// Utilisation de SOPHYA pour faciliter les tests ...
#include <regex.h>
//#include <regexp.h>
#include <stdio.h>

#include "sopnamsp.h"
#include "machdefs.h"

#include <stdlib.h>
#include <dirent.h>
#include <matharr.h>

// include standard c/c++
#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include <map>
#include <functional>
#include <algorithm>
#include <numeric>
#include <list>
#include <exception>

// include sophya mesure ressource CPU/memoire ...
#include "resusage.h"
#include "ctimer.h"
#include "timing.h"
#include "timestamp.h"
#include "strutilxx.h"
#include "ntuple.h"
#include "fioarr.h"
#include "tarrinit.h"
#include "histinit.h"
#include "fitsioserver.h"
#include "fiosinit.h"
#include "ppersist.h"

//-----------------------------------------------
const sa_size_t NUMBER_OF_CHANNELS = 2;
const sa_size_t NUMBER_OF_FREQ     = 8192;
const sa_size_t TOTAL_NUM_CYCLES   = 500;
const r_4    LOWER_FREQUENCY       = 1250.0; //MHz
const r_4    TOTAL_BANDWIDTH       = 250.0;  //MHz
//-----------------------------------------------
//Input parameters
struct Param {
  int debuglev_;      //debug
  string inPath_;     //root directory of the input files
  string outPath_;    //output files are located here
  string sourceName_; //source name & subdirectory of the input files
  string ppfFile_;    //generic name of the input files
  int nSliceInFreq_;  //used by reduceSpectra() fnc
  string typeOfCalib_;//type of calibration to be done
  string calibFreq_;  //freq. value used for calibration
} para;
//--------------------------------------------------------------
//Utility functions

sa_size_t freqTochan(r_4 f){
  return (sa_size_t)((f-LOWER_FREQUENCY)/TOTAL_BANDWIDTH*NUMBER_OF_FREQ);
}
//---------
class median_of_empty_list_exception:public std::exception{
    virtual const char* what() const throw() {
    return "Attempt to take the median of an empty list of numbers.  "
      "The median of an empty list is undefined.";
  }
  };
  template<class RandAccessIter>
    double median(RandAccessIter begin, RandAccessIter end) 
    throw(median_of_empty_list_exception){
    if(begin == end){ throw median_of_empty_list_exception(); }
    std::size_t size = end - begin;
    std::size_t middleIdx = size/2;
    RandAccessIter target = begin + middleIdx;
    std::nth_element(begin, target, end);
    
    if(size % 2 != 0){ //Odd number of elements
      return *target;
    }else{            //Even number of elements
      double a = *target;
      RandAccessIter targetNeighbor= target-1;
      std::nth_element(begin, targetNeighbor, end);
      return (a+*targetNeighbor)/2.0;
    }
  }

//-------------
void split(const string& str, const string& delimiters , vector<string>& tokens) {
    // Skip delimiters at beginning.
    string::size_type lastPos = str.find_first_not_of(delimiters, 0);
    // Find first "non-delimiter".
    string::size_type pos     = str.find_first_of(delimiters, lastPos);

    while (string::npos != pos || string::npos != lastPos)
    {
        // Found a token, add it to the vector.
        tokens.push_back(str.substr(lastPos, pos - lastPos));
        // Skip delimiters.  Note the "not_of"
        lastPos = str.find_first_not_of(delimiters, pos);
        // Find next "non-delimiter"
        pos = str.find_first_of(delimiters, lastPos);
    }
}
//--------------------------------------------------------------
char *regexp (const char *string, const char *patrn, int *begin, int *end) {    
        int i, w=0, len;                 
        char *word = NULL;
        regex_t rgT;
        regmatch_t match;
        regcomp(&rgT,patrn,REG_EXTENDED);
        if ((regexec(&rgT,string,1,&match,0)) == 0) {
                *begin = (int)match.rm_so;
                *end = (int)match.rm_eo;
                len = *end-*begin;
                word=(char*)malloc(len+1);
                for (i=*begin; i<*end; i++) {
                        word[w] = string[i];
                        w++; }
                word[w]=0;
        }
        regfree(&rgT);
        return word;
}
//------- 
sa_size_t round_sa(r_4 r) {
  return static_cast<sa_size_t>((r > 0.0) ? (r + 0.5) : (r - 0.5));
}
//-----
string StringToLower(string strToConvert){
  //change each element of the string to lower case
  for(unsigned int i=0;i<strToConvert.length();i++) {
    strToConvert[i] = tolower(strToConvert[i]);
  }
  return strToConvert;//return the converted string
}
//-----
bool stringCompare( const string &left, const string &right ){
   if( left.size() < right.size() )
      return true;
   for( string::const_iterator lit = left.begin(), rit = right.begin(); lit != left.end() && rit != right.end(); ++lit, ++rit )
      if( tolower( *lit ) < tolower( *rit ) )
         return true;
      else if( tolower( *lit ) > tolower( *rit ) )
         return false;
   return false;
}
//-----
list<string> ListOfFileInDir(string dir, string filePettern) throw(string) {
  list<string> theList;


  DIR *dip;
  struct dirent *dit;
  string msg;  string fileName;
  string fullFileName;
  size_t found;

  if ((dip=opendir(dir.c_str())) == NULL ) {
    msg = "opendir failed on directory "+dir;
    throw msg;
  }
  while ( (dit = readdir(dip)) != NULL ) {
    fileName = dit->d_name;
    found=fileName.find(filePettern);
    if (found != string::npos) {
      fullFileName = dir + "/";
      fullFileName += fileName;
      theList.push_back(fullFileName);
    }
  }//eo while
  if (closedir(dip) == -1) {
    msg = "closedir failed on directory "+dir;
    throw msg;
  }
  
  theList.sort(stringCompare);

  return theList;

}
//
class  StringMatch : public unary_function<string,bool> {
public:
  StringMatch(const string& pattern): pattern_(pattern){}
  bool operator()(const string& aStr) const {


    int b,e;
    regexp(aStr.c_str(),pattern_.c_str(),&b,&e);

//     cout << "investigate " << aStr << " to find " << pattern_ 
// 	 << "[" <<b<<","<<e<<"]" 
// 	 << endl;

    
    if (b != 0) return false;
    if (e != (int)aStr.size()) return false;
    return true;

  }
private:
  string pattern_;
};
//-------------------------------------------------------
//Rebin in frequence + compute mean and sigma
void reduceSpectra(const TMatrix<r_4>& specMtxInPut, 
		    TMatrix<r_4>& meanMtx, 
		    TMatrix<r_4>& sigmaMtx) {
  sa_size_t nSliceFreq = para.nSliceInFreq_;
  sa_size_t deltaFreq =  NUMBER_OF_FREQ/nSliceFreq;
  for (sa_size_t iSlice=0; iSlice<nSliceFreq; iSlice++){
    sa_size_t freqLow= iSlice*deltaFreq;
    sa_size_t freqHigh= freqLow + deltaFreq -1;
    for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; ++iCh){
      TVector<r_4> reducedRow;
      reducedRow = specMtxInPut.SubMatrix(Range(iCh),Range(freqLow,freqHigh)).CompactAllDimensions();
      double mean; 
      double sigma;
      MeanSigma(reducedRow,mean,sigma);
      meanMtx(iCh,iSlice) = mean;
      sigmaMtx(iCh,iSlice) = sigma;
    }//eo loop on channels
  }//eo loop on slices
}
//-------------------------------------------------------
//Compute the mean of Diff ON-OFF BAO-calibrated spectra and also the mean/sigma of rebinned spectra 
//Used like: 
//
// void meanCalibBAODiffOnOffCycles() throw(string) {

//   list<string> listOfFiles;
//   string directoryName;
//   directoryName = para.inPath_ + "/" + para.sourceName_;

//   //Make the listing of the directory
//   listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_);
  
//   list<string>::const_iterator iFile, iFileEnd, iSpecOff, iSpecOffEnd, iSpecOn, iSpecOnEnd;
//   iFileEnd = listOfFiles.end();
  

//   //Loop on files
//   uint_4 nRuns=0;
//   TArray<r_4> tableOfSpectra(NUMBER_OF_FREQ,NUMBER_OF_CHANNELS,TOTAL_NUM_CYCLES); //TOTAL_NUM_CYCLES should be large enough...


//   for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) {
//     if (para.debuglev_>90){
//       cout << "load file <" << *iFile << ">" << endl;
//     }

//     vector<string> tokens;
//     split(*File,"_",tokens);
//     string dateOfRun = tokens[1];
//     string srcLower = tokens[2];
//     if (para.debuglev_>90){
//       cout << "date <" << dateOfRun << ">" << endl;
//     }
    
//     PInPersist fin(*iFile);
//     vector<string> vec = fin.GetNameTags();

//     if (para.typeOfCalib_ == "perRun") {
//       ///////////////////
//       //make the calibration of the mean of all Off and On of the run and perform the difference

//       vector<string> modeList;
//       modeList.push_back("On");
//       modeList.push_back("Off");
//       vector<string>::const_iterator iMode;
//       map<string, TMatrix<r_4> > spectreModeCollect;

//       for (iMode = modeList.begin(); iMode!=modeList.end(); ++iMode) {
// 	///////////////////
// 	//
// 	//Compute the mean of the mode
// 	//
// 	list<string> listOfSpectra;
// 	//Keep only required PPF objects
// 	string matchstr = "specRaw"+(*iMode)+"[0-9]+"; 
// 	std::remove_copy_if(
// 			    vec.begin(), vec.end(), back_inserter(listOfSpectra),
// 			    not1(StringMatch(matchstr))
// 			    );
	
// 	listOfSpectra.sort(stringCompare);
// 	iSpecEnd = listOfSpectra.end();
// 	TMatrix<r_4> meanOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
// 	uint_4 nSpectra=0;
// 	//Loop of spectra matrix
// 	for (iSpec = listOfSpectra.begin(); iSpec!=iSpecEnd;  ++iSpec){
// 	  if (para.debuglev_>90){
// 	    cout << " spactra <" << *iSpec << ">" << endl;
// 	  }
// 	  TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
// 	  fin.GetObject(aSpec,*iSpec);
// 	  //How to see if the GetObject is ok?? Ask Reza
// 	  nSpectra++;
// 	  meanOfSpectra+=aSpec;
// 	}//end loop Off
// 	//Mean
// 	if(nSpectra>0)meanOfSpectra=(r_4)(nSpectra);

// 	//BAO Calibrator
// 	string calibFileName = directoryName + "/" 
// 	  + "calib_" + dateOfRun + "_" + srcLower + "_"+(*iMode)+"_" 
// 	  + para.calibFreq_ +"MHz-All.txt";
// 	if(debuglev_>0) cout << "Read Calib file " << calibFileName << endl;
// 	ifstream ifs(calibFileName.c_str());
// 	if ( ! ifs.is_open() ) {
// 	  rc = 999;
// 	  throw calibFileName + " cannot be opened...";
// 	}	
// 	TVector<r_4> calibBAOfactors;
// 	sa_size_t nr,nc; //values read 
// 	calibBAOfactorsOff.ReadASCII(ifs,nr,nc);
// 	if(debuglev_>9){
// 	  cout << "(nr,nc): "<< nr << "," << nc << endl;
// 	  calibBAOfactors.Print(cout);
// 	}
	
// 	for (sa_size_t iCh=0;iCh<NUMBER_OF_CHANNELS;++iCh){
// 	  meanOfSpectra(Range(iCh), Range::all()) /=calibBAOfactors(iCh);
// 	}
// 	//storage
// 	spectreModeCollect.insert(pair<string, TMatrix<r_4> >(*iMode,TMatrix<r_4>(meanOfSpectra,false))); //do not share data (cf. SOPHYA) 
//       }//end of mode

//       //Take the difference ON-OFF in current run
//       TMatrix<r_4>diffOnOff = spectreModeCollect["On"]-spectreModeCollect["Off"];


//     } else if (para.typeOfCalib_ == "perCycle") {
//       //perform the calibration of the OFF and ON per cycle, then make the mean and take the diff
//     } else {
//       string msg="FATAL (meanCalibBAODiffOnOffCycles); unknown calibration mode " 
// 	+ para.typeOfCalib_ ;
//       throw(msg);
//     }  


//     nRuns++;
    
//   }//eo loop on spectra in a file
// }
void meanCalibBAODiffOnOffCycles() throw(string) {

  list<string> listOfFiles;
  string directoryName;
  directoryName = para.inPath_ + "/" + para.sourceName_;

  //Make the listing of the directory
  listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_);
  
  list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd;
  iFileEnd = listOfFiles.end();

  //Loop on files/run
  uint_4 totalNumberCycles=0; //total number of cycles for normalisation
  for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) {
    if (para.debuglev_>90){
      cout << "load file <" << *iFile << ">" << endl;
    }

    vector<string> tokens;
    split(*iFile,"_",tokens);
    string dateOfRun = tokens[1];
    if (para.debuglev_>90){
      cout << "date <" << dateOfRun << ">" << endl;
    }
    vector<string> tokens2;
    split(tokens[2],".",tokens2);
    string srcLower = tokens2[0];


    
    PInPersist fin(*iFile);
    vector<string> vec = fin.GetNameTags();

    vector<string> modeList;
    modeList.push_back("On");
    modeList.push_back("Off");
    vector<string>::const_iterator iMode;
    
    map<string, list<int> > cycleModeCollect;
    
    for (iMode = modeList.begin(); iMode!=modeList.end(); ++iMode) {
      list<string> listOfSpectra;
      //Keep only required PPF objects
      string matchstr = "specRaw"+(*iMode)+"[0-9]+"; 
      std::remove_copy_if(
			  vec.begin(), vec.end(), back_inserter(listOfSpectra),
			  not1(StringMatch(matchstr))
			  );
      
      listOfSpectra.sort(stringCompare);
      iSpecEnd = listOfSpectra.end();
      
      matchstr = "[0-9]+";
      //Loop of spectra matrix
      list<int> listOfCycles;
      for (iSpec = listOfSpectra.begin(); iSpec!=iSpecEnd;  ++iSpec){
	int b,e;
	regexp(iSpec->c_str(),matchstr.c_str(),&b,&e);
	if (para.debuglev_>90){
	  cout << " spactra <" << *iSpec << ">" << endl;
	  cout << " cycle " << iSpec->substr(b) << endl;
	}
	listOfCycles.push_back(atoi((iSpec->substr(b)).c_str()));
      }//end loop spectra
      cycleModeCollect[*iMode] = listOfCycles;
    }//end of mode    

    //Take the Intersection of the list Of cycles in mode Off and On    
    list<int> commonCycles;
    set_intersection(cycleModeCollect["On"].begin(),
		     cycleModeCollect["On"].end(),
		     cycleModeCollect["Off"].begin(),
		     cycleModeCollect["Off"].end(),
		     back_inserter(commonCycles)
		     );
    
    if (para.debuglev_>90){
      cout << "Liste of cycles common to On & Off: <";
      for (list<int>::iterator i=commonCycles.begin(); i!=commonCycles.end(); ++i){
	cout << *i << " ";
      }
      cout << ">" << endl;
    }
    
    //
    //Load BAO Calibration factors "per Cycle and Channels"
    //Compute the mean per Cycle to 
    //  fill factors "per Run and Channels" with the same cycle list
    //
    //
    //TODO improve the code....

    TMatrix<r_4> calibBAOfactors_Off_Cycle_Ch0;
    TMatrix<r_4> calibBAOfactors_Off_Cycle_Ch1;
    TMatrix<r_4> calibBAOfactors_On_Cycle_Ch0;
    TMatrix<r_4> calibBAOfactors_On_Cycle_Ch1;
    
    string calibFileName;
    ifstream ifs;
    sa_size_t nr,nc; //values read 

    //OFF Cycle per Channel
    calibFileName = directoryName + "/" 
      + "calib_" + dateOfRun + "_" + srcLower + "_Off_" 
      + para.calibFreq_ +"MHz-Ch0Cycles.txt";
    if(para.debuglev_>0) cout << "Read Calib file " << calibFileName << endl;
    ifs.open(calibFileName.c_str());
    if ( ! ifs.is_open() ) {

      throw calibFileName + " cannot be opened...";
    }	
    calibBAOfactors_Off_Cycle_Ch0.ReadASCII(ifs,nr,nc);
    if(para.debuglev_>9){
      cout << "(nr,nc): "<< nr << "," << nc << endl;
      calibBAOfactors_Off_Cycle_Ch0.Print(cout);
    }

    TMatrix<r_4> calibBAOfactors_Off_Run_Ch0(nr,nc);
    calibBAOfactors_Off_Run_Ch0.Column(0) = calibBAOfactors_Off_Cycle_Ch0.Column(0);
    {//Compute the mean
      TVector<r_4> coef(calibBAOfactors_Off_Cycle_Ch0(Range::all(),Range::last()),false);
      double mean,sigma;
      MeanSigma(coef,mean,sigma);
      cout << "Mean: " << mean << " sigma " << sigma << endl;
      calibBAOfactors_Off_Run_Ch0.Column(1).SetCst(mean);
    }
    if(para.debuglev_>9){
      cout << "Fill calib. with mean value " << endl; 
      calibBAOfactors_Off_Run_Ch0.Print(cout);
    }
    ifs.close();

    //
    calibFileName = directoryName + "/" 
      + "calib_" + dateOfRun + "_" + srcLower + "_Off_" 
      + para.calibFreq_ +"MHz-Ch1Cycles.txt";
    if(para.debuglev_>0) cout << "Read Calib file " << calibFileName << endl;
    ifs.open(calibFileName.c_str());
    if ( ! ifs.is_open() ) {

      throw calibFileName + " cannot be opened...";
    }	
    calibBAOfactors_Off_Cycle_Ch1.ReadASCII(ifs,nr,nc);
    if(para.debuglev_>9){
      cout << "(nr,nc): "<< nr << "," << nc << endl;
      calibBAOfactors_Off_Cycle_Ch1.Print(cout);
    }
    TMatrix<r_4> calibBAOfactors_Off_Run_Ch1(nr,nc);
    calibBAOfactors_Off_Run_Ch1.Column(0) = calibBAOfactors_Off_Cycle_Ch1.Column(0);
    {//Compute the mean
      TVector<r_4> coef(calibBAOfactors_Off_Cycle_Ch1(Range::all(),Range::last()),false);
      double mean,sigma;
      MeanSigma(coef,mean,sigma);
      cout << "Mean: " << mean << " sigma " << sigma << endl;
      calibBAOfactors_Off_Run_Ch1.Column(1).SetCst(mean);
    }
    if(para.debuglev_>9){
      cout << "Fill calib. with mean value " << endl; 
      calibBAOfactors_Off_Run_Ch1.Print(cout);
    }
    ifs.close();

    //ON Cycle per Channel
    calibFileName = directoryName + "/" 
      + "calib_" + dateOfRun + "_" + srcLower + "_On_" 
      + para.calibFreq_ +"MHz-Ch0Cycles.txt";
    if(para.debuglev_>0) cout << "Read Calib file " << calibFileName << endl;
    ifs.open(calibFileName.c_str());
    if ( ! ifs.is_open() ) {

      throw calibFileName + " cannot be opened...";
    }	
    calibBAOfactors_On_Cycle_Ch0.ReadASCII(ifs,nr,nc);
    if(para.debuglev_>9){
      cout << "(nr,nc): "<< nr << "," << nc << endl;
      calibBAOfactors_On_Cycle_Ch0.Print(cout);
	
    }

    TMatrix<r_4> calibBAOfactors_On_Run_Ch0(nr,nc);
    calibBAOfactors_On_Run_Ch0.Column(0) = calibBAOfactors_On_Cycle_Ch0.Column(0);
    {//Compute the mean
      TVector<r_4> coef(calibBAOfactors_On_Cycle_Ch0(Range::all(),Range::last()),false);
      double mean,sigma;
      MeanSigma(coef,mean,sigma);
      cout << "Mean: " << mean << " sigma " << sigma << endl;
      calibBAOfactors_On_Run_Ch0.Column(1).SetCst(mean);
    }
    if(para.debuglev_>9){
      cout << "Fill calib. with mean value " << endl; 
      calibBAOfactors_On_Run_Ch0.Print(cout);
    }
    ifs.close();

    
    calibFileName = directoryName + "/" 
      + "calib_" + dateOfRun + "_" + srcLower + "_On_" 
      + para.calibFreq_ +"MHz-Ch1Cycles.txt";
    if(para.debuglev_>0) cout << "Read Calib file " << calibFileName << endl;
    ifs.open(calibFileName.c_str());
    if ( ! ifs.is_open() ) {
      throw calibFileName + " cannot be opened...";
    }	
    calibBAOfactors_On_Cycle_Ch1.ReadASCII(ifs,nr,nc);
    if(para.debuglev_>9){
      cout << "(nr,nc): "<< nr << "," << nc << endl;
      calibBAOfactors_On_Cycle_Ch1.Print(cout);
    }
    TMatrix<r_4> calibBAOfactors_On_Run_Ch1(nr,nc);
    calibBAOfactors_On_Run_Ch1.Column(0) = calibBAOfactors_On_Cycle_Ch1.Column(0);
    {//Compute the mean
      TVector<r_4> coef(calibBAOfactors_On_Cycle_Ch1(Range::all(),Range::last()),false);
      double mean,sigma;
      MeanSigma(coef,mean,sigma);
      cout << "Mean: " << mean << " sigma " << sigma << endl;
      calibBAOfactors_On_Run_Ch1.Column(1).SetCst(mean);
    }
    if(para.debuglev_>9){
      cout << "Fill calib. with mean value " << endl; 
      calibBAOfactors_On_Run_Ch1.Print(cout);
    }

    ifs.close();
    
    //link <cycle> - <calibration coefficient>
    map<int,r_4> calibBAO_Off_Ch0;
    map<int,r_4> calibBAO_Off_Ch1;
    map<int,r_4> calibBAO_On_Ch0;
    map<int,r_4> calibBAO_On_Ch1;
    if (para.typeOfCalib_ == "perRun") {
      sa_size_t nr = calibBAOfactors_Off_Run_Ch0.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_Off_Ch0[(int)calibBAOfactors_Off_Run_Ch0(0,ir)]
	  = calibBAOfactors_Off_Run_Ch0(1,ir);
      }
      nr = calibBAOfactors_Off_Run_Ch1.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_Off_Ch1[(int)calibBAOfactors_Off_Run_Ch1(0,ir)]
	  = calibBAOfactors_Off_Run_Ch1(1,ir);
      }

      nr = calibBAOfactors_On_Run_Ch0.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_On_Ch0[(int)calibBAOfactors_On_Run_Ch0(0,ir)]
	  = calibBAOfactors_On_Run_Ch0(1,ir);
      }
      nr = calibBAOfactors_On_Run_Ch1.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_On_Ch1[(int)calibBAOfactors_On_Run_Ch1(0,ir)]
	  = calibBAOfactors_On_Run_Ch1(1,ir);
      }
      
    } else if (para.typeOfCalib_ == "perCycle") {

      sa_size_t nr = calibBAOfactors_Off_Cycle_Ch0.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_Off_Ch0[(int)calibBAOfactors_Off_Cycle_Ch0(0,ir)]
	  = calibBAOfactors_Off_Cycle_Ch0(1,ir);
      }
      nr = calibBAOfactors_Off_Cycle_Ch1.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_Off_Ch1[(int)calibBAOfactors_Off_Cycle_Ch1(0,ir)]
	  = calibBAOfactors_Off_Cycle_Ch1(1,ir);
      }

      nr = calibBAOfactors_On_Cycle_Ch0.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_On_Ch0[(int)calibBAOfactors_On_Cycle_Ch0(0,ir)]
	  = calibBAOfactors_On_Cycle_Ch0(1,ir);
      }
      nr = calibBAOfactors_On_Cycle_Ch1.NRows();
      for (sa_size_t ir=0; ir<nr; ++ir){
	calibBAO_On_Ch1[(int)calibBAOfactors_On_Cycle_Ch1(0,ir)]
	  = calibBAOfactors_On_Cycle_Ch1(1,ir);
      }

    } else {
      throw "Unknow calibration type: " + para.typeOfCalib_;
    }


    
// 	for (sa_size_t iCh=0;iCh<NUMBER_OF_CHANNELS;++iCh){
// 	  meanOfSpectra(Range(iCh), Range::all()) /=calibBAOfactors(iCh);
// 	}

    //Loop on cyles
    for (list<int>::iterator ic=commonCycles.begin(); ic!=commonCycles.end(); ++ic){
      string ppftag;
      //load ON phase
      stringstream cycle;
      cycle << *ic;
      
      ppftag = "specRawOn"+cycle.str();
      TMatrix<r_4> aSpecON(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
      fin.GetObject(aSpecON,ppftag);

      



      ppftag = "specRawOff"+cycle.str();
      TMatrix<r_4> aSpecOFF(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
      fin.GetObject(aSpecOFF,ppftag);
      
      totalNumberCycles++;
	
    }//eo loop on cycles

  }//eo loop on spectra in a file
}
//-------------------------------------------------------
//Compute the mean of Diff ON-OFF Raw spectra and also the mean/sigma of rebinned spectra 
//Used like:
//
void meanRawDiffOnOffCycles() throw(string) {
  list<string> listOfFiles;
  string directoryName;
  directoryName = para.inPath_ + "/" + para.sourceName_;

  //Make the listing of the directory
  listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_);
  
  list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd;
  iFileEnd = listOfFiles.end();
  
  StringMatch match("specONOFFRaw[0-9]+"); //Tag of the PPF objects
  TMatrix<r_4> meanOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
  uint_4 nSpectra=0;
  //Loop on files
  for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) {
    if (para.debuglev_>90){
      cout << "load file <" << *iFile << ">" << endl;
    }
    PInPersist fin(*iFile);
    vector<string> vec = fin.GetNameTags();
    list<string> listOfSpectra;
    //Keep only required PPF objects
    std::remove_copy_if(
			vec.begin(), vec.end(), back_inserter(listOfSpectra),
			not1(match)
			);
   
    listOfSpectra.sort(stringCompare);
    iSpecEnd = listOfSpectra.end();
    //Loop of spectra matrix
    for (iSpec = listOfSpectra.begin(); iSpec !=iSpecEnd;  ++iSpec){
      if (para.debuglev_>90){
	cout << " spactra <" << *iSpec << ">" << endl;
      }
      TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
      fin.GetObject(aSpec,*iSpec);
      //How to see if the GetObject is ok?? Ask Reza
      nSpectra++;
      meanOfSpectra+=aSpec;
    }//eo loop on spectra in a file
  }//eo loop on files
  
  //Normalisation
  if(nSpectra>0)meanOfSpectra/=(r_4)(nSpectra);

  //Compute the reduced version of the mean and sigma
  TMatrix<r_4> meanRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_);
  TMatrix<r_4> sigmaRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_);
  reduceSpectra(meanOfSpectra,meanRedMtx,sigmaRedMtx);

  {//Save the result
    stringstream tmp;
    tmp << nSpectra;
    string fileName = para.outPath_+"/meanDiffOnOffRaw_"+StringToLower(para.sourceName_)+"-"+tmp.str()+"Cycles.ppf";
    cout << "Save mean based on " <<  nSpectra << " cycles " << endl;
    POutPersist fos(fileName);

    string tag = "mean";
    fos << PPFNameTag(tag) << meanOfSpectra;
    tag = "meanred";
    fos << PPFNameTag(tag) << meanRedMtx;
    tag = "sigmared";
    fos << PPFNameTag(tag) << sigmaRedMtx;
  }
}
//-------------------------------------------------------
//Compute the median of Diff ON-OFF Raw spectra and also the mean/sigma of rebinned spectra 
//Used like:
//
void medianRawDiffOnOffCycles() throw(string) {
  list<string> listOfFiles;
  string directoryName;
  directoryName = para.inPath_ + "/" + para.sourceName_;

  //Make the listing of the directory
  listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_);
  
  list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd;
  iFileEnd = listOfFiles.end();
  

  TArray<r_4> tableOfSpectra(NUMBER_OF_FREQ,NUMBER_OF_CHANNELS,TOTAL_NUM_CYCLES); //TOTAL_NUM_CYCLES should be large enough...

  StringMatch match("specONOFFRaw[0-9]+"); //Tag of the PPF objects
  uint_4 nSpectra=0;
  //Loop on files
  for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) {
    if (para.debuglev_>90){
      cout << "load file <" << *iFile << ">" << endl;
    }
    PInPersist fin(*iFile);
    vector<string> vec = fin.GetNameTags();
    list<string> listOfSpectra;
    //Keep only required PPF objects
    std::remove_copy_if(
			vec.begin(), vec.end(), back_inserter(listOfSpectra),
			not1(match)
			);
   
    listOfSpectra.sort(stringCompare);
    iSpecEnd = listOfSpectra.end();
    //Loop of spectra matrix
    for (iSpec = listOfSpectra.begin(); iSpec !=iSpecEnd && (sa_size_t)nSpectra < TOTAL_NUM_CYCLES ;  ++iSpec){
      if (para.debuglev_>90){
	cout << " spactra <" << *iSpec << ">" << endl;
      }
      TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
      fin.GetObject(aSpec,*iSpec);

      tableOfSpectra(Range::all(),Range::all(),Range(nSpectra)) = aSpec;

      nSpectra++;
    }//eo loop on spectra in a file
  }//eo loop on files
  

 
  TMatrix<r_4> medianOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ);
  //Compute the median for each freq. and Channel
  for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; iCh++){
    for (sa_size_t freq =0; freq<NUMBER_OF_FREQ; freq++){
      TVector<r_4> tmp0(tableOfSpectra(Range(freq),Range(iCh),Range(0,nSpectra-1)).CompactAllDimensions());
      vector<r_4> tmp;
      tmp0.FillTo(tmp);
      medianOfSpectra(iCh,freq) = median(tmp.begin(),tmp.end());
    }
  }


  //Compute the reduced version of the mean and sigma
  TMatrix<r_4> meanRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_);
  TMatrix<r_4> sigmaRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_);
  reduceSpectra(medianOfSpectra,meanRedMtx,sigmaRedMtx);


  sa_size_t f1320=freqTochan(1320.);
  sa_size_t f1345=freqTochan(1345.);
  sa_size_t f1355=freqTochan(1355.);
  sa_size_t f1380=freqTochan(1380.);
  //Compute baseline arround 1350Mhz on [1320-1345] U [1355-1380]
  if (para.debuglev_>9){
    cout << "Compute baseline arround 1350Mhz on [1320-1345] U [1355-1380]" << endl;
  }
  TVector<r_4>meanMed(NUMBER_OF_CHANNELS);
  for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; ++iCh){
    double meanMed1;
    double sigmaMed1;
    TVector<r_4> band1;
    band1 = medianOfSpectra(Range(iCh),Range(f1320,f1345)).CompactAllDimensions();
    MeanSigma(band1,meanMed1,sigmaMed1);
    double meanMed2;
    double sigmaMed2;
    TVector<r_4> band2;
    band2 = medianOfSpectra(Range(iCh),Range(f1355,f1380)).CompactAllDimensions();
    MeanSigma(band2,meanMed2,sigmaMed2);
    meanMed(iCh) = (meanMed1+meanMed2)*0.5;
  }  
  meanMed.Print(cout);
  
  //Compute the sigma in the range 1320MHz-1380MHz
  if (para.debuglev_>9){
    cout << "Compute the sigma in the range 1320MHz-1380MHz" << endl;
  }
  TVector<r_4>sigmaMed(NUMBER_OF_CHANNELS);
  sa_size_t redf1320=(sa_size_t)((1320.0-LOWER_FREQUENCY)/TOTAL_BANDWIDTH*para.nSliceInFreq_);
  sa_size_t redf1380=(sa_size_t)((1380.0-LOWER_FREQUENCY)/TOTAL_BANDWIDTH*para.nSliceInFreq_);

  for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; ++iCh){
    double meanSigma;
    double sigmaSigma;
    TVector<r_4> band;
    band = sigmaRedMtx(Range(iCh),Range(redf1320,redf1380)).CompactAllDimensions();
    MeanSigma(band,meanSigma,sigmaSigma);
    meanSigma *= sqrt(para.nSliceInFreq_); //to scale to orignal spectra
    sigmaMed(iCh) = meanSigma;
  }
  sigmaMed.Print(cout);
  
  
  if (para.debuglev_>9){
    cout << "Compute medianOfSpectraNorm" << endl;
  }
  TMatrix<r_4> medianOfSpectraNorm(medianOfSpectra,false); //do not share the data...
  for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; ++iCh){
    medianOfSpectraNorm.Row(iCh) -= meanMed(iCh);
    medianOfSpectraNorm.Row(iCh) /= sigmaMed(iCh);
  }

  

  {//Save the result
    stringstream tmp;
    tmp << nSpectra;
    string fileName = para.outPath_+"/medianDiffOnOffRaw_"+StringToLower(para.sourceName_)+"-"+tmp.str()+"Cycles.ppf";
    cout << "Save median based on " <<  nSpectra << " cycles " << endl;
    POutPersist fos(fileName);

    string tag = "median";
    fos << PPFNameTag(tag) << medianOfSpectra;

    tag = "medianNorm";
    fos << PPFNameTag(tag) << medianOfSpectraNorm;
    

    tag = "meanmedred";
    fos << PPFNameTag(tag) << meanRedMtx;
    tag = "sigmamedred";
    fos << PPFNameTag(tag) << sigmaRedMtx;
    tag = "cycleVsfreq";
    
    TArray<r_4> tarr(tableOfSpectra(Range::all(),Range::all(),Range(0,nSpectra-1)));
    fos << PPFNameTag(tag) << tarr;
  }
}

//-------------------------------------------------------
int main(int narg, char* arg[]) {
  
  int rc = 0; //return code
  string msg; //message used in Exceptions



  //default value for initial parameters (see Para structure on top of the file)
  string debuglev = "0";
  string action = "meanDiffOnOff";
  string inputPath = "."; 
  string outputPath = "."; 
  string sourceName = "Abell85";
  string ppfFile;
  string nSliceInFreq = "32";
  string typeOfCalib="perRun";
  string calibFreq = "1346";
  
  //  bool okarg=false;
  int ka=1;
  while (ka<narg) {
    if (strcmp(arg[ka],"-h")==0) {
      cout << "Usage:  -act [meanRawDiffOnOff]|medianRawDiffOnOff|meanCalibBAODiffOnOff\n"
	   << " -calibopt [perRun]|perCcyle (cf. in case of calibration to be done)\n"
	   << " -calibfreq <number> (cf. freq. used by calibration operation)\n"
	   << " -src [Abell85]\n -inPath [.]|<top_root_dir of the ppf file>\n" 
	   << " (ex. /sps/baoradio/AmasNancay/JEC/\n " 
	   << " -outPath [.]|<dir of the output> \n"
	   << " -nSliceInFreq [32]|<number of bin in freq. to cumulate>\n"
	   << " -ppfFile <generic name of the input ppf files> (ex. diffOnOffRaw)\n"
	   << " -debug <level> "
	   << endl;
      return 0;
    }
    else if (strcmp(arg[ka],"-debug")==0) {
      debuglev=arg[ka+1];
      ka+=2;
    }
    else if (strcmp(arg[ka],"-act")==0) {
      action=arg[ka+1];
      ka+=2;
    }
    else if (strcmp(arg[ka],"-calibopt")==0) {
      typeOfCalib=arg[ka+1];
      ka+=2;
    }    
    else if (strcmp(arg[ka],"-calibfreq")==0) {
      calibFreq=arg[ka+1];
      ka+=2;
    }    
    else if (strcmp(arg[ka],"-inPath")==0) {
      inputPath=arg[ka+1];
      ka+=2;
    }
    else if (strcmp(arg[ka],"-outPath")==0) {
      outputPath=arg[ka+1];
      ka+=2;
    }
    else if (strcmp(arg[ka],"-src")==0) {
      sourceName=arg[ka+1];
      ka+=2;
    }
    else if (strcmp(arg[ka],"-ppfFile")==0) {
      ppfFile=arg[ka+1];
      ka+=2;
    }
    else if (strcmp(arg[ka],"-nSliceInFreq")==0) {
      nSliceInFreq=arg[ka+1];
      ka+=2;
    }
    else ka++;
  }//eo while

  para.debuglev_   = atoi(debuglev.c_str());
  para.inPath_     = inputPath;
  para.outPath_    = outputPath;
  para.sourceName_ = sourceName;
  para.ppfFile_    = ppfFile;
  para.nSliceInFreq_ = atoi(nSliceInFreq.c_str());
  para.typeOfCalib_ = typeOfCalib;
  para.calibFreq_   = calibFreq;

  cout << "Dump Initial parameters ............" << endl;
  cout << " action = " << action << "\n"
       << " inputPath = " << para.inPath_  << "\n" 
       << " outputPath = " <<  para.outPath_ << "\n"
       << " sourceName = " << para.sourceName_ << "\n"
       << " ppfFile = " <<  para.ppfFile_ << "\n"
       << " nSliceInFreq = " << para.nSliceInFreq_  << "\n"
       << " typeOfCalib = " << para.typeOfCalib_ << "\n"
       << " calibFreq = " <<  para.calibFreq_ << "\n"
       << " debuglev = "  << para.debuglev_   << "\n";
  cout << "...................................." << endl;

  if ( "" == ppfFile ) {
    cerr << "mergeAnaFiles.cc: you have forgotten ppfFile option"
	 << endl;
    return 999;
  }


  try {

//     int b,e;
//     char *match=regexp("truc0machin","[a-z]+[0-9]*",&b,&e);
//     printf("->%s<-\n(b=%d e=%d)\n",match,b,e);

    if ( action == "meanRawDiffOnOff" ) {
      meanRawDiffOnOffCycles();
    } else if (action == "medianRawDiffOnOff") {
      medianRawDiffOnOffCycles();
    } else if (action == "meanCalibBAODiffOnOff") {
      meanCalibBAODiffOnOffCycles();
    } else {
      msg = "Unknown action " + action;
      throw msg;
    }


  }  catch (std::exception& sex) {
    cerr << "mergeRawOnOff.cc std::exception :"  << (string)typeid(sex).name() 
	 << "\n msg= " << sex.what() << endl;
    rc = 78;
  }
  catch ( string str ) {
    cerr << "mergeRawOnOff.cc Exception raised: " << str << endl;
  }
  catch (...) {
    cerr << "mergeRawOnOff.cc catched unknown (...) exception  " << endl; 
    rc = 79; 
  } 

  return 0;

}