConcentration ( bool  _arg)
virtual

◆ SetUseConstrainedStaniszDiffusivity()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedStaniszDiffusivity ( bool  _arg)
virtual

◆ SetUseConstrainedStaniszRadius()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetUseConstrainedStaniszRadius ( bool  _arg)
virtual

◆ SetXTolerance()

template<class InputPixelType, class OutputPixelType>
virtual void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetXTolerance ( double  _arg)
virtual

◆ SparseInitializeSticks()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks ( MCMPointer &  complexModel,
bool  authorizeNegativeB0Value,
std::vector< double > &  observedSignals,
itk::ThreadIdType  threadId 
)
protectedvirtual

Performs initialization from single DTI.

Definition at line 1328 of file animaMCMEstimatorImageFilter.hxx.

References anima::ComputeScalarProduct(), anima::MultiCompartmentModelCreator::GetNewMultiCompartmentModel(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InitializeModelFromSimplifiedOne(), anima::NNLSOptimizer::New(), anima::SpectralClusteringFilter< ScalarType >::SetInputData(), anima::MultiCompartmentModelCreator::SetNumberOfCompartments(), anima::BaseCompartment::SetOrientationPhi(), anima::BaseCompartment::SetOrientationTheta(), and anima::TransformCartesianToSphericalCoordinates().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ComputeAICcValue(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ TensorCoarseGridInitialization()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TensorCoarseGridInitialization ( MCMPointer &  mcmUpdateValue,
CostFunctionBasePointer &  cost,
MCMType::ListType &  workVec,
ParametersType &  p 
)
protected

Coarse grid initialization of tensor model.

Definition at line 1049 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateOptimizer(), anima::MCMAxialDiffusivityAddonLowerBound, and anima::MCMDiffusivityLowerBound.

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ExtraAxonalAndKappaCoarseGridInitialization(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().

◆ WriteMCMOutput()

template<class InputPixelType , class OutputPixelType >
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::WriteMCMOutput ( std::string  fileName)

Definition at line 83 of file animaMCMEstimatorImageFilter.hxx.

References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CheckComputationMask(), and anima::MCMFileWriter< PixelType, ImageDimension >::SetInputImage().

Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GenerateOutputInformation(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetMoseVolume().

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