elxTransformBase.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 __elxTransformBase_h
#define __elxTransformBase_h
 
#include "elxMacro.h"
 
#include "elxBaseComponentSE.h"
#include "itkAdvancedTransform.h"
#include "itkAdvancedCombinationTransform.h"
#include "elxComponentDatabase.h"
#include "elxProgressCommand.h"
 
#include <memory> // For unique_ptr.
 
namespace elastix
{
//using namespace itk; //Not here, because a TransformBase class was added to ITK...
 
template< class TElastix >
class TransformBase :
  public BaseComponentSE< TElastix >
{
public:
  ITK_DISALLOW_COPY_AND_ASSIGN(TransformBase);
 
  typedef TransformBase               Self;
  typedef BaseComponentSE< TElastix > Superclass;
 
  itkTypeMacro( TransformBase, BaseComponentSE );
 
  using typename Superclass::ElastixType;
  using typename Superclass::ElastixPointer;
  using typename Superclass::ConfigurationType;
  using typename Superclass::ConfigurationPointer;
  using typename Superclass::RegistrationType;
  using typename Superclass::RegistrationPointer;
 
  typedef typename ConfigurationType
    ::CommandLineArgumentMapType CommandLineArgumentMapType;
  typedef typename ConfigurationType
    ::CommandLineEntryType CommandLineEntryType;
 
  typedef typename ElastixType::CoordRepType    CoordRepType;
  typedef typename ElastixType::FixedImageType  FixedImageType;
  typedef typename ElastixType::MovingImageType MovingImageType;
 
  typedef ComponentDatabase                               ComponentDatabaseType;
  typedef ComponentDatabaseType::ComponentDescriptionType ComponentDescriptionType;
  typedef ComponentDatabase::PtrToCreator                 PtrToCreator;
 
  typedef elx::ProgressCommand ProgressCommandType;
 
  itkStaticConstMacro( FixedImageDimension,
    unsigned int, FixedImageType::ImageDimension );
 
  itkStaticConstMacro( MovingImageDimension,
    unsigned int, MovingImageType::ImageDimension );
 
  typedef itk::Object ObjectType;
  typedef itk::AdvancedTransform<
    CoordRepType,
    itkGetStaticConstMacro( FixedImageDimension ),
    itkGetStaticConstMacro( MovingImageDimension ) >  ITKBaseType;
  typedef itk::AdvancedCombinationTransform< CoordRepType,
    itkGetStaticConstMacro( FixedImageDimension ) >   CombinationTransformType;
  typedef typename
    CombinationTransformType::InitialTransformType InitialTransformType;
 
  typedef typename ITKBaseType::ParametersType ParametersType;
  typedef typename ParametersType::ValueType   ValueType;
 
  typedef typename ITKBaseType::InputPointType  InputPointType;
  typedef typename ITKBaseType::OutputPointType OutputPointType;
 
  typedef itk::Vector<
    float, FixedImageDimension >                      VectorPixelType;
  typedef itk::Image<
    VectorPixelType, FixedImageDimension >            DeformationFieldImageType;
 
  typedef typename RegistrationType::ITKBaseType      ITKRegistrationType;
  typedef typename ITKRegistrationType::OptimizerType OptimizerType;
  typedef typename OptimizerType::ScalesType          ScalesType;
 
  typedef typename ElastixType::ParameterMapType ParameterMapType;
 
  virtual ITKBaseType * GetAsITKBaseType( void )
  {
    return dynamic_cast< ITKBaseType * >( this );
  }
 
 
  virtual const ITKBaseType * GetAsITKBaseType( void ) const
  {
    return dynamic_cast< const ITKBaseType * >( this );
  }
 
 
  virtual const CombinationTransformType * GetAsCombinationTransform( void ) const
  {
    return dynamic_cast< const CombinationTransformType * >( this );
  }
 
 
  virtual CombinationTransformType * GetAsCombinationTransform( void )
  {
    return dynamic_cast< CombinationTransformType * >( this );
  }
 
 
  int BeforeAllBase( void ) override;
 
  virtual int BeforeAllTransformix( void );
 
  void BeforeRegistrationBase( void ) override;
 
  void AfterRegistrationBase( void ) override;
 
  virtual const InitialTransformType * GetInitialTransform( void ) const;
 
  virtual void SetInitialTransform( InitialTransformType * _arg );
 
  virtual void SetTransformParametersFileName( const char * filename );
 
  itkGetStringMacro( TransformParametersFileName );
 
  virtual void ReadFromFile( void );
 
  virtual void CreateTransformParametersMap(
    const ParametersType & param, ParameterMapType * paramsMap ) const;
 
  virtual void WriteToFile( const ParametersType & param ) const;
 
  virtual void WriteToFile( void ) const;
 
  virtual void SetReadWriteTransformParameters( const bool _arg );
 
  virtual void ReadInitialTransformFromFile(
    const char * transformParameterFileName );
 
  virtual void ReadInitialTransformFromVector( const size_t index );
 
  virtual void TransformPoints( void ) const;
 
  virtual void TransformPointsSomePoints( const std::string filename ) const;
 
  virtual void TransformPointsSomePointsVTK( const std::string filename ) const;
 
  typename DeformationFieldImageType::Pointer GenerateDeformationFieldImage( void ) const;
 
  void WriteDeformationFieldImage( typename DeformationFieldImageType::Pointer ) const;
 
  virtual void TransformPointsAllPoints(void) const;
 
  virtual void ComputeDeterminantOfSpatialJacobian( void ) const;
 
  virtual void ComputeSpatialJacobian( void ) const;
 
  virtual void SetFinalParameters( void );
 
protected:
 
  TransformBase() = default;
  ~TransformBase() override = default;
 
  void AutomaticScalesEstimation( ScalesType & scales ) const;
 
  void AutomaticScalesEstimationStackTransform(
    const unsigned int & numSubTransforms, ScalesType & scales ) const;
 
private:
 
  std::unique_ptr<ParametersType> m_TransformParametersPointer{};
  std::string      m_TransformParametersFileName;
  ParametersType   m_FinalParameters;
 
  bool m_ReadWriteTransformParameters{ true };
 
  std::string GetInitialTransformParametersFileName( void ) const
  {
    if( !this->GetInitialTransform() )
    {
      return "NoInitialTransform";
    }
 
    const Self * t0 = dynamic_cast<const Self *>( this->GetInitialTransform() );
    return t0->GetTransformParametersFileName();
  }
 
  bool m_UseBinaryFormatForTransformationParameters{};
 
};
 
} // end namespace elastix
 
#ifndef ITK_MANUAL_INSTANTIATION
#include "elxTransformBase.hxx"
#endif
 
#endif // end #ifndef __elxTransformBase_h