NDLevel2/src/NDCore.cpp

//
// C/C++ headers
//
#include <fstream>
#include <string.h>
#include <iostream>
#include <cstring>
#include <stdio.h>
//
// ROOT headers
//
#include <TTree.h>
#include <TClassEdit.h>
#include <TObject.h>
#include <TList.h>
#include <TArrayI.h>
#include <TSystem.h>
#include <TSystemDirectory.h>
#include <TString.h>
#include <TFile.h>
#include <TClass.h>
#include <TSQLServer.h>
#include <TSQLRow.h>
#include <TSQLResult.h>
#include <TClonesArray.h>
#include <stdlib.h>
#include <math.h>
//
// RunInfo header
//
#include <RunInfo.h>
#include <GLTables.h>
//
// YODA headers
//
#include <PamelaRun.h>
#include <PscuHeader.h>
#include <PscuEvent.h>
#include <EventHeader.h>
#include <physics/neutronDetector/NeutronEvent.h>
#include <physics/neutronDetector/NeutronRecord.h>
//#include <yodaUtility.h>
//
// RunInfo header
//
//#include <RunInfo.h>
//#include <GLTables.h>
//
// This program headers
//
#include <NDLevel2.h>
#include <NDCore.h>
#include <NDVerl2.h>

using namespace std;

//
// CORE ROUTINE
//
//
int NDCore(UInt_t run, TFile *file, TSQLServer *dbc, Int_t NDargc, char *NDargv[]){
  //  
  Int_t i = 0;
  //
  TString processFolder = "NDFolder";
  //
  // Set these to true to have a very verbose output.
  //
  Bool_t debug = false;
  //
  Bool_t verbose = false;
  //
  if ( NDargc > 0 ){
    i = 0;
    while ( i < NDargc ){
      if ( !strcmp(NDargv[i],"-processFolder") ) {
        if ( NDargc < i+1 ){
          throw -3;
        };
        processFolder = (TString)NDargv[i+1];
        i++;
      };
      if ( (!strcmp(NDargv[i],"--verbose")) || (!strcmp(NDargv[i],"-v")) ) {
        verbose = true;
      };
      if ( (!strcmp(NDargv[i],"--debug")) || (!strcmp(NDargv[i],"-g")) ) {
        verbose= true;
      };
      i++;
    };
  };
  //
  const char* outDir = gSystem->DirName(gSystem->DirName(file->GetPath()));
  // Variables for level2 
  //
  TTree *NDtr = 0;
  UInt_t nevents = 0;
  //
  // variables needed to reprocess data
  //
  TString NDversion;
  ItoRunInfo *runinfo = 0;
  TArrayI *runlist = 0;
  TTree *NDtrclone = 0;
  Bool_t reproc = false;
  Bool_t reprocall = false;
  UInt_t nobefrun = 0;
  UInt_t noaftrun = 0;
  UInt_t numbofrun = 0;
  stringstream ftmpname;
  TString fname;
  UInt_t totfileentries = 0;
  UInt_t idRun = 0;
  Int_t tmpSize =0;
  Float_t yTrig =0;
  Float_t yUpperBackground =0;
  Float_t yBottomBackground =0;
  //
  // variables needed to handle error signals
  //
  Int_t code = 0;
  Int_t sgnl;
  //
  Long64_t maxsize = 10000000000LL;  
  TTree::SetMaxTreeSize(maxsize);
  //
  //
  // ND level2 classes
  //
  NDLevel2 *nd = new NDLevel2();
  NDLevel2 *ndclone = new NDLevel2();
  //
  // define variables for opening and reading level0 file
  //
  TFile *l0File = 0;
  TTree *l0tr = 0;
  TBranch *l0head = 0;
  TBranch *l0ND =0;
  pamela::EventHeader *eh = 0;
  pamela::PscuHeader *ph = 0;
  pamela::neutron::NeutronRecord *l0nr = 0;
  pamela::neutron::NeutronEvent  *l0ne = 0;
  //
  // Define other basic variables
  // 
  UInt_t procev = 0;
  stringstream file2;
  stringstream file3;
  stringstream qy;
  Int_t totevent = 0;
  UInt_t atime = 0;
  UInt_t re = 0;
  //
  // Working filename
  //
  TString outputfile;
  stringstream name;
  name.str("");
  name << outDir << "/";
  //
  // temporary file and folder
  //
  TFile *tempfile = 0;
  TTree *tempND = 0;
  stringstream tempname;
  stringstream NDfolder;
  tempname.str("");
  tempname << outDir;
  tempname << "/" << processFolder.Data();
  NDfolder.str("");
  NDfolder << tempname.str().c_str();
  gSystem->MakeDirectory(NDfolder.str().c_str());
  tempname << "/NDtree_run";
  tempname << run << ".root";  
  //
  // DB classes
  //
  GL_ROOT *glroot = new GL_ROOT();
  GL_TIMESYNC *dbtime = 0;
  //
  // Let's start!
  //
  // As a first thing we must check what we have to do: if run = 0 we must process all events in the file has been passed
  // if run != 0 we must process only that run but first we have to check if the tree MyDetector2 already exist in the file
  // if it exists we are reprocessing data and we must delete that entries, if not we must create it.
  // 
  if ( run == 0 )  reproc = true;
  //
  //
  // Output file is "outputfile"
  //
  if ( !file->IsOpen() ){
    //printf(" ND - ERROR: cannot open file for writing\n");
    throw -601 ;    
  };
  //
  // Retrieve GL_RUN variables from the level2 file
  //  
  NDversion = NDInfo(false); // we should decide how to handle versioning system
  //
  // create an interface to RunInfo called "runinfo"
  //
  runinfo = new ItoRunInfo(file);
  //
  // open "Run" tree in level2 file, if not existing return an error (sngl != 0)
  //
  sgnl = 0;
  sgnl = runinfo->Update(run, "ND",NDversion);
  if ( sgnl ){
    if ( debug ) printf(" ND - ERROR: RunInfo exited with non-zero status\n");
    code = sgnl;
    goto closeandexit;
  } else {
    sgnl = 0;
  };
  //
  // number of events in the file BEFORE the first event of our run
  //
  nobefrun = runinfo->GetFirstEntry();
  //
  // total number of events in the file 
  //
  totfileentries = runinfo->GetFileEntries();
  //
  // first file entry AFTER the last event of our run
  //
  noaftrun = runinfo->GetLastEntry() + 1;
  //
  // number of run to be processed
  //
  numbofrun = runinfo->GetNoRun();
  //
  // Try to access the S4 tree in the file, if it exists we are reprocessing data if not we are processing a new run
  //
  NDtrclone = (TTree*)file->Get("NeutronD");
  //
  if ( !NDtrclone ){
    //
    // tree does not exist, we are not reprocessing
    //
    reproc = false;
    if ( run == 0 ) {
      if (verbose) printf(" ND - WARNING: you are reprocessing data but ND tree does not exist!\n");
    }
    if ( runinfo->IsReprocessing() && run != 0 ) {
      if (verbose) printf(" ND - WARNING: it seems you are not reprocessing data but ND\n versioning information already exists in RunInfo.\n");
    }
  } else {
    //
    NDtrclone->SetAutoSave(900000000000000LL);
    //
    // tree exists, we are reprocessing data. Are we reprocessing a single run or all the file?
    //
    reproc = true;
    //
    // update versioning information 
    //
    if (verbose) printf("\n Preparing the pre-processing...\n");
    //
    if ( run == 0 ){
      //
      // we are reprocessing all the file
      // if we are reprocessing everything we don't need to copy any old event and we can just work with the new tree and delete the old one immediately
      //
      reprocall = true;
      //
      if (verbose) printf("\n ND - WARNING: Reprocessing all runs\n");
      //
    } else {
      //
      // we are reprocessing a single run, we must copy to the new tree the events in the file which preceed the first event of the run
      //
      reprocall = false;
      //
      if (verbose) printf("\n ND - WARNING: Reprocessing run number %u \n",run);
      //
      // copying old tree to a new file
      //
      tempfile = new TFile(tempname.str().c_str(),"RECREATE");
      tempND = NDtrclone->CloneTree(-1,"fast");
      tempND->SetName("NeutronD-old"); 
      tempfile->Write();
      tempfile->Close();  
    }
    //
    // Delete the old tree from old file and memory
    //
    NDtrclone->Delete("all");
    //
    if (verbose) printf(" ...done!\n");
    //
  };
  //
  // create mydetector tree mydect
  // 
  file->cd();
  NDtr = new TTree("NeutronD-new","PAMELA Level2 NeutronD data");
  NDtr->SetAutoSave(900000000000000LL);
  NDtr->Branch("NDLevel2","NDLevel2",&nd);
  //
  if ( reproc && !reprocall ){
    //
    //  open new file and retrieve also tree informations
    //
    tempfile = new TFile(tempname.str().c_str(),"READ");
    NDtrclone = (TTree*)tempfile->Get("NeutronD-old");
    NDtrclone->SetAutoSave(900000000000000LL);
    NDtrclone->SetBranchAddress("NDLevel2",&ndclone);
    //      
    if ( nobefrun > 0 ){
      if (verbose) {
        printf("\n Pre-processing: copying events from the old tree before the processed run\n");   
        printf(" Copying %u events in the file which are before the beginning of the run %u \n",nobefrun,run);
        printf(" Start copying at event number 0, end copying at event number %u \n",nobefrun);
      }
      for (UInt_t j = 0; j < nobefrun; j++){
        //
        NDtrclone->GetEntry(j);   
        //
        // copy ndclone to mydec
        //
        //      nd = new NDLevel2();
        nd->Clear();
        memcpy(&nd,&ndclone,sizeof(ndclone));
        //
        // Fill entry in the new tree
        //
        NDtr->Fill();
        //
      };
      if (verbose) printf(" Finished successful copying!\n");
    };          
  };
  //
  // Get the list of run to be processed, if only one run has to be processed the list will contain one entry only.
  //
  runlist = runinfo->GetRunList();
  //
  // Loop over the run to be processed
  //
  for (UInt_t irun=0; irun < numbofrun; irun++){
    //
    // retrieve the first run ID to be processed using the RunInfo list
    //
    idRun = runlist->At(irun);
    if (verbose) {
      printf("\n\n\n ####################################################################### \n");
      printf("                    PROCESSING RUN NUMBER %u \n",idRun);
      printf(" ####################################################################### \n\n\n");
    }
    //
    runinfo->ID_ROOT_L0 = 0;
    //
    // store in the runinfo class the GL_RUN variables for our run
    //
    sgnl = 0;
    sgnl = runinfo->GetRunInfo(idRun);
    if ( sgnl ){
      if ( debug ) printf(" ND - ERROR: RunInfo exited with non-zero status\n");
      code = sgnl;
      goto closeandexit;
    } else {
      sgnl = 0;
    };
    //
    // now you can access that variables using the RunInfo class this way runinfo->ID_ROOT_L0
    //
    if ( runinfo->ID_ROOT_L0 == 0 ){
      if ( debug ) printf("\n ND - ERROR: no run with ID_RUN = %u \n\n Exiting... \n\n",idRun);
      code = -5;
      goto closeandexit;    
    };
    //
    // prepare the timesync for the db
    //
    if ( !dbc->IsConnected() ) throw -604;
    dbtime = new GL_TIMESYNC(runinfo->ID_ROOT_L0,"ID",dbc);
    //
    // Search in the DB the path and name of the LEVEL0 file to be processed.
    //
    if ( !dbc->IsConnected() ) throw -604;
    glroot->Query_GL_ROOT(runinfo->ID_ROOT_L0,dbc);
    //
    ftmpname.str("");
    ftmpname << glroot->PATH.Data() << "/";
    ftmpname << glroot->NAME.Data();
    fname = ftmpname.str().c_str();
    //
    // print out informations
    //
    totevent = runinfo->NEVENTS;
    if (verbose) {
      printf("\n LEVEL0 data file: %s \n",fname.Data());
      printf(" RUN HEADER absolute time is:  %u \n",runinfo->RUNHEADER_TIME);
      printf(" RUN TRAILER absolute time is: %u \n",runinfo->RUNTRAILER_TIME);
      printf(" %i events to be processed for run %u: from %i to %i \n\n",totevent,idRun,runinfo->EV_FROM,runinfo->EV_FROM+totevent);
    }
    //
    // Open Level0 file
    //
    l0File = new TFile(fname.Data());
    if ( !l0File ) {
      if ( debug ) printf(" ND - ERROR: problems opening  Level0 file\n");
      code = -6;
      goto closeandexit;
    };
    l0tr = (TTree*)l0File->Get("Physics");
    if ( !l0tr ) {
      if ( debug ) printf(" ND - ERROR: no Physics tree in Level0 file\n");
      l0File->Close();
      code = -7;
      goto closeandexit;
    };
    l0head = l0tr->GetBranch("Header");
    if ( !l0head ) {
      if ( debug ) printf(" ND - ERROR: no Header branch in Level0 tree\n");
      l0File->Close();
      code = -8;
      goto closeandexit;    
    };
    l0ND = l0tr->GetBranch("Neutron");
    if ( !l0ND ) {
      if ( debug ) printf(" ND - ERROR: no ND branch in Level0 tree\n");
      l0File->Close();
      code = -603;
      goto closeandexit;
    };

    //
    l0tr->SetBranchAddress("Neutron", &l0ne);
    l0tr->SetBranchAddress("Header", &eh); 
    //
    nevents = l0ND->GetEntries();
    //
    if ( nevents < 1 ) {
      if ( debug ) printf(" ND - ERROR: Level0 file is empty\n\n");
      l0File->Close();
      code = -11;
      goto closeandexit;
    };
    //
    if ( runinfo->EV_TO > nevents-1 ) {
      if ( debug ) printf(" ND - ERROR: too few entries in the tree\n");
      l0File->Close();
      code = -12;
      goto closeandexit;
    };
    //
    // run over all the events of the run
    //
    if (verbose) printf("\n Ready to start! \n\n Processed events: \n\n");
    //
    for ( re = runinfo->EV_FROM; re < (runinfo->EV_FROM+runinfo->NEVENTS); re++){
      //
      if ( procev%1000 == 0 && procev > 0 && verbose ) printf(" %iK \n",procev/1000);   
      //
      l0head->GetEntry(re);
      //
      // absolute time of this event
      //
      ph = eh->GetPscuHeader();
      atime = dbtime->DBabsTime(ph->GetOrbitalTime());  
      //
      // paranoid check
      //
      if ( (atime > runinfo->RUNTRAILER_TIME) || (atime < runinfo->RUNHEADER_TIME)  ) {
        if (verbose) printf(" ND - WARNING: event at time outside the run time window, skipping it\n");
        goto jumpev;
      };
      //
      procev++;
      //
      // start processing
      //
      nd->Clear();
      //
      l0ND->GetEntry(re);
      tmpSize = l0ne->Records->GetEntries();
      if ( tmpSize && l0ne->unpackError == 0 ){
        for (Int_t j = 0; j < tmpSize; j++){
          l0nr = (pamela::neutron::NeutronRecord*)l0ne->Records->At(j);
          yTrig            = yTrig             + (float)l0nr->trigPhysics;
          yUpperBackground  = yUpperBackground  + (float)l0nr->upperBack;
          yBottomBackground = yBottomBackground + (float)l0nr->bottomBack;
        }
        nd->upperBack = yUpperBackground;
        nd->bottomBack = yBottomBackground;
        nd->trigPhysics = yTrig;             
      };
      //
      nd->unpackError = l0ne->unpackError;
      //
      NDtr->Fill();        // Fill tree NDLevel2 in the root file
      //
      yUpperBackground =0;
      yBottomBackground =0;
      yTrig=0;       
      //    
      //
    jumpev:
      debug = false;
      //
    };
    //
    // Here you may want to clear some variables before processing another run  
    //
    delete dbtime;
  }; // process all the runs
  //
  if (verbose) printf("\n Finished processing data \n");
  //
 closeandexit:
  //
  // we have finished processing the run(s). If we processed a single run now we must copy all the events after our run from the old tree to the new one and delete the old tree.
  //
  if ( !reprocall && reproc && code >= 0 ){
    if ( totfileentries > noaftrun ){
      if (verbose) {
      printf("\n Post-processing: copying events from the old tree after the processed run\n");   
      printf(" Copying %i events in the file which are after the end of the run %i \n",(int)(totfileentries-noaftrun),(int)run);
      printf(" Start copying at event number %i end copying at event number %i \n",(int)noaftrun,(int)totfileentries);
      }
      for (UInt_t j = noaftrun; j < totfileentries; j++ ){
        //
        // Get entry from old tree
        //
        NDtrclone->GetEntry(j);   
        //
        // copy ndclone to nd
        //
        nd->Clear();
        memcpy(&nd,&ndclone,sizeof(ndclone));
        //
        // Fill entry in the new tree
        //
        NDtr->Fill();
      };
      if (verbose) printf(" Finished successful copying!\n");
    };
  };
  //
  // Close files, delete old tree(s), write and close level2 file 
  //
  if ( l0File ) l0File->Close();
  if ( tempfile ) tempfile->Close();            
  gSystem->Unlink(tempname.str().c_str());
  //
  if ( runinfo ) runinfo->Close();    
  if ( NDtr ) NDtr->SetName("NeutronD");    
  if ( file ){
    file->cd();
    file->Write();
  };
  //
  gSystem->Unlink(NDfolder.str().c_str());
  //
  // the end
  //
  if ( verbose ) printf("\n Exiting...\n");
  if ( NDtr ) NDtr->Delete();
  //
  if ( nd ) delete nd;
  if ( ndclone ) delete ndclone;
  if ( glroot ) delete glroot;
  if ( runinfo ) delete runinfo; 
  //
  if(code < 0)  throw code;
  return(code);
}


1	mocchiut	1.1	//
2			// C/C++ headers
3			//
4			#include <fstream>
5			#include <string.h>
6			#include <iostream>
7			#include <cstring>
8			#include <stdio.h>
9			//
10			// ROOT headers
11			//
12			#include <TTree.h>
13			#include <TClassEdit.h>
14			#include <TObject.h>
15			#include <TList.h>
16	mocchiut	1.5	#include <TArrayI.h>
17	mocchiut	1.1	#include <TSystem.h>
18			#include <TSystemDirectory.h>
19			#include <TString.h>
20			#include <TFile.h>
21			#include <TClass.h>
22			#include <TSQLServer.h>
23			#include <TSQLRow.h>
24			#include <TSQLResult.h>
25			#include <TClonesArray.h>
26			#include <stdlib.h>
27			#include <math.h>
28			//
29	mocchiut	1.10	// RunInfo header
30			//
31			#include <RunInfo.h>
32			#include <GLTables.h>
33			//
34	mocchiut	1.1	// YODA headers
35			//
36			#include <PamelaRun.h>
37			#include <PscuHeader.h>
38			#include <PscuEvent.h>
39			#include <EventHeader.h>
40			#include <physics/neutronDetector/NeutronEvent.h>
41			#include <physics/neutronDetector/NeutronRecord.h>
42			//#include <yodaUtility.h>
43			//
44			// RunInfo header
45			//
46	mocchiut	1.10	//#include <RunInfo.h>
47			//#include <GLTables.h>
48	mocchiut	1.1	//
49			// This program headers
50			//
51			#include <NDLevel2.h>
52			#include <NDCore.h>
53			#include <NDVerl2.h>
54
55			using namespace std;
56
57			//
58			// CORE ROUTINE
59			//
60			//
61	mocchiut	1.5	int NDCore(UInt_t run, TFile file, TSQLServer dbc, Int_t NDargc, char *NDargv[]){
62	mocchiut	1.1	//
63			Int_t i = 0;
64			//
65			TString processFolder = "NDFolder";
66			//
67			// Set these to true to have a very verbose output.
68			//
69			Bool_t debug = false;
70			//
71			Bool_t verbose = false;
72			//
73			if ( NDargc > 0 ){
74			i = 0;
75			while ( i < NDargc ){
76			if ( !strcmp(NDargv[i],"-processFolder") ) {
77			if ( NDargc < i+1 ){
78			throw -3;
79			};
80			processFolder = (TString)NDargv[i+1];
81			i++;
82			};
83			if ( (!strcmp(NDargv[i],"--verbose")) \|\| (!strcmp(NDargv[i],"-v")) ) {
84			verbose = true;
85			};
86			if ( (!strcmp(NDargv[i],"--debug")) \|\| (!strcmp(NDargv[i],"-g")) ) {
87			verbose= true;
88			};
89			i++;
90			};
91			};
92			//
93			const char* outDir = gSystem->DirName(gSystem->DirName(file->GetPath()));
94			// Variables for level2
95			//
96			TTree *NDtr = 0;
97	mocchiut	1.5	UInt_t nevents = 0;
98	mocchiut	1.1	//
99			// variables needed to reprocess data
100			//
101			TString NDversion;
102			ItoRunInfo *runinfo = 0;
103	mocchiut	1.5	TArrayI *runlist = 0;
104	mocchiut	1.1	TTree *NDtrclone = 0;
105			Bool_t reproc = false;
106			Bool_t reprocall = false;
107			UInt_t nobefrun = 0;
108			UInt_t noaftrun = 0;
109			UInt_t numbofrun = 0;
110			stringstream ftmpname;
111			TString fname;
112	mocchiut	1.5	UInt_t totfileentries = 0;
113			UInt_t idRun = 0;
114	mocchiut	1.1	Int_t tmpSize =0;
115			Float_t yTrig =0;
116			Float_t yUpperBackground =0;
117			Float_t yBottomBackground =0;
118			//
119			// variables needed to handle error signals
120			//
121			Int_t code = 0;
122			Int_t sgnl;
123			//
124	mocchiut	1.9	Long64_t maxsize = 10000000000LL;
125			TTree::SetMaxTreeSize(maxsize);
126			//
127			//
128	mocchiut	1.1	// ND level2 classes
129			//
130			NDLevel2 *nd = new NDLevel2();
131			NDLevel2 *ndclone = new NDLevel2();
132			//
133			// define variables for opening and reading level0 file
134			//
135			TFile *l0File = 0;
136			TTree *l0tr = 0;
137			TBranch *l0head = 0;
138			TBranch *l0ND =0;
139			pamela::EventHeader *eh = 0;
140	mocchiut	1.5	pamela::PscuHeader *ph = 0;
141	mocchiut	1.1	pamela::neutron::NeutronRecord *l0nr = 0;
142			pamela::neutron::NeutronEvent *l0ne = 0;
143			//
144			// Define other basic variables
145			//
146			UInt_t procev = 0;
147			stringstream file2;
148			stringstream file3;
149			stringstream qy;
150			Int_t totevent = 0;
151	mocchiut	1.5	UInt_t atime = 0;
152			UInt_t re = 0;
153	mocchiut	1.1	//
154			// Working filename
155			//
156			TString outputfile;
157			stringstream name;
158			name.str("");
159			name << outDir << "/";
160			//
161			// temporary file and folder
162			//
163			TFile *tempfile = 0;
164			TTree *tempND = 0;
165			stringstream tempname;
166			stringstream NDfolder;
167			tempname.str("");
168			tempname << outDir;
169			tempname << "/" << processFolder.Data();
170			NDfolder.str("");
171			NDfolder << tempname.str().c_str();
172			gSystem->MakeDirectory(NDfolder.str().c_str());
173			tempname << "/NDtree_run";
174			tempname << run << ".root";
175			//
176			// DB classes
177			//
178			GL_ROOT *glroot = new GL_ROOT();
179	mocchiut	1.5	GL_TIMESYNC *dbtime = 0;
180	mocchiut	1.1	//
181			// Let's start!
182			//
183			// As a first thing we must check what we have to do: if run = 0 we must process all events in the file has been passed
184			// if run != 0 we must process only that run but first we have to check if the tree MyDetector2 already exist in the file
185			// if it exists we are reprocessing data and we must delete that entries, if not we must create it.
186			//
187	mocchiut	1.5	if ( run == 0 ) reproc = true;
188	mocchiut	1.1	//
189			//
190			// Output file is "outputfile"
191			//
192			if ( !file->IsOpen() ){
193			//printf(" ND - ERROR: cannot open file for writing\n");
194			throw -601 ;
195			};
196			//
197			// Retrieve GL_RUN variables from the level2 file
198			//
199			NDversion = NDInfo(false); // we should decide how to handle versioning system
200			//
201			// create an interface to RunInfo called "runinfo"
202			//
203			runinfo = new ItoRunInfo(file);
204			//
205			// open "Run" tree in level2 file, if not existing return an error (sngl != 0)
206			//
207			sgnl = 0;
208			sgnl = runinfo->Update(run, "ND",NDversion);
209			if ( sgnl ){
210	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: RunInfo exited with non-zero status\n");
211	mocchiut	1.1	code = sgnl;
212			goto closeandexit;
213			} else {
214			sgnl = 0;
215			};
216			//
217			// number of events in the file BEFORE the first event of our run
218			//
219			nobefrun = runinfo->GetFirstEntry();
220			//
221			// total number of events in the file
222			//
223			totfileentries = runinfo->GetFileEntries();
224			//
225			// first file entry AFTER the last event of our run
226			//
227			noaftrun = runinfo->GetLastEntry() + 1;
228			//
229			// number of run to be processed
230			//
231			numbofrun = runinfo->GetNoRun();
232			//
233			// Try to access the S4 tree in the file, if it exists we are reprocessing data if not we are processing a new run
234			//
235			NDtrclone = (TTree*)file->Get("NeutronD");
236			//
237			if ( !NDtrclone ){
238			//
239			// tree does not exist, we are not reprocessing
240			//
241			reproc = false;
242	mocchiut	1.5	if ( run == 0 ) {
243	mocchiut	1.1	if (verbose) printf(" ND - WARNING: you are reprocessing data but ND tree does not exist!\n");
244			}
245	mocchiut	1.5	if ( runinfo->IsReprocessing() && run != 0 ) {
246	mocchiut	1.1	if (verbose) printf(" ND - WARNING: it seems you are not reprocessing data but ND\n versioning information already exists in RunInfo.\n");
247			}
248			} else {
249			//
250	mocchiut	1.9	NDtrclone->SetAutoSave(900000000000000LL);
251			//
252	mocchiut	1.1	// tree exists, we are reprocessing data. Are we reprocessing a single run or all the file?
253			//
254			reproc = true;
255			//
256			// update versioning information
257			//
258			if (verbose) printf("\n Preparing the pre-processing...\n");
259			//
260	mocchiut	1.5	if ( run == 0 ){
261	mocchiut	1.1	//
262			// we are reprocessing all the file
263			// if we are reprocessing everything we don't need to copy any old event and we can just work with the new tree and delete the old one immediately
264			//
265			reprocall = true;
266			//
267			if (verbose) printf("\n ND - WARNING: Reprocessing all runs\n");
268			//
269			} else {
270			//
271			// we are reprocessing a single run, we must copy to the new tree the events in the file which preceed the first event of the run
272			//
273			reprocall = false;
274			//
275	mocchiut	1.5	if (verbose) printf("\n ND - WARNING: Reprocessing run number %u \n",run);
276	mocchiut	1.1	//
277			// copying old tree to a new file
278			//
279			tempfile = new TFile(tempname.str().c_str(),"RECREATE");
280			tempND = NDtrclone->CloneTree(-1,"fast");
281			tempND->SetName("NeutronD-old");
282			tempfile->Write();
283			tempfile->Close();
284			}
285			//
286			// Delete the old tree from old file and memory
287			//
288			NDtrclone->Delete("all");
289			//
290			if (verbose) printf(" ...done!\n");
291			//
292			};
293			//
294			// create mydetector tree mydect
295			//
296			file->cd();
297			NDtr = new TTree("NeutronD-new","PAMELA Level2 NeutronD data");
298	mocchiut	1.9	NDtr->SetAutoSave(900000000000000LL);
299	mocchiut	1.1	NDtr->Branch("NDLevel2","NDLevel2",&nd);
300			//
301			if ( reproc && !reprocall ){
302			//
303			// open new file and retrieve also tree informations
304			//
305			tempfile = new TFile(tempname.str().c_str(),"READ");
306			NDtrclone = (TTree*)tempfile->Get("NeutronD-old");
307	mocchiut	1.9	NDtrclone->SetAutoSave(900000000000000LL);
308	mocchiut	1.1	NDtrclone->SetBranchAddress("NDLevel2",&ndclone);
309			//
310			if ( nobefrun > 0 ){
311			if (verbose) {
312			printf("\n Pre-processing: copying events from the old tree before the processed run\n");
313	mocchiut	1.5	printf(" Copying %u events in the file which are before the beginning of the run %u \n",nobefrun,run);
314	mocchiut	1.1	printf(" Start copying at event number 0, end copying at event number %u \n",nobefrun);
315			}
316			for (UInt_t j = 0; j < nobefrun; j++){
317			//
318			NDtrclone->GetEntry(j);
319			//
320			// copy ndclone to mydec
321			//
322	mocchiut	1.2	// nd = new NDLevel2();
323			nd->Clear();
324	mocchiut	1.1	memcpy(&nd,&ndclone,sizeof(ndclone));
325			//
326			// Fill entry in the new tree
327			//
328			NDtr->Fill();
329			//
330			};
331			if (verbose) printf(" Finished successful copying!\n");
332			};
333			};
334			//
335			// Get the list of run to be processed, if only one run has to be processed the list will contain one entry only.
336			//
337			runlist = runinfo->GetRunList();
338			//
339			// Loop over the run to be processed
340			//
341			for (UInt_t irun=0; irun < numbofrun; irun++){
342			//
343			// retrieve the first run ID to be processed using the RunInfo list
344			//
345			idRun = runlist->At(irun);
346			if (verbose) {
347			printf("\n\n\n ####################################################################### \n");
348	mocchiut	1.5	printf(" PROCESSING RUN NUMBER %u \n",idRun);
349	mocchiut	1.1	printf(" ####################################################################### \n\n\n");
350			}
351			//
352	mocchiut	1.5	runinfo->ID_ROOT_L0 = 0;
353	mocchiut	1.1	//
354			// store in the runinfo class the GL_RUN variables for our run
355			//
356			sgnl = 0;
357			sgnl = runinfo->GetRunInfo(idRun);
358			if ( sgnl ){
359	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: RunInfo exited with non-zero status\n");
360	mocchiut	1.1	code = sgnl;
361			goto closeandexit;
362			} else {
363			sgnl = 0;
364			};
365			//
366	mocchiut	1.5	// now you can access that variables using the RunInfo class this way runinfo->ID_ROOT_L0
367	mocchiut	1.1	//
368	mocchiut	1.5	if ( runinfo->ID_ROOT_L0 == 0 ){
369			if ( debug ) printf("\n ND - ERROR: no run with ID_RUN = %u \n\n Exiting... \n\n",idRun);
370	mocchiut	1.1	code = -5;
371			goto closeandexit;
372			};
373			//
374	mocchiut	1.5	// prepare the timesync for the db
375			//
376	mocchiut	1.8	if ( !dbc->IsConnected() ) throw -604;
377	mocchiut	1.5	dbtime = new GL_TIMESYNC(runinfo->ID_ROOT_L0,"ID",dbc);
378			//
379	mocchiut	1.1	// Search in the DB the path and name of the LEVEL0 file to be processed.
380			//
381	mocchiut	1.8	if ( !dbc->IsConnected() ) throw -604;
382	mocchiut	1.5	glroot->Query_GL_ROOT(runinfo->ID_ROOT_L0,dbc);
383	mocchiut	1.1	//
384			ftmpname.str("");
385			ftmpname << glroot->PATH.Data() << "/";
386			ftmpname << glroot->NAME.Data();
387			fname = ftmpname.str().c_str();
388			//
389			// print out informations
390			//
391	mocchiut	1.5	totevent = runinfo->NEVENTS;
392	mocchiut	1.1	if (verbose) {
393			printf("\n LEVEL0 data file: %s \n",fname.Data());
394	mocchiut	1.5	printf(" RUN HEADER absolute time is: %u \n",runinfo->RUNHEADER_TIME);
395			printf(" RUN TRAILER absolute time is: %u \n",runinfo->RUNTRAILER_TIME);
396			printf(" %i events to be processed for run %u: from %i to %i \n\n",totevent,idRun,runinfo->EV_FROM,runinfo->EV_FROM+totevent);
397	mocchiut	1.1	}
398			//
399			// Open Level0 file
400			//
401			l0File = new TFile(fname.Data());
402			if ( !l0File ) {
403	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: problems opening Level0 file\n");
404	mocchiut	1.1	code = -6;
405			goto closeandexit;
406			};
407			l0tr = (TTree*)l0File->Get("Physics");
408			if ( !l0tr ) {
409	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: no Physics tree in Level0 file\n");
410	mocchiut	1.1	l0File->Close();
411			code = -7;
412			goto closeandexit;
413			};
414			l0head = l0tr->GetBranch("Header");
415			if ( !l0head ) {
416	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: no Header branch in Level0 tree\n");
417	mocchiut	1.1	l0File->Close();
418			code = -8;
419			goto closeandexit;
420			};
421			l0ND = l0tr->GetBranch("Neutron");
422			if ( !l0ND ) {
423	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: no ND branch in Level0 tree\n");
424	mocchiut	1.1	l0File->Close();
425			code = -603;
426			goto closeandexit;
427			};
428
429			//
430			l0tr->SetBranchAddress("Neutron", &l0ne);
431			l0tr->SetBranchAddress("Header", &eh);
432			//
433	mocchiut	1.5	nevents = l0ND->GetEntries();
434	mocchiut	1.1	//
435			if ( nevents < 1 ) {
436	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: Level0 file is empty\n\n");
437	mocchiut	1.1	l0File->Close();
438			code = -11;
439			goto closeandexit;
440			};
441			//
442	mocchiut	1.5	if ( runinfo->EV_TO > nevents-1 ) {
443			if ( debug ) printf(" ND - ERROR: too few entries in the tree\n");
444	mocchiut	1.1	l0File->Close();
445			code = -12;
446			goto closeandexit;
447			};
448			//
449			// run over all the events of the run
450			//
451			if (verbose) printf("\n Ready to start! \n\n Processed events: \n\n");
452			//
453	mocchiut	1.5	for ( re = runinfo->EV_FROM; re < (runinfo->EV_FROM+runinfo->NEVENTS); re++){
454	mocchiut	1.1	//
455			if ( procev%1000 == 0 && procev > 0 && verbose ) printf(" %iK \n",procev/1000);
456			//
457	mocchiut	1.5	l0head->GetEntry(re);
458	mocchiut	1.1	//
459			// absolute time of this event
460			//
461	mocchiut	1.5	ph = eh->GetPscuHeader();
462			atime = dbtime->DBabsTime(ph->GetOrbitalTime());
463	mocchiut	1.1	//
464			// paranoid check
465			//
466			if ( (atime > runinfo->RUNTRAILER_TIME) \|\| (atime < runinfo->RUNHEADER_TIME) ) {
467			if (verbose) printf(" ND - WARNING: event at time outside the run time window, skipping it\n");
468			goto jumpev;
469			};
470			//
471			procev++;
472			//
473			// start processing
474			//
475	mocchiut	1.2	nd->Clear();
476			//
477	mocchiut	1.5	l0ND->GetEntry(re);
478	mocchiut	1.1	tmpSize = l0ne->Records->GetEntries();
479	mocchiut	1.6	if ( tmpSize && l0ne->unpackError == 0 ){
480			for (Int_t j = 0; j < tmpSize; j++){
481			l0nr = (pamela::neutron::NeutronRecord*)l0ne->Records->At(j);
482			yTrig = yTrig + (float)l0nr->trigPhysics;
483			yUpperBackground = yUpperBackground + (float)l0nr->upperBack;
484			yBottomBackground = yBottomBackground + (float)l0nr->bottomBack;
485			}
486			nd->upperBack = yUpperBackground;
487			nd->bottomBack = yBottomBackground;
488			nd->trigPhysics = yTrig;
489			};
490			//
491	mocchiut	1.7	nd->unpackError = l0ne->unpackError;
492	mocchiut	1.6	//
493	mocchiut	1.1	NDtr->Fill(); // Fill tree NDLevel2 in the root file
494	mocchiut	1.6	//
495	mocchiut	1.1	yUpperBackground =0;
496			yBottomBackground =0;
497			yTrig=0;
498			//
499			//
500			jumpev:
501			debug = false;
502			//
503			};
504			//
505			// Here you may want to clear some variables before processing another run
506			//
507	mocchiut	1.5	delete dbtime;
508	mocchiut	1.1	}; // process all the runs
509			//
510			if (verbose) printf("\n Finished processing data \n");
511			//
512			closeandexit:
513			//
514			// we have finished processing the run(s). If we processed a single run now we must copy all the events after our run from the old tree to the new one and delete the old tree.
515			//
516			if ( !reprocall && reproc && code >= 0 ){
517			if ( totfileentries > noaftrun ){
518			if (verbose) {
519			printf("\n Post-processing: copying events from the old tree after the processed run\n");
520			printf(" Copying %i events in the file which are after the end of the run %i \n",(int)(totfileentries-noaftrun),(int)run);
521			printf(" Start copying at event number %i end copying at event number %i \n",(int)noaftrun,(int)totfileentries);
522			}
523			for (UInt_t j = noaftrun; j < totfileentries; j++ ){
524			//
525			// Get entry from old tree
526			//
527			NDtrclone->GetEntry(j);
528			//
529			// copy ndclone to nd
530			//
531	mocchiut	1.2	nd->Clear();
532	mocchiut	1.1	memcpy(&nd,&ndclone,sizeof(ndclone));
533			//
534			// Fill entry in the new tree
535			//
536			NDtr->Fill();
537			};
538			if (verbose) printf(" Finished successful copying!\n");
539			};
540			};
541			//
542			// Close files, delete old tree(s), write and close level2 file
543			//
544			if ( l0File ) l0File->Close();
545			if ( tempfile ) tempfile->Close();
546			gSystem->Unlink(tempname.str().c_str());
547	mocchiut	1.5	//
548	mocchiut	1.1	if ( runinfo ) runinfo->Close();
549			if ( NDtr ) NDtr->SetName("NeutronD");
550			if ( file ){
551			file->cd();
552			file->Write();
553			};
554			//
555			gSystem->Unlink(NDfolder.str().c_str());
556			//
557			// the end
558			//
559	mocchiut	1.3	if ( verbose ) printf("\n Exiting...\n");
560			if ( NDtr ) NDtr->Delete();
561			//
562			if ( nd ) delete nd;
563			if ( ndclone ) delete ndclone;
564	mocchiut	1.4	if ( glroot ) delete glroot;
565	mocchiut	1.3	if ( runinfo ) delete runinfo;
566			//
567	mocchiut	1.1	if(code < 0) throw code;
568			return(code);
569			}
570
571
572