void ParticleSorterMpi::run()
{
int total_nr_images = MDin.numberOfObjects();
features.resize(total_nr_images, NR_FEATURES);
// Each node does part of the work
long int my_first_image, my_last_image, my_nr_images;
divide_equally(total_nr_images, node->size, node->rank, my_first_image, my_last_image);
my_nr_images = my_last_image - my_first_image + 1;
int barstep;
if (verb > 0)
{
std::cout << "Calculating sorting features for all input particles..." << std::endl;
init_progress_bar(my_nr_images);
barstep = XMIPP_MAX(1, my_nr_images/ 60);
}
long int ipart = 0;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDin)
{
if (ipart >= my_first_image && ipart <= my_last_image)
{
if (verb > 0 && ipart % barstep == 0)
progress_bar(ipart);
calculateFeaturesOneParticle(ipart);
}
ipart++;
}
if (verb > 0)
progress_bar(my_nr_images);
// Combine results from all nodes
MultidimArray<double> allnodes_features;
allnodes_features.resize(features);
MPI_Allreduce(MULTIDIM_ARRAY(features), MULTIDIM_ARRAY(allnodes_features), MULTIDIM_SIZE(features), MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
features = allnodes_features;
// Only the master writes out files
if (verb > 0)
{
normaliseFeatures();
writeFeatures();
}
}
void ParticlePolisherMpi::polishParticlesAllMicrographs()
{
if (!do_start_all_over && exists(fn_out + ".star"))
{
if (verb > 0)
std::cout << std::endl << " + " << fn_out << ".star already exists: skipping polishing of the particles." << std::endl;
return;
}
int total_nr_micrographs = exp_model.average_micrographs.size();
// Each node does part of the work
long int my_first_micrograph, my_last_micrograph, my_nr_micrographs;
divide_equally(total_nr_micrographs, node->size, node->rank, my_first_micrograph, my_last_micrograph);
my_nr_micrographs = my_last_micrograph - my_first_micrograph + 1;
// Loop over all average micrographs
int barstep;
if (verb > 0)
{
std::cout << " + Write out polished particles for all micrographs ... " << std::endl;
init_progress_bar(my_nr_micrographs);
barstep = XMIPP_MAX(1, my_nr_micrographs/ 60);
}
for (long int i = my_first_micrograph; i <= my_last_micrograph; i++)
{
if (verb > 0 && i % barstep == 0)
progress_bar(i);
polishParticlesOneMicrograph(i);
}
if (verb > 0)
progress_bar(my_nr_micrographs);
if (node->isMaster())
writeStarFilePolishedParticles();
MPI_Barrier(MPI_COMM_WORLD);
}
void run()
{
// Get angles ==============================================================
MetaData angles;
angles.read(fnIn);
size_t AngleNo = angles.size();
if (AngleNo == 0 || !angles.containsLabel(MDL_ANGLE_ROT))
REPORT_ERROR(ERR_MD_BADLABEL, "Input file doesn't contain angular information");
double maxWeight = -99.e99;
MultidimArray<double> weight;
weight.initZeros(AngleNo);
if (angles.containsLabel(MDL_WEIGHT))
{
// Find maximum weight
int i=0;
FOR_ALL_OBJECTS_IN_METADATA(angles)
{
double w;
angles.getValue(MDL_WEIGHT,w,__iter.objId);
DIRECT_A1D_ELEM(weight,i++)=w;
maxWeight=XMIPP_MAX(w,maxWeight);
}
}
void MpiProgImageRotationalPCA::createMutexes(size_t Nimgs)
{
fileMutex = new MpiFileMutex(node);
threadMutex = new Mutex();
taskDistributor = new MpiTaskDistributor(Nimgs, XMIPP_MAX(1,Nimgs/(5*node->size)), node);
}
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.;
}
double optimiseTransformationMatrix(bool do_optimise_nr_pairs)
{
std::vector<int> best_pairs_t2u, best_map;
double score, best_score, best_dist=9999.;
if (do_optimise_nr_pairs)
best_score = 0.;
else
best_score = -999999.;
int nn = XMIPP_MAX(1., (rotF-rot0)/rotStep);
nn *= XMIPP_MAX(1., (tiltF-tilt0)/tiltStep);
nn *= XMIPP_MAX(1., (xF-x0)/xStep);
nn *= XMIPP_MAX(1., (yF-y0)/yStep);
int n = 0;
init_progress_bar(nn);
for (double rot = rot0; rot <= rotF; rot+= rotStep)
{
for (double tilt = tilt0; tilt <= tiltF; tilt+= tiltStep)
{
// Assume tilt-axis lies in-plane...
double psi = -rot;
// Rotate all points correspondingly
Euler_angles2matrix(rot, tilt, psi, Pass);
//std::cerr << " Pass= " << Pass << std::endl;
// Zero-translations for now (these are added in the x-y loops below)
MAT_ELEM(Pass, 0, 2) = MAT_ELEM(Pass, 1, 2) = 0.;
mapOntoTilt();
for (int x = x0; x <= xF; x += xStep)
{
for (int y = y0; y <= yF; y += yStep, n++)
{
if (do_optimise_nr_pairs)
score = getNumberOfPairs(x, y);
else
score = -getAverageDistance(x, y); // negative because smaller distance is better!
bool is_best = false;
if (do_optimise_nr_pairs && score==best_score)
{
double dist = getAverageDistance(x, y);
if (dist < best_dist)
{
best_dist = dist;
is_best = true;
}
}
if (score > best_score || is_best)
{
best_score = score;
best_pairs_t2u = pairs_t2u;
best_rot = rot;
best_tilt = tilt;
best_x = x;
best_y = y;
}
if (n%1000==0) progress_bar(n);
}
}
}
}
progress_bar(nn);
// Update pairs with the best_pairs
if (do_optimise_nr_pairs)
pairs_t2u = best_pairs_t2u;
// Update the Passing matrix and the mapping
Euler_angles2matrix(best_rot, best_tilt, -best_rot, Pass);
// Zero-translations for now (these are added in the x-y loops below)
MAT_ELEM(Pass, 0, 2) = MAT_ELEM(Pass, 1, 2) = 0.;
mapOntoTilt();
return best_score;
}
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;
}
//#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;
}
// Fit the beam-induced translations for all average micrographs
void ParticlePolisherMpi::fitMovementsAllMicrographs()
{
int total_nr_micrographs = exp_model.average_micrographs.size();
// Each node does part of the work
long int my_first_micrograph, my_last_micrograph, my_nr_micrographs;
divide_equally(total_nr_micrographs, node->size, node->rank, my_first_micrograph, my_last_micrograph);
my_nr_micrographs = my_last_micrograph - my_first_micrograph + 1;
// Loop over all average micrographs
int barstep;
if (verb > 0)
{
std::cout << " + Fitting straight paths for beam-induced movements in all micrographs ... " << std::endl;
init_progress_bar(my_nr_micrographs);
barstep = XMIPP_MAX(1, my_nr_micrographs/ 60);
}
for (long int i = my_first_micrograph; i <= my_last_micrograph; i++)
{
if (verb > 0 && i % barstep == 0)
progress_bar(i);
fitMovementsOneMicrograph(i);
}
// Wait until all micrographs have been done
MPI_Barrier(MPI_COMM_WORLD);
if (verb > 0)
{
progress_bar(my_nr_micrographs);
}
// Combine results from all nodes
MultidimArray<DOUBLE> allnodes_fitted_movements;
allnodes_fitted_movements.resize(fitted_movements);
MPI_Allreduce(MULTIDIM_ARRAY(fitted_movements), MULTIDIM_ARRAY(allnodes_fitted_movements), MULTIDIM_SIZE(fitted_movements), MY_MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
fitted_movements = allnodes_fitted_movements;
// Set the fitted movements in the xoff and yoff columns of the exp_model.MDimg
for (long int ipart = 0; ipart < exp_model.numberOfParticles(); ipart++)
{
long int part_id = exp_model.particles[ipart].id;
DOUBLE xoff = DIRECT_A2D_ELEM(fitted_movements, part_id, 0);
DOUBLE yoff = DIRECT_A2D_ELEM(fitted_movements, part_id, 1);
exp_model.MDimg.setValue(EMDL_ORIENT_ORIGIN_X, xoff, part_id);
exp_model.MDimg.setValue(EMDL_ORIENT_ORIGIN_Y, yoff, part_id);
}
if (node->isMaster())
{
// Write out the STAR file with all the fitted movements
FileName fn_tmp = fn_in.withoutExtension() + "_" + fn_out + ".star";
exp_model.MDimg.write(fn_tmp);
std::cout << " + Written out all fitted movements in STAR file: " << fn_tmp << std::endl;
}
}
void ParticlePolisherMpi::optimiseBeamTilt()
{
// This function assumes the shiny particles are in exp_mdel.MDimg!!
if (beamtilt_max <= 0. && defocus_shift_max <= 0.)
return;
if (minres_beamtilt < maxres_model)
{
if (verb > 0)
std::cout << " Skipping beamtilt correction, as the resolution of the shiny reconstruction does not go beyond minres_beamtilt of " << minres_beamtilt << " Ang." << std::endl;
return;
}
getBeamTiltGroups();
initialiseSquaredDifferenceVectors();
int total_nr_micrographs = exp_model.micrographs.size();
// Each node does part of the work
long int my_first_micrograph, my_last_micrograph, my_nr_micrographs;
divide_equally(total_nr_micrographs, node->size, node->rank, my_first_micrograph, my_last_micrograph);
my_nr_micrographs = my_last_micrograph - my_first_micrograph + 1;
// Loop over all average micrographs
int barstep;
if (verb > 0)
{
std::cout << " + Optimising beamtilts and/or defocus values in all micrographs ... " << std::endl;
init_progress_bar(my_nr_micrographs);
barstep = XMIPP_MAX(1, my_nr_micrographs/ 60);
}
for (long int i = my_first_micrograph; i <= my_last_micrograph; i++)
{
if (verb > 0 && i % barstep == 0)
progress_bar(i);
optimiseBeamTiltAndDefocusOneMicrograph(i);
}
if (verb > 0)
progress_bar(my_nr_micrographs);
// Combine results from all nodes
if (beamtilt_max > 0.)
{
MultidimArray<DOUBLE> allnodes_diff2_beamtilt;
allnodes_diff2_beamtilt.initZeros(diff2_beamtilt);
MPI_Allreduce(MULTIDIM_ARRAY(diff2_beamtilt), MULTIDIM_ARRAY(allnodes_diff2_beamtilt), MULTIDIM_SIZE(diff2_beamtilt), MY_MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
diff2_beamtilt = allnodes_diff2_beamtilt;
}
if (defocus_shift_max > 0.)
{
MultidimArray<DOUBLE> allnodes_defocus_shift_allmics;
allnodes_defocus_shift_allmics.initZeros(defocus_shift_allmics);
MPI_Allreduce(MULTIDIM_ARRAY(defocus_shift_allmics), MULTIDIM_ARRAY(allnodes_defocus_shift_allmics), MULTIDIM_SIZE(defocus_shift_allmics), MY_MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
defocus_shift_allmics = allnodes_defocus_shift_allmics;
}
// Now get the final optimised beamtilts and defocus shifts, and write results to the MetadataTable
applyOptimisedBeamTiltsAndDefocus();
// Write the new MDTable to disc
if (verb > 0)
exp_model.MDimg.write(fn_out + ".star");
}
//majorAxis and minorAxis is the estimated particle size in px
void ProgSortByStatistics::processInprocessInputPrepareSPTH(MetaData &SF, bool trained)
{
//#define DEBUG
PCAMahalanobisAnalyzer tempPcaAnalyzer0;
PCAMahalanobisAnalyzer tempPcaAnalyzer1;
PCAMahalanobisAnalyzer tempPcaAnalyzer2;
PCAMahalanobisAnalyzer tempPcaAnalyzer3;
PCAMahalanobisAnalyzer tempPcaAnalyzer4;
//Morphology
tempPcaAnalyzer0.clear();
//Signal to noise ratio
tempPcaAnalyzer1.clear();
tempPcaAnalyzer2.clear();
tempPcaAnalyzer3.clear();
//Histogram analysis, to detect black points and saturated parts
tempPcaAnalyzer4.clear();
double sign = 1;//;-1;
int numNorm = 3;
int numDescriptors0=numNorm;
int numDescriptors2=4;
int numDescriptors3=11;
int numDescriptors4 = 10;
MultidimArray<float> v0(numDescriptors0);
MultidimArray<float> v2(numDescriptors2);
MultidimArray<float> v3(numDescriptors3);
MultidimArray<float> v4(numDescriptors4);
if (verbose>0)
{
std::cout << " Sorting particle set by new xmipp method..." << std::endl;
}
int nr_imgs = SF.size();
if (verbose>0)
init_progress_bar(nr_imgs);
int c = XMIPP_MAX(1, nr_imgs / 60);
int imgno = 0, imgnoPCA=0;
bool thereIsEnable=SF.containsLabel(MDL_ENABLED);
bool first=true;
// We assume that at least there is one particle
size_t Xdim, Ydim, Zdim, Ndim;
getImageSize(SF,Xdim,Ydim,Zdim,Ndim);
//Initialization:
MultidimArray<double> nI, modI, tempI, tempM, ROI;
MultidimArray<bool> mask;
nI.resizeNoCopy(Ydim,Xdim);
modI.resizeNoCopy(Ydim,Xdim);
tempI.resizeNoCopy(Ydim,Xdim);
tempM.resizeNoCopy(Ydim,Xdim);
mask.resizeNoCopy(Ydim,Xdim);
mask.initConstant(true);
MultidimArray<double> autoCorr(2*Ydim,2*Xdim);
MultidimArray<double> smallAutoCorr;
Histogram1D hist;
Matrix2D<double> U,V,temp;
Matrix1D<double> D;
MultidimArray<int> radial_count;
MultidimArray<double> radial_avg;
Matrix1D<int> center(2);
MultidimArray<int> distance;
int dim;
center.initZeros();
v0.initZeros(numDescriptors0);
v2.initZeros(numDescriptors2);
v3.initZeros(numDescriptors3);
v4.initZeros(numDescriptors4);
ROI.resizeNoCopy(Ydim,Xdim);
ROI.setXmippOrigin();
FOR_ALL_ELEMENTS_IN_ARRAY2D(ROI)
{
double temp = std::sqrt(i*i+j*j);
if ( temp < (Xdim/2))
A2D_ELEM(ROI,i,j)= 1;
else
A2D_ELEM(ROI,i,j)= 0;
}
Image<double> img;
FourierTransformer transformer(FFTW_BACKWARD);
FOR_ALL_OBJECTS_IN_METADATA(SF)
{
if (thereIsEnable)
{
int enabled;
SF.getValue(MDL_ENABLED,enabled,__iter.objId);
if ( (enabled==-1) )
{
imgno++;
continue;
}
}
img.readApplyGeo(SF,__iter.objId);
if (targetXdim!=-1 && targetXdim!=XSIZE(img()))
selfScaleToSize(LINEAR,img(),targetXdim,targetXdim,1);
MultidimArray<double> &mI=img();
mI.setXmippOrigin();
mI.statisticsAdjust(0,1);
mask.setXmippOrigin();
//The size of v1 depends on the image size and must be declared here
int numDescriptors1 = XSIZE(mI)/2; //=100;
MultidimArray<float> v1(numDescriptors1);
v1.initZeros(numDescriptors1);
double var = 1;
normalize(transformer,mI,tempI,modI,0,var,mask);
modI.setXmippOrigin();
tempI.setXmippOrigin();
nI = sign*tempI*(modI*modI);
tempM = (modI*modI);
A1D_ELEM(v0,0) = (tempM*ROI).sum();
int index = 1;
var+=2;
while (index < numNorm)
{
normalize(transformer,mI,tempI,modI,0,var,mask);
modI.setXmippOrigin();
tempI.setXmippOrigin();
nI += sign*tempI*(modI*modI);
tempM += (modI*modI);
A1D_ELEM(v0,index) = (tempM*ROI).sum();
index++;
var+=2;
}
nI /= tempM;
tempPcaAnalyzer0.addVector(v0);
nI=(nI*ROI);
auto_correlation_matrix(mI,autoCorr);
if (first)
{
radialAveragePrecomputeDistance(autoCorr, center, distance, dim);
first=false;
}
fastRadialAverage(autoCorr, distance, dim, radial_avg, radial_count);
for (int n = 0; n < numDescriptors1; ++n)
A1D_ELEM(v1,n)=(float)DIRECT_A1D_ELEM(radial_avg,n);
tempPcaAnalyzer1.addVector(v1);
#ifdef DEBUG
//String name = "000005@Images/Extracted/run_002/extra/BPV_1386.stk";
String name = "000010@Images/Extracted/run_001/extra/KLH_Dataset_I_Training_0028.stk";
//String name = "001160@Images/Extracted/run_001/DefaultFamily5";
std::cout << img.name() << std::endl;
if (img.name()==name2)
{
FileName fpName = "test_1.txt";
mI.write(fpName);
fpName = "test_2.txt";
nI.write(fpName);
fpName = "test_3.txt";
tempM.write(fpName);
fpName = "test_4.txt";
ROI.write(fpName);
//exit(1);
}
#endif
nI.binarize(0);
int im = labelImage2D(nI,nI,8);
compute_hist(nI, hist, 0, im, im+1);
size_t l;
int k,i,j;
hist.maxIndex(l,k,i,j);
A1D_ELEM(hist,j)=0;
hist.maxIndex(l,k,i,j);
nI.binarizeRange(j-1,j+1);
double x0=0,y0=0,majorAxis=0,minorAxis=0,ellipAng=0;
size_t area=0;
fitEllipse(nI,x0,y0,majorAxis,minorAxis,ellipAng,area);
A1D_ELEM(v2,0)=majorAxis/((img().xdim) );
A1D_ELEM(v2,1)=minorAxis/((img().xdim) );
A1D_ELEM(v2,2)= (fabs((img().xdim)/2-x0)+fabs((img().ydim)/2-y0))/((img().xdim)/2);
A1D_ELEM(v2,3)=area/( (double)((img().xdim)/2)*((img().ydim)/2) );
for (int n=0 ; n < numDescriptors2 ; n++)
{
if ( std::isnan(std::abs(A1D_ELEM(v2,n))))
A1D_ELEM(v2,n)=0;
}
tempPcaAnalyzer2.addVector(v2);
//mI.setXmippOrigin();
//auto_correlation_matrix(mI*ROI,autoCorr);
//auto_correlation_matrix(nI,autoCorr);
autoCorr.window(smallAutoCorr,-5,-5, 5, 5);
smallAutoCorr.copy(temp);
svdcmp(temp,U,D,V);
for (int n = 0; n < numDescriptors3; ++n)
A1D_ELEM(v3,n)=(float)VEC_ELEM(D,n); //A1D_ELEM(v3,n)=(float)VEC_ELEM(D,n)/VEC_ELEM(D,0);
tempPcaAnalyzer3.addVector(v3);
double minVal=0.;
double maxVal=0.;
mI.computeDoubleMinMax(minVal,maxVal);
compute_hist(mI, hist, minVal, maxVal, 100);
for (int n=0 ; n <= numDescriptors4-1 ; n++)
{
A1D_ELEM(v4,n)= (hist.percentil((n+1)*10));
}
tempPcaAnalyzer4.addVector(v4);
#ifdef DEBUG
if (img.name()==name1)
{
FileName fpName = "test.txt";
mI.write(fpName);
fpName = "test3.txt";
nI.write(fpName);
}
#endif
imgno++;
imgnoPCA++;
if (imgno % c == 0 && verbose>0)
progress_bar(imgno);
}
tempPcaAnalyzer0.evaluateZScore(2,20,trained);
tempPcaAnalyzer1.evaluateZScore(2,20,trained);
tempPcaAnalyzer2.evaluateZScore(2,20,trained);
tempPcaAnalyzer3.evaluateZScore(2,20,trained);
tempPcaAnalyzer4.evaluateZScore(2,20,trained);
pcaAnalyzer.push_back(tempPcaAnalyzer0);
pcaAnalyzer.push_back(tempPcaAnalyzer1);
pcaAnalyzer.push_back(tempPcaAnalyzer1);
pcaAnalyzer.push_back(tempPcaAnalyzer3);
pcaAnalyzer.push_back(tempPcaAnalyzer4);
}
void ProgSortByStatistics::processInputPrepare(MetaData &SF)
{
PCAMahalanobisAnalyzer tempPcaAnalyzer;
tempPcaAnalyzer.clear();
Image<double> img;
MultidimArray<double> img2;
MultidimArray<int> radial_count;
MultidimArray<double> radial_avg;
Matrix1D<int> center(2);
center.initZeros();
if (verbose>0)
std::cout << " Processing training set ..." << std::endl;
int nr_imgs = SF.size();
if (verbose>0)
init_progress_bar(nr_imgs);
int c = XMIPP_MAX(1, nr_imgs / 60);
int imgno = 0, imgnoPCA=0;
MultidimArray<float> v;
MultidimArray<int> distance;
int dim;
bool thereIsEnable=SF.containsLabel(MDL_ENABLED);
bool first=true;
FOR_ALL_OBJECTS_IN_METADATA(SF)
{
if (thereIsEnable)
{
int enabled;
SF.getValue(MDL_ENABLED,enabled,__iter.objId);
if (enabled==-1)
continue;
}
img.readApplyGeo(SF,__iter.objId);
if (targetXdim!=-1 && targetXdim!=XSIZE(img()))
selfScaleToSize(LINEAR,img(),targetXdim,targetXdim,1);
MultidimArray<double> &mI=img();
mI.setXmippOrigin();
mI.statisticsAdjust(0,1);
// Overall statistics
Histogram1D hist;
compute_hist(mI,hist,-4,4,31);
// Radial profile
img2.resizeNoCopy(mI);
FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(img2)
{
double val=DIRECT_MULTIDIM_ELEM(mI,n);
DIRECT_MULTIDIM_ELEM(img2,n)=val*val;
}
if (first)
{
radialAveragePrecomputeDistance(img2, center, distance, dim);
first=false;
}
fastRadialAverage(img2, distance, dim, radial_avg, radial_count);
// Build vector
v.initZeros(XSIZE(hist)+XSIZE(img2)/2);
int idx=0;
FOR_ALL_DIRECT_ELEMENTS_IN_ARRAY1D(hist)
v(idx++)=(float)DIRECT_A1D_ELEM(hist,i);
for (size_t i=0; i<XSIZE(img2)/2; i++)
v(idx++)=(float)DIRECT_A1D_ELEM(radial_avg,i);
tempPcaAnalyzer.addVector(v);
if (imgno % c == 0 && verbose>0)
progress_bar(imgno);
imgno++;
imgnoPCA++;
}
if (verbose>0)
progress_bar(nr_imgs);
MultidimArray<double> vavg,vstddev;
tempPcaAnalyzer.computeStatistics(vavg,vstddev);
tempPcaAnalyzer.evaluateZScore(2,20,false);
pcaAnalyzer.insert(pcaAnalyzer.begin(), tempPcaAnalyzer);
}
// 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 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);
}