/*
//
//  Copyright 2012, 2013 SRI International
//
//  This file is part of the Computational Morphometry Toolkit.
//
//  http://www.nitrc.org/projects/cmtk/
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//  The Computational Morphometry Toolkit is free software: you can
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//  warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//  GNU General Public License for more details.
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//  You should have received a copy of the GNU General Public License along
//  with the Computational Morphometry Toolkit.  If not, see
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*/

#ifndef __cmtkFitSplineWarpToXformList_h_included_
#define __cmtkFitSplineWarpToXformList_h_included_

#include <cmtkconfig.h>

#include <Base/cmtkFitAffineToXformList.h>

#include <Base/cmtkXformList.h>
#include <Base/cmtkSplineWarpXform.h>
#include <Base/cmtkCubicSpline.h>
#include <Base/cmtkRegion.h>

namespace
cmtk
{

/** \addtogroup Base */
//@{

/** Fit B-spline-based free-form deformation to list of concatenated transformations, sampled on a discrete grid.
 *\see This class implements the algorithm from: N. J. Tustison, B. B. Avants, and J. C. Gee, "Directly manipulated free-form deformation image registration," IEEE Transactions on Image Processing, vol. 18, no. 3, pp. 624-635, 2009;
 * http://dx.doi.org/10.1109/TIP.2008.2010072
 *\see The implementation itself is more closely following S. Lee, G. Wolberg, and S. Y. Shin, “Scattered data interpolation with multilevel B-splines,” IEEE Transactions on Visualization and Computer Graphics, 
 * vol. 3, no. 3, pp. 228-244, 1997. http://dx.doi.org/10.1109/2945.620490
 *
 *\todo It would be nice to have the same multi-iteration fitting options here as in cmtk::FitSplineWarpToLandmarks.
 */
class FitSplineWarpToXformList
  : private FitAffineToXformList
{
public:
  /// This class.
  typedef FitSplineWarpToXformList Self;

  /// Base class.
  typedef FitAffineToXformList Superclass;

  /// Constructor.
  FitSplineWarpToXformList( const UniformVolume& sampleGrid /*!< Discrete pixel grid where the spline transformation is sampled and residuals are minimized.*/,
			    const XformList& xformList /*!< List of concatenated transformation that the spline transformation is fitted to.*/, 
			    const bool absolute = true /*!< Flag fitting absolute transformation vs. relative deformation field */ ) : Superclass( sampleGrid, xformList, absolute ) {}

  /// Fit spline warp based on final grid dimensions.
  SplineWarpXform::SmartPtr Fit( const SplineWarpXform::ControlPointIndexType& finalDims /*!< Final spline control point grid dimensions.*/, 
				 const int nLevels /*!< Number of levels in the multi-resolution fitting.*/,
				 const bool fitAffineFirst = true /*!< Flag for optional affine transformation to initialize the spline control points.*/ );

  /// Fit spline warp based on final grid spacing.
  SplineWarpXform::SmartPtr Fit( const Types::Coordinate finalSpacing /*!< Final control point spacing of the fitted B-spline free-form deformation*/, 
				 const int nLevels = 1 /*!< Number of levels for optional multi-resolution fit (default: single-resolution fit)*/,
				 const bool fitAffineFirst = true /*!< Flag for optional affine transformation to initialize the spline control points.*/  );
  
private:
  /// Deformation field residuals, i.e., pixel-wise difference between B-spline transformation and deformation field.
  std::vector< FixedVector<3,Types::Coordinate> > m_Residuals;

  /// Compute residuals, i.e., pixel-wise difference between B-spline transformation and deformation field.
  void ComputeResiduals( const SplineWarpXform& splineWarp );

  /// Fit spline warp based on initial warp object.
  void FitSpline( SplineWarpXform& splineWarp, const int nLevels );
};

} // namespace

#endif // #ifndef __cmtkFitSplineWarpToXformList_h_included_
