ANIMA
4.0
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Class computing the 3-class GMM respresenting the NABT, where each Gaussian represents one of the brain tissues WM, GM and CSF. First a model initializer is launched, then the REM algorithm is performed using this initialization. The NABT model can be written in a csv file. More...
#include <animaComputeSolution.h>
Public Types | |
typedef AtlasInitializer< ImageTypeUC, MaskImageType, TAtlasImage > | AtlasInitializerType |
typedef itk::SmartPointer< const Self > | ConstPointer |
typedef GaussianEMEstimator< ImageTypeUC, MaskImageType > | GaussianEMEstimatorType |
typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorType > | GaussianFunctionType |
typedef GaussianREMEstimator< ImageTypeUC, MaskImageType > | GaussianREMEstimatorType |
typedef HierarchicalInitializer< ImageTypeUC, MaskImageType > | HierarchicalType |
typedef ImageTypeUC::Pointer | ImagePointerUC |
typedef itk::Image< PixelTypeUC, 3 > | ImageTypeUC |
typedef itk::ImageRegionConstIterator< InputImageType > | InputConstIteratorType |
typedef InputImageType::ConstPointer | InputImageConstPointer |
typedef TInputImage | InputImageType |
typedef TMaskImage | MaskImageType |
typedef itk::VariableLengthVector< NumericType > | MeasurementVectorType |
typedef double | NumericType |
typedef unsigned char | PixelTypeUC |
typedef itk::SmartPointer< Self > | Pointer |
typedef itk::RescaleIntensityImageFilter< TInputImage, ImageTypeUC > | RescaleFilterType |
typedef ComputeSolution | Self |
typedef itk::ProcessObject | Superclass |
Public Member Functions | |
virtual ::itk::LightObject::Pointer | CreateAnother (void) const |
std::vector< double > | GetAlphas () |
virtual bool | GetEM_before_concentration () |
virtual int | GetEmIter () |
virtual int | GetEmIter_concentration () |
std::vector< GaussianFunctionType::Pointer > | GetGaussianModel () |
virtual unsigned int | GetInitMethodType () |
virtual double | GetMinDistance () |
virtual const char * | GetNameOfClass () const |
virtual double | GetRejRatio () |
virtual double | GetRejRatioHierar () |
virtual double | GetTol () |
virtual bool | GetUseDP () |
virtual bool | GetUseFLAIR () |
virtual bool | GetUseT2 () |
virtual bool | GetVerbose () |
int | PrintSolution (std::vector< double > alphas, std::vector< GaussianFunctionType::Pointer > model) |
int | ReadSolution (std::string filename) |
void | SetAlphas (std::vector< double > alpha) |
virtual void | SetEM_before_concentration (bool _arg) |
virtual void | SetEmIter (int _arg) |
virtual void | SetEmIter_concentration (int _arg) |
void | SetGaussianModel (std::vector< GaussianFunctionType::Pointer > model) |
virtual void | SetInitMethodType (unsigned int _arg) |
void | SetInputCSFAtlas (const TAtlasImage *atlas) |
void | SetInputGMAtlas (const TAtlasImage *atlas) |
void | SetInputImage1 (const InputImageType *image) |
void | SetInputImage2 (const InputImageType *image) |
void | SetInputImage3 (const InputImageType *image) |
void | SetInputWMAtlas (const TAtlasImage *atlas) |
void | SetMask (const TMaskImage *mask) |
virtual void | SetMinDistance (double _arg) |
virtual void | SetRejRatio (double _arg) |
virtual void | SetRejRatioHierar (double _arg) |
void | SetSolutionReadFilename (std::string filename) |
void | SetSolutionWriteFilename (std::string filename) |
virtual void | SetTol (double _arg) |
virtual void | SetUseDP (bool _arg) |
virtual void | SetUseFLAIR (bool _arg) |
virtual void | SetUseT2 (bool _arg) |
virtual void | SetVerbose (bool _arg) |
void | SortGaussianModel () |
virtual void | Update () ITK_OVERRIDE |
void | WriteOutputs () |
int | WriteSolution (std::string filename) |
Static Public Member Functions | |
static void | eventCallback (itk::Object *caller, const itk::EventObject &event, void *clientData) |
static Pointer | New () |
Protected Member Functions | |
void | CheckInputs (void) |
ComputeSolution () | |
TAtlasImage::ConstPointer | GetInputCSFAtlas () |
TAtlasImage::ConstPointer | GetInputGMAtlas () |
InputImageType::ConstPointer | GetInputImage1 () |
InputImageType::ConstPointer | GetInputImage2 () |
InputImageType::ConstPointer | GetInputImage3 () |
TAtlasImage::ConstPointer | GetInputWMAtlas () |
MaskImageType::ConstPointer | GetMask () |
void | RescaleImages (void) |
virtual | ~ComputeSolution () |
Class computing the 3-class GMM respresenting the NABT, where each Gaussian represents one of the brain tissues WM, GM and CSF. First a model initializer is launched, then the REM algorithm is performed using this initialization. The NABT model can be written in a csv file.
Definition at line 26 of file animaComputeSolution.h.
typedef AtlasInitializer<ImageTypeUC,MaskImageType,TAtlasImage> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::AtlasInitializerType |
Definition at line 54 of file animaComputeSolution.h.
typedef itk::SmartPointer<const Self> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::ConstPointer |
Definition at line 34 of file animaComputeSolution.h.
typedef GaussianEMEstimator<ImageTypeUC,MaskImageType> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GaussianEMEstimatorType |
Definition at line 57 of file animaComputeSolution.h.
typedef itk::Statistics::GaussianMembershipFunction< MeasurementVectorType > anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GaussianFunctionType |
Definition at line 64 of file animaComputeSolution.h.
typedef GaussianREMEstimator<ImageTypeUC,MaskImageType> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GaussianREMEstimatorType |
Definition at line 56 of file animaComputeSolution.h.
typedef HierarchicalInitializer<ImageTypeUC,MaskImageType> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::HierarchicalType |
Definition at line 55 of file animaComputeSolution.h.
typedef ImageTypeUC::Pointer anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::ImagePointerUC |
Definition at line 52 of file animaComputeSolution.h.
typedef itk::Image<PixelTypeUC,3> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::ImageTypeUC |
Definition at line 51 of file animaComputeSolution.h.
typedef itk::ImageRegionConstIterator< InputImageType > anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::InputConstIteratorType |
Definition at line 45 of file animaComputeSolution.h.
typedef InputImageType::ConstPointer anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::InputImageConstPointer |
Definition at line 44 of file animaComputeSolution.h.
typedef TInputImage anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::InputImageType |
Type of the input image.
Definition at line 43 of file animaComputeSolution.h.
typedef TMaskImage anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::MaskImageType |
Type of the output images.
Definition at line 48 of file animaComputeSolution.h.
typedef itk::VariableLengthVector<NumericType> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::MeasurementVectorType |
Definition at line 63 of file animaComputeSolution.h.
typedef double anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::NumericType |
Definition at line 62 of file animaComputeSolution.h.
typedef unsigned char anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::PixelTypeUC |
Definition at line 50 of file animaComputeSolution.h.
typedef itk::SmartPointer<Self> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::Pointer |
Definition at line 33 of file animaComputeSolution.h.
typedef itk::RescaleIntensityImageFilter<TInputImage,ImageTypeUC> anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::RescaleFilterType |
Define filter types.
Definition at line 60 of file animaComputeSolution.h.
typedef ComputeSolution anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::Self |
Standard class typedefs.
Definition at line 31 of file animaComputeSolution.h.
typedef itk::ProcessObject anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::Superclass |
Definition at line 32 of file animaComputeSolution.h.
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Definition at line 142 of file animaComputeSolution.h.
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Definition at line 167 of file animaComputeSolution.h.
References anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::CheckInputs(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetInputCSFAtlas(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetInputGMAtlas(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetInputImage1(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetInputImage2(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetInputImage3(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetInputWMAtlas(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::GetMask(), and anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::RescaleImages().
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Definition at line 132 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
virtual::itk::LightObject::Pointer anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::CreateAnother | ( | void | ) | const |
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Definition at line 99 of file animaComputeSolution.h.
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Definition at line 89 of file animaComputeSolution.h.
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Definition at line 86 of file animaComputeSolution.h.
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Definition at line 81 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 88 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 60 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 67 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 74 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 95 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 53 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Run-time type information (and related methods)
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Method for creation through the object factory.
int anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::PrintSolution | ( | std::vector< double > | alphas, |
std::vector< GaussianFunctionType::Pointer > | model | ||
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Definition at line 345 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetAlphas().
int anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::ReadSolution | ( | std::string | filename | ) |
Definition at line 272 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetAlphas().
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Definition at line 178 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::~ComputeSolution().
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Definition at line 90 of file animaComputeSolution.h.
References anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::PrintSolution(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::ReadSolution(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SortGaussianModel(), anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::Update(), and anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::WriteSolution().
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Definition at line 87 of file animaComputeSolution.h.
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void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetInputCSFAtlas | ( | const TAtlasImage * | atlas | ) |
Images for atlas initialisation
Definition at line 33 of file animaComputeSolution.hxx.
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetInputGMAtlas | ( | const TAtlasImage * | atlas | ) |
Definition at line 39 of file animaComputeSolution.hxx.
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetInputImage1 | ( | const InputImageType * | image | ) |
The mri images.
Definition at line 15 of file animaComputeSolution.hxx.
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetInputImage2 | ( | const InputImageType * | image | ) |
Definition at line 21 of file animaComputeSolution.hxx.
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetInputImage3 | ( | const InputImageType * | image | ) |
Definition at line 27 of file animaComputeSolution.hxx.
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetInputWMAtlas | ( | const TAtlasImage * | atlas | ) |
Definition at line 45 of file animaComputeSolution.hxx.
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetMask | ( | const TMaskImage * | mask | ) |
mask in which the segmentation will be performed
Definition at line 9 of file animaComputeSolution.hxx.
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Definition at line 82 of file animaComputeSolution.h.
References anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::WriteOutputs().
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Definition at line 81 of file animaComputeSolution.h.
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void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SortGaussianModel | ( | ) |
Definition at line 104 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetAlphas().
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Definition at line 374 of file animaComputeSolution.hxx.
References eventCallback().
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetAlphas().
void anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::WriteOutputs | ( | ) |
int anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::WriteSolution | ( | std::string | filename | ) |
Definition at line 215 of file animaComputeSolution.hxx.
Referenced by anima::ComputeSolution< TInputImage, TMaskImage, TAtlasImage >::SetAlphas().