elxElastixMain.h

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

  This file is part of the elastix software.

  Copyright (c) University Medical Center Utrecht. All rights reserved.
  See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
  details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE. See the above copyright notices for more information.

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

#ifndef __elxElastixMain_h
#define __elxElastixMain_h

#include "elxComponentDatabase.h"
#include "elxComponentLoader.h"

#include "elxBaseComponent.h"
#include "elxElastixBase.h"
#include "itkObject.h"

#include <iostream>
#include <fstream>

#include "itkParameterMapInterface.h"

namespace elastix
{


extern int xoutSetup( const char * logfilename, bool setupLogging, bool setupCout );

class ElastixMain : public itk::Object
{
public:

  typedef ElastixMain                     Self;
  typedef itk::Object                     Superclass;
  typedef itk::SmartPointer< Self >       Pointer;
  typedef itk::SmartPointer< const Self > ConstPointer;

  itkNewMacro( Self );

  itkTypeMacro( ElastixMain, Object );

  typedef itk::Object             ObjectType;
  typedef ObjectType::Pointer     ObjectPointer;
  typedef itk::DataObject         DataObjectType;
  typedef DataObjectType::Pointer DataObjectPointer;

  typedef ElastixBase                                   ElastixBaseType;
  typedef ElastixBase::ConfigurationType                ConfigurationType;
  typedef ConfigurationType::CommandLineArgumentMapType ArgumentMapType;
  typedef ConfigurationType::Pointer                    ConfigurationPointer;
  typedef ElastixBase::ObjectContainerType              ObjectContainerType;
  typedef ElastixBase::DataObjectContainerType          DataObjectContainerType;
  typedef ElastixBase::ObjectContainerPointer           ObjectContainerPointer;
  typedef ElastixBase::DataObjectContainerPointer       DataObjectContainerPointer;
  typedef ElastixBase::FlatDirectionCosinesType         FlatDirectionCosinesType;

  typedef ComponentDatabase                               ComponentDatabaseType;
  typedef ComponentDatabaseType::Pointer                  ComponentDatabasePointer;
  typedef ComponentDatabaseType::PtrToCreator             PtrToCreator;
  typedef ComponentDatabaseType::ComponentDescriptionType ComponentDescriptionType;
  typedef ComponentDatabaseType::PixelTypeDescriptionType PixelTypeDescriptionType;
  typedef ComponentDatabaseType::ImageDimensionType       ImageDimensionType;
  typedef ComponentDatabaseType::IndexType                DBIndexType;

  typedef ComponentLoader              ComponentLoaderType;
  typedef ComponentLoaderType::Pointer ComponentLoaderPointer;

  typedef itk::ParameterMapInterface::ParameterMapType ParameterMapType;

  itkSetMacro( FixedImagePixelType,   PixelTypeDescriptionType );
  itkSetMacro( MovingImagePixelType,  PixelTypeDescriptionType );
  itkSetMacro( FixedImageDimension,   ImageDimensionType );
  itkSetMacro( MovingImageDimension,  ImageDimensionType );
  itkGetMacro( FixedImagePixelType,   PixelTypeDescriptionType );
  itkGetMacro( MovingImagePixelType,  PixelTypeDescriptionType );
  itkGetMacro( FixedImageDimension,   ImageDimensionType );
  itkGetMacro( MovingImageDimension,  ImageDimensionType );

  itkSetObjectMacro( FixedImageContainer,  DataObjectContainerType );
  itkSetObjectMacro( MovingImageContainer, DataObjectContainerType );
  itkGetObjectMacro( FixedImageContainer,  DataObjectContainerType );
  itkGetObjectMacro( MovingImageContainer, DataObjectContainerType );

  itkSetObjectMacro( FixedMaskContainer, DataObjectContainerType );
  itkSetObjectMacro( MovingMaskContainer, DataObjectContainerType );
  itkGetObjectMacro( FixedMaskContainer, DataObjectContainerType );
  itkGetObjectMacro( MovingMaskContainer, DataObjectContainerType );

  itkSetObjectMacro( ResultImageContainer, DataObjectContainerType );
  itkGetObjectMacro( ResultImageContainer, DataObjectContainerType );

  itkSetObjectMacro( Configuration, ConfigurationType );
  itkGetObjectMacro( Configuration, ConfigurationType );

  itkGetObjectMacro( Elastix, ObjectType );

  virtual ElastixBaseType * GetElastixBase( void ) const;

  itkGetObjectMacro( FinalTransform, ObjectType );

  itkSetObjectMacro( InitialTransform, ObjectType );
  itkGetObjectMacro( InitialTransform, ObjectType );

  virtual void SetOriginalFixedImageDirectionFlat(
    const FlatDirectionCosinesType & arg );

  virtual const FlatDirectionCosinesType & GetOriginalFixedImageDirectionFlat( void ) const;

  void SetElastixLevel( unsigned int level );

  unsigned int GetElastixLevel( void );

  void SetTotalNumberOfElastixLevels( unsigned int levels );

  unsigned int GetTotalNumberOfElastixLevels( void );

  itkGetConstMacro( DBIndex, DBIndexType );

  virtual void EnterCommandLineArguments( ArgumentMapType & argmap );

  virtual void EnterCommandLineArguments( ArgumentMapType & argmap,
    ParameterMapType & inputMap );

  // Version used when elastix is used as a library.
  virtual void EnterCommandLineArguments( ArgumentMapType & argmap,
    std::vector< ParameterMapType > & inputMaps );

  virtual int Run( void );

  virtual int Run( ArgumentMapType & argmap );

  virtual int Run( ArgumentMapType & argmap, ParameterMapType & inputMap );

  virtual void SetProcessPriority( void ) const;

  virtual void SetMaximumNumberOfThreads( void ) const;

  static ComponentDatabase * GetComponentDatabase( void )
  {
    return s_CDB.GetPointer();
  }


  static void SetComponentDatabase( ComponentDatabase * arg )
  {
    if( s_CDB != arg )
    {
      s_CDB = arg;
    }
  }


  virtual ParameterMapType GetTransformParametersMap( void ) const;

  static void UnloadComponents( void );

protected:

  ElastixMain();
  virtual ~ElastixMain();

  ObjectPointer m_Elastix;

  ConfigurationPointer m_Configuration;

  std::vector< ConfigurationPointer > m_Configurations;

  PixelTypeDescriptionType m_FixedImagePixelType;
  ImageDimensionType       m_FixedImageDimension;
  PixelTypeDescriptionType m_MovingImagePixelType;
  ImageDimensionType       m_MovingImageDimension;

  DBIndexType m_DBIndex;

  DataObjectContainerPointer m_FixedImageContainer;
  DataObjectContainerPointer m_MovingImageContainer;
  DataObjectContainerPointer m_FixedMaskContainer;
  DataObjectContainerPointer m_MovingMaskContainer;
  DataObjectContainerPointer m_ResultImageContainer;

  ObjectPointer m_FinalTransform;

  ObjectPointer m_InitialTransform;
  ParameterMapType m_TransformParametersMap;

  FlatDirectionCosinesType m_OriginalFixedImageDirection;

  static ComponentDatabasePointer s_CDB;
  static ComponentLoaderPointer   s_ComponentLoader;
  virtual int LoadComponents( void );

  virtual int InitDBIndex( void );

  virtual ObjectPointer CreateComponent( const ComponentDescriptionType & name );

  virtual ObjectContainerPointer CreateComponents(
    const ComponentDescriptionType & key,
    const ComponentDescriptionType & defaultComponentName,
    int & errorcode,
    bool mandatoryComponent = true );

  void GetImageInformationFromFile( const std::string & filename,
    ImageDimensionType & imageDimension ) const;

private:

  ElastixMain( const Self & );     // purposely not implemented
  void operator=( const Self & );  // purposely not implemented

};

} // end namespace elastix

#endif // end #ifndef __elxElastixMain_h