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>
//
// 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, GL_TABLES *glt, Int_t NDargc, char *NDargv[]){
  //
  // Set these to true to have a verbose output.
  //
  Bool_t debug = false;
  Bool_t verbose = false;
  //
  // Output directory is the working directoy.
  //
  const char* outDir = gSystem->DirName(gSystem->DirName(file->GetPath()));
  //  
  Int_t i = 0;
  TString processFolder = Form("NDFolder_%u",run);
  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")) ) {
        debug = true;
        verbose= true;
      };
      i++;
    };
  };
  //

  // 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;
  Bool_t myfold = false;
  tempname.str("");
  tempname << outDir;
  tempname << "/" << processFolder.Data();
  NDfolder.str("");
  NDfolder << tempname.str().c_str();
  tempname << "/NDtree_run";
  tempname << run << ".root";  
  UInt_t totnorun = 0;
  //
  // 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();
  //
  //
  //
  totnorun = runinfo->GetRunEntries();
  //
  // 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 || totnorun == 1 ){
      //
      // 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
      //
      gSystem->MakeDirectory(NDfolder.str().c_str());
      myfold = true;
      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
    //
    TString host = glt->CGetHost();
    TString user = glt->CGetUser();
    TString psw = glt->CGetPsw();
    TSQLServer *dbc = TSQLServer::Connect(host.Data(),user.Data(),psw.Data());    
    if ( !dbc->IsConnected() ) throw -604;
    stringstream myquery;
    myquery.str("");
    myquery << "SET time_zone='+0:00'";
    dbc->Query(myquery.str().c_str());
    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);
    }
    //
    //    if ( !totevent ) goto closeandexit;
    //
    // 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 && totevent ) {
      if ( debug ) printf(" ND - ERROR: Level0 file is empty\n\n");
      l0File->Close();
      code = -11;
      goto closeandexit;
    };
    //
    if ( runinfo->EV_TO > nevents-1 && totevent ) {
      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");
    //
    if ( dbc ){
      dbc->Close();
      //      delete dbc;
    };
    //
    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+1)) || (atime < (runinfo->RUNHEADER_TIME-1))  ) {
        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();            
  if ( myfold ) gSystem->Unlink(tempname.str().c_str());
  //
  if ( runinfo ) runinfo->Close();    
  if ( NDtr ) NDtr->SetName("NeutronD");    
  if ( file ){
    file->cd();
    file->Write();
  };
  //
  if ( myfold ) 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			//
43			// RunInfo header
44			//
45	mocchiut	1.10	//#include <RunInfo.h>
46			//#include <GLTables.h>
47	mocchiut	1.1	//
48			// This program headers
49			//
50			#include <NDLevel2.h>
51			#include <NDCore.h>
52			#include <NDVerl2.h>
53
54			using namespace std;
55
56			//
57			// CORE ROUTINE
58			//
59			//
60	mocchiut	1.18	int NDCore(UInt_t run, TFile file, GL_TABLES glt, Int_t NDargc, char *NDargv[]){
61	mocchiut	1.1	//
62	pam-rm2	1.11	// Set these to true to have a verbose output.
63	mocchiut	1.1	//
64			Bool_t debug = false;
65	pam-rm2	1.11	Bool_t verbose = false;
66	mocchiut	1.1	//
67	pam-rm2	1.11	// Output directory is the working directoy.
68	mocchiut	1.1	//
69	pam-rm2	1.11	const char* outDir = gSystem->DirName(gSystem->DirName(file->GetPath()));
70			//
71			Int_t i = 0;
72	mocchiut	1.14	TString processFolder = Form("NDFolder_%u",run);
73	mocchiut	1.1	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	mocchiut	1.13	debug = true;
88	mocchiut	1.1	verbose= true;
89			};
90			i++;
91			};
92			};
93			//
94	pam-rm2	1.11
95	mocchiut	1.1	// Variables for level2
96			//
97			TTree *NDtr = 0;
98	mocchiut	1.5	UInt_t nevents = 0;
99	mocchiut	1.1	//
100	pam-rm2	1.11	// Variables needed to reprocess data
101	mocchiut	1.1	//
102			TString NDversion;
103			ItoRunInfo *runinfo = 0;
104	mocchiut	1.5	TArrayI *runlist = 0;
105	mocchiut	1.1	TTree *NDtrclone = 0;
106			Bool_t reproc = false;
107			Bool_t reprocall = false;
108			UInt_t nobefrun = 0;
109			UInt_t noaftrun = 0;
110			UInt_t numbofrun = 0;
111			stringstream ftmpname;
112			TString fname;
113	mocchiut	1.5	UInt_t totfileentries = 0;
114			UInt_t idRun = 0;
115	mocchiut	1.1	Int_t tmpSize =0;
116			Float_t yTrig =0;
117			Float_t yUpperBackground =0;
118			Float_t yBottomBackground =0;
119			//
120			// variables needed to handle error signals
121			//
122			Int_t code = 0;
123			Int_t sgnl;
124			//
125	mocchiut	1.9	Long64_t maxsize = 10000000000LL;
126			TTree::SetMaxTreeSize(maxsize);
127			//
128			//
129	mocchiut	1.1	// ND level2 classes
130			//
131			NDLevel2 *nd = new NDLevel2();
132			NDLevel2 *ndclone = new NDLevel2();
133			//
134			// define variables for opening and reading level0 file
135			//
136			TFile *l0File = 0;
137			TTree *l0tr = 0;
138			TBranch *l0head = 0;
139			TBranch *l0ND =0;
140			pamela::EventHeader *eh = 0;
141	mocchiut	1.5	pamela::PscuHeader *ph = 0;
142	mocchiut	1.1	pamela::neutron::NeutronRecord *l0nr = 0;
143			pamela::neutron::NeutronEvent *l0ne = 0;
144			//
145			// Define other basic variables
146			//
147			UInt_t procev = 0;
148			stringstream file2;
149			stringstream file3;
150			stringstream qy;
151			Int_t totevent = 0;
152	mocchiut	1.5	UInt_t atime = 0;
153			UInt_t re = 0;
154	mocchiut	1.1	//
155			// Working filename
156			//
157			TString outputfile;
158			stringstream name;
159			name.str("");
160			name << outDir << "/";
161			//
162			// temporary file and folder
163			//
164			TFile *tempfile = 0;
165			TTree *tempND = 0;
166			stringstream tempname;
167			stringstream NDfolder;
168	mocchiut	1.16	Bool_t myfold = false;
169	mocchiut	1.1	tempname.str("");
170			tempname << outDir;
171			tempname << "/" << processFolder.Data();
172			NDfolder.str("");
173			NDfolder << tempname.str().c_str();
174			tempname << "/NDtree_run";
175			tempname << run << ".root";
176	mocchiut	1.23	UInt_t totnorun = 0;
177	mocchiut	1.1	//
178			// DB classes
179			//
180			GL_ROOT *glroot = new GL_ROOT();
181	mocchiut	1.5	GL_TIMESYNC *dbtime = 0;
182	mocchiut	1.1	//
183			// Let's start!
184			//
185			// 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
186			// if run != 0 we must process only that run but first we have to check if the tree MyDetector2 already exist in the file
187			// if it exists we are reprocessing data and we must delete that entries, if not we must create it.
188			//
189	mocchiut	1.5	if ( run == 0 ) reproc = true;
190	mocchiut	1.1	//
191			//
192			// Output file is "outputfile"
193			//
194			if ( !file->IsOpen() ){
195			//printf(" ND - ERROR: cannot open file for writing\n");
196			throw -601 ;
197			};
198			//
199			// Retrieve GL_RUN variables from the level2 file
200			//
201			NDversion = NDInfo(false); // we should decide how to handle versioning system
202			//
203			// create an interface to RunInfo called "runinfo"
204			//
205			runinfo = new ItoRunInfo(file);
206			//
207			// open "Run" tree in level2 file, if not existing return an error (sngl != 0)
208			//
209			sgnl = 0;
210			sgnl = runinfo->Update(run, "ND",NDversion);
211			if ( sgnl ){
212	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: RunInfo exited with non-zero status\n");
213	mocchiut	1.1	code = sgnl;
214			goto closeandexit;
215			} else {
216			sgnl = 0;
217			};
218			//
219			// number of events in the file BEFORE the first event of our run
220			//
221			nobefrun = runinfo->GetFirstEntry();
222			//
223			// total number of events in the file
224			//
225			totfileentries = runinfo->GetFileEntries();
226			//
227			// first file entry AFTER the last event of our run
228			//
229			noaftrun = runinfo->GetLastEntry() + 1;
230			//
231			// number of run to be processed
232			//
233			numbofrun = runinfo->GetNoRun();
234			//
235	mocchiut	1.15	//
236			//
237	mocchiut	1.23	totnorun = runinfo->GetRunEntries();
238	mocchiut	1.15	//
239	mocchiut	1.1	// Try to access the S4 tree in the file, if it exists we are reprocessing data if not we are processing a new run
240			//
241			NDtrclone = (TTree*)file->Get("NeutronD");
242			//
243			if ( !NDtrclone ){
244			//
245			// tree does not exist, we are not reprocessing
246			//
247			reproc = false;
248	mocchiut	1.5	if ( run == 0 ) {
249	mocchiut	1.1	if (verbose) printf(" ND - WARNING: you are reprocessing data but ND tree does not exist!\n");
250			}
251	mocchiut	1.5	if ( runinfo->IsReprocessing() && run != 0 ) {
252	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");
253			}
254			} else {
255			//
256	mocchiut	1.9	NDtrclone->SetAutoSave(900000000000000LL);
257			//
258	mocchiut	1.1	// tree exists, we are reprocessing data. Are we reprocessing a single run or all the file?
259			//
260			reproc = true;
261			//
262			// update versioning information
263			//
264			if (verbose) printf("\n Preparing the pre-processing...\n");
265			//
266	mocchiut	1.15	if ( run == 0 \|\| totnorun == 1 ){
267	mocchiut	1.1	//
268			// we are reprocessing all the file
269			// 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
270			//
271			reprocall = true;
272			//
273			if (verbose) printf("\n ND - WARNING: Reprocessing all runs\n");
274			//
275			} else {
276			//
277			// 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
278			//
279			reprocall = false;
280			//
281	mocchiut	1.5	if (verbose) printf("\n ND - WARNING: Reprocessing run number %u \n",run);
282	mocchiut	1.1	//
283			// copying old tree to a new file
284			//
285	mocchiut	1.16	gSystem->MakeDirectory(NDfolder.str().c_str());
286			myfold = true;
287	mocchiut	1.1	tempfile = new TFile(tempname.str().c_str(),"RECREATE");
288			tempND = NDtrclone->CloneTree(-1,"fast");
289			tempND->SetName("NeutronD-old");
290			tempfile->Write();
291			tempfile->Close();
292			}
293			//
294			// Delete the old tree from old file and memory
295			//
296			NDtrclone->Delete("all");
297			//
298			if (verbose) printf(" ...done!\n");
299			//
300			};
301			//
302			// create mydetector tree mydect
303			//
304			file->cd();
305			NDtr = new TTree("NeutronD-new","PAMELA Level2 NeutronD data");
306	mocchiut	1.9	NDtr->SetAutoSave(900000000000000LL);
307	mocchiut	1.1	NDtr->Branch("NDLevel2","NDLevel2",&nd);
308			//
309			if ( reproc && !reprocall ){
310			//
311			// open new file and retrieve also tree informations
312			//
313			tempfile = new TFile(tempname.str().c_str(),"READ");
314			NDtrclone = (TTree*)tempfile->Get("NeutronD-old");
315	mocchiut	1.9	NDtrclone->SetAutoSave(900000000000000LL);
316	mocchiut	1.1	NDtrclone->SetBranchAddress("NDLevel2",&ndclone);
317			//
318			if ( nobefrun > 0 ){
319			if (verbose) {
320			printf("\n Pre-processing: copying events from the old tree before the processed run\n");
321	mocchiut	1.5	printf(" Copying %u events in the file which are before the beginning of the run %u \n",nobefrun,run);
322	mocchiut	1.1	printf(" Start copying at event number 0, end copying at event number %u \n",nobefrun);
323			}
324			for (UInt_t j = 0; j < nobefrun; j++){
325			//
326			NDtrclone->GetEntry(j);
327			//
328			// copy ndclone to mydec
329			//
330	mocchiut	1.2	// nd = new NDLevel2();
331			nd->Clear();
332	mocchiut	1.1	memcpy(&nd,&ndclone,sizeof(ndclone));
333			//
334			// Fill entry in the new tree
335			//
336			NDtr->Fill();
337			//
338			};
339			if (verbose) printf(" Finished successful copying!\n");
340			};
341			};
342			//
343			// Get the list of run to be processed, if only one run has to be processed the list will contain one entry only.
344			//
345			runlist = runinfo->GetRunList();
346			//
347			// Loop over the run to be processed
348			//
349			for (UInt_t irun=0; irun < numbofrun; irun++){
350			//
351			// retrieve the first run ID to be processed using the RunInfo list
352			//
353			idRun = runlist->At(irun);
354			if (verbose) {
355			printf("\n\n\n ####################################################################### \n");
356	mocchiut	1.5	printf(" PROCESSING RUN NUMBER %u \n",idRun);
357	mocchiut	1.1	printf(" ####################################################################### \n\n\n");
358			}
359			//
360	mocchiut	1.5	runinfo->ID_ROOT_L0 = 0;
361	mocchiut	1.1	//
362			// store in the runinfo class the GL_RUN variables for our run
363			//
364			sgnl = 0;
365			sgnl = runinfo->GetRunInfo(idRun);
366			if ( sgnl ){
367	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: RunInfo exited with non-zero status\n");
368	mocchiut	1.1	code = sgnl;
369			goto closeandexit;
370			} else {
371			sgnl = 0;
372			};
373			//
374	mocchiut	1.5	// now you can access that variables using the RunInfo class this way runinfo->ID_ROOT_L0
375	mocchiut	1.1	//
376	mocchiut	1.5	if ( runinfo->ID_ROOT_L0 == 0 ){
377			if ( debug ) printf("\n ND - ERROR: no run with ID_RUN = %u \n\n Exiting... \n\n",idRun);
378	mocchiut	1.1	code = -5;
379			goto closeandexit;
380			};
381			//
382	mocchiut	1.5	// prepare the timesync for the db
383			//
384	mocchiut	1.18	TString host = glt->CGetHost();
385			TString user = glt->CGetUser();
386			TString psw = glt->CGetPsw();
387			TSQLServer *dbc = TSQLServer::Connect(host.Data(),user.Data(),psw.Data());
388			if ( !dbc->IsConnected() ) throw -604;
389	mocchiut	1.19	stringstream myquery;
390			myquery.str("");
391			myquery << "SET time_zone='+0:00'";
392			dbc->Query(myquery.str().c_str());
393	mocchiut	1.5	dbtime = new GL_TIMESYNC(runinfo->ID_ROOT_L0,"ID",dbc);
394			//
395	mocchiut	1.1	// Search in the DB the path and name of the LEVEL0 file to be processed.
396			//
397	mocchiut	1.17	// if ( !dbc->IsConnected() ) throw -604;
398	mocchiut	1.5	glroot->Query_GL_ROOT(runinfo->ID_ROOT_L0,dbc);
399	mocchiut	1.1	//
400			ftmpname.str("");
401			ftmpname << glroot->PATH.Data() << "/";
402			ftmpname << glroot->NAME.Data();
403			fname = ftmpname.str().c_str();
404			//
405			// print out informations
406			//
407	mocchiut	1.5	totevent = runinfo->NEVENTS;
408	mocchiut	1.1	if (verbose) {
409			printf("\n LEVEL0 data file: %s \n",fname.Data());
410	mocchiut	1.5	printf(" RUN HEADER absolute time is: %u \n",runinfo->RUNHEADER_TIME);
411			printf(" RUN TRAILER absolute time is: %u \n",runinfo->RUNTRAILER_TIME);
412			printf(" %i events to be processed for run %u: from %i to %i \n\n",totevent,idRun,runinfo->EV_FROM,runinfo->EV_FROM+totevent);
413	mocchiut	1.1	}
414			//
415	mocchiut	1.21	// if ( !totevent ) goto closeandexit;
416	mocchiut	1.20	//
417	mocchiut	1.1	// Open Level0 file
418			//
419			l0File = new TFile(fname.Data());
420			if ( !l0File ) {
421	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: problems opening Level0 file\n");
422	mocchiut	1.1	code = -6;
423			goto closeandexit;
424			};
425			l0tr = (TTree*)l0File->Get("Physics");
426			if ( !l0tr ) {
427	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: no Physics tree in Level0 file\n");
428	mocchiut	1.1	l0File->Close();
429			code = -7;
430			goto closeandexit;
431			};
432			l0head = l0tr->GetBranch("Header");
433			if ( !l0head ) {
434	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: no Header branch in Level0 tree\n");
435	mocchiut	1.1	l0File->Close();
436			code = -8;
437			goto closeandexit;
438			};
439			l0ND = l0tr->GetBranch("Neutron");
440			if ( !l0ND ) {
441	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: no ND branch in Level0 tree\n");
442	mocchiut	1.1	l0File->Close();
443			code = -603;
444			goto closeandexit;
445			};
446
447			//
448			l0tr->SetBranchAddress("Neutron", &l0ne);
449			l0tr->SetBranchAddress("Header", &eh);
450			//
451	mocchiut	1.5	nevents = l0ND->GetEntries();
452	mocchiut	1.1	//
453	mocchiut	1.21	if ( nevents < 1 && totevent ) {
454	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: Level0 file is empty\n\n");
455	mocchiut	1.1	l0File->Close();
456			code = -11;
457			goto closeandexit;
458			};
459			//
460	mocchiut	1.21	if ( runinfo->EV_TO > nevents-1 && totevent ) {
461	mocchiut	1.5	if ( debug ) printf(" ND - ERROR: too few entries in the tree\n");
462	mocchiut	1.1	l0File->Close();
463			code = -12;
464			goto closeandexit;
465			};
466			//
467			// run over all the events of the run
468			//
469			if (verbose) printf("\n Ready to start! \n\n Processed events: \n\n");
470			//
471	mocchiut	1.17	if ( dbc ){
472			dbc->Close();
473			// delete dbc;
474			};
475			//
476	mocchiut	1.5	for ( re = runinfo->EV_FROM; re < (runinfo->EV_FROM+runinfo->NEVENTS); re++){
477	mocchiut	1.1	//
478			if ( procev%1000 == 0 && procev > 0 && verbose ) printf(" %iK \n",procev/1000);
479			//
480	mocchiut	1.5	l0head->GetEntry(re);
481	mocchiut	1.1	//
482			// absolute time of this event
483			//
484	mocchiut	1.5	ph = eh->GetPscuHeader();
485			atime = dbtime->DBabsTime(ph->GetOrbitalTime());
486	mocchiut	1.1	//
487			// paranoid check
488			//
489	mocchiut	1.22	if ( (atime > (runinfo->RUNTRAILER_TIME+1)) \|\| (atime < (runinfo->RUNHEADER_TIME-1)) ) {
490	mocchiut	1.1	if (verbose) printf(" ND - WARNING: event at time outside the run time window, skipping it\n");
491			goto jumpev;
492			};
493			//
494			procev++;
495			//
496			// start processing
497			//
498	mocchiut	1.2	nd->Clear();
499			//
500	mocchiut	1.5	l0ND->GetEntry(re);
501	mocchiut	1.1	tmpSize = l0ne->Records->GetEntries();
502	mocchiut	1.6	if ( tmpSize && l0ne->unpackError == 0 ){
503			for (Int_t j = 0; j < tmpSize; j++){
504			l0nr = (pamela::neutron::NeutronRecord*)l0ne->Records->At(j);
505			yTrig = yTrig + (float)l0nr->trigPhysics;
506			yUpperBackground = yUpperBackground + (float)l0nr->upperBack;
507			yBottomBackground = yBottomBackground + (float)l0nr->bottomBack;
508			}
509			nd->upperBack = yUpperBackground;
510			nd->bottomBack = yBottomBackground;
511			nd->trigPhysics = yTrig;
512			};
513			//
514	mocchiut	1.7	nd->unpackError = l0ne->unpackError;
515	mocchiut	1.6	//
516	mocchiut	1.1	NDtr->Fill(); // Fill tree NDLevel2 in the root file
517	mocchiut	1.6	//
518	mocchiut	1.1	yUpperBackground =0;
519			yBottomBackground =0;
520			yTrig=0;
521			//
522			//
523			jumpev:
524			debug = false;
525			//
526			};
527			//
528			// Here you may want to clear some variables before processing another run
529			//
530	mocchiut	1.5	delete dbtime;
531	mocchiut	1.1	}; // process all the runs
532			//
533			if (verbose) printf("\n Finished processing data \n");
534			//
535			closeandexit:
536			//
537			// 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.
538			//
539			if ( !reprocall && reproc && code >= 0 ){
540			if ( totfileentries > noaftrun ){
541			if (verbose) {
542			printf("\n Post-processing: copying events from the old tree after the processed run\n");
543			printf(" Copying %i events in the file which are after the end of the run %i \n",(int)(totfileentries-noaftrun),(int)run);
544			printf(" Start copying at event number %i end copying at event number %i \n",(int)noaftrun,(int)totfileentries);
545			}
546			for (UInt_t j = noaftrun; j < totfileentries; j++ ){
547			//
548			// Get entry from old tree
549			//
550			NDtrclone->GetEntry(j);
551			//
552			// copy ndclone to nd
553			//
554	mocchiut	1.2	nd->Clear();
555	mocchiut	1.1	memcpy(&nd,&ndclone,sizeof(ndclone));
556			//
557			// Fill entry in the new tree
558			//
559			NDtr->Fill();
560			};
561			if (verbose) printf(" Finished successful copying!\n");
562			};
563			};
564			//
565			// Close files, delete old tree(s), write and close level2 file
566			//
567			if ( l0File ) l0File->Close();
568			if ( tempfile ) tempfile->Close();
569	mocchiut	1.16	if ( myfold ) gSystem->Unlink(tempname.str().c_str());
570	mocchiut	1.5	//
571	mocchiut	1.1	if ( runinfo ) runinfo->Close();
572			if ( NDtr ) NDtr->SetName("NeutronD");
573			if ( file ){
574			file->cd();
575			file->Write();
576			};
577			//
578	mocchiut	1.16	if ( myfold ) gSystem->Unlink(NDfolder.str().c_str());
579	mocchiut	1.1	//
580			// the end
581			//
582	mocchiut	1.3	if ( verbose ) printf("\n Exiting...\n");
583			if ( NDtr ) NDtr->Delete();
584			//
585			if ( nd ) delete nd;
586			if ( ndclone ) delete ndclone;
587	mocchiut	1.4	if ( glroot ) delete glroot;
588	mocchiut	1.3	if ( runinfo ) delete runinfo;
589			//
590	mocchiut	1.1	if(code < 0) throw code;
591			return(code);
592			}
593
594
595