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