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();
}
// 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));
}
}
}
void FourierTransformer::setReal(MultidimArray<std::complex<double> > &input)
{
bool recomputePlan=false;
if (fComplex==NULL)
recomputePlan=true;
else if (complexDataPtr!=MULTIDIM_ARRAY(input))
recomputePlan=true;
else
recomputePlan=!(fComplex->sameShape(input));
fFourier.resizeNoCopy(input);
fComplex=&input;
if (recomputePlan)
{
int ndim=3;
if (ZSIZE(input)==1)
{
ndim=2;
if (YSIZE(input)==1)
ndim=1;
}
int *N = new int[ndim];
switch (ndim)
{
case 1:
N[0]=XSIZE(input);
break;
case 2:
N[0]=YSIZE(input);
N[1]=XSIZE(input);
break;
case 3:
N[0]=ZSIZE(input);
N[1]=YSIZE(input);
N[2]=XSIZE(input);
break;
}
pthread_mutex_lock(&fftw_plan_mutex);
if (fPlanForward!=NULL)
fftw_destroy_plan(fPlanForward);
fPlanForward=NULL;
fPlanForward = fftw_plan_dft(ndim, N, (fftw_complex*) MULTIDIM_ARRAY(*fComplex),
(fftw_complex*) MULTIDIM_ARRAY(fFourier), FFTW_FORWARD, FFTW_ESTIMATE);
if (fPlanBackward!=NULL)
fftw_destroy_plan(fPlanBackward);
fPlanBackward=NULL;
fPlanBackward = fftw_plan_dft(ndim, N, (fftw_complex*) MULTIDIM_ARRAY(fFourier),
(fftw_complex*) MULTIDIM_ARRAY(*fComplex), FFTW_BACKWARD, FFTW_ESTIMATE);
if (fPlanForward == NULL || fPlanBackward == NULL)
REPORT_ERROR(ERR_PLANS_NOCREATE, "FFTW plans cannot be created");
delete [] N;
complexDataPtr=MULTIDIM_ARRAY(*fComplex);
pthread_mutex_unlock(&fftw_plan_mutex);
}
}
void FourierTransformer::setReal(MultidimArray<double> &input)
{
bool recomputePlan=false;
if (fReal==NULL)
recomputePlan=true;
else if (dataPtr!=MULTIDIM_ARRAY(input))
recomputePlan=true;
else
recomputePlan=!(fReal->sameShape(input));
fFourier.resizeNoCopy(ZSIZE(input),YSIZE(input),XSIZE(input)/2+1);
fReal=&input;
if (recomputePlan)
{
int ndim=3;
if (ZSIZE(input)==1)
{
ndim=2;
if (YSIZE(input)==1)
ndim=1;
}
int N[3];
switch (ndim)
{
case 1:
N[0]=XSIZE(input);
break;
case 2:
N[0]=YSIZE(input);
N[1]=XSIZE(input);
break;
case 3:
N[0]=ZSIZE(input);
N[1]=YSIZE(input);
N[2]=XSIZE(input);
break;
}
pthread_mutex_lock(&fftw_plan_mutex);
if (fPlanForward!=NULL)
fftw_destroy_plan(fPlanForward);
fPlanForward=NULL;
fPlanForward = fftw_plan_dft_r2c(ndim, N, MULTIDIM_ARRAY(*fReal),
(fftw_complex*) MULTIDIM_ARRAY(fFourier), FFTW_ESTIMATE);
if (fPlanBackward!=NULL)
fftw_destroy_plan(fPlanBackward);
fPlanBackward=NULL;
fPlanBackward = fftw_plan_dft_c2r(ndim, N,
(fftw_complex*) MULTIDIM_ARRAY(fFourier), MULTIDIM_ARRAY(*fReal),
FFTW_ESTIMATE);
if (fPlanForward == NULL || fPlanBackward == NULL)
REPORT_ERROR(ERR_PLANS_NOCREATE, "FFTW plans cannot be created");
dataPtr=MULTIDIM_ARRAY(*fReal);
pthread_mutex_unlock(&fftw_plan_mutex);
}
}
void multiplyBySpectrum(MultidimArray<double>& Min,
MultidimArray<double>& spectrum,
bool leave_origin_intact)
{
MultidimArray<Complex > Faux;
Matrix1D<double> f(3);
MultidimArray<double> lspectrum;
FourierTransformer transformer;
double dim3 = XSIZE(Min) * YSIZE(Min) * ZSIZE(Min);
transformer.FourierTransform(Min, Faux, false);
lspectrum = spectrum;
if (leave_origin_intact)
{
lspectrum(0) = 1.;
}
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM(Faux)
{
long int idx = ROUND(sqrt(kp * kp + ip * ip + jp * jp));
dAkij(Faux, k, i, j) *= lspectrum(idx) * dim3;
}
transformer.inverseFourierTransform();
}
/*
FUNCTION: InitNewFont(LOGFONT, COLORREF)
PURPOSE: Prepares a new font for use in the terminal screen
PARAMETERS:
LogFont - New logical font for the screen
rgbColour - New colour for screen painting
*/
void InitNewFont(LOGFONT LogFont, COLORREF rgbColour) {
TEXTMETRIC tm;
HDC hDC;
// If an old font exits, delete it
if (HSCREENFONT(TermInfo)) {
DeleteObject(HSCREENFONT(TermInfo));
}
LFSCREENFONT(TermInfo) = LogFont;
HSCREENFONT(TermInfo) = CreateFontIndirect(&(LFSCREENFONT(TermInfo)));
FGCOLOUR(TermInfo) = rgbColour;
hDC = GetDC(ghWndMain);
SelectObject(hDC, HSCREENFONT(TermInfo));
GetTextMetrics(hDC, &tm);
ReleaseDC(ghWndMain, hDC);
// Character width and height
XCHAR(TermInfo) = tm.tmAveCharWidth;
YCHAR(TermInfo) = tm.tmHeight + tm.tmExternalLeading;
// Set the terminal height and width based on the current font
XSIZE(TermInfo) = tm.tmAveCharWidth * MAXCOLS;
YSIZE(TermInfo) = (tm.tmHeight + tm.tmExternalLeading) * MAXROWS;
}
static void game_compute_size(const game_params *params, int tilesize,
int *x, int *y)
{
struct bbox bb = find_bbox(params);
*x = XSIZE(tilesize, bb, solids[params->solid]);
*y = YSIZE(tilesize, bb, solids[params->solid]);
}
// Really import ==========================================================
void ProgXrayImport::readAndCrop(const FileName &fn, Image<double> &I, int xCropSize, int yCropSize) const
{
I.read(fn);
I().selfWindow(yCropSize,xCropSize,
(int)(YSIZE(I())-yCropSize-1),(int)(XSIZE(I())-xCropSize-1));
I().resetOrigin();
}
/* Filter generation ------------------------------------------------------- */
void Steerable::generate1DFilters(double sigma,
const MultidimArray<double> &Vtomograph,
std::vector< MultidimArray<double> > &hx1,
std::vector< MultidimArray<double> > &hy1,
std::vector< MultidimArray<double> > &hz1){
// Initialization
MultidimArray<double> aux;
aux.initZeros(XSIZE(Vtomograph));
aux.setXmippOrigin();
for (int i=0; i<6; i++) hx1.push_back(aux);
aux.initZeros(YSIZE(Vtomograph));
aux.setXmippOrigin();
for (int i=0; i<6; i++) hy1.push_back(aux);
aux.initZeros(ZSIZE(Vtomograph));
aux.setXmippOrigin();
for (int i=0; i<6; i++) hz1.push_back(aux);
double sigma2=sigma*sigma;
double k1 = 1.0/pow((2.0*PI*sigma),(3.0/2.0));
double k2 = -1.0/(sigma2);
FOR_ALL_ELEMENTS_IN_ARRAY1D(hx1[0])
{
double i2=i*i;
double g = -exp(-i2/(2.0*sigma2));
hx1[0](i) = k1*k2*g*(1.0-(i2/sigma2));
hx1[1](i) = k1*k2*g;
hx1[2](i) = k1*k2*g;
hx1[3](i) = k1*k2*k2*g*i;
hx1[4](i) = k1*k2*k2*g*i;
hx1[5](i) = k1*k2*k2*g;
}
FOR_ALL_ELEMENTS_IN_ARRAY1D(hy1[0])
{
double i2=i*i;
double g = -exp(-i2/(2.0*sigma2));
hy1[0](i) = g;
hy1[1](i) = g*(1.0-(i2/sigma2));
hy1[2](i) = g;
hy1[3](i) = g*i;
hy1[4](i) = g;
hy1[5](i) = g*i;
}
FOR_ALL_ELEMENTS_IN_ARRAY1D(hz1[0])
{
double i2=i*i;
double g = -exp(-i2/(2.0*sigma2));
hz1[0](i) = g;
hz1[1](i) = g;
hz1[2](i) = g*(1.0-(i2/sigma2));
hz1[3](i) = g;
hz1[4](i) = g*i;
hz1[5](i) = g*i;
}
}
void CTF::getCenteredImage(MultidimArray<DOUBLE> &result, DOUBLE Tm,
bool do_abs, bool do_only_flip_phases, bool do_intact_until_first_peak, bool do_damping)
{
result.setXmippOrigin();
DOUBLE xs = (DOUBLE)XSIZE(result) * Tm;
DOUBLE ys = (DOUBLE)YSIZE(result) * Tm;
FOR_ALL_ELEMENTS_IN_ARRAY2D(result)
{
DOUBLE x = (DOUBLE)j / xs;
DOUBLE y = (DOUBLE)i / ys;
A2D_ELEM(result, i, j) = getCTF(x, y, do_abs, do_only_flip_phases, do_intact_until_first_peak, do_damping);
}
}
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::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();
}
void Steerable::singleFilter(const MultidimArray<double>& Vin,
MultidimArray<double> &hx1, MultidimArray<double> &hy1, MultidimArray<double> &hz1,
MultidimArray<double> &Vout){
MultidimArray< std::complex<double> > H, Aux;
Vout.initZeros(Vin);
// Filter in X
#define MINUS_ONE_POWER(n) (((n)%2==0)? 1:-1)
FourierTransformer transformer;
transformer.FourierTransform(hx1,H);
FOR_ALL_ELEMENTS_IN_ARRAY1D(H)
H(i)*= MINUS_ONE_POWER(i);
FourierTransformer transformer2;
MultidimArray<double> aux(XSIZE(Vin));
transformer2.setReal(aux);
for (size_t k=0; k<ZSIZE(Vin); k++)
for (size_t i=0; i<YSIZE(Vin); i++)
{
for (size_t j=0; j<XSIZE(Vin); j++)
DIRECT_A1D_ELEM(aux,j)=DIRECT_A3D_ELEM(Vin,k,i,j);
transformer2.FourierTransform( );
transformer2.getFourierAlias( Aux );
Aux*=H;
transformer2.inverseFourierTransform( );
for (size_t j=0; j<XSIZE(Vin); j++)
DIRECT_A3D_ELEM(Vout,k,i,j)=XSIZE(aux)*DIRECT_A1D_ELEM(aux,j);
}
// Filter in Y
transformer.FourierTransform(hy1,H);
FOR_ALL_ELEMENTS_IN_ARRAY1D(H)
H(i)*= MINUS_ONE_POWER(i);
aux.initZeros(YSIZE(Vin));
transformer2.setReal(aux);
for (size_t k=0; k<ZSIZE(Vin); k++)
for (size_t j=0; j<XSIZE(Vin); j++)
{
for (size_t i=0; i<YSIZE(Vin); i++)
DIRECT_A1D_ELEM(aux,i)=DIRECT_A3D_ELEM(Vout,k,i,j);
transformer2.FourierTransform( );
transformer2.getFourierAlias( Aux );
Aux*=H;
transformer2.inverseFourierTransform( );
for (size_t i=0; i<YSIZE(Vin); i++)
DIRECT_A3D_ELEM(Vout,k,i,j)=XSIZE(aux)*DIRECT_A1D_ELEM(aux,i);
}
// Filter in Z
transformer.FourierTransform(hz1,H);
FOR_ALL_ELEMENTS_IN_ARRAY1D(H)
H(i)*= MINUS_ONE_POWER(i);
aux.initZeros(ZSIZE(Vin));
transformer2.setReal(aux);
for (size_t i=0; i<YSIZE(Vin); i++)
for (size_t j=0; j<XSIZE(Vin); j++)
{
for (size_t k=0; k<ZSIZE(Vin); k++)
DIRECT_A1D_ELEM(aux,k)=DIRECT_A3D_ELEM(Vout,k,i,j);
transformer2.FourierTransform( );
transformer2.getFourierAlias( Aux );
Aux*=H;
transformer2.inverseFourierTransform( );
for (size_t k=0; k<ZSIZE(Vin); k++)
DIRECT_A3D_ELEM(Vout,k,i,j)=XSIZE(aux)*DIRECT_A1D_ELEM(aux,k);
}
// If Missing wedge
if (MW!=NULL)
MW->removeWedge(Vout);
}
void run()
{
MD.read(fn_star);
// Check for rlnImageName label
if (!MD.containsLabel(EMDL_IMAGE_NAME))
REPORT_ERROR("ERROR: Input STAR file does not contain the rlnImageName label");
if (do_split_per_micrograph && !MD.containsLabel(EMDL_MICROGRAPH_NAME))
REPORT_ERROR("ERROR: Input STAR file does not contain the rlnMicrographName label");
Image<DOUBLE> in;
FileName fn_img, fn_mic;
std::vector<FileName> fn_mics;
std::vector<int> mics_ndims;
// First get number of images and their size
int ndim=0;
bool is_first=true;
int xdim, ydim, zdim;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MD)
{
if (is_first)
{
MD.getValue(EMDL_IMAGE_NAME, fn_img);
in.read(fn_img);
xdim=XSIZE(in());
ydim=YSIZE(in());
zdim=ZSIZE(in());
is_first=false;
}
if (do_split_per_micrograph)
{
MD.getValue(EMDL_MICROGRAPH_NAME, fn_mic);
bool have_found = false;
for (int m = 0; m < fn_mics.size(); m++)
{
if (fn_mic == fn_mics[m])
{
have_found = true;
mics_ndims[m]++;
break;
}
}
if (!have_found)
{
fn_mics.push_back(fn_mic);
mics_ndims.push_back(1);
}
}
ndim++;
}
// If not splitting, just fill fn_mics and mics_ndim with one entry (to re-use loop below)
if (!do_split_per_micrograph)
{
fn_mics.push_back("");
mics_ndims.push_back(ndim);
}
// Loop over all micrographs
for (int m = 0; m < fn_mics.size(); m++)
{
ndim = mics_ndims[m];
fn_mic = fn_mics[m];
// Resize the output image
std::cout << "Resizing the output stack to "<< ndim<<" images of size: "<<xdim<<"x"<<ydim<<"x"<<zdim << std::endl;
DOUBLE Gb = ndim*zdim*ydim*xdim*8./1024./1024./1024.;
std::cout << "This will require " << Gb << "Gb of memory...."<< std::endl;
Image<DOUBLE> out(xdim, ydim, zdim, ndim);
int n = 0;
init_progress_bar(ndim);
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MD)
{
FileName fn_mymic;
if (do_split_per_micrograph)
MD.getValue(EMDL_MICROGRAPH_NAME, fn_mymic);
else
fn_mymic="";
if (fn_mymic == fn_mic)
{
MD.getValue(EMDL_IMAGE_NAME, fn_img);
in.read(fn_img);
if (do_apply_trans)
{
DOUBLE xoff = 0.;
DOUBLE yoff = 0.;
DOUBLE psi = 0.;
MD.getValue(EMDL_ORIENT_ORIGIN_X, xoff);
MD.getValue(EMDL_ORIENT_ORIGIN_Y, yoff);
MD.getValue(EMDL_ORIENT_PSI, psi);
// Apply the actual transformation
Matrix2D<DOUBLE> A;
rotation2DMatrix(psi, A);
MAT_ELEM(A,0, 2) = xoff;
MAT_ELEM(A,1, 2) = yoff;
selfApplyGeometry(in(), A, IS_NOT_INV, DONT_WRAP);
}
out().setImage(n, in());
n++;
if (n%100==0) progress_bar(n);
}
}
progress_bar(ndim);
FileName fn_out;
if (do_split_per_micrograph)
{
// Remove any extensions from micrograph names....
fn_out = fn_root + "_" + fn_mic.withoutExtension() + fn_ext;
}
else
fn_out = fn_root + fn_ext;
out.write(fn_out);
std::cout << "Written out: " << fn_out << std::endl;
}
std::cout << "Done!" <<std::endl;
}
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);
}
}
// 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 ProgSSNR::estimateSSNR(int dim, Matrix2D<double> &output)
{
// These vectors are for 1D
Matrix1D<double> S_S21D((int)(XSIZE(S()) / 2 - ring_width)),
S_N21D((int)(XSIZE(S()) / 2 - ring_width)),
K1D((int)(XSIZE(S()) / 2 - ring_width)),
S_SSNR1D;
Matrix1D<double> N_S21D((int)(XSIZE(S()) / 2 - ring_width)),
N_N21D((int)(XSIZE(S()) / 2 - ring_width)),
N_SSNR1D;
// Selfile of the 2D images
MetaData SF_individual;
std::cerr << "Computing the SSNR ...\n";
init_progress_bar(SF_S.size());
int imgno = 1;
Image<double> Is, In;
Projection Iths, Ithn;
MultidimArray< std::complex<double> > FFT_Is, FFT_Iths, FFT_In, FFT_Ithn;
MultidimArray<double> S2s, N2s, S2n, N2n;
FileName fn_img;
FourierTransformer FT(FFTW_BACKWARD);
FourierProjector *Sprojector=NULL;
FourierProjector *Nprojector=NULL;
if (fourierProjections)
{
Sprojector=new FourierProjector(S(),2,0.5,LINEAR);
Nprojector=new FourierProjector(N(),2,0.5,LINEAR);
}
FOR_ALL_OBJECTS_IN_METADATA2(SF_S, SF_N)
{
double rot, tilt, psi;
SF_S.getValue(MDL_ANGLE_ROT,rot, __iter.objId);
SF_S.getValue(MDL_ANGLE_TILT,tilt,__iter.objId);
SF_S.getValue(MDL_ANGLE_PSI,psi,__iter.objId);
SF_S.getValue(MDL_IMAGE,fn_img,__iter.objId);
Is.read(fn_img);
Is().setXmippOrigin();
SF_N.getValue(MDL_IMAGE,fn_img,__iter2.objId);
In.read(fn_img);
In().setXmippOrigin();
if (fourierProjections)
{
projectVolume(*Sprojector, Iths, YSIZE(Is()), XSIZE(Is()), rot, tilt, psi);
projectVolume(*Nprojector, Ithn, YSIZE(Is()), XSIZE(Is()), rot, tilt, psi);
}
else
{
projectVolume(S(), Iths, YSIZE(Is()), XSIZE(Is()), rot, tilt, psi);
projectVolume(N(), Ithn, YSIZE(Is()), XSIZE(Is()), rot, tilt, psi);
}
#ifdef DEBUG
Image<double> save;
save() = Is();
save.write("PPPread_signal.xmp");
save() = In();
save.write("PPPread_noise.xmp");
save() = Iths();
save.write("PPPtheo_signal.xmp");
save() = Ithn();
save.write("PPPtheo_noise.xmp");
#endif
Is() -= Iths();
In() -= Ithn(); // According to the article: should we not subtract here (simply remove this line)
// "...except that there is no subtraction in the denominator because the
// underlying signal is zero by definition."
if (dim == 2)
{
FT.completeFourierTransform(Is(), FFT_Is);
FT.completeFourierTransform(Iths(), FFT_Iths);
FT.completeFourierTransform(In(), FFT_In);
FT.completeFourierTransform(Ithn(), FFT_Ithn);
}
else
{
FT.FourierTransform(Is(), FFT_Is);
FT.FourierTransform(Iths(), FFT_Iths);
FT.FourierTransform(In(), FFT_In);
FT.FourierTransform(Ithn(), FFT_Ithn);
}
#ifdef DEBUG
Image< std::complex<double> > savec;
savec() = FFT_Is;
savec.write("PPPFFTread_signal.xmp");
savec() = FFT_In;
savec.write("PPPFFTread_noise.xmp");
savec() = FFT_Iths;
savec.write("PPPFFTtheo_signal.xmp");
savec() = FFT_Ithn;
savec.write("PPPFFTtheo_noise.xmp");
#endif
// Compute the amplitudes
S2s.resizeNoCopy(FFT_Iths);
N2s.resizeNoCopy(FFT_Iths);
S2n.resizeNoCopy(FFT_Iths);
N2n.resizeNoCopy(FFT_Iths);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(FFT_Iths)
{
DIRECT_MULTIDIM_ELEM(S2s, n) = abs(DIRECT_MULTIDIM_ELEM(FFT_Iths, n));
DIRECT_MULTIDIM_ELEM(S2s, n) *= DIRECT_MULTIDIM_ELEM(S2s, n);
DIRECT_MULTIDIM_ELEM(N2s, n) = abs(DIRECT_MULTIDIM_ELEM(FFT_Is, n));
DIRECT_MULTIDIM_ELEM(N2s, n) *= DIRECT_MULTIDIM_ELEM(N2s, n);
DIRECT_MULTIDIM_ELEM(S2n, n) = abs(DIRECT_MULTIDIM_ELEM(FFT_Ithn, n));
DIRECT_MULTIDIM_ELEM(S2n, n) *= DIRECT_MULTIDIM_ELEM(S2n, n);
DIRECT_MULTIDIM_ELEM(N2n, n) = abs(DIRECT_MULTIDIM_ELEM(FFT_In, n));
DIRECT_MULTIDIM_ELEM(N2n, n) *= DIRECT_MULTIDIM_ELEM(N2n, n);
}
#ifdef DEBUG
save() = S2s();
save.write("PPPS2s.xmp");
save() = N2s();
save.write("PPPN2s.xmp");
save() = S2n();
save.write("PPPS2n.xmp");
save() = N2n();
save.write("PPPN2n.xmp");
#endif
if (dim == 2)
{
// Compute the SSNR image
Image<double> SSNR2D;
SSNR2D().initZeros(S2s);
const MultidimArray<double> & SSNR2Dmatrix=SSNR2D();
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(S2s)
{
double ISSNR = 0, alpha = 0, SSNR = 0;
double aux = DIRECT_MULTIDIM_ELEM(N2s,n);
if (aux > min_power)
ISSNR = DIRECT_MULTIDIM_ELEM(S2s,n) / aux;
aux = DIRECT_MULTIDIM_ELEM(N2n,n);
if (aux > min_power)
alpha = DIRECT_MULTIDIM_ELEM(S2n,n) / aux;
if (alpha > min_power)
{
aux = ISSNR / alpha - 1.0;
SSNR = XMIPP_MAX(aux, 0.0);
}
if (SSNR > min_power)
DIRECT_MULTIDIM_ELEM(SSNR2Dmatrix,n) = 10.0 * log10(SSNR + 1.0);
}
CenterFFT(SSNR2D(), true);
#ifdef DEBUG
save() = SSNR2Dmatrix;
save.write("PPPSSNR2D.xmp");
#endif
// Save image
FileName fn_img_out;
fn_img_out.compose(imgno, fn_out_images, "stk");
SSNR2D.write(fn_img_out);
size_t objId = SF_individual.addObject();
SF_individual.setValue(MDL_IMAGE,fn_img_out,objId);
SF_individual.setValue(MDL_ANGLE_ROT,rot,objId);
SF_individual.setValue(MDL_ANGLE_TILT,tilt,objId);
SF_individual.setValue(MDL_ANGLE_PSI,psi,objId);
}
static void game_redraw(drawing *dr, game_drawstate *ds,
const game_state *oldstate, const game_state *state,
int dir, const game_ui *ui,
float animtime, float flashtime)
{
int i, j;
struct bbox bb = find_bbox(&state->params);
struct solid *poly;
const int *pkey, *gkey;
float t[3];
float angle;
int square;
draw_rect(dr, 0, 0, XSIZE(GRID_SCALE, bb, state->solid),
YSIZE(GRID_SCALE, bb, state->solid), COL_BACKGROUND);
if (dir < 0) {
const game_state *t;
/*
* This is an Undo. So reverse the order of the states, and
* run the roll timer backwards.
*/
assert(oldstate);
t = oldstate;
oldstate = state;
state = t;
animtime = ROLLTIME - animtime;
}
if (!oldstate) {
oldstate = state;
angle = 0.0;
square = state->current;
pkey = state->dpkey;
gkey = state->dgkey;
} else {
angle = state->angle * animtime / ROLLTIME;
square = state->previous;
pkey = state->spkey;
gkey = state->sgkey;
}
state = oldstate;
for (i = 0; i < state->grid->nsquares; i++) {
int coords[8];
for (j = 0; j < state->grid->squares[i].npoints; j++) {
coords[2*j] = ((int)(state->grid->squares[i].points[2*j] * GRID_SCALE)
+ ds->ox);
coords[2*j+1] = ((int)(state->grid->squares[i].points[2*j+1]*GRID_SCALE)
+ ds->oy);
}
draw_polygon(dr, coords, state->grid->squares[i].npoints,
GET_SQUARE(state, i) ? COL_BLUE : COL_BACKGROUND,
COL_BORDER);
}
/*
* Now compute and draw the polyhedron.
*/
poly = transform_poly(state->solid, state->grid->squares[square].flip,
pkey[0], pkey[1], angle);
/*
* Compute the translation required to align the two key points
* on the polyhedron with the same key points on the current
* face.
*/
for (i = 0; i < 3; i++) {
float tc = 0.0;
for (j = 0; j < 2; j++) {
float grid_coord;
if (i < 2) {
grid_coord =
state->grid->squares[square].points[gkey[j]*2+i];
} else {
grid_coord = 0.0;
}
tc += (grid_coord - poly->vertices[pkey[j]*3+i]);
}
t[i] = tc / 2;
}
for (i = 0; i < poly->nvertices; i++)
for (j = 0; j < 3; j++)
poly->vertices[i*3+j] += t[j];
/*
* Now actually draw each face.
*/
for (i = 0; i < poly->nfaces; i++) {
float points[8];
int coords[8];
for (j = 0; j < poly->order; j++) {
int f = poly->faces[i*poly->order + j];
points[j*2] = (poly->vertices[f*3+0] -
poly->vertices[f*3+2] * poly->shear);
points[j*2+1] = (poly->vertices[f*3+1] -
poly->vertices[f*3+2] * poly->shear);
}
for (j = 0; j < poly->order; j++) {
coords[j*2] = (int)floor(points[j*2] * GRID_SCALE) + ds->ox;
coords[j*2+1] = (int)floor(points[j*2+1] * GRID_SCALE) + ds->oy;
}
/*
* Find out whether these points are in a clockwise or
* anticlockwise arrangement. If the latter, discard the
* face because it's facing away from the viewer.
*
* This would involve fiddly winding-number stuff for a
* general polygon, but for the simple parallelograms we'll
* be seeing here, all we have to do is check whether the
* corners turn right or left. So we'll take the vector
* from point 0 to point 1, turn it right 90 degrees,
* and check the sign of the dot product with that and the
* next vector (point 1 to point 2).
*/
{
float v1x = points[2]-points[0];
float v1y = points[3]-points[1];
float v2x = points[4]-points[2];
float v2y = points[5]-points[3];
float dp = v1x * v2y - v1y * v2x;
if (dp <= 0)
continue;
}
draw_polygon(dr, coords, poly->order,
state->facecolours[i] ? COL_BLUE : COL_BACKGROUND,
COL_BORDER);
}
sfree(poly);
draw_update(dr, 0, 0, XSIZE(GRID_SCALE, bb, state->solid),
YSIZE(GRID_SCALE, bb, state->solid));
/*
* Update the status bar.
*/
{
char statusbuf[256];
if (state->completed) {
strcpy(statusbuf, _("COMPLETED!"));
strcpy(statusbuf+strlen(statusbuf), " ");
} else statusbuf[0] = '\0';
sprintf(statusbuf+strlen(statusbuf), _("Moves: %d"),
(state->completed ? state->completed : state->movecount));
status_bar(dr, statusbuf);
}
}
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 Projector::rotate3D(MultidimArray<Complex > &f3d, Matrix2D<DOUBLE> &A, bool inv)
{
DOUBLE fx, fy, fz, xp, yp, zp;
int x0, x1, y0, y1, z0, z1, y, z, y2, z2, r2;
bool is_neg_x;
Complex d000, d010, d100, d110, d001, d011, d101, d111, dx00, dx10, dxy0, dx01, dx11, dxy1;
Matrix2D<DOUBLE> Ainv;
// f3d should already be in the right size (ori_size,orihalfdim)
// AND the points outside max_r should already be zero...
// f3d.initZeros();
// Use the inverse matrix
if (inv)
Ainv = A;
else
Ainv = A.transpose();
// The f3d 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(f3d) - 1);
// Go from the 3D rotated coordinates to the original 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(f3d)= "<< XSIZE(f3d) << std::endl;
std::cerr << " YSIZE(f3d)= "<< YSIZE(f3d) << 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 k=0; k < ZSIZE(f3d); k++)
{
// Don't search beyond square with side max_r
if (k <= my_r_max)
{
z = k;
}
else if (k >= ZSIZE(f3d) - my_r_max)
{
z = k - ZSIZE(f3d);
}
else
continue;
z2 = z * z;
for (int i=0; i < YSIZE(f3d); i++)
{
// Don't search beyond square with side max_r
if (i <= my_r_max)
{
y = i;
}
else if (i >= YSIZE(f3d) - my_r_max)
{
y = i - YSIZE(f3d);
}
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 + z2;
if (r2 > max_r2)
continue;
// Get logical coordinates in the 3D map
xp = Ainv(0,0) * x + Ainv(0,1) * y + Ainv(0,2) * z;
yp = Ainv(1,0) * x + Ainv(1,1) * y + Ainv(1,2) * z;
zp = Ainv(2,0) * x + Ainv(2,1) * y + Ainv(2,2) * z;
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;
zp = -zp;
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;
z0 = FLOOR(zp);
fz = zp - z0;
z0 -= STARTINGZ(data);
z1 = z0 + 1;
// Matrix access can be accelerated through pre-calculation of z0*xydim etc.
d000 = DIRECT_A3D_ELEM(data, z0, y0, x0);
d001 = DIRECT_A3D_ELEM(data, z0, y0, x1);
d010 = DIRECT_A3D_ELEM(data, z0, y1, x0);
d011 = DIRECT_A3D_ELEM(data, z0, y1, x1);
d100 = DIRECT_A3D_ELEM(data, z1, y0, x0);
d101 = DIRECT_A3D_ELEM(data, z1, y0, x1);
d110 = DIRECT_A3D_ELEM(data, z1, y1, x0);
d111 = DIRECT_A3D_ELEM(data, z1, y1, x1);
// Set the interpolated value in the 2D output array
// interpolate in x
#ifndef FLOAT_PRECISION
__m256d __fx = _mm256_set1_pd(fx);
__m256d __interpx1 = LIN_INTERP_AVX(_mm256_setr_pd(d000.real, d000.imag, d100.real, d100.imag),
_mm256_setr_pd(d001.real, d001.imag, d101.real, d101.imag),
__fx);
__m256d __interpx2 = LIN_INTERP_AVX(_mm256_setr_pd(d010.real, d010.imag, d110.real, d110.imag),
_mm256_setr_pd(d011.real, d011.imag, d111.real, d111.imag),
__fx);
// interpolate in y
__m256d __fy = _mm256_set1_pd(fy);
__m256d __interpy = LIN_INTERP_AVX(__interpx1, __interpx2, __fy);
#else
__m128 __fx = _mm_set1_ps(fx);
__m128 __interpx1 = LIN_INTERP_AVX(_mm_setr_ps(d000.real, d000.imag, d100.real, d100.imag),
_mm_setr_ps(d001.real, d001.imag, d101.real, d101.imag),
__fx);
__m128 __interpx2 = LIN_INTERP_AVX(_mm_setr_ps(d010.real, d010.imag, d110.real, d110.imag),
_mm_setr_ps(d011.real, d011.imag, d111.real, d111.imag),
__fx);
// interpolate in y
__m128 __fy = _mm_set1_ps(fy);
__m128 __interpy = LIN_INTERP_AVX(__interpx1, __interpx2, __fy);
#endif
Complex* interpy = (Complex*)&__interpy;
//interpolate in z
DIRECT_A3D_ELEM(f3d, k, i, x) = LIN_INTERP(fz, interpy[0], interpy[1]);
// Take complex conjugated for half with negative x
if (is_neg_x)
DIRECT_A3D_ELEM(f3d, k, i, x) = conj(DIRECT_A3D_ELEM(f3d, k, i, x));
} // endif TRILINEAR
else if (interpolator == NEAREST_NEIGHBOUR )
{
x0 = ROUND(xp);
y0 = ROUND(yp);
z0 = ROUND(zp);
if (x0 < 0)
DIRECT_A3D_ELEM(f3d, k, i, x) = conj(A3D_ELEM(data, -z0, -y0, -x0));
else
DIRECT_A3D_ELEM(f3d, k, i, x) = A3D_ELEM(data, z0, y0, x0);
} // endif NEAREST_NEIGHBOUR
else
REPORT_ERROR("Unrecognized interpolator in Projector::project");
} // endif x-loop
} // endif y-loop
} // endif z-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();
}
void runThread(ThreadArgument &thArg)
{
int thread_id = thArg.thread_id;
ProgXrayImport * ptrProg= (ProgXrayImport *)thArg.workClass;
MetaData localMD;
Image<double> Iaux;
FileName fnImgIn, fnImgOut;
size_t first = 0, last = 0;
MultidimArray<char> mask;
while (ptrProg->td->getTasks(first, last))
{
for (size_t i=first; i<=last; i++)
{
ptrProg->inMD.getValue(MDL_IMAGE, fnImgIn, ptrProg->objIds[i]);
MDRow rowGeo;
ptrProg->readGeoInfo(fnImgIn, rowGeo);
// ptrProg->readAndCrop(fnImgIn, Iaux, ptrProg->cropSizeX, ptrProg->cropSizeY);
Iaux.read(fnImgIn);
Iaux().selfWindow(ptrProg->cropSizeYi,ptrProg->cropSizeXi,
(int)(YSIZE(Iaux())-ptrProg->cropSizeYe-1),(int)(XSIZE(Iaux())-ptrProg->cropSizeXe-1));
Iaux().resetOrigin();
if (XSIZE(ptrProg->IavgDark())!=0)
{
Iaux()-=ptrProg->IavgDark();
forcePositive(Iaux());
}
double currentBeam = 1;
double expTime = 1;
double slitWidth = 1;
if ( ptrProg->dSource == ptrProg->MISTRAL )
{
size_t idx = fnImgIn.getPrefixNumber();
currentBeam = dMi(ptrProg->cBeamArray, idx-1);
expTime = dMi(ptrProg->expTimeArray, idx-1);
slitWidth = dMi(ptrProg->slitWidthArray, idx-1);
}
else
ptrProg->readCorrectionInfo(fnImgIn, currentBeam, expTime, slitWidth);
Iaux() *= 1.0/(currentBeam*expTime*slitWidth);
if (XSIZE(ptrProg->IavgFlat())!=0)
Iaux()/=ptrProg->IavgFlat();
// Assign median filter to zero valued pixels to avoid -inf when applying log10
Iaux().equal(0,mask);
mask.resizeNoCopy(Iaux());
if (XSIZE(ptrProg->bpMask()) != 0)
mask += ptrProg->bpMask();
boundMedianFilter(Iaux(), mask);
if (ptrProg->logFix)
{
Iaux().selfLog();
if (ptrProg->selfAttFix)
Iaux() *= -1.;
}
fnImgOut.compose(i+1, ptrProg->fnOut);
size_t objId = localMD.addObject();
localMD.setValue(MDL_IMAGE,fnImgOut,objId);
localMD.setRow(rowGeo, objId); //
// localMD.setValue(MDL_ANGLE_TILT,Iaux.tilt(),objId);
Iaux.write(fnImgOut);
if (thread_id==0)
progress_bar(i);
}
}
//Lock for update the total counter
ptrProg->mutex.lock();
ptrProg->outMD.unionAll(localMD);
ptrProg->mutex.unlock();
}
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");
}
}
void ProgXrayImport::run()
{
// Delete output stack if it exists
fnOut = fnRoot + ".mrc";
fnOut.deleteFile();
/* Turn off error handling */
H5Eset_auto(H5E_DEFAULT, NULL, NULL);
if (dSource == MISTRAL)
H5File.openFile(fnInput, H5F_ACC_RDONLY);
// Reading bad pixels mask
if ( !fnBPMask.empty() )
{
std::cerr << "Reading bad pixels mask from "+fnBPMask << "." << std::endl;
bpMask.read(fnBPMask);
if ( (cropSizeX + cropSizeY ) > 0 )
bpMask().selfWindow(cropSizeY,cropSizeX,
(int)(YSIZE(bpMask())-cropSizeY-1),(int)(XSIZE(bpMask())-cropSizeX-1));
STARTINGX(bpMask()) = STARTINGY(bpMask()) = 0;
}
// Setting the image projections list
switch (dSource)
{
case MISTRAL:
{
inMD.read(fnInput);
H5File.getDataset("NXtomo/data/rotation_angle", anglesArray, false);
H5File.getDataset("NXtomo/instrument/sample/ExpTimes", expTimeArray, false);
H5File.getDataset("NXtomo/instrument/sample/current", cBeamArray);
/* In case there is no angles information we set them to to an increasing sequence
* just to be able to continue importing data */
if ( anglesArray.size() != inMD.size() )
{
reportWarning("Input file does not contains angle information. Default sequence used.");
anglesArray.resizeNoCopy(inMD.size());
anglesArray.enumerate();
}
// If expTime is empty or only one single value in nexus file then we fill with 1
if (expTimeArray.size() < 2)
{
reportWarning("Input file does not contains tomogram exposition time information.");
expTimeArray.initConstant(anglesArray.size(), 1.);
}
// If current is empty or only one single value in nexus file then we fill with 1
if (cBeamArray.size() < 2)
{
reportWarning("Input file does not contains tomogram current beam information.");
cBeamArray.initConstant(anglesArray.size(), 1.);
}
// Since Alba does not provide slit width, we set to ones
slitWidthArray.initConstant(anglesArray.size(), 1.);
}
break;
case BESSY:
{
size_t objId;
for (size_t i = tIni; i <= tEnd; ++i)
{
objId = inMD.addObject();
inMD.setValue(MDL_IMAGE, fnInput + formatString("/img%d.spe", i), objId);
}
break;
}
case GENERIC:
{
// Get Darkfield
std::cerr << "Getting darkfield from "+fnInput << " ..." << std::endl;
getDarkfield(fnInput, IavgDark);
if (XSIZE(IavgDark())!=0)
IavgDark.write(fnRoot+"_darkfield.xmp");
std::vector<FileName> listDir;
fnInput.getFiles(listDir);
size_t objId;
for (size_t i = 0; i < listDir.size(); ++i)
{
if (!listDir[i].hasImageExtension())
continue;
objId = inMD.addObject();
inMD.setValue(MDL_IMAGE, fnInput+"/"+listDir[i], objId);
}
}
break;
}
inMD.findObjects(objIds);
size_t nIm = inMD.size();
// Create empty output stack file
getImageInfo(inMD, imgInfo);
/* Get the flatfield:: We get the FF after the image list because we need the image size to adapt the FF
* in case they were already cropped.
*/
if (!fnFlat.empty())
{
std::cout << "Getting flatfield from "+fnFlat << " ..." << std::endl;
getFlatfield(fnFlat,IavgFlat);
if ( XSIZE(IavgFlat()) != 0 )
{
FileName ffName = fnRoot+"_flatfield_avg.xmp";
IavgFlat.write(ffName);
fMD.setValue(MDL_IMAGE, ffName, fMD.addObject());
}
}
createEmptyFile(fnOut, imgInfo.adim.xdim-cropSizeXi-cropSizeXe, imgInfo.adim.ydim-cropSizeYi-cropSizeYe, 1, nIm);
// Process images
td = new ThreadTaskDistributor(nIm, XMIPP_MAX(1, nIm/30));
tm = new ThreadManager(thrNum, this);
std::cerr << "Getting data from " << fnInput << " ...\n";
init_progress_bar(nIm);
tm->run(runThread);
progress_bar(nIm);
// Write Metadata and angles
MetaData MDSorted;
MDSorted.sort(outMD,MDL_ANGLE_TILT);
MDSorted.write("tomo@"+fnRoot + ".xmd");
if ( fMD.size() > 0 )
fMD.write("flatfield@"+fnRoot + ".xmd", MD_APPEND);
// We also reference initial and final images at 0 degrees for Mistral tomograms
if ( dSource == MISTRAL )
{
fMD.clear();
FileName degree0Fn = "NXtomo/instrument/sample/0_degrees_initial_image";
if ( H5File.checkDataset(degree0Fn.c_str()))
fMD.setValue(MDL_IMAGE, degree0Fn + "@" + fnInput, fMD.addObject());
degree0Fn = "NXtomo/instrument/sample/0_degrees_final_image";
if ( H5File.checkDataset(degree0Fn.c_str()))
fMD.setValue(MDL_IMAGE, degree0Fn + "@" + fnInput, fMD.addObject());
if ( fMD.size() > 0 )
fMD.write("degree0@"+fnRoot + ".xmd", MD_APPEND);
}
// Write tlt file for IMOD
std::ofstream fhTlt;
fhTlt.open((fnRoot+".tlt").c_str());
if (!fhTlt)
REPORT_ERROR(ERR_IO_NOWRITE,fnRoot+".tlt");
FOR_ALL_OBJECTS_IN_METADATA(MDSorted)
{
double tilt;
MDSorted.getValue(MDL_ANGLE_TILT,tilt,__iter.objId);
fhTlt << tilt << std::endl;
}
fhTlt.close();
delete td;
delete tm;
}
// Evaluate plane ----------------------------------------------------------
double evaluatePlane(double rot, double tilt,
const MultidimArray<double> *V, const MultidimArray<double> *Vmag,
double maxFreq, double planeWidth, int direction,
MultidimArray<double> *Vdraw=NULL,
bool setPos=false, double rotPos=0, double tiltPos=0)
{
if (rot<0 || rot>360 || tilt<-90 || tilt>90)
return 0;
Matrix2D<double> E, Einv;
Euler_angles2matrix(rot,tilt,0,E);
Einv=E.transpose();
if (setPos)
{
Matrix2D<double> Epos;
Euler_angles2matrix(rotPos,tiltPos,0,Epos);
double angle=acos(E(2,0)*Epos(2,0)+E(2,1)*Epos(2,1)+E(2,2)*Epos(2,2));
angle=RAD2DEG(angle);
if (fabs(angle)<20 || fabs(180-angle)<20)
return 0;
}
size_t N=XMIPP_MAX(XSIZE(*Vmag),YSIZE(*Vmag)/2);
N=XMIPP_MAX(N,ZSIZE(*Vmag)/2);
double df=0.5/N;
Matrix1D<double> freq(3), freqp(3);
Matrix1D<int> idx(3);
double sumNeg=0, sumPos=0;
int Nneg=0, Npos=0;
double maxFreq2=maxFreq*maxFreq;
int iPlaneWidth=(int)ceil(planeWidth);
for (double ix=0; ix<=N; ix++)
{
XX(freq)=ix*df;
double fx2=XX(freq)*XX(freq);
if (fx2>maxFreq2)
continue;
for (double iy=-(int)N; iy<=N; iy++)
{
YY(freq)=iy*df;
double fx2fy2=fx2+YY(freq)*YY(freq);
if (fx2fy2>maxFreq2)
continue;
for (int iz=-iPlaneWidth; iz<=iPlaneWidth; iz++)
{
if (iz==0 || ix==0 || iy==0)
continue;
// Frequency in the coordinate system of the plane
ZZ(freq)=iz*df;
// Frequency in the coordinate system of the volume
SPEED_UP_temps012;
M3x3_BY_V3x1(freqp,Einv,freq);
bool inverted=false;
if (XX(freqp)<0)
{
XX(freqp)=-XX(freqp);
YY(freqp)=-YY(freqp);
ZZ(freqp)=-ZZ(freqp);
inverted=true;
}
// Get the corresponding index
DIGFREQ2FFT_IDX(ZZ(freqp), ZSIZE(*V), ZZ(idx));
DIGFREQ2FFT_IDX(YY(freqp), YSIZE(*V), YY(idx));
DIGFREQ2FFT_IDX(XX(freqp), XSIZE(*V), XX(idx));
if (XX(idx) < STARTINGX(*Vmag) || XX(idx) > FINISHINGX(*Vmag) ||
YY(idx) < STARTINGY(*Vmag) || YY(idx) > FINISHINGY(*Vmag) ||
ZZ(idx) < STARTINGZ(*Vmag) || ZZ(idx) > FINISHINGZ(*Vmag))
continue;
// Make the corresponding sums
bool negativeSum;
if (direction==1)
negativeSum=iz<0;
else
negativeSum=iz>0;
double val=A3D_ELEM(*Vmag,ZZ(idx),YY(idx),XX(idx));
if ((negativeSum && !inverted) || (!negativeSum && inverted)) // XOR
{
sumNeg+=val;
Nneg++;
if (Vdraw!=NULL)
(*Vdraw)(idx)=2*direction*val;
}
else
{
sumPos+=val;
Npos++;
if (Vdraw!=NULL)
(*Vdraw)(idx)=1.0/2.0*direction*val;
}
}
}
}
if (fabs(Nneg-Npos)/(0.5*(Nneg+Npos))>0.5)
// If there is a difference of more than 50%
return 1e38;
if (Nneg!=0)
sumNeg/=Nneg;
else
return 1e38;
if (Npos!=0)
sumPos/=Npos;
else
return 1e38;
return -(sumPos-sumNeg);
}
void FourierTransformer::setReal(MultidimArray<double>& input)
{
bool recomputePlan = false;
if (fReal == NULL)
{
recomputePlan = true;
}
else if (dataPtr != MULTIDIM_ARRAY(input))
{
recomputePlan = true;
}
else
{
recomputePlan = !(fReal->sameShape(input));
}
fFourier.resize(ZSIZE(input), YSIZE(input), XSIZE(input) / 2 + 1);
fReal = &input;
if (recomputePlan)
{
int ndim = 3;
if (ZSIZE(input) == 1)
{
ndim = 2;
if (YSIZE(input) == 1)
{
ndim = 1;
}
}
int* N = new int[ndim];
switch (ndim)
{
case 1:
N[0] = XSIZE(input);
break;
case 2:
N[0] = YSIZE(input);
N[1] = XSIZE(input);
break;
case 3:
N[0] = ZSIZE(input);
N[1] = YSIZE(input);
N[2] = XSIZE(input);
break;
}
// Destroy both forward and backward plans if they already exist
destroyPlans();
// Make new plans
pthread_mutex_lock(&fftw_plan_mutex);
fPlanForward = fftw_plan_dft_r2c(ndim, N, MULTIDIM_ARRAY(*fReal),
(fftw_complex*) MULTIDIM_ARRAY(fFourier), FFTW_ESTIMATE);
fPlanBackward = fftw_plan_dft_c2r(ndim, N,
(fftw_complex*) MULTIDIM_ARRAY(fFourier), MULTIDIM_ARRAY(*fReal),
FFTW_ESTIMATE);
pthread_mutex_unlock(&fftw_plan_mutex);
if (fPlanForward == NULL || fPlanBackward == NULL)
{
REPORT_ERROR("FFTW plans cannot be created");
}
#ifdef DEBUG_PLANS
std::cerr << " SETREAL fPlanForward= " << fPlanForward << " fPlanBackward= " << fPlanBackward << " this= " << this << std::endl;
#endif
delete [] N;
dataPtr = MULTIDIM_ARRAY(*fReal);
}
}
//#define DEBUG
void ProgResolutionIBW::run()
{
V.read(fnVol);
//Mask generation
Image<double> aux;
double bg_mean;
MultidimArray<double> Vmask;
detectBackground(V(),aux(),0.1,bg_mean);
#ifdef DEBUG
aux.write("PPPmask_no_ero_03.vol");
#endif
//Mask volume erosion to expand the mask boundaries
Vmask.initZeros(V());
erode3D(aux(),Vmask, 18,0,2);
//Correction of some flaws produced in the edges of the mask volume
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY3D(Vmask)
if (k<=4 || i<=4 || j<=4 ||
k>=ZSIZE(Vmask)-4 || i>=YSIZE(Vmask)-4 || j>=XSIZE(Vmask)-4)
DIRECT_A3D_ELEM(Vmask,k,i,j)=1;
aux()=Vmask;
#ifdef DEBUG
aux.write("PPPmask_ero_03.vol");
#endif
//Sobel edge detection applied to original volume
Image<double> Vedge;
computeEdges(V(),Vedge());
#ifdef DEBUG
Vedge.write("PPPvolume_sobel_unmask_03.vol");
#endif
//Masked volume generation
const MultidimArray<double> &mVedge=Vedge();
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mVedge)
if (DIRECT_MULTIDIM_ELEM(Vmask,n)==1)
DIRECT_MULTIDIM_ELEM(mVedge,n)=0;
#ifdef DEBUG
Vedge.write("volume_sobel_mask_03.vol");
#endif
double minval, maxval, avg, stddev;
//Invert the mask to meet computeStats_within_binary_mask requirements
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vmask)
if (DIRECT_MULTIDIM_ELEM(Vmask,n)==1)
DIRECT_MULTIDIM_ELEM(Vmask,n)=0;
else
DIRECT_MULTIDIM_ELEM(Vmask,n)=1;
//Threshold is 3 times the standard deviation of unmasked pixel values
double thresh;
computeStats_within_binary_mask(Vmask,mVedge,minval, maxval, avg, stddev);
thresh=3*stddev;
//Final edge volume generated by setting to 1 positions with values > threshold
Image<double> Vaux;
Vaux().initZeros(mVedge);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mVedge)
if (DIRECT_MULTIDIM_ELEM(mVedge,n)>=thresh)
DIRECT_MULTIDIM_ELEM(Vaux(),n)=1;
#ifdef DEBUG
Vaux.write("volumen_bordes_definitivo_03.vol");
#endif
const MultidimArray<double> &mVaux=Vaux();
//Spline coefficient volume from original volume, to allow <1 step sizes
MultidimArray<double> Volcoeffs;
Volcoeffs.initZeros(V());
produceSplineCoefficients(3,Volcoeffs,V());
//Width parameter volume initialization
Image<double> widths;
widths().resizeNoCopy(V());
widths().initConstant(1e5);
double step=0.25;
Matrix1D<double> direction(3);
//Calculation of edge width for 10 different directions, if a smaller value is found for a different
//direction on a given position the former value is overwritten
//Direction (1,0,0)
VECTOR_R3(direction,1,0,0);
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (0,1,0)
VECTOR_R3(direction,0,1,0);
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (0,0,1)
VECTOR_R3(direction,0,0,1);
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (1,1,0)
VECTOR_R3(direction,(1/sqrt(2)),(1/sqrt(2)),0);
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (1,0,1)
VECTOR_R3(direction,(1/sqrt(2)),0,(1/sqrt(2)));
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (0,1,1)
VECTOR_R3(direction,0,(1/sqrt(2)),(1/sqrt(2)));
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (1,1,1)
VECTOR_R3(direction,(1/sqrt(3)),(1/sqrt(3)),(1/sqrt(3)));
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (-1,1,1)
VECTOR_R3(direction,-(1/sqrt(3)),(1/sqrt(3)),(1/sqrt(3)));
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (1,1,-1)
VECTOR_R3(direction,(1/sqrt(3)),(1/sqrt(3)),-(1/sqrt(3)));
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
//Direction (1,-1,1)
VECTOR_R3(direction,(1/sqrt(3)),-(1/sqrt(3)),(1/sqrt(3)));
edgeWidth(Volcoeffs, mVaux, widths(), direction, step);
#ifdef DEBUG
std::cout << "width stats: ";
widths().printStats();
std::cout << std::endl;
widths.write("PPPwidths.vol");
#endif
double ibw=calculateIBW(widths());
std::cout << "Resolution ibw= " << ibw << std::endl;
if (fnOut!="")
widths.write(fnOut);
}
/* Run --------------------------------------------------------------------- */
void ProgAngularProjectLibrary::run()
{
/////////////////////////////
// PreRun for all nodes but not for all works
/////////////////////////////
//only rank 0
mysampling.verbose=verbose;
show();
//all ranks
mysampling.setSampling(sampling);
srand ( time(NULL) );
//process the symmetry file
//only checks symmetry and set pg_order and pg_group, no memory allocation
if (!mysampling.SL.isSymmetryGroup(fn_sym, symmetry, sym_order))
REPORT_ERROR(ERR_VALUE_INCORRECT,
(std::string)"Invalid symmetry" + fn_sym);
if(perturb_projection_vector!=0)
{
int my_seed;
my_seed=rand();
// set noise deviation and seed
mysampling.setNoise(perturb_projection_vector,my_seed);
}
if(angular_distance_bool!=0)
mysampling.setNeighborhoodRadius(angular_distance);//irrelevant
//true -> half_sphere
mysampling.computeSamplingPoints(false,max_tilt_angle,min_tilt_angle);
//only rank 0
//mysampling.createSymFile(fn_sym,symmetry, sym_order);
//all nodes
mysampling.SL.readSymmetryFile(fn_sym);
//store symmetry matrices, this is faster than computing them each time
mysampling.fillLRRepository();
//mpi_barrier here
//all working nodes must read symmetry file
//and experimental docfile if apropiate
//symmetry_file = symmetry + ".sym";
//SL.readSymmetryFile(symmetry_file)
// We first sample The whole sphere
// Then we remove point redundant due to sampling symmetry
// use old symmetry, this is geometric does not use L_R
mysampling.removeRedundantPoints(symmetry, sym_order);
//=========================
//======================
//recompute symmetry with neigh symmetry
// If uncomment neighbour are not OK. BE CAREFULL
#define BREAKSIMMETRY
#ifdef BREAKSIMMETRY
if (!mysampling.SL.isSymmetryGroup(fn_sym_neigh, symmetry, sym_order))
REPORT_ERROR(ERR_VALUE_INCORRECT,
(std::string)"Invalid neig symmetry" + fn_sym_neigh);
mysampling.SL.readSymmetryFile(fn_sym_neigh);
mysampling.fillLRRepository();
#endif
#undef BREAKSIMMETRY
//precompute product between symmetry matrices and experimental data
if (FnexperimentalImages.size() > 0)
mysampling.fillExpDataProjectionDirectionByLR(FnexperimentalImages);
//remove points not close to experimental points, only for no symmetric cases
if (FnexperimentalImages.size() > 0 &&
remove_points_far_away_from_experimental_data_bool)
{
// here we remove points no close to experimental data, neight symmetry must be use
mysampling.removePointsFarAwayFromExperimentalData();
}
if(compute_closer_sampling_point_bool)
{
//find sampling point closer to experimental point (only 0) and bool
//and save docfile with this information
// use neight symmetry
mysampling.findClosestSamplingPoint(FnexperimentalImages,output_file_root);
}
//only rank 0
//write docfile with vectors and angles
mysampling.createAsymUnitFile(output_file_root);
//all nodes
//If there is no reference available exit
try
{
inputVol.read(input_volume);
}
catch (XmippError XE)
{
std::cout << XE;
exit(0);
}
inputVol().setXmippOrigin();
Xdim = XSIZE(inputVol());
Ydim = YSIZE(inputVol());
if (compute_neighbors_bool)
{
// new symmetry
mysampling.computeNeighbors(only_winner);
mysampling.saveSamplingFile(output_file_root,false);
}
//release some memory
mysampling.exp_data_projection_direction_by_L_R.clear();
unlink(output_file.c_str());
//mpi master should divide doc in chuncks
//in this serial program there is a unique chunck
//angle information is in
//mysampling.no_redundant_sampling_points_vector[i]
//Run for all works
project_angle_vector(0,
mysampling.no_redundant_sampling_points_angles.size()-1,verbose);
//only rank 0 create sel file
MetaData mySFin, mySFout;
FileName fn_temp;
mySFin.read(output_file_root+"_angles.doc");
size_t myCounter=0;
size_t id;
int ref;
for (double mypsi=0;mypsi<360;mypsi += psi_sampling)
{
FOR_ALL_OBJECTS_IN_METADATA(mySFin)
{
double x,y,z, rot, tilt, psi;
mySFin.getValue(MDL_ANGLE_ROT,rot,__iter.objId);
mySFin.getValue(MDL_ANGLE_TILT,tilt,__iter.objId);
mySFin.getValue(MDL_ANGLE_PSI,psi,__iter.objId);
mySFin.getValue(MDL_X,x,__iter.objId);
mySFin.getValue(MDL_Y,y,__iter.objId);
mySFin.getValue(MDL_Z,z,__iter.objId);
mySFin.getValue(MDL_REF,ref,__iter.objId);
fn_temp.compose( ++myCounter,output_file);
id = mySFout.addObject();
mySFout.setValue(MDL_IMAGE,fn_temp,id);
mySFout.setValue(MDL_ENABLED,1,id);
mySFout.setValue(MDL_ANGLE_ROT,rot,id);
mySFout.setValue(MDL_ANGLE_TILT,tilt,id);
mySFout.setValue(MDL_ANGLE_PSI,psi+mypsi,id);
mySFout.setValue(MDL_X,x,id);
mySFout.setValue(MDL_Y,y,id);
mySFout.setValue(MDL_Z,z,id);
mySFout.setValue(MDL_SCALE,1.0,id);
mySFout.setValue(MDL_REF,ref,id);
}
}
mySFout.setComment("x,y,z refer to the coordinates of the unitary vector at direction given by the euler angles");
mySFout.write(output_file_root+".doc");
unlink((output_file_root+"_angles.doc").c_str());
if (fn_groups!="")
createGroupSamplingFiles();
}
void ProgVolumePCA::run()
{
show();
produce_side_info();
const MultidimArray<int> &imask=mask.imask;
size_t Nvoxels=imask.sum();
MultidimArray<float> v;
v.initZeros(Nvoxels);
// Add all volumes to the analyzer
FileName fnVol;
FOR_ALL_OBJECTS_IN_METADATA(mdVols)
{
mdVols.getValue(MDL_IMAGE,fnVol,__iter.objId);
V.read(fnVol);
// Construct vector
const MultidimArray<double> &mV=V();
size_t idx=0;
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
{
if (DIRECT_MULTIDIM_ELEM(imask,n))
DIRECT_MULTIDIM_ELEM(v,idx++)=DIRECT_MULTIDIM_ELEM(mV,n);
}
analyzer.addVector(v);
}
// Construct PCA basis
analyzer.subtractAvg();
analyzer.learnPCABasis(NPCA,100);
// Project onto the PCA basis
Matrix2D<double> proj;
analyzer.projectOnPCABasis(proj);
std::vector<double> dimredProj;
dimredProj.resize(NPCA);
int i=0;
FOR_ALL_OBJECTS_IN_METADATA(mdVols)
{
memcpy(&dimredProj[0],&MAT_ELEM(proj,i,0),NPCA*sizeof(double));
mdVols.setValue(MDL_DIMRED,dimredProj,__iter.objId);
i++;
}
if (fnVolsOut!="")
mdVols.write(fnVolsOut);
else
mdVols.write(fnVols);
// Save the basis
const MultidimArray<double> &mV=V();
for (int i=NPCA-1; i>=0; --i)
{
V().initZeros();
size_t idx=0;
const MultidimArray<double> &mPCA=analyzer.PCAbasis[i];
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(mV)
{
if (DIRECT_MULTIDIM_ELEM(imask,n))
DIRECT_MULTIDIM_ELEM(mV,n)=DIRECT_MULTIDIM_ELEM(mPCA,idx++);
}
if (fnBasis!="")
V.write(fnBasis,i+1,true,WRITE_OVERWRITE);
}
// Generate the PCA volumes
if (listOfPercentiles.size()>0 && fnOutStack!="" && fnAvgVol!="")
{
Image<double> Vavg;
if (fnAvgVol!="")
Vavg.read(fnAvgVol);
else
Vavg().initZeros(V());
Matrix1D<double> p;
proj.toVector(p);
Matrix1D<double> psorted=p.sort();
Image<double> Vpca;
Vpca()=Vavg();
createEmptyFile(fnOutStack,(int)XSIZE(Vavg()),(int)YSIZE(Vavg()),(int)ZSIZE(Vavg()),listOfPercentiles.size());
std::cout << "listOfPercentiles.size()=" << listOfPercentiles.size() << std::endl;
for (size_t i=0; i<listOfPercentiles.size(); i++)
{
int idx=(int)round(textToFloat(listOfPercentiles[i].c_str())/100.0*VEC_XSIZE(p));
std::cout << "Percentile " << listOfPercentiles[i] << " -> idx=" << idx << " p(idx)=" << psorted(idx) << std::endl;
Vpca()+=psorted(idx)*V();
Vpca.write(fnOutStack,i+1,true,WRITE_REPLACE);
}
}
}
