Medical Imaging Interaction Toolkit
2016.11.0
Medical Imaging Interaction Toolkit
|
This filter provides the fit of the kurtosis (non-IVIM) signal to the data. More...
#include <itkDiffusionKurtosisReconstructionImageFilter.h>
Classes | |
struct | KurtosisSnapshot |
Struct describing a result (and the data) of a Kurtosis model fit. More... | |
Public Types | |
typedef DiffusionKurtosisReconstructionImageFilter | Self |
typedef SmartPointer< Self > | Pointer |
typedef SmartPointer< const Self > | ConstPointer |
typedef ImageToImageFilter< VectorImage< TInputPixelType, 3 >, Image< TOutputPixelType, 3 > > | Superclass |
typedef TOutputPixelType | OutputPixelType |
typedef TInputPixelType | InputPixelType |
typedef Superclass::InputImageType | InputImageType |
typedef Image< OutputPixelType, 3 > | OutputImageType |
typedef itk::Image< short, 3 > | MaskImageType |
typedef Superclass::OutputImageRegionType | OutputImageRegionType |
typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType | GradientDirectionContainerType |
typedef itk::VectorImage< float, 3 > | VectorImageType |
typedef itk::Image< itk::Vector< double, 3 >, 3 > | InitialFitImageType |
Public Member Functions | |
Pointer | Clone () const |
virtual const char * | GetClassName () const |
void | SetInitialSolution (const vnl_vector< double > &x0) |
void | SetOmitUnweightedValue (bool flag) |
KurtosisSnapshot | GetSnapshot (const itk::VariableLengthVector< TInputPixelType > &input, vnl_vector< double > bvalues, KurtosisFitConfiguration kf_conf) |
KurtosisSnapshot | GetSnapshot (const itk::VariableLengthVector< TInputPixelType > &input, GradientDirectionContainerType::Pointer, float bvalue, KurtosisFitConfiguration kf_conf) |
KurtosisSnapshot | GetCurrentSnapshot (bool omit_bzero) |
void | SetReferenceBValue (double bvalue) |
void | SetGradientDirections (GradientDirectionContainerType::Pointer gradients) |
void | SetMapOutputRegion (OutputImageRegionType region) |
void | SetImageMask (MaskImageType::Pointer mask) |
void | SetSmoothingSigma (double sigma) |
void | SetUseSmoothingPriorToFitting (bool flag) |
void | SetBoundariesForKurtosis (double lower, double upper) |
void | SetMaximalBValueUsedForFitting (double max_bvalue) |
void | SetFittingScale (FitScale scale) |
Static Public Member Functions | |
static Pointer | New () |
Protected Member Functions | |
DiffusionKurtosisReconstructionImageFilter () | |
virtual | ~DiffusionKurtosisReconstructionImageFilter () |
void | GenerateOutputInformation () override |
void | AfterThreadedGenerateData () override |
void | BeforeThreadedGenerateData () override |
void | ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) override |
Protected Attributes | |
double | m_ReferenceBValue |
vnl_vector< double > | m_BValues |
vnl_vector< double > | m_InitialPosition |
bool | m_OmitBZero |
OutputImageRegionType | m_MapOutputRegion |
MaskImageType::Pointer | m_MaskImage |
InputImageType::Pointer | m_ProcessedInputImage |
bool | m_ApplyPriorSmoothing |
double | m_SmoothingSigma |
bool | m_UseKBounds |
vnl_vector_fixed< double, 2 > | m_KurtosisBounds |
double | m_MaxFitBValue |
FitScale | m_ScaleForFitting |
This filter provides the fit of the kurtosis (non-IVIM) signal to the data.
It has two main modes of operation, either as an image filter to compute the D and K maps, i.e. fitting the values to each voxel or a computation on a single voxel or a voxel group (with mask) can be triggered by
Definition at line 246 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef SmartPointer<const Self> itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::ConstPointer |
Definition at line 282 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::GradientDirectionContainerType |
Holds each magnetic field gradient used to acquire one DWImage
Definition at line 306 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef itk::Image<itk::Vector<double, 3>, 3> itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::InitialFitImageType |
Definition at line 310 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef Superclass::InputImageType itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::InputImageType |
Definition at line 296 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef TInputPixelType itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::InputPixelType |
Definition at line 294 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef itk::Image< short , 3> itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::MaskImageType |
Definition at line 299 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef Superclass::OutputImageRegionType itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::OutputImageRegionType |
Definition at line 301 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef Image< OutputPixelType, 3 > itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::OutputImageType |
Definition at line 297 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef TOutputPixelType itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::OutputPixelType |
Definition at line 293 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef SmartPointer<Self> itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::Pointer |
Definition at line 281 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef DiffusionKurtosisReconstructionImageFilter itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::Self |
Definition at line 280 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef ImageToImageFilter< VectorImage< TInputPixelType, 3>, Image< TOutputPixelType,3 > > itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::Superclass |
Definition at line 284 of file itkDiffusionKurtosisReconstructionImageFilter.h.
typedef itk::VectorImage<float,3> itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::VectorImageType |
Definition at line 309 of file itkDiffusionKurtosisReconstructionImageFilter.h.
|
protected |
Definition at line 123 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_InitialPosition, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_KurtosisBounds, and mitk::New().
|
inlineprotectedvirtual |
Definition at line 393 of file itkDiffusionKurtosisReconstructionImageFilter.h.
|
overrideprotected |
Definition at line 254 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
|
overrideprotected |
Definition at line 170 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
References mitkThrow, and mitk::New().
Pointer itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::Clone | ( | ) | const |
|
overrideprotected |
Definition at line 155 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
|
virtual |
Runtime information support.
KurtosisSnapshot itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::GetCurrentSnapshot | ( | bool | omit_bzero | ) |
Returns the value of the current data presented to the filter.
If a mask is set, the voxels are first averaged before passed to the fitting procedure
itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::GetSnapshot | ( | const itk::VariableLengthVector< TInputPixelType > & | input, |
vnl_vector< double > | bvalues, | ||
KurtosisFitConfiguration | kf_conf | ||
) |
Trigger a single computation of the Kurtosis values from the given input vector and the bvalues and returns the result as a KurtosisSnapshot object
Definition at line 288 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::bvalues, mitk::eps, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::fit_bvalues, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::fit_measurements, FitSingleVoxel(), itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::m_BzeroFit, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::m_D, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::m_f, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::m_fittedBZero, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::m_K, itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot::measurements, and itk::KurtosisFitConfiguration::omit_bzero.
itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::KurtosisSnapshot itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::GetSnapshot | ( | const itk::VariableLengthVector< TInputPixelType > & | input, |
GradientDirectionContainerType::Pointer | gradients, | ||
float | bvalue, | ||
KurtosisFitConfiguration | kf_conf | ||
) |
Trigger a single computation of the kurtosis values, first the bvalues vector is computed internally but then also stored into the returend snapshot
Definition at line 274 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
|
static |
Method for creation through the object factory.
|
inline |
Set boundaries enforced by penalty terms in the fitting procedure
Definition at line 368 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_KurtosisBounds, and itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_UseKBounds.
|
inline |
Select the method used in fitting of the data
STRAIHT - fit the exponential signal equation S / S_0 = exp [ ... ] LOGARITHMIC - fit the logarithmic signal equation ln( S / S_0 ) = []
Definition at line 386 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_ScaleForFitting.
void itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetGradientDirections | ( | GradientDirectionContainerType::Pointer | gradients | ) |
Set the gradient directions
Definition at line 375 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
void itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetImageMask | ( | MaskImageType::Pointer | mask | ) |
Definition at line 163 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
void itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetInitialSolution | ( | const vnl_vector< double > & | x0 | ) |
Set the initial solution for fitting, make sure the length and the values correspond to the parameters x0 = ( S_0, ADC_0, AKC_0 ) when also the S_0 is estimated x0 = ( ADC_0, AKC_0 ) when the S_0 is used in fitting
Definition at line 407 of file itkDiffusionKurtosisReconstructionImageFilter.cxx.
|
inline |
Restrict map generation to an image region
Definition at line 346 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_ApplyPriorSmoothing, and itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_MapOutputRegion.
|
inline |
Exclude measurements associated with b-values higher than max_bvalue from fitting
Definition at line 376 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_MaxFitBValue.
|
inline |
Set whether the S_0 value is fitted or used in fitting
Definition at line 320 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_OmitBZero.
|
inline |
Set the reference bvalue of the input DW image
Definition at line 339 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_ReferenceBValue.
|
inline |
Set smoothing sigma (default = 1.5 ), automatically enables smoothing prior to fitting
Definition at line 355 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_ApplyPriorSmoothing, and itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_SmoothingSigma.
|
inline |
Activate/Deactivate the gaussian smoothing applied to the input prior to fitting ( default = off )
Definition at line 362 of file itkDiffusionKurtosisReconstructionImageFilter.h.
References itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::m_ApplyPriorSmoothing.
|
overrideprotected |
|
protected |
Definition at line 417 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetMapOutputRegion(), itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetSmoothingSigma(), and itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetUseSmoothingPriorToFitting().
|
protected |
Definition at line 405 of file itkDiffusionKurtosisReconstructionImageFilter.h.
|
protected |
Definition at line 407 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::DiffusionKurtosisReconstructionImageFilter().
|
protected |
Definition at line 421 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::DiffusionKurtosisReconstructionImageFilter(), and itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetBoundariesForKurtosis().
|
protected |
Definition at line 411 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetMapOutputRegion().
|
protected |
Definition at line 413 of file itkDiffusionKurtosisReconstructionImageFilter.h.
|
protected |
Definition at line 422 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetMaximalBValueUsedForFitting().
|
protected |
Definition at line 409 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetOmitUnweightedValue().
|
protected |
Definition at line 415 of file itkDiffusionKurtosisReconstructionImageFilter.h.
|
protected |
Definition at line 403 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetReferenceBValue().
|
protected |
Definition at line 424 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetFittingScale().
|
protected |
Definition at line 418 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetSmoothingSigma().
|
protected |
Definition at line 420 of file itkDiffusionKurtosisReconstructionImageFilter.h.
Referenced by itk::DiffusionKurtosisReconstructionImageFilter< TInputPixelType, TOutputPixelType >::SetBoundariesForKurtosis().