//! Return the signal to noise ratio
float Pulsar::AdaptiveSNR::get_snr (const Profile* profile)
{
Reference::To<PhaseWeight> baseline;
if (baseline_estimator)
baseline = baseline_estimator->operate (profile);
else
baseline = profile->baseline();
Estimate<double> mean = baseline->get_mean();
Estimate<double> variance = baseline->get_variance();
unsigned nbin = profile->get_nbin();
unsigned off_pulse = baseline->get_nonzero_weight_count();
unsigned on_pulse = nbin - off_pulse;
double energy = profile->sum() - mean.val * nbin;
double snr = energy / sqrt(variance.val*on_pulse);
if (Profile::verbose)
{
double rms = sqrt (variance.val);
cerr << "Pulsar::AdaptiveSNR::get_snr " << off_pulse << " out of " << nbin
<< " bins in baseline\n mean=" << mean << " rms=" << rms
<< " energy=" << energy << " S/N=" << snr << endl;
}
if (energy < 0)
return 0.0;
return snr;
}
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();
}
void Pulsar::RemoveBaseline::Each::transform (Archive* archive)
{
const unsigned nsub = archive->get_nsubint();
const unsigned nchan = archive->get_nchan();
const unsigned npol = archive->get_npol();
bool pscrunch = (archive->get_state() == Signal::Coherence ||
archive->get_state() == Signal::PPQQ);
for (unsigned isub=0; isub < nsub; isub++)
{
Integration* subint = archive->get_Integration (isub);
for (unsigned ichan=0; ichan < nchan; ichan++)
{
Reference::To<Profile> profile = subint->get_Profile (0,ichan);
if (pscrunch)
{
profile = profile->clone();
profile->sum (subint->get_Profile (1,ichan));
}
Reference::To<PhaseWeight> baseline = profile->baseline();
for (unsigned ipol=0; ipol < npol; ipol++)
{
Profile* p = subint->get_Profile(ipol, ichan);
baseline->set_Profile (p);
p->offset (-baseline->get_mean().val);
}
}
}
};
void Pulsar::ComponentModel::fit (const Profile *profile)
{
build ();
unsigned nbin = profile->get_nbin();
vector<float> data (nbin);
float mean = 0.0;
float variance = 1.0;
if (fit_derivative)
{
vector<complex<float> > spec(nbin/2+2);
// FFT
FTransform::frc1d(nbin, (float*)&spec[0], profile->get_amps());
unsigned ic, nc=nbin/2+1;
float scale = 1.0/nbin;
for (ic=0; ic < nc; ic++)
spec[ic] *= complex<float>(0.0f, ic) // scale by i*frequency
* scale; // correction for DFT normalisation
// IFFT
FTransform::bcr1d (nbin, &data[0], (float*)&spec[0]);
}
else // normal profile
{
Reference::To<PhaseWeight> baseline = profile->baseline();
variance = baseline->get_variance().get_value();
mean = baseline->get_mean().get_value();
if (verbose)
cerr << "Pulsar::ComponentModel::fit mean=" << mean
<< " variance=" << variance << endl;
// copy data
for (unsigned i=0; i < nbin; i++)
data[i] = profile->get_amps()[i] - mean;
}
Axis<double> argument;
model->set_argument (0, &argument);
vector< Axis<double>::Value > xval;
vector< Estimate<double> > yval;
unsigned nfree = 0;
for (unsigned i=0; i < nbin; i++)
{
double radians = (i+0.5)/nbin * 2*M_PI;
xval.push_back( argument.get_Value(radians) );
yval.push_back( Estimate<double>(data[i], variance) );
nfree ++;
}
for (unsigned i=0; i<model->get_nparam(); i++)
if (model->get_infit(i))
{
if (nfree == 0)
throw Error (InvalidState, "Pulsar::ComponentModel::fit",
"more free parameters than data");
nfree --;
}
// fit
LevenbergMarquardt<double> fit;
fit.verbose = Function::verbose;
chisq = fit.init (xval, yval, *model);
// fit.singular_threshold = 1e-15; // dodge covariance problems
unsigned iter = 1;
unsigned not_improving = 0;
string result = "RMS";
if (variance)
result = "chisq";
unsigned max_iter = 100;
while (not_improving < 25 && iter < max_iter)
{
if (verbose)
cerr << "iteration " << iter;
float nchisq = fit.iter (xval, yval, *model);
if (verbose)
cerr << " " << result << " = " << nchisq << endl;
if (nchisq < chisq)
{
float diffchisq = chisq - nchisq;
chisq = nchisq;
not_improving = 0;
if (diffchisq/chisq < threshold && diffchisq > 0)
{
if (verbose)
cerr << "converged, delta " << result << " = " << diffchisq << endl;
break;
}
}
else
not_improving ++;
iter ++;
}
std::vector<std::vector<double> > covar;
fit.result (*model, covar);
for (unsigned iparam=0; iparam < model->get_nparam(); iparam++)
{
double variance = covar[iparam][iparam];
if (verbose)
cerr << "Pulsar::ComponentModel::fit"
" variance[" << iparam << "]=" << variance << endl;
if (!finite(variance))
throw Error (InvalidState,
"Pulsar::ComponentModel::fit",
"non-finite variance "
+ model->get_param_name(iparam));
if (!model->get_infit(iparam) && variance != 0)
throw Error (InvalidState,
"Pulsar::ComponentModel::fit",
"non-zero unfit variance "
+ model->get_param_name(iparam)
+ " = " + tostring(variance) );
if (variance < 0)
throw Error (InvalidState,
"Pulsar::ComponentModel::fit",
"invalid variance " + model->get_param_name(iparam)
+ " = " + tostring(variance) );
// cerr << iparam << ".var=" << variance << endl;
model->set_variance (iparam, variance);
}
if (fit_derivative) // copy best-fit parameters back
{
for (unsigned icomp=0; icomp < components.size(); icomp++)
{
components[icomp]->set_centre(derivative[icomp]->get_centre());
components[icomp]->set_concentration
(derivative[icomp]->get_concentration());
components[icomp]->set_height(derivative[icomp]->get_height());
}
}
}