source: tags/release-1.0.5/src/param.cc @ 184

#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <string>
#include <math.h>
#include <wcs.h>
#include <wcsunits.h>
#include <param.hh>
#include <config.h>
#include <duchamp.hh>
#include <Utils/utils.hh>

// Define funtion to print bools as words, in case the compiler doesn't recognise
// the setf(ios::boolalpha) command...
#ifdef HAVE_STDBOOL_H
string stringize(bool b){
  std::stringstream ss;
  ss.setf(std::ios::boolalpha);
  ss << b;
  return ss.str();
}
#else
string stringize(bool b){
  std::string output;
  if(b) output="true";
  else output="false";
  return output;
}
#endif

using std::setw;
using std::endl;

/****************************************************************/
///////////////////////////////////////////////////
//// Functions for FitsHeader class:
///////////////////////////////////////////////////

FitsHeader::FitsHeader(){
  this->wcs = new wcsprm;
  this->wcs->flag=-1;
  wcsini(true,3,this->wcs); 
  this->wcsIsGood = false;
  this->nwcs = 0;
  this->scale=1.;
  this->offset=0.;
  this->power=1.;
  this->fluxUnits="counts";
}

FitsHeader::FitsHeader(const FitsHeader& h){
  this->wcs = new wcsprm;
  this->wcs->flag=-1;
  wcsini(true,h.wcs->naxis,this->wcs); 
  wcscopy(true,h.wcs,this->wcs); 
  wcsset(this->wcs);
  this->nwcs = h.nwcs;
  this->wcsIsGood = h.wcsIsGood;
  this->spectralUnits = h.spectralUnits;
  this->fluxUnits = h.fluxUnits;
  this->intFluxUnits = h.intFluxUnits;
  this->beamSize = h.beamSize;
  this->bmajKeyword = h.bmajKeyword;
  this->bminKeyword = h.bminKeyword;
  this->blankKeyword = h.blankKeyword;
  this->bzeroKeyword = h.bzeroKeyword;
  this->bscaleKeyword = h.bscaleKeyword;
  this->scale = h.scale;
  this->offset = h.offset;
  this->power = h.power;
}

FitsHeader& FitsHeader::operator= (const FitsHeader& h){
  this->wcs = new wcsprm;
  this->wcs->flag=-1;
  wcsini(true,h.wcs->naxis,this->wcs); 
  wcscopy(true,h.wcs,this->wcs); 
  wcsset(this->wcs);
  this->nwcs = h.nwcs;
  this->wcsIsGood = h.wcsIsGood;
  this->spectralUnits = h.spectralUnits;
  this->fluxUnits = h.fluxUnits;
  this->intFluxUnits = h.intFluxUnits;
  this->beamSize = h.beamSize;
  this->bmajKeyword = h.bmajKeyword;
  this->bminKeyword = h.bminKeyword;
  this->blankKeyword = h.blankKeyword;
  this->bzeroKeyword = h.bzeroKeyword;
  this->bscaleKeyword = h.bscaleKeyword;
  this->scale = h.scale;
  this->offset = h.offset;
  this->power = h.power;
}

void FitsHeader::setWCS(wcsprm *w)
{
  /** 
   * FitsHeader::setWCS(wcsprm *)
   *  A function that assigns the wcs parameters, and runs
   *   wcsset to set it up correctly.
   *  Performs a check to see if the WCS is good (by looking at 
   *   the lng and lat wcsprm parameters), and sets the wcsIsGood 
   *   flag accordingly.
   */
  wcscopy(true,w,this->wcs);
  wcsset(this->wcs);
  if( (w->lng!=-1) && (w->lat!=-1) ) this->wcsIsGood = true;
}

wcsprm *FitsHeader::getWCS()
{
  /** 
   * FitsHeader::getWCS()
   *  A function that returns a wcsprm object corresponding to the WCS.
   */
  wcsprm *wNew = new wcsprm;
  wNew->flag=-1;
  wcsini(true,this->wcs->naxis,wNew); 
  wcscopy(true,this->wcs,wNew); 
  wcsset(wNew);
  return wNew;
}

int     FitsHeader::wcsToPix(const double *world, double *pix){
  return wcsToPixSingle(this->wcs,world,pix);}
int     FitsHeader::wcsToPix(const double *world, double *pix, const int npts){
  return wcsToPixMulti(this->wcs,world,pix,npts);}
int     FitsHeader::pixToWCS(const double *pix, double *world){
  return pixToWCSSingle(this->wcs,pix,world);}
int     FitsHeader::pixToWCS(const double *pix, double *world, const int npts){
  return pixToWCSMulti(this->wcs,pix,world,npts);}

double  FitsHeader::pixToVel(double &x, double &y, double &z)
{
  double vel;
  if(this->wcsIsGood){
    double *pix   = new double[3]; 
    double *world = new double[3];
    pix[0] = x; pix[1] = y; pix[2] = z;
    pixToWCSSingle(this->wcs,pix,world);
    vel = this->specToVel(world[2]);
    delete [] pix;
    delete [] world;
  }
  else vel = z;
  return vel;
}

double* FitsHeader::pixToVel(double &x, double &y, double *zarray, int size)
{
  double *newzarray = new double[size];
  if(this->wcsIsGood){
    double *pix   = new double[size*3];
    for(int i=0;i<size;i++){
      pix[3*i] = x; pix[3*i+1] = y; pix[3*i+2] = zarray[i];
    }
    double *world = new double[size*3];
    pixToWCSMulti(this->wcs,pix,world,size);
    delete [] pix;
    double *newzarray = new double[size];
    for(int i=0;i<size;i++) newzarray[i] = this->specToVel(world[3*i+2]);
    delete [] world;
  }
  else for(int i=0;i<size;i++) newzarray[i] = zarray[i];
  return newzarray;
}

double  FitsHeader::specToVel(const double &coord)
{
  double vel;
  if(power==1.0) vel =  coord*this->scale + this->offset;
  else vel = pow( (coord*this->scale + this->offset), this->power);
  return vel;
}

double  FitsHeader::velToSpec(const float &velocity)
{
//   return velToCoord(this->wcs,velocity,this->spectralUnits);};
  return (pow(velocity, 1./this->power) - this->offset) / this->scale;}

string  FitsHeader::getIAUName(double ra, double dec)
{
  if(strcmp(this->wcs->lngtyp,"RA")==0) return getIAUNameEQ(ra, dec, this->wcs->equinox);
  else return getIAUNameGAL(ra, dec);
}

void FitsHeader::fixUnits(Param &par)
{
  // define spectral units from the param set
  this->spectralUnits = par.getSpectralUnits();

  double sc=1.;
  double of=0.;
  double po=1.;;
  if(this->wcsIsGood){
    int flag = wcsunits( this->wcs->cunit[wcs->spec], 
                         this->spectralUnits.c_str(), 
                         &sc, &of, &po);
    if(flag>0){
      std::stringstream errmsg;
      errmsg << "WCSUNITS Error, Code = " << flag 
             << ": "<< wcsunits_errmsg[flag];
      if(flag==10) errmsg << "\nTried to get conversion from '" 
                          << wcs->cunit[wcs->spec] << "' to '" 
                          << this->spectralUnits.c_str() << "'\n";
      this->spectralUnits = this->wcs->cunit[wcs->spec];
      if(this->spectralUnits==""){
        errmsg << "Setting coordinates to 'XX' for clarity.\n";
        this->spectralUnits = "XX";
      }
      duchampError("fixUnits", errmsg.str());
      
    }
  }
  this->scale = sc;
  this->offset= of;
  this->power = po;

  // Work out the integrated flux units, based on the spectral units.
  // If flux is per beam, trim the /beam from the flux units and multiply 
  //  by the spectral units.
  // Otherwise, just muliply by the spectral units.
  if(this->fluxUnits.size()>0){
    if(this->fluxUnits.substr(this->fluxUnits.size()-5,
                              this->fluxUnits.size()   ) == "/beam"){
      this->intFluxUnits = this->fluxUnits.substr(0,this->fluxUnits.size()-5)
        +" " +this->spectralUnits;
    }
    else this->intFluxUnits = this->fluxUnits + " " + this->spectralUnits;
  }

}

/****************************************************************/
///////////////////////////////////////////////////
//// Accessor Functions for Parameter class:
///////////////////////////////////////////////////
Param::Param(){
  /** 
   * Param()
   *  Default intial values for the parameters.
   * imageFile has no default value!
   */
  // Input files
  this->imageFile       = "";
  this->flagSubsection  = false;
  this->subsection      = "[*,*,*]";
  this->flagReconExists = false;
  this->reconFile       = "";
  // Output files
  this->flagLog         = true;
  this->logFile         = "duchamp-Logfile.txt";
  this->outFile         = "duchamp-Results.txt";
  this->spectraFile     = "duchamp-Spectra.ps";
  this->flagOutputRecon = false;
  this->flagOutputResid = false;
  this->flagVOT         = false;
  this->votFile         = "duchamp-Results.xml";
  this->flagKarma       = false;
  this->karmaFile       = "duchamp-Results.ann";
  this->flagMaps        = true;
  this->detectionMap    = "duchamp-DetectionMap.ps";
  this->momentMap       = "duchamp-MomentMap.ps";
  // Cube related parameters 
  this->flagBlankPix    = true;
  this->blankPixValue   = -8.00061;
  this->blankKeyword    = 1;
  this->bscaleKeyword   = -8.00061;
  this->bzeroKeyword    = 0.;
  this->flagUsingBlank  = false;
  this->flagMW          = false;
  this->maxMW           = 112;
  this->minMW           = 75;
  this->numPixBeam      = 10.;
  this->flagUsingBeam   = false;
  // Trim-related         
  this->flagTrimmed     = false;
  this->borderLeft      = 0;
  this->borderRight     = 0;
  this->borderBottom    = 0;
  this->borderTop       = 0;
  // Subsection offsets
  this->xSubOffset      = 0;
  this->ySubOffset      = 0;
  this->zSubOffset      = 0;
  // Baseline related
  this->flagBaseline    = false;
  // Detection-related    
  this->flagNegative    = false;
  // Object growth        
  this->flagGrowth      = false;
  this->growthCut       = 2.;
  // FDR analysis         
  this->flagFDR         = false;
  this->alphaFDR        = 0.01;
  // Other detection      
  this->snrCut          = 3.;
  // A trous reconstruction parameters
  this->flagATrous      = true;
  this->reconDim        = 3;
  this->scaleMin        = 1;
  this->snrRecon        = 4.;
  this->filterCode      = 1;
  // Volume-merging parameters
  this->flagAdjacent    = true;
  this->threshSpatial   = 3.;
  this->threshVelocity  = 7.;
  this->minChannels     = 3;
  this->minPix          = 2;
  // Input-Output related
  this->spectralMethod  = "peak";
  this->borders         = true;
  this->blankEdge       = true;
  this->verbose         = true;
  this->spectralUnits   = "km/s";
};

Param& Param::operator= (const Param& p)
{
  this->imageFile       = p.imageFile;
  this->flagSubsection  = p.flagSubsection; 
  this->subsection      = p.subsection;     
  this->flagReconExists = p.flagReconExists;
  this->reconFile       = p.reconFile;      
  this->flagLog         = p.flagLog;        
  this->logFile         = p.logFile;       
  this->outFile         = p.outFile;        
  this->spectraFile     = p.spectraFile;    
  this->flagOutputRecon = p.flagOutputRecon;
  this->flagOutputResid = p.flagOutputResid;
  this->flagVOT         = p.flagVOT;         
  this->votFile         = p.votFile;        
  this->flagKarma       = p.flagKarma;      
  this->karmaFile       = p.karmaFile;      
  this->flagMaps        = p.flagMaps;       
  this->detectionMap    = p.detectionMap;   
  this->momentMap       = p.momentMap;      
  this->flagBlankPix    = p.flagBlankPix;   
  this->blankPixValue   = p.blankPixValue;  
  this->blankKeyword    = p.blankKeyword;   
  this->bscaleKeyword   = p.bscaleKeyword;  
  this->bzeroKeyword    = p.bzeroKeyword;   
  this->flagUsingBlank  = p.flagUsingBlank; 
  this->flagMW          = p.flagMW;         
  this->maxMW           = p.maxMW;          
  this->minMW           = p.minMW;         
  this->numPixBeam      = p.numPixBeam;     
  this->flagTrimmed     = p.flagTrimmed;    
  this->borderLeft      = p.borderLeft;     
  this->borderRight     = p.borderRight;    
  this->borderBottom    = p.borderBottom;   
  this->borderTop       = p.borderTop;      
  this->xSubOffset      = p.xSubOffset;     
  this->ySubOffset      = p.ySubOffset;     
  this->zSubOffset      = p.zSubOffset;
  this->flagBaseline    = p.flagBaseline;
  this->flagNegative    = p.flagNegative;
  this->flagGrowth      = p.flagGrowth;
  this->growthCut       = p.growthCut;
  this->flagFDR         = p.flagFDR;
  this->alphaFDR        = p.alphaFDR;
  this->snrCut          = p.snrCut;
  this->flagATrous      = p.flagATrous;
  this->reconDim        = p.reconDim;
  this->scaleMin        = p.scaleMin;
  this->snrRecon        = p.snrRecon;
  this->filterCode      = p.filterCode;
  this->flagAdjacent    = p.flagAdjacent;
  this->threshSpatial   = p.threshSpatial;
  this->threshVelocity  = p.threshVelocity;
  this->minChannels     = p.minChannels;
  this->minPix          = p.minPix;
  this->spectralMethod  = p.spectralMethod;
  this->borders         = p.borders;
  this->verbose         = p.verbose;
  this->spectralUnits   = p.spectralUnits;
}

/****************************************************************/
///////////////////////////////////////////////////
//// Other Functions using the  Parameter class:
///////////////////////////////////////////////////

inline string makelower( string s )
{
  // "borrowed" from Matt Howlett's 'fred'
  string out = "";
  for( int i=0; i<s.size(); ++i ) {
    out += tolower(s[i]);
  }
  return out;
}

inline bool boolify( string s )
{
  /**
   * bool boolify(string)
   *  Convert a string to a bool variable
   *  "1" and "true" get converted to true
   *  "0" and "false" (and anything else) get converted to false
   */
  if((s=="1") || (makelower(s)=="true")) return true;
  else if((s=="0") || (makelower(s)=="false")) return false;
  else return false;
}

inline string readSval(std::stringstream& ss)
{
  string val; ss >> val; return val;
}

inline bool readFlag(std::stringstream& ss)
{
  string val; ss >> val; return boolify(val);
}

inline float readFval(std::stringstream& ss)
{
  float val; ss >> val; return val;
}

inline int readIval(std::stringstream& ss)
{
  int val; ss >> val; return val;
}

int Param::readParams(string paramfile)
{

  std::ifstream fin(paramfile.c_str());
  if(!fin.is_open()) return FAILURE;
  string line;
  while( !std::getline(fin,line,'\n').eof()){

    if(line[0]!='#'){
      std::stringstream ss;
      ss.str(line);
      string arg;
      ss >> arg;
      arg = makelower(arg);
      if(arg=="imagefile")       this->imageFile = readSval(ss);
      if(arg=="flagsubsection")  this->flagSubsection = readFlag(ss); 
      if(arg=="subsection")      this->subsection = readSval(ss); 
      if(arg=="flagreconexists") this->flagReconExists = readFlag(ss); 
      if(arg=="reconfile")       this->reconFile = readSval(ss); 

      if(arg=="flaglog")         this->flagLog = readFlag(ss); 
      if(arg=="logfile")         this->logFile = readSval(ss); 
      if(arg=="outfile")         this->outFile = readSval(ss); 
      if(arg=="spectrafile")     this->spectraFile = readSval(ss); 
      if(arg=="flagoutputrecon") this->flagOutputRecon = readFlag(ss); 
      if(arg=="flagoutputresid") this->flagOutputResid = readFlag(ss); 
      if(arg=="flagvot")         this->flagVOT = readFlag(ss); 
      if(arg=="votfile")         this->votFile = readSval(ss); 
      if(arg=="flagkarma")       this->flagKarma = readFlag(ss); 
      if(arg=="karmafile")       this->karmaFile = readSval(ss); 
      if(arg=="flagmaps")        this->flagMaps = readFlag(ss); 
      if(arg=="detectionmap")    this->detectionMap = readSval(ss); 
      if(arg=="momentmap")       this->momentMap = readSval(ss); 

      if(arg=="flagnegative")    this->flagNegative = readFlag(ss);
      if(arg=="flagblankpix")    this->flagBlankPix = readFlag(ss); 
      if(arg=="blankpixvalue")   this->blankPixValue = readFval(ss); 
      if(arg=="flagmw")          this->flagMW = readFlag(ss); 
      if(arg=="maxmw")           this->maxMW = readIval(ss); 
      if(arg=="minmw")           this->minMW = readIval(ss); 
      if(arg=="beamsize")        this->numPixBeam = readFval(ss); 

      if(arg=="flagbaseline")    this->flagBaseline = readFlag(ss); 
      if(arg=="minpix")          this->minPix = readIval(ss); 
      if(arg=="flaggrowth")      this->flagGrowth = readFlag(ss); 
      if(arg=="growthcut")       this->growthCut = readFval(ss); 

      if(arg=="flagfdr")         this->flagFDR = readFlag(ss); 
      if(arg=="alphafdr")        this->alphaFDR = readFval(ss); 

      if(arg=="snrcut")          this->snrCut = readFval(ss); 

      if(arg=="flagatrous")      this->flagATrous = readFlag(ss); 
      if(arg=="recondim")        this->reconDim = readIval(ss); 
      if(arg=="scalemin")        this->scaleMin = readIval(ss); 
      if(arg=="snrrecon")        this->snrRecon = readFval(ss); 
      if(arg=="filtercode")      this->filterCode = readIval(ss); 

      if(arg=="flagadjacent")    this->flagAdjacent = readFlag(ss); 
      if(arg=="threshspatial")   this->threshSpatial = readFval(ss); 
      if(arg=="threshvelocity")  this->threshVelocity = readFval(ss); 
      if(arg=="minchannels")     this->minChannels = readIval(ss); 

      if(arg=="spectralmethod")  this->spectralMethod=makelower(readSval(ss));
      if(arg=="spectralunits")   this->spectralUnits=makelower(readSval(ss));
      if(arg=="drawborders")     this->borders = readFlag(ss); 
      if(arg=="drawblankedges")  this->blankEdge = readFlag(ss); 
      if(arg=="verbose")         this->verbose = readFlag(ss); 
    }
  }
  return SUCCESS;
}


std::ostream& operator<< ( std::ostream& theStream, Param& par)
{
  // Only show the [blankPixValue] bit if we are using the parameter
  // otherwise we have read it from the FITS header.
  string blankParam = "";
  if(par.getFlagUsingBlank()) blankParam = "[blankPixValue]";
  string beamParam = "";
  if(par.getFlagUsingBeam()) beamParam = "[beamSize]";

  // BUG -- can get error: `boolalpha' is not a member of type `ios' -- old compilers: gcc 2.95.3?
  //   theStream.setf(std::ios::boolalpha);
  theStream.setf(std::ios::left);
  theStream  <<"---- Parameters ----"<<endl;
  theStream  << std::setfill('.');
  if(par.getFlagSubsection())
    theStream<<setw(38)<<"Image to be analysed"                 
             <<setw(18)<<setiosflags(std::ios::right)  <<"[imageFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<(par.getImageFile()+par.getSubsection()) <<endl;
  else 
    theStream<<setw(38)<<"Image to be analysed"                 
             <<setw(18)<<setiosflags(std::ios::right)  <<"[imageFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getImageFile()      <<endl;
  if(par.getFlagReconExists() && par.getFlagATrous()){
    theStream<<setw(38)<<"Reconstructed array exists?"          
             <<setw(18)<<setiosflags(std::ios::right)  <<"[reconExists]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagReconExists())<<endl;
    theStream<<setw(38)<<"FITS file containing reconstruction"  
             <<setw(18)<<setiosflags(std::ios::right)  <<"[reconFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getReconFile()      <<endl;
  }
  theStream  <<setw(38)<<"Intermediate Logfile"
             <<setw(18)<<setiosflags(std::ios::right)  <<"[logFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getLogFile()        <<endl;
  theStream  <<setw(38)<<"Final Results file"                   
             <<setw(18)<<setiosflags(std::ios::right)  <<"[outFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getOutFile()        <<endl;
  theStream  <<setw(38)<<"Spectrum file"                        
             <<setw(18)<<setiosflags(std::ios::right)  <<"[spectraFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getSpectraFile()    <<endl;
  if(par.getFlagVOT()){
    theStream<<setw(38)<<"VOTable file"                         
             <<setw(18)<<setiosflags(std::ios::right)  <<"[votFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getVOTFile()        <<endl;
  }
  if(par.getFlagKarma()){
    theStream<<setw(38)<<"Karma annotation file"                
             <<setw(18)<<setiosflags(std::ios::right)  <<"[karmaFile]"
             <<"  =  " <<resetiosflags(std::ios::right)
             
             <<par.getKarmaFile()      <<endl;
  }
  if(par.getFlagMaps()){
    theStream<<setw(38)<<"0th Moment Map"                       
             <<setw(18)<<setiosflags(std::ios::right)  <<"[momentMap]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getMomentMap()      <<endl;
    theStream<<setw(38)<<"Detection Map"                        
             <<setw(18)<<setiosflags(std::ios::right)  <<"[detectionMap]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getDetectionMap()   <<endl;
  }
  if(par.getFlagATrous()){                             
    theStream<<setw(38)<<"Saving reconstructed cube?"           
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagoutputrecon]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagOutputRecon())<<endl;
    theStream<<setw(38)<<"Saving residuals from reconstruction?"
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagoutputresid]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagOutputResid())<<endl;
  }                                                    
  theStream  <<"------"<<endl;
  theStream  <<setw(38)<<"Searching for Negative features?"     
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagNegative]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagNegative())   <<endl;
  theStream  <<setw(38)<<"Fixing Blank Pixels?"                 
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagBlankPix]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagBlankPix())   <<endl;
  if(par.getFlagBlankPix()){
    theStream<<setw(38)<<"Blank Pixel Value"                    
             <<setw(18)<<setiosflags(std::ios::right)  << blankParam
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getBlankPixVal()    <<endl;
  }
  theStream  <<setw(38)<<"Removing Milky Way channels?"         
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagMW]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagMW())         <<endl;
  if(par.getFlagMW()){
    theStream<<setw(38)<<"Milky Way Channels"                   
             <<setw(18)<<setiosflags(std::ios::right)  <<"[minMW - maxMW]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getMinMW()
             <<"-" <<par.getMaxMW()          <<endl;
  }
  theStream  <<setw(38)<<"Beam Size (pixels)"                   
             <<setw(18)<<setiosflags(std::ios::right)  << beamParam
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getBeamSize()       <<endl;
  theStream  <<setw(38)<<"Removing baselines before search?"    
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagBaseline]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagBaseline())   <<endl;
  theStream  <<setw(38)<<"Minimum # Pixels in a detection"      
             <<setw(18)<<setiosflags(std::ios::right)  <<"[minPix]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getMinPix()         <<endl;
  theStream  <<setw(38)<<"Minimum # Channels in a detection"    
             <<setw(18)<<setiosflags(std::ios::right)  <<"[minChannels]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getMinChannels()    <<endl;
  theStream  <<setw(38)<<"Growing objects after detection?"     
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagGrowth]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagGrowth())     <<endl;
  if(par.getFlagGrowth()) {                            
    theStream<<setw(38)<<"SNR Threshold for growth"             
             <<setw(18)<<setiosflags(std::ios::right)  <<"[growthCut]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getGrowthCut()      <<endl;
  }
  theStream  <<setw(38)<<"Using A Trous reconstruction?"        
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagATrous]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagATrous())     <<endl;
  if(par.getFlagATrous()){                             
    theStream<<setw(38)<<"Number of dimensions in reconstruction"      
             <<setw(18)<<setiosflags(std::ios::right)  <<"[reconDim]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getReconDim()       <<endl;
    theStream<<setw(38)<<"Minimum scale in reconstruction"      
             <<setw(18)<<setiosflags(std::ios::right)  <<"[scaleMin]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getMinScale()       <<endl;
    theStream<<setw(38)<<"SNR Threshold within reconstruction"  
             <<setw(18)<<setiosflags(std::ios::right)  <<"[snrRecon]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getAtrousCut()      <<endl;
    theStream<<setw(38)<<"Filter being used for reconstruction" 
             <<setw(18)<<setiosflags(std::ios::right)  <<"[filterCode]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getFilterCode() 
             << " (" << par.getFilterName()  << ")" <<endl;
  }                                                    
  theStream  <<setw(38)<<"Using FDR analysis?"                  
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagFDR]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagFDR())        <<endl;
  if(par.getFlagFDR()){                                
    theStream<<setw(38)<<"Alpha value for FDR analysis"         
             <<setw(18)<<setiosflags(std::ios::right)  <<"[alphaFDR]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getAlpha()          <<endl;
  }                                                    
  else {
    theStream<<setw(38)<<"SNR Threshold"                        
             <<setw(18)<<setiosflags(std::ios::right)  <<"[snrCut]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getCut()            <<endl;
  }
  theStream  <<setw(38)<<"Using Adjacent-pixel criterion?"      
             <<setw(18)<<setiosflags(std::ios::right)  <<"[flagAdjacent]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<stringize(par.getFlagAdjacent())   <<endl;
  if(!par.getFlagAdjacent()){
    theStream<<setw(38)<<"Max. spatial separation for merging"  
             <<setw(18)<<setiosflags(std::ios::right)  <<"[threshSpatial]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getThreshS()        <<endl;
  }
  theStream  <<setw(38)<<"Max. velocity separation for merging" 
             <<setw(18)<<setiosflags(std::ios::right)  <<"[threshVelocity]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getThreshV()        <<endl;
  theStream  <<setw(38)<<"Method of spectral plotting"          
             <<setw(18)<<setiosflags(std::ios::right)  <<"[spectralMethod]"
             <<"  =  " <<resetiosflags(std::ios::right)
             <<par.getSpectralMethod() <<endl;
  theStream  <<"--------------------"<<endl;
  theStream  << std::setfill(' ');
  theStream.unsetf(std::ios::left);
  //  theStream.unsetf(std::ios::boolalpha);
}


void Param::copyHeaderInfo(FitsHeader &head)
{
  /**
   *  Param::copyHeaderInfo(FitsHeader &head)
   * A function to copy across relevant header keywords from the 
   *  FitsHeader class to the Param class, as they are needed by
   *  functions in the Param class.
   */

  this->blankKeyword  = head.getBlankKeyword();
  this->bscaleKeyword = head.getBscaleKeyword();
  this->bzeroKeyword  = head.getBzeroKeyword();
  this->blankPixValue = this->blankKeyword * this->bscaleKeyword + 
    this->bzeroKeyword;

  this->numPixBeam    = head.getBeamSize();
}

bool Param::isBlank(float &value)
{
  /** 
   *  Param::isBlank(float)
   *   Tests whether the value passed as the argument is BLANK or not.
   *   If flagBlankPix is false, return false.
   *   Otherwise, compare to the relevant FITS keywords, using integer 
   *     comparison.
   *   Return a bool.
   */

  return this->flagBlankPix &&
    (this->blankKeyword == int((value-this->bzeroKeyword)/this->bscaleKeyword));
}

string Param::outputReconFile()
{
  /** 
   *  outputReconFile()
   *
   *   This function produces the required filename in which to save
   *    the reconstructed array. If the input image is image.fits, then
   *    the output will be eg. image.RECON-3-2-4-1.fits, where the numbers are
   *    3=reconDim, 2=filterCode, 4=snrRecon, 1=minScale
   */
  string inputName = this->imageFile;
  std::stringstream ss;
  ss << inputName.substr(0,inputName.size()-5);  // remove the ".fits" on the end.
  if(this->flagSubsection) ss<<".sub";
  ss << ".RECON-" << this->reconDim 
     << "-"       << this->filterCode
     << "-"       << this->snrRecon
     << "-"       << this->scaleMin
     << ".fits";
  return ss.str();
}

string Param::outputResidFile()
{
  /** 
   *  outputResidFile()
   *
   *   This function produces the required filename in which to save
   *    the reconstructed array. If the input image is image.fits, then
   *    the output will be eg. image.RESID-3-2-4-1.fits, where the numbers are
   *    3=reconDim, 2=filterCode, 4=snrRecon, 1=scaleMin
   */
  string inputName = this->imageFile;
  std::stringstream ss;
  ss << inputName.substr(0,inputName.size()-5);  // remove the ".fits" on the end.
  if(this->flagSubsection) ss<<".sub";
  ss << ".RESID-" << this->reconDim 
     << "-"       << this->filterCode
     << "-"       << this->snrRecon
     << "-"       << this->scaleMin
     << ".fits";
  return ss.str();
}