itkMultiphaseFiniteDifferenceImageFilter.h

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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 itkMultiphaseFiniteDifferenceImageFilter_h
#define itkMultiphaseFiniteDifferenceImageFilter_h
 
#include "itkInPlaceImageFilter.h"
#include "itkFiniteDifferenceFunction.h"
#include "vnl/vnl_vector.h"
#include "itkImageRegionIterator.h"
 
#include "itkListSample.h"
#include "itkKdTreeGenerator.h"
 
namespace itk
{
template <typename TInputImage,
          typename TFeatureImage,
          typename TOutputImage,
          typename TFiniteDifferenceFunction = FiniteDifferenceFunction<TOutputImage>,
          typename TIdCell = unsigned int>
class ITK_TEMPLATE_EXPORT MultiphaseFiniteDifferenceImageFilter : public InPlaceImageFilter<TFeatureImage, TOutputImage>
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(MultiphaseFiniteDifferenceImageFilter);
 
  using Self = MultiphaseFiniteDifferenceImageFilter;
  using Superclass = InPlaceImageFilter<TFeatureImage, TOutputImage>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;
 
  itkOverrideGetNameOfClassMacro(MultiphaseFiniteDifferenceImageFilter);
 
  static constexpr unsigned int ImageDimension = TOutputImage::ImageDimension;
 
  using InputImageType = TInputImage;
  using InputImagePointer = typename InputImageType::Pointer;
  using InputPointType = typename InputImageType::PointType;
  using InputCoordinateType = typename InputPointType::CoordinateType;
#ifndef ITK_FUTURE_LEGACY_REMOVE
  using InputCoordRepType ITK_FUTURE_DEPRECATED(
    "ITK 6 discourages using `InputCoordRepType`. Please use `InputCoordinateType` instead!") = InputCoordinateType;
#endif
  using InputIndexType = typename InputImageType::IndexType;
  using InputIndexValueType = typename InputIndexType::IndexValueType;
  using InputSizeType = typename InputImageType::SizeType;
  using InputSizeValueType = typename InputSizeType::SizeValueType;
  using InputRegionType = typename InputImageType::RegionType;
  using InputPixelType = typename InputImageType::PixelType;
  using InputSpacingType = typename InputImageType::SpacingType;
  using InputOffsetValueType = typename InputImageType::OffsetValueType;
 
  using FeatureImageType = TFeatureImage;
  using FeatureImagePointer = typename FeatureImageType::Pointer;
  using FeatureRegionType = typename FeatureImageType::RegionType;
  using FeatureSizeType = typename FeatureImageType::SizeType;
  using FeatureSpacingType = typename FeatureImageType::SpacingType;
  using FeaturePointType = typename FeatureImageType::PointType;
  using FeaturePixelType = typename FeatureImageType::PixelType;
 
  using OutputImageType = TOutputImage;
  using OutputImagePointer = typename OutputImageType::Pointer;
  using OutputPixelType = typename OutputImageType::PixelType;
  using OutputRegionType = typename OutputImageType::RegionType;
  using OutputSizeType = typename OutputImageType::SizeType;
  using OutputSizeValueType = typename OutputImageType::SizeValueType;
  using OutputIndexType = typename OutputImageType::IndexType;
  using OutputIndexValueType = typename OutputImageType::IndexValueType;
 
  using IdCellType = TIdCell;
  using VectorIdCellType = std::vector<IdCellType>;
 
  using FiniteDifferenceFunctionType = TFiniteDifferenceFunction;
  using FiniteDifferenceFunctionPointer = typename FiniteDifferenceFunctionType::Pointer;
  using TimeStepType = typename FiniteDifferenceFunctionType::TimeStepType;
  using TimeStepVectorType = typename std::vector<TimeStepType>;
  using RadiusType = typename FiniteDifferenceFunctionType::RadiusType;
 
  using CentroidVectorType = Vector<float, Self::ImageDimension>;
  using SampleType = Statistics::ListSample<CentroidVectorType>;
  using KdTreeGeneratorType = Statistics::KdTreeGenerator<SampleType>;
  using KdTreeGeneratorPointer = typename KdTreeGeneratorType::Pointer;
  using KdTreeType = typename KdTreeGeneratorType::KdTreeType;
  using KdTreePointer = typename KdTreeType::Pointer;
 
  virtual const FiniteDifferenceFunctionPointer
  GetDifferenceFunction(const IdCellType & functionIndex) const
  {
    if (functionIndex < m_FunctionCount)
    {
      return (this->m_DifferenceFunctions[functionIndex]);
    }
    else
    {
      return nullptr;
    }
  }
  virtual void
  SetDifferenceFunction(const IdCellType & functionIndex, FiniteDifferenceFunctionPointer function)
  {
    if (functionIndex < m_FunctionCount)
    {
      this->m_DifferenceFunctions[functionIndex] = function;
    }
  }
  itkSetMacro(NumberOfIterations, unsigned int);
  itkGetConstReferenceMacro(NumberOfIterations, unsigned int);
  itkSetMacro(UseImageSpacing, bool);
  itkBooleanMacro(UseImageSpacing);
  itkGetConstReferenceMacro(UseImageSpacing, bool);
  itkSetMacro(MaximumRMSError, double);
  itkGetConstReferenceMacro(MaximumRMSError, double);
  itkSetMacro(RMSChange, double);
  itkGetConstReferenceMacro(RMSChange, double);
  itkSetMacro(InitializedState, bool);
  itkGetConstReferenceMacro(InitializedState, bool);
  itkBooleanMacro(InitializedState);
  itkSetMacro(ManualReinitialization, bool);
  itkGetConstReferenceMacro(ManualReinitialization, bool);
  itkBooleanMacro(ManualReinitialization);
  itkSetMacro(ElapsedIterations, unsigned int);
 
  itkGetConstReferenceMacro(ElapsedIterations, unsigned int);
 
  void
  SetLevelSet(const IdCellType & i, const InputImageType * levelSet)
  {
    m_LevelSet[i] = InputImageType::New();
    m_LevelSet[i]->SetRequestedRegion(levelSet->GetRequestedRegion());
    m_LevelSet[i]->SetBufferedRegion(levelSet->GetBufferedRegion());
    m_LevelSet[i]->SetLargestPossibleRegion(levelSet->GetLargestPossibleRegion());
    m_LevelSet[i]->Allocate();
    m_LevelSet[i]->CopyInformation(levelSet);
 
    ImageRegionConstIterator<InputImageType> in(levelSet, levelSet->GetBufferedRegion());
    ImageRegionIterator<InputImageType>      cp(m_LevelSet[i], levelSet->GetBufferedRegion());
 
    in.GoToBegin();
    cp.GoToBegin();
 
    while (!in.IsAtEnd())
    {
      cp.Set(in.Get());
      ++in;
      ++cp;
    }
  }
 
  InputImagePointer
  GetLevelSet(const IdCellType & i)
  {
    if (i >= m_FunctionCount)
    {
      itkExceptionMacro("Request for level set #" << i << " but there are only " << m_FunctionCount);
    }
    else
    {
      return m_LevelSet[i];
    }
  }
 
  void
  SetLookup(VectorIdCellType lookup)
  {
    this->m_Lookup = lookup;
  }
 
  void
  SetKdTree(KdTreeType * kdtree)
  {
    this->m_KdTree = kdtree;
  }
 
  void
  SetFunctionCount(const IdCellType & n)
  {
    m_FunctionCount = n;
 
    m_DifferenceFunctions.resize(m_FunctionCount, nullptr);
 
    constexpr auto radius = MakeFilled<RadiusType>(1);
 
    for (unsigned int i = 0; i < this->m_FunctionCount; ++i)
    {
      this->m_DifferenceFunctions[i] = FiniteDifferenceFunctionType::New();
      this->m_DifferenceFunctions[i]->Initialize(radius);
    }
 
    // Initialize the images
    m_LevelSet.resize(m_FunctionCount, nullptr);
 
    // Initialize the lookup table
    this->m_Lookup.resize(m_FunctionCount);
 
    IdCellType k = 1;
 
    {
      auto it = this->m_Lookup.begin();
      auto _end = this->m_Lookup.end();
      while (it != _end)
      {
        *it = k;
        ++it;
        ++k;
      }
    }
  }
 
protected:
  MultiphaseFiniteDifferenceImageFilter()
  {
    this->m_KdTree = nullptr;
    this->m_ElapsedIterations = 0;
    this->m_MaximumRMSError = itk::Math::eps;
    this->m_RMSChange = NumericTraits<double>::max();
    this->m_UseImageSpacing = true;
    this->m_ManualReinitialization = false;
    this->m_InitializedState = false;
    this->m_NumberOfIterations = NumericTraits<unsigned int>::max();
    this->m_FunctionCount = 0;
    this->InPlaceOff();
  }
 
  ~MultiphaseFiniteDifferenceImageFilter() override = default;
 
  IdCellType                     m_FunctionCount{};
  std::vector<InputImagePointer> m_LevelSet{};
  VectorIdCellType               m_Lookup{};
  KdTreePointer                  m_KdTree{};
 
  unsigned int m_ElapsedIterations{};
  double       m_MaximumRMSError{};
  double       m_RMSChange{};
  unsigned int m_NumberOfIterations{};
 
  std::vector<FiniteDifferenceFunctionPointer> m_DifferenceFunctions{};
 
  bool m_UseImageSpacing{};
 
  void
  PrintSelf(std::ostream & os, Indent indent) const override;
 
  virtual void
  AllocateUpdateBuffer() = 0;
 
  virtual void
  ApplyUpdate(TimeStepType dt) = 0;
 
  virtual TimeStepType
  CalculateChange() = 0;
 
  virtual void
  CopyInputToOutput() = 0;
 
  void
  GenerateData() override;
 
  void
  GenerateInputRequestedRegion() override;
 
  virtual bool
  Halt();
 
  virtual bool
  ThreadedHalt(void * itkNotUsed(threadInfo))
  {
    return this->Halt();
  }
 
  virtual void
  Initialize()
  {}
 
  virtual void
  InitializeIteration()
  {
    for (IdCellType i = 0; i < this->m_FunctionCount; ++i)
    {
      this->m_DifferenceFunctions[i]->InitializeIteration();
    }
  }
  inline TimeStepType
  ResolveTimeStep(const TimeStepVectorType & timeStepList, const std::vector<uint8_t> & valid);
 
  virtual void
  PostProcessOutput()
  {}
 
private:
  bool m_ManualReinitialization{};
 
  bool m_InitializedState{};
};
} // end namespace itk
 
#ifndef ITK_MANUAL_INSTANTIATION
#  include "itkMultiphaseFiniteDifferenceImageFilter.hxx"
#endif
 
#endif