source/*cc

source/ArrayModel.cc

+#include "Model.h"
+
+ArrayModel::ArrayModel(const Exposure &exposure, const CountsMap &counts, const Psf &psf, const Sources &sources, const Parameters &pars, const Skymap<char> &filter, unsigned int configure) :
+	BaseModel(counts,exposure,psf,sources,pars, filter, configure), fmodels(0)
+{
+}
+
+void ArrayModel::setModels( const std::vector<BaseModel*> & models) {
+	//Check for null pointers in the array
+	for (int i = 0; i < models.size(); ++i){
+		if (models[i] == 0) {
+			throw(ModelError("Null pointer in array model, aborting"));
+		}
+	}
+	//Clear up the variables
+	fvariables.clear();
+	
+	//Set the model array to the new models
+	fmodels = models;
+
+	//Join the variables
+	for (int i = 0; i < fmodels.size(); ++i){
+		fvariables.add(fmodels[i]->getVariables());
+	}
+}
+
+void ArrayModel::getMap(const Variables & vars, Skymap<double> &map) {
+	for (int i = 0; i < fmodels.size(); ++i){
+		fmodels[i]->getMap(vars, map);
+	}
+}
+
+BaseModel::gradMap ArrayModel::getComponents(const Variables & vars, const std::string &prefix){
+	gradMap output;
+	for (int i = 0; i < fmodels.size(); ++i){
+		gradMap tmp(fmodels[i]->getComponents(vars, prefix));
+		for (gradMap::iterator it = tmp.begin(); it != tmp.end(); ++it){
+		   //Check if something exists, if it does, add the new map
+		   //rather than replace it
+		   gradMap::iterator it2 = output.find((*it).first);
+		   if (it2 == output.end()) {
+			output[(*it).first] = (*it).second;
+		   } else {
+			output[(*it).first] += (*it).second;
+		   }
+		}
+	}
+	return output;
+}
+
+void ArrayModel::getGrads(const Variables & vars, const std::string & varName, Skymap<double> &map) {
+	for (int i = 0; i < fmodels.size(); ++i){
+		fmodels[i]->getGrads(vars,varName, map);
+	}
+}
+
+BaseModel::gradMap ArrayModel::getSecDer(const Variables & vars, const std::string & varName1, const std::string & varName2) {
+	gradMap output;
+	//Loop over the models and add to output
+	for (int i = 0; i < fmodels.size(); ++i){
+		gradMap tmp(fmodels[i]->getSecDer(vars,varName1,varName2));
+		for (gradMap::iterator it = tmp.begin(); it != tmp.end(); ++it){
+		   //Check if something exists, if it does, add the new map
+		   //rather than replace it
+		   gradMap::iterator it2 = output.find((*it).first);
+		   if (it2 == output.end()) {
+			output[(*it).first] = (*it).second;
+		   } else {
+			output[(*it).first] += (*it).second;
+		   }
+		}
+	}
+	return output;
+}
+
+void ArrayModel::modifySources(const Variables & vars, Sources &sources) const {
+	for (int i = 0; i < fmodels.size(); ++i) {
+		fmodels[i]->modifySources(vars,sources);
+	}
+}

source/CAT.cc

+using namespace std;
+// for slalib version which uses: if defined (__cplusplus) extern "C"
+// but this does not work, use version without this 
+// #define __cplusplus
+
+#include<iostream>
+#include"fitsio.h"
+#include"slalib.h"
+
+#include"CAT.h"
+
+
+
+//////////////////////////////////////////////////////
+  
+  
+///////////////////////////////////////////////////////
+  int CAT:: read (char *directory)
+{
+  char infile[500];
+
+  char err_text[100];
+  char comment[100];
+
+  fitsfile *fptr;
+  int status;
+  int hdunum,hdutype,total_hdus,colnum;
+  int n_columns,n_rows;
+  double nulval=0.;
+  int anynul   =0;
+  char nulstr[100];strcpy(nulstr,"null");
+  double dtr=acos(-1.0)/180.;
+  int i,j,k;
+
+
+  //char catalogue_file[]="gnrl_refr_cat_0020_reformatted.fits";
+  //char catalogue_file[]="isgriCat_2nd_Tony.fits";
+    char catalogue_file[]="isgri_2nd_cat_revised.fits";
+ 
+
+
+
+  cout<< "CAT::read  (" << directory<<")" <<endl;
+
+  
+  strcpy(infile,directory);
+  strcat(infile,catalogue_file);
+
+  
+  cout<<"   infile "<<infile<<endl;
+
+  status=0; // needed
+  fits_open_file(&fptr,infile,READONLY,&status) ;
+  cout<<"FITS read open status= "<<status<<" "<<infile<<endl;
+
+  fits_get_errstatus(status,err_text);
+  cout<<err_text<<endl;
+
+fits_get_num_hdus(fptr,&total_hdus,&status);
+  cout<<"total number of header units="<<total_hdus<<endl;
+
+  hdunum=1;
+
+  fits_movabs_hdu(fptr,hdunum+1,&hdutype,&status );
+  cout<<"FITS movabs_hdu hdunum="<<hdunum
+      <<" status= "<<status<<" hdutype="<<hdutype<<endl  ;
+
+   fits_read_key(fptr,TLONG,"TFIELDS",&n_columns,comment,&status);
+   cout<<" n_columns ="<<n_columns ;
+   fits_read_key(fptr,TLONG,"NAXIS2",&n_rows  ,comment,&status);
+   cout<<" n_rows    ="<<n_rows    <<endl;
+
+
+   n_sources=n_rows;
+
+   ra      =new double[n_rows];
+   dec     =new double[n_rows];
+   flux    =new double[n_rows];//AWS20060110
+   flux_err=new double[n_rows];//AWS20060110
+
+  fits_get_colnum(fptr,CASEINSEN,"RA_OBJ",&colnum,&status);
+  cout<<"RA_OBJ column ="<< colnum<<endl;
+  fits_read_col(fptr, TDOUBLE, colnum, 1,1,n_rows,&nulval,ra, &anynul,&status);
+
+  fits_get_colnum(fptr,CASEINSEN,"DEC_OBJ",&colnum,&status);
+  cout<<"DEC_OBJ column ="<< colnum<<endl;
+  fits_read_col(fptr, TDOUBLE, colnum, 1,1,n_rows,&nulval,dec, &anynul,&status);
+
+
+  // cout<<"ra :";for (i=0;i<n_rows;i++)cout<<" "<<ra [i];cout<<endl;
+  //cout<<"dec:";for (i=0;i<n_rows;i++)cout<<" "<<dec[i];cout<<endl;
+
+
+ fits_get_colnum(fptr,CASEINSEN,"NAME",&colnum,&status);
+ cout<<"NAME column ="<< colnum<<endl;
+ name=new char*[n_rows];
+ for (i=0;i<n_rows;i++)     name[i]=new char[100];
+ fits_read_col_str(fptr,  colnum, 1,1, n_rows,nulstr,  name, &anynul,&status);
+
+ // for (i=0;i<n_rows;i++)  cout<<   name[i] <<" ra="<<ra[i]<<" dec="<<dec[i]<<endl;
+
+  longitude =new double[n_rows];
+  latitude  =new double[n_rows];
+
+ for (i=0;i<n_rows;i++) 
+   {
+     // NB had to compile sla_c since undefined symbol using lib from osa4.2
+
+  slaEqgal(ra[i]*dtr, dec[i]*dtr,  &longitude[i],  &latitude[i]);
+  longitude[i]/=dtr;
+   latitude[i]/=dtr;
+   }
+
+
+
+  return 0;
+}
+///////////////////////////////////////////////////////
+  int CAT:: read (char *directory,char *filename) //AWS20060110
+{
+  char infile[500];
+
+  char err_text[100];
+  char comment[100];
+
+  fitsfile *fptr;
+  int status;
+  int hdunum,hdutype,total_hdus,colnum;
+  int n_columns,n_rows;
+  double nulval=0.;
+  int anynul   =0;
+  char nulstr[100];strcpy(nulstr,"null");
+  double dtr=acos(-1.0)/180.;
+  int i,j,k;
+
+
+  
+
+
+  cout<< "CAT::read  (" << directory<<"/"<<filename<<")" <<endl;
+
+  
+  strcpy(infile,directory);
+  strcat(infile,filename);
+
+  
+  cout<<"CAT::read   infile= "<<infile<<endl;
+
+  status=0; // needed
+  fits_open_file(&fptr,infile,READONLY,&status) ;
+  cout<<"FITS read open status= "<<status<<" "<<infile<<endl;
+
+  fits_get_errstatus(status,err_text);
+  cout<<err_text<<endl;
+
+  fits_get_num_hdus(fptr,&total_hdus,&status);
+  cout<<"total number of header units="<<total_hdus<<endl;
+
+  hdunum=total_hdus-1; // because spimodfit output has also grouping extension, make it thus more general assuming catalogue is last extension
+
+  fits_movabs_hdu(fptr,hdunum+1,&hdutype,&status );
+  cout<<"FITS movabs_hdu hdunum="<<hdunum
+      <<" status= "<<status<<" hdutype="<<hdutype<<endl  ;
+
+   fits_read_key(fptr,TLONG,"TFIELDS",&n_columns,comment,&status);
+   cout<<" n_columns ="<<n_columns ;
+   fits_read_key(fptr,TLONG,"NAXIS2",&n_rows  ,comment,&status);
+   cout<<" n_rows    ="<<n_rows    <<endl;
+
+
+   n_sources=n_rows;
+
+  ra      =new double[n_rows];
+  dec     =new double[n_rows];
+  flux    =new double[n_rows];
+  flux_err=new double[n_rows];
+
+  fits_get_colnum(fptr,CASEINSEN,"RA_OBJ",&colnum,&status);
+  cout<<"RA_OBJ column ="<< colnum<<endl;
+  fits_read_col(fptr, TDOUBLE, colnum, 1,1,n_rows,&nulval,ra, &anynul,&status);
+
+  fits_get_colnum(fptr,CASEINSEN,"DEC_OBJ",&colnum,&status);
+  cout<<"DEC_OBJ column ="<< colnum<<endl;
+  fits_read_col(fptr, TDOUBLE, colnum, 1,1,n_rows,&nulval,dec, &anynul,&status);
+
+  fits_get_colnum(fptr,CASEINSEN,"FLUX  ",&colnum,&status);
+  cout<<"FLUX    column ="<< colnum<<endl;
+  // read only first value of spectrum vector
+  for (i=0;i<n_rows;i++)
+  fits_read_col(fptr, TDOUBLE, colnum,i+ 1,1,1,&nulval,&flux[i],   &anynul,&status);
+
+  fits_get_colnum(fptr,CASEINSEN,"FLUX_ERR",&colnum,&status);
+  cout<<"FLUX_ERR column ="<< colnum<<endl;
+  // read only first value of spectrum vector
+  for (i=0;i<n_rows;i++)
+  fits_read_col(fptr, TDOUBLE, colnum,i+ 1,1,1,&nulval,&flux_err[i],&anynul,&status);
+
+  // cout<<"ra :";for (i=0;i<n_rows;i++)cout<<" "<<ra [i];cout<<endl;
+  //cout<<"dec:";for (i=0;i<n_rows;i++)cout<<" "<<dec[i];cout<<endl;
+  //cout<<"flux:    ";for (i=0;i<n_rows;i++)cout<<" "<<flux[i]    ;cout<<endl;
+  //cout<<"flux_err:";for (i=0;i<n_rows;i++)cout<<" "<<flux_err[i];cout<<endl;
+
+ fits_get_colnum(fptr,CASEINSEN,"NAME",&colnum,&status);
+ cout<<"NAME column ="<< colnum<<endl;
+ name=new char*[n_rows];
+ for (i=0;i<n_rows;i++)     name[i]=new char[100];
+ fits_read_col_str(fptr,  colnum, 1,1, n_rows,nulstr,  name, &anynul,&status);
+
+ // for (i=0;i<n_rows;i++)  cout<<   name[i] <<" ra="<<ra[i]<<" dec="<<dec[i]<<endl;
+
+  longitude =new double[n_rows];
+  latitude  =new double[n_rows];
+
+ for (i=0;i<n_rows;i++) 
+   {
+     // NB had to compile sla_c since undefined symbol using lib from osa4.2
+
+  slaEqgal(ra[i]*dtr, dec[i]*dtr,  &longitude[i],  &latitude[i]);
+  longitude[i]/=dtr;
+   latitude[i]/=dtr;
+   }
+
+
+
+  return 0;
+}
+
+////////////////////////////////////////////////////////////////
+void CAT:: print ()
+{
+
+  int i;
+  cout<<"CAT::print"<<endl;
+
+  for (i=0;i<n_sources;i++)  cout<<"source #"<<i<<"   "<<   name[i]
+                                 <<"    ra = "<<ra[i]<<" dec = "<<dec[i]
+				 <<"     l = "<<longitude[i]<<"  b = "<<latitude[i]
+				 <<"  flux = "<<flux     [i]<<" +-   "<<flux_err[i]
+                                 <<endl;
+
+  cout<<"end CAT::print"<<endl;
+}
+////////////////////////////////////////////////////////////////
+
+void CAT:: find (char *name_, double *ra_, double *dec_, double *longitude_, double *latitude_)
+{
+
+  int i;
+  int found;
+
+  cout<<"CAT::find"<<endl;
+
+  found=0;
+
+  for (i=0;i<n_sources;i++) 
+  {
+    /*
+     cout<<"source #"<<i<<"   "<<   name[i]
+                                     <<"    ra = "<<ra[i]<<" dec = "<<dec[i]
+	       			 <<"     l = "<<longitude[i]<<"  b = "<<latitude[i]
+                                 <<endl;
+    */
+ if(strcmp(name[i],name_)==0) found=1;
+ if(strcmp(name[i],name_)==0) break;
+
+    }
+
+  if(found==0)
+  {
+   *ra_              =-999.;
+   *dec_             =-999.;
+   *longitude_       =-999.;
+   *latitude_        =-999.;
+
+   cout<<"source "<<name_<< "   not found in catalogue !"<<endl;
+  }
+
+  if(found==1)
+  {
+   cout<<"found source #"<<i<<"   "<<   name[i]
+                                 <<"    ra = "<<ra[i]<<" dec = "<<dec[i]
+				 <<"     l = "<<longitude[i]<<"  b = "<<latitude[i]
+                                 <<endl;
+
+   *ra_              =ra[i];
+   *dec_            =dec[i];
+   *longitude_=longitude[i];
+   *latitude_ = latitude[i];
+
+   }
+
+  cout<<"end CAT::find"<<endl;
+}
+

source/Configure.cc

+
+//**.****|****.****|****.****|****.****|****.****|****.****|****.****|****.****|
+// * Configure.cc *                                galprop package * 4/14/2000 
+//**"****!****"****!****"****!****"****!****"****!****"****!****"****!****"****|
+using namespace std;//AWS20050919
+#include<iostream>  //AWS20050919
+#include <cstring>  //AWS20111010 for sles11 gcc 4.3.4
+
+#include"Configure.h"
+
+int Configure::init()
+{
+   cout<<">>>>Configure"<<endl;
+   directory_length=100;
+   galdef_directory=new char[directory_length];
+   fits_directory=new char[directory_length];
+   adjunct_directory=new char[directory_length];
+   strcpy(galdef_directory, "../GALDEF/");
+   strcpy(  fits_directory, "../FITS/"  );
+   strcpy(adjunct_directory,"../adjunct/"  );
+   cout<<"Configure: galdef_directory:  "<< galdef_directory<<endl;
+   cout<<"Configure:   fits_directory:  "<<   fits_directory<<endl;
+   cout<<"Configure:adjunct_directory:  "<<adjunct_directory<<endl;
+   cout<<"<<<<Configure"<<endl;
+   return 0;
+}

source/Coordinate.cc

+#include "Coordinate.h"
+#include "pointing.h"
+#include "PhysicalConstants.h"
+#include <iostream>
+
+SM::Coordinate::Coordinate(const pointing &point) {
+   m_b = 90 - point.theta/utl::kConvertDegreesToRadians;
+   m_l = point.phi/utl::kConvertDegreesToRadians;
+}
+
+pointing SM::Coordinate::healpixAng() const{
+   const double theta = utl::kPi/2 - utl::kConvertDegreesToRadians*m_b;
+   const double phi = utl::kConvertDegreesToRadians*m_l;
+   return pointing(theta,phi);
+}
+
+namespace SM {
+std::ostream & operator << (std::ostream &os, const SM::Coordinate &coord) {
+   os << "(" << coord.l() <<","<<coord.b()<<")";
+   return os;
+}
+}

source/Counts.cc

+#include "Counts.h"
+#include <valarray>
+#include <CCfits/CCfits>
+#include <cmath>
+#include <fstream>
+#include "Parameters.h"
+
+
+CountsMap::CountsMap(const Parameters &pars){
+  
+	//Start by trying a cached old file
+	std::string countsOutFile="NONE";
+
+{
+		//Read from countsFile
+		std::string countsFile;
+		pars.getParameter("countsFile", countsFile);
+		std::cout<<"Reading counts from file "<<countsFile<<std::endl;
+		//Check the parameters for order and energy binning parameters.  If not
+		//found, assume this is binned healpix output
+		//TODO check the file for headers.
+		int order = 0;
+		try{
+			pars.getParameter("countOrder", order);
+		}catch (Parameters::ParameterError){ }
+		//Check for order, if set we assume FT1 files
+		if (order) {
+			std::string energyBinning;
+			std::valarray<double> eMinArr, eMaxArr;
+			pars.getParameter("energyBinning", energyBinning);
+			if (energyBinning == "linear" || energyBinning == "log"){
+				int nEnergyBins;
+				double eMin, eMax;
+				pars.getParameter("nEnergyBins", nEnergyBins);
+				pars.getParameter("eMin", eMin);
+				pars.getParameter("eMax", eMax);
+				eMinArr.resize(nEnergyBins);
+				eMaxArr.resize(nEnergyBins);
+				if (energyBinning == "linear" ){
+					double binsize = (eMax-eMin)/nEnergyBins;
+					for (int i = 0; i < nEnergyBins; ++i){
+						eMinArr[i] = eMin+i*binsize;
+						eMaxArr[i] = eMin+(i+1)*binsize;
+					}
+				}else {
+					double binsize = log(eMax/eMin)/nEnergyBins;
+					for (int i = 0; i < nEnergyBins; ++i){
+						eMinArr[i] = eMin*exp(i*binsize);
+						eMaxArr[i] = eMin*exp((i+1)*binsize);
+					}
+				}
+			}else if(energyBinning == "list"){
+				std::vector<double> eMinVec;
+				std::vector<double> eMaxVec;
+				pars.getParameter("eMinList", eMinVec);
+				pars.getParameter("eMaxList", eMaxVec);
+				eMinArr.resize(eMinVec.size());
+				eMaxArr.resize(eMaxVec.size());
+				eMinArr = std::valarray<double>(&eMinVec[0], eMinVec.size());
+				eMaxArr = std::valarray<double>(&eMaxVec[0], eMaxVec.size());
+			}else{
+				std::cout<<"Energy binning specified \""<<energyBinning<<"\" not available!"<<std::endl;
+				std::cout<<"Available values (case sensitive): linear, log and list"<<std::endl;
+				throw (CountsMapException("Energy binning specified \""+energyBinning+"\" not available!\nAvailable values (case sensitive): linear, log and list"));
+			}
+			//Try to get the filter from the parameters
+			std::string filter;
+			try{
+				pars.getParameter("FT1filter", filter);
+			}catch (Parameters::ParameterError){ }
+			//Get the energy column from the parameters
+			fEnergyCol = "ENERGY";
+			try{
+			   pars.getParameter("FT1EnergyCol", fEnergyCol);
+			} catch (Parameters::ParameterError) {}
+			reset(order, eMinArr, eMaxArr);
+			addFile(countsFile, filter);
+		}else{
+			ReadHealpixFits(countsFile);
+		}
+		if (countsOutFile != "NONE"){
+			write(countsOutFile);
+		}
+	}
+}
+
+CountsMap::CountsMap(const std::string &fileName): fLost(0){
+	ReadHealpixFits(fileName);
+}	
+
+CountsMap::CountsMap(int order, std::valarray<double> & eMin, std::valarray<double> & eMax){
+	reset(order, eMin, eMax);
+}
+
+CountsMap::CountsMap(const CountsMap & oldCountsMap){
+	(*this) = oldCountsMap;
+}
+
+CountsMap::CountsMap(const std::string &fileName, int order, std::valarray<double> & eMin, std::valarray<double> & eMax, const std::string & filter) :fLost(0){
+	reset(order, eMin, eMax);
+	addFile(fileName, filter);
+}
+
+void CountsMap::addPhotons(const std::valarray< std::pair< SM::Coordinate, double > > & photonArray){
+	for (int i = 0; i < photonArray.size(); ++i){
+		Add(photonArray[i]);
+	}
+}
+
+void CountsMap::addFile(const std::string & fileName, const std::string & filter){
+	//Open the file and throw exception if failure occurs
+	std::ifstream is(fileName.c_str());
+	if (is.fail()){
+		throw(CountsMapException("Failed to open file \""+fileName+"\""));
+	}
+	
+	//Read the first line and look for SIMPLE keyword.  If found, read the file
+	//directly, otherwise, loop over each line in the file, assuming it is a text
+	//file containing list of FT1 files
+	std::string line;
+	std::getline(is, line);
+	if (line.compare(0,6,"SIMPLE") == 0) {
+		//We have a FITS file
+		ReadFT1Fits(fileName, filter);
+	}else{
+		//Assume we have a list of FITS files, one per line
+		while (true) {
+			ReadFT1Fits(line, filter);
+			std::getline(is, line);
+			if (is.eof()){
+				break;
+			}
+			if (is.fail()){
+				throw(CountsMapException("Error parsing file \""+fileName+"\" assuming it contains a list of FT1 FITS filenames, one per line"));
+			}
+		}
+	}
+}
+
+void CountsMap::reset(int order, std::valarray<double> &eMin, std::valarray<double> & eMax){
+	//Check the valarrays are the same size and in each case, EMin[i] < EMax[i]
+	//and EMax[i] <= EMin[i+1];
+	if (eMin.size() != eMax.size()){
+		throw(CountsMapException("Boundary array sizes do not conform."));
+	}else{
+		if (eMin.size() < 1){
+			throw(CountsMapException("Must have at least one energy bin."));
+		}
+		for (int i = 0; i < eMin.size(); ++i){
+			if (eMin[i] >= eMax[i]){
+				throw(CountsMapException("Energy bins must have size > 0"));
+			}
+			if (i != eMin.size() - 1 && eMax[i] > eMin[i+1]){
+				throw(CountsMapException("The energy bins can't ovelap and must be in ascending order!"));
+			}
+		}
+	}