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/// \file neuron.cc
/// \brief Main program of the dna/neuron example

// This example is provided by the Geant4-DNA collaboration
// Any report or published results obtained using the Geant4-DNA software
// shall cite the following Geant4-DNA collaboration publication:
// Med. Phys. 37 (2010) 4692-4708
// and papers
// M. Batmunkh et al. J Radiat Res Appl Sci 8 (2015) 498-507
// O. Belov et al. Physica Medica 32 (2016) 1510-1520
// The Geant4-DNA web site is available at http://geant4-dna.org
//
// -------------------------------------------------------------------
// November 2016
// -------------------------------------------------------------------
//
//
//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo....
#include "ActionInitialization.hh"
#include "CommandLineParser.hh"
#include "DetectorConstruction.hh"
#include "PhysicsList.hh"

#include "G4DNAChemistryManager.hh"
#include "G4RunManagerFactory.hh"
#include "G4Timer.hh"
#include "G4Types.hh"
#include "G4UIExecutive.hh"
#include "G4UImanager.hh"
#include "G4VisExecutive.hh"

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

using namespace std;
using namespace G4DNAPARSER;

CommandLineParser* parser(0);

void Parse(int& argc, char** argv);

int main(int argc, char** argv)
{
  // run time in Geant4
  G4Timer* timer = new G4Timer();
  timer->Start();

  //////////
  // Parse options given in commandLine
  //
  Parse(argc, argv);

  //////////
  // Construct the run manager according to whether MT is activated or not
  //
  Command* commandLine(0);

  auto* runManager = G4RunManagerFactory::CreateRunManager();

  if ((commandLine = parser->GetCommandIfActive("-mt"))) {
    G4int nThreads = 2;

    if (commandLine->GetOption() == "NMAX") {
      nThreads = G4Threading::G4GetNumberOfCores();
    }
    else {
      nThreads = G4UIcommand::ConvertToInt(commandLine->GetOption());
    }
    runManager->SetNumberOfThreads(nThreads);

    G4cout << "===== neuron is started with " << runManager->GetNumberOfThreads()
           << " threads of MT MODE =====" << G4endl;
  }

  // Set mandatory user initialization classes
  DetectorConstruction* detector = new DetectorConstruction;
  runManager->SetUserInitialization(detector);
  runManager->SetUserInitialization(new PhysicsList);

  // User action initialization
  runManager->SetUserInitialization(new ActionInitialization(detector));

  // Initialize visualization
  G4VisManager* visManager = new G4VisExecutive;
  visManager->Initialize();

  // Get the pointer to the User Interface manager
  G4UImanager* UImanager = G4UImanager::GetUIpointer();
  G4UIExecutive* ui(0);

  // interactive mode : define UI session
  if ((commandLine = parser->GetCommandIfActive("-gui"))) {
    ui = new G4UIExecutive(argc, argv, commandLine->GetOption());

    if (ui->IsGUI()) UImanager->ApplyCommand("/control/execute gui.mac");

    if (parser->GetCommandIfActive("-novis") == 0)
    // visualization is used by default
    {
      if ((commandLine = parser->GetCommandIfActive("-vis")))
      // select a visualization driver if needed (e.g. HepFile)
      {
        UImanager->ApplyCommand(G4String("/vis/open ") + commandLine->GetOption());
      }
      else
      // by default OGL is used
      {
        UImanager->ApplyCommand("/vis/open OGL 800x600-0+0");
      }
      UImanager->ApplyCommand("/control/execute vis.mac");
    }
  }
  else
  // to be use visualization file (= store the visualization into
  // an external file:
  // ASCIITree ;  DAWNFILE ; HepRepFile ; VRML(1,2)FILE ; gMocrenFile ...
  {
    if ((commandLine = parser->GetCommandIfActive("-vis"))) {
      UImanager->ApplyCommand(G4String("/vis/open ") + commandLine->GetOption());
      UImanager->ApplyCommand("/control/execute vis.mac");
    }
  }

  if ((commandLine = parser->GetCommandIfActive("-mac"))) {
    G4String command = "/control/execute ";
    UImanager->ApplyCommand(command + commandLine->GetOption());
  }
  else {
    UImanager->ApplyCommand("/control/execute ");  // neuron.in
  }

  if ((commandLine = parser->GetCommandIfActive("-gui"))) {
    ui->SessionStart();
    delete ui;
  }

  // calculation time
  timer->Stop();
  G4cout << " Calculation time                      = " << timer->GetRealElapsed() << " s \n"
         << G4endl;

  delete visManager;
  delete runManager;

  return 0;
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void GetNameAndPathOfExecutable(char** argv, G4String& executable, G4String& path)
{
  // Get the last position of '/'
  std::string aux(argv[0]);

  // get '/' or '\\' depending on unix/mac or windows.
#if defined(_WIN32) || defined(WIN32)
  int pos = aux.rfind('\\');
#else
  int pos = aux.rfind('/');
#endif

  // Get the path and the name
  path = aux.substr(0, pos + 1);
  executable = aux.substr(pos + 1);
}

//....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......

void Parse(int& argc, char** argv)
{
  //////////
  // Parse options given in commandLine
  //
  parser = CommandLineParser::GetParser();

  parser->AddCommand("-gui", Command::OptionNotCompulsory,
                     "Select geant4 UI or just launch a geant4 terminal session", "qt");

  parser->AddCommand("-mac", Command::WithOption, "Give a mac file to execute", "macFile.mac");

  // You cann your own command, as for instance:
  //  parser->AddCommand("-seed",
  //                     Command::WithOption,
  //                     "Give a seed value in argument to be tested", "seed");
  // it is then up to you to manage this option

  parser->AddCommand("-mt", Command::WithOption, "Launch in MT mode (events computed in parallel)",
                     " NOT RECOMMANDED WITH CHEMISTRY)", "2");

  parser->AddCommand("-sXY", Command::OptionNotCompulsory,
                     "Initial beam position uniformly spread on a square!");
  parser->AddCommand("-dXY", Command::OptionNotCompulsory,
                     "Initial beam position uniformly spread on a disk!");

  parser->AddCommand("-dnaliv", Command::OptionNotCompulsory, "Activate Livermore + DNAPhysics");
  parser->AddCommand("-dnachemON", Command::OptionNotCompulsory,
                     "Activate Livermore + DNAPhysics + DNAChemistry");
  parser->AddCommand("-dnahad", Command::OptionNotCompulsory,
                     "Activate Hadronic + Livermore + DNAPhysics");

  parser->AddCommand("-swc", Command::WithOption, "Give a SWC file to simulation", "fileName.swc");

  parser->AddCommand("-network",
                     Command::WithOption,  // OptionNotCompulsory,
                     "Give a DAT file to simulation", "fileName.dat");

  parser->AddCommand("-vis", Command::WithOption, "Select a visualization driver",
                     "OGL 600x600-0+0");

  parser->AddCommand("-novis", Command::WithoutOption, "Deactivate visualization when using GUI");

  G4String exec;
  G4String path;
  GetNameAndPathOfExecutable(argv, exec, path);

  parser->AddCommand("-out", Command::OptionNotCompulsory, "Output files", exec);

  //////////
  // If -h or --help is given in option : print help and exit
  //
  if (parser->Parse(argc, argv) != 0)  // help is being printed
  {
    // if you are using ROOT, create a TApplication in this condition in order
    // to print the help from ROOT as well
    CommandLineParser::DeleteInstance();
    std::exit(0);
  }
  ///////////
  // Kill application if wrong argument in command line
  //
  if (parser->CheckIfNotHandledOptionsExists(argc, argv)) {
    // if you are using ROOT, you should initialise your TApplication
    // before this condition
    abort();
  }
}