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);
}
boost::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
boost::shared_ptr<BFMatrix> hess;
if (bf.HasGlobalSupport()) hess = boost::shared_ptr<BFMatrix>(new FullBFMatrix(bf.CoefSz(),bf.CoefSz()));
else {
if (prec == BFMatrixDoublePrecision) hess = boost::shared_ptr<BFMatrix>(new SparseBFMatrix<double>(bf.CoefSz(),bf.CoefSz()));
else hess = boost::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);
}
void FnirtFileWriter::common_coef_construction(const string& fname,
const basisfield& fieldx,
const basisfield& fieldy,
const basisfield& fieldz,
const Matrix& aff)
{
volume4D<float> coefs(fieldx.CoefSz_x(),fieldx.CoefSz_y(),fieldx.CoefSz_z(),3);
vector<float> ksp(3,1.0);
try {
const splinefield& f = dynamic_cast<const splinefield& >(fieldx);
ksp[0] = float(f.Ksp_x()); ksp[1] = float(f.Ksp_y()); ksp[2] = float(f.Ksp_z());
if (f.Order() == 2) coefs.set_intent(FSL_QUADRATIC_SPLINE_COEFFICIENTS,f.Vxs_x(),f.Vxs_y(),f.Vxs_z());
else if (f.Order() == 3) coefs.set_intent(FSL_CUBIC_SPLINE_COEFFICIENTS,f.Vxs_x(),f.Vxs_y(),f.Vxs_z());
}
catch (...) {
try {
const dctfield& f = dynamic_cast<const dctfield& >(fieldx);
coefs.set_intent(FSL_DCT_COEFFICIENTS,f.Vxs_x(),f.Vxs_y(),f.Vxs_z());
throw FnirtFileWriterException("common_coef_construction: Saving of DCT coefficients not yet implemented");
}
catch (...) {
throw FnirtFileWriterException("common_coef_construction: Unknown field type");
}
}
coefs.setxdim(ksp[0]); coefs.setydim(ksp[1]); coefs.setzdim(ksp[2]);
Matrix qform(4,4);
qform = IdentityMatrix(4);
qform(1,4) = fieldx.FieldSz_x();
qform(2,4) = fieldx.FieldSz_y();
qform(3,4) = fieldx.FieldSz_z();
coefs.set_qform(NIFTI_XFORM_SCANNER_ANAT,qform);
coefs.set_sform(NIFTI_XFORM_SCANNER_ANAT,aff);
vector<shared_ptr<ColumnVector> > coefp(3);
coefp[0]=fieldx.GetCoef(); coefp[1]=fieldy.GetCoef(); coefp[2]=fieldz.GetCoef();
for (unsigned int v=0; v<3; v++) {
ColumnVector c = *(coefp[v]);
for (unsigned int k=0, vindx=0; k<fieldx.CoefSz_z(); k++) {
for (unsigned int j=0; j<fieldx.CoefSz_y(); j++) {
for (unsigned int i=0; i<fieldx.CoefSz_x(); i++) {
coefs(i,j,k,v) = c.element(vindx++);
}
}
}
}
save_orig_volume4D(coefs,fname);
}