void FourierProjector::produceSideInfo()
{
// Zero padding
MultidimArray<double> Vpadded;
int paddedDim=(int)(paddingFactor*volumeSize);
volume->window(Vpadded,FIRST_XMIPP_INDEX(paddedDim),FIRST_XMIPP_INDEX(paddedDim),FIRST_XMIPP_INDEX(paddedDim),
LAST_XMIPP_INDEX(paddedDim),LAST_XMIPP_INDEX(paddedDim),LAST_XMIPP_INDEX(paddedDim));
volume->clear();
// Make Fourier transform, shift the volume origin to the volume center and center it
MultidimArray< std::complex<double> > Vfourier;
transformer3D.completeFourierTransform(Vpadded,Vfourier);
ShiftFFT(Vfourier, FIRST_XMIPP_INDEX(XSIZE(Vpadded)), FIRST_XMIPP_INDEX(YSIZE(Vpadded)), FIRST_XMIPP_INDEX(ZSIZE(Vpadded)));
CenterFFT(Vfourier,true);
Vfourier.setXmippOrigin();
// Compensate for the Fourier normalization factor
double K=(double)(XSIZE(Vpadded)*XSIZE(Vpadded)*XSIZE(Vpadded))/(double)(volumeSize*volumeSize);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vfourier)
DIRECT_MULTIDIM_ELEM(Vfourier,n)*=K;
Vpadded.clear();
// Compute Bspline coefficients
if (BSplineDeg==3)
{
MultidimArray< double > VfourierRealAux, VfourierImagAux;
Complex2RealImag(Vfourier, VfourierRealAux, VfourierImagAux);
Vfourier.clear();
produceSplineCoefficients(BSPLINE3,VfourierRealCoefs,VfourierRealAux);
produceSplineCoefficients(BSPLINE3,VfourierImagCoefs,VfourierImagAux);
//VfourierRealAux.clear();
//VfourierImagAux.clear();
}
else
Complex2RealImag(Vfourier, VfourierRealCoefs, VfourierImagCoefs);
// Allocate memory for the 2D Fourier transform
projection().initZeros(volumeSize,volumeSize);
projection().setXmippOrigin();
transformer2D.FourierTransform(projection(),projectionFourier,false);
}
void FourierProjector::produceSideInfo()
{
// Zero padding
MultidimArray<double> Vpadded;
int paddedDim=(int)(paddingFactor*volumeSize);
// JMRT: TODO: I think it is a very poor design to modify the volume passed
// in the construct, it will be padded anyway, so new memory should be allocated
volume->window(Vpadded,FIRST_XMIPP_INDEX(paddedDim),FIRST_XMIPP_INDEX(paddedDim),FIRST_XMIPP_INDEX(paddedDim),
LAST_XMIPP_INDEX(paddedDim),LAST_XMIPP_INDEX(paddedDim),LAST_XMIPP_INDEX(paddedDim));
volume->clear();
// Make Fourier transform, shift the volume origin to the volume center and center it
MultidimArray< std::complex<double> > Vfourier;
transformer3D.completeFourierTransform(Vpadded,Vfourier);
ShiftFFT(Vfourier, FIRST_XMIPP_INDEX(XSIZE(Vpadded)), FIRST_XMIPP_INDEX(YSIZE(Vpadded)), FIRST_XMIPP_INDEX(ZSIZE(Vpadded)));
CenterFFT(Vfourier,true);
Vfourier.setXmippOrigin();
// Compensate for the Fourier normalization factor
double K=(double)(XSIZE(Vpadded)*XSIZE(Vpadded)*XSIZE(Vpadded))/(double)(volumeSize*volumeSize);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vfourier)
DIRECT_MULTIDIM_ELEM(Vfourier,n)*=K;
Vpadded.clear();
// Compute Bspline coefficients
if (BSplineDeg==3)
{
MultidimArray< double > VfourierRealAux, VfourierImagAux;
Complex2RealImag(Vfourier, VfourierRealAux, VfourierImagAux);
Vfourier.clear();
produceSplineCoefficients(BSPLINE3,VfourierRealCoefs,VfourierRealAux);
produceSplineCoefficients(BSPLINE3,VfourierImagCoefs,VfourierImagAux);
//VfourierRealAux.clear();
//VfourierImagAux.clear();
}
else
Complex2RealImag(Vfourier, VfourierRealCoefs, VfourierImagCoefs);
// Allocate memory for the 2D Fourier transform
projection().initZeros(volumeSize,volumeSize);
projection().setXmippOrigin();
transformer2D.FourierTransform(projection(),projectionFourier,false);
// Calculate phase shift terms
phaseShiftImgA.initZeros(projectionFourier);
phaseShiftImgB.initZeros(projectionFourier);
double shift=-FIRST_XMIPP_INDEX(volumeSize);
double xxshift = -2 * PI * shift / volumeSize;
for (size_t i=0; i<YSIZE(projectionFourier); ++i)
{
double phasey=(double)(i) * xxshift;
for (size_t j=0; j<XSIZE(projectionFourier); ++j)
{
// Phase shift to move the origin of the image to the corner
double dotp = (double)(j) * xxshift + phasey;
sincos(dotp,&DIRECT_A2D_ELEM(phaseShiftImgB,i,j),&DIRECT_A2D_ELEM(phaseShiftImgA,i,j));
}
}
}
void FourierProjector::project(double rot, double tilt, double psi)
{
double freqy, freqx;
std::complex< double > f;
Euler_angles2matrix(rot,tilt,psi,E);
projectionFourier.initZeros();
double shift=-FIRST_XMIPP_INDEX(volumeSize);
double xxshift = -2 * PI * shift / volumeSize;
double maxFreq2=maxFrequency*maxFrequency;
double volumePaddedSize=XSIZE(VfourierRealCoefs);
for (size_t i=0; i<YSIZE(projectionFourier); ++i)
{
FFT_IDX2DIGFREQ(i,volumeSize,freqy);
double freqy2=freqy*freqy;
double phasey=(double)(i) * xxshift;
double freqYvol_X=MAT_ELEM(E,1,0)*freqy;
double freqYvol_Y=MAT_ELEM(E,1,1)*freqy;
double freqYvol_Z=MAT_ELEM(E,1,2)*freqy;
for (size_t j=0; j<XSIZE(projectionFourier); ++j)
{
// The frequency of pairs (i,j) in 2D
FFT_IDX2DIGFREQ(j,volumeSize,freqx);
// Do not consider pixels with high frequency
if ((freqy2+freqx*freqx)>maxFreq2)
continue;
// Compute corresponding frequency in the volume
double freqvol_X=freqYvol_X+MAT_ELEM(E,0,0)*freqx;
double freqvol_Y=freqYvol_Y+MAT_ELEM(E,0,1)*freqx;
double freqvol_Z=freqYvol_Z+MAT_ELEM(E,0,2)*freqx;
double c,d;
if (BSplineDeg==0)
{
// 0 order interpolation
// Compute corresponding index in the volume
int kVolume=(int)round(freqvol_Z*volumePaddedSize);
int iVolume=(int)round(freqvol_Y*volumePaddedSize);
int jVolume=(int)round(freqvol_X*volumePaddedSize);
c = A3D_ELEM(VfourierRealCoefs,kVolume,iVolume,jVolume);
d = A3D_ELEM(VfourierImagCoefs,kVolume,iVolume,jVolume);
}
else if (BSplineDeg==1)
{
// B-spline linear interpolation
double kVolume=freqvol_Z*volumePaddedSize;
double iVolume=freqvol_Y*volumePaddedSize;
double jVolume=freqvol_X*volumePaddedSize;
c=VfourierRealCoefs.interpolatedElement3D(jVolume,iVolume,kVolume);
d=VfourierImagCoefs.interpolatedElement3D(jVolume,iVolume,kVolume);
}
else
{
// B-spline cubic interpolation
double kVolume=freqvol_Z*volumePaddedSize;
double iVolume=freqvol_Y*volumePaddedSize;
double jVolume=freqvol_X*volumePaddedSize;
c=VfourierRealCoefs.interpolatedElementBSpline3D(jVolume,iVolume,kVolume);
d=VfourierImagCoefs.interpolatedElementBSpline3D(jVolume,iVolume,kVolume);
}
// Phase shift to move the origin of the image to the corner
double dotp = (double)(j) * xxshift + phasey;
double a,b;
sincos(dotp,&b,&a);
// Multiply Fourier coefficient in volume times phase shift
double ac = a * c;
double bd = b * d;
double ab_cd = (a + b) * (c + d);
// And store the multiplication
double *ptrI_ij=(double *)&DIRECT_A2D_ELEM(projectionFourier,i,j);
*ptrI_ij = ac - bd;
*(ptrI_ij+1) = ab_cd - ac - bd;
}
}
//VfourierRealCoefs.clear();
//VfourierImagCoefs.clear();
transformer2D.inverseFourierTransform();
}
