// Inforce Hermitian symmetry ---------------------------------------------
void FourierTransformer::enforceHermitianSymmetry()
{
int ndim = 3;
if (ZSIZE(*fReal) == 1)
{
ndim = 2;
if (YSIZE(*fReal) == 1)
{
ndim = 1;
}
}
long int yHalf = YSIZE(*fReal) / 2;
if (YSIZE(*fReal) % 2 == 0)
{
yHalf--;
}
long int zHalf = ZSIZE(*fReal) / 2;
if (ZSIZE(*fReal) % 2 == 0)
{
zHalf--;
}
switch (ndim)
{
case 2:
for (long int i = 1; i <= yHalf; i++)
{
long int isym = intWRAP(-i, 0, YSIZE(*fReal) - 1);
Complex mean = 0.5 * (
DIRECT_A2D_ELEM(fFourier, i, 0) +
conj(DIRECT_A2D_ELEM(fFourier, isym, 0)));
DIRECT_A2D_ELEM(fFourier, i, 0) = mean;
DIRECT_A2D_ELEM(fFourier, isym, 0) = conj(mean);
}
break;
case 3:
for (long int k = 0; k < ZSIZE(*fReal); k++)
{
long int ksym = intWRAP(-k, 0, ZSIZE(*fReal) - 1);
for (long int i = 1; i <= yHalf; i++)
{
long int isym = intWRAP(-i, 0, YSIZE(*fReal) - 1);
Complex mean = 0.5 * (
DIRECT_A3D_ELEM(fFourier, k, i, 0) +
conj(DIRECT_A3D_ELEM(fFourier, ksym, isym, 0)));
DIRECT_A3D_ELEM(fFourier, k, i, 0) = mean;
DIRECT_A3D_ELEM(fFourier, ksym, isym, 0) = conj(mean);
}
}
for (long int k = 1; k <= zHalf; k++)
{
long int ksym = intWRAP(-k, 0, ZSIZE(*fReal) - 1);
Complex mean = 0.5 * (
DIRECT_A3D_ELEM(fFourier, k, 0, 0) +
conj(DIRECT_A3D_ELEM(fFourier, ksym, 0, 0)));
DIRECT_A3D_ELEM(fFourier, k, 0, 0) = mean;
DIRECT_A3D_ELEM(fFourier, ksym, 0, 0) = conj(mean);
}
break;
}
}
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));
}
}
}
TEST_F( FftwTest, directFourierTransformComplex)
{
MultidimArray< std::complex< double > > FFT1, complxDouble;
FourierTransformer transformer1;
typeCast(mulDouble, complxDouble);
transformer1.FourierTransform(complxDouble, FFT1, false);
transformer1.inverseFourierTransform();
transformer1.inverseFourierTransform();
MultidimArray<std::complex<double> > auxFFT;
auxFFT.resize(3,3);
DIRECT_A2D_ELEM(auxFFT,0,0) = std::complex<double>(2.77778,0);
DIRECT_A2D_ELEM(auxFFT,0,1) = std::complex<double>(-0.0555556,0.096225);
DIRECT_A2D_ELEM(auxFFT,0,2) = std::complex<double>(-0.0555556,-0.096225);
DIRECT_A2D_ELEM(auxFFT,1,0) = std::complex<double>(-0.388889,0.673575) ;
DIRECT_A2D_ELEM(auxFFT,1,1) = std::complex<double>(-0.388889,-0.096225);
DIRECT_A2D_ELEM(auxFFT,1,2) = std::complex<double>(-0.0555556,-0.288675);
DIRECT_A2D_ELEM(auxFFT,2,0) = std::complex<double>(-0.388889,-0.673575) ;
DIRECT_A2D_ELEM(auxFFT,2,1) = std::complex<double>(-0.0555556,0.288675) ;
DIRECT_A2D_ELEM(auxFFT,2,2) = std::complex<double>(-0.388889,0.096225) ;
EXPECT_EQ(FFT1,auxFFT);
transformer1.cleanup();
}
void actualPhaseFlip(MultidimArray<double> &I, CTFDescription ctf)
{
// Perform the Fourier transform
FourierTransformer transformer;
MultidimArray< std::complex<double> > M_inFourier;
transformer.FourierTransform(I,M_inFourier,false);
Matrix1D<double> freq(2); // Frequencies for Fourier plane
int yDim=YSIZE(I);
int xDim=XSIZE(I);
double iTm=1.0/ctf.Tm;
for (size_t i=0; i<YSIZE(M_inFourier); ++i)
{
FFT_IDX2DIGFREQ(i, yDim, YY(freq));
YY(freq) *= iTm;
for (size_t j=0; j<XSIZE(M_inFourier); ++j)
{
FFT_IDX2DIGFREQ(j, xDim, XX(freq));
XX(freq) *= iTm;
ctf.precomputeValues(XX(freq),YY(freq));
if (ctf.getValuePureWithoutDampingAt()<0)
DIRECT_A2D_ELEM(M_inFourier,i,j)*=-1;
}
}
// Perform inverse Fourier transform and finish
transformer.inverseFourierTransform();
}
//init metadatas
virtual void SetUp()
{
mulDouble.resize(3,3);
DIRECT_A2D_ELEM(mulDouble,0,0) = 1;
DIRECT_A2D_ELEM(mulDouble,0,1) = 2;
DIRECT_A2D_ELEM(mulDouble,0,2) = 3;
DIRECT_A2D_ELEM(mulDouble,1,0) = 3;
DIRECT_A2D_ELEM(mulDouble,1,1) = 2;
DIRECT_A2D_ELEM(mulDouble,1,2) = 1;
DIRECT_A2D_ELEM(mulDouble,2,0) = 4;
DIRECT_A2D_ELEM(mulDouble,2,1) = 4;
DIRECT_A2D_ELEM(mulDouble,2,2) = 5;
}
/* Generate a complete CTF Image ------------------------------------------------------ */
void CTF::getFftwImage(MultidimArray<DOUBLE> &result, int orixdim, int oriydim, DOUBLE angpix,
bool do_abs, bool do_only_flip_phases, bool do_intact_until_first_peak, bool do_damping)
{
DOUBLE xs = (DOUBLE)orixdim * angpix;
DOUBLE ys = (DOUBLE)oriydim * angpix;
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM2D(result)
{
DOUBLE x = (DOUBLE)jp / xs;
DOUBLE y = (DOUBLE)ip / ys;
DIRECT_A2D_ELEM(result, i, j) = getCTF(x, y, do_abs, do_only_flip_phases, do_intact_until_first_peak, do_damping);
}
}
EnsembleNaiveBayes::EnsembleNaiveBayes(
const std::vector < MultidimArray<double> > &features,
const Matrix1D<double> &priorProbs,
int discreteLevels, int numberOfClassifiers,
double samplingFeatures, double samplingIndividuals,
const std::string &newJudgeCombination)
{
int NFeatures=XSIZE(features[0]);
int NsubFeatures=CEIL(NFeatures*samplingFeatures);
K=features.size();
judgeCombination=newJudgeCombination;
#ifdef WEIGHTED_SAMPLING
// Measure the classification power of each variable
NaiveBayes *nb_weights=new NaiveBayes(features, priorProbs, discreteLevels);
MultidimArray<double> weights=nb_weights->__weights;
delete nb_weights;
double sumWeights=weights.sum();
#endif
for (int n=0; n<numberOfClassifiers; n++)
{
// Produce the set of features for this subclassifier
MultidimArray<int> subFeatures(NsubFeatures);
FOR_ALL_ELEMENTS_IN_ARRAY1D(subFeatures)
{
#ifdef WEIGHTED_SAMPLING
double random_sum_weight=rnd_unif(0,sumWeights);
int j=0;
do
{
double wj=DIRECT_A1D_ELEM(weights,j);
if (wj<random_sum_weight)
{
random_sum_weight-=wj;
j++;
if (j==NFeatures)
{
j=NFeatures-1;
break;
}
}
else
break;
}
while (true);
DIRECT_A1D_ELEM(subFeatures,i)=j;
#else
DIRECT_A1D_ELEM(subFeatures,i)=round(rnd_unif(0,NFeatures-1));
#endif
}
// Container for the new training sample
std::vector< MultidimArray<double> > newFeatures;
// Produce the data set for each class
for (int k=0; k<K; k++)
{
int NIndividuals=YSIZE(features[k]);
int NsubIndividuals=CEIL(NIndividuals*samplingIndividuals);
MultidimArray<int> subIndividuals(NsubIndividuals);
FOR_ALL_ELEMENTS_IN_ARRAY1D(subIndividuals)
subIndividuals(i)=ROUND(rnd_unif(0,NsubIndividuals-1));
MultidimArray<double> newFeaturesK;
newFeaturesK.initZeros(NsubIndividuals,NsubFeatures);
const MultidimArray<double>& features_k=features[k];
FOR_ALL_ELEMENTS_IN_ARRAY2D(newFeaturesK)
DIRECT_A2D_ELEM(newFeaturesK,i,j)=DIRECT_A2D_ELEM(features_k,
DIRECT_A1D_ELEM(subIndividuals,i),
DIRECT_A1D_ELEM(subFeatures,j));
newFeatures.push_back(newFeaturesK);
}
// Create a Naive Bayes classifier with this data
NaiveBayes *nb=new NaiveBayes(newFeatures, priorProbs, discreteLevels);
ensemble.push_back(nb);
ensembleFeatures.push_back(subFeatures);
}
}
// Split several histograms within the indexes l0 and lF so that
// the entropy after division is maximized
int splitHistogramsUsingEntropy(const std::vector<Histogram1D> &hist,
size_t l0, size_t lF)
{
// Number of classes
int K = hist.size();
// Set everything outside l0 and lF to zero, and make it a PDF
std::vector<Histogram1D> histNorm;
for (int k = 0; k < K; k++)
{
Histogram1D histaux = hist[k];
for (size_t l = 0; l < XSIZE(histaux); l++)
if (l < l0 || l > lF)
DIRECT_A1D_ELEM(histaux,l) = 0;
histaux *= 1.0/histaux.sum();
histNorm.push_back(histaux);
}
// Compute for each class the probability of being l<=l0 and l>l0
MultidimArray<double> p(K, 2);
for (int k = 0; k < K; k++)
{
const Histogram1D& histogram=histNorm[k];
DIRECT_A2D_ELEM(p,k, 0) = DIRECT_A1D_ELEM(histogram,l0);
DIRECT_A2D_ELEM(p,k, 1) = 0;
for (size_t l = l0 + 1; l <= lF; l++)
DIRECT_A2D_ELEM(p,k, 1) += DIRECT_A1D_ELEM(histogram,l);
}
// Compute the splitting l giving maximum entropy
double maxEntropy = 0;
int lmaxEntropy = -1;
size_t l = l0;
while (l < lF)
{
// Compute the entropy of the classes if we split by l
double entropy = 0;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(p)
{
double aux=DIRECT_MULTIDIM_ELEM(p,n);
if (aux != 0)
entropy -= aux * log10(aux);
}
#ifdef DEBUG_SPLITTING_USING_ENTROPY
std::cout << "Splitting at " << l << " entropy=" << entropy
<< std::endl;
#endif
// Check if this is the maximum
if (entropy > maxEntropy)
{
maxEntropy = entropy;
lmaxEntropy = l;
}
// Move to next split point
++l;
// Update probabilities of being l<=l0 and l>l0
for (int k = 0; k < K; k++)
{
const Histogram1D& histogram=histNorm[k];
double aux=DIRECT_A1D_ELEM(histogram,l);
DIRECT_A2D_ELEM(p,k, 0) += aux;
DIRECT_A2D_ELEM(p,k, 1) -= aux;
}
}
#ifdef DEBUG_SPLITTING_USING_ENTROPY
std::cout << "Finally in l=[" << l0 << "," << lF
<< " Max Entropy:" << maxEntropy
<< " lmax=" << lmaxEntropy << std::endl;
#endif
// If the point giving the maximum entropy is too much on the extreme,
// substitute it by the middle point
if (lmaxEntropy<=2 || lmaxEntropy>=(int)lF-2)
lmaxEntropy = (int)ceil((lF + l0)/2.0);
return lmaxEntropy;
}
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();
}
// Fit the beam-induced translations for all average micrographs
void ParticlePolisherMpi::fitMovementsAllMicrographs()
{
int total_nr_micrographs = exp_model.average_micrographs.size();
// Each node does part of the work
long int my_first_micrograph, my_last_micrograph, my_nr_micrographs;
divide_equally(total_nr_micrographs, node->size, node->rank, my_first_micrograph, my_last_micrograph);
my_nr_micrographs = my_last_micrograph - my_first_micrograph + 1;
// Loop over all average micrographs
int barstep;
if (verb > 0)
{
std::cout << " + Fitting straight paths for beam-induced movements in all micrographs ... " << std::endl;
init_progress_bar(my_nr_micrographs);
barstep = XMIPP_MAX(1, my_nr_micrographs/ 60);
}
for (long int i = my_first_micrograph; i <= my_last_micrograph; i++)
{
if (verb > 0 && i % barstep == 0)
progress_bar(i);
fitMovementsOneMicrograph(i);
}
// Wait until all micrographs have been done
MPI_Barrier(MPI_COMM_WORLD);
if (verb > 0)
{
progress_bar(my_nr_micrographs);
}
// Combine results from all nodes
MultidimArray<DOUBLE> allnodes_fitted_movements;
allnodes_fitted_movements.resize(fitted_movements);
MPI_Allreduce(MULTIDIM_ARRAY(fitted_movements), MULTIDIM_ARRAY(allnodes_fitted_movements), MULTIDIM_SIZE(fitted_movements), MY_MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
fitted_movements = allnodes_fitted_movements;
// Set the fitted movements in the xoff and yoff columns of the exp_model.MDimg
for (long int ipart = 0; ipart < exp_model.numberOfParticles(); ipart++)
{
long int part_id = exp_model.particles[ipart].id;
DOUBLE xoff = DIRECT_A2D_ELEM(fitted_movements, part_id, 0);
DOUBLE yoff = DIRECT_A2D_ELEM(fitted_movements, part_id, 1);
exp_model.MDimg.setValue(EMDL_ORIENT_ORIGIN_X, xoff, part_id);
exp_model.MDimg.setValue(EMDL_ORIENT_ORIGIN_Y, yoff, part_id);
}
if (node->isMaster())
{
// Write out the STAR file with all the fitted movements
FileName fn_tmp = fn_in.withoutExtension() + "_" + fn_out + ".star";
exp_model.MDimg.write(fn_tmp);
std::cout << " + Written out all fitted movements in STAR file: " << fn_tmp << std::endl;
}
}
// Shift an image through phase-shifts in its Fourier Transform (without pretabulated sine and cosine)
void shiftImageInFourierTransform(MultidimArray<Complex >& in,
MultidimArray<Complex >& out,
double oridim, Matrix1D<double> shift)
{
out.resize(in);
shift /= -oridim;
double dotp, a, b, c, d, ac, bd, ab_cd, x, y, z, xshift, yshift, zshift;
switch (in.getDim())
{
case 1:
xshift = XX(shift);
if (ABS(xshift) < XMIPP_EQUAL_ACCURACY)
{
out = in;
return;
}
for (long int j = 0; j < XSIZE(in); j++)
{
x = j;
dotp = 2 * PI * (x * xshift);
a = cos(dotp);
b = sin(dotp);
c = DIRECT_A1D_ELEM(in, j).real;
d = DIRECT_A1D_ELEM(in, j).imag;
ac = a * c;
bd = b * d;
ab_cd = (a + b) * (c + d); // (ab_cd-ac-bd = ad+bc : but needs 4 multiplications)
DIRECT_A1D_ELEM(out, j) = Complex(ac - bd, ab_cd - ac - bd);
}
break;
case 2:
xshift = XX(shift);
yshift = YY(shift);
if (ABS(xshift) < XMIPP_EQUAL_ACCURACY && ABS(yshift) < XMIPP_EQUAL_ACCURACY)
{
out = in;
return;
}
for (long int i = 0; i < XSIZE(in); i++)
for (long int j = 0; j < XSIZE(in); j++)
{
x = j;
y = i;
dotp = 2 * PI * (x * xshift + y * yshift);
a = cos(dotp);
b = sin(dotp);
c = DIRECT_A2D_ELEM(in, i, j).real;
d = DIRECT_A2D_ELEM(in, i, j).imag;
ac = a * c;
bd = b * d;
ab_cd = (a + b) * (c + d);
DIRECT_A2D_ELEM(out, i, j) = Complex(ac - bd, ab_cd - ac - bd);
}
for (long int i = YSIZE(in) - 1; i >= XSIZE(in); i--)
{
y = i - YSIZE(in);
for (long int j = 0; j < XSIZE(in); j++)
{
x = j;
dotp = 2 * PI * (x * xshift + y * yshift);
a = cos(dotp);
b = sin(dotp);
c = DIRECT_A2D_ELEM(in, i, j).real;
d = DIRECT_A2D_ELEM(in, i, j).imag;
ac = a * c;
bd = b * d;
ab_cd = (a + b) * (c + d);
DIRECT_A2D_ELEM(out, i, j) = Complex(ac - bd, ab_cd - ac - bd);
}
}
break;
case 3:
xshift = XX(shift);
yshift = YY(shift);
zshift = ZZ(shift);
if (ABS(xshift) < XMIPP_EQUAL_ACCURACY && ABS(yshift) < XMIPP_EQUAL_ACCURACY && ABS(zshift) < XMIPP_EQUAL_ACCURACY)
{
out = in;
return;
}
for (long int k = 0; k < ZSIZE(in); k++)
{
z = (k < XSIZE(in)) ? k : k - ZSIZE(in);
for (long int i = 0; i < YSIZE(in); i++)
{
y = (i < XSIZE(in)) ? i : i - YSIZE(in);
for (long int j = 0; j < XSIZE(in); j++)
{
x = j;
dotp = 2 * PI * (x * xshift + y * yshift + z * zshift);
a = cos(dotp);
b = sin(dotp);
c = DIRECT_A3D_ELEM(in, k, i, j).real;
d = DIRECT_A3D_ELEM(in, k, i, j).imag;
ac = a * c;
bd = b * d;
ab_cd = (a + b) * (c + d);
DIRECT_A3D_ELEM(out, k, i, j) = Complex(ac - bd, ab_cd - ac - bd);
}
}
}
break;
default:
REPORT_ERROR("shiftImageInFourierTransform ERROR: dimension should be 1, 2 or 3!");
}
}
void Projector::rotate2D(MultidimArray<Complex > &f2d, Matrix2D<DOUBLE> &A, bool inv)
{
DOUBLE fx, fy, xp, yp;
int x0, x1, y0, y1, y, y2, r2;
bool is_neg_x;
Complex d00, d01, d10, d11, dx0, dx1;
Matrix2D<DOUBLE> Ainv;
// f2d should already be in the right size (ori_size,orihalfdim)
// AND the points outside max_r should already be zero...
// f2d.initZeros();
// Use the inverse matrix
if (inv)
Ainv = A;
else
Ainv = A.transpose();
// The f2d image may be smaller than r_max, in that case also make sure not to fill the corners!
int my_r_max = XMIPP_MIN(r_max, XSIZE(f2d) - 1);
// Go from the 2D slice coordinates to the map coordinates
Ainv *= (DOUBLE)padding_factor; // take scaling into account directly
int max_r2 = my_r_max * my_r_max;
int min_r2_nn = r_min_nn * r_min_nn;
#ifdef DEBUG
std::cerr << " XSIZE(f2d)= "<< XSIZE(f2d) << std::endl;
std::cerr << " YSIZE(f2d)= "<< YSIZE(f2d) << std::endl;
std::cerr << " XSIZE(data)= "<< XSIZE(data) << std::endl;
std::cerr << " YSIZE(data)= "<< YSIZE(data) << std::endl;
std::cerr << " STARTINGX(data)= "<< STARTINGX(data) << std::endl;
std::cerr << " STARTINGY(data)= "<< STARTINGY(data) << std::endl;
std::cerr << " STARTINGZ(data)= "<< STARTINGZ(data) << std::endl;
std::cerr << " max_r= "<< r_max << std::endl;
std::cerr << " Ainv= " << Ainv << std::endl;
#endif
for (int i=0; i < YSIZE(f2d); i++)
{
// Don't search beyond square with side max_r
if (i <= my_r_max)
{
y = i;
}
else if (i >= YSIZE(f2d) - my_r_max)
{
y = i - YSIZE(f2d);
}
else
continue;
y2 = y * y;
for (int x=0; x <= my_r_max; x++)
{
// Only include points with radius < max_r (exclude points outside circle in square)
r2 = x * x + y2;
if (r2 > max_r2)
continue;
// Get logical coordinates in the 3D map
xp = Ainv(0,0) * x + Ainv(0,1) * y;
yp = Ainv(1,0) * x + Ainv(1,1) * y;
if (interpolator == TRILINEAR || r2 < min_r2_nn)
{
// Only asymmetric half is stored
if (xp < 0)
{
// Get complex conjugated hermitian symmetry pair
xp = -xp;
yp = -yp;
is_neg_x = true;
}
else
{
is_neg_x = false;
}
// Trilinear interpolation (with physical coords)
// Subtract STARTINGY to accelerate access to data (STARTINGX=0)
// In that way use DIRECT_A3D_ELEM, rather than A3D_ELEM
x0 = FLOOR(xp);
fx = xp - x0;
x1 = x0 + 1;
y0 = FLOOR(yp);
fy = yp - y0;
y0 -= STARTINGY(data);
y1 = y0 + 1;
// Matrix access can be accelerated through pre-calculation of z0*xydim etc.
d00 = DIRECT_A2D_ELEM(data, y0, x0);
d01 = DIRECT_A2D_ELEM(data, y0, x1);
d10 = DIRECT_A2D_ELEM(data, y1, x0);
d11 = DIRECT_A2D_ELEM(data, y1, x1);
// Set the interpolated value in the 2D output array
#ifndef FLOAT_PRECISION
__m256d __interpx = LIN_INTERP_AVX(_mm256_setr_pd(d00.real, d00.imag, d10.real, d10.imag),
_mm256_setr_pd(d01.real, d01.imag, d11.real, d11.imag),
_mm256_set1_pd(fx));
#else
__m128 __interpx = LIN_INTERP_AVX(_mm_setr_ps(d00.real, d00.imag, d10.real, d10.imag),
_mm_setr_ps(d01.real, d01.imag, d11.real, d11.imag),
_mm_set1_ps(fx));
#endif
Complex* interpx = (Complex*)&__interpx;
DIRECT_A2D_ELEM(f2d, i, x) = LIN_INTERP(fy, interpx[0], interpx[1]);
// Take complex conjugated for half with negative x
if (is_neg_x)
DIRECT_A2D_ELEM(f2d, i, x) = conj(DIRECT_A2D_ELEM(f2d, i, x));
} // endif TRILINEAR
else if (interpolator == NEAREST_NEIGHBOUR )
{
x0 = ROUND(xp);
y0 = ROUND(yp);
if (x0 < 0)
DIRECT_A2D_ELEM(f2d, i, x) = conj(A2D_ELEM(data, -y0, -x0));
else
DIRECT_A2D_ELEM(f2d, i, x) = A2D_ELEM(data, y0, x0);
} // endif NEAREST_NEIGHBOUR
else
REPORT_ERROR("Unrecognized interpolator in Projector::project");
} // endif x-loop
} // endif y-loop
}
void FourierProjector::project(double rot, double tilt, double psi, const MultidimArray<double> *ctf)
{
double freqy, freqx;
std::complex< double > f;
Euler_angles2matrix(rot,tilt,psi,E);
projectionFourier.initZeros();
double maxFreq2=maxFrequency*maxFrequency;
int Xdim=(int)XSIZE(VfourierRealCoefs);
int Ydim=(int)YSIZE(VfourierRealCoefs);
int Zdim=(int)ZSIZE(VfourierRealCoefs);
for (size_t i=0; i<YSIZE(projectionFourier); ++i)
{
FFT_IDX2DIGFREQ(i,volumeSize,freqy);
double freqy2=freqy*freqy;
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;
// Commented for speed-up, the corresponding code is below
// c=VfourierRealCoefs.interpolatedElementBSpline3D(jVolume,iVolume,kVolume);
// d=VfourierImagCoefs.interpolatedElementBSpline3D(jVolume,iVolume,kVolume);
// The code below is a replicate for speed reasons of interpolatedElementBSpline3D
double z=kVolume;
double y=iVolume;
double x=jVolume;
// Logical to physical
z -= STARTINGZ(VfourierRealCoefs);
y -= STARTINGY(VfourierRealCoefs);
x -= STARTINGX(VfourierRealCoefs);
int l1 = (int)ceil(x - 2);
int l2 = l1 + 3;
int m1 = (int)ceil(y - 2);
int m2 = m1 + 3;
int n1 = (int)ceil(z - 2);
int n2 = n1 + 3;
c = d = 0.0;
double aux;
for (int nn = n1; nn <= n2; nn++)
{
int equivalent_nn=nn;
if (nn<0)
equivalent_nn=-nn-1;
else if (nn>=Zdim)
equivalent_nn=2*Zdim-nn-1;
double yxsumRe = 0.0, yxsumIm = 0.0;
for (int m = m1; m <= m2; m++)
{
int equivalent_m=m;
if (m<0)
equivalent_m=-m-1;
else if (m>=Ydim)
equivalent_m=2*Ydim-m-1;
double xsumRe = 0.0, xsumIm = 0.0;
for (int l = l1; l <= l2; l++)
{
double xminusl = x - (double) l;
int equivalent_l=l;
if (l<0)
equivalent_l=-l-1;
else if (l>=Xdim)
equivalent_l=2*Xdim-l-1;
double CoeffRe = (double) DIRECT_A3D_ELEM(VfourierRealCoefs,equivalent_nn,equivalent_m,equivalent_l);
double CoeffIm = (double) DIRECT_A3D_ELEM(VfourierImagCoefs,equivalent_nn,equivalent_m,equivalent_l);
BSPLINE03(aux,xminusl);
xsumRe += CoeffRe * aux;
xsumIm += CoeffIm * aux;
}
double yminusm = y - (double) m;
BSPLINE03(aux,yminusm);
yxsumRe += xsumRe * aux;
yxsumIm += xsumIm * aux;
}
double zminusn = z - (double) nn;
BSPLINE03(aux,zminusn);
c += yxsumRe * aux;
d += yxsumIm * aux;
}
}
// Phase shift to move the origin of the image to the corner
double a=DIRECT_A2D_ELEM(phaseShiftImgA,i,j);
double b=DIRECT_A2D_ELEM(phaseShiftImgB,i,j);
if (ctf!=NULL)
{
double ctfij=DIRECT_A2D_ELEM(*ctf,i,j);
a*=ctfij;
b*=ctfij;
}
// 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;
}
}
transformer2D.inverseFourierTransform();
}