elastix

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00001 /*======================================================================
00002 
00003   This file is part of the elastix software.
00004 
00005   Copyright (c) University Medical Center Utrecht. All rights reserved.
00006   See src/CopyrightElastix.txt or http://elastix.isi.uu.nl/legal.php for
00007   details.
00008 
00009      This software is distributed WITHOUT ANY WARRANTY; without even
00010      the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
00011      PURPOSE. See the above copyright notices for more information.
00012 
00013 ======================================================================*/
00014 
00024 #ifndef __elxElastixBase_h
00025 #define __elxElastixBase_h
00026 
00027 #include "elxBaseComponent.h"
00028 #include "elxComponentDatabase.h"
00029 #include "elxConfiguration.h"
00030 #include "itkObject.h"
00031 #include "itkDataObject.h"
00032 #include "elxMacro.h"
00033 #include "xoutmain.h"
00034 #include "itkVectorContainer.h"
00035 #include "itkImageFileReader.h"
00036 #include "itkChangeInformationImageFilter.h"
00037 
00038 #include <fstream>
00039 #include <iomanip>
00040 
00047 #define elxGetObjectMacro(_name,_type) \
00048   virtual _type * Get##_name (void) const \
00049   { \
00050     return this->m_##_name .GetPointer(); \
00051   }
00052 //end elxGetObjectMacro
00053 
00054 #define elxSetObjectMacro(_name,_type) \
00055   virtual void Set##_name (_type * _arg) \
00056   { \
00057     if ( this->m_##_name != _arg ) \
00058     { \
00059       this->m_##_name = _arg; \
00060       this->GetAsITKBaseType()->Modified(); \
00061     } \
00062   }
00063 //end elxSetObjectMacro
00064 
00066 #define elxGetNumberOfMacro(_name) \
00067   virtual unsigned int GetNumberOf##_name##s(void) const \
00068   { \
00069     if ( this->Get##_name##Container() != 0 ) \
00070     { \
00071       return this->Get##_name##Container()->Size(); \
00072     } \
00073     return 0; \
00074   }
00075 // end elxGetNumberOfMacro
00076 
00077 namespace elastix
00078 {
00079 using namespace itk;
00080 
00132 class ElastixBase : public BaseComponent
00133 {
00134 public:
00135 
00137   typedef ElastixBase       Self;
00138   typedef BaseComponent     Superclass;
00139 
00141   typedef Configuration                       ConfigurationType;
00142   typedef ConfigurationType::Pointer          ConfigurationPointer;
00143   typedef itk::Object                         ObjectType; //for the components
00144   typedef ObjectType::Pointer                 ObjectPointer;
00145   typedef itk::DataObject                     DataObjectType; //for the images
00146   typedef DataObjectType::Pointer             DataObjectPointer;
00147   typedef itk::VectorContainer<
00148     unsigned int, ObjectPointer>              ObjectContainerType;
00149   typedef ObjectContainerType::Pointer        ObjectContainerPointer;
00150   typedef itk::VectorContainer<
00151     unsigned int, DataObjectPointer>          DataObjectContainerType;
00152   typedef DataObjectContainerType::Pointer    DataObjectContainerPointer;
00153   typedef itk::VectorContainer<
00154     unsigned int, std::string >               FileNameContainerType;
00155   typedef FileNameContainerType::Pointer      FileNameContainerPointer;
00156 
00158   typedef ComponentDatabase                   ComponentDatabaseType;
00159   typedef ComponentDatabaseType::Pointer      ComponentDatabasePointer;
00160   typedef ComponentDatabaseType::IndexType    DBIndexType;
00161   typedef std::vector<double>                 FlatDirectionCosinesType;
00162 
00166   typedef Object      ITKBaseType;
00167 
00169   virtual ITKBaseType * GetAsITKBaseType( void )
00170   {
00171     return dynamic_cast<ITKBaseType *>( this );
00172   }
00173 
00175   elxGetObjectMacro( Configuration, ConfigurationType );
00176   elxSetObjectMacro( Configuration, ConfigurationType );
00177 
00179   virtual void SetDBIndex( DBIndexType _arg );
00180   virtual DBIndexType GetDBIndex( void )
00181   {
00182     return this->m_DBIndex;
00183   }
00184 
00189   elxGetObjectMacro( ComponentDatabase, ComponentDatabaseType );
00190   elxSetObjectMacro( ComponentDatabase, ComponentDatabaseType );
00191 
00196   elxGetObjectMacro( RegistrationContainer, ObjectContainerType );
00197   elxGetObjectMacro( FixedImagePyramidContainer, ObjectContainerType );
00198   elxGetObjectMacro( MovingImagePyramidContainer, ObjectContainerType );
00199   elxGetObjectMacro( InterpolatorContainer, ObjectContainerType );
00200   elxGetObjectMacro( ImageSamplerContainer, ObjectContainerType );
00201   elxGetObjectMacro( MetricContainer, ObjectContainerType );
00202   elxGetObjectMacro( OptimizerContainer, ObjectContainerType );
00203   elxGetObjectMacro( ResamplerContainer, ObjectContainerType );
00204   elxGetObjectMacro( ResampleInterpolatorContainer, ObjectContainerType );
00205   elxGetObjectMacro( TransformContainer, ObjectContainerType );
00206 
00211   elxSetObjectMacro( RegistrationContainer, ObjectContainerType );
00212   elxSetObjectMacro( FixedImagePyramidContainer, ObjectContainerType );
00213   elxSetObjectMacro( MovingImagePyramidContainer, ObjectContainerType );
00214   elxSetObjectMacro( InterpolatorContainer, ObjectContainerType );
00215   elxSetObjectMacro( ImageSamplerContainer, ObjectContainerType );
00216   elxSetObjectMacro( MetricContainer, ObjectContainerType );
00217   elxSetObjectMacro( OptimizerContainer, ObjectContainerType );
00218   elxSetObjectMacro( ResamplerContainer, ObjectContainerType );
00219   elxSetObjectMacro( ResampleInterpolatorContainer, ObjectContainerType );
00220   elxSetObjectMacro( TransformContainer, ObjectContainerType );
00221 
00223   elxGetObjectMacro( FixedImageContainer, DataObjectContainerType );
00224   elxGetObjectMacro( MovingImageContainer, DataObjectContainerType );
00225   elxSetObjectMacro( FixedImageContainer, DataObjectContainerType );
00226   elxSetObjectMacro( MovingImageContainer, DataObjectContainerType );
00227 
00229   elxGetObjectMacro( FixedMaskContainer, DataObjectContainerType );
00230   elxGetObjectMacro( MovingMaskContainer, DataObjectContainerType );
00231   elxSetObjectMacro( FixedMaskContainer, DataObjectContainerType );
00232   elxSetObjectMacro( MovingMaskContainer, DataObjectContainerType );
00233 
00237   elxGetObjectMacro( FixedImageFileNameContainer, FileNameContainerType );
00238   elxGetObjectMacro( MovingImageFileNameContainer, FileNameContainerType );
00239   elxSetObjectMacro( FixedImageFileNameContainer, FileNameContainerType );
00240   elxSetObjectMacro( MovingImageFileNameContainer, FileNameContainerType );
00241 
00245   elxGetObjectMacro( FixedMaskFileNameContainer, FileNameContainerType );
00246   elxGetObjectMacro( MovingMaskFileNameContainer, FileNameContainerType );
00247   elxSetObjectMacro( FixedMaskFileNameContainer, FileNameContainerType );
00248   elxSetObjectMacro( MovingMaskFileNameContainer, FileNameContainerType );
00249 
00251   elxGetNumberOfMacro( Registration );
00252   elxGetNumberOfMacro( FixedImagePyramid );
00253   elxGetNumberOfMacro( MovingImagePyramid );
00254   elxGetNumberOfMacro( Interpolator );
00255   elxGetNumberOfMacro( ImageSampler );
00256   elxGetNumberOfMacro( Metric );
00257   elxGetNumberOfMacro( Optimizer );
00258   elxGetNumberOfMacro( Resampler );
00259   elxGetNumberOfMacro( ResampleInterpolator );
00260   elxGetNumberOfMacro( Transform );
00261   elxGetNumberOfMacro( FixedImage );
00262   elxGetNumberOfMacro( MovingImage );
00263   elxGetNumberOfMacro( FixedImageFileName );
00264   elxGetNumberOfMacro( MovingImageFileName );
00265   elxGetNumberOfMacro( FixedMask );
00266   elxGetNumberOfMacro( MovingMask );
00267   elxGetNumberOfMacro( FixedMaskFileName );
00268   elxGetNumberOfMacro( MovingMaskFileName );
00269 
00274   elxSetObjectMacro( InitialTransform, ObjectType );
00275   elxGetObjectMacro( InitialTransform, ObjectType );
00276 
00283   elxSetObjectMacro( FinalTransform, ObjectType );
00284   elxGetObjectMacro( FinalTransform, ObjectType );
00285 
00287   virtual int Run( void ) = 0;
00288 
00290   virtual int ApplyTransform( void ) = 0;
00291 
00295   virtual int BeforeAllBase( void );
00296 
00300   virtual int BeforeAllTransformixBase( void );
00301 
00305   virtual void BeforeRegistrationBase( void );
00306   virtual void AfterRegistrationBase( void );
00307 
00312   virtual int GetDefaultOutputPrecision( void ) const
00313   {
00314     return this->m_DefaultOutputPrecision;
00315   }
00316 
00320   virtual bool GetUseDirectionCosines( void ) const;
00321 
00324   virtual void SetOriginalFixedImageDirectionFlat(
00325     const FlatDirectionCosinesType & arg );
00326   virtual const FlatDirectionCosinesType &
00327     GetOriginalFixedImageDirectionFlat( void ) const;
00328 
00329 protected:
00330 
00331   ElastixBase();
00332   virtual ~ElastixBase() {};
00333 
00334   ConfigurationPointer      m_Configuration;
00335   DBIndexType               m_DBIndex;
00336   ComponentDatabasePointer  m_ComponentDatabase;
00337 
00338   FlatDirectionCosinesType     m_OriginalFixedImageDirection;
00339 
00352   template < class TImage >
00353   class MultipleImageLoader
00354   {
00355   public:
00356     typedef TImage                              ImageType;
00357     typedef typename ImageType::Pointer         ImagePointer;
00358     typedef ImageFileReader<ImageType>          ImageReaderType;
00359     typedef typename ImageReaderType::Pointer   ImageReaderPointer;
00360     typedef typename ImageType::DirectionType   DirectionType;
00361     typedef ChangeInformationImageFilter<ImageType> ChangeInfoFilterType;
00362     typedef typename ChangeInfoFilterType::Pointer  ChangeInfoFilterPointer;
00363 
00364     static DataObjectContainerPointer GenerateImageContainer(
00365       FileNameContainerType * fileNameContainer, const std::string & imageDescription,
00366       bool useDirectionCosines, DirectionType * originalDirectionCosines = NULL )
00367     {
00368       DataObjectContainerPointer imageContainer = DataObjectContainerType::New();
00369 
00371       for ( unsigned int i = 0; i < fileNameContainer->Size(); ++i )
00372       {
00374         ImageReaderPointer imageReader = ImageReaderType::New();
00375         imageReader->SetFileName( fileNameContainer->ElementAt( i ).c_str() );
00376         ChangeInfoFilterPointer infoChanger = ChangeInfoFilterType::New();
00377         DirectionType direction;
00378         direction.SetIdentity();
00379         infoChanger->SetOutputDirection( direction );
00380         infoChanger->SetChangeDirection( !useDirectionCosines );
00381         infoChanger->SetInput( imageReader->GetOutput() );
00382 
00384         try
00385         {
00386           infoChanger->Update();
00387         }
00388         catch( itk::ExceptionObject & excp )
00389         {
00391           std::string err_str = excp.GetDescription();
00392           err_str += "\nError occurred while reading the image described as "
00393             + imageDescription + ", with file name " + imageReader->GetFileName() + "\n";
00394           excp.SetDescription( err_str );
00396           throw excp;
00397         }
00398 
00400         ImagePointer image = infoChanger->GetOutput();
00401         imageContainer->CreateElementAt(i) = image.GetPointer();
00402 
00404         if ( originalDirectionCosines )
00405         {
00406           *originalDirectionCosines = imageReader->GetOutput()->GetDirection();
00407         }
00408 
00409       } // end for i
00410 
00411       return imageContainer;
00412 
00413     } // end static method GenerateImageContainer
00414 
00415     MultipleImageLoader(){};
00416     ~MultipleImageLoader(){};
00417 
00418   }; // end class MultipleImageLoader
00419 
00420 private:
00421 
00422   ElastixBase( const Self& );     // purposely not implemented
00423   void operator=( const Self& );  // purposely not implemented
00424 
00425   xl::xoutrow_type      m_IterationInfo;
00426 
00427   int m_DefaultOutputPrecision;
00428 
00432   ObjectContainerPointer m_FixedImagePyramidContainer;
00433   ObjectContainerPointer m_MovingImagePyramidContainer;
00434   ObjectContainerPointer m_InterpolatorContainer;
00435   ObjectContainerPointer m_ImageSamplerContainer;
00436   ObjectContainerPointer m_MetricContainer;
00437   ObjectContainerPointer m_OptimizerContainer;
00438   ObjectContainerPointer m_RegistrationContainer;
00439   ObjectContainerPointer m_ResamplerContainer;
00440   ObjectContainerPointer m_ResampleInterpolatorContainer;
00441   ObjectContainerPointer m_TransformContainer;
00442 
00444   DataObjectContainerPointer m_FixedImageContainer;
00445   DataObjectContainerPointer m_MovingImageContainer;
00446   DataObjectContainerPointer m_FixedMaskContainer;
00447   DataObjectContainerPointer m_MovingMaskContainer;
00448 
00450   FileNameContainerPointer    m_FixedImageFileNameContainer;
00451   FileNameContainerPointer    m_MovingImageFileNameContainer;
00452   FileNameContainerPointer    m_FixedMaskFileNameContainer;
00453   FileNameContainerPointer    m_MovingMaskFileNameContainer;
00454 
00456   ObjectPointer m_InitialTransform;
00457   ObjectPointer m_FinalTransform;
00458 
00460   bool m_UseDirectionCosines;
00461 
00469   FileNameContainerPointer GenerateFileNameContainer(
00470     const std::string & optionkey,
00471     int & errorcode,
00472     bool printerrors,
00473     bool printinfo ) const;
00474 
00475 };  // end class ElastixBase
00476 
00477 
00478 } // end namespace elastix
00479 
00480 #undef elxGetObjectMacro
00481 #undef elxSetObjectMacro
00482 #undef elxGetNumberOfMacro
00483 
00484 #endif // end #ifndef __elxElastixBase_h
00485