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