int
main (int argc, char **argv)
{
VERBOSE = 1;
struct params p;
processArgsAnalyze (argc, argv, p);
gsl_matrix *atomsNonCrop = ReadFitsImg_gsl_matrix (p.atomsfile);
//gsl_matrix *noatoms = ReadFitsImg_gsl_matrix (p.noatomsfile);
gsl_matrix *atoms = cropImage (p.reportfile, atomsNonCrop);
//gsl_matrix *cnoatoms = cropImage (p.reportfile, noatoms);
double com[2];
COM (atoms, com);
cout << "COM_X = " << com[0] << endl;
cout << "COM_Y = " << com[1] << endl;
setINI_num (p.reportfile, "CPP", "COM_X", com[0]);
setINI_num (p.reportfile, "CPP", "COM_Y", com[1]);
gsl_matrix_free (atomsNonCrop);
gsl_matrix_free (atoms);
}
int
main (int argc, char **argv)
{
struct params p;
processArgsBasler (argc, argv, p);
VERBOSE = p.verbose;
Basler *b = new Basler (&p);
b->LoadFLUOR ();
b->ComputeColumnDensity ();
b->Fit2DGauss ();
setINI_num (p.reportfile, "FLUORCPP", "offset",
b->gaus2dfit[5] * b->GetNPixels ());
double nfit = b->gaus2dfit[4] * 3.14159 * b->gaus2dfit[1] * b->gaus2dfit[3];
double peakd = b->gaus2dfit[4] / (pow (M_PI * b->gaus2dfit[1] * b->gaus2dfit[3], 0.5)) / pow (p.magnif, 3); // cm^-3
setINI_num (p.reportfile, "FLUORCPP", "nfit", nfit);
setINI_num (p.reportfile, "FLUORCPP", "peakd", peakd);
setINI_num (p.reportfile, "FLUORCPP", "ax0w", b->gaus2dfit[1] * p.magnif);
setINI_num (p.reportfile, "FLUORCPP", "ax1w", b->gaus2dfit[3] * p.magnif);
setINI_num (p.reportfile, "FLUORCPP", "ax0w_err",
b->gaus2dfit_err[1] * p.magnif);
setINI_num (p.reportfile, "FLUORCPP", "ax1w_err",
b->gaus2dfit_err[3] * p.magnif);
setINI_num (p.reportfile, "FLUORCPP", "ax0c", b->abs_ci);
setINI_num (p.reportfile, "FLUORCPP", "ax1c", b->abs_cj);
cout << p.
shotnum << " nfit = " << nfit << setprecision (3) << " , peakd = " <<
peakd << " , sizes = (" << b->gaus2dfit[1] *
p.
magnif << " +/- " << b->gaus2dfit_err[1] *
p.magnif << "," << b->gaus2dfit[3] *
p.magnif << " +/- " << b->gaus2dfit_err[3] *
p.
magnif << ") , center = (" << setiosflags (ios::
fixed) << setprecision (0) <<
b->abs_ci << "," << b->abs_cj << ")" << endl;
cout << resetiosflags (ios::fixed) << setprecision (6);
// f->ComputeRadialAxialDensity ();
return EXIT_SUCCESS;
}
int
main (int argc, char **argv)
{
struct params p;
processArgsAnalyze (argc, argv, p);
VERBOSE = p.verbose;
init_params (&p);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "phcdet", p.det);
Fermions *f = new Fermions (&p);
f->LoadFITS (); // LoadFITS already computes the column density
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "maxOD", f->maxOD);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "maxPHI", f->maxPHI);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "maxPHCSIG",
f->maxPHCSIG);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "maxCD", f->maxCD);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "maxI", f->maxI);
if (p.onlyCD)
{
f->SaveColumnDensity ();
return EXIT_SUCCESS;
}
// f->FindMoments ();
if (!p.keeproi)
{
f->MinimalCrop (5.0);
}
f->Fit2DGauss (p.gaus2d_mott);
f->SaveColumnDensity ();
if (!p.keeproi)
{
f->MinimalCrop (3.5);
f->Fit2DGauss ();
f->SaveColumnDensity ();
}
// f->FitScatt2DGauss ();
// f->FitProbe2DGauss ();
//Get center of cloud with respect to the Andor full frame
f->abs_ci += f->gaus2dfit[0];
f->abs_cj += f->gaus2dfit[2];
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "offset",
f->gaus2dfit[5] * f->GetNPixels ());
if (p.gaus2d_mott)
{
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "nfit_mott",
f->nfit_mott);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "r0_mott",
f->gaus2dfit_mott[5]);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "peakd_mott",
f->peakd_mott);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax0w_mott",
f->gaus2dfit_mott[1] * p.magnif);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax1w_mott",
f->gaus2dfit_mott[3] * p.magnif);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax0c_mott",
f->abs_ci - f->gaus2dfit[0] + f->gaus2dfit_mott[0]);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax1c_mott",
f->abs_cj - f->gaus2dfit[2] + f->gaus2dfit_mott[2]);
}
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "nfit", f->nfit);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "nfit_err",
f->nfit_err);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "peakd", f->peakd);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "peakd_sph",
f->peakd_sph);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax0w",
f->gaus2dfit[1] * p.magnif);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax1w",
f->gaus2dfit[3] * p.magnif);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax0c", f->abs_ci);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ax1c", f->abs_cj);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "TF", f->TF);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ph_per_at",
f->Tsp / f->nfit);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "peak_cd",
f->gaus2dfit[4]);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "photons_in_pulse",
f->Tp0);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "alphastar",
p.alphastar);
f->GetAzimuthalAverageEllipse ();
if (p.fermiazimuth)
{
//f->GetAzimuthalAverage ();
f->FitAzimuthalFermi ();
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "n0_az", f->n0_az);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "BetaMu_az",
f->BetaMu_az);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "r_az", f->r_az);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "B_az", f->B_az);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "mx_az", f->mx_az);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "TF_az", f->TF_az);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "T_az", f->T_az);
}
if (p.fermi2d)
{
f->Fit2DFermi ();
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "n0_Fermi", f->n0);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "BetaMU_Fermi",
f->BetaMu);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ri_Fermi",
f->ri_Fermi);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "rj_Fermi",
f->rj_Fermi);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "ci_Fermi",
f->ci_Fermi);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "cj_Fermi",
f->cj_Fermi);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "B_Fermi",
f->B_Fermi);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "TF_2d", f->TF_2d);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "T_2d_rd",
f->T_2d_rd);
setINI_num (p.reportfile, p.andor2 ? "CPP2" : "CPP", "T_2d_ax",
f->T_2d_ax);
}
if (p.fitfermi1D || p.fermiazimuth || p.fermi2d || true)
{
f->ComputeIntegrated1DDensity ();
f->MakePlots ();
}
printf ("%s %sN = %.2e%s", p.shotnum.c_str (), KCYN, f->nfit, KNRM);
//Print number
if (f->nfit_err * 50. > f->nfit)
{
printf
("\nNumber determination uncertainty might be too high: N = %.2e +/- %.0e\n",
f->nfit, f->nfit_err);
}
if (!p.phc && !p.fluor)
{
//Print number from scattered photons
//printf (", Nsp = %.2e", f->Nsp);
//Print total number of photons in probe pulse
//printf (", Ph = %.2e", f->Tp0);
//Print average number of photons scattered per atom
printf (", Ph/At = %.0f", f->Tsp / f->nfit);
//Print peak density
printf (", n = %.2e", f->peakd);
//Print peak density
printf (", %sn_sph = %.2e%s", KMAG, f->peakd_sph, KNRM);
//Print axial size
printf (", ax0w = %.1f +/- %.1f", f->gaus2dfit[1] * p.magnif,
f->gaus2dfit_err[1] * p.magnif);
//Print center
printf (", %sc = (%.0f,%.0f)%s", KGRN, f->abs_ci, f->abs_cj, KNRM);
//Print max intensity
//printf (", Imax = %.2f", f->maxI);
//Print max intensity smoothed
//printf (", Imax(smoothed) = %.2f", f->maxIsmooth);
//Print average intensity
//printf (", Iave = %.2f", f->aveI);
//Print average intensity
printf (", I/Isat = %.2f", f->aveIweighted);
//Print max optical density
printf (", ODmax = %.1f", f->maxOD);
//Print max column density
printf (", CDmax = %.1f", f->maxCD);
}
else if (p.fluor || p.Nframes == 2)
{
printf (", MAX Counts/Px = %.1f", f->maxCD);
//Print axial size
printf (", ax0w = %.1f +/- %.1f", f->gaus2dfit[1] * p.magnif,
f->gaus2dfit_err[1] * p.magnif);
//Print center
printf (", c = (%.0f,%.0f)", f->abs_ci, f->abs_cj);
//Print range of counts in atoms and noatoms frames
printf (", atoms:(%d to %d), noatoms:(%d to %d)", (int) f->minCA,
(int) f->maxCA, (int) f->minCN, (int) f->maxCN);
}
else
{
//Print total number of photons in probe pulse
printf (", Ph = %.2e", f->Tp0);
//Print peak density
printf (", n = %.2e", f->peakd);
//Print peak density
printf (", %sn_sph = %.2e%s", KMAG, f->peakd_sph, KNRM);
//Print axial size
printf (", ax0w = %.1f +/- %.1f", f->gaus2dfit[1] * p.magnif,
f->gaus2dfit_err[1] * p.magnif);
//Print center
printf (", %sc = (%.0f,%.0f)%s", KGRN, f->abs_ci, f->abs_cj, KNRM);
//Print max intensity
//printf (", Imax = %.2f", f->maxI);
//Print average intensity
printf (", I/Isat = %.2f", f->aveIweighted);
//Print max phase shift
printf (", PHImax = %.3f", f->maxPHI);
//Print max phase-contrast signal
printf (", SIGmax = %.3f", f->maxPHCSIG);
//Print max column density
printf (", CDmax = %.1f", f->maxCD);
//Print sqrt(N)/n parameter
printf (", %ssqrt(N)/n = %.2e%s", KYEL, sqrt (f->nfit) / f->peakd_sph,
KNRM);
}
// printf
// ("%s N = %.2e +/- %.0e, n = %.2e , ax0w = %.1f +/- %.1f, c = (%.0f,%.0f), I_max = %.2f, OD_max = %.1f",
// p.shotnum.c_str (), f->nfit, f->nfit_err, f->peakd,
// f->wi_1e * p.magnif, f->gaus2dfit_err[1] * p.magnif, f->abs_ci,
// f->abs_cj, f->maxI, f->maxOD);
if (p.fermi2d)
printf (", T/TF_2d = %.2f, z = %.2f, f(z) = %.2f", f->TF_2d,
f->Fugacity_Fermi, f->f_Fermi);
if (p.fermiazimuth)
printf (", T/TF_az = %.2f, z = %.2f, f(z) = %.2f", f->TF_az,
f->Fugacity_az, f->f_az);
printf ("\n");
/*
double pos[2];
double cts = img_counts (signal);
double peak = img_peak (signal, pos);
setINI_num (p.reportfile, p.andor2?"CPP2":"CPP", "peak", peak);
setINI_num (p.reportfile, p.andor2?"CPP2":"CPP", "ipeak", pos[0]);
setINI_num (p.reportfile, p.andor2?"CPP2":"CPP", "jpeak", pos[1]);
cout << "#" << p.
shotnum << " Counts=" << img_counts (signal) << " Peak=" << peak << endl;
*/
return EXIT_SUCCESS;
}
