cmtkVolumeInjectionReconstruction.h

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/*
//
//  Copyright 1997-2009 Torsten Rohlfing
//
//  Copyright 2004-2010 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: 2398 $
//
//  $LastChangedDate: 2010-10-05 14:54:37 -0700 (Tue, 05 Oct 2010) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#ifndef __cmtkVolumeInjectionReconstruction_h_included_
#define __cmtkVolumeInjectionReconstruction_h_included_

#include <cmtkconfig.h>

#include <Registration/cmtkAffineRegistration.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkXform.h>
#include <Base/cmtkUniformVolume.h>

#include "Numerics/ap.h"

#include <vector>

namespace
cmtk
{


class VolumeInjectionReconstruction
{
public:
  typedef VolumeInjectionReconstruction Self;

  VolumeInjectionReconstruction( const UniformVolume* originalImage, const int numberOfPasses, const int interleaveAxis );

  VolumeInjectionReconstruction( const UniformVolume* reconstructionGrid, std::vector<UniformVolume::SmartPtr>& images );

  virtual ~VolumeInjectionReconstruction() {}

  static int GuessInterleaveAxis( 
    const UniformVolume* image, 
    const int defaultAxis = 2 
    );

  void ComputeTransformationsToPassImages( const int registrationMetric = 0 );

  void SetTransformationsToPassImages( std::vector<Xform::SmartPtr>& transformations )
  {
    this->m_TransformationsToPassImages = transformations;
  }

  Xform::SmartPtr& GetTransformationToPassImage( const size_t passIdx )
  {
    if ( passIdx < this->m_TransformationsToPassImages.size() )
      return this->m_TransformationsToPassImages[passIdx];
    else
      return Xform::SmartPtr::Null;
  }

  std::vector<Xform::SmartPtr>& GetTransformationsToPassImages()
  {
    return this->m_TransformationsToPassImages;
  }

  void VolumeInjectionIsotropic
  ( const Types::Coordinate kernelSigma, 
    const Types::Coordinate kernelRadius 
    );

  void VolumeInjectionAnisotropic
  ( const Types::Coordinate kernelSigmaFactor, 
    const Types::Coordinate kernelRadiusFactor 
    );

  UniformVolume::SmartPtr& GetCorrectedImage();
  
  void SetReferenceImage( UniformVolume::SmartPtr& referenceImage );  

  void SetPassWeight( const size_t pass, const Types::Coordinate weight )
  {
    this->m_PassWeights[pass] = weight;
  }

  ap::real_value_type GetOriginalToCorrectedImageKLD( const ap::real_1d_array& x );
  
protected:
  int m_NumberOfPasses;

  std::vector<Types::Coordinate> m_PassWeights;

  Types::DataItemRange m_OriginalImageRange;

  std::vector<UniformVolume::SmartPtr> m_OriginalPassImages;

  typedef Histogram<double> HistogramType;

  HistogramType::SmartPtr m_OriginalImageHistogram;

  HistogramType::SmartPtr m_CorrectedImageHistogram;

  std::vector<HistogramType::BinType> m_OriginalImageIntensityNoiseKernel;

  UniformVolume::SmartPtr m_ReferenceImage;

  std::vector<Xform::SmartPtr> m_TransformationsToPassImages;

  UniformVolume::SmartPtr m_CorrectedImage;

  std::vector<ap::real_value_type> m_CorrectedImageLaplacians;  

  ap::real_value_type ComputeCorrectedImageLaplacianNorm( 
    const ap::real_1d_array& correctedImagePixels 
    );
  
  void AddLaplacianGradientImage( 
    ap::real_1d_array& g, 
    const ap::real_1d_array& correctedImagePixels,
    const ap::real_value_type weight ) const;

  ap::real_1d_array m_NeighorhoodMaxPixelValues;
  
  ap::real_1d_array m_NeighorhoodMinPixelValues;
  
private:
  static const unsigned int NumberOfHistogramBins = 64;

  void SetupHistogramKernels( const TypedArray* originalData );
};


} // namespace cmtk

#endif // #ifndef __cmtkVolumeInjectionReconstruction_h_included_