experiments_utility.hpp

#ifndef SIM_EXP_H
#define SIM_EXP_H

#include "io/arg_parse.hpp"
#include "measurement/oscillation.hpp"
#include "measurement/basic.hpp"
#include "measurement/bad_simulation_error.hpp"
#include "utility/style.hpp"
#include "utility/common_utils.hpp"
#include "io/csvr_sim.hpp"
#include "io/csvw_sim.hpp"
#include "sim/determ/determ.hpp"
#include "sim/stoch/fast_gillespie_direct_simulation.hpp"
#include "sim/stoch/next_reaction_simulation.hpp"
#include "sim/stoch/sorting_direct_simulation.hpp"
#include "sim/stoch/log_direct_method.hpp"
#include "model_impl.hpp"
#include "io/ezxml/ezxml.h"
#include "arg_parse.hpp"
#include "parse_analysis_entries.hpp"

using dense::run_simulation;
using dense::Sim_Builder;
using dense::parse_analysis_entries;
using dense::Sorting_Direct_Simulation;



template<class Sim>
std::vector<Real> simulate_experiment(int ac, char** av, Static_Args* args, std::string type){
  using Simulation = Sim;
  Sim_Builder<Simulation> sim = Sim_Builder<Simulation>(args->perturbation_factors, args->gradient_factors, args->adj_graph, ac, av);
  std::vector<std::pair<std::string, std::unique_ptr<Analysis<Simulation>>>> names_and_analysis = parse_analysis_entries<Simulation>(ac, av, args->adj_graph.num_vertices());
  for(auto& entry : names_and_analysis){
    entry.first = "output/" + type + ".csv";
  }
  std::vector<std::vector<Real>> perf = run_simulation<Simulation>(args->simulation_duration, args->analysis_interval, std::move(sim.get_simulations(args->param_sets)), std::move(names_and_analysis));
  
  return perf[0];
}

void performance_out(std::string type, std::vector<std::vector<Real>> perf, std::string perf_sims){
  csvw performance_out("performance/" + type + "_performance.csv");
  perf_sims = perf_sims.substr(0,perf_sims.size()-1);
  performance_out << perf_sims + "\n";
  
  //Obnoxiously primitive fix for seg fault(should be made better eventually)
  for(int i = 0; (unsigned)i < perf.size(); i++){
    std::cout << perf[i].size() <<'\n';
  }
  
  for(int i = 0; (unsigned)i < perf.size(); i++){
      performance_out << perf[i].at(0);
      if(i + 1 == perf.size()){
      } else {
        performance_out << ",";
      }
    }
  performance_out << "\n";
}

#endif