itkStripTsImageFilter.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 itkStripTsImageFilter_h
#define itkStripTsImageFilter_h

#include "itkImageToImageFilter.h"

#include "itkImageDuplicator.h"
#include "itkRescaleIntensityImageFilter.h"

#include "itkMultiResolutionImageRegistrationMethod.h"
#include "itkResampleImageFilter.h"
#include "itkNearestNeighborInterpolateImageFunction.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkCenteredTransformInitializer.h"
#include "itkVersorRigid3DTransform.h"
#include "itkAffineTransform.h"
#include "itkVersorRigid3DTransformOptimizer.h"
#include "itkRegularStepGradientDescentOptimizer.h"
#include "itkMattesMutualInformationImageToImageMetric.h"

#include "itkBinaryBallStructuringElement.h"
#include "itkBinaryErodeImageFilter.h"

#include "itkBinaryThresholdImageFilter.h"
#include "itkGradientAnisotropicDiffusionImageFilter.h"
#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
#include "itkSigmoidImageFilter.h"
#include "itkGeodesicActiveContourLevelSetImageFilter.h"
#include "itkCastImageFilter.h"

#include "itkTimeProbesCollectorBase.h"
#include "itkProgressAccumulator.h"

namespace itk
{

template <class TImageType, class TAtlasImageType, class TAtlasLabelType>
class ITK_EXPORT
StripTsImageFilter : public ImageToImageFilter<TImageType, TAtlasLabelType>
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(StripTsImageFilter);

  // standard class type alias
  using Self = StripTsImageFilter;
  using Superclass = ImageToImageFilter<TImageType,TAtlasLabelType>;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  // method for creation through the object factory
  itkNewMacro(Self);

  // run-time type information (and related methods)
  itkTypeMacro(StripTsImageFilter, ImageToImageFilter);

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

  // image and label templates
  using ImageType = TImageType;
  using ImagePointer = typename ImageType::Pointer;
  using ImageConstPointer = typename ImageType::ConstPointer;

  using AtlasImageType = TAtlasImageType;
  using AtlasImagePointer = typename AtlasImageType::Pointer;
  using AtlasImageConstPointer = typename AtlasImageType::ConstPointer;

  using AtlasLabelType = TAtlasLabelType;
  using AtlasLabelPointer = typename AtlasLabelType::Pointer;
  using AtlasLabelConstPointer = typename AtlasLabelType::ConstPointer;

  using ProgressPointer = typename ProgressAccumulator::Pointer;

  void SetAtlasImage( const TAtlasImageType * ptr );
  void SetAtlasBrainMask( const TAtlasLabelType * ptr );

  const std::string &GetTimerReport() const
  {
    return m_TimerReport;
  }

protected:

  StripTsImageFilter();
  ~StripTsImageFilter();

  // does the real work
  void GenerateData() override;


private:
  ImagePointer            m_PatientImage;
  AtlasImagePointer       m_AtlasImage;
  AtlasLabelPointer       m_AtlasLabels;
  ProgressPointer         m_Progress;
  TimeProbesCollectorBase m_Timer;
  std::string             m_TimerReport;

  void RescaleImages();
  void DownsampleImage();
  void RigidRegistration();
  void AffineRegistration();
  void BinaryErosion();
  void MultiResLevelSet();
  void PyramidFilter(int isoSpacing);
  void InversePyramidFilter();
  void LevelSetRefinement(int isoSpacing);
  void UpsampleLabels();

}; // end of class

} // end namespace itk

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

#endif