ANIMA  4.0
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
anima::GcStremMsLesionsSegmentationFilter< TInputImage > Class Template Reference

Class performing lesion segmentation. More...

#include <animaGcStremMsLesionsSegmentationFilter.h>

+ Inheritance diagram for anima::GcStremMsLesionsSegmentationFilter< TInputImage >:
+ Collaboration diagram for anima::GcStremMsLesionsSegmentationFilter< TInputImage >:

Public Types

typedef itk::BinaryThresholdImageFilter< ImageTypeD, ImageTypeUCBinaryThresholdImageFilterType_F_UC
 
typedef itk::BinaryThresholdImageFilter< ImageTypeUC, ImageTypeUCBinaryThresholdImageFilterType_UC_UC
 
typedef anima::CheckStructureNeighborFilter< ImageTypeUC, ImageTypeUCCheckStructureNeighborFilterFilterType
 
typedef anima::ComputeMahalanobisImagesFilter< ImageTypeUC, ImageTypeUC, ImageTypeDComputeMahalanobisImagesFilterType
 
typedef anima::ComputeSolution< ImageTypeUC, ImageTypeUC, ImageTypeDComputeSolutionType
 
typedef itk::ConnectedComponentImageFilter< ImageTypeUC, ImageTypeIntConnectedComponentType
 
typedef itk::SmartPointer< const SelfConstPointer
 
typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorTypeGaussianFunctionType
 
typedef anima::GraphCutFilter< TInputImage, ImageTypeUCGraphCutFilterType
 
typedef itk::ImageRegionConstIterator< InputImageTypeImageIteratorTypeConstInput
 
typedef itk::ImageRegionConstIterator< ImageTypeUCImageIteratorTypeConstUC
 
typedef itk::ImageRegionIterator< ImageTypeDImageIteratorTypeD
 
typedef itk::ImageRegionIterator< ImageTypeIntImageIteratorTypeInt
 
typedef itk::ImageRegionIterator< ImageTypeUCImageIteratorTypeUC
 
typedef itk::Image< PixelTypeD, 3 > ImageTypeD
 
typedef itk::Image< PixelTypeInt, 3 > ImageTypeInt
 
typedef itk::Image< PixelTypeUC, 3 > ImageTypeUC
 
typedef TInputImage InputImageType
 
typedef itk::IntensityWindowingImageFilter< ImageTypeUC, ImageTypeDIntensityWindowingImageFilterType
 
typedef itk::MaskImageFilter< ImageTypeD, ImageTypeUCMaskFilterType_F_UC
 
typedef itk::MaskImageFilter< ImageTypeUC, ImageTypeUCMaskFilterType_UC_UC
 
typedef itk::MaximumImageFilter< ImageTypeD, ImageTypeD, ImageTypeDMaximumFilterType
 
typedef itk::VariableLengthVector< double > MeasurementVectorType
 
typedef itk::MinimumImageFilter< ImageTypeD, ImageTypeD, ImageTypeDMinimumFilterTypeF
 
typedef itk::MinimumImageFilter< ImageTypeUC, ImageTypeUC, ImageTypeUCMinimumFilterTypeUC
 
typedef OutputImageType::Pointer OutputImagePointer
 
typedef TOutputImage OutputImageType
 
typedef itk::ImageRegionIterator< OutputImageTypeOutputIteratorType
 
typedef OutputImageType::PixelType OutputPixelType
 
typedef double PixelTypeD
 
typedef int PixelTypeInt
 
typedef unsigned char PixelTypeUC
 
typedef itk::SmartPointer< SelfPointer
 
typedef itk::RelabelComponentImageFilter< ImageTypeInt, ImageTypeIntRelabelComponentType
 
typedef anima::RemoveTouchingBorderFilter< ImageTypeUC, ImageTypeUC, ImageTypeUCRemoveTouchingBorderFilterType
 
typedef itk::RescaleIntensityImageFilter< TInputImage, ImageTypeUCRescaleFilterType
 
typedef GcStremMsLesionsSegmentationFilter Self
 
typedef itk::ImageToImageFilter< TInputImage, TOutputImageSuperclass
 
typedef anima::TLinksFilter< TInputImage, ImageTypeDTLinksFilterType
 
typedef itk::Image< unsigned char, 3 > TOutputImage
 

Public Member Functions

void ApplyHeuristicRules ()
 
void CheckInputImages ()
 
void ComputeAutomaticInitialization ()
 
void ComputeNABT ()
 
virtual ::itk::LightObject::Pointer CreateAnother (void) const
 
void CreateFuzzyRuleImage ()
 
void GenerateData () ITK_OVERRIDE
 
virtual double GetAlpha ()
 
virtual bool GetEM_before_concentration ()
 
virtual int GetEmIter ()
 
virtual int GetEmIter_concentration ()
 
std::string GetFuzzyOutputObjectFilename ()
 
virtual double GetFuzzyRuleMax ()
 
virtual double GetFuzzyRuleMin ()
 
virtual unsigned int GetInitMethodType ()
 
virtual double GetIntensityDPFactor ()
 
virtual double GetIntensityFLAIRFactor ()
 
virtual double GetIntensityT2Factor ()
 
virtual double GetLesionPriorProportion ()
 
LesionSegmentationType GetLesionSegmentationType ()
 
virtual double GetMahalanobisThCSF ()
 
virtual double GetMahalanobisThGM ()
 
virtual double GetMahalanobisThWM ()
 
std::string GetMatrixGradFilename ()
 
virtual double GetMinDistance ()
 
virtual double GetMinLesionsSize ()
 
virtual double GetMultiVarSinks ()
 
virtual double GetMultiVarSources ()
 
virtual const char * GetNameOfClass () const
 
TOutputImageGetOutputCSF ()
 
std::string GetOutputCSFFilename ()
 
itk::Image< double, 3 > * GetOutputFuzzyObjectImage ()
 
std::string GetOutputGCFilename ()
 
TOutputImageGetOutputGM ()
 
std::string GetOutputGMFilename ()
 
TOutputImageGetOutputGraphCut ()
 
TOutputImageGetOutputIntensityImage1 ()
 
std::string GetOutputIntensityImage1Filename ()
 
TOutputImageGetOutputIntensityImage2 ()
 
std::string GetOutputIntensityImage2Filename ()
 
std::string GetOutputLesionFile ()
 
TOutputImageGetOutputLesions ()
 
std::string GetOutputMahaCSFFilename ()
 
itk::Image< double, 3 > * GetOutputMahaCSFImage ()
 
std::string GetOutputMahaGMFilename ()
 
itk::Image< double, 3 > * GetOutputMahaGMImage ()
 
std::string GetOutputMahaMaximumFilename ()
 
itk::Image< double, 3 > * GetOutputMahaMaximumImage ()
 
std::string GetOutputMahaMinimumFilename ()
 
itk::Image< double, 3 > * GetOutputMahaMinimumImage ()
 
std::string GetOutputMahaWMFilename ()
 
itk::Image< double, 3 > * GetOutputMahaWMImage ()
 
TOutputImageGetOutputStrem ()
 
TOutputImageGetOutputStremCSF ()
 
std::string GetOutputStremCSFFilename ()
 
std::string GetOutputStremFilename ()
 
TOutputImageGetOutputStremGM ()
 
std::string GetOutputStremGMFilename ()
 
TOutputImageGetOutputStremWM ()
 
std::string GetOutputStremWMFilename ()
 
std::string GetOutputWholeFilename ()
 
TOutputImageGetOutputWholeSeg ()
 
TOutputImageGetOutputWM ()
 
std::string GetOutputWMFilename ()
 
virtual double GetRatioContourWM ()
 
virtual double GetRejRatio ()
 
virtual double GetRejRatioHierar ()
 
virtual bool GetRemoveBorder ()
 
virtual double GetSigma ()
 
std::vector< GaussianFunctionType::Pointer > GetSolution ()
 
virtual double GetThresoldWMmap ()
 
virtual bool GetUseDP ()
 
virtual bool GetUseFLAIR ()
 
virtual bool GetUseSpecGrad ()
 
virtual bool GetUseT2 ()
 
virtual bool GetVerbose ()
 
void GraphCut ()
 
void RescaleImages ()
 
virtual void SetAlpha (double _arg)
 
virtual void SetEM_before_concentration (bool _arg)
 
virtual void SetEmIter (int _arg)
 
virtual void SetEmIter_concentration (int _arg)
 
virtual void SetFuzzyRuleMax (double _arg)
 
virtual void SetFuzzyRuleMin (double _arg)
 
void SetGaussianModel (std::vector< GaussianFunctionType::Pointer > solution)
 
virtual void SetInitMethodType (unsigned int _arg)
 
void SetInputCSFAtlas (const ImageTypeD *image)
 
void SetInputGMAtlas (const ImageTypeD *image)
 
void SetInputImageDP (const InputImageType *image)
 
void SetInputImageFLAIR (const InputImageType *image)
 
void SetInputImageT1 (const InputImageType *image)
 
void SetInputImageT1Gd (const InputImageType *image)
 
void SetInputImageT2 (const InputImageType *image)
 
void SetInputLesionPrior (const ImageTypeD *image)
 
void SetInputWMAtlas (const ImageTypeD *image)
 
virtual void SetIntensityDPFactor (double _arg)
 
virtual void SetIntensityFLAIRFactor (double _arg)
 
virtual void SetIntensityT2Factor (double _arg)
 
virtual void SetLesionPriorProportion (double _arg)
 
void SetLesionSegmentationType (LesionSegmentationType type)
 
virtual void SetMahalanobisThCSF (double _arg)
 
virtual void SetMahalanobisThGM (double _arg)
 
virtual void SetMahalanobisThWM (double _arg)
 
void SetMask (const TInputImage *MaskImage)
 
void SetMatrixGradFilename (std::string fn)
 
virtual void SetMinDistance (double _arg)
 
virtual void SetMinLesionsSize (double _arg)
 
virtual void SetMultiVarSinks (double _arg)
 
virtual void SetMultiVarSources (double _arg)
 
void SetOutputCSFFilename (std::string fn)
 
void SetOutputFuzzyObjectFilename (std::string fn)
 
void SetOutputGCFilename (std::string fn)
 
void SetOutputGMFilename (std::string fn)
 
void SetOutputIntensityImage1Filename (std::string fn)
 
void SetOutputIntensityImage2Filename (std::string fn)
 
void SetOutputLesionFilename (std::string fn)
 
void SetOutputMahaCSFFilename (std::string fn)
 
void SetOutputMahaGMFilename (std::string fn)
 
void SetOutputMahaMaximumFilename (std::string fn)
 
void SetOutputMahaMinimumFilename (std::string fn)
 
void SetOutputMahaWMFilename (std::string fn)
 
void SetOutputStremCSFFilename (std::string fn)
 
void SetOutputStremFilename (std::string fn)
 
void SetOutputStremGMFilename (std::string fn)
 
void SetOutputStremWMFilename (std::string fn)
 
void SetOutputWholeFilename (std::string fn)
 
void SetOutputWMFilename (std::string fn)
 
virtual void SetRatioContourWM (double _arg)
 
virtual void SetRejRatio (double _arg)
 
virtual void SetRejRatioHierar (double _arg)
 
virtual void SetRemoveBorder (bool _arg)
 
virtual void SetSigma (double _arg)
 
void SetSinksMask (const ImageTypeUC *MaskImage)
 
void SetSolutionReadFilename (std::string fn)
 
void SetSolutionWriteFilename (std::string fn)
 
void SetSourcesMask (const ImageTypeUC *MaskImage)
 
virtual void SetThresoldWMmap (double _arg)
 
void SetTol (const double tol)
 
virtual void SetUseDP (bool _arg)
 
virtual void SetUseFLAIR (bool _arg)
 
virtual void SetUseSpecGrad (bool _arg)
 
virtual void SetUseT2 (bool _arg)
 
virtual void SetVerbose (bool _arg)
 
void StremThreshold ()
 
void WriteOutputs ()
 

Static Public Member Functions

static Pointer New ()
 

Protected Member Functions

void EmitProgress (int prog)
 
 GcStremMsLesionsSegmentationFilter ()
 
ImageTypeD::ConstPointer GetInputCSFAtlas ()
 
ImageTypeD::ConstPointer GetInputGMAtlas ()
 
InputImageType::ConstPointer GetInputImageDP ()
 
InputImageType::ConstPointer GetInputImageFLAIR ()
 
InputImageType::ConstPointer GetInputImageT1 ()
 
InputImageType::ConstPointer GetInputImageT1Gd ()
 
InputImageType::ConstPointer GetInputImageT2 ()
 
ImageTypeD::ConstPointer GetInputLesionPrior ()
 
ImageTypeD::ConstPointer GetInputWMAtlas ()
 
InputImageType::ConstPointer GetMask ()
 
ImageTypeUC::ConstPointer GetSinksMask ()
 
ImageTypeUC::ConstPointer GetSourcesMask ()
 
itk::DataObject::Pointer MakeOutput (unsigned int idx)
 
 ~GcStremMsLesionsSegmentationFilter ()
 

Static Protected Member Functions

static void ManageProgress (itk::Object *caller, const itk::EventObject &event, void *clientData)
 

Protected Attributes

MaximumFilterType::Pointer m_FilterMaxSinks
 
MaximumFilterType::Pointer m_FilterMaxSources
 
GraphCutFilterType::Pointer m_GraphCutFilter
 
ComputeMahalanobisImagesFilterType::Pointer m_MahalanobisFilter
 
TLinksFilterType::Pointer m_TLinksFilter
 

Detailed Description

template<typename TInputImage>
class anima::GcStremMsLesionsSegmentationFilter< TInputImage >

Class performing lesion segmentation.

The segmentation method has three steps:

1) Estimation of the NABT model: The NABT model computation requires strictly 3 sequences: T1-w and two sequences among T2-w, DP and FLAIR.

2) Detection of candidate lesions: The lesion detection can be done two different ways:

3) Application of a priori heuristic rules to extract the MS lesions from others outliers: The heuritic rules that can be used to refine the segmentation are:

Additionally to the lesions segmentation, the filter provides a segmentation of the healthy tissues based on the NABT estimation.

Definition at line 71 of file animaGcStremMsLesionsSegmentationFilter.h.

Member Typedef Documentation

◆ BinaryThresholdImageFilterType_F_UC

template<typename TInputImage >
typedef itk::BinaryThresholdImageFilter<ImageTypeD, ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::BinaryThresholdImageFilterType_F_UC

Definition at line 126 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ BinaryThresholdImageFilterType_UC_UC

template<typename TInputImage >
typedef itk::BinaryThresholdImageFilter<ImageTypeUC, ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::BinaryThresholdImageFilterType_UC_UC

Definition at line 127 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ CheckStructureNeighborFilterFilterType

Definition at line 116 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ComputeMahalanobisImagesFilterType

Definition at line 119 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ComputeSolutionType

Definition at line 120 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ConnectedComponentType

template<typename TInputImage >
typedef itk::ConnectedComponentImageFilter<ImageTypeUC,ImageTypeInt> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ConnectedComponentType

Definition at line 131 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ConstPointer

template<typename TInputImage >
typedef itk::SmartPointer<const Self> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ConstPointer

Definition at line 80 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GaussianFunctionType

template<typename TInputImage >
typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorType > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GaussianFunctionType

Definition at line 112 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GraphCutFilterType

template<typename TInputImage >
typedef anima::GraphCutFilter< TInputImage, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCutFilterType

Define filters.

Definition at line 115 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageIteratorTypeConstInput

template<typename TInputImage >
typedef itk::ImageRegionConstIterator<InputImageType> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeConstInput

Definition at line 90 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageIteratorTypeConstUC

template<typename TInputImage >
typedef itk::ImageRegionConstIterator<ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeConstUC

Definition at line 101 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageIteratorTypeD

template<typename TInputImage >
typedef itk::ImageRegionIterator<ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeD

Definition at line 105 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageIteratorTypeInt

template<typename TInputImage >
typedef itk::ImageRegionIterator<ImageTypeInt> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeInt

Definition at line 109 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageIteratorTypeUC

template<typename TInputImage >
typedef itk::ImageRegionIterator<ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageIteratorTypeUC

Definition at line 100 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageTypeD

template<typename TInputImage >
typedef itk::Image<PixelTypeD,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeD

Definition at line 104 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageTypeInt

template<typename TInputImage >
typedef itk::Image<PixelTypeInt,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeInt

Definition at line 108 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ ImageTypeUC

template<typename TInputImage >
typedef itk::Image<PixelTypeUC,3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ImageTypeUC

Definition at line 99 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ InputImageType

template<typename TInputImage >
typedef TInputImage anima::GcStremMsLesionsSegmentationFilter< TInputImage >::InputImageType

Type of the input images.

Definition at line 89 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ IntensityWindowingImageFilterType

template<typename TInputImage >
typedef itk::IntensityWindowingImageFilter<ImageTypeUC, ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::IntensityWindowingImageFilterType

Definition at line 128 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ MaskFilterType_F_UC

template<typename TInputImage >
typedef itk::MaskImageFilter< ImageTypeD, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaskFilterType_F_UC

Definition at line 130 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ MaskFilterType_UC_UC

template<typename TInputImage >
typedef itk::MaskImageFilter< ImageTypeUC, ImageTypeUC > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaskFilterType_UC_UC

Definition at line 129 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ MaximumFilterType

template<typename TInputImage >
typedef itk::MaximumImageFilter<ImageTypeD,ImageTypeD,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MaximumFilterType

Definition at line 123 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ MeasurementVectorType

template<typename TInputImage >
typedef itk::VariableLengthVector<double> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MeasurementVectorType

Definition at line 111 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ MinimumFilterTypeF

template<typename TInputImage >
typedef itk::MinimumImageFilter<ImageTypeD,ImageTypeD,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MinimumFilterTypeF

Definition at line 124 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ MinimumFilterTypeUC

template<typename TInputImage >
typedef itk::MinimumImageFilter<ImageTypeUC,ImageTypeUC,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MinimumFilterTypeUC

Definition at line 125 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ OutputImagePointer

template<typename TInputImage >
typedef OutputImageType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputImagePointer

Definition at line 94 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ OutputImageType

template<typename TInputImage >
typedef TOutputImage anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputImageType

Type of the output images.

Definition at line 93 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ OutputIteratorType

template<typename TInputImage >
typedef itk::ImageRegionIterator< OutputImageType > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputIteratorType

Definition at line 95 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ OutputPixelType

template<typename TInputImage >
typedef OutputImageType::PixelType anima::GcStremMsLesionsSegmentationFilter< TInputImage >::OutputPixelType

Definition at line 96 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ PixelTypeD

template<typename TInputImage >
typedef double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeD

Definition at line 103 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ PixelTypeInt

template<typename TInputImage >
typedef int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeInt

Definition at line 107 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ PixelTypeUC

template<typename TInputImage >
typedef unsigned char anima::GcStremMsLesionsSegmentationFilter< TInputImage >::PixelTypeUC

Definition at line 98 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ Pointer

template<typename TInputImage >
typedef itk::SmartPointer<Self> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Pointer

Definition at line 79 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ RelabelComponentType

template<typename TInputImage >
typedef itk::RelabelComponentImageFilter< ImageTypeInt, ImageTypeInt > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RelabelComponentType

Definition at line 132 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ RemoveTouchingBorderFilterType

Definition at line 117 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ RescaleFilterType

template<typename TInputImage >
typedef itk::RescaleIntensityImageFilter<TInputImage,ImageTypeUC> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RescaleFilterType

Definition at line 122 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ Self

template<typename TInputImage >
typedef GcStremMsLesionsSegmentationFilter anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Self

Standard class typedefs.

Definition at line 76 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ Superclass

template<typename TInputImage >
typedef itk::ImageToImageFilter< TInputImage, TOutputImage > anima::GcStremMsLesionsSegmentationFilter< TInputImage >::Superclass

Definition at line 78 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ TLinksFilterType

template<typename TInputImage >
typedef anima::TLinksFilter<TInputImage,ImageTypeD> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::TLinksFilterType

Definition at line 118 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ TOutputImage

template<typename TInputImage >
typedef itk::Image<unsigned char, 3> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::TOutputImage

Definition at line 77 of file animaGcStremMsLesionsSegmentationFilter.h.

Constructor & Destructor Documentation

◆ GcStremMsLesionsSegmentationFilter()

template<typename TInputImage >
anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GcStremMsLesionsSegmentationFilter ( )
inlineprotected

◆ ~GcStremMsLesionsSegmentationFilter()

template<typename TInputImage >
anima::GcStremMsLesionsSegmentationFilter< TInputImage >::~GcStremMsLesionsSegmentationFilter ( )
inlineprotected

Member Function Documentation

◆ ApplyHeuristicRules()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ApplyHeuristicRules ( )

Intensity Rule: MS lesions are known to be hyperintense compared to the WM intensity on T2-w and PD-w and FLAIR sequences. We use the information given by the NABT model to define hyper-intensity. A voxel is considered to be hyper-intense for a given sequence if its intensity y is greater than a threshold T that is defined by the probability of the Gaussian distribution and an intensity factor intensityFactor: For example the hyperintensity threshold T in T2 is defined as: T = meanT2 + intensityFactor * stdT2 meanT2 and stdT2 being the mean and standard deviation of the white matter in the sequence T2. If the voxel is not considered hyper-intense on T2-w, PD and FLAIR, it is discarded as a lesion voxel.

Size Rule: In order to avoid false positives, candidate lesions smaller than 9 mm3 in size are rejected. These small candidate lesions are usually produced by noise or flow artifacts. In clinical practice, lesions must have a radius of 3 mm on one image slice to be considered as such.

Definition at line 897 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References HierarchicalDP, and manualGC.

◆ CheckInputImages()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CheckInputImages ( )

Definition at line 391 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC.

◆ ComputeAutomaticInitialization()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeAutomaticInitialization ( )

Definition at line 534 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ ComputeNABT()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ComputeNABT ( )

Definition at line 1127 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC.

◆ CreateAnother()

template<typename TInputImage >
virtual::itk::LightObject::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CreateAnother ( void  ) const

◆ CreateFuzzyRuleImage()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::CreateFuzzyRuleImage ( )

Definition at line 695 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ EmitProgress()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::EmitProgress ( int  prog)
protected

◆ GenerateData()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GenerateData ( )

Definition at line 1230 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC, and strem.

◆ GetAlpha()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetAlpha ( )
virtual

◆ GetEM_before_concentration()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetEM_before_concentration ( )
virtual

◆ GetEmIter()

template<typename TInputImage >
virtual int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetEmIter ( )
virtual

◆ GetEmIter_concentration()

template<typename TInputImage >
virtual int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetEmIter_concentration ( )
virtual

◆ GetFuzzyOutputObjectFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetFuzzyOutputObjectFilename ( )
inline

Definition at line 314 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetFuzzyRuleMax()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetFuzzyRuleMax ( )
virtual

◆ GetFuzzyRuleMin()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetFuzzyRuleMin ( )
virtual

◆ GetInitMethodType()

template<typename TInputImage >
virtual unsigned int anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInitMethodType ( )
virtual

◆ GetInputCSFAtlas()

template<typename TInputImage >
itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputCSFAtlas ( )
protected

◆ GetInputGMAtlas()

template<typename TInputImage >
itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputGMAtlas ( )
protected

◆ GetInputImageDP()

template<typename TInputImage >
TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageDP ( )
protected

◆ GetInputImageFLAIR()

template<typename TInputImage >
TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageFLAIR ( )
protected

◆ GetInputImageT1()

template<typename TInputImage >
TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT1 ( )
protected

◆ GetInputImageT1Gd()

template<typename TInputImage >
TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT1Gd ( )
protected

◆ GetInputImageT2()

template<typename TInputImage >
TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputImageT2 ( )
protected

◆ GetInputLesionPrior()

template<typename TInputImage >
itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputLesionPrior ( )
protected

◆ GetInputWMAtlas()

template<typename TInputImage >
itk::Image< double, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetInputWMAtlas ( )
protected

◆ GetIntensityDPFactor()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetIntensityDPFactor ( )
virtual

◆ GetIntensityFLAIRFactor()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetIntensityFLAIRFactor ( )
virtual

◆ GetIntensityT2Factor()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetIntensityT2Factor ( )
virtual

◆ GetLesionPriorProportion()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetLesionPriorProportion ( )
virtual

◆ GetLesionSegmentationType()

template<typename TInputImage >
LesionSegmentationType anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetLesionSegmentationType ( )
inline

Definition at line 281 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetMahalanobisThCSF()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMahalanobisThCSF ( )
virtual

◆ GetMahalanobisThGM()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMahalanobisThGM ( )
virtual

◆ GetMahalanobisThWM()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMahalanobisThWM ( )
virtual

◆ GetMask()

template<typename TInputImage >
TInputImage::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMask ( )
protected

◆ GetMatrixGradFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMatrixGradFilename ( )
inline

Definition at line 344 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetMinDistance()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMinDistance ( )
virtual

◆ GetMinLesionsSize()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMinLesionsSize ( )
virtual

◆ GetMultiVarSinks()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMultiVarSinks ( )
virtual

◆ GetMultiVarSources()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetMultiVarSources ( )
virtual

◆ GetNameOfClass()

template<typename TInputImage >
virtual const char* anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetNameOfClass ( ) const
virtual

Run-time type information (and related methods)

◆ GetOutputCSF()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputCSF ( )

Definition at line 219 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputCSFFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputCSFFilename ( )
inline

Definition at line 287 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputFuzzyObjectImage()

template<typename TInputImage >
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputFuzzyObjectImage ( )

Definition at line 269 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputGCFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGCFilename ( )
inline

Definition at line 299 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputGM()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGM ( )

Definition at line 224 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputGMFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGMFilename ( )
inline

Definition at line 290 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputGraphCut()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputGraphCut ( )

Definition at line 299 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputIntensityImage1()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage1 ( )

Definition at line 259 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputIntensityImage1Filename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage1Filename ( )
inline

Definition at line 332 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputIntensityImage2()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage2 ( )

Definition at line 264 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputIntensityImage2Filename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputIntensityImage2Filename ( )
inline

Definition at line 335 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputLesionFile()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputLesionFile ( )
inline

Definition at line 284 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputLesions()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputLesions ( )

Definition at line 214 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputMahaCSFFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaCSFFilename ( )
inline

Definition at line 317 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputMahaCSFImage()

template<typename TInputImage >
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaCSFImage ( )

Definition at line 274 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputMahaGMFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaGMFilename ( )
inline

Definition at line 320 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputMahaGMImage()

template<typename TInputImage >
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaGMImage ( )

Definition at line 279 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputMahaMaximumFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMaximumFilename ( )
inline

Definition at line 326 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputMahaMaximumImage()

template<typename TInputImage >
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMaximumImage ( )

Definition at line 294 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputMahaMinimumFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMinimumFilename ( )
inline

Definition at line 329 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputMahaMinimumImage()

template<typename TInputImage >
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaMinimumImage ( )

Definition at line 289 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputMahaWMFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaWMFilename ( )
inline

Definition at line 323 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputMahaWMImage()

template<typename TInputImage >
itk::Image< double, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputMahaWMImage ( )

Definition at line 284 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputStrem()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStrem ( )

Definition at line 239 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputStremCSF()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremCSF ( )

Definition at line 244 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputStremCSFFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremCSFFilename ( )
inline

Definition at line 305 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputStremFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremFilename ( )
inline

Definition at line 302 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputStremGM()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremGM ( )

Definition at line 249 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputStremGMFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremGMFilename ( )
inline

Definition at line 308 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputStremWM()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremWM ( )

Definition at line 254 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputStremWMFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputStremWMFilename ( )
inline

Definition at line 311 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputWholeFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWholeFilename ( )
inline

Definition at line 296 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetOutputWholeSeg()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWholeSeg ( )

Definition at line 234 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputWM()

template<typename TInputImage >
itk::Image< unsigned char, 3 > * anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWM ( )

Definition at line 229 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ GetOutputWMFilename()

template<typename TInputImage >
std::string anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetOutputWMFilename ( )
inline

Definition at line 293 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetRatioContourWM()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRatioContourWM ( )
virtual

◆ GetRejRatio()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRejRatio ( )
virtual

◆ GetRejRatioHierar()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRejRatioHierar ( )
virtual

◆ GetRemoveBorder()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetRemoveBorder ( )
virtual

◆ GetSigma()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSigma ( )
virtual

◆ GetSinksMask()

template<typename TInputImage >
itk::Image< unsigned char, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSinksMask ( )
protected

◆ GetSolution()

template<typename TInputImage >
std::vector<GaussianFunctionType::Pointer> anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSolution ( )
inline

Definition at line 339 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ GetSourcesMask()

template<typename TInputImage >
itk::Image< unsigned char, 3 >::ConstPointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetSourcesMask ( )
protected

◆ GetThresoldWMmap()

template<typename TInputImage >
virtual double anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetThresoldWMmap ( )
virtual

◆ GetUseDP()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseDP ( )
virtual

◆ GetUseFLAIR()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseFLAIR ( )
virtual

◆ GetUseSpecGrad()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseSpecGrad ( )
virtual

◆ GetUseT2()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetUseT2 ( )
virtual

◆ GetVerbose()

template<typename TInputImage >
virtual bool anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GetVerbose ( )
virtual

◆ GraphCut()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::GraphCut ( )

◆ MakeOutput()

template<typename TInputImage >
itk::DataObject::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::MakeOutput ( unsigned int  idx)
protected

◆ ManageProgress()

template<typename TInputImage >
static void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::ManageProgress ( itk::Object *  caller,
const itk::EventObject &  event,
void *  clientData 
)
staticprotected

◆ New()

template<typename TInputImage >
static Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::New ( )
static

Method for creation through the object factory.

◆ RescaleImages()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::RescaleImages ( void  )

Definition at line 427 of file animaGcStremMsLesionsSegmentationFilter.hxx.

References manualGC.

◆ SetAlpha()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetAlpha ( double  _arg)
virtual

◆ SetEM_before_concentration()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetEM_before_concentration ( bool  _arg)
virtual

◆ SetEmIter()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetEmIter ( int  _arg)
virtual

◆ SetEmIter_concentration()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetEmIter_concentration ( int  _arg)
virtual

◆ SetFuzzyRuleMax()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetFuzzyRuleMax ( double  _arg)
virtual

◆ SetFuzzyRuleMin()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetFuzzyRuleMin ( double  _arg)
virtual

◆ SetGaussianModel()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetGaussianModel ( std::vector< GaussianFunctionType::Pointer >  solution)
inline

Definition at line 338 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetInitMethodType()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInitMethodType ( unsigned int  _arg)
virtual

Setter/Getter for parameters

◆ SetInputCSFAtlas()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputCSFAtlas ( const ImageTypeD image)

Definition at line 60 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputGMAtlas()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputGMAtlas ( const ImageTypeD image)

Definition at line 68 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputImageDP()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageDP ( const InputImageType image)

Definition at line 33 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputImageFLAIR()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageFLAIR ( const InputImageType image)

Definition at line 42 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputImageT1()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT1 ( const InputImageType image)

Setter for images

Definition at line 15 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputImageT1Gd()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT1Gd ( const InputImageType image)

Definition at line 51 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputImageT2()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputImageT2 ( const InputImageType image)

Definition at line 24 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputLesionPrior()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputLesionPrior ( const ImageTypeD image)

Definition at line 84 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetInputWMAtlas()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetInputWMAtlas ( const ImageTypeD image)

Definition at line 76 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetIntensityDPFactor()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetIntensityDPFactor ( double  _arg)
virtual

◆ SetIntensityFLAIRFactor()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetIntensityFLAIRFactor ( double  _arg)
virtual

◆ SetIntensityT2Factor()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetIntensityT2Factor ( double  _arg)
virtual

◆ SetLesionPriorProportion()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetLesionPriorProportion ( double  _arg)
virtual

◆ SetLesionSegmentationType()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetLesionSegmentationType ( LesionSegmentationType  type)
inline

Definition at line 282 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetMahalanobisThCSF()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMahalanobisThCSF ( double  _arg)
virtual

◆ SetMahalanobisThGM()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMahalanobisThGM ( double  _arg)
virtual

◆ SetMahalanobisThWM()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMahalanobisThWM ( double  _arg)
virtual

◆ SetMask()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMask ( const TInputImage *  MaskImage)

Definition at line 7 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetMatrixGradFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMatrixGradFilename ( std::string  fn)
inline

Definition at line 345 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetMinDistance()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMinDistance ( double  _arg)
virtual

◆ SetMinLesionsSize()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMinLesionsSize ( double  _arg)
virtual

◆ SetMultiVarSinks()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMultiVarSinks ( double  _arg)
virtual

◆ SetMultiVarSources()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetMultiVarSources ( double  _arg)
virtual

◆ SetOutputCSFFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputCSFFilename ( std::string  fn)
inline

Definition at line 288 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputFuzzyObjectFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputFuzzyObjectFilename ( std::string  fn)
inline

Definition at line 315 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputGCFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputGCFilename ( std::string  fn)
inline

Definition at line 300 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputGMFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputGMFilename ( std::string  fn)
inline

Definition at line 291 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputIntensityImage1Filename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputIntensityImage1Filename ( std::string  fn)
inline

Definition at line 333 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputIntensityImage2Filename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputIntensityImage2Filename ( std::string  fn)
inline

Definition at line 336 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputLesionFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputLesionFilename ( std::string  fn)
inline

Definition at line 285 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputMahaCSFFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaCSFFilename ( std::string  fn)
inline

Definition at line 318 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputMahaGMFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaGMFilename ( std::string  fn)
inline

Definition at line 321 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputMahaMaximumFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaMaximumFilename ( std::string  fn)
inline

Definition at line 327 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputMahaMinimumFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaMinimumFilename ( std::string  fn)
inline

Definition at line 330 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputMahaWMFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputMahaWMFilename ( std::string  fn)
inline

Definition at line 324 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputStremCSFFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremCSFFilename ( std::string  fn)
inline

Definition at line 306 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputStremFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremFilename ( std::string  fn)
inline

Definition at line 303 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputStremGMFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremGMFilename ( std::string  fn)
inline

Definition at line 309 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputStremWMFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputStremWMFilename ( std::string  fn)
inline

Definition at line 312 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputWholeFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputWholeFilename ( std::string  fn)
inline

Definition at line 297 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetOutputWMFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetOutputWMFilename ( std::string  fn)
inline

Definition at line 294 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetRatioContourWM()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRatioContourWM ( double  _arg)
virtual

◆ SetRejRatio()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRejRatio ( double  _arg)
virtual

◆ SetRejRatioHierar()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRejRatioHierar ( double  _arg)
virtual

◆ SetRemoveBorder()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetRemoveBorder ( bool  _arg)
virtual

◆ SetSigma()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSigma ( double  _arg)
virtual

◆ SetSinksMask()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSinksMask ( const ImageTypeUC MaskImage)

Definition at line 100 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetSolutionReadFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSolutionReadFilename ( std::string  fn)
inline

Definition at line 341 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetSolutionWriteFilename()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSolutionWriteFilename ( std::string  fn)
inline

Definition at line 342 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetSourcesMask()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetSourcesMask ( const ImageTypeUC MaskImage)

Definition at line 92 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ SetThresoldWMmap()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetThresoldWMmap ( double  _arg)
virtual

◆ SetTol()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetTol ( const double  tol)
inline

Definition at line 184 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ SetUseDP()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseDP ( bool  _arg)
virtual

◆ SetUseFLAIR()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseFLAIR ( bool  _arg)
virtual

◆ SetUseSpecGrad()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseSpecGrad ( bool  _arg)
virtual

◆ SetUseT2()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetUseT2 ( bool  _arg)
virtual

◆ SetVerbose()

template<typename TInputImage >
virtual void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::SetVerbose ( bool  _arg)
virtual

◆ StremThreshold()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::StremThreshold ( )

Definition at line 610 of file animaGcStremMsLesionsSegmentationFilter.hxx.

◆ WriteOutputs()

template<typename TInputImage >
void anima::GcStremMsLesionsSegmentationFilter< TInputImage >::WriteOutputs ( )

Member Data Documentation

◆ m_FilterMaxSinks

template<typename TInputImage >
MaximumFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_FilterMaxSinks
protected

Definition at line 351 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ m_FilterMaxSources

template<typename TInputImage >
MaximumFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_FilterMaxSources
protected

Definition at line 350 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ m_GraphCutFilter

template<typename TInputImage >
GraphCutFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_GraphCutFilter
protected

Definition at line 348 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ m_MahalanobisFilter

template<typename TInputImage >
ComputeMahalanobisImagesFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_MahalanobisFilter
protected

Definition at line 352 of file animaGcStremMsLesionsSegmentationFilter.h.

◆ m_TLinksFilter

template<typename TInputImage >
TLinksFilterType::Pointer anima::GcStremMsLesionsSegmentationFilter< TInputImage >::m_TLinksFilter
protected

Definition at line 349 of file animaGcStremMsLesionsSegmentationFilter.h.


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