#if !defined(__CLING__) || defined(__ROOTCLING__)

#include <TStopwatch.h>

#include "DetectorsBase/GeometryManager.h"

#include "ITSReconstruction/ClustererTask.h"

#include "ITSMFTReconstruction/Clusterer.h"

#include "ITSMFTBase/DPLAlpideParam.h"

#include "CommonConstants/LHCConstants.h"

#include "DetectorsCommonDataFormats/NameConf.h"

#include "FairLogger.h"

#endif

// Clusterization avoiding FairRunAna management.

// Works both with MC digits and with "raw" data (in this case the last argument must be

// set to true). The raw data should be prepared beforeahand from the MC digits using e.g.

// o2::itsmft::RawPixelReader<o2::itsmft::ChipMappingITS> reader;

// reader.convertDigits2Raw("dig.raw","o2dig.root","o2sim","ITSDigit");

//

// Use for MC mode:

// root -b -q run_clus_itsSA.C+\(\"o2clus_its.root\",\"o2dig.root\"\) 2>&1 | tee clusSA.log

//

// Use for RAW mode:

// root -b -q run_clus_itsSA.C+\(\"o2clus_its.root\",\"dig.raw\"\) 2>&1 | tee clusSARAW.log

//

void run_clus_itsSA(std::string inputfile = "rawits.bin", // input file name

std::string outputfile = "clr.root", // output file name (root or raw)

bool raw = true, // flag if this is raw data

int strobeBC = -1, // strobe length in BC for masking, if <0, get automatically (assume cont. readout)

std::string dictionaryfile = "",

bool withPatterns = true)

{

// Initialize logger

FairLogger* logger = FairLogger::GetLogger();

logger->SetLogVerbosityLevel("LOW");

logger->SetLogScreenLevel("INFO");

TStopwatch timer;

// Setup clusterizer

Bool_t useMCTruth = kTRUE; // kFALSE if no comparison with MC needed

o2::its::ClustererTask* clus = new o2::its::ClustererTask(useMCTruth, raw);

clus->setMaxROframe(2 << 21); // about 3 cluster files per a raw data chunk

if (dictionaryfile.empty()) {

dictionaryfile = o2::base::NameConf::getDictionaryFileName(o2::detectors::DetID::ITS, "", ".bin");

}

std::ifstream file(dictionaryfile.c_str());

if (file.good()) {

LOG(INFO) << "Running with dictionary: " << dictionaryfile.c_str();

clus->loadDictionary(dictionaryfile.c_str());

} else {

LOG(INFO) << "Running without dictionary !";

}

// Mask fired pixels separated by <= this number of BCs (for overflow pixels).

// In continuos mode strobe lenght should be used, in triggered one: signal shaping time (~7mus)

if (strobeBC < 0) {

const auto& dgParams = o2::itsmft::DPLAlpideParam<o2::detectors::DetID::ITS>::Instance();

strobeBC = dgParams.roFrameLengthInBC;

}

clus->getClusterer().setMaxBCSeparationToMask(strobeBC + 10);

clus->getClusterer().print();

clus->run(inputfile, outputfile);

timer.Stop();

timer.Print();

}