elxElastixMain.h

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

  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