Rename mass_profile to src; Add install & uninstall to Makefile

1 files changed, 0 insertions, 586 deletions

diff --git a/mass_profile/fit_dbeta_sbp.cpp b/mass_profile/fit_dbeta_sbp.cpp
deleted file mode 100644
index 71b3089..0000000
--- a/mass_profile/fit_dbeta_sbp.cpp
+++ /dev/null
@@ -1,586 +0,0 @@
-/*
-  Perform a double-beta density model fitting to the surface brightness data
-  Author: Junhua Gu
-  Last modified: 2016.06.07
-  This code is distributed with no warrant
-*/
-
-
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <list>
-#include "vchisq.hpp"
-#include "dbeta.hpp"
-#include "beta_cfg.hpp"
-#include <data_sets/default_data_set.hpp>
-#include <methods/powell/powell_method.hpp>
-#include <core/freeze_param.hpp>
-#include <error_estimator/error_estimator.hpp>
-#include "spline.hpp"
-
-using namespace std;
-using namespace opt_utilities;
-//double s=5.63136645E20;
-const double kpc=3.086E21;//kpc in cm
-const double Mpc=kpc*1000;
-
-double dbeta_func(double r, double n01, double rc1, double beta1,
-                  double n02, double rc2, double beta2)
-{
-  double v1 = abs(n01) * pow(1+r*r/rc1/rc1, -3./2.*abs(beta1));
-  double v2 = abs(n02) * pow(1+r*r/rc2/rc2, -3./2.*abs(beta2));
-  return v1 + v2;
-}
-
-//calculate critical density from z, under following cosmological constants
-static double calc_critical_density(double z,
-				    const double H0=2.3E-18,
-				      const double Omega_m=.27)
-{
-  const double G=6.673E-8;//cm^3 g^-1 s^2
-  const double E=std::sqrt(Omega_m*(1+z)*(1+z)*(1+z)+1-Omega_m);
-  const double H=H0*E;
-  return 3*H*H/8/pi/G;
-}
-
-
-//A class enclosing the spline interpolation method
-class spline_func_obj
-  :public func_obj<double,double>
-{
-  //has an spline object
-  spline<double> spl;
-public:
-  //This function is used to calculate the intepolated value
-  double do_eval(const double& x)
-  {
-    return spl.get_value(x);
-  }
-
-  //we need this function, when this object is performing a clone of itself
-  spline_func_obj* do_clone()const
-  {
-    return new spline_func_obj(*this);
-  }
-
-public:
-  //add points to the spline object, after which the spline will be initialized
-  void add_point(double x,double y)
-  {
-    spl.push_point(x,y);
-  }
-
-  //before getting the intepolated value, the spline should be initialzied by calling this function
-  void gen_spline()
-  {
-    spl.gen_spline(0,0);
-  }
-};
-
-int main(int argc,char* argv[])
-{
-  if(argc!=2)
-    {
-      cerr<<argv[0]<<" <configure file>"<<endl;
-      return -1;
-    }
-  //initialize the parameters list
-  ifstream cfg_file(argv[1]);
-  assert(cfg_file.is_open());
-  cfg_map cfg=parse_cfg_file(cfg_file);
-
-  const double z=cfg.z;
-
-  //initialize the radius list, sbp list and sbp error list
-  std::vector<double> radii;
-  std::vector<double> sbps;
-  std::vector<double> sbpe;
-  std::vector<double> radii_all;
-  std::vector<double> sbps_all;
-  std::vector<double> sbpe_all;
-  //prepend the zero point to radius list
-  radii.push_back(0.0);
-  radii_all.push_back(0.0);
-  //read sbp and sbp error data
-  ifstream ifs(cfg.sbp_data.c_str());
-  std::string line;
-  if (ifs.is_open())
-    {
-      while(std::getline(ifs, line))
-        {
-          if (line.empty())
-            continue;
-
-          std::istringstream iss(line);
-          double x, xe, y, ye;
-          if ((iss >> x >> xe >> y >> ye))
-            {
-              std::cerr << "sbprofile data: "
-                        << x << ", " << xe << ", " << y << ", " << ye
-                        << std::endl;
-              radii.push_back(x+xe);  /* NOTE: use outer radii of regions */
-              radii_all.push_back(x+xe);
-              sbps.push_back(y);
-              sbps_all.push_back(y);
-              sbpe.push_back(ye);
-              sbpe_all.push_back(ye);
-            }
-          else
-            {
-              std::cerr << "skipped line: " << line << std::endl;
-            }
-        }
-    }
-  else
-    {
-      std::cerr << "ERROR: cannot open file: " << cfg.sbp_data.c_str()
-                << std::endl;
-      return 1;
-    }
-
-  //initialize the cm/pixel value
-  double cm_per_pixel=cfg.cm_per_pixel;
-  double rmin;
-  if(cfg.rmin_pixel>0)
-    {
-      rmin=cfg.rmin_pixel;
-    }
-  else
-    {
-      rmin=cfg.rmin_kpc*kpc/cm_per_pixel;
-    }
-
-  cerr<<"rmin="<<rmin<<" (pixel)"<<endl;
-  std::list<double> radii_tmp,sbps_tmp,sbpe_tmp;
-  radii_tmp.resize(radii.size());
-  sbps_tmp.resize(sbps.size());
-  sbpe_tmp.resize(sbpe.size());
-  copy(radii.begin(),radii.end(),radii_tmp.begin());
-  copy(sbps.begin(),sbps.end(),sbps_tmp.begin());
-  copy(sbpe.begin(),sbpe.end(),sbpe_tmp.begin());
-  for(list<double>::iterator i=radii_tmp.begin();i!=radii_tmp.end();)
-    {
-      if(*i<rmin)
-	{
-	  radii_tmp.pop_front();
-	  sbps_tmp.pop_front();
-	  sbpe_tmp.pop_front();
-	  i=radii_tmp.begin();
-	  continue;
-	}
-      ++i;
-    }
-  radii.resize(radii_tmp.size());
-  sbps.resize(sbps_tmp.size());
-  sbpe.resize(sbpe_tmp.size());
-  copy(radii_tmp.begin(),radii_tmp.end(),radii.begin());
-  copy(sbps_tmp.begin(),sbps_tmp.end(),sbps.begin());
-  copy(sbpe_tmp.begin(),sbpe_tmp.end(),sbpe.begin());
-
-  //read cooling function data
-  spline_func_obj cf;
-  for(ifstream ifs(cfg.cfunc_profile.c_str());;)
-    {
-      assert(ifs.is_open());
-      double x,y;
-      ifs>>x>>y;
-      if(!ifs.good())
-	{
-	  break;
-	}
-      cerr<<x<<"\t"<<y<<endl;
-      if(x>radii.back())
-	{
-	  break;
-	}
-      cf.add_point(x,y);
-    }
-  cf.gen_spline();
-
-  //read temperature profile data
-  spline_func_obj Tprof;
-  int tcnt=0;
-  for(ifstream ifs1(cfg.tprofile.c_str());;++tcnt)
-    {
-      assert(ifs1.is_open());
-      double x,y;
-      ifs1>>x>>y;
-      if(!ifs1.good())
-      {
-	break;
-      }
-      cerr<<x<<"\t"<<y<<endl;
-#if 0
-      if(tcnt==0)
-	{
-	  Tprof.add_point(0,y);
-	}
-#endif
-      Tprof.add_point(x,y);
-    }
-
-
-  Tprof.gen_spline();
-
-  default_data_set<std::vector<double>,std::vector<double> > ds;
-  ds.add_data(data<std::vector<double>,std::vector<double> >(radii,sbps,sbpe,sbpe,radii,radii));
-
-  //initial fitter
-  fitter<vector<double>,vector<double>,vector<double>,double> f;
-  f.load_data(ds);
-  //initial the object, which is used to calculate projection effect
-  projector<double> a;
-  bool tie_beta=false;
-  if(cfg.param_map.find("beta")!=cfg.param_map.end()
-     &&cfg.param_map.find("beta1")==cfg.param_map.end()
-     &&cfg.param_map.find("beta2")==cfg.param_map.end())
-    {
-      dbeta2<double> dbetao;
-      a.attach_model(dbetao);
-      tie_beta=true;
-    }
-  else if((cfg.param_map.find("beta1")!=cfg.param_map.end()
-	   ||cfg.param_map.find("beta2")!=cfg.param_map.end())
-	  &&cfg.param_map.find("beta")==cfg.param_map.end())
-    {
-      dbeta<double> dbetao;
-      a.attach_model(dbetao);
-      tie_beta=false;
-    }
-  else
-    {
-      cerr<<"Error, cannot decide whether to tie beta together or let them vary freely!"<<endl;
-      assert(0);
-    }
-
-  //attach the cooling function
-  a.attach_cfunc(cf);
-  a.set_cm_per_pixel(cm_per_pixel);
-
-  f.set_model(a);
-  //chi^2 statistic
-  vchisq<double> c;
-  c.verbose(true);
-  c.set_limit();
-  f.set_statistic(c);
-  //optimization method
-  f.set_opt_method(powell_method<double,std::vector<double> >());
-  //initialize the initial values
-  double n01=0;
-  double rc1=0;
-  double n02=0;
-  double rc2=0;
-  double beta=0;
-  double bkg_level=0;
-  if(tie_beta)
-    {
-      f.set_param_value("beta",.7);
-      f.set_param_lower_limit("beta",.3);
-      f.set_param_upper_limit("beta",1.4);
-    }
-  else
-    {
-      f.set_param_value("beta1",.7);
-      f.set_param_lower_limit("beta1",.3);
-      f.set_param_upper_limit("beta1",1.4);
-      f.set_param_value("beta2",.7);
-      f.set_param_lower_limit("beta2",.3);
-      f.set_param_upper_limit("beta2",1.4);
-    }
-  for(std::map<std::string,std::vector<double> >::iterator i=cfg.param_map.begin();
-      i!=cfg.param_map.end();++i)
-    {
-      std::string pname=i->first;
-      f.set_param_value(pname,i->second.at(0));
-      if(i->second.size()==3)
-	{
-	  double a1=i->second[1];
-	  double a2=i->second[2];
-	  double u=std::max(a1,a2);
-	  double l=std::min(a1,a2);
-	  f.set_param_upper_limit(pname,u);
-	  f.set_param_lower_limit(pname,l);
-	}
-      else
-	{
-	  if(pname=="beta"||pname=="beta1"||pname=="beta2")
-	    {
-	      f.set_param_lower_limit(pname,.3);
-	      f.set_param_upper_limit(pname,1.4);
-	    }
-	}
-    }
-
-
-
-  //perform the fitting, first freeze beta1, beta2, rc1, and rc2
-  if(tie_beta)
-    {
-      f.set_param_modifier(freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("beta")+
-			   freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("rc1")+
-			   freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("rc2")
-			   );
-    }
-  else
-    {
-      f.set_param_modifier(freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("beta1")+
-			   freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("beta2")+
-			   freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("rc1")+
-			   freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("rc2")
-			   );
-    }
-
-  f.fit();
-
-  f.clear_param_modifier();
-
-  //then perform the fitting, freeze beta1 and beta2
-  //f.set_param_modifier(freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("beta"));
-  //f.set_param_modifier(freeze_param<std::vector<double>,std::vector<double>,std::vector<double>,std::string>("bkg"));
-  f.fit();
-  //f.clear_param_modifier();
-
-  //finally thaw all parameters
-  f.fit();
-  double beta1=0;
-  double beta2=0;
-
-  n01=f.get_param_value("n01");
-  rc1=f.get_param_value("rc1");
-  n02=f.get_param_value("n02");
-  rc2=f.get_param_value("rc2");
-  if(tie_beta)
-    {
-      beta=f.get_param_value("beta");
-      beta1=beta;
-      beta2=beta;
-    }
-  else
-    {
-      beta1=f.get_param_value("beta1");
-      beta2=f.get_param_value("beta2");
-    }
-  //output the params
-  ofstream param_output("dbeta_param.txt");
-  //output the datasets and fitting results
-  for(size_t i=0;i<f.get_num_params();++i)
-    {
-      if(f.get_param_info(i).get_name()=="rc1")
-	{
-	  cerr<<"rc1_kpc"<<"\t"<<abs(f.get_param_info(i).get_value())*cm_per_pixel/kpc<<endl;
-	  param_output<<"rc1_kpc"<<"\t"<<abs(f.get_param_info(i).get_value())*cm_per_pixel/kpc<<endl;
-	}
-      if(f.get_param_info(i).get_name()=="rc2")
-	{
-	  cerr<<"rc2_kpc"<<"\t"<<abs(f.get_param_info(i).get_value())*cm_per_pixel/kpc<<endl;
-	  param_output<<"rc2_kpc"<<"\t"<<abs(f.get_param_info(i).get_value())*cm_per_pixel/kpc<<endl;
-	}
-      cerr<<f.get_param_info(i).get_name()<<"\t"<<abs(f.get_param_info(i).get_value())<<endl;
-      param_output<<f.get_param_info(i).get_name()<<"\t"<<abs(f.get_param_info(i).get_value())<<endl;
-    }
-  cerr<<"reduced_chi^2="<<f.get_statistic_value()/(radii.size()-f.get_model().get_num_free_params())<<endl;
-  param_output<<"reduced_chi^2="<<f.get_statistic_value()/(radii.size()-f.get_model().get_num_free_params())<<endl;
-
-  //c.verbose(false);
-  //f.set_statistic(c);
-  //f.fit();
-  std::vector<double> p=f.get_all_params();
-  f.clear_param_modifier();
-  std::vector<double> mv=f.eval_model(radii,p);
-
-
-  ofstream ofs_sbp("sbp_fit.qdp");
-  ofs_sbp<<"read serr 2"<<endl;
-  ofs_sbp<<"skip single"<<endl;
-
-  ofs_sbp<<"line on 2"<<endl;
-  ofs_sbp<<"line on 3"<<endl;
-  ofs_sbp<<"line on 4"<<endl;
-  ofs_sbp<<"line on 5"<<endl;
-  ofs_sbp<<"line on 7"<<endl;
-  ofs_sbp<<"ls 2 on 7"<<endl;
-  ofs_sbp<<"ls 2 on 3"<<endl;
-  ofs_sbp<<"ls 2 on 4"<<endl;
-  ofs_sbp<<"ls 2 on 5"<<endl;
-
-
-
-  ofs_sbp<<"!LAB  POS Y  4.00"<<endl;
-  ofs_sbp<<"!LAB  ROT"<<endl;
-  ofs_sbp<<"win 1"<<endl;
-  ofs_sbp<<"yplot 1 2 3 4 5"<<endl;
-  ofs_sbp<<"loc 0 0 1 1"<<endl;
-  ofs_sbp<<"vie .1 .4 .9 .9"<<endl;
-  ofs_sbp<<"la y cnt/s/pixel/cm^2"<<endl;
-  ofs_sbp<<"log x"<<endl;
-  ofs_sbp<<"log y"<<endl;
-  ofs_sbp<<"r x "<<(radii[1]+radii[0])/2*cm_per_pixel/kpc<<" "<<(radii[sbps.size()-2]+radii[sbps.size()-1])/2*cm_per_pixel/kpc<<endl;
-  ofs_sbp<<"win 2"<<endl;
-  ofs_sbp<<"yplot 6 7"<<endl;
-  ofs_sbp<<"loc 0 0 1 1"<<endl;
-  ofs_sbp<<"vie .1 .1 .9 .4"<<endl;
-  ofs_sbp<<"la x radius (kpc)"<<endl;
-  ofs_sbp<<"la y chi"<<endl;
-  ofs_sbp<<"log x"<<endl;
-  ofs_sbp<<"log y off"<<endl;
-  ofs_sbp<<"r x "<<(radii[1]+radii[0])/2*cm_per_pixel/kpc<<" "<<(radii[sbps.size()-2]+radii[sbps.size()-1])/2*cm_per_pixel/kpc<<endl;
-  for(size_t i=1;i<sbps.size();++i)
-    {
-      double x=(radii[i]+radii[i-1])/2;
-      double y=sbps[i-1];
-      double ye=sbpe[i-1];
-      //double ym=mv[i-1];
-      ofs_sbp<<x*cm_per_pixel/kpc<<"\t"<<y<<"\t"<<ye<<endl;
-    }
-  ofs_sbp<<"no no no"<<endl;
-  for(size_t i=1;i<sbps.size();++i)
-    {
-      double x=(radii[i]+radii[i-1])/2;
-      //double y=sbps[i-1];
-      //double ye=sbpe[i-1];
-      double ym=mv[i-1];
-      ofs_sbp<<x*cm_per_pixel/kpc<<"\t"<<ym<<"\t"<<0<<endl;
-    }
-  //bkg
-  ofs_sbp<<"no no no"<<endl;
-  bkg_level=abs(f.get_param_value("bkg"));
-  for(size_t i=0;i<sbps.size();++i)
-    {
-      double x=(radii[i]+radii[i-1])/2;
-      ofs_sbp<<x*cm_per_pixel/kpc<<"\t"<<bkg_level<<"\t0"<<endl;
-    }
-  //rc1
-  ofs_sbp<<"no no no"<<endl;
-  double rc1_kpc=abs(f.get_param_value("rc1")*cm_per_pixel/kpc);
-  double max_sbp=*max_element(sbps.begin(),sbps.end());
-  double min_sbp=*min_element(sbps.begin(),sbps.end());
-  for(double x=min_sbp;x<=max_sbp;x+=(max_sbp-min_sbp)/100)
-    {
-      ofs_sbp<<rc1_kpc<<"\t"<<x<<"\t"<<"0"<<endl;
-    }
-  //rc2
-  ofs_sbp<<"no no no"<<endl;
-  double rc2_kpc=abs(f.get_param_value("rc2")*cm_per_pixel/kpc);
-  for(double x=min_sbp;x<=max_sbp;x+=(max_sbp-min_sbp)/100)
-    {
-      ofs_sbp<<rc2_kpc<<"\t"<<x<<"\t"<<"0"<<endl;
-    }
-  //resid
-  ofs_sbp<<"no no no"<<endl;
-  for(size_t i=1;i<sbps.size();++i)
-    {
-      double x=(radii[i]+radii[i-1])/2;
-      //double y=sbps[i-1];
-      //double ye=sbpe[i-1];
-      double ym=mv[i-1];
-      ofs_sbp<<x*cm_per_pixel/kpc<<"\t"<<(ym-sbps[i-1])/sbpe[i-1]<<"\t"<<1<<endl;
-    }
-  //zero level in resid map
-  ofs_sbp<<"no no no"<<endl;
-  for(size_t i=1;i<sbps.size();++i)
-    {
-      double x=(radii[i]+radii[i-1])/2;
-      //double y=sbps[i-1];
-      //double ye=sbpe[i-1];
-      //double ym=mv[i-1];
-      ofs_sbp<<x*cm_per_pixel/kpc<<"\t"<<0<<"\t"<<0<<endl;
-    }
-
-
-  mv=f.eval_model_raw(radii,p);
-  ofstream ofs_rho("rho_fit.qdp");
-  ofstream ofs_rho_data("rho_fit.dat");
-  ofstream ofs_entropy("entropy.qdp");
-  ofs_rho<<"la x radius (kpc)"<<endl;
-  ofs_rho<<"la y density (cm\\u-3\\d)"<<endl;
-  /*
-  for(int i=1;i<sbps.size();++i)
-    {
-      double x=(radii[i]+radii[i-1])/2;
-      double ym=mv[i-1];
-      ofs_rho<<x*cm_per_pixel/kpc<<"\t"<<ym<<endl;
-    }
-  */
-
-  //double lower,upper;
-  double dr=1;
-  //calculate the mass profile
-  //const double G=6.673E-8;//cm^3 g^-1 s^-2
-  // Molecular weight per electron
-  // Reference: Ettori et al. 2013, Space Sci. Rev., 177, 119-154; Eq.(9) below
-  static const double mu=1.155;
-  static const double mp=1.67262158E-24;//g
-  static const double M_sun=1.98892E33;//g
-  //static const double k=1.38E-16;
-
-  ofstream ofs_mass("mass_int.qdp");
-  ofstream ofs_mass_dat("mass_int.dat");
-  ofstream ofs_overdensity("overdensity.qdp");
-  ofstream ofs_gas_mass("gas_mass_int.qdp");
-  //ofs_mass<<"la x radius (kpc)"<<endl;
-  //ofs_mass<<"la y mass enclosed (solar mass)"<<endl;
-  //ofs_overdensity<<"la x radius (kpc)"<<endl;
-  //ofs_overdensity<<"la y overdensity"<<endl;
-  double gas_mass=0;
-  for(double r=1;r<200000;r+=dr)
-    {
-      dr=r/100;
-      double r1=r+dr;
-      double r_cm=r*cm_per_pixel;
-      double r1_cm=r1*cm_per_pixel;
-      double dr_cm=dr*cm_per_pixel;
-      double V_cm3=4./3.*pi*(dr_cm*(r1_cm*r1_cm+r_cm*r_cm+r_cm*r1_cm));
-      double ne=dbeta_func(r,n01,rc1,beta1,
-			   n02,rc2,beta2);//cm^3
-
-      double dmgas=V_cm3*ne*mu*mp/M_sun;
-      gas_mass+=dmgas;
-
-      ofs_gas_mass<<r*cm_per_pixel/kpc<<"\t"<<gas_mass<<endl;
-      double ne_beta1=dbeta_func(r,n01,rc1,beta1, 0,rc2,beta2);
-
-      double ne_beta2=dbeta_func(r,0,rc1,beta1, n02,rc2,beta2);
-
-      double ne1=dbeta_func(r1,n01,rc1,beta1, n02,rc2,beta2);//cm^3
-
-      double T_keV=Tprof(r);
-      double T1_keV=Tprof(r1);
-
-      //double T_K=T_keV*11604505.9;
-      //double T1_K=T1_keV*11604505.9;
-
-      double dlnT=log(T1_keV/T_keV);
-      double dlnr=log(r+dr)-log(r);
-      double dlnn=log(ne1/ne);
-
-      //double r_kpc=r_cm/kpc;
-      double r_Mpc=r_cm/Mpc;
-      //double M=-r_cm*T_K*k/G/mu/mp*(dlnT/dlnr+dlnn/dlnr);
-      //ref:http://adsabs.harvard.edu/abs/2012MNRAS.422.3503W
-      //Walker et al. 2012
-      double M=-3.68E13*M_sun*T_keV*r_Mpc*(dlnT/dlnr+dlnn/dlnr);
-      double rho=M/(4./3.*pi*r_cm*r_cm*r_cm);
-
-      double S=T_keV/pow(ne,2./3.);
-      //cout<<r<<"\t"<<M/M_sun<<endl;
-      //cout<<r<<"\t"<<T_keV<<endl;
-
-      ofs_rho<<r*cm_per_pixel/kpc<<"\t"<<ne<<"\t"<<ne_beta1<<"\t"<<ne_beta2<<endl;
-      ofs_rho_data<<r*cm_per_pixel/kpc<<"\t"<<ne<<endl;
-      ofs_entropy<<r*cm_per_pixel/kpc<<"\t"<<S<<endl;
-#if 0
-      if(r*cm_per_pixel/kpc<5)
-	{
-	  continue;
-	}
-#endif
-      ofs_mass<<r*cm_per_pixel/kpc<<"\t"<<M/M_sun<<endl;
-      if(r<radii.back())
-	{
-	  ofs_mass_dat<<r*cm_per_pixel/kpc<<"\t0\t"<<M/M_sun<<"\t"<<M/M_sun*.1<<endl;
-	}
-      ofs_overdensity<<r*cm_per_pixel/kpc<<"\t"<<rho/calc_critical_density(z)<<endl;
-
-    }
-}