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// Utilisation de SOPHYA pour faciliter les tests ...
#include "sopnamsp.h"
#include "machdefs.h"

/* ---------------------------------------------------------- 
   Projet BAORadio/PAON4 - (C) LAL/IRFU  2017

   visiavg: programme de lecture des fichiers matrices de 
   visibilites de PAON4, calcul de visibilities moyennes 
    en bin de temps et de frequence
   O. Perdereau, R.Ansari   -  LAL
   ---------------------------------------------------------- */

// include standard c/c++
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#include <iostream>
#include <string>

#include "pexceptions.h"
#include "tvector.h"
#include "fioarr.h"
// #include "tarrinit.h"
#include "ntuple.h" 
#include "datatable.h" 
#include "histinit.h" 
#include "matharr.h" 
#include "timestamp.h"
#include <utilarr.h>

// include sophya mesure ressource CPU/memoire ...
#include "resusage.h"
#include "ctimer.h"
#include "timing.h"

// include lecteur de fichiers visibilites 
#include "p4autils.h"
#include "visip4reader.h"
#include "p4gnugain.h"

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#include "fitsioserver.h"
#include "fiosinit.h"

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int Usage(void);
int Usage(void)
{
  cout << " --- visiavg.cc : Read PPF files produced by mfacq time-frequency\n" << endl;
  cout << " Usage: visiavg [-arguments] \n" << endl;
  P4AnaParams::UsageOptions();
  cout<< endl;
  return 1;
}

//----------------------------------------------------
int main(int narg, const char* arg[])
{
  // --- Decoding parameters 
  if( (narg<2) || ((narg>1)&&(strcmp(arg[1],"-h")==0) ) )  return Usage();
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  FitsIOServerInit();
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  P4AnaParams params;
  params.DecodeArgs(narg, arg);
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  string outfile = params.outfile_;
  if (outfile.length()<1)  outfile = "visavg.ppf";
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  string fitsoutfile = params.fitsoutfile_;
  if (fitsoutfile.length()>=1) {
    fitsoutfile = "!"+fitsoutfile ; // adds '!' ?
  }
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  int deltaIavg = params.TFMtimebin_;
  sa_size_t TFMfbin = params.TFMfreqbin_;
  int Imin = params.Imin_, Imax = params.Imax_, Istep = params.Istep_; 
  int prtlev = params.prtlev_;
  bool FgTFMAC = true;
  bool FgTFMCX = true;
  string desctfmap;
  bool FgTFM = params.fgTFM_;   // true -> create time-frequency maps

  params.Print(cout);
  cout <<"visiavg/Info: Path BAO5:"<<params.inpath5_<<" BAO6:"<<params.inpath6_<<"\n"
       <<"fgreorderfreq="<<params.fgreorderfreq_<<"\n"
       <<"Imin,max,step="<<Imin<<","<<Imax<<","<<Istep<<" DeltaIAvg="<<deltaIavg<<"\n"
       <<"outfile="<<outfile<<" PrtLev="<<prtlev<<endl;

  if (!FgTFM) {
    cout<<" visiavg/parameter error : specify Time-Frequency map parameter with -tfm "<<endl;
    return 5;
  }

  P4AVisiNumEncoder  visiencod;
  vector<sa_size_t> KVAC = visiencod.getAllAutoCor();
  vector<sa_size_t> KVCXHH = visiencod.getAllHCrossCor();
  cout << " List of AutoCorrelation rows:"<<endl;
  for(size_t k=0; k<KVAC.size(); k++) {
    cout << "KVAC["<<k<<"]="<<KVAC[k]<<"  ->"<<visiencod.Convert2VisiName(KVAC[k])<<endl;
  }
  cout << " List of HH X-cor rows:"<<endl;
  for(size_t k=0; k<KVCXHH.size(); k++) {
    cout << "KVCXHH["<<k<<"]="<<KVCXHH[k]<<"  ->"<<visiencod.Convert2VisiName(KVCXHH[k])<<endl;
  }
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  // ---
  HiStatsInitiator _inia;
  int rc = 0;
  try {
    ResourceUsage resu;

    // Gain correction class
    P4gnuGain p4g(params.gain_gnu_file_);

    // setting up input visi reader
    vector<string> paths; 
    paths.push_back(params.inpath5_); 
    paths.push_back(params.inpath6_);

    
    VisiP4ReaderBase * reader = VisiP4ReaderBase::getReader(paths);
    VisiP4ReaderBase & vreader = (*reader);
    vreader.setFreqReordering(params.fgreorderfreq_);
    if (!params.fgserall_ && !params.fgtmsel_) {
      cout << " vreader.SelectSerialNum(Imin="<<Imin<<" ,Imax="<<Imax<<" ,Istep="<<Istep<<")"<<endl;
      vreader.SelectSerialNum(Imin,Imax,Istep);
    }
    else if (params.fgserall_) {
      cout << " vreader.SelectAll() ... " << endl;
      vreader.SelectAll();
    }
    else {
      TimeStamp tustart = params.tmsel_tu_;  tustart.ShiftSeconds(-params.tmsel_duration_*30.);
      TimeStamp tuend = params.tmsel_tu_;  tuend.ShiftSeconds(params.tmsel_duration_*30.);
      cout << " vreader.SelectTimeFrame(TUStart="<<tustart.ToString()<<" ,TUEnd="<<tuend.ToString()
	   <<" ,Istep="<<Istep<<")"<<endl;
      vreader.SelectTimeFrame(tustart, tuend, Istep);
    }
    vreader.setPrintLevel(prtlev);

    Imin = vreader.getSerialFirst(); Imax =  vreader.getSerialLast();   Istep =  vreader.getSerialStep();
    cout << "visiavg/Info: processing visibility matrix serial/sequence number range "
	 <<Imin<<" <= seq <= " << Imax << " with step="<<Istep<<endl;

    bool fgok=true;
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    // vecteur de noms 
    vector <string> ext_names;
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    // un vecteur avec les temps 
    TVector< double > timevec((Imax-Imin)/Istep/deltaIavg); 
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    TVector< double > ravec((Imax-Imin)/Istep/deltaIavg); 
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    TMatrix< complex<r_4> > vismtx;
    TMatrix< complex<r_4> > acsum;
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    TMatrix< r_4 > acsum_sq; // wil sum only the real part ^2
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    TMatrix< complex<r_4> > cxsum;
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    // for sums of real and imag parts 
    TMatrix< r_4 > cxsum_sq_rp;
    TMatrix< r_4 > cxsum_sq_ip;
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    TimeStamp dateobs, cfdate,datestart;
    TimeStamp dateorg(2015,1,1,12,0,0.);  // Date origine 1 jan 2015
    double mttag;
    int cnt=0, cntnt=0, pcntnt=0;
    int I=0; 
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    // for
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    //----- 6 H-H cross-cor TimeFrequency maps 
    vector< TArray< complex<r_4> > > vtfm;
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    //----- 6 H-H cross-cor TimeFrequency maps for the variances of real and imag parts 
    vector< TArray< r_4 > > vtfm_rp_sq;
    vector< TArray< r_4 > > vtfm_ip_sq;

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    //----- 8 auto-corr TimeFrequency maps 
    vector< TArray< r_4 > > vtfmac;
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    //----- 8 auto-corr TimeFrequency variance maps 
    vector< TArray< r_4 > > vtfmac_sq;
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    //---- for the time-freqency map filling    
    sa_size_t TFMtmidx=0;
    sa_size_t tfmSX, tfmSY;

    while (fgok) {
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      //reads next visimtx
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      fgok=vreader.ReadNext(vismtx, cfdate, mttag);
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      if (!fgok)  break;
      // Apply gain g(nu)
      p4g.applyGain(vismtx);
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      if (cnt==0)  {    //resizing matrices for sum of auto-correlations and sum of 6 cross-correlations 
	acsum.SetSize(8, vismtx.NCols());
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	acsum_sq.SetSize(8, vismtx.NCols());
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	cxsum.SetSize(6, vismtx.NCols());
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	cxsum_sq_rp.SetSize(6, vismtx.NCols());
	cxsum_sq_ip.SetSize(6, vismtx.NCols());

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	tfmSX=(Imax-Imin)/Istep/deltaIavg;
	tfmSY=vismtx.NCols()/TFMfbin;
	//allocating 8 Auto-Corr time-frequency maps 
	cout<<"visiavg/Info: allocating 8 AutoCor Time-Frequency maps : Time->NX="<<tfmSX<<" x Freq->NY="<<tfmSY<<endl;
	for(int k=0; k<8; k++) vtfmac.push_back( TArray< r_4 >(tfmSX, tfmSY) ); 
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	cout <<" and 8 for the the variance maps "<<endl;
	for(int k=0; k<8; k++) vtfmac_sq.push_back( TArray< r_4 >(tfmSX, tfmSY) ); 

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	//allocating 6 Cross-Corr H-H time-frequency maps 
	cout<<"visiavg/Info: allocating H-H cross-cor Time-Frequency maps : Time->NX="<<tfmSX<<" x Freq->NY="<<tfmSY<<endl;
	for(int k=0; k<6; k++) vtfm.push_back( TArray< complex<r_4> >(tfmSX, tfmSY) );
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	cout << "and the 2x6 for squares of rela & imag parts " << endl;
	for(int k=0; k<6; k++) vtfm_rp_sq.push_back( TArray< r_4 >(tfmSX, tfmSY) );
	for(int k=0; k<6; k++) vtfm_ip_sq.push_back( TArray< r_4 >(tfmSX, tfmSY) );
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	// recupere le jour de depart @ 0h
	datestart = TimeStamp(cfdate.DaysPart(),0.);
 
      }
      if (I==0) {   // start filling a new time bin 
	dateobs=cfdate;
	if (prtlev>0) 
	  cout<<"visiavg/Info:  dateobs="<<dateobs<<" SecondsPart()="<<dateobs.SecondsPart()<<endl;
	acsum = complex<r_4>(0.,0.);
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	acsum_sq = 0.;
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	cxsum = complex<r_4>(0.,0.);
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	cxsum_sq_rp = 0.;
	cxsum_sq_ip = 0.;
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      }
      
      //   sum (integration) along the time axis 
      for(size_t k=0; k<KVAC.size(); k++)      acsum.Row(k) += vismtx.Row(KVAC[k]);     // Les auto-correlations 
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      for(size_t k=0; k<KVAC.size(); k++)      {
	TVector<r_4> tmp = real(vismtx.Row(KVAC[k]));
	acsum_sq.Row(k) += tmp.MulElt(tmp,tmp) ;
      }

      for(size_t k=0; k<KVCXHH.size(); k++){
	cxsum.Row(k) += vismtx.Row(KVCXHH[k]);   // les cross-correlations 

	TVector<r_4> tmp = real(vismtx.Row(KVCXHH[k]));
	cxsum_sq_rp.Row(k) +=  tmp.MulElt(tmp,tmp) ;

	tmp = imag(vismtx.Row(KVCXHH[k]));
	cxsum_sq_ip.Row(k) +=  tmp.MulElt(tmp,tmp) ;

      }


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      I++;    // incrementing DeltaTime counter 
      
      if (I==deltaIavg) {
	//---- On s'occupe d'abord des autocorrelations P1 ... P8 
	for(size_t k=0; k<KVAC.size(); k++) {  // Loop over the 8 auto-correlations 
	  TVector<r_4> vac = real(acsum.Row(k));
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	  TVector<r_4> vacsq = acsum_sq.Row(k);
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	  if (TFMtmidx<tfmSX) {  // we check that our time index did not go beyond the allocated array size (might not be necessary)
	    TArray< r_4 > & tfmap = vtfmac[k];
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	    TArray< r_4 > & tfmap_sq = vtfmac_sq[k];
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	    for(sa_size_t jy=0; jy<tfmSY; jy++) {  // frequency binning 
	      tfmap(TFMtmidx, jy) = vac( Range(jy*TFMfbin, (jy+1)*TFMfbin-1) ).Sum();
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	      tfmap_sq(TFMtmidx, jy) = vacsq( Range(jy*TFMfbin, (jy+1)*TFMfbin-1) ).Sum();

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	    } 
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	  }
  
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	}  //----- end of loop over the 8 AutoCor
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	//---- On s'occupe des 6 cross-correlations  1H-2H ... 3H-4H 
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 	for(size_t k=0; k<KVCXHH.size(); k++)   {   // loop over the 6 Xcor 	  
	  TVector< complex<r_4> > vcx = cxsum.Row(k);
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	  TVector<r_4>  vcxprsq = cxsum_sq_rp.Row(k);
	  TVector<r_4>  vcxpisq = cxsum_sq_ip.Row(k);
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	  if (TFMtmidx<tfmSX) {  // we check that our time index did not go beyond the allocated array size (might not be necessary) 
	    TArray< complex<r_4> > & tfmap = vtfm[k];
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	    TArray< r_4 > & tfmapsqpr = vtfm_rp_sq[k];
	    TArray< r_4 > & tfmapsqpi = vtfm_ip_sq[k];
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	    for(sa_size_t jy=0; jy<tfmSY; jy++) {
	      tfmap(TFMtmidx, jy) = vcx( Range(jy*TFMfbin, (jy+1)*TFMfbin-1) ).Sum();
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	      tfmapsqpr(TFMtmidx, jy) = vcxprsq( Range(jy*TFMfbin, (jy+1)*TFMfbin-1) ).Sum();
	      tfmapsqpi(TFMtmidx, jy) = vcxpisq( Range(jy*TFMfbin, (jy+1)*TFMfbin-1) ).Sum();
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	    } 
	  }  
	}  //----- end of loop over the 6 Xcor 
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	double tdif =  cfdate.TimeDifferenceSeconds(cfdate,dateobs)/2.;
	timevec(TFMtmidx) = dateobs.TimeDifferenceSeconds(dateobs.ShiftSeconds (tdif ),datestart);	// centre du bin 
	ravec(TFMtmidx) = P4Coords::RAFromTimeTU(dateobs);
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	TFMtmidx++;
	//  ... done 
	I=0;  cntnt++;
      }
      cnt++;
      if ((cnt>0)&&(cntnt%10==0)&&(cntnt>pcntnt)) {
	cout<<"visiavg/Info: TFM-Map fill cnt="<<cntnt<<" VisMtxCount="<<cnt<<" /Max="<<Imax<<" DateObs="<<dateobs<<endl;
	pcntnt=cntnt;
      }
    }
    cout<<"visiavg/Info: count="<<cnt<<" visimtx read "<<endl;

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    // --- Sauvegarde cartes temps-frequence en fits 
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    //FitsABTWriter * fbtw = NULL;
    FitsInOutFile  * fos = NULL ;
    if (fitsoutfile.length()>=1){
      //cout<<">>>>> Creating a new fits file with FitsABTWriter"<<endl;
      //fbtw = new FitsABTWriter(fitsoutfile,BINARY_TBL,3);
      //fbtw->SetExtName("Test fits table 1");
      //i1 = fbtw.AddCol("Time",NULL,"unit1",TDOUBLE);

      cout << " fitsoutfile" <<fitsoutfile<< endl;
      fos = new FitsInOutFile(fitsoutfile, FitsInOutFile::Fits_Create);
    }
    
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    POutPersist potfm(outfile);
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    char bufnam[10];
    int numkey =0;
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    // --- renormalizing and saving AutoCorr time-frequency maps 
    cout<<"  visiavg/Info: Saving 8 AutoCorr time-frequency maps to PPF file "<<outfile<<endl;
    const char* tfm_names[8]={"TFM_1H", "TFM_2H", "TFM_3H", "TFM_4H", "TFM_1V", "TFM_2V", "TFM_3V", "TFM_4V"};
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    const char* tfmsq_names[8]={"VARTFM_1H", "VARTFM_2H", "VARTFM_3H", "VARTFM_4H", "VARTFM_1V", "VARTFM_2V", "VARTFM_3V", "VARTFM_4V"};
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    for(int k=0; k<8; k++)  {   // loop over the 8 AutoCorr 
      TArray< r_4 > & tfmap = vtfmac[k];
      tfmap *= (r_4)(1./((double)deltaIavg*(double)TFMfbin));
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      TArray< r_4 > & tfmapsq = vtfmac_sq[k];
      tfmapsq *= (r_4)(1./((double)deltaIavg*(double)TFMfbin));
      tfmapsq = tfmapsq - tfmap.MulElt(tfmap,tfmap) ; 
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      potfm << PPFNameTag(tfm_names[k]) << tfmap;
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      potfm << PPFNameTag(tfmsq_names[k]) << tfmapsq;
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      if (fos != NULL) {
	ext_names.push_back(tfm_names[k]);
	(*fos)<<  tfmap;
	ext_names.push_back(tfmsq_names[k]);
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	(*fos)<<  tfmapsq;
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      }
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    }
    // --- renormalizing and saving H-H Cross-Corr time-frequency maps 
    cout<<"  visiavg/Info: Saving 6 H-H cross-corr time-frequency maps to PPF file "<<outfile<<endl;
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    const char* tfmCC_names[6]={"TFM_1H2H", "TFM_1H3H", "TFM_1H4H", "TFM_2H3H", "TFM_2H4H", "TFM_3H4H"};
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    const char* vrtfmCC_names[6]={"RVARTFM_1H2H", "RVARTFM_1H3H", "RVARTFM_1H4H", "RVARTFM_2H3H", "RVARTFM_2H4H", "RVARTFM_3H4H"};
    const char* vitfmCC_names[6]={"IVARTFM_1H2H", "IVARTFM_1H3H", "IVARTFM_1H4H", "IVARTFM_2H3H", "IVARTFM_2H4H", "IVARTFM_3H4H"};

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    for(int k=0; k<6; k++)  {   // loop over the 6 Xcor 
      TArray< complex<r_4> > & tfmap = vtfm[k];
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      TArray< r_4 > & tfmap_sqpr = vtfm_rp_sq[k];
      TArray< r_4 > & tfmap_sqpi = vtfm_ip_sq[k];
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      tfmap *= complex<r_4>((r_4)(1./((double)deltaIavg*(double)TFMfbin)), 0.);
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      TArray< r_4 >  tfmapr = real(tfmap);
      TArray< r_4 >  tfmapi = imag(tfmap);

      tfmap_sqpr *= ((r_4)(1./((double)deltaIavg*(double)TFMfbin)));
      tfmap_sqpi *= ((r_4)(1./((double)deltaIavg*(double)TFMfbin)));
      tfmapr = tfmapr.MulElt(tfmapr,tfmapr) ;
      tfmap_sqpr -= tfmapr ;
      tfmapi = tfmapi.MulElt(tfmapi,tfmapi) ;
      tfmap_sqpi -= tfmapi;
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      potfm << PPFNameTag(tfmCC_names[k]) << tfmap;
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      potfm << PPFNameTag(vrtfmCC_names[k]) << tfmap_sqpr;
      potfm << PPFNameTag(vitfmCC_names[k]) << tfmap_sqpi;
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      if (fos != NULL) {
	ext_names.push_back(string(tfmCC_names[k])+"_real");
	(*fos)<<  real(tfmap);
	ext_names.push_back(string(tfmCC_names[k])+"_imag");
	(*fos)<<  imag(tfmap);
	ext_names.push_back(vrtfmCC_names[k]);
	(*fos)<<  tfmap_sqpr;
	ext_names.push_back(vitfmCC_names[k]);
	(*fos)<<  tfmap_sqpi;
      }
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    }
    potfm << PPFNameTag("TimeVec") << timevec ;
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    potfm << PPFNameTag("RAVec") << ravec ;
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    // --- FIN sauvegarde cartes temps-frequence 
    //    resu.Update();
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    P4FreqBand myp4fre;
    TVector <double> avg_freqs( myp4fre.getP4NbFreqChannels()/TFMfbin);
    double frbase =  myp4fre.freqstart_ + myp4fre.getP4FreqResolution()/2. ;

    for (int kf=0 ; kf< myp4fre.getP4NbFreqChannels()/TFMfbin ; kf++,frbase +=myp4fre.getP4FreqResolution() )
      avg_freqs(kf) = frbase ;
    potfm << PPFNameTag("FreqVec") << avg_freqs;
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    if (fos != NULL) {
      ext_names.push_back("Frequences");
      (*fos)<< avg_freqs ;
      ext_names.push_back("RAs");
      (*fos)<<  ravec;
      ext_names.push_back("Times");
      (*fos)<<  timevec;
      cout << " number of objs in fits "<< ext_names.size() << endl;
      cout << ext_names << endl;
      delete(fos);
    }
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    cout << resu;   // Update est fait lors du print
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  }
  catch (PException& exc) {
    cerr << " visiavg.cc catched PException " << exc.Msg() << endl;
    rc = 77;
  }  
  catch (std::exception& sex) {
    cerr << "\n visiavg.cc std::exception :" 
         << (string)typeid(sex).name() << "\n msg= " 
         << sex.what() << endl;
    rc = 78;
  }
  catch (...) {
    cerr << " visiavg.cc catched unknown (...) exception  " << endl; 
    rc = 79; 
  } 

  cout << ">>>> visiavg.cc ------- END ----------- RC=" << rc << endl;
  return rc;

}