void initialise()
{
// Get the MDs for both untilted and tilted particles
MDu.read(fn_unt);
MDt.read(fn_til);
if (MDu.numberOfObjects() != MDt.numberOfObjects())
REPORT_ERROR("Tiltpair plot ERROR: untilted and tilted STAR files have unequal number of entries.");
// Get the symmetry point group
int pgGroup, pgOrder;
SL.isSymmetryGroup(fn_sym, pgGroup, pgOrder);
SL.read_sym_file(fn_sym);
// Make postscript header
fh_eps.open(fn_eps.c_str(), std::ios::out);
if (!fh_eps)
REPORT_ERROR("Tiltpair plot ERROR: Cannot open " + fn_eps + " for output");
fh_eps << "%%!PS-Adobe-2.0\n";
fh_eps << "%% Creator: Tilt pair analysis \n";
fh_eps << "%% Pages: 1\n";
fh_eps << "0 setgray\n";
fh_eps << "0.1 setlinewidth\n";
// Draw circles on postscript: 250pixels=plot_max_tilt
fh_eps << "300 400 83 0 360 arc closepath stroke\n";
fh_eps << "300 400 167 0 360 arc closepath stroke\n";
fh_eps << "300 400 250 0 360 arc closepath stroke\n";
fh_eps << "300 150 newpath moveto 300 650 lineto stroke\n";
fh_eps << "50 400 newpath moveto 550 400 lineto stroke\n";
}
void run()
{
EMDLabel label1, label2, label3;
MD1.read(fn1);
MD2.read(fn2);
label1 = EMDL::str2Label(fn_label1);
label2 = (fn_label2 == "") ? EMDL_UNDEFINED : EMDL::str2Label(fn_label2);
label3 = (fn_label3 == "") ? EMDL_UNDEFINED : EMDL::str2Label(fn_label3);
compareMetaDataTable(MD1, MD2, MDboth, MDonly1, MDonly2, label1, eps, label2, label3);
std::cout << MDboth.numberOfObjects() << " entries occur in both input STAR files." << std::endl;
std::cout << MDonly1.numberOfObjects() << " entries occur only in the 1st input STAR file." << std::endl;
std::cout << MDonly2.numberOfObjects() << " entries occur only in the 2nd input STAR file." << std::endl;
if (fn_both != "")
MDboth.write(fn_both);
if (fn_only1 != "")
MDonly1.write(fn_only1);
if (fn_only2 != "")
MDonly2.write(fn_only2);
}
void correctMapForMTF(MultidimArray<Complex >& FT, int ori_size, FileName& fn_mtf)
{
MetaDataTable MDmtf;
if (!fn_mtf.isStarFile())
{
REPORT_ERROR("correctMapForMTF ERROR: input MTF file is not a STAR file.");
}
MDmtf.read(fn_mtf);
MultidimArray<double> mtf_resol, mtf_value;
mtf_resol.resize(MDmtf.numberOfObjects());
mtf_value.resize(mtf_resol);
int i = 0;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDmtf)
{
MDmtf.getValue(EMDL_RESOLUTION_INVPIXEL, DIRECT_A1D_ELEM(mtf_resol, i)); // resolution needs to be given in 1/pix
MDmtf.getValue(EMDL_POSTPROCESS_MTF_VALUE, DIRECT_A1D_ELEM(mtf_value, i));
if (DIRECT_A1D_ELEM(mtf_value, i) < 1e-10)
{
std::cerr << " i= " << i << " mtf_value[i]= " << DIRECT_A1D_ELEM(mtf_value, i) << std::endl;
REPORT_ERROR("Postprocessing::sharpenMap ERROR: zero or negative values encountered in MTF curve!");
}
i++;
}
double xsize = (double)ori_size;
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM(FT)
{
int r2 = kp * kp + ip * ip + jp * jp;
double res = sqrt((double)r2) / xsize; // get resolution in 1/pixel
if (res < 0.5)
{
// Find the suitable MTF value
int i_0 = 0;
for (int ii = 0; ii < XSIZE(mtf_resol); ii++)
{
if (DIRECT_A1D_ELEM(mtf_resol, ii) > res)
{
break;
}
i_0 = ii;
}
// linear interpolation: y = y_0 + (y_1 - y_0)*(x-x_0)/(x1_x0)
double mtf;
double x_0 = DIRECT_A1D_ELEM(mtf_resol, i_0);
if (i_0 == MULTIDIM_SIZE(mtf_resol) - 1 || i_0 == 0) // check boundaries of the array
{
mtf = DIRECT_A1D_ELEM(mtf_value, i_0);
}
else
{
double x_1 = DIRECT_A1D_ELEM(mtf_resol, i_0 + 1);
double y_0 = DIRECT_A1D_ELEM(mtf_value, i_0);
double y_1 = DIRECT_A1D_ELEM(mtf_value, i_0 + 1);
mtf = y_0 + (y_1 - y_0) * (res - x_0) / (x_1 - x_0);
}
// Divide Fourier component by the MTF
DIRECT_A3D_ELEM(FT, k, i, j) /= mtf;
}
}
}
void Postprocessing::divideByMtf(MultidimArray<Complex > &FT)
{
if (fn_mtf != "")
{
if (verb > 0)
{
std::cout << "== Dividing map by the MTF of the detector ..." << std::endl;
std::cout.width(35); std::cout << std::left <<" + mtf STAR-file: "; std::cout << fn_mtf << std::endl;
}
MetaDataTable MDmtf;
if (!fn_mtf.isStarFile())
REPORT_ERROR("Postprocessing::divideByMtf ERROR: input MTF file is not a STAR file.");
MDmtf.read(fn_mtf);
MultidimArray<DOUBLE> mtf_resol, mtf_value;
mtf_resol.resize(MDmtf.numberOfObjects());
mtf_value.resize(mtf_resol);
int i =0;
FOR_ALL_OBJECTS_IN_METADATA_TABLE(MDmtf)
{
MDmtf.getValue(EMDL_RESOLUTION_INVPIXEL, DIRECT_A1D_ELEM(mtf_resol, i) ); // resolution needs to be given in 1/pix
MDmtf.getValue(EMDL_POSTPROCESS_MTF_VALUE, DIRECT_A1D_ELEM(mtf_value, i) );
if (DIRECT_A1D_ELEM(mtf_value, i) < 1e-10)
{
std::cerr << " i= " << i << " mtf_value[i]= " << DIRECT_A1D_ELEM(mtf_value, i) << std::endl;
REPORT_ERROR("Postprocessing::sharpenMap ERROR: zero or negative values encountered in MTF curve!");
}
i++;
}
DOUBLE xsize = (DOUBLE)XSIZE(I1());
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM(FT)
{
int r2 = kp * kp + ip * ip + jp * jp;
DOUBLE res = sqrt((DOUBLE)r2)/xsize; // get resolution in 1/pixel
if (res < 0.5 )
{
// Find the suitable MTF value
int i_0 = 0;
for (int ii = 0; ii < XSIZE(mtf_resol); ii++)
{
if (DIRECT_A1D_ELEM(mtf_resol, ii) > res)
break;
i_0 = ii;
}
// linear interpolation: y = y_0 + (y_1 - y_0)*(x-x_0)/(x1_x0)
DOUBLE mtf;
DOUBLE x_0 = DIRECT_A1D_ELEM(mtf_resol, i_0);
if (i_0 == MULTIDIM_SIZE(mtf_resol) - 1 || i_0 == 0) // check boundaries of the array
mtf = DIRECT_A1D_ELEM(mtf_value, i_0);
else
{
DOUBLE x_1 = DIRECT_A1D_ELEM(mtf_resol, i_0 + 1);
DOUBLE y_0 = DIRECT_A1D_ELEM(mtf_value, i_0);
DOUBLE y_1 = DIRECT_A1D_ELEM(mtf_value, i_0 + 1);
mtf = y_0 + (y_1 - y_0)*(res - x_0)/(x_1 - x_0);
}
// Divide Fourier component by the MTF
DIRECT_A3D_ELEM(FT, k, i, j) /= mtf;
}
}
}
}
