Tempo::toa Pulsar::ArrivalTime::get_toa (Estimate<double>& shift,
const Pulsar::Integration* subint,
unsigned ichan)
{
Tempo::toa toa (format);
// phase shift in turns
toa.set_phase_shift (shift.get_value());
// topocentric folding period
double period = subint->get_folding_period();
// epoch of the integration (rise time of bin 0 in each profile)
MJD epoch = subint->get_epoch ();
// arrival time
toa.set_arrival (epoch + shift.get_value() * period);
// arrival time error in microseconds
toa.set_error (shift.get_error() * period * 1e6);
if (subint->get_dedispersed())
toa.set_frequency (subint->get_centre_frequency());
else
toa.set_frequency (subint->get_centre_frequency(ichan));
toa.set_channel (ichan);
// would like to see this go somewhere else
if (format == Tempo::toa::Parkes || format == Tempo::toa::Psrclock)
toa.set_auxilliary_text( tostring(ichan) );
return toa;
}
Estimate<double> Pulsar::FourierDomainFit::get_shift () const
{
Profile prfcopy = *observation;
Reference::To<Profile> obs_p = &prfcopy;
if (error_method=="mcmc")
fit.set_error_method(ProfileShiftFit::MCMC_Variance);
else if (error_method=="trad")
fit.set_error_method(ProfileShiftFit::Traditional_Chi2);
else if (error_method=="num")
fit.set_error_method(ProfileShiftFit::Numerical);
else
throw Error (InvalidParam, "Pulsar::FourierDomainFit::get_shift",
"Uncertainty method '" + error_method + "' not known");
fit.set_Profile(obs_p);
fit.compute();
reduced_chisq = fit.get_reduced_chisq();
snr = fit.get_snr();
// Change shift range from 0->1 to -0.5->0.5
Estimate<double> result = fit.get_shift();
if (result.get_value() > 0.5) { result -= 1.0; }
return result;
}
void Pulsar::LastHarmonic::build ()
{
if (!profile)
throw Error (InvalidState, "Pulsar::LastHarmonic::build",
"Profile not set");
if (!baseline_estimator)
throw Error (InvalidState, "Pulsar::LastHarmonic::build",
"Baseline estimator not set");
Reference::To<PhaseWeight> baseline = baseline_estimator->baseline (profile);
Estimate<double> mean = baseline->get_mean ();
Estimate<double> var = baseline->get_variance ();
Estimate<double> rms = sqrt(var);
#ifdef _DEBUG
cerr << "Pulsar::LastHarmonic::build mean=" << mean
<< " rms=" << rms << endl;
#endif
significant.find (profile, rms.get_value());
// skip the DC term
bin_rise = 1;
bin_fall = significant.get();
}
//! Set the Stokes parameters of the model
void MEAL::ModeCoherency::set_stokes (const Stokes<Estimate<double> >& stokes)
{
if (stokes[0].get_value() <= 0.0)
throw Error (InvalidParam, "MEAL::ModeCoherency::set_stokes",
"total intensity I=%lf <= 0", stokes[0].get_value());
Estimate<double> p = stokes.abs_vect() / stokes[0];
if (p.get_value() >= 1)
throw Error (InvalidParam, "MEAL::ModeCoherency::set_stokes",
"degree of polarization p=%lf >= 1", p.get_value());
if (p.get_value() == 0.0)
throw Error (InvalidParam, "MEAL::ModeCoherency::set_stokes",
"degree of polarization p==0");
log_intensity->set_value ( log( 0.5 * stokes[0] * sqrt(1-p*p) ) );
log_beta->set_value ( log(atanh(p)) );
axis->set_vector (stokes.get_vector());
}
void Pulsar::ComponentModel::align (const Profile *profile)
{
Profile modelprof(*profile);
evaluate (modelprof.get_amps(), modelprof.get_nbin());
Estimate<double> shift = profile->shift (modelprof);
if (verbose)
cerr << "Pulsar::ComponentModel::align shift=" << shift << endl;
if (phase)
{
float normalization = profile->sum() / modelprof.sum();
if (verbose)
cerr << "Pulsar::ComponentModel::align normalization="
<< normalization << endl;
for (unsigned icomp=0; icomp < components.size(); icomp++)
{
Estimate<double> height = components[icomp]->get_height();
components[icomp]->set_height ( height * normalization );
}
phase->set_value (phase->get_value() + shift.get_value() * 2*M_PI);
return;
}
// Dick requires this
cout << setprecision(6) << fixed << "Shift= " << shift.val << endl;
for (unsigned icomp=0; icomp < components.size(); icomp++)
{
Estimate<double> centre = components[icomp]->get_centre() + shift * 2*M_PI;
if (centre.val >= M_PI)
centre -= 2*M_PI;
if (centre.val < -M_PI)
centre += 2*M_PI;
components[icomp]->set_centre(centre);
}
}
/* returns the phase shift and scale that aligns the profile with the model */
void Pulsar::ComponentModel::get_best_alignment (const Profile* profile, double& the_phase, double& the_scale)
{
Profile modelprof (profile->get_nbin());
if (verbose)
cerr << "Pulsar::ComponentModel::get_best_alignment calling evaluate" << endl;
evaluate (modelprof.get_amps(), modelprof.get_nbin());
Estimate<double> shift = profile->shift (modelprof);
if (verbose)
cerr << "Pulsar::ComponentModel::get_best_alignment shift=" << shift << endl;
the_phase = shift.get_value();
the_scale = profile->sum() / modelprof.sum();
if (verbose)
cerr << "Pulsar::ComponentModel::get_best_alignment scale=" << the_scale << endl;
}
void psrflux::process (Pulsar::Archive* archive)
{
// Convert to total intensity
archive->convert_state(Signal::Intensity);
// Set self-standard if needed
if (stdfile=="") set_standard(archive);
// Test for single-profile data
bool single_profile = archive->get_nsubint()==1 && archive->get_nchan()==1;
// Access to the flux computation
StandardFlux *flux = dynamic_cast<StandardFlux*>(ds.get_flux_method().get());
// If shifts not fit, need to dedisperse and possibly align total
// with standard.
if (noalign) {
archive->dedisperse();
flux->set_fit_shift(false);
} else if (align==false && single_profile==false) {
archive->dedisperse();
Reference::To<Archive> arch_tot = archive->total();
Estimate<double> shift =
arch_tot->get_Profile(0,0,0)->shift(stdarch->get_Profile(0,0,0));
stdarch->get_Profile(0,0,0)->rotate_phase(-1.0*shift.get_value());
flux->set_fit_shift(false);
} else {
flux->set_fit_shift(true);
}
// Compute DS
ds.set_Archive(archive);
ds.compute();
// Unload archive with .sm extension
std::string outf = archive->get_filename() + "." + ext;
cerr << "psrflux: unloading " << outf << endl;
ds.unload(outf, command);
}
