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 "elxComponentDatabase.h"
#include "elxComponentLoader.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 );
  itkGetModifiableObjectMacro( FixedImageContainer,  DataObjectContainerType );
  itkGetModifiableObjectMacro( MovingImageContainer, DataObjectContainerType );
 
  itkSetObjectMacro( FixedMaskContainer, DataObjectContainerType );
  itkSetObjectMacro( MovingMaskContainer, DataObjectContainerType );
  itkGetModifiableObjectMacro( FixedMaskContainer, DataObjectContainerType );
  itkGetModifiableObjectMacro( MovingMaskContainer, DataObjectContainerType );
 
  itkSetObjectMacro( ResultImageContainer, DataObjectContainerType );
  itkGetModifiableObjectMacro( ResultImageContainer, DataObjectContainerType );
 
  itkSetObjectMacro( ResultDeformationFieldContainer, DataObjectContainerType );
  itkGetModifiableObjectMacro( ResultDeformationFieldContainer, DataObjectContainerType );
 
  itkSetObjectMacro( Configuration, ConfigurationType );
  itkGetModifiableObjectMacro( Configuration, ConfigurationType );
 
  itkGetModifiableObjectMacro( Elastix, ObjectType );
 
  virtual ElastixBaseType * GetElastixBase( void ) const;
 
  itkGetModifiableObjectMacro( FinalTransform, ObjectType );
 
  itkSetObjectMacro( InitialTransform, ObjectType );
  itkGetModifiableObjectMacro( 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( const ArgumentMapType & argmap );
 
  virtual void EnterCommandLineArguments( const ArgumentMapType & argmap,
    const ParameterMapType & inputMap );
 
  // Version used when elastix is used as a library.
  virtual void EnterCommandLineArguments( const ArgumentMapType & argmap,
    const std::vector< ParameterMapType > & inputMaps );
 
  virtual int Run( void );
 
  virtual int Run( const ArgumentMapType & argmap );
 
  virtual int Run( const ArgumentMapType & argmap, const 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();
  ~ElastixMain() override;
 
  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;
  DataObjectContainerPointer m_ResultDeformationFieldContainer;
 
  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