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

#include <TStopwatch.h>

#include "DetectorsBase/GeometryManager.h"

#include "MFTReconstruction/ClustererTask.h"

#include "ITSMFTReconstruction/Clusterer.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::ChipMappingMFT> reader;

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

//

// 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_mftSA(std::string outputfile, // output file name

std::string inputfile, // input file name (root or raw)

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

float strobe = 6000.) // strobe length of ALPIDE readout

{

// Initialize logger

FairLogger* logger = FairLogger::GetLogger();

logger->SetLogVerbosityLevel("LOW");

logger->SetLogScreenLevel("INFO");

TStopwatch timer;

o2::base::GeometryManager::loadGeometry(); // needed provisionary, only to write full clusters

// Setup clusterizer

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

Bool_t entryPerROF = kTRUE; // write single tree entry for every ROF. If false, just 1 entry will be saved

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

// 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)

clus->getClusterer().setMaxBCSeparationToMask(strobe / o2::constants::lhc::LHCBunchSpacingNS + 10);

clus->getClusterer().setWantFullClusters(true); // require clusters with coordinates and full pattern

clus->getClusterer().setWantCompactClusters(true); // require compact clusters with patternID

clus->run(inputfile, outputfile, entryPerROF);

timer.Stop();

timer.Print();

}