void PolyZernikes::fit(const Matrix1D<int> & coef, MultidimArray<double> & im, MultidimArray<double> &weight,
MultidimArray<bool> & ROI, int verbose)
{
this->create(coef);
size_t xdim = XSIZE(im);
size_t ydim = YSIZE(im);
//int numZer = (size_t)coef.sum();
int numZer = (size_t)coef.sum();
//Actually polOrder corresponds to the polynomial order +1
int polOrder=(int)ZERNIKE_ORDER(coef.size());
im.setXmippOrigin();
Matrix2D<double> polValue(polOrder,polOrder);
//First argument means number of images
//Second argument means number of pixels
WeightedLeastSquaresHelper weightedLeastSquaresHelper;
Matrix2D<double>& zerMat=weightedLeastSquaresHelper.A;
zerMat.resizeNoCopy((size_t)ROI.sum(), numZer);
double iMaxDim2 = 2./std::max(xdim,ydim);
size_t pixel_idx=0;
weightedLeastSquaresHelper.b.resizeNoCopy((size_t)ROI.sum());
weightedLeastSquaresHelper.w.resizeNoCopy(weightedLeastSquaresHelper.b);
FOR_ALL_ELEMENTS_IN_ARRAY2D(im)
{
if ( (A2D_ELEM(ROI,i,j)))
{
//For one i we swap the different j
double y=i*iMaxDim2;
double x=j*iMaxDim2;
//polValue = [ 0 y y2 y3 ...
// x xy xy2 xy3 ...
// x2 x2y x2y2 x2y3 ]
//dMij(polValue,py,px) py es fila, px es columna
for (int py = 0; py < polOrder; ++py)
{
double ypy=std::pow(y,py);
for (int px = 0; px < polOrder; ++px)
dMij(polValue,px,py) = ypy*std::pow(x,px);
}
Matrix2D<int> *fMat;
//We generate the representation of the Zernike polynomials
for (int k=0; k < numZer; ++k)
{
fMat = &fMatV[k];
if (fMat == NULL)
continue;
double temp = 0;
for (size_t px = 0; px < (*fMat).Xdim(); ++px)
for (size_t py = 0; py < (*fMat).Ydim(); ++py)
temp += dMij(*fMat,py,px)*dMij(polValue,py,px);
dMij(zerMat,pixel_idx,k) = temp;
}
VEC_ELEM(weightedLeastSquaresHelper.b,pixel_idx)=A2D_ELEM(im,i,j);
VEC_ELEM(weightedLeastSquaresHelper.w,pixel_idx)=std::abs(A2D_ELEM(weight,i,j));
++pixel_idx;
}
}
Matrix1D<double> zernikeCoefficients;
weightedLeastSquares(weightedLeastSquaresHelper, zernikeCoefficients);
fittedCoeffs = zernikeCoefficients;
// Pointer to the image to be fitted
MultidimArray<double> reconstructed;
reconstructed.resizeNoCopy(im);
pixel_idx=0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(im)
if (A2D_ELEM(ROI,i,j))
{
double temp=0;
for (int k=0; k < numZer; ++k)
temp+=dMij(zerMat,pixel_idx,k)*VEC_ELEM(fittedCoeffs,k);
A2D_ELEM(reconstructed,i,j)=temp;
if ( fabs(A2D_ELEM(reconstructed,i,j)-A2D_ELEM(im,i,j)) > PI)
A2D_ELEM(ROI,i,j) = false;
++pixel_idx;
}
pixel_idx=0;
if (verbose > 0)
{
Image<double> save;
save()=reconstructed;
save.write("reconstructedZernikes.xmp");
ROI.write("ROI.txt");
}
}
void PolyZernikes::zernikePols(const Matrix1D<int> coef, MultidimArray<double> & im, MultidimArray<bool> & ROI, int verbose)
{
this->create(coef);
int polOrder=(int)ZERNIKE_ORDER(coef.size());
int numZer = coef.size();
int xdim = XSIZE(im);
int ydim = YSIZE(im);
im.setXmippOrigin();
Matrix2D<double> polValue(polOrder,polOrder);
double iMaxDim2 = 2./std::max(xdim,ydim);
double temp = 0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(im)
{
if (A2D_ELEM(ROI,i,j))
{
//For one i we swap the different j
double y=i*iMaxDim2;
double x=j*iMaxDim2;
//polValue = [ 0 y y2 y3 ...
// x xy xy2 xy3 ...
// x2 x2y x2y2 x2y3 ]
//dMij(polValue,py,px) py es fila, px es columna
for (int py = 0; py < polOrder; ++py)
{
double ypy=std::pow(y,py);
for (int px = 0; px < polOrder; ++px)
dMij(polValue,px,py) = ypy*std::pow(x,px);
}
Matrix2D<int> *fMat;
//We generate the representation of the Zernike polynomials
for (int k=0; k < numZer; ++k)
{
fMat = &fMatV[k];
if ( (dMij(*fMat,0,0) == 0) && MAT_SIZE(*fMat) == 1 )
continue;
for (size_t px = 0; px < (*fMat).Xdim(); ++px)
for (size_t py = 0; py < (*fMat).Ydim(); ++py)
temp += dMij(*fMat,py,px)*dMij(polValue,py,px)*VEC_ELEM(coef,k);
}
A2D_ELEM(im,i,j) = temp;
temp = 0;
}
}
STARTINGX(im)=STARTINGY(im)=0;
if (verbose == 1)
{
Image<double> save;
save()=im;
save.write("PPP1.xmp");
}
}
