itkImageRegistrationMethodv4.h

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/*=========================================================================
 *
 *  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 itkImageRegistrationMethodv4_h
#define itkImageRegistrationMethodv4_h

#include "itkProcessObject.h"

#include "itkCompositeTransform.h"
#include "itkDataObjectDecorator.h"
#include "itkObjectToObjectMetricBase.h"
#include "itkObjectToObjectMultiMetricv4.h"
#include "itkObjectToObjectOptimizerBase.h"
#include "itkImageToImageMetricv4.h"
#include "itkPointSetToPointSetMetricv4.h"
#include "itkShrinkImageFilter.h"
#include "itkIdentityTransform.h"
#include "itkTransformParametersAdaptorBase.h"

#include <vector>

namespace itk
{

template<typename TFixedImage,
         typename TMovingImage,
         typename TOutputTransform = Transform<double, TFixedImage::ImageDimension, TFixedImage::ImageDimension>,
         typename TVirtualImage = TFixedImage,
         typename TPointSet = PointSet<unsigned int, TFixedImage::ImageDimension> >
class ITK_TEMPLATE_EXPORT ImageRegistrationMethodv4
:public ProcessObject
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(ImageRegistrationMethodv4);

  using Self = ImageRegistrationMethodv4;
  using Superclass = ProcessObject;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  itkNewMacro( Self );

  static constexpr unsigned int ImageDimension = TFixedImage::ImageDimension;

  itkTypeMacro( ImageRegistrationMethodv4, ProcessObject );

  using FixedImageType = TFixedImage;
  using FixedImagePointer = typename FixedImageType::Pointer;
  using FixedImageConstPointer = typename FixedImageType::ConstPointer;
  using FixedImagesContainerType = std::vector<FixedImageConstPointer>;
  using MovingImageType = TMovingImage;
  using MovingImagePointer = typename MovingImageType::Pointer;
  using MovingImageConstPointer = typename MovingImageType::ConstPointer;
  using MovingImagesContainerType = std::vector<MovingImageConstPointer>;

  using PointSetType = TPointSet;
  using PointSetConstPointer = typename PointSetType::ConstPointer;
  using PointSetsContainerType = std::vector<PointSetConstPointer>;

  using OutputTransformType = TOutputTransform;
  using OutputTransformPointer = typename OutputTransformType::Pointer;
  using RealType = typename OutputTransformType::ScalarType;
  using DerivativeType = typename OutputTransformType::DerivativeType;
  using DerivativeValueType = typename DerivativeType::ValueType;

  using InitialTransformType = Transform<RealType, ImageDimension, ImageDimension>;
  using InitialTransformPointer = typename InitialTransformType::Pointer;

  using CompositeTransformType = CompositeTransform<RealType, ImageDimension>;
  using CompositeTransformPointer = typename CompositeTransformType::Pointer;

  using MetricType = ObjectToObjectMetricBaseTemplate<RealType>;
  using MetricPointer = typename MetricType::Pointer;

  using VectorType = Vector<RealType, ImageDimension>;

  using VirtualImageType = TVirtualImage;
  using VirtualImagePointer = typename VirtualImageType::Pointer;
  using VirtualImageBaseType = ImageBase<ImageDimension>;
  using VirtualImageBaseConstPointer = typename VirtualImageBaseType::ConstPointer;

  using MultiMetricType = ObjectToObjectMultiMetricv4<ImageDimension, ImageDimension, VirtualImageType, RealType>;
  using ImageMetricType = ImageToImageMetricv4<FixedImageType, MovingImageType, VirtualImageType, RealType>;
  using PointSetMetricType = PointSetToPointSetMetricv4<PointSetType, PointSetType, RealType>;

  using FixedImageMaskType = typename ImageMetricType::FixedImageMaskType;
  using FixedImageMaskConstPointer = typename FixedImageMaskType::ConstPointer;
  using FixedImageMasksContainerType = std::vector<FixedImageMaskConstPointer>;
  using MovingImageMaskType = typename ImageMetricType::MovingImageMaskType;
  using MovingImageMaskConstPointer = typename MovingImageMaskType::ConstPointer;
  using MovingImageMasksContainerType = std::vector<MovingImageMaskConstPointer>;

  using DecoratedOutputTransformType = DataObjectDecorator<OutputTransformType>;
  using DecoratedOutputTransformPointer = typename DecoratedOutputTransformType::Pointer;
  using DecoratedInitialTransformType = DataObjectDecorator<InitialTransformType>;
  using DecoratedInitialTransformPointer = typename DecoratedInitialTransformType::Pointer;

  using ShrinkFilterType = ShrinkImageFilter<FixedImageType, VirtualImageType>;
  using ShrinkFactorsPerDimensionContainerType = typename ShrinkFilterType::ShrinkFactorsType;

  using ShrinkFactorsArrayType = Array<SizeValueType>;

  using SmoothingSigmasArrayType = Array<RealType>;
  using MetricSamplingPercentageArrayType = Array<RealType>;

  using TransformParametersAdaptorType = TransformParametersAdaptorBase<InitialTransformType>;
  using TransformParametersAdaptorPointer = typename TransformParametersAdaptorType::Pointer;
  using TransformParametersAdaptorsContainerType = std::vector<TransformParametersAdaptorPointer>;

  using OptimizerType = ObjectToObjectOptimizerBaseTemplate<RealType>;
  using OptimizerPointer = typename OptimizerType::Pointer;

  using OptimizerWeightsType = typename OptimizerType::ScalesType;

  enum MetricSamplingStrategyType { NONE, REGULAR, RANDOM };

  using MetricSamplePointSetType = typename ImageMetricType::FixedSampledPointSetType;

  virtual void SetFixedImage( const FixedImageType *image )
    {
    this->SetFixedImage( 0, image );
    }
  virtual const FixedImageType * GetFixedImage() const
    {
    return this->GetFixedImage( 0 );
    }
  virtual void SetFixedImage( SizeValueType, const FixedImageType * );
  virtual const FixedImageType * GetFixedImage( SizeValueType ) const;

  virtual void SetMovingImage( const MovingImageType *image )
    {
    this->SetMovingImage( 0, image );
    }
  virtual const MovingImageType * GetMovingImage() const
    {
    return this->GetMovingImage( 0 );
    }
  virtual void SetMovingImage( SizeValueType, const MovingImageType * );
  virtual const MovingImageType * GetMovingImage( SizeValueType ) const;

  virtual void SetFixedPointSet( const PointSetType *pointSet )
    {
    this->SetFixedPointSet( 0, pointSet );
    }
  virtual const PointSetType * GetFixedPointSet() const
    {
    return this->GetFixedPointSet( 0 );
    }
  virtual void SetFixedPointSet( SizeValueType, const PointSetType * );
  virtual const PointSetType * GetFixedPointSet( SizeValueType ) const;

  virtual void SetMovingPointSet( const PointSetType *pointSet )
    {
    this->SetMovingPointSet( 0, pointSet );
    }
  virtual const PointSetType * GetMovingPointSet() const
    {
    return this->GetMovingPointSet( 0 );
    }
  virtual void SetMovingPointSet( SizeValueType, const PointSetType * );
  virtual const PointSetType * GetMovingPointSet( SizeValueType ) const;

  itkSetObjectMacro( Optimizer, OptimizerType );
  itkGetModifiableObjectMacro( Optimizer, OptimizerType );

  void SetOptimizerWeights( OptimizerWeightsType & );
  itkGetConstMacro( OptimizerWeights, OptimizerWeightsType );

  itkSetObjectMacro( Metric, MetricType );
  itkGetModifiableObjectMacro( Metric, MetricType );

  itkSetMacro( MetricSamplingStrategy, MetricSamplingStrategyType );
  itkGetConstMacro( MetricSamplingStrategy, MetricSamplingStrategyType );

  void MetricSamplingReinitializeSeed();
  void MetricSamplingReinitializeSeed(int seed);

  void SetMetricSamplingPercentage( const RealType );

  virtual void SetMetricSamplingPercentagePerLevel( const MetricSamplingPercentageArrayType  &samplingPercentages );
  itkGetConstMacro( MetricSamplingPercentagePerLevel, MetricSamplingPercentageArrayType );

  itkSetGetDecoratedObjectInputMacro( FixedInitialTransform, InitialTransformType );

  itkSetGetDecoratedObjectInputMacro( MovingInitialTransform, InitialTransformType );

  itkSetGetDecoratedObjectInputMacro(InitialTransform, InitialTransformType);

  void SetTransformParametersAdaptorsPerLevel( TransformParametersAdaptorsContainerType & );
  const TransformParametersAdaptorsContainerType & GetTransformParametersAdaptorsPerLevel() const;

  void SetNumberOfLevels( const SizeValueType );
  itkGetConstMacro( NumberOfLevels, SizeValueType );

  void SetShrinkFactorsPerLevel( ShrinkFactorsArrayType factors )
    {
    for( unsigned int level = 0; level < factors.Size(); ++level )
      {
      ShrinkFactorsPerDimensionContainerType shrinkFactors;
      shrinkFactors.Fill( factors[level] );
      this->SetShrinkFactorsPerDimension( level, shrinkFactors );
      }
    }

  ShrinkFactorsPerDimensionContainerType GetShrinkFactorsPerDimension( const unsigned int level ) const
    {
    if( level >= this->m_ShrinkFactorsPerLevel.size() )
      {
      itkExceptionMacro( "Requesting level greater than the number of levels." );
      }
    return this->m_ShrinkFactorsPerLevel[level];
    }

  void SetShrinkFactorsPerDimension( unsigned int level, ShrinkFactorsPerDimensionContainerType factors )
    {
    if( level >= this->m_ShrinkFactorsPerLevel.size() )
      {
      this->m_ShrinkFactorsPerLevel.resize( level + 1 );
      }
    this->m_ShrinkFactorsPerLevel[level] = factors;
    this->Modified();
    }

  itkSetMacro( SmoothingSigmasPerLevel, SmoothingSigmasArrayType );
  itkGetConstMacro( SmoothingSigmasPerLevel, SmoothingSigmasArrayType );

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

  using DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType;
  using Superclass::MakeOutput;
  DataObjectPointer MakeOutput( DataObjectPointerArraySizeType ) override;

  virtual DecoratedOutputTransformType * GetOutput();
  virtual const DecoratedOutputTransformType * GetOutput() const;

  virtual DecoratedOutputTransformType * GetTransformOutput() { return this->GetOutput(); }
  virtual const DecoratedOutputTransformType * GetTransformOutput() const { return this->GetOutput(); }

  virtual OutputTransformType * GetModifiableTransform();
  virtual const OutputTransformType * GetTransform() const;

  itkGetConstMacro( CurrentLevel, SizeValueType );

  itkGetConstReferenceMacro( CurrentIteration, SizeValueType );

  /* Get the current metric value.  This is a helper function for reporting observations. */
  itkGetConstReferenceMacro( CurrentMetricValue, RealType );

  itkGetConstReferenceMacro( CurrentConvergenceValue, RealType );

  itkGetConstReferenceMacro( IsConverged, bool );

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

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

  void InitializeCenterOfLinearOutputTransform();

protected:
  ImageRegistrationMethodv4();
  ~ImageRegistrationMethodv4() override = default;
  void PrintSelf( std::ostream & os, Indent indent ) const override;

  void  GenerateData() override;

  virtual void AllocateOutputs();

  virtual void InitializeRegistrationAtEachLevel( const SizeValueType );

  virtual VirtualImageBaseConstPointer GetCurrentLevelVirtualDomainImage();

  virtual void SetMetricSamplePoints();

  SizeValueType                                                   m_CurrentLevel;
  SizeValueType                                                   m_NumberOfLevels;
  SizeValueType                                                   m_CurrentIteration;
  RealType                                                        m_CurrentMetricValue;
  RealType                                                        m_CurrentConvergenceValue;
  bool                                                            m_IsConverged;

  FixedImagesContainerType                                        m_FixedSmoothImages;
  MovingImagesContainerType                                       m_MovingSmoothImages;
  FixedImageMasksContainerType                                    m_FixedImageMasks;
  MovingImageMasksContainerType                                   m_MovingImageMasks;
  VirtualImagePointer                                             m_VirtualDomainImage;
  PointSetsContainerType                                          m_FixedPointSets;
  PointSetsContainerType                                          m_MovingPointSets;
  SizeValueType                                                   m_NumberOfFixedObjects;
  SizeValueType                                                   m_NumberOfMovingObjects;

  OptimizerPointer                                                m_Optimizer;
  OptimizerWeightsType                                            m_OptimizerWeights;
  bool                                                            m_OptimizerWeightsAreIdentity;

  MetricPointer                                                   m_Metric;
  MetricSamplingStrategyType                                      m_MetricSamplingStrategy;
  MetricSamplingPercentageArrayType                               m_MetricSamplingPercentagePerLevel;
  SizeValueType                                                   m_NumberOfMetrics;
  int                                                             m_FirstImageMetricIndex;
  std::vector<ShrinkFactorsPerDimensionContainerType>             m_ShrinkFactorsPerLevel;
  SmoothingSigmasArrayType                                        m_SmoothingSigmasPerLevel;
  bool                                                            m_SmoothingSigmasAreSpecifiedInPhysicalUnits;

  bool                                                            m_ReseedIterator;
  int                                                             m_RandomSeed;
  int                                                             m_CurrentRandomSeed;


  TransformParametersAdaptorsContainerType                        m_TransformParametersAdaptorsPerLevel;

  CompositeTransformPointer                                       m_CompositeTransform;

  //TODO: m_OutputTransform should be removed and replaced with a named input parameter for
  //      the pipeline
  OutputTransformPointer                                          m_OutputTransform;


private:
  bool                                                            m_InPlace;

  bool                                                            m_InitializeCenterOfLinearOutputTransform;

  // helper function to create the right kind of concrete transform
  template<typename TTransform>
  static void MakeOutputTransform(SmartPointer<TTransform> &ptr)
    {
    ptr = TTransform::New();
    }

  static void MakeOutputTransform(SmartPointer<InitialTransformType> &ptr)
    {
    ptr = IdentityTransform<RealType, ImageDimension>::New().GetPointer();
    }

};
} // end namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkImageRegistrationMethodv4.hxx"
#endif

#endif