itkMRIBiasFieldCorrectionFilter.h

Go to the documentation of this file.

/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkMRIBiasFieldCorrectionFilter_h
#define itkMRIBiasFieldCorrectionFilter_h

#include <ctime>

#include "itkImageToImageFilter.h"
#include "itkArray2D.h"
#include "itkMRASlabIdentifier.h"
#include "itkCompositeValleyFunction.h"
#include "itkMultivariateLegendrePolynomial.h"
#include "itkNormalVariateGenerator.h"
#include "itkOnePlusOneEvolutionaryOptimizer.h"
#include "itkImageRegionIterator.h"

namespace itk
{
template< typename TImage, typename TImageMask, typename TBiasField >
class ITK_TEMPLATE_EXPORT MRIBiasEnergyFunction : public SingleValuedCostFunction
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(MRIBiasEnergyFunction);

  using Self = MRIBiasEnergyFunction;
  using Superclass = SingleValuedCostFunction;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkTypeMacro(MRIBiasEnergyFunction, SingleValuedCostFunction);

  itkNewMacro(Self);

  using ImageType = TImage;
  using ImagePointer = typename ImageType::Pointer;
  using ImageElementType = typename ImageType::PixelType;
  using ImageIndexType = typename ImageType::IndexType;
  using ImageRegionType = typename ImageType::RegionType;
  using MaskType = TImageMask;
  using MaskPointer = typename MaskType::Pointer;
  using MaskElementType = typename MaskType::PixelType;

  using BiasFieldType = TBiasField;

  using ParametersType = typename Superclass::ParametersType;

  using DerivativeType = Superclass::DerivativeType;

  using MeasureType = Superclass::MeasureType;

  static constexpr unsigned int SpaceDimension = 3;

  using InternalEnergyFunction = CompositeValleyFunction;

  typedef unsigned int SamplingFactorType[SpaceDimension];

  itkSetObjectMacro(Image, ImageType);

  itkSetObjectMacro(Mask, MaskType);

  itkSetMacro(Region, ImageRegionType);

  void SetBiasField(BiasFieldType *bias)
  { m_BiasField = bias; }

  void SetSamplingFactors(SamplingFactorType factor)
  {
    for ( unsigned int i = 0; i < SpaceDimension; i++ )
      {
      m_SamplingFactor[i] = factor[i];
      }
  }

  double GetEnergy0(double diff)
  {
    return ( *m_InternalEnergyFunction )( diff );
  }

  MeasureType GetValue(const ParametersType & parameters) const override;

  void GetDerivative( const ParametersType & itkNotUsed(parameters),
                      DerivativeType & itkNotUsed(derivative) ) const override
  {}

  void InitializeDistributions(Array< double > classMeans,
                               Array< double > classSigmas);

  unsigned int GetNumberOfParameters() const override;

protected:
  MRIBiasEnergyFunction();

  ~MRIBiasEnergyFunction() override;

private:
  BiasFieldType        *m_BiasField;

  ImagePointer m_Image;

  MaskPointer m_Mask;

  ImageRegionType m_Region;

  InternalEnergyFunction *m_InternalEnergyFunction;

  SamplingFactorType m_SamplingFactor;
};                                     // end of class

template< typename TInputImage, typename TOutputImage, typename TMaskImage >
class ITK_TEMPLATE_EXPORT MRIBiasFieldCorrectionFilter :
  public ImageToImageFilter< TInputImage, TOutputImage >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(MRIBiasFieldCorrectionFilter);

  using Self = MRIBiasFieldCorrectionFilter;
  using Superclass = ImageToImageFilter< TInputImage, TOutputImage >;
  using Pointer = SmartPointer< Self >;
  using ConstPointer = SmartPointer< const Self >;

  itkNewMacro(Self);

  itkTypeMacro(MRIBiasFieldCorrectionFilter, ImageToImageFilter);

  static constexpr unsigned int ImageDimension = TOutputImage::ImageDimension;

  using OutputImageType = TOutputImage;
  using OutputImagePointer = typename TOutputImage::Pointer;
  using OutputImageIndexType = typename TOutputImage::IndexType;
  using OutputImagePixelType = typename TOutputImage::PixelType;
  using OutputImageSizeType = typename TOutputImage::SizeType;
  using OutputImageRegionType = typename TOutputImage::RegionType;

  using InputImageType = TInputImage;
  using InputImagePointer = typename TInputImage::Pointer;
  using InputImageIndexType = typename TInputImage::IndexType;
  using InputImagePixelType = typename TInputImage::PixelType;
  using InputImageSizeType = typename TInputImage::SizeType;
  using InputImageRegionType = typename TInputImage::RegionType;

  using ImageMaskType = TMaskImage;
  using ImageMaskPointer = typename ImageMaskType::Pointer;
  using ImageMaskRegionType = typename ImageMaskType::RegionType;

  using InternalImageType = Image< float, Self::ImageDimension >;
  using InternalImagePixelType = typename InternalImageType::PixelType;
  using InternalImagePointer = typename InternalImageType::Pointer;
  using InternalImageRegionType = typename InternalImageType::RegionType;

  using MRASlabIdentifierType = MRASlabIdentifier< InputImageType >;
  using SlabRegionVectorType = typename MRASlabIdentifierType::SlabRegionVectorType;
  using SlabRegionVectorIteratorType = typename SlabRegionVectorType::iterator;

  using BiasFieldType = MultivariateLegendrePolynomial;

  using EnergyFunctionType = MRIBiasEnergyFunction< InternalImageType,
                                 ImageMaskType,
                                 BiasFieldType >;
  using EnergyFunctionPointer = typename EnergyFunctionType::Pointer;

  using NormalVariateGeneratorType = Statistics::NormalVariateGenerator;

  using OptimizerType = OnePlusOneEvolutionaryOptimizer;

  using ScheduleType = Array2D< unsigned int >;

  void SetInputMask(ImageMaskType *inputMask);
  itkGetModifiableObjectMacro(InputMask, ImageMaskType);

  void SetOutputMask(ImageMaskType *outputMask);
  itkGetModifiableObjectMacro(OutputMask, ImageMaskType);

#if defined ( ITK_LEGACY_REMOVE )

  void IsBiasFieldMultiplicative(bool flag)
  { m_BiasFieldMultiplicative = flag; }
#endif // defined ( ITK_LEGACY_REMOVE )

  itkSetMacro(BiasFieldMultiplicative, bool);
  itkGetConstMacro(BiasFieldMultiplicative, bool);
  itkBooleanMacro(BiasFieldMultiplicative);

#if defined ( ITK_LEGACY_REMOVE )

  bool IsBiasFieldMultiplicative()
  { return m_BiasFieldMultiplicative; }
#endif // defined ( ITK_LEGACY_REMOVE )

  itkSetMacro(UsingInterSliceIntensityCorrection, bool);
  itkGetConstMacro(UsingInterSliceIntensityCorrection, bool);
  itkBooleanMacro(UsingInterSliceIntensityCorrection);

  itkSetMacro(UsingSlabIdentification, bool);
  itkGetConstMacro(UsingSlabIdentification, bool);
  itkBooleanMacro(UsingSlabIdentification);

  itkSetMacro(SlabBackgroundMinimumThreshold, InputImagePixelType);
  itkGetConstReferenceMacro(SlabBackgroundMinimumThreshold,
                            InputImagePixelType);

  itkSetMacro(SlabNumberOfSamples, unsigned int);
  itkGetConstReferenceMacro(SlabNumberOfSamples, unsigned int);

  itkSetMacro(SlabTolerance, double);
  itkGetConstReferenceMacro(SlabTolerance, double);

  itkSetMacro(UsingBiasFieldCorrection, bool);
  itkGetConstMacro(UsingBiasFieldCorrection, bool);
  itkBooleanMacro(UsingBiasFieldCorrection);

  itkSetMacro(GeneratingOutput, bool);
  itkGetConstMacro(GeneratingOutput, bool);
  itkBooleanMacro(GeneratingOutput);

  itkSetMacro(SlicingDirection, int);
  itkGetConstMacro(SlicingDirection, int);

  itkSetMacro(BiasFieldDegree, int);
  itkGetConstMacro(BiasFieldDegree, int);

  void SetInitialBiasFieldCoefficients(const
                                       BiasFieldType::CoefficientArrayType
                                       & coefficients)
  { this->Modified(); m_BiasFieldCoefficients = coefficients; }

  BiasFieldType::CoefficientArrayType GetEstimatedBiasFieldCoefficients()
  { return m_EstimatedBiasFieldCoefficients; }

  void SetTissueClassStatistics(const Array< double > & means,
                                const Array< double > & sigmas);

  itkSetMacro(VolumeCorrectionMaximumIteration, int);
  itkGetConstMacro(VolumeCorrectionMaximumIteration, int);

  itkSetMacro(InterSliceCorrectionMaximumIteration, int);
  itkGetConstMacro(InterSliceCorrectionMaximumIteration, int);

  itkSetMacro(OptimizerInitialRadius, double);
  itkGetConstMacro(OptimizerInitialRadius, double);

  itkSetMacro(OptimizerGrowthFactor, double);
  itkGetConstMacro(OptimizerGrowthFactor, double);

  itkSetMacro(OptimizerShrinkFactor, double);
  itkGetConstMacro(OptimizerShrinkFactor, double);

  void SetNumberOfLevels(unsigned int num);

  itkGetConstMacro(NumberOfLevels, unsigned int);

  void SetSchedule(const ScheduleType & schedule);

  itkGetConstReferenceMacro(Schedule, ScheduleType);

  void SetStartingShrinkFactors(unsigned int factor);

  void SetStartingShrinkFactors(unsigned int *factors);

  const unsigned int * GetStartingShrinkFactors() const;

  static bool IsScheduleDownwardDivisible(const ScheduleType & schedule);

  void Initialize();

  BiasFieldType EstimateBiasField(InputImageRegionType region,
                                  unsigned int degree,
                                  int maximumIteration);

  void CorrectImage(BiasFieldType & bias,
                    InputImageRegionType region);

  void CorrectInterSliceIntensityInhomogeneity(InputImageRegionType region);

protected:
  MRIBiasFieldCorrectionFilter();
  ~MRIBiasFieldCorrectionFilter() override = default;
  void PrintSelf(std::ostream & os, Indent indent) const override;

  bool CheckMaskImage(ImageMaskType *mask);

protected:
  void Log1PImage(InternalImageType *source,
                  InternalImageType *target);

  void ExpImage(InternalImageType *source,
                InternalImageType *target);

  template< typename TSource, typename TTarget >
  void CopyAndConvertImage(const TSource *source,
                           TTarget *target,
                           typename TTarget::RegionType requestedRegion)
  {
    using SourceIterator = ImageRegionConstIterator< TSource >;
    using TargetIterator = ImageRegionIterator< TTarget >;
    using TargetPixelType = typename TTarget::PixelType;

    SourceIterator s_iter(source, requestedRegion);
    TargetIterator t_iter(target, requestedRegion);

    s_iter.GoToBegin();
    t_iter.GoToBegin();
    while ( !s_iter.IsAtEnd() )
      {
      t_iter.Set( static_cast< TargetPixelType >( s_iter.Get() ) );
      ++s_iter;
      ++t_iter;
      }
  }

  void GetBiasFieldSize(InputImageRegionType region,
                        BiasFieldType::DomainSizeType & domainSize);

  void AdjustSlabRegions(SlabRegionVectorType & slabs,
                         OutputImageRegionType requestedRegion);

  void GenerateData() override;

private:
  EnergyFunctionPointer m_EnergyFunction;

  NormalVariateGeneratorType::Pointer m_NormalVariateGenerator;

  ImageMaskPointer m_InputMask;

  ImageMaskPointer m_OutputMask;

  InternalImagePointer m_InternalInput;

  SlabRegionVectorType m_Slabs;

  int m_SlicingDirection;

  bool m_BiasFieldMultiplicative{ true };

  bool m_UsingInterSliceIntensityCorrection;
  bool m_UsingSlabIdentification{ false };
  bool m_UsingBiasFieldCorrection{ true };
  bool m_GeneratingOutput{ true };

  unsigned int        m_SlabNumberOfSamples{ 200 };
  InputImagePixelType m_SlabBackgroundMinimumThreshold;
  double              m_SlabTolerance{ 0.0 };

  int m_BiasFieldDegree{ 3 };

  unsigned int m_NumberOfLevels{ 0 };

  ScheduleType m_Schedule;

  BiasFieldType::CoefficientArrayType m_BiasFieldCoefficients;

  BiasFieldType::CoefficientArrayType m_EstimatedBiasFieldCoefficients;

  int m_VolumeCorrectionMaximumIteration{ 2000 };

  int m_InterSliceCorrectionMaximumIteration{ 4000 };

  double m_OptimizerInitialRadius{ 1.01 };

  double m_OptimizerGrowthFactor{ 1.05 };

  double m_OptimizerShrinkFactor;

  Array< double > m_TissueClassMeans;

  Array< double > m_TissueClassSigmas;
};

} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkMRIBiasFieldCorrectionFilter.hxx"
#endif

#endif