Exemple #1
0
void dsp::Archiver::set (Pulsar::Archive* archive, const PhaseSeries* phase)
try
{
  if (verbose > 2)
    cerr << "dsp::Archiver::set Pulsar::Archive" << endl;

  if (!archive)
    throw Error (InvalidParam, "dsp::Archiver::set Pulsar::Archive",
        	 "no Archive");

  if (!phase)
    throw Error (InvalidParam, "dsp::Archiver::set Pulsar::Archive",
        	 "no PhaseSeries");

  const unsigned npol  = get_npol (phase);
  const unsigned nchan = phase->get_nchan();
  const unsigned nbin  = phase->get_nbin();
  const unsigned nsub  = 1;

  if (verbose > 2)
    cerr << "dsp::Archiver::set Pulsar::Archive nsub=" << nsub 
         << " npol=" << npol << " nchan=" << nchan 
         << " nbin=" << nbin << " fourth=" << fourth_moments << endl;

  archive-> resize (nsub, npol, nchan, nbin);

  Pulsar::FITSHdrExtension* ext;
  ext = archive->get<Pulsar::FITSHdrExtension>();
  
  if (ext)
  {
    if (verbose > 2)
      cerr << "dsp::Archiver::set Pulsar::Archive FITSHdrExtension" << endl;

    // Make sure the start time is aligned with pulse phase zero
    // as this is what the PSRFITS format expects.

    MJD initial = phase->get_start_time();

    if (phase->has_folding_predictor())
    {
      Pulsar::Phase inphs = phase->get_folding_predictor()->phase(initial);
      double dtime = inphs.fracturns() * phase->get_folding_period();
      initial -= dtime;
    }

    ext->set_start_time (initial);

    // In keeping with tradition, I'll set this to a value that should
    // work in most places for the next 50 years or so ;)

    ext->set_coordmode("J2000");

    // Set the ASCII date stamp from the system clock (in UTC)

    time_t thetime;
    time(&thetime);
    string time_str = asctime(gmtime(&thetime));

    // Cut off the line feed character
    time_str = time_str.substr(0,time_str.length() - 1);

    ext->set_date_str(time_str);
  }

  archive-> set_telescope ( phase->get_telescope() );
  archive-> set_type ( phase->get_type() );

  switch (phase->get_state())
  {
  case Signal::NthPower:
  case Signal::PP_State:
  case Signal::QQ_State:
    archive->set_state (Signal::Intensity);
    break;
  
  case Signal::FourthMoment:
    archive->set_state (Signal::Stokes);
    break;

  default:
    archive-> set_state ( phase->get_state() );
  }

  archive-> set_scale ( Signal::FluxDensity );

  if (verbose > 2)
    cerr << "dsp::Archiver::set Archive source=" << phase->get_source()
         << "\n  coord=" << phase->get_coordinates()
         << "\n  bw=" << phase->get_bandwidth()
         << "\n  freq=" << phase->get_centre_frequency () << endl;

  archive-> set_source ( phase->get_source() );
  archive-> set_coordinates ( phase->get_coordinates() );
  archive-> set_bandwidth ( phase->get_bandwidth() );
  archive-> set_centre_frequency ( phase->get_centre_frequency() );
  archive-> set_dispersion_measure ( phase->get_dispersion_measure() );

  archive-> set_dedispersed( archive_dedispersed );
  archive-> set_faraday_corrected (false);

  /* *********************************************************************
     *********************************************************************

     Set any available extensions

     *********************************************************************
     ********************************************************************* */

  /*
    A valid Backend extension may have already been created; e.g. by
    the OutputArchive extension class.  Therefore, if the Backend extension
    already exists, do not modifiy it.
  */

  Pulsar::Backend* backend = archive -> get<Pulsar::Backend>();
  if (!backend)
  {
    backend = new Pulsar::Backend;

    if (verbose > 2)
      cerr << "dsp::Archiver::set Pulsar::Backend extension" << endl;

    set (backend);

    archive->add_extension( backend );
  }


  // Note, this is now called before the set(Integration,...) call below
  // so that the DigitiserCounts extension gets set up correctly the
  // first time.

  Pulsar::dspReduction* dspR = archive -> getadd<Pulsar::dspReduction>();
  if (dspR)
  {
    if (verbose > 2)
      cerr << "dsp::Archiver::set Pulsar::dspReduction extension" << endl;
    set (dspR);
  }

  for (unsigned isub=0; isub < nsub; isub++)
    set (archive->get_Integration(isub), phase, isub, nsub);

  if (store_dynamic_extensions)
  {
    Pulsar::TwoBitStats* tbc = archive -> getadd<Pulsar::TwoBitStats>();
    if (tbc)
    {
      if (verbose > 2)
        cerr << "dsp::Archiver::set Pulsar::TwoBitStats extension" << endl;
      set (tbc);
    }

    Pulsar::Passband* pband = archive -> getadd<Pulsar::Passband>();
    if (pband)
    {
      if (verbose > 2)
        cerr << "dsp::Archiver::set Pulsar::Passband extension" << endl;
      set (pband);
    }
  }

  Pulsar::Telescope* telescope = archive -> getadd<Pulsar::Telescope>();

  try
  {
    telescope->set_coordinates ( phase -> get_telescope() );
  }
  catch (Error& error)
  {
    if (verbose > 2)
      cerr << "dsp::Archiver WARNING could not set telescope coordinates\n\t"
           << error.get_message() << endl;
  }

  // default Receiver extension
  Pulsar::Receiver* receiver = archive -> getadd<Pulsar::Receiver>();
  receiver->set_name ( phase -> get_receiver() );
  receiver->set_basis ( phase -> get_basis() );

  for (unsigned iext=0; iext < extensions.size(); iext++)
    archive -> add_extension ( extensions[iext] );

  // set_model must be called after the Integration::MJD has been set
  if( phase->has_folding_predictor() )
  {
    if (verbose > 2)
      cerr << "dsp::Archiver::set has predictor" << endl;
    archive-> set_model ( phase->get_folding_predictor(), false );
  }
  else if (verbose > 2)
    cerr << "dsp::Archiver::set PhaseSeries has no predictor" << endl;

  if (phase->has_pulsar_ephemeris())
    archive-> set_ephemeris( phase->get_pulsar_ephemeris(), false );

  archive-> set_filename (get_filename (phase));

  if (verbose > 2) cerr << "dsp::Archiver set archive filename to '"
        	    << archive->get_filename() << "'" << endl;
}
catch (Error& error)
{
  throw error += "dsp::Archiver::set Pulsar::Archive";
}
Exemple #2
0
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;
}