ANIMA
4.0
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#include <animaMCMEstimatorImageFilter.h>
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 |
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) |
Definition at line 21 of file animaMCMEstimatorImageFilter.h.
typedef anima::BaseCompartment anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BaseCompartmentType |
Definition at line 45 of file animaMCMEstimatorImageFilter.h.
typedef anima::MultiCompartmentModelCreator::CompartmentType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CompartmentType |
Definition at line 44 of file animaMCMEstimatorImageFilter.h.
typedef itk::SmartPointer<const Self> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ConstPointer |
Definition at line 35 of file animaMCMEstimatorImageFilter.h.
typedef CostFunctionBaseType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CostFunctionBasePointer |
Definition at line 54 of file animaMCMEstimatorImageFilter.h.
typedef itk::CostFunction anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CostFunctionBaseType |
Definition at line 53 of file animaMCMEstimatorImageFilter.h.
typedef vnl_vector_fixed<double,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GradientType |
Definition at line 88 of file animaMCMEstimatorImageFilter.h.
typedef itk::Image<InputPixelType,4> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Image4DType |
Definition at line 29 of file animaMCMEstimatorImageFilter.h.
typedef InputImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InputImagePointer |
Definition at line 79 of file animaMCMEstimatorImageFilter.h.
typedef Superclass::InputImageRegionType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InputImageRegionType |
Definition at line 85 of file animaMCMEstimatorImageFilter.h.
typedef TInputImage anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::InputImageType |
Image typedef support
Definition at line 77 of file animaMCMEstimatorImageFilter.h.
typedef Superclass::MaskImageType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MaskImageType |
Superclass typedefs.
Definition at line 84 of file animaMCMEstimatorImageFilter.h.
typedef anima::MultiCompartmentModelCreator anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMCreatorType |
Definition at line 43 of file animaMCMEstimatorImageFilter.h.
typedef MCMCreatorType::MCMPointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMPointer |
Definition at line 47 of file animaMCMEstimatorImageFilter.h.
typedef MCMCreatorType::MCMType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMType |
Definition at line 46 of file animaMCMEstimatorImageFilter.h.
typedef MCMType::ListType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMVectorType |
Definition at line 48 of file animaMCMEstimatorImageFilter.h.
typedef anima::MCMImage<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ModelImageType |
Definition at line 28 of file animaMCMEstimatorImageFilter.h.
typedef MoseImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MoseImagePointer |
Definition at line 38 of file animaMCMEstimatorImageFilter.h.
typedef itk::Image<unsigned char,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MoseImageType |
Definition at line 37 of file animaMCMEstimatorImageFilter.h.
typedef OptimizerType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizerPointer |
Definition at line 51 of file animaMCMEstimatorImageFilter.h.
typedef itk::NonLinearOptimizer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OptimizerType |
Definition at line 50 of file animaMCMEstimatorImageFilter.h.
typedef OutputImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputImagePointer |
Definition at line 81 of file animaMCMEstimatorImageFilter.h.
typedef Superclass::OutputImageRegionType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputImageRegionType |
Definition at line 86 of file animaMCMEstimatorImageFilter.h.
typedef TOutputImage anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputImageType |
Definition at line 78 of file animaMCMEstimatorImageFilter.h.
typedef OutputScalarImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputScalarImagePointer |
Definition at line 32 of file animaMCMEstimatorImageFilter.h.
typedef itk::Image<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::OutputScalarImageType |
Definition at line 31 of file animaMCMEstimatorImageFilter.h.
typedef OptimizerType::ParametersType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::ParametersType |
Definition at line 52 of file animaMCMEstimatorImageFilter.h.
typedef itk::SmartPointer<Self> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Pointer |
Definition at line 34 of file animaMCMEstimatorImageFilter.h.
typedef MCMEstimatorImageFilter<InputPixelType, OutputPixelType> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Self |
Standard class typedefs.
Definition at line 26 of file animaMCMEstimatorImageFilter.h.
typedef anima::MaskedImageToImageFilter< TInputImage, TOutputImage > anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::Superclass |
Definition at line 33 of file animaMCMEstimatorImageFilter.h.
typedef itk::Image<InputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TInputImage |
Definition at line 27 of file animaMCMEstimatorImageFilter.h.
typedef anima::MCMImage<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TOutputImage |
Definition at line 30 of file animaMCMEstimatorImageFilter.h.
typedef OutputImageType::PixelType anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::VariableLengthVectorType |
Definition at line 80 of file animaMCMEstimatorImageFilter.h.
typedef VectorImageType::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::VectorImagePointer |
Definition at line 41 of file animaMCMEstimatorImageFilter.h.
typedef itk::VectorImage<OutputPixelType,3> anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::VectorImageType |
Definition at line 40 of file animaMCMEstimatorImageFilter.h.
enum anima::MCMEstimatorImageFilter::MaximumLikelihoodEstimationMode |
Enumerator | |
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Marginal | |
Profile | |
VariableProjection |
Definition at line 63 of file animaMCMEstimatorImageFilter.h.
enum anima::MCMEstimatorImageFilter::SignalNoiseType |
Denotes noise type on input signal. Based on this, a different cost function should be created.
Enumerator | |
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Gaussian | |
NCC |
Definition at line 57 of file animaMCMEstimatorImageFilter.h.
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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.
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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().
void anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::AddGradientDirection | ( | unsigned int | i, |
GradientType & | grad | ||
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Definition at line 33 of file animaMCMEstimatorImageFilter.hxx.
References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNewMCMCreatorInstance().
Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SetGradientStrengths().
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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().
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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().
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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().
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Computes extra axonal and kappa coarse grids (used for NODDI and DDI initialization)
Definition at line 374 of file animaMCMEstimatorImageFilter.hxx.
Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::~MCMEstimatorImageFilter().
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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().
virtual::itk::LightObject::Pointer anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CreateAnother | ( | void | ) | const |
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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().
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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().
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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().
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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().
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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().
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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().
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Definition at line 143 of file animaMCMEstimatorImageFilter.h.
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Definition at line 144 of file animaMCMEstimatorImageFilter.h.
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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().
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Definition at line 137 of file animaMCMEstimatorImageFilter.h.
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Definition at line 134 of file animaMCMEstimatorImageFilter.h.
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Definition at line 139 of file animaMCMEstimatorImageFilter.h.
References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::GetNewMCMCreatorInstance().
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Definition at line 148 of file animaMCMEstimatorImageFilter.h.
References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::WriteMCMOutput().
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Run-time type information (and related methods)
Reimplemented from anima::MaskedImageToImageFilter< itk::Image< InputPixelType, 3 >, anima::MCMImage< OutputPixelType, 3 > >.
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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().
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Definition at line 132 of file animaMCMEstimatorImageFilter.h.
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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().
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Definition at line 145 of file animaMCMEstimatorImageFilter.h.
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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().
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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().
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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().
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Method for creation through the object factory.
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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().
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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().
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Definition at line 91 of file animaMCMEstimatorImageFilter.h.
References anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::AddGradientDirection().
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Definition at line 147 of file animaMCMEstimatorImageFilter.h.
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Definition at line 98 of file animaMCMEstimatorImageFilter.h.
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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().
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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().
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().