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 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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 itkMultiResolutionPDEDeformableRegistration_h
#define itkMultiResolutionPDEDeformableRegistration_h

#include "itkImage.h"
#include "itkDemonsRegistrationFilter.h"
#include "itkMultiResolutionPyramidImageFilter.h"
#include "itkResampleImageFilter.h"
#include "itkArray.h"

namespace itk
{
/**
 * \class MultiResolutionPDEDeformableRegistration
 * \brief Framework for performing multi-resolution PDE
 * deformable registration.
 *
 * MultiResolutionPDEDeformableRegistration provides a generic framework
 * to perform multi-resolution deformable registration.
 *
 * At each resolution level a PDEDeformableRegistrationFilter is used
 * to register two images by computing the deformation field which will
 * map a moving image onto a fixed image.
 *
 * A deformation field is represented as an image whose pixel type is some
 * vector type with at least N elements, where N is the dimension of
 * the fixed image. The vector type must support element access via operator
 * []. It is assumed that the vector elements behave like floating point
 * scalars.
 *
 * The internal PDEDeformationRegistrationFilter can be set using
 * SetRegistrationFilter. By default a DemonsRegistrationFilter is used.
 *
 * The input fixed and moving images are set via methods SetFixedImage
 * and SetMovingImage respectively. An initial deformation field maybe set via
 * SetInitialDisplacementField if is matches the characteristics of the coarsest
 * pyramid level. If no such assumption can be made (e.g. the deformation field
 * has the same characteristics as the input images), an initial deformation
 * field can still be set via SetArbitraryInitialDisplacementField or
 * SetInput. The filter will then take care of matching the coarsest level
 * characteristics. If no initial field is set a zero field is used as the
 * initial condition.
 *
 * MultiResolutionPyramidImageFilters are used to downsample the fixed
 * and moving images. A ResampleImageFilter is used to upsample
 * the deformation as we move from a coarse to fine solution.
 *
 * This class is templated over the fixed image type, the moving image type,
 * and the Deformation Field type.
 *
 * \warning This class assumes that the fixed, moving and deformation
 * field image types all have the same number of dimensions.
 *
 * \sa PDEDeformableRegistrationFilter
 * \sa DemonsRegistrationFilter
 * \sa MultiResolutionPyramidImageFilter
 * \sa ResampleImageFilter
 *
 * The current implementation of this class does not support streaming.
 *
 * \ingroup DeformableImageRegistration
 * \ingroup ITKPDEDeformableRegistration
 */
template <
  typename TFixedImage,
  typename TMovingImage,
  typename TDisplacementField,
  typename TRealType = float,
  typename TFloatImageType = Image<TRealType, TFixedImage::ImageDimension>,
  typename TRegistrationType = PDEDeformableRegistrationFilter<TFloatImageType, TFloatImageType, TDisplacementField>,
  typename TDefaultRegistrationType = DemonsRegistrationFilter<TFloatImageType, TFloatImageType, TDisplacementField>>
class ITK_TEMPLATE_EXPORT MultiResolutionPDEDeformableRegistration
  : public ImageToImageFilter<TDisplacementField, TDisplacementField>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(MultiResolutionPDEDeformableRegistration);

  /** Standard class type aliases */
  using Self = MultiResolutionPDEDeformableRegistration;
  using Superclass = ImageToImageFilter<TDisplacementField, TDisplacementField>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  /** Method for creation through the object factory. */
  itkNewMacro(Self);

  /** \see LightObject::GetNameOfClass() */
  itkOverrideGetNameOfClassMacro(MultiResolutionPDEDeformableRegistration);

  /** Fixed image type. */
  using FixedImageType = TFixedImage;
  using FixedImagePointer = typename FixedImageType::Pointer;
  using FixedImageConstPointer = typename FixedImageType::ConstPointer;

  /** Moving image type. */
  using MovingImageType = TMovingImage;
  using MovingImagePointer = typename MovingImageType::Pointer;
  using MovingImageConstPointer = typename MovingImageType::ConstPointer;

  /** Deformation field image type. */
  using DisplacementFieldType = TDisplacementField;
  using DisplacementFieldPointer = typename DisplacementFieldType::Pointer;

  /** ImageDimension. */
  static constexpr unsigned int ImageDimension = FixedImageType::ImageDimension;

  /** Internal float image type. */
  using FloatImageType = TFloatImageType;

  /** The internal registration type. */
  using RegistrationType = TRegistrationType;
  using RegistrationPointer = typename RegistrationType::Pointer;

  /** The default registration type. */
  using DefaultRegistrationType = TDefaultRegistrationType;

  /** The fixed multi-resolution image pyramid type. */
  using FixedImagePyramidType = MultiResolutionPyramidImageFilter<FixedImageType, FloatImageType>;
  using FixedImagePyramidPointer = typename FixedImagePyramidType::Pointer;

  /** The moving multi-resolution image pyramid type. */
  using MovingImagePyramidType = MultiResolutionPyramidImageFilter<MovingImageType, FloatImageType>;
  using MovingImagePyramidPointer = typename MovingImagePyramidType::Pointer;

  /** The deformation field expander type. */
  using FieldExpanderType = ResampleImageFilter<DisplacementFieldType, DisplacementFieldType>;
  using FieldExpanderPointer = typename FieldExpanderType::Pointer;

  using NumberOfIterationsType = Array<unsigned int>;

  /** Set the fixed image. */
  virtual void
  SetFixedImage(const FixedImageType * ptr);

  /** Get the fixed image. */
  const FixedImageType *
  GetFixedImage() const;

  /** Set the moving image. */
  virtual void
  SetMovingImage(const MovingImageType * ptr);

  /** Get the moving image. */
  const MovingImageType *
  GetMovingImage() const;

  /** Set initial deformation field to be used as is (no smoothing, no
   *  subsampling at the coarsest level of the pyramid. */
  virtual void
  SetInitialDisplacementField(DisplacementFieldType * ptr)
  {
    this->m_InitialDisplacementField = ptr;
  }

  /** Set initial deformation field. No assumption is made on the
   *  input. It will therefore be smoothed and resampled to match the
   *  images characteristics at the coarsest level of the pyramid. */
  virtual void
  SetArbitraryInitialDisplacementField(DisplacementFieldType * ptr)
  {
    this->SetInput(ptr);
  }

  /** Get output deformation field. */
  const DisplacementFieldType *
  GetDisplacementField()
  {
    return this->GetOutput();
  }

  /** Get the number of valid inputs.  For
   * MultiResolutionPDEDeformableRegistration, this checks whether the
   * fixed and moving images have been set. While
   * MultiResolutionPDEDeformableRegistration can take a third input
   * as an initial deformation field, this input is not a required input.
   */
  std::vector<SmartPointer<DataObject>>::size_type
  GetNumberOfValidRequiredInputs() const override;

  /** Get/Set the internal registrator. */
  itkSetObjectMacro(RegistrationFilter, RegistrationType);
  itkGetModifiableObjectMacro(RegistrationFilter, RegistrationType);

  /** Get/Set the fixed image pyramid. */
  itkSetObjectMacro(FixedImagePyramid, FixedImagePyramidType);
  itkGetModifiableObjectMacro(FixedImagePyramid, FixedImagePyramidType);

  /** Get/Set the moving image pyramid. */
  itkSetObjectMacro(MovingImagePyramid, MovingImagePyramidType);
  itkGetModifiableObjectMacro(MovingImagePyramid, MovingImagePyramidType);

  /** Set number of multi-resolution levels. */
  virtual void
  SetNumberOfLevels(unsigned int num);

  /** Get number of multi-resolution levels. */
  itkGetConstReferenceMacro(NumberOfLevels, unsigned int);

  /** Get the current resolution level being processed. */
  itkGetConstReferenceMacro(CurrentLevel, unsigned int);

  /** Get/Set the moving image pyramid. */
  itkSetObjectMacro(FieldExpander, FieldExpanderType);
  itkGetModifiableObjectMacro(FieldExpander, FieldExpanderType);

  /** Set number of iterations per multi-resolution levels. */
  itkSetMacro(NumberOfIterations, NumberOfIterationsType);
  itkSetVectorMacro(NumberOfIterations, unsigned int, m_NumberOfLevels);

  /** Get number of iterations per multi-resolution levels. */
  itkGetConstReferenceMacro(NumberOfIterations, NumberOfIterationsType);

  /** Stop the registration after the current iteration. */
  virtual void
  StopRegistration();

protected:
  MultiResolutionPDEDeformableRegistration();
  ~MultiResolutionPDEDeformableRegistration() override = default;

  void
  PrintSelf(std::ostream & os, Indent indent) const override;

  /** Generate output data by performing the registration at each resolution level.
   *
   * Performs a the deformable registration using a multiresolution scheme using an internal mini-pipeline
   *
   *  ref_pyramid ->  registrator  ->  field_expander --|| tempField
   * test_pyramid ->           |                              |
   *                           |                              |
   *                           --------------------------------
   *
   * A tempField image is used to break the cycle between the registrator and field_expander.
   */
  void
  GenerateData() override;

  /** The current implementation of this class does not support
   * streaming. As such it requires the largest possible region
   * for the moving, fixed and input deformation field. */
  void
  GenerateInputRequestedRegion() override;

  /** By default, the output deformation field has the same
   * spacing, origin and LargestPossibleRegion as the input/initial
   * deformation field.
   *
   * If the initial deformation field is not set, the output
   * information is copied from the fixed image. */
  void
  GenerateOutputInformation() override;

  /** The current implementation of this class does not support
   * streaming. As such it produces the output for the largest
   * possible region. */
  void
  EnlargeOutputRequestedRegion(DataObject * ptr) override;

  /** This method returns true to indicate that the registration should
   * terminate at the current resolution level. */
  virtual bool
  Halt();

  /** Override VerifyInputInformation() since this filter's inputs do
   * not need to occupy the same physical space.
   *
   * \sa ProcessObject::VerifyInputInformation
   */
  void
  VerifyInputInformation() ITKv5_CONST override
  {}

private:
  RegistrationPointer       m_RegistrationFilter{};
  FixedImagePyramidPointer  m_FixedImagePyramid{};
  MovingImagePyramidPointer m_MovingImagePyramid{};
  FieldExpanderPointer      m_FieldExpander{};
  DisplacementFieldPointer  m_InitialDisplacementField{};

  unsigned int           m_NumberOfLevels{};
  unsigned int           m_CurrentLevel{};
  NumberOfIterationsType m_NumberOfIterations{};

  /** Flag to indicate user stop registration request. */
  bool m_StopRegistrationFlag{};
};
} // end namespace itk

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

#endif