mitkDemonsRegistration.cpp

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/*===================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.

This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.

See LICENSE.txt or http://www.mitk.org for details.

===================================================================*/

#include <mitkImageCast.h>

#include "itkImageFileWriter.h"
#include "itkImageRegionIterator.h"
#include "itkWarpImageFilter.h"

#include "mitkDemonsRegistration.h"

namespace mitk
{
  DemonsRegistration::DemonsRegistration()
    : m_Iterations(50),
      m_StandardDeviation(1.0),
      m_FieldName("newField.mhd"),
      m_ResultName("deformedImage.mhd"),
      m_SaveField(true),
      m_SaveResult(true),
      m_DeformationField(nullptr)
  {
  }

  DemonsRegistration::~DemonsRegistration() {}
  void DemonsRegistration::SetNumberOfIterations(int iterations) { m_Iterations = iterations; }
  void DemonsRegistration::SetStandardDeviation(float deviation) { m_StandardDeviation = deviation; }
  void DemonsRegistration::SetSaveDeformationField(bool saveField) { m_SaveField = saveField; }
  void DemonsRegistration::SetDeformationFieldFileName(const char *fieldName) { m_FieldName = fieldName; }
  void DemonsRegistration::SetSaveResult(bool saveResult) { m_SaveResult = saveResult; }
  void DemonsRegistration::SetResultFileName(const char *resultName) { m_ResultName = resultName; }
  itk::Image<itk::Vector<float, 3>, 3>::Pointer DemonsRegistration::GetDeformationField() { return m_DeformationField; }
  template <typename TPixel, unsigned int VImageDimension>
  void DemonsRegistration::GenerateData2(const itk::Image<TPixel, VImageDimension> *itkImage1)
  {
    typedef typename itk::Image<TPixel, VImageDimension> FixedImageType;
    typedef typename itk::Image<TPixel, VImageDimension> MovingImageType;

    typedef float InternalPixelType;
    typedef typename itk::Image<InternalPixelType, VImageDimension> InternalImageType;
    typedef typename itk::CastImageFilter<FixedImageType, InternalImageType> FixedImageCasterType;
    typedef typename itk::CastImageFilter<MovingImageType, InternalImageType> MovingImageCasterType;
    typedef typename itk::Image<InternalPixelType, VImageDimension> InternalImageType;
    typedef typename itk::Vector<float, VImageDimension> VectorPixelType;
    typedef typename itk::Image<VectorPixelType, VImageDimension> DeformationFieldType;
    typedef typename itk::DemonsRegistrationFilter<InternalImageType, InternalImageType, DeformationFieldType>
      RegistrationFilterType;
    typedef typename itk::WarpImageFilter<MovingImageType, MovingImageType, DeformationFieldType> WarperType;
    typedef typename itk::LinearInterpolateImageFunction<MovingImageType, double> InterpolatorType;

    typedef TPixel OutputPixelType;
    typedef typename itk::Image<OutputPixelType, VImageDimension> OutputImageType;
    typedef typename itk::CastImageFilter<MovingImageType, OutputImageType> CastFilterType;
    typedef typename itk::ImageFileWriter<OutputImageType> WriterType;
    typedef typename itk::ImageFileWriter<DeformationFieldType> FieldWriterType;

    typename FixedImageType::Pointer fixedImage = FixedImageType::New();
    mitk::CastToItkImage(m_ReferenceImage, fixedImage);
    typename MovingImageType::ConstPointer movingImage = itkImage1;

    if (fixedImage.IsNotNull() && movingImage.IsNotNull())
    {
      typename RegistrationFilterType::Pointer filter = RegistrationFilterType::New();

      this->AddStepsToDo(4);
      typename itk::ReceptorMemberCommand<DemonsRegistration>::Pointer command =
        itk::ReceptorMemberCommand<DemonsRegistration>::New();
      command->SetCallbackFunction(this, &DemonsRegistration::SetProgress);
      filter->AddObserver(itk::IterationEvent(), command);

      typename FixedImageCasterType::Pointer fixedImageCaster = FixedImageCasterType::New();
      fixedImageCaster->SetInput(fixedImage);
      filter->SetFixedImage(fixedImageCaster->GetOutput());
      typename MovingImageCasterType::Pointer movingImageCaster = MovingImageCasterType::New();
      movingImageCaster->SetInput(movingImage);
      filter->SetMovingImage(movingImageCaster->GetOutput());
      filter->SetNumberOfIterations(m_Iterations);
      filter->SetStandardDeviations(m_StandardDeviation);
      filter->Update();

      typename WarperType::Pointer warper = WarperType::New();
      typename InterpolatorType::Pointer interpolator = InterpolatorType::New();

      warper->SetInput(movingImage);
      warper->SetInterpolator(interpolator);
      warper->SetOutputSpacing(fixedImage->GetSpacing());
      warper->SetOutputOrigin(fixedImage->GetOrigin());
      warper->SetOutputDirection(fixedImage->GetDirection());
      warper->SetDisplacementField(filter->GetOutput());
      warper->Update();
      Image::Pointer outputImage = this->GetOutput();
      mitk::CastToMitkImage(warper->GetOutput(), outputImage);

      typename WriterType::Pointer writer = WriterType::New();
      typename CastFilterType::Pointer caster = CastFilterType::New();

      writer->SetFileName(m_ResultName);

      caster->SetInput(warper->GetOutput());
      writer->SetInput(caster->GetOutput());
      if (m_SaveResult)
      {
        writer->Update();
      }

      if (VImageDimension == 2)
      {
        typedef DeformationFieldType VectorImage2DType;
        typedef typename DeformationFieldType::PixelType Vector2DType;

        typename VectorImage2DType::ConstPointer vectorImage2D = filter->GetOutput();

        typename VectorImage2DType::RegionType region2D = vectorImage2D->GetBufferedRegion();
        typename VectorImage2DType::IndexType index2D = region2D.GetIndex();
        typename VectorImage2DType::SizeType size2D = region2D.GetSize();

        typedef typename itk::Vector<float, 3> Vector3DType;
        typedef typename itk::Image<Vector3DType, 3> VectorImage3DType;

        typedef typename itk::ImageFileWriter<VectorImage3DType> WriterType;

        typename WriterType::Pointer writer3D = WriterType::New();

        typename VectorImage3DType::Pointer vectorImage3D = VectorImage3DType::New();

        typename VectorImage3DType::RegionType region3D;
        typename VectorImage3DType::IndexType index3D;
        typename VectorImage3DType::SizeType size3D;

        index3D[0] = index2D[0];
        index3D[1] = index2D[1];
        index3D[2] = 0;

        size3D[0] = size2D[0];
        size3D[1] = size2D[1];
        size3D[2] = 1;

        region3D.SetSize(size3D);
        region3D.SetIndex(index3D);

        typename VectorImage2DType::SpacingType spacing2D = vectorImage2D->GetSpacing();
        typename VectorImage3DType::SpacingType spacing3D;

        spacing3D[0] = spacing2D[0];
        spacing3D[1] = spacing2D[1];
        spacing3D[2] = 1.0;

        vectorImage3D->SetSpacing(spacing3D);

        vectorImage3D->SetRegions(region3D);
        vectorImage3D->Allocate();

        typedef typename itk::ImageRegionConstIterator<VectorImage2DType> Iterator2DType;

        typedef typename itk::ImageRegionIterator<VectorImage3DType> Iterator3DType;

        Iterator2DType it2(vectorImage2D, region2D);
        Iterator3DType it3(vectorImage3D, region3D);

        it2.GoToBegin();
        it3.GoToBegin();

        Vector2DType vector2D;
        Vector3DType vector3D;

        vector3D[2] = 0; // set Z component to zero.

        while (!it2.IsAtEnd())
        {
          vector2D = it2.Get();
          vector3D[0] = vector2D[0];
          vector3D[1] = vector2D[1];
          it3.Set(vector3D);
          ++it2;
          ++it3;
        }

        writer3D->SetInput(vectorImage3D);
        m_DeformationField = vectorImage3D;

        writer3D->SetFileName(m_FieldName);

        try
        {
          if (m_SaveField)
          {
            writer3D->Update();
          }
        }
        catch (itk::ExceptionObject &excp)
        {
          MITK_ERROR << excp << std::endl;
        }
      }
      else
      {
        typename FieldWriterType::Pointer fieldwriter = FieldWriterType::New();
        fieldwriter->SetFileName(m_FieldName);
        fieldwriter->SetInput(filter->GetOutput());
        m_DeformationField = (itk::Image<itk::Vector<float, 3>, 3> *)(filter->GetOutput());
        if (m_SaveField)
        {
          fieldwriter->Update();
        }
      }
      this->SetRemainingProgress(4);
    }
  }
} // end namespace