/* This algorithm uses zero padding in the fourier domain to
interpolate the cross correlation function in the time domain. The
technique is described at:
http://www.dspguru.com/howto/tech/zeropad2.htm
*/
Estimate<double> Pulsar::ZeroPadShift::get_shift () const
{
// First compute the standard cross correlation function:
Reference::To<Pulsar::Profile> ptr = observation->clone();
Reference::To<Pulsar::Profile> stp = standard->clone();
// Remove the baseline
*ptr -= ptr->mean(ptr->find_min_phase(0.15));
// Perform the correlation
ptr->correlate (standard);
// Remove the baseline
*ptr -= ptr->mean(ptr->find_min_phase(0.15));
vector< Estimate<float> > correlation;
const unsigned nbin = observation->get_nbin();
for (unsigned i = 0; i < nbin; i++) {
correlation.push_back(ptr->get_amps()[i]);
}
vector< Estimate<float> > interpolated;
interpolated.resize(correlation.size() * interpolate);
// Perform the zero-pad interpolation
fft::interpolate(interpolated, correlation);
// Find the peak of the correlation function
float maxval = 0.0;
float maxloc = 0.0;
for (unsigned i = 0; i < interpolated.size(); i++) {
if (interpolated[i].val > maxval) {
maxval = interpolated[i].val;
maxloc = float(i) / interpolate;
}
}
// Error estimate (???)
float ephase = 1.0 / float(nbin);
double shift = double(maxloc) / double(nbin);
if (shift < -0.5)
shift += 1.0;
else if (shift > 0.5)
shift -= 1.0;
return Estimate<double>(shift,ephase*ephase);
}
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();
}
int main (int argc, char *argv[])
{
bool verbose = false;
bool gaussian = false;
float factor = 5.0;
bool log = false;
bool shownoise = false;
int method = 0;
int bins = 30;
float cphs = 0.0;
float dcyc = 0.0;
float norm = 0.0;
int gotc = 0;
while ((gotc = getopt(argc, argv, "qvVhlg:p:w:n:b:Gs")) != -1) {
switch (gotc) {
case 'h':
usage ();
return 0;
case 'v':
Pulsar::Archive::set_verbosity(2);
verbose = true;
break;
case 'V':
verbose = true;
Pulsar::Archive::set_verbosity(3);
break;
case 'l':
log = true;
break;
case 'g':
factor = atof(optarg);
break;
case 'n':
norm = atof(optarg);
break;
case 'p':
cphs = atof(optarg);
if (cphs > 0.0 && cphs < 1.0) {
method = 2;
}
else {
method = 1;
}
break;
case 'w':
dcyc = atof(optarg);
break;
case 'b':
bins = atoi(optarg);
break;
case 'G':
gaussian = true;
break;
case 's':
shownoise = true;
break;
default:
cout << "Unrecognised option: " << gotc << endl;
}
}
vector<string> archives;
vector<pulse> pulses;
vector<pulse> noise;
vector<pulse> pgiants;
vector<pulse> ngiants;
vector<hbin> pdata;
vector<hbin> ndata;
Reference::To<Pulsar::Archive> arch;
for (int ai = optind; ai < argc; ai++) // extract filenames
dirglob (&archives, argv[ai]);
try {
cout << "Loading archives and extracting data..." << endl;
for (unsigned i = 0; i < archives.size(); i++) {
if (verbose) cerr << "Loading " << archives[i] << endl;
arch = Pulsar::Archive::load(archives[i]);
arch->fscrunch(); // remove frequency and polarisation resolution
arch->pscrunch();
arch->remove_baseline(); // Remove the baseline level
scan_pulses(arch, pulses, method, cphs, dcyc);
if (shownoise)
scan_pulses(arch, noise, 2, arch->find_min_phase(dcyc), dcyc);
}
float offset = 2.0;
if (shownoise) {
offset = noise[0].flx;
for (unsigned i = 1; i < noise.size(); i++)
if (noise[i].flx < offset) offset = noise[i].flx;
offset = fabs(offset);
offset /= norm;
}
float threshold = find_giants(pulses, pgiants, factor, norm, offset);
cout << "Detection threshold is roughly " << threshold << endl;
display_giants(pgiants);
prob_hist(pulses, pdata, bins);
float submin = pdata[0].x;
float submax = pdata[0].x;
for (unsigned i = 1; i < pdata.size(); i++) {
if (pdata[i].x > submax) submax = pdata[i].x;
if (pdata[i].x < submin) submin = pdata[i].x;
}
if (shownoise) {
find_giants(noise, ngiants, factor, norm, offset);
prob_hist(noise, ndata, bins, submin, submax);
}
unsigned useful = 0;
if (log) {
vector<hbin>::iterator it = pdata.begin();
while (it != pdata.end()) {
if (pdata[useful].x < 0) {
pdata.erase(it);
continue;
}
else {
pdata[useful].x = logf(pdata[useful].x);
it++;
useful++;
}
}
threshold = logf(threshold);
}
float xmin, xmax, ymin, ymax;
xmin = xmax = pdata[0].x;
ymin = ymax = pdata[0].y;
// Find the extremes of the data set
for (unsigned i = 1; i < pdata.size(); i++) {
if (pdata[i].x > xmax) xmax = pdata[i].x;
if (pdata[i].x < xmin) xmin = pdata[i].x;
if (pdata[i].y > ymax) ymax = pdata[i].y;
if (pdata[i].y < ymin) ymin = pdata[i].y;
}
// Plot pulse intensity probability distribution
cpgopen("?");
cpgsvp(0.1,0.9,0.15,0.9);
cpgsci(7);
cpgsch(1.3);
cpgswin(xmin-(xmin/100.0), xmax+(xmax/100.0),
logf(ymin-(ymin/2.0)), logf(ymax+(ymax/2.0)));
cpgbox("BCNST", 0.0, 0, "BCNST", 0.0, 0);
cpgsci(8);
if (log)
cpglab("Log (Normalised Pulse Flux)", "Log (P(I))", "");
else
cpglab("Normalised Pulse Flux", "Log (P(I))", "");
cpgsci(5);
// Plot the pulse detection threshold
cpgsls(3);
cpgsci(3);
cpgmove(threshold, logf(ymin-(ymin/2.0)));
cpgdraw(threshold, logf(ymax+(ymax/2.0)));
cpgsls(1);
// Plot points and associated error bars
for (unsigned i = 0; i < pdata.size(); i++) {
cpgpt1(pdata[i].x, logf(pdata[i].y), 4);
cpgerr1(6, pdata[i].x, logf(pdata[i].y), pdata[i].e/pdata[i].y, 1.0);
}
if (gaussian) {
MEAL::Gaussian gm1;
fit_gauss(pdata, gm1);
gm1.set_abscissa(xmin);
cpgmove(xmin,logf(gm1.evaluate()));
cpgsci(2);
cpgsls(2);
float xval = 0.0;
for (unsigned i = 1; i < 1000; i++) {
xval = xmin+((xmax-xmin)/1000.0*i);
gm1.set_abscissa(xval);
cpgdraw(xval,logf(gm1.evaluate()));
}
if (shownoise) {
MEAL::Gaussian ngm;
fit_gauss(ndata, ngm);
ngm.set_abscissa(xmin);
cpgmove(xmin,logf(ngm.evaluate()));
cpgsci(5);
cpgsls(4);
for (unsigned i = 1; i < 1000; i++) {
xval = xmin + ((xmax-xmin)/250.0*i);
ngm.set_abscissa(xval);
if (log)
cpgdraw(logf(xval),logf(ngm.evaluate()));
else
cpgdraw(xval,logf(ngm.evaluate()));
}
}
}
cpgclos();
// Free any used memory
archives.clear();
pulses.clear();
noise.clear();
pgiants.clear();
ngiants.clear();
pdata.clear();
ndata.clear();
}
catch (Error& error) {
fflush(stdout);
cerr << error << endl;
exit(1);
}
fflush(stdout);
return 0;
}