cmtkVoxelRegistration.h

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/*
//
//  Copyright 1997-2009 Torsten Rohlfing
//
//  Copyright 2004-2011 SRI International
//
//  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 __cmtkVoxelRegistration_h_included_
#define __cmtkVoxelRegistration_h_included_

#include <cmtkconfig.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 <Registration/cmtkRegistrationCallback.h>
#include <Registration/cmtkOptimizer.h>
#include <Base/cmtkInterpolator.h>

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

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

namespace
cmtk
{


class VoxelRegistration 
{
protected:
  cmtkGetSetMacro(int,Metric);

  cmtkGetSetMacro(int,Algorithm);

  cmtkGetSetMacro(double,Exploration);

  cmtkGetSetMacro(double,Accuracy);

  double CoarsestResolution;

  cmtkGetSetMacro(bool,UseOriginalData);
 
  double OptimizerStepFactor;

  bool UseMaxNorm;

  Optimizer::ReturnType m_DeltaFThreshold;

  cmtkGetSetMacro(Types::Coordinate,Sampling);

  cmtkGetSetMacroString(Protocol);

  cmtkGetSetMacro(UniformVolume::SmartPtr,Volume_1);

  cmtkGetSetMacro(UniformVolume::SmartPtr,Volume_2);

  cmtkGetSetMacro(UniformVolume::SmartPtr,ReferenceVolume);

  cmtkGetSetMacro(UniformVolume::SmartPtr,FloatingVolume);

  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;

    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;
  
  bool SwitchVolumes;

  cmtkGetSetMacro(RegistrationCallback::SmartPtr,Callback);

  cmtkGetSetMacro(AffineXform::SmartPtr,InitialTransformation);

  cmtkGetSetMacro(bool,InitialXformIsInverse);

  Xform::SmartPtr m_Xform;

  std::stack<Functional::SmartPtr> FunctionalStack;

  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 {};

  VoxelRegistration ();

  virtual ~VoxelRegistration ();

  virtual CallbackResult Register ();

  double GetTotalElapsedTime() const 
  {
    return cmtk::Timers::GetTimeProcess() - TimeStartRegistration;
  }
  
  double GetLevelElapsedTime() const 
  {
    return cmtk::Timers::GetTimeProcess() - TimeStartLevel;
  }
  
  double GetTotalElapsedWalltime() const 
  {
    return cmtk::Timers::GetWalltime() - WalltimeStartRegistration;
  }
  
  double GetLevelElapsedWalltime() const 
  {
    return cmtk::Timers::GetWalltime() - WalltimeStartLevel;
  }
  
  double GetThreadTotalElapsedTime() const 
  {
    return cmtk::Timers::GetTimeThread() - ThreadTimeStartRegistration;
  }
  
  double GetThreadLevelElapsedTime() const 
  {
    return cmtk::Timers::GetTimeThread() - ThreadTimeStartLevel;
  }

private:
  double TimeStartRegistration;

  double TimeStartLevel;

  double WalltimeStartRegistration;

  double WalltimeStartLevel;

  double ThreadTimeStartRegistration;

  double ThreadTimeStartLevel;
};


} // namespace cmtk

#endif // #ifndef __cmtkVoxelRegistration_h_included_