void paz::setup ()
{
if (!killfile.empty ())
{
FILE *fptr = fopen (killfile.c_str (), "r");
if (!fptr)
throw Error (FailedSys, "paz::setup", "fopen " + killfile);
char *buffer = new char[4096];
while (fgets (buffer, 4096, fptr))
{
char* key = strtok (buffer, whitespace);
while (key)
{
chans_to_zero.push_back (fromstring<unsigned>(key));
key = strtok (NULL, whitespace);
}
}
}
zero_channels = chans_to_zero.size()
|| freqs_to_zero.size() || freq_ranges_to_zero.size();
bool zero_subints = subs_to_zero.size ();
if (zero_intersection && !(zero_channels && zero_subints))
throw Error (InvalidState, "paz::setup",
"must use -I with both -s|S|k *and* -w|W");
if (mow_all_subints || subints_to_mow.size())
mower = new Pulsar::LawnMower;
if (median_zap || median_zap_bybin || median_zap_window)
{
median_zapper = new Pulsar::ChannelZapMedian;
median_zapper->set_bybin (median_zap_bybin);
median_zapper->set_paz_report (true);
if (median_zap_window)
median_zapper->set_window_size (median_zap_window);
}
if (edge_zap_percent < 0.0 || edge_zap_percent >= 100.0)
throw Error (InvalidState, "paz::setup",
"invalid parameter to option -E");
if (!std_filename.empty())
{
Reference::To<Pulsar::Archive> data = Pulsar::Archive::load (std_filename);
data->pscrunch ();
data->fscrunch ();
data->tscrunch ();
thestd = data->get_Profile (0, 0, 0);
standard_snr.set_standard (thestd);
Pulsar::Profile::snr_strategy.get_value().set (&standard_snr,
&Pulsar::StandardSNR::get_snr);
}
}
void psrpca::setup ()
{
arrival->set_shift_estimator ( new PhaseGradShift );
try
{
std_archive->fscrunch();
std_archive->pscrunch();
arrival->set_standard ( std_archive );
} catch (Error& error)
{
cerr << error << endl;
cerr << "psrpca::setup setting standard failed" << endl;
exit ( -1 );
}
}
/**
* Zap a specified range of bins by substituting their values with the
* baseline mean for each profile.
*/
void zap_bins(Pulsar::Archive* arch, Pulsar::Archive* old_arch,
const unsigned s, const unsigned start_bin, const unsigned end_bin)
{
const unsigned npol = old_arch->get_npol();
const unsigned nchan = old_arch->get_nchan();
// Get the baseline region from what is displayed on screen (pscrunched
// and fscrunched integration).
Reference::To<Pulsar::Archive> copy = old_arch->clone();
copy->pscrunch();
copy->fscrunch();
Reference::To<Pulsar::PhaseWeight> baseline_weights =
copy->get_Profile(s,0,0)->baseline();
vector<float> weights;
baseline_weights->get_weights(weights);
for (unsigned ipol = 0; ipol < npol; ++ipol) {
for (unsigned ichan = 0; ichan < nchan; ++ichan) {
// Apply the baseline region to each profile and get the mean.
baseline_weights->set_Profile(old_arch->get_Profile(s,ipol,ichan));
const double baseline_mean = baseline_weights->get_mean().get_value();
float* bins = old_arch->get_Profile(s,ipol,ichan)->get_amps();
// Set all the bins between start_bin and end_bin to the mean of the
// baseline.
for (unsigned ibin = start_bin; ibin <= end_bin; ++ibin) {
bins[ibin] = baseline_mean;
}
}
}
*arch = *old_arch;
arch->set_dispersion_measure(0);
arch->pscrunch();
arch->fscrunch();
arch->remove_baseline();
}
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;
}
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 paz::process (Pulsar::Archive* arch)
{
if (periodic_zap)
{
if (arch->get_nchan () == 1)
cout << periodic_zap_warning << endl;
for (unsigned pol = 0; pol < arch->get_npol (); pol++)
for (unsigned chan = 0; chan < arch->get_nchan (); chan++)
for (unsigned subint = 0; subint < arch->get_nsubint (); subint++)
zap_periodic_spikes (arch->get_Profile (subint, pol, chan),
periodic_zap_period, periodic_zap_phase,
periodic_zap_width);
}
if (pol_to_delete != -1)
{
/*
Delete either PP=(pol 0) or QQ=(pol 1) by resizing to npol = 1
If PP is to be deleted, PP and QQ are first swapped.
*/
if (pol_to_delete != 0 && pol_to_delete != 1)
throw Error (InvalidState, "paz::process",
"--pol = either 0 or 1, not %d", pol_to_delete);
if (arch->get_state() == Signal::Stokes)
arch->convert_state( Signal::Coherence );
Signal::State state = arch->get_state();
if (state != Signal::Coherence && state != Signal::PPQQ)
throw Error (InvalidState, "paz::process",
"cannot delete polarization when state = %s",
Signal::state_string(state));
if (verbose)
cerr << "paz: deleting ipol=" << pol_to_delete
<< " current state=" << Signal::state_string(state) << endl;
const unsigned nchan = arch->get_nchan ();
const unsigned nsub = arch->get_nsubint ();
for (unsigned isub = 0; isub < nsub; isub++)
{
// ensure that the sub-integration is loaded from file
Pulsar::Integration* subint = arch->get_Integration (isub);
if (pol_to_delete == 0)
{
// Swap pol 0 and pol 1 in each sub-integration and frequency channel
for (unsigned ichan = 0; ichan < nchan; ichan++)
subint->expert()->swap_profiles (0, ichan, 1, ichan);
}
}
// resize to npol = 1
arch->resize (nsub, 1);
arch->set_state( Signal::Intensity );
}
// To fix early wide-band correlator problem
if (eightBinZap)
{
for (unsigned pol = 0; pol < arch->get_npol (); pol++) {
for (unsigned chan = 0; chan < arch->get_nchan (); chan++) {
for (unsigned subint = 0; subint < arch->get_nsubint (); subint++) {
Pulsar::Profile * prof = arch->get_Profile (subint, pol, chan);
float *amps = prof->get_amps ();
for (unsigned i = 5; i < arch->get_nbin (); i += 8) {
// Interpolate between previous and later point if possible
if (i == arch->get_nbin () - 1)
amps[i] = amps[i - 1];
else {
float amp1 = amps[i - 1];
float amp2 = amps[i + 1];
amps[i] = 0.5 * (amp1 + amp2);
}
}
prof->set_amps (amps);
}
}
}
}
unsigned nchan = arch->get_nchan ();
double chan_bw = fabs(arch->get_bandwidth() / (double)nchan);
if (subs_to_delete.size())
{
unsigned zapped = 0;
unsigned orig_nsubint = arch->get_nsubint ();
for (unsigned i = 0; i < orig_nsubint; i++)
for (unsigned j = 0; j < subs_to_delete.size (); j++)
if (subs_to_delete[j] == i)
{
if (verbose)
cout << "Deleting subint " << i << endl;
// after each subint is zapped, it is necessary to offset the index
arch->erase (i - zapped);
zapped ++;
}
if (verbose)
cerr << "paz: deletion completed" << endl;
}
if (subs_no_delete.size())
{
unsigned zapped = 0;
unsigned orig_nsubint = arch->get_nsubint ();
for (unsigned i = 0; i < orig_nsubint; i++)
{
bool keep = false;
for (unsigned j = 0; j < subs_no_delete.size (); j++)
if (subs_no_delete[j] == i)
keep = true;
if (!keep)
{
if (verbose)
cout << "Deleting subint " << i << endl;
// after each subint is zapped, it is necessary to offset the index
arch->erase (i - zapped);
zapped ++;
}
}
if (verbose)
cerr << "paz: deletion completed" << endl;
}
if (median_zapper)
{
cout << "Using median smoothed difference zapper" << endl;
(*median_zapper) (arch);
}
if (modulation_zapper)
{
cout << "Using modulation index zapper" << endl;
(*modulation_zapper) (arch);
}
if (simple)
{
cout << "Using simple mean offset zapper" << endl;
zapper->zap_chans (arch);
cout << "Zapping complete" << endl;
}
if (subs_to_zero.size() && !zero_intersection)
{
vector<float> mask (nchan, 0.0);
zapper->zap_very_specific (arch, mask, subs_to_zero);
}
if (bins_to_zap.size ())
{
for (unsigned i = 0; i < bins_to_zap.size(); ++i)
zap_bin_in_archive(arch, bins_to_zap[i]);
}
if (zero_channels)
{
vector<float> mask (nchan, 1.0);
for (unsigned i = 0; i < chans_to_zero.size (); i++)
{
if (chans_to_zero[i] >= nchan || chans_to_zero[i] < 0)
throw Error (InvalidRange, "paz::process",
"channel %d is out of range (nchan=%d)",
chans_to_zero[i], nchan);
mask[chans_to_zero[i]] = 0.0;
}
for (unsigned i = 0; i < freqs_to_zero.size (); i++)
{
for (unsigned ic=0; ic<nchan; ic++)
{
double chan_freq=arch->get_Integration(0)->get_centre_frequency(ic);
if ( freqs_to_zero[i] > chan_freq - chan_bw/2.0
&& freqs_to_zero[i] < chan_freq + chan_bw/2.0 )
mask[ic] = 0.0;
}
}
for (unsigned i=0; i< freq_ranges_to_zero.size(); i++)
{
for (unsigned ic=0; ic<nchan; ic++)
{
FreqRange chan;
chan.lo=arch->get_Integration(0)->get_centre_frequency(ic)
- chan_bw/2.0;
chan.hi=arch->get_Integration(0)->get_centre_frequency(ic)
+ chan_bw/2.0;
if (chan.lo > freq_ranges_to_zero[i].lo
&& chan.lo < freq_ranges_to_zero[i].hi)
mask[ic] = 0.0;
else if (chan.hi > freq_ranges_to_zero[i].lo
&& chan.hi < freq_ranges_to_zero[i].hi)
mask[ic] = 0.0;
else if (freq_ranges_to_zero[i].lo > chan.lo
&& freq_ranges_to_zero[i].lo < chan.hi)
mask[ic] = 0.0;
}
}
if (zero_intersection)
zapper->zap_very_specific (arch, mask, subs_to_zero);
else
zapper->zap_specific (arch, mask);
}
if (edge_zap_percent)
{
float fraction = edge_zap_percent / 100.0;
unsigned buffer = unsigned (float (nchan) * fraction);
vector < float >mask (nchan, 0.0);
for (unsigned i = buffer; i < (nchan - buffer); i++)
mask[i] = 1.0;
zapper->zap_specific (arch, mask);
}
if (ston_cutoff > 0.0)
{
double theston = 0.0;
Reference::To<Pulsar::Archive> cloned = arch->clone();
cloned->pscrunch ();
for (unsigned isub = 0; isub < arch->get_nsubint (); isub++) {
for (unsigned ichan = 0; ichan < arch->get_nchan (); ichan++) {
theston = cloned->get_Profile (isub, 0, ichan)->snr ();
if (theston < ston_cutoff) {
arch->get_Integration (isub)->set_weight (ichan, 0.0);
}
}
}
}
if (dropout_sigma)
{
Reference::To < Pulsar::Archive > cloned = arch->clone ();
Reference::To < Pulsar::Profile > testprof = 0;
cloned->pscrunch ();
cloned->fscrunch ();
cloned->remove_baseline ();
vector < double >mins;
for (unsigned isub = 0; isub < arch->get_nsubint (); isub++) {
testprof = cloned->get_Profile (isub, 0, 0);
mins.push_back (fabs (testprof->min ()));
}
cloned->tscrunch ();
double mean, vari, varm;
testprof = cloned->get_Profile (0, 0, 0);
testprof->stats (&mean, &vari, &varm);
for (unsigned isub = 0; isub < arch->get_nsubint (); isub++) {
if (mins[isub] > dropout_sigma * sqrt (vari)) {
cerr << "Zapping integration " << isub << endl;
arch->get_Integration (isub)->uniform_weight (0.0);
}
}
}
if (mower)
{
if (mow_all_subints)
{
subints_to_mow.resize (arch->get_nsubint ());
for (unsigned isub = 0; isub < arch->get_nsubint (); isub++)
subints_to_mow[isub] = isub;
}
for (unsigned isub = 0; isub < subints_to_mow.size (); isub++)
{
cerr << "paz: mowing subint " << subints_to_mow[isub] << endl;
mower->transform (arch->get_Integration (subints_to_mow[isub]));
}
}
}
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;
}
