// Definitions of class used for point-matching in FNIRT
//
// matching_points.cpp
//
// Jesper Andersson, FMRIB Image Analysis Group
//
// Copyright (C) 2008 University of Oxford 
//
/*  Part of FSL - FMRIB's Software Library
    http://www.fmrib.ox.ac.uk/fsl
    fsl@fmrib.ox.ac.uk
    
    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
    Imaging of the Brain), Department of Clinical Neurology, Oxford
    University, Oxford, UK
    
    
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#include <cstdlib>
#include <string>
#include <vector>
#include <boost/shared_ptr.hpp>
#include "newmat.h"
#include "newimage/newimageall.h"
#include "miscmaths/bfmatrix.h"
#include "basisfield/basisfield.h"
#include "basisfield/splinefield.h"
#include "basisfield/dctfield.h"
#include "warpfns/point_list.h"
#include "matching_points.h"

using namespace std;
using namespace boost;
using namespace NEWMAT;
using namespace NEWIMAGE;
using namespace BASISFIELD;
using namespace FNIRT;

///////////////////////////////////////////////////////////////////////////////////////////////
//
// Member functions for class MatchingPoints
//
///////////////////////////////////////////////////////////////////////////////////////////////

///////////////////////////////////////////////////////////////////////////////////////////////
//
// Returns the difference in position in dimension dim for point-pair given by index
//
///////////////////////////////////////////////////////////////////////////////////////////////

double MatchingPoints::Diff(unsigned int indx, unsigned int dim, const BASISFIELD::basisfield& bf) const
{
  ColumnVector ref_pnt = _in_ref->Point(indx);
  ColumnVector rrp = _in_ref->RawPoint(indx);  // Raw Ref Point
  rrp = bf.mm2vox(3) * rrp;
  ColumnVector in_pnt = _in_in->Point(indx);
  return(in_pnt(dim+1) - (ref_pnt(dim+1) + bf(rrp(1),rrp(2),rrp(3))));
}

///////////////////////////////////////////////////////////////////////////////////////////////
//
// Returns the sum-of-squared differences for the dimension given by dim
//
///////////////////////////////////////////////////////////////////////////////////////////////

double MatchingPoints::SSD(unsigned int dim, const basisfield& bf) const
{
  if (dim > 2) throw MatchingPointsException("SSD: dim must be 0--2");

  double ssd = 0.0;
  for (unsigned int i=0; i<_in_ref->NPoints(); i++) {
    ssd += MISCMATHS::Sqr(Diff(i,dim,bf));
  }
  return(ssd);
}

///////////////////////////////////////////////////////////////////////////////////////////////
//
// Returns the gradient of the sum-of-squared differences for the dimension given by dim
//
///////////////////////////////////////////////////////////////////////////////////////////////

ReturnMatrix MatchingPoints::SSD_Gradient(unsigned int dim, const basisfield& bf) const
{
  if (dim > 2) throw MatchingPointsException("SSD: dim must be 0--2");

  ColumnVector grad(bf.CoefSz());
  grad = 0.0;
  for (unsigned int pti=0; pti<_in_ref->NPoints(); pti++) {
    ColumnVector rrp = _in_ref->RawPoint(pti);  // Raw Ref Point
    rrp = bf.mm2vox(3) * rrp;
    vector<unsigned int>  first(3,0);
    vector<unsigned int>  last(3,0);
    bf.RangeOfBasesWithSupportAtXyz(rrp,first,last);
    // cout << "rrp = " << rrp(1) << "  " << rrp(2) << "  " << rrp(3) << endl;
    // cout << "first = " << first[0] << "  " << first[1] << "  " << first[2] << endl;
    // cout << "last = " << last[0] << "  " << last[1] << "  " << last[2] << endl;
    vector<unsigned int>  ci(3,0);
    double diff = Diff(pti,dim,bf);
    for (ci[2]=first[2]; ci[2]<last[2]; ci[2]++) {
      for (ci[1]=first[1]; ci[1]<last[1]; ci[1]++) {
	for (ci[0]=first[0]; ci[0]<last[0]; ci[0]++) {
          unsigned int lindx = ci[2]*bf.CoefSz_x()*bf.CoefSz_y()+ci[1]*bf.CoefSz_x()+ci[0];
          grad(lindx+1) += -2.0 * diff * bf.ValueOfBasisLmnAtXyz(ci,rrp);
	}
      }
    }
  }
  grad.Release();
  return(grad);  
}

///////////////////////////////////////////////////////////////////////////////////////////////
//
// Returns the Hessian of the sum-of-squared differences for the dimension given by dim
//
///////////////////////////////////////////////////////////////////////////////////////////////

shared_ptr<BFMatrix> MatchingPoints::SSD_Hessian(unsigned int dim, const basisfield& bf, BFMatrixPrecisionType prec) const
{
  if (dim > 2) throw MatchingPointsException("SSD: dim must be 0--2");

  // Make sure matrix is of correct type
  shared_ptr<BFMatrix>  hess;
  if (bf.HasGlobalSupport()) hess = shared_ptr<BFMatrix>(new FullBFMatrix(bf.CoefSz(),bf.CoefSz()));
  else {
    if (prec == BFMatrixDoublePrecision) hess = shared_ptr<BFMatrix>(new SparseBFMatrix<double>(bf.CoefSz(),bf.CoefSz()));
    else hess = shared_ptr<BFMatrix>(new SparseBFMatrix<float>(bf.CoefSz(),bf.CoefSz()));
  }
  
  for (unsigned int pti=0; pti<_in_ref->NPoints(); pti++) {
    ColumnVector rrp = _in_ref->RawPoint(pti);  // Raw Ref Point
    rrp = bf.mm2vox(3) * rrp;
    vector<unsigned int>  first(3,0);
    vector<unsigned int>  last(3,0);
    bf.RangeOfBasesWithSupportAtXyz(rrp,first,last);
    vector<unsigned int>  rci(3,0);
    for (rci[2]=first[2]; rci[2]<last[2]; rci[2]++) {
      for (rci[1]=first[1]; rci[1]<last[1]; rci[1]++) {
	for (rci[0]=first[0]; rci[0]<last[0]; rci[0]++) {
          unsigned int row_lindx = rci[2]*bf.CoefSz_x()*bf.CoefSz_y()+rci[1]*bf.CoefSz_x()+rci[0];
          double row_val = bf.ValueOfBasisLmnAtXyz(rci,rrp);
	  vector<unsigned int>  cci(3,0);
          for (cci[2]=first[2]; cci[2]<last[2]; cci[2]++) {
            for (cci[1]=first[1]; cci[1]<last[1]; cci[1]++) {
	      for (cci[0]=first[0]; cci[0]<last[0]; cci[0]++) {
                unsigned int col_lindx = cci[2]*bf.CoefSz_x()*bf.CoefSz_y()+cci[1]*bf.CoefSz_x()+cci[0];
                double col_val = bf.ValueOfBasisLmnAtXyz(cci,rrp);
                hess->AddTo(row_lindx+1,col_lindx+1,2.0*row_val*col_val);
	      }
	    }
	  }
	}
      }
    }
  }
  return(hess);        
}