void Pulsar::SquareWave::get_transitions (const Profile* profile,
vector<unsigned>& up,
vector<unsigned>& down)
{
unsigned nbin = profile->get_nbin();
unsigned scrunch = 1;
Reference::To<Profile> clone;
if (use_nbin && nbin > use_nbin) {
clone = profile->clone();
scrunch = nbin/use_nbin;
clone->bscrunch(scrunch);
profile = clone;
nbin = profile->get_nbin();
}
unsigned offset = (unsigned) (risetime * nbin);
cerr << "nbin=" << nbin << " offset=" << offset << endl;
// differentiate the profile
Reference::To<Profile> difference = differentiate (profile, offset);
float* amps = difference->get_amps();
// find the phase window in which the mean is closest to zero
BaselineWindow window;
window.set_find_mean (0.0);
window.get_smooth()->set_turns (0.2);
float zero = window.find_phase (nbin, amps);
// get the noise statistics of the zero mean region
double mean = 0;
double variance = 0;
difference->stats (zero, &mean, &variance);
cerr << "mean=" << mean << " rms=" << sqrt(variance) << endl;
// check that the mean is actually zero
double rms = sqrt(variance);
if (mean > rms)
throw Error (InvalidState, "Pulsar::SquareWave::get_transitions",
"mean=%lf > rms=%lf", mean, rms);
float cutoff = threshold * rms;
find_transitions (nbin, amps, up, cutoff);
find_transitions (nbin, amps, down, -cutoff);
}
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);
}
}
}
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
{
// 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 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