elxElastixMain.h

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/*=========================================================================
 *
 *  Copyright UMC Utrecht and contributors
 *
 *  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 elxElastixMain_h
#define elxElastixMain_h
 
#include "elxMainBase.h"
 
 
namespace elastix
{

 
class ElastixMain : public MainBase
{
public:
  ITK_DISALLOW_COPY_AND_MOVE(ElastixMain);

  using Self = ElastixMain;
  using Superclass = MainBase;
  using Pointer = itk::SmartPointer<Self>;
  using ConstPointer = itk::SmartPointer<const Self>;

  itkNewMacro(Self);

  itkOverrideGetNameOfClassMacro(ElastixMain);

  itkSetObjectMacro(FixedImageContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(FixedImageContainer, DataObjectContainerType);

  itkSetObjectMacro(FixedMaskContainer, DataObjectContainerType);
  itkSetObjectMacro(MovingMaskContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(FixedMaskContainer, DataObjectContainerType);
  itkGetModifiableObjectMacro(MovingMaskContainer, DataObjectContainerType);
 
  itkSetConstObjectMacro(FixedPoints, itk::Object);
  itkSetConstObjectMacro(MovingPoints, itk::Object);

  itkGetModifiableObjectMacro(FinalTransform, itk::Object);

  itkSetObjectMacro(InitialTransform, itk::Object);
  itkGetModifiableObjectMacro(InitialTransform, itk::Object);

  virtual void
  SetOriginalFixedImageDirectionFlat(const FlatDirectionCosinesType & arg);
 
  virtual const FlatDirectionCosinesType &
  GetOriginalFixedImageDirectionFlat() const;

  void
  SetElastixLevel(unsigned int level);
 
  unsigned int
  GetElastixLevel() const;

  void
  SetTotalNumberOfElastixLevels(unsigned int levels);
 
  unsigned int
  GetTotalNumberOfElastixLevels() const;
 
  using Superclass::Run;

  int
  Run() override;
 
  int
  RunWithInitialTransformParameterMaps(const ArgumentMapType &               argmap,
                                       const ParameterMapType &              inputMap,
                                       const std::vector<ParameterMapType> & initialTransformParameterMaps);

  virtual ParameterMapType
  GetTransformParameterMap() const;
 
protected:
  ElastixMain();
  ~ElastixMain() override;

  int
  InitDBIndex() override;

  void
  GetImageInformationFromFile(const std::string & filename, ImageDimensionType & imageDimension) const;
 
private:
  DataObjectContainerPointer m_FixedImageContainer{ nullptr };
  DataObjectContainerPointer m_FixedMaskContainer{ nullptr };
  DataObjectContainerPointer m_MovingMaskContainer{ nullptr };
  DataObjectContainerPointer m_ResultImageContainer{ nullptr };
 
  itk::SmartPointer<const itk::Object> m_FixedPoints{ nullptr };
  itk::SmartPointer<const itk::Object> m_MovingPoints{ nullptr };
 

  ObjectPointer m_FinalTransform{ nullptr };

  ObjectPointer m_InitialTransform{ nullptr };

  ParameterMapType m_TransformParameterMap{};
 
  FlatDirectionCosinesType m_OriginalFixedImageDirectionFlat{};
};
 
} // end namespace elastix
 
#endif // end #ifndef elxElastixMain_h