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itkMRIBiasFieldCorrectionFilter.h

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00001 /*========================================================================= 00002 00003 Program: Insight Segmentation & Registration Toolkit 00004 Module: $RCSfile: itkMRIBiasFieldCorrectionFilter.h,v $ 00005 Language: C++ 00006 Date: $Date: 2003/09/10 14:28:34 $ 00007 Version: $Revision: 1.28 $ 00008 00009 Copyright (c) Insight Software Consortium. All rights reserved. 00010 See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details. 00011 00012 This software is distributed WITHOUT ANY WARRANTY; without even 00013 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00014 PURPOSE. See the above copyright notices for more information. 00015 00016 =========================================================================*/ 00017 #ifndef __itkMRIBiasFieldCorrectionFilter_h 00018 #define __itkMRIBiasFieldCorrectionFilter_h 00019 00020 #include "itkImageToImageFilter.h" 00021 #include "itkImage.h" 00022 00023 #include "itkMRASlabIdentifier.h" 00024 #include "itkCompositeValleyFunction.h" 00025 #include "itkMultivariateLegendrePolynomial.h" 00026 #include "Statistics/itkNormalVariateGenerator.h" 00027 #include "itkOnePlusOneEvolutionaryOptimizer.h" 00028 #include "itkArray.h" 00029 #include "itkImageRegionConstIterator.h" 00030 00031 00032 namespace itk 00033 { 00045 template<class TImage, class TImageMask, class TBiasField> 00046 class MRIBiasEnergyFunction : public SingleValuedCostFunction 00047 { 00048 public: 00050 typedef MRIBiasEnergyFunction Self; 00051 typedef SingleValuedCostFunction Superclass; 00052 typedef SmartPointer<Self> Pointer; 00053 typedef SmartPointer<const Self> ConstPointer; 00054 00056 itkTypeMacro( SingleValuedCostFunction, CostFunction ); 00057 00059 itkNewMacro(Self); 00060 00062 typedef TImage ImageType ; 00063 typedef TImageMask MaskType ; 00064 typedef typename ImageType::Pointer ImagePointer ; 00065 typedef typename MaskType::Pointer MaskPointer ; 00066 typedef typename ImageType::PixelType ImageElementType ; 00067 typedef typename MaskType::PixelType MaskElementType ; 00068 typedef typename ImageType::IndexType ImageIndexType ; 00069 typedef typename ImageType::RegionType ImageRegionType ; 00070 00072 typedef TBiasField BiasFieldType; 00073 00076 typedef typename Superclass::ParametersType ParametersType ; 00077 00079 typedef Superclass::DerivativeType DerivativeType; 00080 00082 typedef Superclass::MeasureType MeasureType; 00083 00085 itkStaticConstMacro(SpaceDimension, unsigned int, 3); 00086 00088 typedef CompositeValleyFunction InternalEnergyFunction ; 00089 00091 itkSetObjectMacro( Image, ImageType ); 00092 00094 itkSetObjectMacro( Mask, MaskType ); 00095 00097 itkSetMacro( Region, ImageRegionType ); 00098 00100 void SetBiasField(BiasFieldType* bias) 00101 { m_BiasField = bias ; } 00102 00105 double GetEnergy0(double diff) 00106 { return (*m_InternalEnergyFunction)(diff); } 00107 00110 MeasureType GetValue(const ParametersType & parameters ) const ; 00111 00114 void GetDerivative( const ParametersType & itkNotUsed(parameters), 00115 DerivativeType & itkNotUsed(derivative) ) const 00116 { } 00117 00122 void InitializeDistributions( Array<double> classMeans, 00123 Array<double> classSigmas ); 00124 00125 unsigned int GetNumberOfParameters(void) const; 00126 00127 private: 00129 BiasFieldType * m_BiasField ; 00130 00132 ImagePointer m_Image ; 00133 00135 MaskPointer m_Mask ; 00136 00138 ImageRegionType m_Region ; 00139 00141 InternalEnergyFunction* m_InternalEnergyFunction ; 00142 00143 protected: 00145 MRIBiasEnergyFunction(); 00146 00148 virtual ~MRIBiasEnergyFunction(); 00149 00150 00151 private: 00152 00153 MRIBiasEnergyFunction(const Self&); //purposely not implemented 00154 void operator=(const Self&); //purposely not implemented 00155 00156 } ; // end of class 00157 00158 00159 00197 template <class TInputImage, class TOutputImage, class TMaskImage> 00198 class ITK_EXPORT MRIBiasFieldCorrectionFilter : 00199 public ImageToImageFilter< TInputImage, TOutputImage > 00200 { 00201 public: 00203 typedef MRIBiasFieldCorrectionFilter Self; 00204 typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass; 00205 typedef SmartPointer<Self> Pointer; 00206 typedef SmartPointer<const Self> ConstPointer; 00207 00209 itkNewMacro(Self); 00210 00212 itkTypeMacro(MRIBiasFieldCorrectionFilter, ImageToImageFilter); 00213 00215 itkStaticConstMacro(ImageDimension, unsigned int, 00216 TOutputImage::ImageDimension); 00217 00219 typedef TOutputImage OutputImageType ; 00220 typedef TInputImage InputImageType ; 00221 typedef typename TOutputImage::Pointer OutputImagePointer ; 00222 typedef typename TOutputImage::IndexType OutputImageIndexType ; 00223 typedef typename TOutputImage::PixelType OutputImagePixelType ; 00224 typedef typename TOutputImage::SizeType OutputImageSizeType; 00225 typedef typename TOutputImage::RegionType OutputImageRegionType; 00226 typedef typename TInputImage::Pointer InputImagePointer ; 00227 typedef typename TInputImage::IndexType InputImageIndexType; 00228 typedef typename TInputImage::PixelType InputImagePixelType; 00229 typedef typename TInputImage::SizeType InputImageSizeType; 00230 typedef typename TInputImage::RegionType InputImageRegionType; 00231 00233 typedef TMaskImage ImageMaskType ; 00234 typedef typename ImageMaskType::Pointer ImageMaskPointer ; 00235 typedef typename ImageMaskType::RegionType ImageMaskRegionType ; 00236 00238 typedef Image< float, itkGetStaticConstMacro(ImageDimension) > InternalImageType ; 00239 typedef typename InternalImageType::PixelType InternalImagePixelType ; 00240 typedef typename InternalImageType::Pointer InternalImagePointer ; 00241 typedef typename InternalImageType::RegionType InternalImageRegionType ; 00242 00244 typedef MRASlabIdentifier<InputImageType> MRASlabIdentifierType; 00245 typedef typename MRASlabIdentifierType::SlabRegionVectorType 00246 SlabRegionVectorType; 00247 typedef typename SlabRegionVectorType::iterator SlabRegionVectorIteratorType; 00248 00250 typedef MultivariateLegendrePolynomial BiasFieldType; 00251 00253 typedef MRIBiasEnergyFunction<InternalImageType, ImageMaskType, BiasFieldType> 00254 EnergyFunctionType; 00255 typedef typename EnergyFunctionType::Pointer EnergyFunctionPointer; 00256 00258 typedef Statistics::NormalVariateGenerator NormalVariateGeneratorType ; 00259 00261 typedef OnePlusOneEvolutionaryOptimizer OptimizerType ; 00262 00266 void SetInputMask(ImageMaskType* inputMask); 00267 itkGetObjectMacro( InputMask, ImageMaskType ); 00268 00271 void SetOutputMask(ImageMaskType* outputMask) ; 00272 00274 itkGetObjectMacro( OutputMask, ImageMaskType ); 00275 00279 void IsBiasFieldMultiplicative(bool flag) 00280 { m_BiasMultiplicative = flag ; } 00281 00283 bool IsBiasFieldMultiplicative() 00284 { return m_BiasMultiplicative ; } 00285 00289 itkSetMacro( UsingInterSliceIntensityCorrection, bool ); 00290 itkGetConstMacro( UsingInterSliceIntensityCorrection, bool ); 00291 00297 itkSetMacro( UsingSlabIdentification, bool ); 00298 itkGetConstMacro( UsingSlabIdentification, bool ); 00299 00300 itkSetMacro( SlabBackgroundMinimumThreshold, InputImagePixelType ); 00301 itkGetConstMacro( SlabBackgroundMinimumThreshold, InputImagePixelType ); 00302 00303 itkSetMacro( SlabNumberOfSamples, unsigned int ); 00304 itkGetConstMacro( SlabNumberOfSamples, unsigned int ); 00305 00306 itkSetMacro( SlabTolerance, double ); 00307 itkGetConstMacro( SlabTolerance, double ); 00308 00314 itkSetMacro( UsingBiasFieldCorrection, bool ); 00315 itkGetConstMacro( UsingBiasFieldCorrection, bool ); 00316 00319 itkSetMacro( GeneratingOutput, bool ); 00320 itkGetConstMacro( GeneratingOutput, bool ); 00321 00324 itkSetMacro( SlicingDirection , int ); 00325 00327 itkSetMacro( BiasFieldDegree, int ); 00328 itkGetMacro( BiasFieldDegree, int ); 00329 00332 void SetInitialBiasFieldCoefficients 00333 (const BiasFieldType::CoefficientArrayType &coefficients) 00334 { m_BiasFieldCoefficients = coefficients ; } 00335 00339 BiasFieldType::CoefficientArrayType GetEstimatedBiasFieldCoefficients() 00340 { return m_EstimatedBiasFieldCoefficients ; } 00341 00345 void SetTissueClassStatistics(const Array<double> & means, 00346 const Array<double> & sigmas) 00347 throw (ExceptionObject) ; 00348 00350 itkSetMacro( VolumeCorrectionMaximumIteration, int ); 00351 itkGetMacro( VolumeCorrectionMaximumIteration, int ); 00352 itkSetMacro( InterSliceCorrectionMaximumIteration, int ); 00353 itkGetMacro( InterSliceCorrectionMaximumIteration, int ); 00354 00356 void SetOptimizerInitialRadius(double initRadius) 00357 { m_OptimizerInitialRadius = initRadius ; } 00358 double GetOptimizerInitialRadius() 00359 { return m_OptimizerInitialRadius ; } 00360 00362 itkSetMacro( OptimizerGrowthFactor, double ); 00363 itkGetMacro( OptimizerGrowthFactor, double ); 00364 00367 itkSetMacro( OptimizerShrinkFactor, double ); 00368 itkGetMacro( OptimizerShrinkFactor, double ); 00369 00376 void Initialize() throw (ExceptionObject) ; 00377 00380 BiasFieldType EstimateBiasField(InputImageRegionType region, 00381 unsigned int degree, 00382 int maximumIteration) ; 00383 00387 void CorrectImage(BiasFieldType& bias, 00388 InputImageRegionType region) ; 00389 00392 void CorrectInterSliceIntensityInhomogeneity(InputImageRegionType region) ; 00393 00394 protected: 00395 MRIBiasFieldCorrectionFilter() ; 00396 virtual ~MRIBiasFieldCorrectionFilter() ; 00397 void PrintSelf(std::ostream& os, Indent indent) const; 00398 00401 bool CheckMaskImage(ImageMaskType* mask) ; 00402 00403 protected: 00407 void Log1PImage(InternalImageType* source, 00408 InternalImageType* target) ; 00409 00412 void ExpImage(InternalImageType* source, 00413 InternalImageType* target) ; 00414 00417 template<class TSource, class TTarget> 00418 void CopyAndConvertImage(const TSource * source, 00419 TTarget * target, 00420 typename TTarget::RegionType requestedRegion) 00421 { 00422 typedef ImageRegionConstIterator<TSource> SourceIterator ; 00423 typedef ImageRegionIterator<TTarget> TargetIterator ; 00424 typedef typename TTarget::PixelType TargetPixelType ; 00425 00426 SourceIterator s_iter(source, requestedRegion) ; 00427 TargetIterator t_iter(target, requestedRegion) ; 00428 00429 s_iter.GoToBegin() ; 00430 t_iter.GoToBegin() ; 00431 while (!s_iter.IsAtEnd()) 00432 { 00433 t_iter.Set(static_cast<TargetPixelType>( s_iter.Get() ) ) ; 00434 ++s_iter ; 00435 ++t_iter ; 00436 } 00437 } 00438 00443 void GetBiasFieldSize(InputImageRegionType region, 00444 BiasFieldType::DomainSizeType& domainSize) ; 00445 00449 void AdjustSlabRegions(SlabRegionVectorType& slabs, 00450 OutputImageRegionType requestedRegion) ; 00451 00452 void GenerateData() ; 00453 00454 private: 00455 MRIBiasFieldCorrectionFilter(const Self&); //purposely not implemented 00456 void operator=(const Self&); //purposely not implemented 00457 00459 EnergyFunctionPointer m_EnergyFunction ; 00460 00462 NormalVariateGeneratorType::Pointer m_NormalVariateGenerator ; 00463 00465 ImageMaskPointer m_InputMask ; 00466 00468 ImageMaskPointer m_OutputMask ; 00469 00471 InternalImagePointer m_InternalInput ; 00472 00474 SlabRegionVectorType m_Slabs ; 00475 00477 int m_SlicingDirection ; 00478 00480 bool m_BiasMultiplicative ; 00481 00483 bool m_UsingInterSliceIntensityCorrection ; 00484 bool m_UsingSlabIdentification ; 00485 bool m_UsingBiasFieldCorrection ; 00486 bool m_GeneratingOutput ; 00487 00488 unsigned int m_SlabNumberOfSamples ; 00489 InputImagePixelType m_SlabBackgroundMinimumThreshold ; 00490 double m_SlabTolerance ; 00492 int m_BiasFieldDegree ; 00493 00496 BiasFieldType::CoefficientArrayType m_BiasFieldCoefficients ; 00497 00500 BiasFieldType::CoefficientArrayType m_EstimatedBiasFieldCoefficients ; 00501 00503 int m_VolumeCorrectionMaximumIteration ; 00504 00506 int m_InterSliceCorrectionMaximumIteration ; 00507 00509 double m_OptimizerInitialRadius ; 00510 00512 double m_OptimizerGrowthFactor ; 00513 00515 double m_OptimizerShrinkFactor ; 00516 00518 Array<double> m_TissueClassMeans ; 00519 00521 Array<double> m_TissueClassSigmas ; 00522 }; 00523 00524 00525 // ================================== 00526 00527 00528 } // end namespace itk 00529 00530 #ifndef ITK_MANUAL_INSTANTIATION 00531 #include "itkMRIBiasFieldCorrectionFilter.txx" 00532 #endif 00533 00534 #endif

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