void psrspa::matched_finder ( const Archive* arch )
{
string name = arch->get_filename ();
for ( unsigned isub = 0; isub < arch->get_nsubint(); isub++ )
{
Reference::To<Profile> profile = arch->get_Profile(isub,0,0)->clone();
while (profile->get_nbin() > 256)
{
finder->set_Profile( profile ); // might finder optimize on &profile?
PhaseWeight weight;
finder->get_weight( &weight );
matched_report (name, isub, weight, *profile);
profile->bscrunch (2);
}
}
}
void Pulsar::SpectrumPlot::get_spectra (const Archive* data)
{
unsigned nchan = data->get_nchan();
spectra.resize(1);
spectra[0].resize(nchan);
Reference::To<ProfileStats> stats;
Reference::To<TextInterface::Parser> parser;
if (!expression.empty())
{
stats = new ProfileStats;
parser = stats->get_interface ();
}
Reference::To<const Integration> subint;
subint = get_Integration (data, isubint);
for (unsigned ichan=0; ichan<nchan; ichan++)
{
Reference::To<const Profile> profile;
profile = get_Profile (subint, ipol, ichan);
if (profile -> get_weight() == 0.0)
spectra[0][ichan] = 0.0;
else if (stats)
{
stats->set_Profile (profile);
string value = process( parser, expression );
spectra[0][ichan] = fromstring<float>( value );
}
else if (ibin.get_integrate())
spectra[0][ichan] = profile->sum() / (float)profile->get_nbin();
else
spectra[0][ichan] = profile->get_amps()[ibin.get_value()];
}
}
void psrpca::finalize ()
{
arrival->set_observation ( total );
arrival->get_toas(toas);
if ( remove_std_baseline )
std_archive -> remove_baseline ();
Reference::To<Profile> std_prof = std_archive->get_Profile(0, 0, 0);
float *s_amps = std_prof->get_amps ();
const float nbin = std_prof->get_nbin ();
double scale, offset, snr;
if ( total_count < nbin )
cerr << "WARNING: psrpca::finalize - not enough observations provided, "
"covariance matrix will not have full rank" << endl;
//total->remove_baseline();
gsl_matrix *profiles = gsl_matrix_alloc ( (unsigned)nbin, total_count );
for (unsigned i_subint = 0; i_subint < total->get_nsubint(); i_subint++ )
{
Reference::To<Profile> prof = total->get_Profile ( i_subint, 0, 0 );
if ( apply_shift )
prof->rotate_phase ( toas[i_subint].get_phase_shift() );
snr = prof->snr ();
//calculate the scale
float *p_amps = prof->get_amps ();
scale = 0.0;
for ( unsigned i_bin = 0; i_bin < nbin; i_bin++ )
{
scale += s_amps[i_bin] * p_amps[i_bin];
}
scale = (prof->get_nbin()* scale - prof->sum() * std_prof->sum()) /
(prof->get_nbin()* std_prof->sumsq() - std_prof->sum() * std_prof->sum());
// calculate the baseline offset
offset = (scale * std_prof->sum() - prof->sum()) / nbin;
if ( prof_to_std )
{
//match the profile to standard and subtract the standard
if ( apply_offset )
prof->offset ( offset );
if ( apply_scale )
prof->scale ( 1.0/scale );
prof->diff ( std_prof );
double* damps;
damps = new double [ (unsigned)nbin ];
transform( prof->get_amps(), prof->get_amps() + (unsigned)nbin, damps, CastToDouble() );
gsl_vector_const_view view = gsl_vector_const_view_array( damps, nbin );
gsl_matrix_set_col ( profiles, i_subint, &view.vector );
t_cov->add_Profile ( prof, snr );
}
else
{// prof_to_std is false
Reference::To<Profile> diff = prof->clone ();
diff->set_amps ( std_prof->get_amps () );
if ( apply_offset )
diff->offset( -offset );
if ( apply_scale )
diff->scale (scale);
diff->diff ( prof );
diff->scale (-1);
double* damps;
damps = new double [ (unsigned)nbin ];
transform( diff->get_amps(), diff->get_amps() + (unsigned)nbin, damps, CastToDouble() );
gsl_vector_const_view view = gsl_vector_const_view_array( damps, nbin );
gsl_matrix_set_col ( profiles, i_subint, &view.vector );
t_cov->add_Profile ( diff, snr );
prof->set_amps ( diff->get_amps() );
}
}
covariance = gsl_matrix_alloc ( (int) nbin, (int) nbin );
t_cov->get_covariance_matrix_gsl ( covariance );
// write the covariance matrix and difference profiles
FILE *out;
if ( save_covariance_matrix )
{
out = fopen ( (prefix+"_covariance.dat").c_str(), "w" );
gsl_matrix_fprintf(out, covariance, "%g");
fclose ( out );
} // save covariance matrix
if ( save_diffs )
total->unload ( prefix+"_diffs.ar" );
//solve the eigenproblem
gsl_matrix_view m = gsl_matrix_submatrix ( covariance, 0, 0, (int)nbin, (int)nbin );
gsl_vector *eval = gsl_vector_alloc ( (int)nbin );
gsl_matrix *evec = gsl_matrix_alloc ( (int)nbin, (int)nbin );
gsl_eigen_symmv_workspace *w = gsl_eigen_symmv_alloc ( (int)nbin );
gsl_eigen_symmv ( &m.matrix, eval, evec, w );
gsl_eigen_symmv_free ( w );
gsl_eigen_symmv_sort ( eval, evec, GSL_EIGEN_SORT_VAL_DESC );
// save evectors
if ( save_evecs )
{
Reference::To<Archive> evecs_archive = total->clone();
gsl_vector *evec_copy = gsl_vector_alloc ( (int)nbin );
for (unsigned iext=0; iext < evecs_archive->get_nextension(); iext++)
{
delete evecs_archive->get_extension(iext);
}
evecs_archive->resize ( (unsigned)nbin, 1, 1, (unsigned)nbin );
for (unsigned i_evec = 0; i_evec < (unsigned)nbin; i_evec++ )
{
gsl_vector_view view = gsl_matrix_column(evec, i_evec);
gsl_vector_memcpy ( evec_copy, &view.vector );
evecs_archive->get_Profile ( i_evec, 0, 0 ) -> set_amps ( evec_copy->data );
}
evecs_archive->unload ( prefix+"_evecs.ar" );
} // save evectors
if ( save_evals )
{
out = fopen ( (prefix+"_evals.dat").c_str(), "w" );
gsl_vector_fprintf ( out, eval, "%g" );
fclose ( out );
} // save_evals
// decompose profiles onto eigenvectors
gsl_matrix *decompositions = gsl_matrix_alloc ( (unsigned)nbin, total_count );
gsl_blas_dgemm ( CblasTrans, CblasNoTrans, 1.0, evec, profiles, 0.0, decompositions );
if ( save_decomps )
{
out = fopen ( (prefix + "_decomposition.dat").c_str(), "w" );
gsl_matrix_fprintf ( out, decompositions, "%g");
fclose ( out );
} // save decompositions
if ( !residuals_file.empty() )
{
//read in the residuals:
double tmp;
unsigned residual_count = 0;
gsl_vector *mjds = gsl_vector_alloc ( total->get_nsubint() );
gsl_vector *residuals = gsl_vector_alloc ( total->get_nsubint() );
gsl_vector *residuals_err = gsl_vector_alloc ( total->get_nsubint() );
//TODO check the format of the input
ifstream inFile( residuals_file.c_str() );
if ( inFile.is_open() )
{
while ( inFile.good() )
{
inFile >> tmp;
if ( !inFile.good() )
break;
gsl_vector_set(mjds, residual_count, tmp);
inFile >> tmp;
gsl_vector_set(residuals, residual_count, tmp*1e6);
inFile >> tmp;
gsl_vector_set(residuals_err, residual_count, tmp);
residual_count ++ ;
}
inFile.close ();
if ( residual_count != total->get_nsubint() )
{
cerr << "psrpca::finalize wrong number of residuals provided. Got " << residual_count
<< " while needed " << total->get_nsubint()<< endl;
exit (-1) ;
}
}
else
{
int main (int argc, char** argv) try
{
// the multiple component model
ComponentModel model;
string model_filename_in;
string model_filename_out = "paas.m";
string details_filename = "paas.txt";
string std_filename = "paas.std";
bool fit = false;
vector<string> new_components;
string fit_flags;
int bscrunch = 1;
string pgdev;
bool line_plot=false;
bool interactive = false;
bool centre_model = false, rotate_peak=false;
float rotate_amount = 0.0;
bool align = false;
const char* args = "hb:r:w:c:fF:it:d:Dl:j:Ws:CpR:a";
int c;
while ((c = getopt(argc, argv, args)) != -1)
switch (c) {
case 'h':
usage ();
return 0;
case 'r':
model_filename_in = optarg;
break;
case 'w':
model_filename_out = optarg;
break;
case 'f':
fit = true;
break;
case 'W':
model.set_fit_derivative (true);
break;
case 'c':
new_components.push_back(optarg);
break;
case 'F':
fit_flags = optarg;
break;
case 'b':
bscrunch = atoi (optarg);
break;
case 't':
model.set_threshold( atof(optarg) );
break;
case 'd':
pgdev = optarg;
break;
case 'i':
interactive = true;
case 'D':
pgdev = "/xs";
break;
case 'l':
line_plot = true;
break;
case 's':
std_filename = optarg;
break;
case 'C':
centre_model = true;
break;
case 'p':
rotate_peak = true;
break;
case 'R':
rotate_amount = atof(optarg);
break;
case 'a':
align = true;
break;
case 'j':
details_filename = optarg;
break;
default:
cerr << "invalid param '" << c << "'" << endl;
}
if (!pgdev.empty())
{
cpgopen(pgdev.c_str());
cpgask(0);
cpgsvp(0.1, 0.9, 0.1, 0.9);
}
Reference::To<Archive> archive = Archive::load (argv[optind]);
// preprocess
archive->fscrunch();
archive->tscrunch();
archive->pscrunch();
// phase up as requested
if (centre_model)
archive->centre();
else if (rotate_peak)
archive->centre_max_bin(0.0);
if (rotate_amount != 0.0)
archive->rotate_phase(-rotate_amount);
archive->remove_baseline();
// load from file if specified
if (!model_filename_in.empty())
{
cerr << "paas: loading model from " << model_filename_in << endl;
model.load(model_filename_in.c_str());
// align to profile first if asked
if (align)
model.align(archive->get_Integration(0)->get_Profile(0,0));
}
// add any new components specified
unsigned ic, nc=new_components.size();
double centre, concentration, height;
int name_start;
for (ic=0; ic < nc; ic++)
{
if (sscanf(new_components[ic].c_str(),
"%lf %lf %lf %n", ¢re, &concentration, &height,
&name_start)!=3)
{
cerr << "Could not parse component " << ic << endl;
return -1;
}
model.add_component(centre, concentration, height,
new_components[ic].c_str()+name_start);
}
bool iterate = true;
while (iterate)
{
iterate = false;
// fit if specified
if (fit)
{
// set fit flags
model.set_infit(fit_flags.c_str());
// fit
model.fit(archive->get_Integration(0)->get_Profile(0,0));
}
// plot
if (!pgdev.empty())
{
Reference::To<Pulsar::Archive> scrunched;
scrunched = archive->clone();
if (bscrunch > 1)
scrunched->bscrunch(bscrunch);
cpgpage();
Profile *prof = scrunched->get_Integration(0)->get_Profile(0,0);
float ymin = prof->min();
float ymax = prof->max();
float extra = 0.05*(ymax-ymin);
ymin -= extra;
ymax += extra;
cpgswin(0.0, 1.0, ymin, ymax);
cpgbox("bcnst", 0, 0, "bcnst", 0, 0);
cpglab("Pulse phase", "Intensity", "");
unsigned i, npts=prof->get_nbin();
cpgsci(14);
for (ic=0; ic < model.get_ncomponents(); ic++)
plot(model, npts, true, ic);
vector<float> xvals(npts);
cpgsci(4);
for (i=0; i < npts; i++)
xvals[i] = i/((double)npts);
if (line_plot)
cpgline(npts, &xvals[0], prof->get_amps());
else
cpgbin(npts, &xvals[0], prof->get_amps(), 0);
cpgsci(2);
plot_difference(model, prof, line_plot);
cpgsci(1);
plot(model, npts, true);
}
while (interactive)
{
iterate = true;
fit = false;
cerr << "Enter command ('h' for help)" << endl;
float curs_x=0, curs_y=0;
char key = ' ';
if (cpgband(6,0,0,0,&curs_x, &curs_y, &key) != 1 || key == 'q')
{
cerr << "Quitting ..." << endl;
iterate = false;
break;
}
if (key == 'h')
{
cerr <<
"\n"
"left click - add a component at cursor position\n"
"f key - fit current set of components\n"
"q key - quit\n"
"\n"
"After left click:\n"
" 1) any key - select width of new component, then \n"
" 2) any key - select height of new component \n"
"\n"
" right click or <Escape> to abort addition of new component \n"
<< endl;
continue;
}
if (key == 'f')
{
cerr << "Fitting components" << endl;
fit = true;
break;
}
if (key == 'a' || key == 65)
{
cerr << "Adding component centred at pulse phase " << curs_x << endl;
double centre = curs_x;
cerr << "Select width and hit any key" << endl;
if (cpgband(4, 1, curs_x, curs_y, &curs_x, &curs_y, &key) != 1) {
cerr << "paas: cpgband error" << endl;
return -1;
}
// right click or escape to abort
if (key == 88 || key == 27)
continue;
double width = fabs(centre - curs_x);
cerr << "Select height and hit any key" << endl;
if (cpgband(5,0,0,0,&curs_x, &curs_y, &key) != 1) {
cerr << "paas: cpgband error" << endl;
return -1;
}
// right click or escape to abort
if (key == 88 || key == 27)
continue;
double height = curs_y;
model.add_component (centre, 0.25/(width*width), height, "");
break;
}
cerr << "Unrecognized command" << endl;
}
}
// write out if specified
if (!model_filename_out.empty())
{
cerr << "paas: writing model to " << model_filename_out << endl;
model.unload (model_filename_out.c_str());
}
Reference::To<Pulsar::Archive> copy = archive->clone();
// write out standard
model.evaluate (archive->get_Integration(0)->get_Profile(0,0)->get_amps(),
archive->get_nbin());
write_details_to_file (model, copy, archive, details_filename);
cerr << "paas: writing standard to " << std_filename << endl;
archive->unload (std_filename);
if (!pgdev.empty())
cpgend();
return 0;
}
catch (Error& error)
{
cerr << error << endl;
return -1;
}
void Pulsar::PolnSpectrumStats::build () try
{
if (!profile)
return;
fourier = fourier_transform (profile, plan);
// convert to Stokes parameters and drop the Nyquist bin
fourier->convert_state (Signal::Stokes);
fourier->resize( profile->get_nbin() );
// form the power spectral density
Reference::To<PolnProfile> psd = fourier_to_psd (fourier);
// separate fourier into real and imaginary components
Reference::To<PolnProfile> re = psd->clone();
Reference::To<PolnProfile> im = psd->clone();
unsigned npol = 4;
unsigned nbin = psd -> get_nbin();
for (unsigned ipol=0; ipol < npol; ipol++)
{
float* C_ptr = fourier->get_Profile(ipol)->get_amps();
float* re_ptr = re->get_Profile(ipol)->get_amps();
float* im_ptr = im->get_Profile(ipol)->get_amps();
for (unsigned ibin=0; ibin < nbin; ibin++)
{
re_ptr[ibin] = C_ptr[ibin*2];
im_ptr[ibin] = C_ptr[ibin*2+1];
}
}
if (!regions_set)
{
LastHarmonic last;
last.set_Profile( psd->get_Profile(0) );
last.get_weight (&onpulse);
last.get_baseline_estimator()->get_weight (&baseline);
last_harmonic = last.get_last_harmonic();
#ifdef _DEBUG
cerr << "Pulsar::PolnSpectrumStats::build last harmonic="
<< last_harmonic << " nbin on=" << onpulse.get_weight_sum() << endl;
#endif
real->set_regions (onpulse, baseline);
imag->set_regions (onpulse, baseline);
}
if (onpulse.get_nbin () != re->get_nbin())
{
PhaseWeight on_temp = onpulse;
PhaseWeight off_temp = baseline;
on_temp.resize( re->get_nbin() );
off_temp.resize( re->get_nbin() );
if (re->get_nbin() > onpulse.get_nbin ())
{
copy_pad( on_temp, onpulse, 0 );
copy_pad( off_temp, baseline, 1 );
}
real->set_regions (on_temp, off_temp);
imag->set_regions (on_temp, off_temp);
}
real->set_profile (re.release());
imag->set_profile (im.release());
}
catch (Error& error)
{
throw error += "Pulsar::PolnSpectrumStats::build";
}
int scan_pulses(Reference::To<Pulsar::Archive> arch, vector<pulse>& data,
int method, float cphs, float dcyc)
{
/* Find and store the flux and phase of each pulse in the file
to the data vector. */
pulse newentry;
Reference::To<Pulsar::Profile> prof;
newentry.file = arch->get_filename();
double nm, nv, vm;
int nbin = arch->get_nbin();
int bwid = int(float(nbin) * dcyc);
int cbin = 0;
for (unsigned i = 0; i < arch->get_nsubint(); i++) {
newentry.intg = i;
prof = arch->get_Profile(i, 0, 0);
prof->stats(prof->find_min_phase(), &nm, &nv, &vm);
newentry.err = sqrt(nv);
switch (method) {
case 0: // Method of total flux
newentry.flx = prof->sum();
newentry.phs = prof->find_max_phase();
break;
case 1: // Method of maximum amplitude
if (dcyc == 0.0) {
newentry.flx = prof->max();
newentry.phs = prof->find_max_phase();
}
else {
cbin = int(prof->find_max_phase(dcyc) * float(nbin));
newentry.flx = prof->sum(cbin - bwid/2, cbin + bwid/2);
newentry.phs = prof->find_max_phase(dcyc);
}
break;
case 2: // User-defined phase centre
cbin = int(float(nbin) * cphs);
if (dcyc == 0.0) {
newentry.flx = (prof->get_amps())[cbin];
newentry.phs = cphs;
}
else {
newentry.flx = prof->sum(cbin - bwid/2, cbin + bwid/2);
newentry.phs = cphs;
}
break;
default:
cerr << "No phase selection method chosen!" << endl;
}
data.push_back(newentry);
}
return data.size();
}