void Pulsar::CalibratorSpectrum::prepare (const Archive* data)
{
Reference::To<Archive> clone;
if (plot_Ip && data->get_state() != Signal::Stokes)
{
clone = data -> clone();
clone->convert_state(Signal::Stokes);
data = clone;
}
vector< vector< Estimate<double> > > hi;
vector< vector< Estimate<double> > > lo;
unsigned nchan = data->get_nchan();
unsigned npol = data->get_npol();
Reference::To<const Integration> subint = get_Integration(data, isubint);
ReferenceCalibrator::get_levels (subint, nchan, hi, lo);
assert (hi.size() == npol);
unsigned ipol, ipt, npt = hi[0].size();
if (!plot_total)
for (ipol=0; ipol<npol; ipol++)
for (ipt=0; ipt<npt; ipt++)
hi[ipol][ipt] -= lo[ipol][ipt];
if (plot_low)
for (ipol=0; ipol<npol; ipol++)
for (ipt=0; ipt<npt; ipt++)
hi[ipol][ipt] = lo[ipol][ipt];
if (plot_Ip)
{
for (ipt=0; ipt<npt; ipt++)
if (hi[0][ipt].get_variance() != 0)
hi[1][ipt] = sqrt( sqr(hi[1][ipt]) +
sqr(hi[2][ipt]) +
sqr(hi[3][ipt]) );
npol = 2;
}
double cfreq = data->get_centre_frequency();
double bw = data->get_bandwidth();
plotter.clear ();
plotter.set_xrange (cfreq-0.5*bw, cfreq+0.5*bw);
for (ipol=0; ipol<npol; ipol++)
plotter.add_plot (hi[ipol]);
get_frame()->get_y_scale()->set_minmax (plotter.get_y_min(),
plotter.get_y_max());
}
void psrflux::set_standard(Archive *arch)
{
// Convert
stdarch = arch->total();
stdarch->convert_state(Signal::Intensity);
// Set up DS calculation
Reference::To<StandardFlux> flux = new StandardFlux;
flux->set_fit_shift(true); // always init with true, choose later
flux->set_standard(stdarch->get_Profile(0,0,0));
ds.set_flux_method(flux);
}
int main (int argc, char *argv[]) try {
bool verbose = false;
char* metafile = 0;
string ulpath;
bool save = false;
string ext;
bool tscr = false;
int tscr_fac = 0;
bool fscr = false;
int fscr_fac = 0;
bool bscr = false;
int bscr_fac = 0;
bool newdm = false;
double dm = 0.0;
bool scattered_power_correction = false;
bool defaraday = false;
bool newrm = false;
double rm = 0.0;
bool reset_weights = false;
float new_weight = 1.0;
float smear_dc = 0.0;
bool rotate = false;
double rphase = 0.0;
bool dedisperse = false;
bool dededisperse = false;
bool pscr = false;
bool invint = false;
bool stokesify = false;
bool unstokesify = false;
bool flipsb = false;
bool flip_freq = false;
double flip_freq_mhz = 0.0;
Pulsar::Parameters* new_eph = 0;
string command = "pam";
char* archive_class = 0;
int new_nchn = 0;
int new_nsub = 0;
int new_nbin = 0;
float tsub = 0.0;
bool circ = false;
bool lin = false;
unsigned ronsub = 0;
bool cbppo = false;
bool cbpao = false;
bool cblpo = false;
bool cblao = false;
int subint_extract_start = -1;
int subint_extract_end = -1;
bool new_cfreq = false;
double new_fr = 0.0;
Signal::Source new_type = Signal::Unknown;
string instrument;
bool reverse_freqs = false;
string site;
string name;
float mult = -1.0;
double new_folding_period = -1.0;
bool update_dm_from_eph = false;
double aux_rm = 0.0;
Reference::To<Pulsar::IntegrationOrder> myio;
Reference::To<Pulsar::Receiver> install_receiver;
Pulsar::ReflectStokes reflections;
int c = 0;
const int TYPE = 1208;
const int INST = 1209;
const int REVERSE_FREQS = 1210;
const int SITE = 1211;
const int NAME = 1212;
const int DD = 1213;
const int RR = 1214;
const int SPC = 1215;
const int RM = 1216;
const int MULT = 1218;
const int PERIOD=1219;
const int SS = 1220;
const int FLIP = 1221;
const int UPDATE_DM = 1222;
const int AUX_RM = 1223;
while (1) {
int options_index = 0;
static struct option long_options[] = {
{"setnchn", 1, 0, 200},
{"setnsub", 1, 0, 201},
{"setnbin", 1, 0, 202},
{"binphsperi", 1, 0, 203},
{"binphsasc", 1, 0, 204},
{"binlngperi", 1, 0, 205},
{"binlngasc", 1, 0, 206},
{"receiver", 1, 0, 207},
{"settsub", 1, 0, 208},
{"type", 1, 0, TYPE},
{"inst", 1, 0, INST},
{"reverse_freqs",no_argument,0,REVERSE_FREQS},
{"flip", 1 ,0, FLIP},
{"site", 1, 0, SITE},
{"name", 1, 0, NAME},
{"DD", no_argument, 0,DD},
{"RR", no_argument, 0,RR},
{"RM", required_argument,0,RM},
{"spc", no_argument, 0,SPC},
{"mult", required_argument,0,MULT},
{"period", required_argument,0,PERIOD},
{"SS", no_argument, 0,SS},
{"update_dm", no_argument, 0,UPDATE_DM},
{"aux_rm", required_argument,0,AUX_RM},
{0, 0, 0, 0}
};
c = getopt_long(argc, argv, "hqvViM:mn:a:e:E:TFpIt:f:b:d:o:s:r:u:w:DSBLCx:R:",
long_options, &options_index);
if (c == -1)
break;
switch (c) {
case 'h':
usage();
return (0);
break;
case 'q':
Pulsar::Archive::set_verbosity(0);
break;
case 'v':
verbose = true;
Pulsar::Archive::set_verbosity(2);
break;
case 'V':
verbose = true;
Pulsar::Archive::set_verbosity(3);
break;
case 'i':
cout << "$Id: pam.C,v 1.101 2010/10/05 23:59:50 jonathan_khoo Exp $" << endl;
return 0;
case 'm':
save = true;
break;
case 'M':
metafile = optarg;
break;
case 'L':
lin = true;
break;
case 'C':
circ = true;
break;
case 'a':
archive_class = optarg;
break;
case 'e':
ext = optarg;
if( !ext.empty() )
save = true;
break;
case 'E':
try {
new_eph = factory<Pulsar::Parameters> (optarg);
}
catch (Error& error) {
cerr << "Could not load new ephemeris from " << optarg << endl;
return -1;
}
command += " -E";
break;
case 'T':
tscr = true;
command += " -T";
break;
case 'F':
fscr = true;
command += " -F";
break;
case 'p':
pscr = true;
command += " -p";
break;
case 'I':
invint = true;
pscr = false;
command += " -I";
break;
case 'f':
fscr = true;
if (sscanf(optarg, "%d", &fscr_fac) != 1) {
cout << "That is not a valid fscrunch factor" << endl;
return -1;
}
command += " -f ";
command += optarg;
break;
case 'n':
reflections.add_reflection( optarg[0] );
command += " -n ";
command += optarg;
break;
case 'o':
new_cfreq = true;
if (sscanf(optarg, "%lf", &new_fr) != 1) {
cout << "That is not a valid centre frequency" << endl;
return -1;
}
command += " -o ";
command += optarg;
break;
case 't':
tscr = true;
if (sscanf(optarg, "%d", &tscr_fac) != 1) {
cout << "That is not a valid tscrunch factor" << endl;
return -1;
}
command += " -t ";
command += optarg;
break;
case 'b':
bscr = true;
if (sscanf(optarg, "%d", &bscr_fac) != 1) {
cout << "That is not a valid bscrunch factor" << endl;
return -1;
}
if (bscr_fac <= 0) {
cout << "That is not a valid bscrunch factor" << endl;
return -1;
}
command += " -b ";
command += optarg;
break;
case 'd':
newdm = true;
if (sscanf(optarg, "%lf", &dm) != 1) {
cout << "That is not a valid dispersion measure" << endl;
return -1;
}
command += " -d ";
command += optarg;
break;
case 'D':
dedisperse = true;
command += " -D ";
break;
case 'R':
if (sscanf(optarg, "%lf", &rm) != 1) {
cout << "That is not a valid rotation measure" << endl;
return -1;
}
newrm = true;
defaraday = true;
command += " -R ";
command += optarg;
break;
case 's':
if (sscanf(optarg, "%f", &smear_dc) != 1) {
cout << "That is not a valid smearing duty cycle" << endl;
return -1;
}
command += " -s ";
command += optarg;
break;
case 'r':
rotate = true;
if (sscanf(optarg, "%lf", &rphase) != 1) {
cout << "That is not a valid rotation phase" << endl;
return -1;
}
if (rphase <= -1.0 || rphase >= 1.0) {
cout << "That is not a valid rotation phase" << endl;
return -1;
}
command += " -r ";
command += optarg;
break;
case 'u':
ulpath = optarg;
if( !ulpath.empty() )
{
save = true;
if (ulpath.substr(ulpath.length()-1,1) != "/")
ulpath += "/";
}
break;
case 'w':
reset_weights = true;
if (sscanf(optarg, "%f", &new_weight) != 1) {
cout << "That is not a valid weight" << endl;
return -1;
}
command += " -w ";
command += optarg;
break;
case 'S':
stokesify = true;
break;
case SS:
unstokesify = true;
break;
case 'B':
flipsb = true;
break;
case 'x' :
if (sscanf(optarg, "%d %d",
&subint_extract_start, &subint_extract_end) !=2 ) {
cout << "That is not a valid subint range" << endl;
return -1;
}
subint_extract_end++;
break;
case 200:
fscr = true;
if (sscanf(optarg, "%d", &new_nchn) != 1) {
cout << "That is not a valid number of channels" << endl;
return -1;
}
if (new_nchn <= 0) {
cout << "That is not a valid number of channels" << endl;
return -1;
}
command += " --setnchn ";
command += optarg;
break;
case 201:
tscr = true;
if (sscanf(optarg, "%d", &new_nsub) != 1) {
cout << "That is not a valid number of subints" << endl;
return -1;
}
if (new_nsub <= 0) {
cout << "That is not a valid number of subints" << endl;
return -1;
}
command += " --setnsub ";
command += optarg;
break;
case 202:
bscr = true;
if (sscanf(optarg, "%d", &new_nbin) != 1) {
cout << "That is not a valid number of bins" << endl;
return -1;
}
if (new_nbin <= 0) {
cout << "That is not a valid number of bins" << endl;
return -1;
}
command += " --setnbin ";
command += optarg;
break;
case 203: {
if (cbpao || cblpo || cblao) {
cerr << "You can only specify one re-ordering scheme!"
<< endl;
return -1;
}
if (sscanf(optarg, "%ud", &ronsub) != 1) {
cerr << "Invalid nsub given" << endl;
return -1;
}
cbppo = true;
break;
}
case 204: {
if (cbppo || cblpo || cblao) {
cerr << "You can only specify one re-ordering scheme!"
<< endl;
return -1;
}
if (sscanf(optarg, "%ud", &ronsub) != 1) {
cerr << "Invalid nsub given" << endl;
return -1;
}
cbpao = true;
break;
}
case 205: {
if (cblao || cbppo || cbpao) {
cerr << "You can only specify one re-ordering scheme!"
<< endl;
return -1;
}
if (sscanf(optarg, "%ud", &ronsub) != 1) {
cerr << "Invalid nsub given" << endl;
return -1;
}
cblpo = true;
break;
}
case 206: {
if (cblpo || cbppo || cbpao) {
cerr << "You can only specify one re-ordering scheme!"
<< endl;
return -1;
}
if (sscanf(optarg, "%ud", &ronsub) != 1) {
cerr << "Invalid nsub given" << endl;
return -1;
}
cblao = true;
break;
}
case 207: try {
install_receiver = Pulsar::Receiver::load (optarg);
break;
}
catch (Error& error) {
cerr << "pam: Error loading Receiver from " << optarg << endl
<< error.get_message() << endl;
return -1;
}
case 208: {
if (sscanf(optarg, "%f", &tsub) != 1) {
cerr << "Invalid tsub given" << endl;
return -1;
}
tscr = true;
break;
}
case TYPE:
{
string s = optarg;
if(s=="Pulsar") new_type = Signal::Pulsar;
else if(s=="PolnCal") new_type = Signal::PolnCal;
else if(s=="FluxCalOn") new_type = Signal::FluxCalOn;
else if(s=="FluxCalOff") new_type = Signal::FluxCalOff;
else if(s=="Calibrator") new_type = Signal::Calibrator;
else{
fprintf(stderr,"Unrecognised argument to --type: '%s'\n",optarg);
exit(-1);
}
command += " --type " + s;
}
break;
case INST: instrument = optarg; break;
case REVERSE_FREQS: reverse_freqs = true; break;
case SITE: site = optarg; break;
case NAME: name = optarg; break;
case DD: dededisperse = true; break;
case RM:
aux_rm = fromstring<double>(optarg);
newrm = true;
command += " --RM ";
command += optarg;
break;
case SPC: scattered_power_correction = true; break;
case MULT: mult = atof(optarg); break;
case PERIOD: new_folding_period = fromstring<double>(optarg); break;
case FLIP: flip_freq = true; flip_freq_mhz = atof(optarg); break;
case UPDATE_DM: update_dm_from_eph = true; break;
case AUX_RM:
aux_rm = fromstring<double>(optarg);
command += " --aux_rm ";
command += optarg;
break;
default:
cout << "Unrecognised option" << endl;
}
}
if (verbose)
cerr << "pam: parsing filenames" << endl;
vector <string> filenames;
if (metafile)
stringfload (&filenames, metafile);
else
for (int ai=optind; ai<argc; ai++)
dirglob (&filenames, argv[ai]);
if (filenames.empty())
{
cerr << "pam: no filenames were specified" << endl;
exit(-1);
}
Reference::To<Pulsar::Archive> arch;
if (!save)
{
cout << "Changes will not be saved. Use -m, -u or -e to write results to disk"
<< endl;
}
if (stokesify && unstokesify)
{
cerr << "pam: Both -S and --SS options were given. Poln state will not be changed!" << endl;
stokesify = false;
unstokesify = false;
}
int flip_option_count=0;
if (flipsb) flip_option_count++;
if (flip_freq) flip_option_count++;
if (reverse_freqs) flip_option_count++;
if (flip_option_count > 1) {
cerr << "pam: More than one band-flip option was given, exiting." << endl;
exit(-1);
}
for (unsigned i = 0; i < filenames.size(); i++) try
{
if (verbose)
cerr << "Loading " << filenames[i] << endl;
arch = Pulsar::Archive::load(filenames[i]);
if( mult > 0.0 ){
for( unsigned isub=0; isub<arch->get_nsubint();isub++)
for( unsigned ichan=0; ichan<arch->get_nchan();ichan++)
for( unsigned ipol=0; ipol<arch->get_npol();ipol++)
arch->get_Profile(isub,ipol,ichan)->scale( mult );
}
if( new_folding_period > 0.0 ){
Pulsar::counter_drift( arch, new_folding_period, 0.0);
for( unsigned isub=0; isub<arch->get_nsubint();isub++)
arch->get_Integration(isub)->set_folding_period( new_folding_period );
}
if (install_receiver) {
if (verbose)
cerr << "pam: Installing receiver: " << install_receiver->get_name()
<< " in archive" << endl;
arch->add_extension (install_receiver);
}
if (lin || circ) {
Pulsar::Receiver* receiver = arch->get<Pulsar::Receiver>();
if (!receiver)
cerr << "No Receiver Extension in " << filenames[i] << endl;
else {
if (lin) {
receiver->set_basis (Signal::Linear);
cout << "Feed basis set to Linear" << endl;
}
if (circ) {
receiver->set_basis (Signal::Circular);
cout << "Feed basis set to Circular" << endl;
}
}
}
reflections.transform( arch );
if (new_cfreq)
{
double nc = arch->get_nchan();
double bw = arch->get_bandwidth();
double cw = bw / nc;
double fr = new_fr - (bw / 2.0) + (cw / 2.0);
for (unsigned i = 0; i < arch->get_nsubint(); i++) {
for (unsigned j = 0; j < arch->get_nchan(); j++) {
arch->get_Integration(i)->set_centre_frequency(j,(fr + (j*cw)));
}
}
arch->set_centre_frequency(new_fr);
}
if( new_type != Signal::Unknown )
arch->set_type( new_type );
if( instrument != string() ){
Pulsar::Backend* b = arch->get<Pulsar::Backend>();
if( !b )
fprintf(stderr,"Could not change instrument name- archive does not have Backend extension\n");
else
b->set_name(instrument);
}
if( site != string() )
arch->set_telescope( site );
if( name != string() )
arch->set_source( name );
if (new_eph) try
{
arch->set_ephemeris(new_eph);
if (update_dm_from_eph) {
update_dm(arch);
}
}
catch (Error& error)
{
cerr << "Error while installing new ephemeris: "
<< error.get_message() << endl;
continue;
}
if (flipsb) {
for (unsigned i = 0; i < arch->get_nsubint(); i++) {
vector<double> labels;
labels.resize(arch->get_nchan());
for (unsigned j = 0; j < arch->get_nchan(); j++) {
labels[j] = arch->get_Integration(i)->get_centre_frequency(j);
}
for (unsigned j = 0; j < arch->get_nchan(); j++) {
double new_frequency = labels[labels.size()-1-j];
arch->get_Integration(i)->set_centre_frequency(j,new_frequency);
}
}
arch->set_bandwidth(-1.0 * arch->get_bandwidth());
}
if (flip_freq) {
for (unsigned isub = 0; isub < arch->get_nsubint(); isub++) {
Reference::To<Pulsar::Integration>
subint = arch->get_Integration(isub);
for (unsigned ichan = 0; ichan < arch->get_nchan(); ichan++) {
double new_freq = flip_freq_mhz
- (subint->get_centre_frequency(ichan) - flip_freq_mhz);
subint->set_centre_frequency(ichan, new_freq);
}
}
arch->set_bandwidth(-1.0 * arch->get_bandwidth());
}
if( reverse_freqs ) {
// Of course it would be nice to do this with pointers.... but oh well I guess copying will have to do HSK 27/8/04
unsigned nchan = arch->get_nchan();
for( unsigned isub=0; isub<arch->get_nsubint(); isub++){
for( unsigned ipol =0; ipol<arch->get_npol(); ipol++){
for( unsigned ichan=0; ichan<nchan/2; ichan++){
Reference::To<Pulsar::Profile> lo = arch->get_Profile(isub,ipol,ichan);
Reference::To<Pulsar::Profile> tmp = lo->clone();
Reference::To<Pulsar::Profile> hi = arch->get_Profile(isub,ipol,nchan-1-ichan);
lo->operator=(*hi);
hi->operator=(*tmp);
}
}
}
arch->set_bandwidth( -1.0 * arch->get_bandwidth() );
}
if (reset_weights) {
arch->uniform_weight(new_weight);
if (verbose)
cout << "All profile weights set to " << new_weight << endl;
}
if (rotate)
arch->rotate_phase (rphase);
if (scattered_power_correction) {
Pulsar::ScatteredPowerCorrection spc;
if (arch->get_state() == Signal::Stokes)
arch->convert_state(Signal::Coherence);
spc.correct (arch);
}
if (newdm)
{
arch->set_dispersion_measure(dm);
if (verbose)
cout << "Archive dispersion measure set to " << dm << endl;
if (arch->get_dedispersed())
{
arch->dedisperse();
if (verbose)
cout << "Archive re-dedipsersed" << endl;
}
}
if (dedisperse)
{
arch->dedisperse();
if (verbose)
cout << "Archive dedipsersed" << endl;
}
if (dededisperse)
{
Pulsar::Dispersion correction;
correction.revert (arch);
}
if (stokesify) {
if (arch->get_npol() != 4)
throw Error(InvalidState, "Convert to Stokes",
"Not enough polarisation information");
arch->convert_state(Signal::Stokes);
if (verbose)
cout << "Archive converted to Stokes parameters" << endl;
}
if (unstokesify) {
if (arch->get_npol() != 4)
throw Error(InvalidState, "Convert to coherence",
"Not enough polarisation information");
arch->convert_state(Signal::Coherence);
if (verbose)
cout << "Archive converted to coherence parameters" << endl;
}
if (cbppo) {
myio = new Pulsar::PeriastronOrder();
arch->add_extension(myio);
myio->organise(arch, ronsub);
}
if (cbpao) {
myio = new Pulsar::BinaryPhaseOrder();
arch->add_extension(myio);
myio->organise(arch, ronsub);
}
if (cblpo) {
myio = new Pulsar::BinLngPeriOrder();
arch->add_extension(myio);
myio->organise(arch, ronsub);
}
if (cblao) {
myio = new Pulsar::BinLngAscOrder();
arch->add_extension(myio);
myio->organise(arch, ronsub);
}
if( subint_extract_start >= 0 && subint_extract_end >= 0 ) {
vector<unsigned> subints;
unsigned isub = subint_extract_start;
while ( isub<arch->get_nsubint() && isub<unsigned(subint_extract_end) ) {
subints.push_back( isub );
isub++;
}
Reference::To<Pulsar::Archive> extracted( arch->extract(subints) );
extracted->set_filename( arch->get_filename() );
arch = extracted;
}
if (tscr) {
if (tsub > 0.0) {
unsigned factor =
unsigned (tsub / arch->get_Integration(0)->get_duration());
if (factor == 0) {
cerr << "Warning: subints already too long" << endl;
}
else {
arch->tscrunch(factor);
}
if (verbose)
cout << arch->get_filename() << " tscrunched by a factor of "
<< factor << endl;
}
else if (new_nsub > 0) {
arch->tscrunch_to_nsub(new_nsub);
if (verbose)
cout << arch->get_filename() << " tscrunched to "
<< new_nsub << " subints" << endl;
}
else if (tscr_fac > 0) {
arch->tscrunch(tscr_fac);
if (verbose)
cout << arch->get_filename() << " tscrunched by a factor of "
<< tscr_fac << endl;
}
else {
arch->tscrunch();
if (verbose)
cout << arch->get_filename() << " tscrunched" << endl;
}
}
if (pscr) {
arch->pscrunch();
if (verbose)
cout << arch->get_filename() << " pscrunched" << endl;
}
if (invint) {
arch->invint();
if (verbose)
cout << arch->get_filename() << " invinted" << endl;
}
if (newrm) {
arch->set_rotation_measure (rm);
if (verbose)
cout << arch->get_filename() << " RM set to " << rm << endl;
}
if (defaraday) {
arch->defaraday();
if (verbose)
cout << arch->get_filename() << " defaradayed" <<endl;
}
if (aux_rm)
{
if (verbose)
cout << "pam: correct auxiliary Faraday rotation; iono RM="
<< aux_rm << endl;
correct_auxiliary_rm (arch, aux_rm);
}
if (fscr) {
if (new_nchn > 0) {
arch->fscrunch_to_nchan(new_nchn);
if (verbose)
cout << arch->get_filename() << " fscrunched to "
<< new_nchn << " channels" << endl;
}
else if (fscr_fac > 0) {
arch->fscrunch(fscr_fac);
if (verbose)
cout << arch->get_filename() << " fscrunched by a factor of "
<< fscr_fac << endl;
}
else {
arch->fscrunch();
if (verbose)
cout << arch->get_filename() << " fscrunched" << endl;
}
}
if (bscr) {
if (new_nbin > 0) {
arch->bscrunch_to_nbin(new_nbin);
if (verbose)
cout << arch->get_filename() << " bscrunched to "
<< new_nbin << " bins" << endl;
}
else {
arch->bscrunch(bscr_fac);
if (verbose)
cout << arch->get_filename() << " bscrunched by a factor of "
<< bscr_fac << endl;
}
}
if (smear_dc) {
for (unsigned i = 0; i < arch->get_nsubint(); i++) {
for (unsigned j = 0; j < arch->get_npol(); j++) {
for (unsigned k = 0; k < arch->get_nchan(); k++) {
smear (arch->get_Profile(i,j,k), smear_dc);
}
}
}
}
if (save) {
if (archive_class) {
// unload an archive of the specified class
Reference::To<Pulsar::Archive> output;
output = Pulsar::Archive::new_Archive (archive_class);
output -> copy (*arch);
output -> set_filename ( arch->get_filename() );
arch = output;
}
// See if the archive contains a history that should be updated:
Pulsar::ProcHistory* fitsext = arch->get<Pulsar::ProcHistory>();
if (fitsext) {
if (command.length() > 80) {
cout << "WARNING: ProcHistory command string truncated to 80 chars"
<< endl;
fitsext->set_command_str(command.substr(0, 80));
}
else {
fitsext->set_command_str(command);
}
}
string out_filename = arch->get_filename();
if( !ext.empty() )
out_filename = replace_extension( out_filename, ext );
if( !ulpath.empty() )
out_filename = ulpath + basename(out_filename);
arch->unload( out_filename );
cout << out_filename << " written to disk" << endl;
}
}
catch (Error& error) {
cerr << error << endl;
}
return 0;
}
catch(Error& er)
{
cerr << er << endl;
return -1;
}
catch (string& error)
{
cerr << "exception thrown: " << error << endl;
return -1;
}
catch (bad_alloc& ba)
{
cerr << "Caught a bad_alloc: '" << ba.what() << "'" << endl ;
return -1;
}
catch (exception& e)
{
cerr << "caught an exception of type '"
<< typeid(e).name() << "'" << endl;
return -1;
}
catch(...)
{
fprintf(stderr,"Unknown exception caught\n");
return -1;
}
int main(int argc, char* argv[]) try
{
if (argc < 2) {
usage();
return EXIT_SUCCESS;
}
int gotc = 0;
while ((gotc = getopt(argc, argv, "hvV")) != -1) {
switch (gotc) {
case 'h':
usage();
return EXIT_SUCCESS;
case 'V':
Pulsar::Archive::set_verbosity(3);
break;
case 'v':
Pulsar::Archive::set_verbosity(2);
break;
}
}
if (optind >= argc)
{
cerr << "pazi: please specify filename" << endl;
return -1;
}
string filename = argv[optind];
string extension = filename.substr(filename.length() - 2, 2);
if (extension == "rf")
extension = "rz";
else if (extension == "cf")
extension = "cz";
else
extension = "pazi";
string write_filename = filename + ".";
write_filename += extension;
cerr << "pazi: loading data" << endl;
base_archive = Archive::load(filename);
if (base_archive->get_npol() == 4)
{
original_state = base_archive->get_state();
base_archive->convert_state( Signal::Stokes );
}
backup_archive = base_archive->clone();
cerr << "pazi: making fscrunched clone" << endl;
mod_archive = base_archive->clone();
mod_archive->pscrunch();
mod_archive->remove_baseline();
mod_archive->dedisperse();
mod_archive->fscrunch();
scrunched_archive = mod_archive->clone();
scrunched_archive->tscrunch();
ranges.second = get_max_value(base_archive, plot_type);
positive_direction = base_archive->get_bandwidth() < 0.0;
time_orig_plot = factory.construct("time");
time_mod_plot = factory.construct("time");
time_fui = time_mod_plot->get_frame_interface();
freq_orig_plot = factory.construct("freq");
freq_mod_plot = factory.construct("freq");
freq_fui = freq_mod_plot->get_frame_interface();
total_plot = factory.construct("flux");
total_plot->configure("info=1");
subint_orig_plot = new ProfilePlot;
subint_mod_plot = new ProfilePlot;
subint_fui = subint_mod_plot->get_frame_interface();
subint_orig_plot->configure("info=1");
subint_mod_plot->configure("info=1");
unsigned window = 0;
char device [8];
for (unsigned i=0; i<2; i++) do {
window ++;
snprintf (device, 8, "%u/XS", window);
}
while ( cpgopen (device) < 0 );
cpgask(0);
cerr << endl << "Total S/N = " <<
scrunched_archive->get_Profile(0,0,0)->snr() << endl << endl;
total_plot->plot(scrunched_archive);
cpgslct(1);
time_orig_plot->plot(mod_archive);
do
{
cpgswin(0, 1, 0, 1);
// plot:
// frequency = horizontal mouse band
// time = horizontal mouse band
// profile = vertical mouse band
int band = 0;
if (prune_start != UNDEF_MOUSE)
{
band = BOX_ANCHOR;
mouse_ref = prune_start;
}
else if (mouse_ref != UNDEF_MOUSE)
{
if (plot_type == FscrunchedSubint)
band = VERTICAL_ANCHOR;
else
band = HORIZONTAL_ANCHOR;
}
else
{
if (plot_type == FscrunchedSubint)
band = VERTICAL_LINE;
else
band = HORIZONTAL_LINE;
}
cpgband(band, 0, mouse_ref.first, mouse_ref.second, &(mouse.first),
&(mouse.second), &ch);
switch (ch)
{
case 'A': // zoom
{
constrain_range(mouse.first);
constrain_range(mouse.second);
if (mouse_ref == UNDEF_MOUSE)
{
mouse_ref = mouse;
continue;
}
// store the current range so it can be restored if the user selects
// a zoom region too small
const RangeType old_ranges = ranges;
bool horizontal = plot_type == FscrunchedSubint ? false : true;
ranges = get_range(mouse_ref, mouse, ranges, horizontal);
// ignore mouse clicks if the index values are too close (< 1)
if (ranges.first == ranges.second) {
ranges = old_ranges;
break;
}
zoomed = true;
const unsigned max_value = get_max_value(base_archive, plot_type);
const string zoom_option = get_zoom_option(ranges, max_value);
switch (plot_type) {
case PhaseVsTime:
time_fui->set_value("y:range", zoom_option);
redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed);
break;
case PhaseVsFrequency:
freq_fui->set_value("y:range", zoom_option);
freq_redraw(mod_archive, base_archive, freq_orig_plot,
freq_mod_plot, zoomed);
break;
case FscrunchedSubint:
subint_fui->set_value("x:range", zoom_option);
redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed);
break;
}
}
break; // case 'A'
case 'h':
usage();
break;
case 'b': // plot specific subint
if (plot_type == PhaseVsTime) {
plot_type = FscrunchedSubint;
zoomed = false;
*mod_archive = *base_archive;
mod_archive->set_dispersion_measure(0);
mod_archive->fscrunch();
mod_archive->pscrunch();
mod_archive->remove_baseline();
subint = get_indexed_value(mouse);
ranges.first = 0;
ranges.second = get_max_value(base_archive, plot_type);
char add[3];
sprintf(add, "%d", subint);
string subint_option = "subint=";
subint_option += add;
subint_orig_plot->configure(subint_option);
subint_mod_plot->configure(subint_option);
cpgeras();
subint_orig_plot->plot(mod_archive);
update_total(scrunched_archive, base_archive, total_plot);
}
break;
/*case 'c': // center pulse
set_centre(mod_archive, base_archive, centered, plot_type, dedispersed);
if (plot_type == "freq")
redraw(mod_archive, freq_orig_plot, freq_mod_plot, zoomed);
else if (plot_type == "time")
redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed);
update_total(scrunched_archive, base_archive, total_plot);
break;*/
case 'd': // toggle dedispersion on/off
set_dedispersion(mod_archive, base_archive, dedispersed);
if (plot_type == PhaseVsFrequency) {
mod_archive->tscrunch();
redraw(mod_archive, freq_orig_plot, freq_mod_plot, zoomed);
} else if (plot_type == PhaseVsTime) {
mod_archive->fscrunch();
redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed);
}
update_total(scrunched_archive, base_archive, total_plot);
break;
case 'f': // frequency plot
plot_type = PhaseVsFrequency;
ranges.first = 0;
ranges.second = get_max_value(base_archive, plot_type);
zoomed = false;
freq_redraw(mod_archive, base_archive, freq_orig_plot, freq_mod_plot, zoomed);
break;
case 'm':
if (plot_type != FscrunchedSubint)
{
cerr << "pazi: can only mow lawn in binzap-subint mode" << endl;
continue;
}
cerr << "pazi: mowing lawn" << endl;
mowlawn (mod_archive, base_archive, subint);
cerr << "pazi: replotting" << endl;
redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed);
cerr << "pazi: updating total" << endl;
update_total(scrunched_archive, base_archive, total_plot);
break;
case 'x': // prune
if (plot_type != FscrunchedSubint)
{
cerr << "pazi: can only prune hedge in binzap-subint mode" << endl;
continue;
}
constrain_range(mouse.first);
constrain_range(mouse.second);
if (prune_start == UNDEF_MOUSE)
{
prune_start = mouse;
continue;
}
prune_end = mouse;
cerr << "pazi: pruning hedge" << endl;
prune_hedge (mod_archive, base_archive, subint);
cerr << "pazi: replotting" << endl;
redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed);
cerr << "pazi: updating total" << endl;
update_total(scrunched_archive, base_archive, total_plot);
break;
case 'o': // toggle frequency scrunching on/off
if (plot_type == PhaseVsTime)
{
if (fscrunched) {
fscrunched = false;
*mod_archive = *base_archive;
}
else {
fscrunched = true;
mod_archive->fscrunch();
}
redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed);
}
break;
case 'q': // quit
cpgclos();
return EXIT_SUCCESS;
case 'p':
print_command(channels_to_zap, subints_to_zap, extension, filename);
break;
case 'r': // reset zoom
zoomed = false;
ranges.first = 0;
ranges.second = get_max_value(base_archive, plot_type);
switch (plot_type) {
case PhaseVsTime:
redraw(mod_archive, time_orig_plot, time_mod_plot, zoomed);
break;
case PhaseVsFrequency:
freq_redraw(mod_archive, base_archive, freq_orig_plot,
freq_mod_plot, zoomed);
break;
case FscrunchedSubint:
redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed);
break;
}
break;
case 's': // save current archive changes:
{
Pulsar::ProcHistory* ext = base_archive->get<Pulsar::ProcHistory>();
if (ext) {
ext->set_command_str("pazi");
}
if ( base_archive->get_npol() == 4 )
base_archive->convert_state( original_state );
base_archive->unload(write_filename);
if ( base_archive->get_npol() == 4 )
base_archive->convert_state( Signal::Stokes );
break;
}
case 't': // time plot
plot_type = PhaseVsTime;
ranges.first = 0;
ranges.second = get_max_value(base_archive, plot_type);
zoomed = false;
time_redraw(mod_archive, base_archive, time_orig_plot, time_mod_plot, zoomed);
break;
case 'u': // undo last change
if (mouse_ref != UNDEF_MOUSE) {
mouse_ref = UNDEF_MOUSE;
continue;
}
switch (plot_type) {
case PhaseVsTime:
{
const unsigned value = get_indexed_value(mouse);
remove_channel(value, subints_to_zap);
time_unzap_subint(base_archive, backup_archive, value);
time_redraw(mod_archive, base_archive, time_orig_plot,
time_mod_plot, zoomed);
}
break;
case PhaseVsFrequency:
{
const unsigned value = get_indexed_value(mouse);
remove_channel(value, channels_to_zap);
freq_unzap_chan(base_archive, backup_archive, value);
freq_redraw(mod_archive, base_archive, freq_orig_plot,
freq_mod_plot, zoomed);
}
break;
case FscrunchedSubint:
if (bins_to_zap.size()) {
bins_to_zap.erase(bins_to_zap.end() - 5, bins_to_zap.end());
*base_archive = *backup_archive;
*mod_archive = *backup_archive;
mod_archive->set_dispersion_measure(0);
mod_archive->pscrunch();
mod_archive->fscrunch();
mod_archive->remove_baseline();
redraw(mod_archive, subint_orig_plot, subint_mod_plot, zoomed);
}
break;
}
update_total(scrunched_archive, base_archive, total_plot);
break;
case 'z':
case 'X': // zap single channel
if (mouse_ref == UNDEF_MOUSE)
zap_single ();
else
zap_multiple ();
break;
}
prune_start = UNDEF_MOUSE;
mouse_ref = UNDEF_MOUSE;
} while (ch != 'q');
return 0;
} // end main
catch (Error& error) {
cerr << "pazi: " << error << endl;
return -1;
}
void psrspa::create_histograms ( Reference::To<Archive> archive )
{
if ( verbose )
cerr << "psrspa::create_histograms entered" << endl;
// ensure Stokes parameters if creating polarisation histograms
if ( create_polar_degree || create_polar_angle )
{
archive->convert_state ( Signal::Stokes );
if ( verbose )
cerr << "psrspa::create_histograms converted state of the archive to Stokes" << endl;
}
// auxillary vectors
//vector< Estimate<float > > aux_vec_f;
vector< Estimate<double > > aux_vec_d;
// Full Stokes profile
Reference::To<PolnProfile> profile;
// Polarized flux
Reference::To<Profile> P;
P = new Profile;
// Total flux
float *T_amps = new float [ nbin ];
float *P_amps = new float [ nbin ];
unsigned bin_min, bin_max;
if ( verbose && max_bscrunch > 1 )
cerr << "psrspa::create_histograms entering the bscrunch loop for the " << archive->get_filename () << " archive" << endl;
// TODO Uh, this should be fixed up. The first idea was to enable the phase resolved histograms to be bscrunch-aware as well, but I think it doesn't make much sense so I decided to keep only the max flux bscrunch aware. This can be done much more neatly probably in such a case
for ( current_bscrunch = 1 ; current_bscrunch <= max_bscrunch ; current_bscrunch *= 2 )
{
// in each passage, we bscrunch by a factor of 2
if ( current_bscrunch > 1 )
{
if ( verbose )
cerr << "psrspa::create_histograms bscrunching the archive " << archive->get_filename () << " by a factor of 2" << endl;
archive->bscrunch ( 2 );
}
if ( verbose )
cerr << "psrspa::create_histograms entering the loop through subints of the " << archive->get_filename () << " archive" << endl;
// loop through subints
for ( unsigned isub = 0; isub < archive->get_nsubint (); isub++ )
{
if ( verbose )
cerr << "psrspa::create_histograms creating necessary profiles for subint " << isub << " of " << archive->get_filename () << endl;
if ( create_polar_angle || create_polar_degree && current_bscrunch == 1 )
{
profile = archive->get_Integration(isub)->new_PolnProfile(0);
if ( verbose )
cerr << "psrspa::create_histograms retrieved PolnProfile for subint " << isub << " of " << archive->get_filename () << endl;
}
if ( create_polar_angle && current_bscrunch == 1 )
{
profile->get_orientation ( aux_vec_d, 0 );
if ( verbose )
cerr << "psrspa::create_histograms retrieved polarisation angle for subint " << isub << " of " << archive->get_filename () << endl;
}
if ( create_polar_degree || create_flux || find_max_amp_in_range )
{
stats.set_profile ( archive->get_Profile ( isub, 0, 0 ) );
b_sigma = sqrt ( stats.get_baseline_variance ().get_value () );
T_amps = archive->get_Profile ( isub, 0, 0 )->get_amps ();
if ( verbose )
cerr << "psrspa::create_histograms retrieved total flux amps for subint " << isub << " of " << archive->get_filename () << endl;
if ( create_polar_degree && current_bscrunch == 1 )
{
profile->get_polarized ( P );
if ( verbose )
cerr << "psrspa::create_histograms retrieved polarized flux profile for subint " << isub << " of " << archive->get_filename () << endl;
P_amps = P->get_amps ();
if ( verbose )
cerr << "psrspa::create_histograms retrieved polarized flux amps for subint " << isub << " of " << archive->get_filename () << endl;
}
}
if ( verbose )
cerr << "psrspa::create_histograms looping through the provided phase ranges for subint " << isub << " of " << archive->get_filename () << endl;
unsigned curr_hist = 0;
// loop through phase ranges
for ( unsigned irange = 0; irange < phase_range.size () ; irange++ )
{
if ( irange%2 == 0)
{
bin_min = unsigned( floor ( phase_range[irange] * float(nbin / current_bscrunch ) + 0.5 ) );
if ( verbose )
cerr << "psrspa::create_histograms set minimal bin to " << bin_min << endl;
}
else
{
bin_max = unsigned( floor ( phase_range[irange] * float(nbin / current_bscrunch ) + 0.5 ) );
if ( bin_max == nbin )
bin_max = nbin - 1 ;
if ( verbose )
cerr << "psrspa::create_histograms set maximum bin to " << bin_max << endl;
// loop through bins in the given phase range
for ( unsigned ibin = bin_min; ibin <= bin_max; ibin++ )
{
if ( create_polar_angle && current_bscrunch == 1 )
{
int result = gsl_histogram_increment ( h_polar_angle_vec[curr_hist], aux_vec_d[ibin].get_value () / 180.0 * M_PI );
if ( result == GSL_EDOM )
{
if ( dynamic_histogram )
{
gsl_histogram *temp_hist = gsl_histogram_clone ( h_polar_angle_vec[curr_hist] );
h_flux_pr_vec[curr_hist] = update_histogram_range ( temp_hist, aux_vec_d[ibin].get_value () / 180.0 * M_PI );
}
else {
warn << "WARNING psrspa::create_histograms polarisation angle the histogram range for the bin " << ibin << " in the subint " << isub << " of archive " << archive->get_filename () << endl;
}
}
}
if ( create_polar_degree && current_bscrunch == 1 )
{
// if P_amps[ibin] or T_amps[ibin] < 3 sigma, set polar degree to zero
int result = gsl_histogram_increment ( h_polar_degree_vec[curr_hist], ( fabs ( P_amps[ibin] ) < 3.0 * b_sigma || fabs ( T_amps[ibin] ) < 3.0 * b_sigma ) ? 0.0 : P_amps[ibin] / T_amps[ibin] );
if ( result == GSL_EDOM )
{
if ( dynamic_histogram )
{
gsl_histogram *temp_hist = gsl_histogram_clone ( h_polar_degree_vec[curr_hist] );
h_flux_pr_vec[curr_hist] = update_histogram_range ( temp_hist, ( fabs ( P_amps[ibin] ) < 3.0 * b_sigma || fabs ( T_amps[ibin] ) < 3.0 * b_sigma ) ? 0.0 : P_amps[ibin] / T_amps[ibin] );
}
else {
warn << "WARNING psrspa::create_histograms polarisation degree outside the histogram range for the bin " << ibin << " in the subint " << isub << " of archive " << archive->get_filename () << endl;
}
}
}
if ( create_flux && current_bscrunch == 1 )
{
int result = 0;
if ( log && T_amps[ibin] > 0.0 )
{
result = gsl_histogram_increment ( h_flux_pr_vec[curr_hist], log10f ( T_amps[ibin] ) );
}
else if ( !log )
{
result = gsl_histogram_increment ( h_flux_pr_vec[curr_hist], T_amps[ibin] );
}
if ( result == GSL_EDOM )
{
if ( dynamic_histogram )
{
gsl_histogram *temp_hist = gsl_histogram_clone ( h_flux_pr_vec[curr_hist] );
h_flux_pr_vec[curr_hist] = update_histogram_range ( temp_hist, log ? log10f ( T_amps[ibin] ) : T_amps[ibin] );
}
else {
warn << "WARNING psrspa::create_histograms phase resolved flux outside the histogram range for the bin " << ibin << " in the subint " << isub << " of archive " << archive->get_filename () << " flux = " << T_amps[ibin] << endl;
}
}
}
// increment the histogram id
curr_hist ++;
} // loop through bins in the given phase range
// find the maximum amplitude in given phase range.
if ( find_max_amp_in_range )
{
if ( verbose )
cerr << "psrspa::create_histograms finding the maximum amplitude in the phase range " << irange << " of the subint " << isub << " (archive " << archive->get_filename () << ")" << endl;
int max_bin = archive->get_Profile ( isub, 0, 0 )->find_max_bin ( (int)bin_min, (int)bin_max );
identifier current_identifier = { archive->get_filename (), isub, bin_min, bin_max, current_bscrunch,
(unsigned)max_bin, T_amps[max_bin], b_sigma };
max_amp_info.push_back ( current_identifier );
} // find maximal amplitude in the given phase range
} // handle given phase range
} // loop through phase ranges
} // loop through subints
} // bscrunch loop
if ( verbose )
cerr << "psrspa::create_histograms finished" << endl;
}// create_histograms
