/* Footprint of a blob ----------------------------------------------------- */
void footprint_blob(
ImageOver &blobprint, // blob foot_print table
const struct blobtype &blob, // blob description
int istep, // number of foot-print samples per one sample
// on projection plane in u,v directions
int normalise) // set to 1 if you want normalise. Usually
// you may omit it and no normalisation is performed
{
// Resize output image and redefine the origin of it
int footmax = CEIL(blob.radius);
blobprint.init(-footmax, footmax, istep, -footmax, footmax, istep);
// Run for Imge class indexes
for (int i = STARTINGY(blobprint()); i <= FINISHINGY(blobprint()); i++)
for (int j = STARTINGX(blobprint()); j <= FINISHINGX(blobprint()); j++)
{
// Compute oversampled index and blob value
double vi, ui;
IMG2OVER(blobprint, i, j, vi, ui);
double r = sqrt(vi * vi + ui * ui);
IMGPIXEL(blobprint, i, j) = blob_proj(r, blob);
}
// Adjust the footprint structure
if (normalise)
blobprint() /= blobprint().sum();
}
// Show a complex array ---------------------------------------------------
std::ostream& operator<<(std::ostream& ostrm,
const MultidimArray< Complex >& v)
{
if (v.xdim == 0)
ostrm << "NULL MultidimArray\n";
else
ostrm << std::endl;
for (int l = 0; l < NSIZE(v); l++)
{
if (NSIZE(v)>1) ostrm << "Image No. " << l << std::endl;
for (int k = STARTINGZ(v); k <= FINISHINGZ(v); k++)
{
if (ZSIZE(v) > 1) ostrm << "Slice No. " << k << std::endl;
for (int i = STARTINGY(v); i <= FINISHINGY(v); i++)
{
for (int j = STARTINGX(v); j <= FINISHINGX(v); j++)
ostrm << "(" << A3D_ELEM(v, k, i, j).real << "," << A3D_ELEM(v, k, i, j).imag << ")" << ' ';
ostrm << std::endl;
}
}
}
return ostrm;
}
//#define DEBUG
void spatial_Bspline032voxels(const GridVolume &vol_splines,
MultidimArray<double> *vol_voxels, int Zdim, int Ydim, int Xdim)
{
// Resize and set starting corner .......................................
if (Zdim == 0 || Ydim == 0 || Xdim == 0)
{
Matrix1D<double> size = vol_splines.grid(0).highest -
vol_splines.grid(0).lowest;
Matrix1D<double> corner = vol_splines.grid(0).lowest;
(*vol_voxels).initZeros(CEIL(ZZ(size)), CEIL(YY(size)), CEIL(XX(size)));
STARTINGX(*vol_voxels) = FLOOR(XX(corner));
STARTINGY(*vol_voxels) = FLOOR(YY(corner));
STARTINGZ(*vol_voxels) = FLOOR(ZZ(corner));
}
else
{
(*vol_voxels).initZeros(Zdim, Ydim, Xdim);
(*vol_voxels).setXmippOrigin();
}
// Convert each subvolume ...............................................
for (size_t i = 0; i < vol_splines.VolumesNo(); i++)
{
spatial_Bspline032voxels_SimpleGrid(vol_splines(i)(), vol_splines.grid(i),
vol_voxels);
#ifdef DEBUG
std::cout << "Spline grid no " << i << " stats: ";
vol_splines(i)().printStats();
std::cout << std::endl;
std::cout << "So far vol stats: ";
(*vol_voxels).printStats();
std::cout << std::endl;
VolumeXmipp save;
save() = *vol_voxels;
save.write((std::string)"PPPvoxels" + integerToString(i));
#endif
}
// Now normalise the resulting volume ..................................
double inorm = 1.0 / sum_spatial_Bspline03_Grid(vol_splines.grid());
FOR_ALL_ELEMENTS_IN_ARRAY3D(*vol_voxels)
A3D_ELEM(*vol_voxels, k, i, j) *= inorm;
// Set voxels outside interest region to minimum value .................
double R = vol_splines.grid(0).get_interest_radius();
if (R != -1)
{
double R2 = (R - 6) * (R - 6);
// Compute minimum value within sphere
double min_val = A3D_ELEM(*vol_voxels, 0, 0, 0);
FOR_ALL_ELEMENTS_IN_ARRAY3D(*vol_voxels)
if (j*j + i*i + k*k <= R2 - 4)
min_val = XMIPP_MIN(min_val, A3D_ELEM(*vol_voxels, k, i, j));
// Substitute minimum value
R2 = (R - 2) * (R - 2);
FOR_ALL_ELEMENTS_IN_ARRAY3D(*vol_voxels)
if (j*j + i*i + k*k >= R2)
A3D_ELEM(*vol_voxels, k, i, j) = min_val;
}
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;
}
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 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;
FourierTransformer transformer3D;
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);
// Release memory as soon as you can
VfourierRealAux.clear();
// Remove all those coefficients we are sure we will not use during the projections
volumePaddedSize=XSIZE(VfourierRealCoefs);
int idxMax=maxFrequency*XSIZE(VfourierRealCoefs)+10; // +10 is a safety guard
idxMax=std::min(FINISHINGX(VfourierRealCoefs),idxMax);
int idxMin=std::max(-idxMax,STARTINGX(VfourierRealCoefs));
VfourierRealCoefs.selfWindow(idxMin,idxMin,idxMin,idxMax,idxMax,idxMax);
produceSplineCoefficients(BSPLINE3,VfourierImagCoefs,VfourierImagAux);
VfourierImagAux.clear();
VfourierImagCoefs.selfWindow(idxMin,idxMin,idxMin,idxMax,idxMax,idxMax);
}
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 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");
}
}
// 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);
}