TGRSIint.cxx

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#include "TGRSIint.h"
 
#include "GRootGuiFactory.h"
#include "GVersion.h"
#include "Getline.h"
#include "Globals.h"
#include "TDataParser.h"
#include "TGRSIOptions.h"
#include "TGRSIUtilities.h"
#include "GValue.h"
#include "TROOT.h"
#include "GCanvas.h"
 
#include "StoppableThread.h"
#include "TAnalysisHistLoop.h"
#include "TAnalysisWriteLoop.h"
#include "TDataLoop.h"
#include "TDetBuildingLoop.h"
#include "TEventBuildingLoop.h"
#include "TFragHistLoop.h"
#include "TFragWriteLoop.h"
#include "TFragmentChainLoop.h"
#include "TTerminalLoop.h"
#include "TUnpackingLoop.h"
#include "TPPG.h"
#include "TSortingDiagnostics.h"
#include "TParserLibrary.h"
 
#include "GRootCommands.h"
#include "TRunInfo.h"
 
#include "TInterpreter.h"
#include "TGHtmlBrowser.h"
//#include <pstream.h>
 
#include <thread>
#include <utility>
 
#include <pwd.h>
 
extern void PopupLogo(bool);
extern void WaitLogo();
 
TGRSIint* TGRSIint::fTGRSIint = nullptr;
 
TEnv* TGRSIint::fGRSIEnv = nullptr;
 
void ReadTheNews();
 
TChain* gFragment = nullptr;
TChain* gAnalysis = nullptr;
 
TGRSIint* TGRSIint::instance(int argc, char** argv, void*, int, bool, const char* appClassName)
{
   /// Singleton constructor instance
   if(fTGRSIint == nullptr) {
      fTGRSIint = new TGRSIint(argc, argv, nullptr, 0, true, appClassName);
      fTGRSIint->ApplyOptions();
   }
   return fTGRSIint;
}
 
TGRSIint::TGRSIint(int argc, char** argv, void*, int, bool noLogo, const char* appClassName)
   : TRint(appClassName, new int(0), argv, nullptr, 0, noLogo), fKeepAliveTimer(nullptr),
     main_thread_id(std::this_thread::get_id()), fIsTabComplete(false), fAllowedToTerminate(true), fRootFilesOpened(0),
     fRawFilesOpened(0)
{
   /// Singleton constructor
   fGRSIEnv = gEnv;
 
   GetSignalHandler()->Remove();
   auto* interruptHandler = new TGRSIInterruptHandler();
   interruptHandler->Add();
 
   try {
      TGRSIOptions* opt = TGRSIOptions::Get(argc, argv);
      if(opt->ShouldExit()) {
         exit(0);
      }
   } catch(ParseError& e) {
      exit(1);
   }
 
   PrintLogo(TGRSIOptions::Get()->ShowLogo());
   SetPrompt("GRSI [%d] ");
   std::string grsipath = getenv("GRSISYS");
   gInterpreter->AddIncludePath(Form("%s/include", grsipath.c_str()));
}
 
void TGRSIint::ApplyOptions()
{
   /// Applies options from TGRSIOptions. This include things such as batch sorting,
   /// reading material, and logo. Also includes the setup of what to do with mid
   /// and root files that are input.
   TGRSIOptions* opt = TGRSIOptions::Get();
 
   if(opt->Batch()) {
      MakeBatch();
   }
 
   bool missing_raw_file = !AllFilesExist(opt->InputFiles());
 
   LoadGROOTGraphics();
 
   if(opt->ReadingMaterial()) {
      std::thread fnews = std::thread(ReadTheNews);
      fnews.detach();
   }
 
   ////////////////////////////////////////////////////////
   ////////////////////////////////////////////////////////
   //////           Start of redoing section        ///////
   ////////////////////////////////////////////////////////
   ////////////////////////////////////////////////////////
 
   // load parser library if provided
   if(!opt->ParserLibrary().empty()) {
      try {
         TParserLibrary::Get()->Load();
      } catch(std::runtime_error& e) {
         // if we failed to load the library, try to continue w/o it
         std::cerr << DRED << e.what() << RESET_COLOR << std::endl;
      }
   }
 
   TRunInfo::ClearVersion();
   TRunInfo::SetVersion(GRSI_RELEASE);
 
   TRunInfo::ClearFullVersion();
   TRunInfo::SetFullVersion(GRSI_GIT_COMMIT);
 
   TRunInfo::ClearDate();
   TRunInfo::SetDate(GRSI_GIT_COMMIT_TIME);
 
   for(const auto& rawFile : opt->InputFiles()) {
      OpenRawFile(rawFile);
   }
 
   for(const auto& filename : opt->RootInputFiles()) {
      // this will populate gChain if able.
      //   TChannels from the root file will be loaded as file is opened.
      //   GValues from the root file will be loaded as file is opened.
      OpenRootFile(filename);
   }
 
   SetupPipeline();
 
   if(opt->StartGui()) {
      StartGUI();
   }
 
   for(const auto& filename : opt->MacroInputFiles()) {
      RunMacroFile(filename);
   }
 
   std::cout << StoppableThread::AllThreadHeader() << std::endl;
   LoopUntilDone();
   if(opt->CloseAfterSort()) {
      int exit_status = missing_raw_file ? 1 : 0;
      Terminate(exit_status);
   }
}
 
void TGRSIint::LoopUntilDone()
{
   /// Outputs the thread status until all of the threads are complete.
   int iter = 0;
   while(StoppableThread::AnyThreadRunning()) {
      std::this_thread::sleep_for(std::chrono::seconds(1));
 
      // We need to process events in case a different thread is asking for a file to be opened.
      // However, if there is no stdin, ProcessEvents() will call Terminate().
      // This prevents the terminate from taking effect while in this context.
      fAllowedToTerminate = false;
      gSystem->ProcessEvents();
      fAllowedToTerminate = true;
 
      ++iter;
      if(TGRSIOptions::Get()->StatusInterval() > 0 && iter % TGRSIOptions::Get()->StatusInterval() == 0) {
         std::cout << "\r" << StoppableThread::AllThreadStatus() << std::endl;
      }
      std::cout << "\r" << StoppableThread::AllThreadProgress() << std::flush;
   }
   std::cout << std::endl;
}
 
bool TGRSIint::HandleTermInput()
{
   /// Handles terminal input via TRint
   return TRint::HandleTermInput();
}
 
void TGRSIint::Terminate(Int_t status)
{
   /// Kills all of the threads if the process is allowed to terminate. This
   /// sends an error to TSortingDiagnostics if an analysis tree is being created
   if(!fAllowedToTerminate) {
      std::cout << "Not allowed to terminate, sorry!" << std::endl;
      return;
   }
 
   StoppableThread::SendStop();
   LoopUntilDone();
   StoppableThread::StopAll();
 
   if(TGRSIOptions::Get()->MakeAnalysisTree()) {
      TSortingDiagnostics::Get()->Print("error");
   }
 
   if((clock() % 60) == 0) {
      std::cout << "DING!" << std::flush;
      gSystem->Sleep(500);   // 500 ms
      std::cout << "\r              \r" << std::flush;
   }
 
   TSeqCollection* canvases = gROOT->GetListOfCanvases();
   while(canvases->GetEntries() > 0) {
      static_cast<GCanvas*>(canvases->At(0))->Close();
   }
 
   // TChannel::DeleteAllChannels();
   TRint::Terminate(status);
}
 
Int_t TGRSIint::TabCompletionHook(char* buf, int* pLoc, std::ostream& out)
{
   /// Tries to do a tab completion. Returns false if unsuccsessful
   fIsTabComplete = true;
   auto result    = TRint::TabCompletionHook(buf, pLoc, out);
   fIsTabComplete = false;
   return result;
}
 
Long_t TGRSIint::ProcessLine(const char* inputLine, Bool_t sync, Int_t* error)
{
   /// This takes over the native root command line. There are two main reasons for this
   /// 1. To keep the command line thread-safe.
   /// 2. To block TCanvas from opening, and to instead use our GCanvas.
 
   // If you print while fIsTabComplete is true, you will break tab complete.
   // Any diagnostic print statements should be done after this if statement.
   if(fIsTabComplete) {
      Long_t res = TRint::ProcessLine(inputLine, sync, error);
      return res;
   }
 
   // loop over the input line and replace all instances of "TCanvas" with "GCanvas"
   std::string line(inputLine);
   size_t      pos = 0;
   while((pos = line.find("TCanvas", pos)) != std::string::npos) {
      line[pos] = 'G';
   }
 
   if(std::this_thread::get_id() != main_thread_id) {
      return DelayedProcessLine(line);
   }
 
   return TRint::ProcessLine(line.c_str(), sync, error);
}
 
void ReadTheNews()
{
   /// Opens a random wikipedia page for your enjoyment
#ifdef __APPLE__
   gROOT->ProcessLine(".! open http://en.wikipedia.org/wiki/Special:Random > /dev/null 2>&1;");
#else
   gROOT->ProcessLine(".! xdg-open http://en.wikipedia.org/wiki/Special:Random > /dev/null 2>&1;");
#endif
}
 
void TGRSIint::PrintLogo(bool print)
{
   /// Prints the GRSISort logo to terminal
   if(print) {
#ifdef LINUX
      const std::string& ref       = ProgramName();
      const unsigned int reflength = ref.length() - 78;
#else
      const std::string& ref       = "Sorting Program for Online and Offline Nuclear Data";
      const unsigned int reflength = 53;
#endif
 
      const unsigned int width = reflength + (reflength % 2);
      printf("\t*%s*\n", std::string(width, '*').c_str());
      printf("\t*%*s%*s*\n", width / 2 + 4, "GRSI Sort", width / 2 - 4, "");
      printf("\t*%*s%*s*\n", width / 2 + 12, "a remake of GRSI SPOON", width / 2 - 12, "");
      printf("\t*%*s%*s*\n", width / 2 + reflength / 2, ref.c_str(), width / 2 - reflength / 2, "");
      printf("\t*%*s%*s*\n", width / 2 + 14, "A lean, mean sorting machine", width / 2 - 14, "");
      printf("\t*%*s%*s*\n", width / 2 + 9, "version " GRSI_RELEASE, width / 2 - 9, "");
      printf("\t*%s*\n", std::string(width, '*').c_str());
 
      std::thread drawlogo(&TGRSIint::DrawLogo);   //, this);
      drawlogo.detach();
   } else {
      std::cout << "\tgrsisort version " << GRSI_RELEASE << std::endl;
   }
}
 
TFile* TGRSIint::OpenRootFile(const std::string& filename, Option_t* opt)
{
   /// Opens root files provided on the command line. Also tells you where these files
   /// are stored (ie _file0). If these files are analysis or fragment trees, they are
   /// automatically chained into chains called gFragment and gAnalysis. Once this is
   /// complete, the TChannels, GValues and RunInfo are also read in.
   TString sopt(opt);
   sopt.ToLower();
 
   TFile* file = nullptr;
   if(sopt.Contains("recreate") || sopt.Contains("new")) {
      // We are being asked to make a new file.
      file = new TFile(filename.c_str(), "RECREATE");
      if(file != nullptr && file->IsOpen()) {
         // Give access to the file inside the interpreter.
         const char* command = Form("TFile* _file%i = (TFile*)%luL;", fRootFilesOpened, reinterpret_cast<unsigned long>(file));
         TRint::ProcessLine(command);
         fRootFilesOpened++;
      } else {
         std::cout << "Could not create " << filename << std::endl;
      }
   } else {
      // Open an already existing file.
      file = new TFile(filename.c_str(), opt);
      if(file != nullptr && file->IsOpen()) {
         // Give access to the file inside the interpreter.
         const char* command = Form("TFile* _file%i = (TFile*)%luL;", fRootFilesOpened, reinterpret_cast<unsigned long>(file));
         TRint::ProcessLine(command);
         std::cout << "\tfile " << BLUE << file->GetName() << RESET_COLOR << " opened as " << BLUE << "_file"
                   << fRootFilesOpened << RESET_COLOR << std::endl;
 
         // If FragmentTree exists, add the file to the chain.
         if(file->FindObjectAny("FragmentTree") != nullptr) {
            if(gFragment == nullptr) {
               // TODO: Once we have a notifier set up
               gFragment = new TChain("FragmentChain");
               // gFragment->SetNotify(GrutNotifier::Get());
            }
            std::cout << "file " << file->GetName() << " added to gFragment." << std::endl;
            gFragment->AddFile(file->GetName(), TTree::kMaxEntries, "FragmentTree");
         }
 
         // If AnalysisTree exists, add the file to the chain.
         if(file->FindObjectAny("AnalysisTree") != nullptr) {
            if(gAnalysis == nullptr) {
               gAnalysis = new TChain("AnalysisChain");
               // TODO: Once we have a notifier set up
               // gAnalysis->SetNotify(GrutNotifier::Get());
            }
            std::cout << "file " << file->GetName() << " added to gAnalysis." << std::endl;
            gAnalysis->AddFile(file->GetName(), TTree::kMaxEntries, "AnalysisTree");
         }
 
         if(file->FindObjectAny("Channel") != nullptr) {
            // not necessary to do anything as FindObjectAny already seems to call the streamer?
            // file->Get("Channel"); // this calls TChannel::Streamer
         }
         if(file->FindObjectAny("Values") != nullptr) {
            file->Get("Values");
         }
         fRootFilesOpened++;
      } else {
         std::cout << "Could not open " << filename << std::endl;
      }
   }
 
   AddFileToGUI(file);
   TRunInfo::ReadInfoFromFile();
 
   return file;
}
 
TRawFile* TGRSIint::OpenRawFile(const std::string& filename)
{
   /// Opens Raw input file and stores them in _raw if successfuly opened.
   if(!FileExists(filename.c_str())) {
      std::cerr << R"(File ")" << filename << R"(" does not exist)" << std::endl;
      return nullptr;
   }
 
   // create new raw file
   try {
      auto* file = TParserLibrary::Get()->CreateRawFile(filename);
      fRawFiles.push_back(file);
 
      if(file != nullptr) {
         const char* command = Form("TRawFile* _raw%i = (TRawFile*)%luL;", fRawFilesOpened, reinterpret_cast<unsigned long>(file));
         ProcessLine(command);
 
         std::cout << "\tfile " << BLUE << filename << RESET_COLOR << " opened as "
                   << BLUE << "_raw" << fRawFilesOpened << RESET_COLOR << std::endl;
      }
      fRawFilesOpened++;
      return file;
   } catch(std::runtime_error& e) {
      std::cout << e.what();
   }
   return nullptr;
}
 
void TGRSIint::SetupPipeline()
{
   /// Finds all of the files input as well as flags provided and makes all
   /// of the decisions about what to sort and what order to open everything up
   /// in. This also creates the output files. Starts the threads and gets the
   /// sorting going. This is really the brains of the command line sorting routine.
   TGRSIOptions* opt = TGRSIOptions::Get();
 
   // Determining which parts of the pipeline need to be set up.
 
   bool missing_raw_file = false;
   for(const auto& filename : opt->InputFiles()) {
      if(!FileExists(filename.c_str())) {
         missing_raw_file = true;
         std::cerr << "File not found: " << filename << std::endl;
      }
   }
 
   // Which input files do we have
   bool has_raw_file            = !opt->InputFiles().empty() && opt->SortRaw() && !missing_raw_file && !fRawFiles.empty();
   bool has_input_fragment_tree = gFragment != nullptr;   // && opt->SortRoot();
   bool has_input_analysis_tree = gAnalysis != nullptr;   // && opt->SortRoot();
 
   // Which output files are could possibly be made
   bool able_to_write_fragment_histograms =
      ((has_raw_file || has_input_fragment_tree) && opt->FragmentHistogramLib().length() > 0);
   bool able_to_write_fragment_tree       = (has_raw_file && !missing_raw_file);
   bool able_to_write_analysis_histograms = ((has_raw_file || has_input_fragment_tree || has_input_analysis_tree) &&
                                             opt->AnalysisHistogramLib().length() > 0);
   bool able_to_write_analysis_tree       = (able_to_write_fragment_tree || has_input_fragment_tree);
 
   // Which output files will we make
   bool write_fragment_histograms = (able_to_write_fragment_histograms && opt->MakeHistos());
   bool write_fragment_tree       = able_to_write_fragment_tree && opt->WriteFragmentTree();
   bool write_analysis_histograms =
      (able_to_write_analysis_histograms && opt->MakeHistos());   // TODO: make it so we aren't always trying to generate both frag and analysis histograms
   bool write_analysis_tree = (able_to_write_analysis_tree && opt->MakeAnalysisTree());
 
   // Which steps need to be performed to get from the inputs to the outputs
   bool self_stopping = opt->CloseAfterSort();
 
   bool read_from_raw = (has_raw_file && (write_fragment_histograms || write_fragment_tree ||
                                          write_analysis_histograms || write_analysis_tree));
 
   bool read_from_fragment_tree =
      (has_input_fragment_tree && (write_fragment_histograms || write_analysis_histograms || write_analysis_tree));
 
   bool generate_analysis_data =
      ((read_from_raw || read_from_fragment_tree) && (write_analysis_histograms || write_analysis_tree));
 
   bool read_from_analysis_tree =
      (has_input_analysis_tree && (write_analysis_histograms || write_analysis_tree) && !generate_analysis_data);
 
   // Extract the run number and sub run number from whatever we were given
   int run_number     = 0;
   int sub_run_number = 0;
   if(read_from_raw) {
      run_number     = fRawFiles[0]->GetRunNumber();
      sub_run_number = fRawFiles[0]->GetSubRunNumber();
   } else if(read_from_fragment_tree) {
      const auto* run_title = gFragment->GetListOfFiles()->At(0)->GetTitle();
      run_number            = GetRunNumber(run_title);
      sub_run_number        = GetSubRunNumber(run_title);
   } else if(read_from_analysis_tree) {
      const auto* run_title = gAnalysis->GetListOfFiles()->At(0)->GetTitle();
      run_number            = GetRunNumber(run_title);
      sub_run_number        = GetSubRunNumber(run_title);
   }
 
   // Choose output file names for the 4 possible output files
   std::string output_fragment_tree_filename = opt->OutputFragmentFile();
   if(output_fragment_tree_filename.length() == 0) {
      if(sub_run_number == -1) {
         output_fragment_tree_filename = Form("fragment%05i.root", run_number);
      } else {
         output_fragment_tree_filename = Form("fragment%05i_%03i.root", run_number, sub_run_number);
      }
   }
 
   std::string output_fragment_hist_filename = opt->OutputFragmentHistogramFile();
   if(output_fragment_hist_filename.length() == 0) {
      if(sub_run_number == -1) {
         output_fragment_hist_filename = Form("hist_fragment%05i.root", run_number);
      } else {
         output_fragment_hist_filename = Form("hist_fragment%05i_%03i.root", run_number, sub_run_number);
      }
   }
 
   std::string output_analysis_tree_filename = opt->OutputAnalysisFile();
   if(output_analysis_tree_filename.length() == 0) {
      if(sub_run_number == -1) {
         if(opt->UseRnTuple()) {
            output_analysis_tree_filename = Form("rntuple%05i.root", run_number);
         } else {
            output_analysis_tree_filename = Form("analysis%05i.root", run_number);
         }
      } else {
         if(opt->UseRnTuple()) {
            output_analysis_tree_filename = Form("rntuple%05i_%03i.root", run_number, sub_run_number);
         } else {
            output_analysis_tree_filename = Form("analysis%05i_%03i.root", run_number, sub_run_number);
         }
      }
   }
 
   std::string output_analysis_hist_filename = opt->OutputAnalysisHistogramFile();
   if(output_analysis_hist_filename.length() == 0) {
      if(sub_run_number == -1) {
         output_analysis_hist_filename = Form("hist_analysis%05i.root", run_number);
      } else {
         output_analysis_hist_filename = Form("hist_analysis%05i_%03i.root", run_number, sub_run_number);
      }
   }
 
   if(read_from_analysis_tree) {
      std::cerr << "Reading from analysis tree not currently supported" << std::endl;
   }
 
   ////////////////////////////////////////////////////
   ////////////  Setting up the loops  ////////////////
   ////////////////////////////////////////////////////
 
   if(!write_fragment_histograms && !write_fragment_tree && !write_analysis_histograms && !write_analysis_tree) {
      // We still might want to read the calibration, values, or run info files
      for(const auto& cal_filename : opt->CalInputFiles()) {
         TChannel::ReadCalFile(cal_filename.c_str());
      }
      for(const auto& val_filename : opt->ValInputFiles()) {
         GValue::ReadValFile(val_filename.c_str());
      }
      for(const auto& info_filename : opt->ExternalRunInfo()) {
         TRunInfo::ReadInfoFile(info_filename.c_str());
      }
      return;
   }
   // Set the width of the status and each column
   StoppableThread::ColumnWidth(TGRSIOptions::Get()->ColumnWidth());
   StoppableThread::StatusWidth(TGRSIOptions::Get()->StatusWidth());
 
   // Different queues that can show up
   std::vector<std::shared_ptr<ThreadsafeQueue<std::shared_ptr<const TFragment>>>> fragmentQueues;
   std::vector<std::shared_ptr<ThreadsafeQueue<std::shared_ptr<TEpicsFrag>>>>      scalerQueues;
   std::vector<std::shared_ptr<ThreadsafeQueue<std::shared_ptr<TUnpackedEvent>>>>  analysisQueues;
 
   // The different loops that can run
   TDataLoop*          dataLoop          = nullptr;
   TUnpackingLoop*     unpackLoop        = nullptr;
   TFragmentChainLoop* fragmentChainLoop = nullptr;
   TEventBuildingLoop* eventBuildingLoop = nullptr;
   TDetBuildingLoop*   detBuildingLoop   = nullptr;
 
   // If needed, read from the raw file
   if(read_from_raw) {
      if(fRawFiles.size() > 1) {
         std::cerr << "I'm going to ignore all but first .mid" << std::endl;
      }
 
      dataLoop = TDataLoop::Get("1_input_loop", fRawFiles[0]);
      dataLoop->SetSelfStopping(self_stopping);
 
      unpackLoop               = TUnpackingLoop::Get("2_unpack_loop");
      unpackLoop->InputQueue() = dataLoop->OutputQueue();
   }
 
   // If needed, read from the fragment tree
   if(read_from_fragment_tree) {
      fragmentChainLoop = TFragmentChainLoop::Get("1_chain_loop", gFragment);
      fragmentChainLoop->SetSelfStopping(self_stopping);
   }
 
   // if I am passed any calibrations, lets load those, this
   // will overwrite any with the same address previously read in.
   for(const auto& cal_filename : opt->CalInputFiles()) {
      TChannel::ReadCalFile(cal_filename.c_str());
   }
   // Set the run number and sub-run number
   if(!fRawFiles.empty()) {
      TRunInfo::SetRunInfo(fRawFiles[0]->GetRunNumber(), fRawFiles[0]->GetSubRunNumber());
   } else {
      TRunInfo::SetRunInfo(0, -1);
   }
 
   for(const auto& val_filename : opt->ValInputFiles()) {
      GValue::ReadValFile(val_filename.c_str());
   }
   for(const auto& info_filename : opt->ExternalRunInfo()) {
      TRunInfo::ReadInfoFile(info_filename.c_str());
   }
 
   TEventBuildingLoop::EBuildMode event_build_mode = TEventBuildingLoop::EBuildMode::kDefault;
   if(TRunInfo::GetDetectorInformation() != nullptr) {
      // call DetectorInformation::Set again, in case the calibration files we've loaded now changed things
      TRunInfo::GetDetectorInformation()->Set();
      event_build_mode = TRunInfo::GetDetectorInformation()->BuildMode();
   } else {
      std::cout << "no detector information, can't set build mode" << std::endl;
   }
 
   // If requested, write the fragment histograms
   if(write_fragment_histograms) {
      TFragHistLoop* loop = TFragHistLoop::Get("3_frag_hist_loop");
      loop->SetOutputFilename(output_fragment_hist_filename);
      if(unpackLoop != nullptr) {
         loop->InputQueue() = unpackLoop->AddGoodOutputQueue();
      }
      if(fragmentChainLoop != nullptr) {
         loop->InputQueue() = fragmentChainLoop->AddOutputQueue();
      }
      fragmentQueues.push_back(loop->InputQueue());
   }
 
   // If requested, write the fragment tree
   if(write_fragment_tree) {
      TFragWriteLoop* loop = TFragWriteLoop::Get("4_frag_write_loop", output_fragment_tree_filename);
      fNewFragmentFile     = output_fragment_tree_filename;
      if(unpackLoop != nullptr) {
         loop->InputQueue()       = unpackLoop->AddGoodOutputQueue(TGRSIOptions::Get()->FragmentWriteQueueSize());
         loop->BadInputQueue()    = unpackLoop->BadOutputQueue();
         loop->ScalerInputQueue() = unpackLoop->ScalerOutputQueue();
         scalerQueues.push_back(loop->ScalerInputQueue());
      }
      if(fragmentChainLoop != nullptr) {
         loop->InputQueue() = fragmentChainLoop->AddOutputQueue();
      }
      fragmentQueues.push_back(loop->InputQueue());
   }
 
   // If needed, generate the individual detectors from the TFragments
   if(generate_analysis_data) {
      TGRSIOptions::AnalysisOptions()->Print();
      eventBuildingLoop = TEventBuildingLoop::Get("5_event_build_loop", event_build_mode, TGRSIOptions::AnalysisOptions()->BuildWindow());
      eventBuildingLoop->SetSortDepth(opt->SortDepth());
      if(unpackLoop != nullptr) {
         eventBuildingLoop->InputQueue() = unpackLoop->AddGoodOutputQueue();
      }
      if(fragmentChainLoop != nullptr) {
         eventBuildingLoop->InputQueue() = fragmentChainLoop->AddOutputQueue();
      }
      fragmentQueues.push_back(eventBuildingLoop->InputQueue());
 
      detBuildingLoop               = TDetBuildingLoop::Get("6_det_build_loop");
      detBuildingLoop->InputQueue() = eventBuildingLoop->OutputQueue();
   }
 
   // If requested, write the analysis histograms
   if(write_analysis_histograms) {
      TAnalysisHistLoop* loop = TAnalysisHistLoop::Get("7_analysis_hist_loop");
      loop->SetOutputFilename(output_analysis_hist_filename);
      if(detBuildingLoop != nullptr) {   // TODO: This needs to be extended to being able to read from an analysis tree
         loop->InputQueue() = detBuildingLoop->AddOutputQueue();
      } else {
         std::cerr << DRED << "Error, writing analysis histograms is enabled, but no detector building loop was found!"
                   << RESET_COLOR << std::endl;
         exit(1);
      }
 
      analysisQueues.push_back(loop->InputQueue());
   }
 
   // If requested, write the analysis tree
   if(write_analysis_tree) {
      auto* loop         = TAnalysisWriteLoop::Get("8_analysis_write_loop", output_analysis_tree_filename);
      loop->InputQueue() = detBuildingLoop->AddOutputQueue(TGRSIOptions::Get()->AnalysisWriteQueueSize());
      if(TGRSIOptions::Get()->SeparateOutOfOrder()) {
         loop->OutOfOrderQueue() = eventBuildingLoop->OutOfOrderQueue();
      }
      analysisQueues.push_back(loop->InputQueue());
   }
 
   StoppableThread::ResumeAll();
}
 
void TGRSIint::RunMacroFile(const std::string& filename)
{
   /// Runs a macro file. This happens when a .C file is provided on the command line
   if(FileExists(filename.c_str())) {
      const char* command = Form(".x %s", filename.c_str());
      ProcessLine(command);
   } else {
      // check if commandline arguments were supplied
      size_t beginning_pos = filename.find_first_of('(');
      if(beginning_pos != std::string::npos && filename.back() == ')') {
         std::string trueFilename = filename.substr(0, beginning_pos);
         std::string arguments    = filename.substr(beginning_pos, std::string::npos);
         if(FileExists(trueFilename.c_str())) {
            const char* command = Form(".L %s", trueFilename.c_str());
            ProcessLine(command);
            command = Form("%s%s", trueFilename.substr(0, filename.find_first_of('.')).c_str(), arguments.c_str());
            ProcessLine(command);
         } else {
            std::cerr << R"(File ")" << trueFilename << R"(" does not exist)" << std::endl;
         }
      } else {
         std::cerr << R"(File ")" << filename << R"(" does not exist)" << std::endl;
      }
   }
}
 
void TGRSIint::DrawLogo()
{
   /// Draws the logo. Can be suppressed with -l
   PopupLogo(false);
   WaitLogo();
}
 
void TGRSIint::LoadGROOTGraphics()
{
   /// Loads root graphics in unless -b is used for batch mode.
   if(gROOT->IsBatch()) {
      return;
   }
   // force Canvas to load, this ensures global GUI Factory ptr exists.
   gROOT->LoadClass("TCanvas", "Gpad");
   gGuiFactory = new GRootGuiFactory();
}
 
void TGRSIint::PrintHelp(bool print)
{
   /// Prints the help. Not sure this is used anymore.
   if(print) {
      std::cout << DRED << BG_WHITE << "     Sending Help!!     " << RESET_COLOR << std::endl;
      new TGHtmlBrowser(gSystem->ExpandPathName("${GRSISYS}/README.html"));
   }
}
 
bool TGRSIInterruptHandler::Notify()
{
   /// When ctrl-c is pressed, this takes over. This can be used in the future
   /// for safe cleanup.
   if(!StoppableThread::AnyThreadRunning()) {
      std::cout << std::endl
                << DRED << BG_WHITE << "   Control-c was pressed in interactive mode.   " << RESET_COLOR << std::endl;
      exit(1);
   }
   static int timesPressed = 0;
   timesPressed++;
   switch(timesPressed) {
   case 1:
      std::cout << std::endl
                << DRED << BG_WHITE << "   Control-c was pressed, terminating input loop.   " << RESET_COLOR << std::endl;
      TGRSIint::instance()->Terminate();
      break;
   case 2:
      std::cout << std::endl
                << DRED << BG_WHITE << "   Control-c was pressed, stopping all queues.   " << RESET_COLOR << std::endl;
      StoppableThread::ClearAllQueues();
      break;
   default:
      std::cout << std::endl
                << DRED << BG_WHITE << "   No you shutup!   " << RESET_COLOR << std::endl;
      exit(1);
   }
   return true;
}
 
//   These variables are to be accessed only from DelayedProcessLine
// and DelayedProcessLine_Action, nowhere else.
//   These are used to pass information between the two functions.
// DelayedProcessLine_Action() should ONLY be called from a TTimer running
// on the main thread.  DelayedProcessLine may ONLY be called
// from inside ProcessLine().
namespace {
std::mutex              g__CommandListMutex;
std::mutex              g__ResultListMutex;
std::mutex              g__CommandWaitingMutex;
std::condition_variable g__NewResult;
 
std::string g__LineToProcess;
bool        g__ProcessingNeeded;
 
Long_t g__CommandResult;
bool   g__CommandFinished;
}   // namespace
 
Long_t TGRSIint::DelayedProcessLine(std::string command)
{
   std::lock_guard<std::mutex> any_command_lock(g__CommandWaitingMutex);
 
   g__LineToProcess    = std::move(command);
   g__CommandFinished  = false;
   g__ProcessingNeeded = true;
   TTimer::SingleShot(0, "TGRSIint", this, "DelayedProcessLine_Action()");
 
   std::unique_lock<std::mutex> lock(g__ResultListMutex);
   while(!g__CommandFinished) {
      g__NewResult.wait(lock);
   }
 
   return g__CommandResult;
}
 
void TGRSIint::DelayedProcessLine_Action()
{
   std::string message;
   {
      std::lock_guard<std::mutex> lock(g__CommandListMutex);
      if(!g__ProcessingNeeded) {
         return;
      }
      message = g__LineToProcess;
   }
 
   Long_t result = ProcessLine(message.c_str());
   Getlinem(EGetLineMode::kInit, (static_cast<TRint*>(gApplication))->GetPrompt());
 
   {
      std::lock_guard<std::mutex> lock(g__ResultListMutex);
      g__CommandResult    = result;
      g__CommandFinished  = true;
      g__ProcessingNeeded = false;
   }
 
   g__NewResult.notify_one();
}