void Projector::initialiseData(int current_size)
{
// By default r_max is half ori_size
if (current_size < 0)
r_max = ori_size / 2;
else
r_max = current_size / 2;
// Never allow r_max beyond Nyquist...
r_max = XMIPP_MIN(r_max, ori_size / 2);
// Set pad_size
pad_size = 2 * (padding_factor * r_max + 1) + 1;
// Short side of data array
switch (ref_dim)
{
case 2:
data.resize(pad_size, pad_size / 2 + 1);
break;
case 3:
data.resize(pad_size, pad_size, pad_size / 2 + 1);
break;
default:
REPORT_ERROR("Projector::resizeData%%ERROR: Dimension of the data array should be 2 or 3");
}
// Set origin in the y.z-center, but on the left side for x.
data.setXmippOrigin();
data.xinit=0;
}
void read(int argc, char **argv)
{
parser.setCommandLine(argc, argv);
int general_section = parser.addSection("General Options");
fn_unt = parser.getOption("--u", "STAR file with the untilted xy-coordinates");
fn_til = parser.getOption("--t", "STAR file with the untilted xy-coordinates");
size = textToInteger(parser.getOption("--size", "Largest dimension of the micrograph (in pixels), e.g. 4096"));
dim = textToInteger(parser.getOption("--dim", "Dimension of boxed particles (for EMAN .box files in pixels)", "200"));
acc = textToFloat(parser.getOption("--acc", "Allowed accuracy (in pixels), e.g. half the particle diameter"));
tilt = textToFloat(parser.getOption("--tilt", "Fix tilt angle (in degrees)", "99999."));
rot = textToFloat(parser.getOption("--rot", "Fix direction of the tilt axis (in degrees), 0 = along y, 90 = along x", "99999."));
do_opt = !parser.checkOption("--dont_opt", "Skip optimization of the transformation matrix");
mind2 = ROUND(acc * acc);
int angle_section = parser.addSection("Specified tilt axis and translational search ranges");
tilt0 = textToFloat(parser.getOption("--tilt0", "Minimum tilt angle (in degrees)","0."));
tiltF = textToFloat(parser.getOption("--tiltF", "Maximum tilt angle (in degrees)","99999."));
if (tiltF == 99999.) tiltF = tilt0;
tiltStep = textToFloat(parser.getOption("--tiltStep", "Tilt angle step size (in degrees)","1."));
rot0 = textToFloat(parser.getOption("--rot0", "Minimum rot angle (in degrees)","0."));
rotF = textToFloat(parser.getOption("--rotF", "Maximum rot angle (in degrees)","99999."));
if (rotF == 99999.) rotF = rot0;
rotStep = textToFloat(parser.getOption("--rotStep", "Rot angle step size (in degrees)","1."));
x0 = textToInteger(parser.getOption("--x0", "Minimum X offset (pixels)","-99999"));
xF = textToInteger(parser.getOption("--xF", "Maximum X offset (pixels)","99999"));
xStep = textToInteger(parser.getOption("--xStep", "X offset step size (pixels)","-1"));
y0 = textToInteger(parser.getOption("--y0", "Minimum Y offset (pixels)","-99999"));
yF = textToInteger(parser.getOption("--yF", "Maximum Y offset (pixels)","99999"));
yStep = textToInteger(parser.getOption("--yStep", "Y offset step size (pixels)","-1"));
// Check for errors in the command-line option
if (parser.checkForErrors())
REPORT_ERROR("Errors encountered on the command line, exiting...");
// If tilt and rot were given: do not search those
if (tilt != 99999.)
{
tilt0 = tiltF = tilt;
tiltStep = 1.;
}
if (rot != 99999.)
{
rot0 = rotF = rot;
rotStep = 1.;
}
// By default search the entire micrograph
x0 = XMIPP_MAX(x0, -size);
xF = XMIPP_MIN(xF, size);
// By default use a xStep of one third the accuracy
if (xStep < 0)
xStep = acc / 3;
// By default treat y search in the same way as the x-search
if (y0 == -99999)
y0 = x0;
if (yF == 99999)
yF = xF;
if (yStep < 0)
yStep = xStep;
// Done reading, now fill p_unt and p_til
MDunt.read(fn_unt);
MDtil.read(fn_til);
// Check for the correct labels
if (!MDunt.containsLabel(EMDL_IMAGE_COORD_X) || !MDunt.containsLabel(EMDL_IMAGE_COORD_Y))
REPORT_ERROR("ERROR: Untilted STAR file does not contain the rlnCoordinateX or Y labels");
if (!MDtil.containsLabel(EMDL_IMAGE_COORD_X) || !MDtil.containsLabel(EMDL_IMAGE_COORD_Y))
REPORT_ERROR("ERROR: Tilted STAR file does not contain the rlnCoordinateX or Y labels");
double x, y;
p_unt.clear();
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDunt)
{
MDunt.getValue(EMDL_IMAGE_COORD_X, x);
MDunt.getValue(EMDL_IMAGE_COORD_Y, y);
p_unt.push_back((int)x);
p_unt.push_back((int)y);
}
p_til.clear();
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDtil)
{
MDtil.getValue(EMDL_IMAGE_COORD_X, x);
MDtil.getValue(EMDL_IMAGE_COORD_Y, y);
p_til.push_back((int)x);
p_til.push_back((int)y);
}
// Initialize best transformation params
best_x = best_y = 9999;
best_rot = best_tilt = 9999.;
}
//#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;
}
//#define DEBUG
double spatial_Bspline03_proj(
const Matrix1D<double> &r, const Matrix1D<double> &u)
{
// Avoids divisions by zero and allows orthogonal rays computation
static Matrix1D<double> ur(3);
if (XX(u) == 0) XX(ur) = XMIPP_EQUAL_ACCURACY;
else XX(ur) = XX(u);
if (YY(u) == 0) YY(ur) = XMIPP_EQUAL_ACCURACY;
else YY(ur) = YY(u);
if (ZZ(u) == 0) ZZ(ur) = XMIPP_EQUAL_ACCURACY;
else ZZ(ur) = ZZ(u);
// Some precalculated variables
double x_sign = SGN(XX(ur));
double y_sign = SGN(YY(ur));
double z_sign = SGN(ZZ(ur));
// Compute the minimum and maximum alpha for the ray
double alpha_xmin = (-2 - XX(r)) / XX(ur);
double alpha_xmax = (2 - XX(r)) / XX(ur);
double alpha_ymin = (-2 - YY(r)) / YY(ur);
double alpha_ymax = (2 - YY(r)) / YY(ur);
double alpha_zmin = (-2 - ZZ(r)) / ZZ(ur);
double alpha_zmax = (2 - ZZ(r)) / ZZ(ur);
double alpha_min = XMIPP_MAX(XMIPP_MIN(alpha_xmin, alpha_xmax),
XMIPP_MIN(alpha_ymin, alpha_ymax));
alpha_min = XMIPP_MAX(alpha_min, XMIPP_MIN(alpha_zmin, alpha_zmax));
double alpha_max = XMIPP_MIN(XMIPP_MAX(alpha_xmin, alpha_xmax),
XMIPP_MAX(alpha_ymin, alpha_ymax));
alpha_max = XMIPP_MIN(alpha_max, XMIPP_MAX(alpha_zmin, alpha_zmax));
if (alpha_max - alpha_min < XMIPP_EQUAL_ACCURACY) return 0.0;
#ifdef DEBUG
std::cout << "Pixel: " << r.transpose() << std::endl
<< "Dir: " << ur.transpose() << std::endl
<< "Alpha x:" << alpha_xmin << " " << alpha_xmax << std::endl
<< " " << (r + alpha_xmin*ur).transpose() << std::endl
<< " " << (r + alpha_xmax*ur).transpose() << std::endl
<< "Alpha y:" << alpha_ymin << " " << alpha_ymax << std::endl
<< " " << (r + alpha_ymin*ur).transpose() << std::endl
<< " " << (r + alpha_ymax*ur).transpose() << std::endl
<< "Alpha z:" << alpha_zmin << " " << alpha_zmax << std::endl
<< " " << (r + alpha_zmin*ur).transpose() << std::endl
<< " " << (r + alpha_zmax*ur).transpose() << std::endl
<< "alpha :" << alpha_min << " " << alpha_max << std::endl
<< std::endl;
#endif
// Compute the first point in the volume intersecting the ray
static Matrix1D<double> v(3);
V3_BY_CT(v, ur, alpha_min);
V3_PLUS_V3(v, r, v);
#ifdef DEBUG
std::cout << "First entry point: " << v.transpose() << std::endl;
std::cout << " Alpha_min: " << alpha_min << std::endl;
#endif
// Follow the ray
double alpha = alpha_min;
double ray_sum = 0;
do
{
double alpha_x = (XX(v) + x_sign - XX(r)) / XX(ur);
double alpha_y = (YY(v) + y_sign - YY(r)) / YY(ur);
double alpha_z = (ZZ(v) + z_sign - ZZ(r)) / ZZ(ur);
// Which dimension will ray move next step into?, it isn't neccesary to be only
// one.
double diffx = ABS(alpha - alpha_x);
double diffy = ABS(alpha - alpha_y);
double diffz = ABS(alpha - alpha_z);
double diff_alpha = XMIPP_MIN(XMIPP_MIN(diffx, diffy), diffz);
ray_sum += spatial_Bspline03_integral(r, ur, alpha, alpha + diff_alpha);
// Update alpha and the next entry point
if (ABS(diff_alpha - diffx) <= XMIPP_EQUAL_ACCURACY) alpha = alpha_x;
if (ABS(diff_alpha - diffy) <= XMIPP_EQUAL_ACCURACY) alpha = alpha_y;
if (ABS(diff_alpha - diffz) <= XMIPP_EQUAL_ACCURACY) alpha = alpha_z;
XX(v) += diff_alpha * XX(ur);
YY(v) += diff_alpha * YY(ur);
ZZ(v) += diff_alpha * ZZ(ur);
#ifdef DEBUG
std::cout << "Alpha x,y,z: " << alpha_x << " " << alpha_y
<< " " << alpha_z << " ---> " << alpha << std::endl;
std::cout << " Next entry point: " << v.transpose() << std::endl
<< " diff_alpha: " << diff_alpha << std::endl
<< " ray_sum: " << ray_sum << std::endl
<< " Alfa tot: " << alpha << "alpha_max: " << alpha_max <<
std::endl;
#endif
}
while ((alpha_max - alpha) > XMIPP_EQUAL_ACCURACY);
return ray_sum;
}
//#define DEBUG
void normalize_tomography(MultidimArray<double> &I, double tilt, double &mui,
double &sigmai, bool tiltMask, bool tomography0,
double mu0, double sigma0)
{
// Tilt series are always 2D
I.checkDimension(2);
const int L=2;
// Build a mask using the tilt angle
I.setXmippOrigin();
MultidimArray<int> mask;
mask.initZeros(I);
int Xdimtilt=(int)XMIPP_MIN(FLOOR(0.5*(XSIZE(I)*cos(DEG2RAD(tilt)))),
0.5*(XSIZE(I)-(2*L+1)));
int N=0;
for (int i=STARTINGY(I); i<=FINISHINGY(I); i++)
for (int j=-Xdimtilt; j<=Xdimtilt;j++)
{
A2D_ELEM(mask,i,j)=1;
N++;
}
// Estimate the local variance
MultidimArray<double> localVariance;
localVariance.initZeros(I);
double meanVariance=0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(I)
{
// Center a mask of size 5x5 and estimate the variance within the mask
double meanPiece=0, variancePiece=0;
double Npiece=0;
for (int ii=i-L; ii<=i+L; ii++)
{
if (INSIDEY(I,ii))
for (int jj=j-L; jj<=j+L; jj++)
{
if (INSIDEX(I,jj))
{
double pixval=A2D_ELEM(I,ii,jj);
meanPiece+=pixval;
variancePiece+=pixval*pixval;
++Npiece;
}
}
}
meanPiece/=Npiece;
variancePiece=variancePiece/(Npiece-1)-
Npiece/(Npiece-1)*meanPiece*meanPiece;
A2D_ELEM(localVariance,i,j)=variancePiece;
meanVariance+=variancePiece;
}
meanVariance*=1.0/N;
// Test the hypothesis that the variance in this piece is
// the same as the variance in the whole image
double iFu=1/icdf_FSnedecor(4*L*L+4*L,N-1,0.975);
double iFl=1/icdf_FSnedecor(4*L*L+4*L,N-1,0.025);
double iMeanVariance=1.0/meanVariance;
FOR_ALL_ELEMENTS_IN_ARRAY2D(localVariance)
{
if (A2D_ELEM(localVariance,i,j)==0)
A2D_ELEM(mask,i,j)=-2;
if (A2D_ELEM(mask,i,j)==1)
{
double ratio=A2D_ELEM(localVariance,i,j)*iMeanVariance;
double thl=ratio*iFu;
double thu=ratio*iFl;
if (thl>1 || thu<1)
A2D_ELEM(mask,i,j)=-1;
}
}
#ifdef DEBUG
Image<double> save;
save()=I;
save.write("PPP.xmp");
save()=localVariance;
save.write("PPPLocalVariance.xmp");
Image<int> savemask;
savemask()=mask;
savemask.write("PPPmask.xmp");
#endif
// Compute the statistics again in the reduced mask
double avg, stddev, min, max;
computeStats_within_binary_mask(mask, I, min, max, avg, stddev);
double cosTilt=cos(DEG2RAD(tilt));
double iCosTilt=1.0/cosTilt;
if (tomography0)
{
double iadjustedStddev=1.0/(sigma0*cosTilt);
FOR_ALL_ELEMENTS_IN_ARRAY2D(I)
switch (A2D_ELEM(mask,i,j))
{
case -2:
A2D_ELEM(I,i,j)=0;
break;
case 0:
if (tiltMask)
A2D_ELEM(I,i,j)=0;
else
A2D_ELEM(I,i,j)=(A2D_ELEM(I,i,j)*iCosTilt-mu0)*iadjustedStddev;
break;
case -1:
case 1:
A2D_ELEM(I,i,j)=(A2D_ELEM(I,i,j)*iCosTilt-mu0)*iadjustedStddev;
break;
}
}
else
{
void busca()
{
static float f[22][22];
float pi = 3.141592653;
short in1, mu5, i, mu3, ind, ind1, indice, iflag, j, ix=0, iy=0, k;
float h, th, costh, sinth, fi, anc, xk0, yk0, hpi, x, y, z, xx, yy;
float b, g, d1, e1, ext;
int count = 0;
suaviza();
in = XMIPP_MIN(in, 10);
mu1 = mu - 1;
m = 2 * mu;
mu4 = mu * ncic;
mt = 2 * m;
ntot = mt * ncic;
ntot4 = ntot + mu4 + ncic;
zzz0 = ntot;
ncic2 = 2 * ncic;
in1 = in + 1;
h = 2. * pi / ntot;
idz = 2 - ntot;
th = ncic * h;
costh = cos(th);
sinth = sin(th);
b = 2. / (th * th) * (1. + costh * costh - sin(2. * th) / th);
g = 4. / (th * th) * (sinth / th - costh);
d1 = 2. * th / 45.;
e1 = d1 * sinth * 2.;
d1 *= sin(2. * th);
mu5 = mu4 - 1;
for (i = 1; i <= mu5; i++)
{
fi = i * h;
coseno[i] = sin(fi);
}
coseno[mu4] = 1.;
mu3 = 2 * mu4;
for (i = 1; i <= mu5; i++)
{
coseno[mu3-i] = coseno[i];
coseno[mu3+i] = -coseno[i];
coseno[ntot-i] = -coseno[i];
coseno[ntot+i] = coseno[i];
}
coseno[mu3] = 0.;
coseno[mu3+mu4] = -1.;
coseno[ntot] = 0.;
coseno[ntot+mu4] = 1.;
ind = 2 * in + 1;
ind1 = ind - 1;
indice = 0;
iflag = 0;
e9:
if (indice >= ni)
goto e10;
if (iflag == 2)
goto e22;
anc = (int)(3. + in * del);
xk0 = xc0;
yk0 = yc0;
rh = XMIPP_MIN(rh, r2);
rh = XMIPP_MIN(rh, xk0 - anc - 1.);
rh = XMIPP_MIN(rh, yk0 - anc - 1.);
rh = XMIPP_MIN(rh, largo - xk0 - anc);
rh = XMIPP_MIN(rh, lancho - yk0 - anc);
ir = (int)((rh - r1) / r3 + 1);
hpi = h / 2. / pi / ir;
cxp1 = 2. * b * e1 * hpi;
cxp2 = -2. * g * d1 * hpi;
cxp3 = 2. * (g * e1 - b * d1) * hpi;
cxm1 = (b * b + e1 * e1) * hpi;
cxm2 = (g * g + d1 * d1) * hpi;
cxm3 = 2. * (b * g - d1 * e1) * hpi;
/* if(iflag == 1) goto 21 */
if (iflag == 2)
goto e22;
x = xc0 - in * del;
for (i = 1; i <= ind; i++) /* do 5 */
{ y = yc0 - in * del;
for (j = 1; j <= ind; j++) /*do 4 */
{ ergrot(x, y, &z);
/* printf ("%10.3f%10.3f%10.5f%10.3f%10.3f AA\n", x,y,z,del,rh);*/
printf(".");
fflush(stdout);
z = 100. + indmul * z;
f[i][j] = z;
y += del;
}
x += del;
}
// Introduced by Sjors dd 28.9.2004 to avoid infinite loops
count++;
if (count > 1000)
goto s1;
e23:
ext = -1000000.;
for (i = 1; i <= ind; i++) /* do 7 */
for (j = 1; j <= ind; j++) /* do 7 */
{ if (f[i][j] > ext)
{
ix = i;
iy = j;
ext = f[i][j];
}
}
xc0 = xc0 + (ix - in - 1) * del;
yc0 = yc0 + (iy - in - 1) * del;
if (ix == 1 || ix == ind || iy == 1 || iy == ind)
goto e8;
del /= in;
iflag = 2;
indice++;
goto e9;
e8:
iflag = 1;
goto e9;
e22:
f[1][1] = f[ix-1][iy-1];
f[ind][1] = f[ix+1][iy-1];
f[1][ind] = f[ix-1][iy+1];
f[ind][ind] = f[ix+1][iy+1];
f[1][in1] = f[ix-1][iy];
f[in1][1] = f[ix][iy-1];
f[ind][in1] = f[ix+1][iy];
f[in1][ind] = f[ix][iy+1];
f[in1][in1] = f[ix][iy];
x = xc0 - (in - 1) * del;
for (i = 2; i < ind1; i++) /* do 11 */
{ y = yc0 - (in - 1) * del;
for (j = 2;j <= ind1; j++) /* do 12 */
{ if (i == in1 && j == in1)
goto e13;
ergrot(x, y, &z);
/* printf ("%10.3f%10.3f%10.5f%10.3f BB \n", x,y,z,del);*/
printf(".");
fflush(stdout);
z = 100. + indmul * z;
f[i][j] = z;
e13:
y += del;
}
x += del;
}
x = xc0 - (in - 1) * del;
y = yc0 - (in - 1) * del;
for (k = 2; k <= ind1; k++) /* do 16 */
{ if (k == in1)
goto e17;
xx = xc0 - in * del;
ergrot(xx, y, &z);
/* printf ("%10.3f%10.3f%10.5f%10.3f CC \n", xx,y,z,del);*/
printf(".");
fflush(stdout);
z = 100. + indmul * z;
f[1][k] = z;
yy = yc0 - in * del;
ergrot(x, yy, &z);
/* printf ("%10.3f%10.3f%10.5f%10.3f DD \n", xx,y,z,del);*/
printf(".");
fflush(stdout);
z = 100. + indmul * z;
f[k][1] = z;
xx = xc0 + in * del;
ergrot(xx, y, &z);
/* printf ("%10.3f%10.3f%10.5f%10.3f EE \n", xx,y,z,del);*/
printf(".");
fflush(stdout);
z = 100. + indmul * z;
f[ind][k] = z;
yy = yc0 + in * del;
ergrot(x, yy, &z);
/* printf ("%10.3f%10.3f%10.5f%10.3f FF\n", x,yy,z,del);*/
printf(".");
fflush(stdout);
z = 100. + indmul * z;
f[k][ind] = z;
e17:
x += del;
y += del;
}
goto e23;
e10:
std::cout << "\nOptimal center coordinates: x= " << yc0-1 << " ,y= " << xc0-1 << " " << std::endl;
return;
s1:
yc0=xc0=-1;
printf("\nNot-converged\n");
return;
}
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
}
