cmtkImagePairRegistration.h

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/*
//
//  Copyright 2004-2011 SRI International
//
//  Copyright 1997-2009 Torsten Rohlfing
//
//  This file is part of the Computational Morphometry Toolkit.
//
//  http://www.nitrc.org/projects/cmtk/
//
//  The Computational Morphometry Toolkit is free software: you can
//  redistribute it and/or modify it under the terms of the GNU General Public
//  License as published by the Free Software Foundation, either version 3 of
//  the License, or (at your option) any later version.
//
//  The Computational Morphometry Toolkit is distributed in the hope that it
//  will be useful, but WITHOUT ANY WARRANTY; without even the implied
//  warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//  GNU General Public License for more details.
//
//  You should have received a copy of the GNU General Public License along
//  with the Computational Morphometry Toolkit.  If not, see
//  <http://www.gnu.org/licenses/>.
//
//  $Revision: 2752 $
//
//  $LastChangedDate: 2011-01-17 11:33:31 -0800 (Mon, 17 Jan 2011) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#ifndef __cmtkImagePairRegistration_h_included_
#define __cmtkImagePairRegistration_h_included_

#include <cmtkconfig.h>

#include <System/cmtkTimers.h>
#include <System/cmtkCommandLine.h>

#include <Base/cmtkMacros.h>
#include <Base/cmtkTypes.h>
#include <Base/cmtkXform.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkFunctional.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkVector.h>
#include <Base/cmtkInterpolator.h>

#include <Registration/cmtkRegistrationCallback.h>
#include <Registration/cmtkOptimizer.h>

#include <IO/cmtkClassStream.h>

#include <stack>
#include <string.h>

namespace
cmtk
{


class ImagePairRegistration 
{
public:
  typedef ImagePairRegistration Self;

  typedef SmartPointer<Self> SmartPtr;

protected:
  int m_Metric;
  
  cmtkGetSetMacro(Interpolators::InterpolationEnum,FloatingImageInterpolation);
  
  cmtkGetSetMacro(int,Algorithm);

  unsigned int m_AutoMultiLevels;

  double m_MaxStepSize;

  double m_MinStepSize;

  double m_CoarsestResolution;

  bool m_UseOriginalData;
 
  double m_OptimizerStepFactor;

  bool m_UseMaxNorm;

  Optimizer::ReturnType m_DeltaFThreshold;

  Types::Coordinate m_Sampling;

  bool m_ForceOutsideFlag;

  Types::DataItem m_ForceOutsideValue;

  cmtkGetSetMacro(UniformVolume::SmartPtr,Volume_1);

  cmtkGetSetMacro(UniformVolume::SmartPtr,Volume_2);

  cmtkGetSetMacro(UniformVolume::SmartPtr,ReferenceVolume);

  cmtkGetSetMacro(UniformVolume::SmartPtr,FloatingVolume);

  virtual void SetForceOutside( const bool flag = true, const Types::DataItem value = 0 )
  {
    this->m_ForceOutsideFlag = flag;
    this->m_ForceOutsideValue = value;
  }

  class ImagePreprocessor
  {
  public:
    const char* m_DataClassString;

    DataClass m_DataClass;
    
    bool m_PaddingFlag;
    
    Types::DataItem m_PaddingValue;

    bool m_LowerThresholdActive;

    Types::DataItem m_LowerThresholdValue;
  
    bool m_UpperThresholdActive;

    Types::DataItem m_UpperThresholdValue;

    bool m_UsePruneHistogramBins;

    unsigned int m_PruneHistogramBins;

    bool m_HistogramEqualization;

    int m_MedianFilterRadius;

    bool m_SobelFilter;

    const char* m_CropIndex;

    const char* m_CropWorld;

    bool m_AutoCropFlag;

    Types::DataItem m_AutoCropLevel;
    
    ImagePreprocessor( const char* name,  
                       const char* key 
      );
    
    void AttachToCommandLine( CommandLine& cl 
      ); 
    
    UniformVolume::SmartPtr GetProcessedImage( const UniformVolume* original );
    
    void WriteSettings( ClassStream& stream ) const;

  private:
    const char* m_Name;

    const char* m_Key;
  };

  ImagePreprocessor m_PreprocessorRef;

  ImagePreprocessor m_PreprocessorFlt;
  
  cmtkGetSetMacro(RegistrationCallback::SmartPtr,Callback);

  cmtkGetSetMacro(AffineXform::SmartPtr,InitialTransformation);

  cmtkGetSetMacro(bool,InitialXformIsInverse);

  Xform::SmartPtr m_Xform;

  class LevelParameters
  {
  public:
    typedef LevelParameters Self;

    typedef SmartPointer<Self> SmartPtr;

    virtual ~LevelParameters() {}
  };

  std::stack<Self::LevelParameters::SmartPtr> m_ParameterStack;

  virtual Functional* MakeFunctional( const int level, const Self::LevelParameters* levelParameters ) = 0;

  Optimizer::SmartPtr m_Optimizer;

  virtual CallbackResult InitRegistration ();

  virtual void OutputResult ( const CoordinateVector* v ) { UNUSED(v); }
  
  virtual void DoneRegistration ( const CoordinateVector* v = NULL);

  virtual void EnterResolution( CoordinateVector::SmartPtr& v, Functional::SmartPtr& f, const int idx, const int total );

  virtual int DoneResolution( CoordinateVector::SmartPtr&, Functional::SmartPtr&, const int, const int ) { return 1; }

public:
  class ConstructorFailed {};

  ImagePairRegistration ();

  virtual ~ImagePairRegistration () {}

  virtual CallbackResult Register ();

  double GetTotalElapsedTime() const 
  {
    return cmtk::Timers::GetTimeProcess() - this->m_TimeStartRegistration;
  }
  
  double GetLevelElapsedTime() const 
  {
    return cmtk::Timers::GetTimeProcess() - this->m_TimeStartLevel;
  }
  
  double GetTotalElapsedWalltime() const 
  {
    return cmtk::Timers::GetWalltime() - this->m_WalltimeStartRegistration;
  }
  
  double GetLevelElapsedWalltime() const 
  {
    return cmtk::Timers::GetWalltime() - this->m_WalltimeStartLevel;
  }
  
  double GetThreadTotalElapsedTime() const 
  {
    return cmtk::Timers::GetTimeThread() - this->m_ThreadTimeStartRegistration;
  }
  
  double GetThreadLevelElapsedTime() const 
  {
    return cmtk::Timers::GetTimeThread() - this->m_ThreadTimeStartLevel;
  }

private:
  double m_TimeStartRegistration;

  double m_TimeStartLevel;

  double m_WalltimeStartRegistration;

  double m_WalltimeStartLevel;

  double m_ThreadTimeStartRegistration;

  double m_ThreadTimeStartLevel;
};


} // namespace cmtk

#endif // #ifndef __cmtkImagePairRegistration_h_included_