add task for AliAnalysisTaskV0ForRAA
[u/mrichter/AliRoot.git] / PWGJE / macros / AnalysisTrainPWGJets.C
1 //===================== ANALYSIS TRAIN =========================================
2 // To use: copy this macro to your work directory, modify the global part to match
3 // your needs, then run root.
4 //    root[0] .L AnalysisTrain.C
5 // Grid full mode as below (other modes: test, offline, submit, terminate)
6 //    root[1] AnalysisTrainPWG-244Jets("grid", "full")
7 // CAF mode (requires root v5-23-02 + aliroot v4-16-Rev08)
8 //    root[2] AnalysisTrainPWG4Jets("proof")
9 // Local mode requires AliESds.root or AliAOD.root in ./data directory
10 //    root[3] AnalysisTrainPWG4Jets("local")
11 // In proof and grid modes, a token is needed and sourcing the produced environment file.
12 //
13 // If 'saveTrain' flag is set, the train will generate a directory name and run
14 // in this directory. A configuration file 'ConfigTrain.C' will be generated. 
15 // One can replay at any time the train via:
16 //    root[1] AnalysisTrainPWG4Jets(ana_mode, plugin_mode, "train_default_<date>/ConfigTrain.C")
17
18 // For Usage with fastjet run in "offline" first and then "submit"
19 // jdl and analysismacro are automatically patched after "offline" mode
20
21 // =============================================================================
22 // ### General Steering variables
23 // =============================================================================
24 //== general setup variables
25 TString     kTrainName         = "testAnalysis"; // *CHANGE ME* (no blancs or special characters)
26 TString     kJobTag            = "PWGJE Jet Tasks analysis train configured"; // *CHANGE ME*
27
28 // Usage of par files ONLY in grid mode and ONLY if the code is not available
29 // in the deployed AliRoot versions. Par file search path: local dir, if not there $ALICE_ROOT.
30 // To refresh par files, remove the ones in the workdir, then do "make <target.par>" in 
31 // AliRoot.
32 Bool_t      kUsePAR             = kFALSE;  // use par files for extra libs
33 Bool_t      kUseCPAR            = kFALSE;  // use par files for common libs
34 Bool_t      kFillAOD = kTRUE;  // switch of AOD filling for on the fly analysis
35 Bool_t      kFilterAOD = kTRUE;
36 Float_t     kJetTriggerPtCut = 20; // pT for jet trigger in case of iFilter==2
37 Int_t       kSaveAOD = 8;        // Bit switch 1 = Full AOD 2 = Jet AOD , 4 = PartCorr, 8 = JCORRAN 
38 //== general input and output variables
39
40 Int_t       iAODanalysis       = 1;      // Analysis on input AOD's
41 Int_t       iFilterAnalysis       = 0;      // Analysis on input AOD's
42 Int_t       iAODhandler        = 1;      // Analysis produces an AOD or dAOD's
43 Int_t       iCentralitySelection  = 0;      // Use the centrality
44 Int_t       iESDfilter         = 0;      // ESD to AOD filter (barrel + muon tracks)
45 Int_t       iPhysicsSelection  = 1;      // ESD to AOD filter (barrel + muon tracks)
46 UInt_t      iPhysicsSelectionFlag = 1; // set by pyshics selection and passed to the task, kMB, kUserDefined etc
47 Bool_t      useTender           = kFALSE; // use tender wagon 
48 Bool_t      kUseKinefilter     = kFALSE; // use Kinematics filter
49 Bool_t      kUseMuonfilter     = kFALSE; // use Kinematics filter
50 TString     kCommonOutputFileName = "PWGJE_JetTasksOutput.root";
51 TString     kCaloQAOutputFileName = "PWGJE_CaloQAOutput.root";
52
53
54 //== general process variables
55
56 // ### Other flags to steer the analysis
57 //==============================================================================
58 Bool_t      kSkipTerminate      = kTRUE; // Do not call Teminate
59 Bool_t      kUseDate            = kFALSE; // use date in train name
60 Bool_t      kUseDebug           = kTRUE; // activate debugging
61 Int_t         kErrorIgnoreLevel = -1; // takes the errror print level from .rootrc 
62 // From TError.h:
63 // const Int_t kUnset    =  -1;
64 // const Int_t kPrint    =   0;
65 // const Int_t kInfo     =   1000;
66 // const Int_t kWarning  =   2000;
67 // const Int_t kError    =   3000;
68 // const Int_t kBreak    =   4000;
69 // const Int_t kSysError =   5000;
70 // const Int_t kFatal    =   6000; 
71 Int_t         kUseSysInfo         = 0; // activate debugging
72 Long64_t    kNumberOfEvents     = 1234567890; // Number of events to process from the chain
73 Bool_t      kUseMC              = kTRUE;  // use MC info
74 Bool_t      kIsMC               = kTRUE;  // is MC info, if false it overwrites Use(AOD)MC
75 Bool_t      kUseAODMC           = kTRUE;  // use MC infA
76 Bool_t      kUseESDTags         = kFALSE; // use ESD tags for selection
77 Bool_t      kUseTR              = kFALSE;  // use track references
78 Bool_t      kUseAODTags         = kFALSE;  // use AOD tags
79 Bool_t      kSaveTrain          = kFALSE;  // save train configuration as: 
80 Bool_t      kIsPbPb             = kFALSE;  // Pb+Pb
81
82
83 // ### Analysis modules to be included. Some may not be yet fully implemented.
84 //==============================================================================
85 Int_t       iJETAN             = 1;      // Jet analysis  // 1 write standard 2 write non-standard jets, 3 wrtie both
86 Int_t       iJETANReader       = 0;      // Jet analysis  // DEV
87 Int_t       iJETANFinder       = 0;      // Jet analysis  // DEV
88 Int_t       iJETSUBTRACT        = 0;      // Jet background subtration
89 TList       kJetListSpectrum;             // list of jets contains TObjString of possible jet finder names
90 TExMap      kJetMapSpectrum;             // Maps the jet finder pairs to be used in the spectrum task second number negative no pair other wise (j1+1) + (1000 * (j2+1)) +10000 * (j3+1)
91 TExMap      kJetBackMapSpectrum;             // Maps the jet finder pairs with the background branch used, just for countint of trackrefs
92 Int_t       kJetMapOffset[3] = {10000,100,1};
93 TString     kDefaultJetBranch     = "";      // is currently set when filled (iJETAN or clusters) or from config macro 
94 TString     kDefaultJetBackgroundBranch            = "";      // is currently set when filled (jet clsuters  
95 TString     kDefaultJetBackgroundBranchCut1        = "";      // is currently set when filled (jet clsuters  
96 TString     kDefaultJetBackgroundBranchCut2        = "";      // is currently set when filled (jet clsuters  
97 TString     kDefaultJetBackgroundBranch_extra     = "";      // is currently set when filled (jet clsuters) 
98 TString     kJetSubtractBranches     = "";      // is currently set when filled (jet clsuters  
99 TString     kJetSubtractBranchesCut1     = "";      // is currently set when filled (jet clsuters  
100 TString     kJetSubtractBranchesCut2     = "";      // is currently set when filled (jet clsuters  
101 TString     kJetSubtractBranches_extra     = "";      // is currently set when filled (jet clsuters  
102
103 TString     kDefaultJetBranchMC     = "";      // is currently set when filled (iJETAN or clusters) or from config macro 
104 TString     kDefaultJetBackgroundBranchMC     = "";      // is currently set when filled (jet clsuters  
105 TString     kDefaultJetBranchMC2     = "";      // is currently set when filled (iJETAN or clusters) or from config macro 
106 TString     kDefaultJetBackgroundBranchMC2     = "";      // is currently set when filled (jet clsuters  
107 TString     kJetSubtractMask1 = "B0";
108 TString     kJetSubtractMask2 = "B%d";
109 Int_t       iDIJETAN           = 1;
110 Int_t       iJETANLib          = 1;
111 Int_t       iJETANdevLib       = 0;
112 Int_t       iPWGPPQASym         = 0;      // Eva's QA task compiled on the fly...
113 Int_t       iPWG4FastEmbedding = 0;      // Generate non-standard AOD for embedding
114 Int_t       iPWG4JetTasks      = 0;      // all jet tasks flag for lib laoding
115 Int_t       iPWG4JetServices   = 0;      // jet spectrum analysis
116 Int_t       iPWG4JetSpectrum   = 0;      // jet spectrum analysis
117 Int_t       iPWG4JetResponse   = 0;      // jet response matrix
118 Int_t       iPWG4JCORRAN       = 0;      // JCORRAN module
119 Int_t       iPWG4UE            = 0;      // Underlying Event analysis
120 Int_t       iPWG4LeadingUE     = 0;      // Underlying Event analysis
121 Int_t       iPWG4CorrectionsUE = 0;      // Underlying Event analysis
122 Int_t       iPWG4TmpSourceSara = 0;      // Underlying Event analysis not in svn
123 Int_t       iPWG4Fragmentation = 1;      // Official Fragmentation
124 Int_t       iPWG4JetChem       = 0;      // Jet chemistry 
125 Int_t       iPWG4PtQAMC        = 0;      // Marta's QA tasks 
126 Int_t       iPWG4PtTrackQA     = 0;      // Marta's QA tasks  
127 Int_t       iPWG4PtSpectra     = 0;      // Marta's QA tasks 
128 Int_t       iPWG4PtQATPC       = 0;      // Marta's QA tasks 
129 Int_t       iPWG4Cosmics     = 0;      // Marta's Cosmics Taks 
130 Int_t       iPWG4ThreeJets     = 0;      // Sona's thrust task
131 Int_t       iPWG4QGSep     = 0;          // Sona's QG Separation task
132 Int_t       iPWG4Minijet       = 0;      // Eva's Mini Jet Task cluster task 
133 Int_t       iPWG4KMeans        = 0;      // Andreas' KMeans task 
134 Int_t       iPWG4Cluster       = 0;      // CKB cluster task 
135 Int_t       iEMCUtilLibs       = 0;      // Flag to satisfy dependence on EMC utils
136 Int_t       iPWG4PartCorrLibs  = 0;      // Gustavo's part corr analysis
137 Int_t       iPWG4PartCorr      = 0;      // Gustavo's part corr analysis
138 Int_t       iPWG4CaloQA        = 0;      // Gustavo's part corr analysis
139 Int_t       iPWG4JetCorr       = 0;     // Paul's jet corr analysis
140 Int_t       iPWG4Tagged        = 0;      // Gustavo's part corr analysis
141 Int_t       iPWG4omega3pi      = 0;      // Omega to 3 pi analysis (PWG4) 
142 Int_t       iPWG4GammaConvLib     = 0;      // Gamma Conversio
143 Int_t       iPWG4GammaConv     = 0;      // Gamma Conversio
144 Int_t       iPWG4CaloConv     = 0;      // Gamma Conversio
145 Int_t       kHighPtFilterMask  = 32;     // change depending on the used AOD Filter
146 TString     kDeltaAODJetName   = "AliAOD.Jets.root";     
147 TString     kDeltaAODJetNameInput   = "";     
148 TString     kDeltaAODJCORRANName   = "AliAOD.JCORRAN.root";     
149 TString     kDeltaAODPartCorrName   = "AliAOD.PartCorr.root";     
150 TString     kFastEmbeddingAOD  = "emb/AliAOD.root";
151 TString     kFastEmbAODList    = "";
152
153 //==============================================================================
154 // ### PROOF Steering varibales
155 //==============================================================================
156 //== proof setup variables
157 TString     kProofCluster      = "alicecaf.cern.ch";
158 Bool_t      kProofUseAFPAR     = kFALSE;  // use AF special par file
159 TString     kProofAFversion          = "AF-v4-17";
160 //== proof input and output variables
161 TString     kProofDataSet      = "/COMMON/COMMON/LHC09a4_run8100X#/esdTree";
162 Bool_t      kProofSaveToAlien   = kFALSE; // save proof outputs in AliEn train_[trainName]_ddMonthyyyy_time.C
163 TString     kProofOutdir       = "";
164 Bool_t      kProofClearPackages = kFALSE;
165 Int_t       kProofEvents = 10000;
166 Int_t       kProofOffset = 0;
167 //== proof process variables
168
169
170 //==============================================================================
171 // ### Grid plugin Steering varibiables
172 //==============================================================================
173 //== grid plugin setup variables
174 Bool_t      kPluginUse         = kTRUE;   // do not change
175 Bool_t      kPluginUseProductionMode  = kFALSE;   // use the plugin in production mode
176 TString     kPluginRootVersion       = "v5-30-02";  // *CHANGE ME IF MORE RECENT IN GRID*
177 TString     kPluginAliRootVersion    = "v4-21-01a-AN";  // *CHANGE ME IF MORE RECENT IN GRID*                                          
178 Bool_t      kPluginMergeViaJDL       = kTRUE;  // merge via JDL
179 Bool_t      kPluginFastReadOption   = kFALSE;  // use xrootd tweaks
180 Bool_t      kPluginOverwriteMode    = kTRUE;  // overwrite existing collections
181 Int_t       kPluginOutputToRunNumber = 1;     // write the output to subdirs named after run number
182 // TString kPluginExecutableCommand = "root -b -q";
183 TString     kPluginExecutableCommand = "source /Users/kleinb/setup_32bit_aliroot_trunk_clean_root_trunk.sh; alienroot -b -q ";
184
185 // == grid plugin input and output variables
186 TString     kGridDatadir      = "/alice/sim/PDC_08b/LHC09a1/AOD/";
187 Int_t         kGridMaxRunsFromList = 999999999;
188 Int_t         kGridOffsetRunFromList = 0; // skip the first n runs from the list
189 TString     kGridLocalRunList = "";
190 TString     kGridOutdir       = ""; // AliEn output directory. If blank will become output_<kTrainName>
191 TString     kGridDataSet      = ""; // sub working directory not to confuse different run xmls 
192 TString     kGridExtraAliendirLevel = ""; // sub working directory not to confuse different run xmls 
193 Int_t         kGridRunRange[2]       =  {0, -1}; // Set the run range
194 TString     kGridRunPattern        = "%03d"; // important for leading zeroes!!
195 TString     kGridPassPattern       = "";
196 TString     kGridExtraFiles        = ""; // files that will be added to the input list in the JDL...
197 Int_t         kGridMaxMergeFiles      = 25; // Number of files merged in a chunk grid run range
198 TString     kGridMergeExclude       = "AliAOD.root"; // Files that should not be merged
199 TString     kGridOutputStorages      = "disk=2"; // Make replicas on the storages
200 // == grid process variables
201 Int_t       kGridRunsPerMaster     = 100; // Number of runs per master job
202 Int_t       kGridFilesPerJob       = 100; // Maximum number of files per job (gives size of AOD)
203
204 //==============================================================================
205 // ### Local Steering variables
206 //==============================================================================
207 //== local setup variables
208 //== local input and output variables
209 TString     kLocalXMLDataset   = ""; // Change local xml dataset for local interactive analysis
210 TString     kLocalDataList   = "local_deltaaod.txt"; // Change local xml dataset for local interactive analysis
211 // == local process variables
212
213 TString kPluginMode = "";
214 TString kAnalysisMode = "";
215
216
217 // Temporaries.
218 TString anaPars = "";
219 TString anaLibs = "";
220 TString anaLibsExtra = "";
221 TString anaSources = "";
222 // Function signatures
223 class AliAnalysisAlien;
224 class AliAnalysisManager;
225
226 //______________________________________________________________________________
227 void AnalysisTrainPWGJets(const char *analysis_mode="local", 
228                            const char *plugin_mode="",
229                            const char *config_file="",Int_t iOffset = 0,Int_t iTotal = 0)
230 {
231 // Main analysis train macro. If a configuration file is provided, all parameters
232 // are taken from there but may be altered by CheckModuleFlags.
233
234   // these flag may be needed by the config file
235   kPluginMode   = plugin_mode;
236   kAnalysisMode = analysis_mode;
237   
238   if (strlen(config_file) && !LoadConfig(config_file)) return;
239   if(iTotal>0)kGridMaxRunsFromList = iTotal; // overwrites the settings from config file
240   if(iOffset)kGridOffsetRunFromList = iOffset;
241   if(iOffset)kProofOffset = iOffset;
242
243
244    TString smode(analysis_mode);
245    smode.ToUpper();
246    if (kSaveTrain)WriteConfig();
247    // Check compatibility of selected modules 
248    CheckModuleFlags(smode);
249    //     gROOT->ProcessLine(".trace");
250
251    printf("==================================================================\n");
252    printf("===========    RUNNING ANALYSIS TRAIN %s IN %s MODE   ==========\n", kTrainName.Data(),smode.Data());
253    printf("==================================================================\n");
254                               printf("=  Configuring analysis train for:                               =\n");
255    if (iAODanalysis) printf("=  AOD analysis                                                  =\n");
256    else                     printf("=  ESD analysis                                                  =\n");
257    if (iPhysicsSelection)   printf("=  Physics selection                                                =\n");
258    if(iCentralitySelection)printf("=  Centrality selection                                                =\n");
259    if (useTender)   printf("=  Using tender                                                =\n");
260    if (iESDfilter)   printf("=  ESD filter                                                    =\n");
261    if (iJETAN)       printf("=  Jet analysis                                                  =\n");
262    if (iJETANReader)       printf("=  Jet analysis Reader (DEV)                              =\n");
263    if (iJETANFinder)       printf("=  Jet analysis Finder (DEV)                              =\n");
264    printf("==================================================================\n");
265
266    char *printMask = ":: %20s  %10d\n";
267    printf(printMask,"Fill AOD",(UInt_t)kFillAOD);
268    printf(printMask,"Save AOD", (UInt_t)kSaveAOD);
269    printf(printMask,"MC truth", (UInt_t)kUseMC);
270    printf(printMask,"KINE filter", (UInt_t)kUseKinefilter);
271    printf(printMask,"track refs", (UInt_t)kUseTR);
272    printf(printMask,"tags", (UInt_t)kUseESDTags);
273    printf(printMask,"AOD tags", (UInt_t)kUseAODTags);
274    printf(printMask,"debugging", (UInt_t)kUseDebug);
275    printf(printMask,"PAR files", (UInt_t)kUsePAR);
276    printf(printMask,"AliEn plugin", (UInt_t)kPluginUse);
277    printf(printMask,"JETAN subtract", (UInt_t)iJETSUBTRACT);
278    printf(printMask,"PWGPP QA sym", iPWGPPQASym);
279    printf(printMask,"PWG4 Source Sara",iPWG4TmpSourceSara);
280    printf(printMask,"PWG4 Fragmentation",iPWG4Fragmentation);
281    printf(printMask,"PWG4 Jet Chem",iPWG4JetChem);
282    printf(printMask,"PWG4 Jet tasks",iPWG4JetTasks);
283    printf(printMask,"PWG4 Jet Services",iPWG4JetServices);     
284    printf(printMask,"PWG4 Jet Spectrum",iPWG4JetSpectrum);
285    printf(printMask,"PWG4 JCORRAN",iPWG4JCORRAN);
286    printf(printMask,"PWG4 UE",iPWG4UE); 
287    printf(printMask,"PWG4 Leading UE",iPWG4LeadingUE); 
288    printf(printMask,"PWG4 Corrections UE",iPWG4CorrectionsUE); 
289    printf(printMask,"PWG4 Pt QA MC",iPWG4PtQAMC);
290    printf(printMask,"PWG4 Pt QA track",iPWG4PtTrackQA);
291    printf(printMask,"PWG4 Pt Spectra",iPWG4PtSpectra);
292    printf(printMask,"PWG4 Pt QA TPC",iPWG4PtQATPC);     
293    printf(printMask,"PWG4 Cosmics",iPWG4Cosmics);     
294    printf(printMask,"PWG4 Three Jets",iPWG4ThreeJets);
295    printf(printMask,"PWG4 QGSep",iPWG4QGSep);
296    printf(printMask,"PWG4 Minijet",iPWG4Minijet);
297    printf(printMask,"PWG4 KMeans",iPWG4KMeans);
298    printf(printMask,"PWG4 Cluster",iPWG4Cluster);
299    printf(printMask,"PWG4 Part Corr",iPWG4PartCorr);
300    printf(printMask,"PWG4 Calo QA",iPWG4CaloQA);
301    printf(printMask,"PWG4 Jet Corr",iPWG4JetCorr);
302    printf(printMask,"PWG4 JCORRAN",iPWG4JCORRAN);
303    printf(printMask,"PWG4 Tagged",iPWG4Tagged);
304    printf(printMask,"PWG4 omega to 3 pi ",iPWG4omega3pi);
305    printf(printMask,"PWG4 Gamma Conv",iPWG4GammaConv);
306    printf(printMask,"PWG4 Calo Conv",iPWG4CaloConv);
307    printf(printMask,"HighPt FilterMask",kHighPtFilterMask);    
308    
309    //==========================================================================
310    // Connect to back-end system
311    if (!Connect(smode)) {
312       ::Error("AnalysisTrain", "Could not connect to %s back-end", analysis_mode);
313       return;
314    }   
315
316    // Load common libraries and set include path
317    if (!LoadCommonLibraries(smode)) {
318       ::Error("AnalysisTrain", "Could not load common libraries");
319       return;
320    }
321
322
323    
324
325
326    // Make the analysis manager and connect event handlers
327    AliAnalysisManager *mgr  = new AliAnalysisManager("PWG4Train", "pwg4 mini train");
328    if (kCommonOutputFileName.Length()>0)mgr->SetCommonFileName(kCommonOutputFileName.Data());
329    if (kProofSaveToAlien) mgr->SetSpecialOutputLocation(kProofOutdir);
330    mgr->SetNSysInfo(0);
331    if (!strcmp(plugin_mode, "test")) mgr->SetNSysInfo(1);
332    if (kUseSysInfo)mgr->SetNSysInfo(kUseSysInfo);
333    mgr->SetSkipTerminate(kSkipTerminate);
334
335    // Load analysis specific libraries
336    if (!LoadAnalysisLibraries(smode)) {
337       ::Error("AnalysisTrain", "Could not load analysis libraries");
338      return;
339    }   
340
341    gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/ConfigLegoTrainPWGJE.C");
342    ConfigLegoTrainPWGJE(1013);
343    // Create input handler (input container created automatically)
344    if (iAODanalysis) {
345    // AOD input handler
346       AliAODInputHandler *aodH = new AliAODInputHandler();
347       mgr->SetInputEventHandler(aodH);
348       if (kDeltaAODJetNameInput.Length()){
349         Printf("Adding Friend %s",kDeltaAODJetNameInput.Data());
350         aodH->AddFriend(kDeltaAODJetNameInput.Data());
351       }
352       //      if (iPWG4PartCorr) aodH->AddFriend(Form("deltas/%s"kDeltaAODJetName.Data()));
353    } else {   
354    // ESD input handler
355       AliESDInputHandler *esdHandler = new AliESDInputHandler();
356       if (kUseESDTags) esdHandler->SetReadTags();
357       esdHandler->SetReadFriends(kFALSE);
358       mgr->SetInputEventHandler(esdHandler);       
359       //      if(iPWG4PtQATPC&& !kTrainName.Contains("pass5"))esdHandler->SetActiveBranches("ESDfriend");
360
361    }
362
363
364
365    // Monte Carlo handler
366    if (kUseMC && !iAODanalysis) {
367       AliMCEventHandler* mcHandler = new AliMCEventHandler();
368       mgr->SetMCtruthEventHandler(mcHandler);
369       mcHandler->SetReadTR(kUseTR); 
370    }   
371    // AOD output container, created automatically when setting an AOD handler
372    if (iAODhandler) {
373       // AOD output handler
374       AliAODHandler* aodHandler   = new AliAODHandler();
375       aodHandler->SetOutputFileName("AliAOD.root");
376       aodHandler->SetFillAODforRun(kFillAOD);
377       //
378       mgr->SetOutputEventHandler(aodHandler);
379       AliAnalysisDataContainer * cout_aod = mgr->GetCommonOutputContainer();
380       cout_aod->SetSpecialOutput();
381    }
382    // Debugging if needed
383
384    if (kUseDebug){
385      mgr->SetDebugLevel(3);
386    }
387    if(kUseSysInfo>0){
388      mgr->RegisterExtraFile("syswatch.root");
389      if(kGridMergeExclude.Length())kGridMergeExclude += " ";
390      kGridMergeExclude += "syswatch.root";
391    }
392    else{
393      AliLog::SetGlobalLogLevel(AliLog::kError);
394    }
395
396
397    //==========================================================================
398    // Create the chain. In this example it is created only from ALIEN files but
399    // can be done to work in batch or grid mode as well.
400    TChain *chain = CreateChain(smode, plugin_mode);
401         
402    //==========================================================================
403    // Load the tasks configuration macros for all wagons. These files are supposed now to be
404    // in the current workdir, but in AliEn they will be in the file catalog, 
405    // mapped from AliRoot and pecified in the jdl input list.
406     
407    // For now connection to top input container and common AOD output container
408    // is done in this macro, but in future these containers will be connected
409    // from each task configuration macro.
410    
411    //                                                                                                                              
412    // Tender and supplies. Needs to be called for every event.                                                                     
413    //                                                                                                                              
414
415    if (useTender) {
416       gROOT->LoadMacro("$ALICE_ROOT/ANALYSIS/TenderSupplies/AddTaskTender.C");
417       AliAnalysisTaskSE *tender = AddTaskTender(kTRUE);
418       //      tender->SelectCollisionCandidates();                                                                                      
419       tender->SetDebugLevel(2);
420    }
421
422    
423    Float_t fTrackEtaWindow = 0.9;
424    Float_t fJetEtaWindow   = 0.5;
425    Float_t fVertexWindow =  10;
426    /*
427    if(kIsPbPb){// for pass1
428      Float_t fTrackEtaWindow = 0.8;
429      Float_t fJetEtaWindow   = 0.4;
430    }
431    */
432
433
434    if(iPhysicsSelection && !iAODanalysis){
435      gROOT->LoadMacro("$ALICE_ROOT/ANALYSIS/macros/AddTaskPhysicsSelection.C");
436      Int_t iTriggerHIC = 0;
437      Bool_t rejectBkg = true;
438      if(kIsPbPb){
439        iTriggerHIC = 2;
440        rejectBkg = false; // for the moment...
441      }
442      AliPhysicsSelectionTask* physSelTask = AddTaskPhysicsSelection(kIsMC,true,rejectBkg);  
443
444      //     mgr->RegisterExtraFile("event_stat.root");
445      mgr->AddStatisticsTask();
446    }
447    else{
448      iPhysicsSelectionFlag = AliVEvent::kMB;
449    }
450    
451    if(kIsPbPb&&!iAODanalysis){
452
453      // has to run before AOD filter
454      gROOT->LoadMacro("$ALICE_ROOT/ANALYSIS/macros/AddTaskCentrality.C");
455      AliCentralitySelectionTask *taskC = AddTaskCentrality();
456       if (!taskC) ::Warning("AnalysisTrainPWG4Jets", "AliCentralitySelectionTask cannot run for this train conditions - EXCLUDED");
457
458
459      gROOT->LoadMacro("$ALICE_ROOT/ANALYSIS/macros/AddTaskEventplane.C");
460      AliEPSelectionTask *taskEP = AddTaskEventplane();
461      if (!taskEP) ::Warning("AnalysisTrainPWG4Jets", "AliEventplan cannot run for this train conditions - EXCLUDED");
462    }
463    
464    if (iESDfilter && !iAODanalysis) {
465       //  ESD filter task configuration.
466       gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskESDFilterPWG4Train.C");
467       // switch on centrality make for PbPb
468       AliAnalysisTaskESDfilter *taskesdfilter = AddTaskESDFilterPWG4Train(kUseKinefilter); // carefull, if physics selection is enabled you may get not primary vertex pointer later on...
469       taskesdfilter->SetEnableFillAOD(!kFilterAOD);
470       taskesdfilter->DisableV0s();
471       taskesdfilter->DisableCascades();
472       taskesdfilter->DisableKinks();
473       taskesdfilter->DisablePmdClusters();
474       taskesdfilter->DisableCaloClusters();
475       taskesdfilter->DisableCells();
476
477       if(kIsMC){
478         mgr->RegisterExtraFile("pyxsec_hists.root");
479         if(kGridMergeExclude.Length())kGridMergeExclude += " ";
480         kGridMergeExclude += "pyxsec_hists.root";
481
482       }
483    }   
484
485    // AOD tags
486    if (kUseAODTags) {
487       AliAnalysisTaskTagCreator* tagTask = new AliAnalysisTaskTagCreator("AOD Tag Creator");
488       mgr->AddTask(tagTask);
489       AliAnalysisDataContainer *coutTags = mgr->CreateContainer("cTag",  TTree::Class(), 
490                                            AliAnalysisManager::kOutputContainer, "AOD.tag.root");
491       mgr->ConnectInput (tagTask, 0, mgr->GetCommonInputContainer());
492       mgr->ConnectOutput(tagTask, 1, coutTags);
493    }   
494
495    if (iPWG4FastEmbedding) {
496      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskFastEmbedding.C");
497      AliAnalysisTaskFastEmbedding *taskEmbedding = 0;
498      if(kFastEmbAODList.Length()) taskEmbedding = AddTaskFastEmbedding(kFastEmbAODList, 1);
499      else                         taskEmbedding = AddTaskFastEmbedding(kFastEmbeddingAOD, 0);
500      taskEmbedding->SetJetBranch("jetsAOD_UA104_B0_Filter00256_Cut01000");
501      // taskEmbedding->SetEvtSelecMode(AliAnalysisTaskFastEmbedding::kEventsAll);
502      // taskEmbedding->SetDebugLevel(10);
503    }
504
505     // Jet analysis
506    if (iJETAN) {
507       gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJets.C");
508       AliAnalysisTaskJets *taskjets = 0;
509       if(iJETAN&1){
510         /*
511         taskjets = AddTaskJets(kHighPtFilterMask); 
512         taskjets->SetName("StandardJets");
513         taskjets->SetNonStdBranch("");
514         */
515       }
516       if(iJETAN&2){
517         // Set only few jet finders  backgroudn subtraction w an wo 
518         
519         taskjets = AddTaskJets("AOD","UA1",0.4,kHighPtFilterMask,1.,0); // no background subtraction
520         if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
521         TString cTmp("");       
522         cTmp = taskjets->GetNonStdBranch();
523         if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
524
525         taskjets = AddTaskJets("AOD","UA1",0.4,kHighPtFilterMask,2.,0); // no background subtraction
526         if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
527         TString cTmp("");       
528         cTmp = taskjets->GetNonStdBranch();
529         if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
530
531
532         // STANDARD UA jet finders pT cut 1 GeV background mode 2 R = 0.4
533         if(kIsPbPb){
534           taskjets = AddTaskJets("AOD","UA1",0.4,kHighPtFilterMask,1.,2); // background subtraction
535           if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
536           cTmp = taskjets->GetNonStdBranch();
537           if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
538           taskjets = AddTaskJets("AOD","UA1",0.4,kHighPtFilterMask,2.,2); // background subtraction
539           if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
540           cTmp = taskjets->GetNonStdBranch();
541           if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
542         }
543
544
545
546         // SICONE 
547         /*
548         taskjets = AddTaskJets("AOD","SISCONE",0.4,kHighPtFilterMask,0.15,0); //no background subtraction to be done later....
549         if(kDeltaAODJetName.Length()>0)taskjets->SetNonStdOutputFile(kDeltaAODJetName.Data());
550         cTmp = taskjets->GetNonStdBranch();
551         if(cTmp.Length()>0)kJetSubtractBranches += Form("%s ",cTmp.Data());
552         if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
553         */
554         if(kUseAODMC){
555           // STANDARD UA jet finders pT cut 1 GeV background mode 2 R = 0.4
556           if(kIsPbPb){
557             taskjets = AddTaskJets("AODMC","UA1",0.4,kHighPtFilterMask,1.,2); // background subtraction
558             cTmp = taskjets->GetNonStdBranch();
559             if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
560             taskjets = AddTaskJets("AODMC2","UA1",0.4,kHighPtFilterMask,1.,2); // background subtraction
561             cTmp = taskjets->GetNonStdBranch();
562             if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
563           }
564           else{
565             taskjets = AddTaskJets("AODMC","UA1",0.4,kHighPtFilterMask,1.,0); // no background subtraction
566             cTmp = taskjets->GetNonStdBranch();
567             if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
568             taskjets = AddTaskJets("AODMC2","UA1",0.4,kHighPtFilterMask,1.,0); // no background subtraction
569             cTmp = taskjets->GetNonStdBranch();
570             if(cTmp.Length())kJetListSpectrum.Add(new TObjString(cTmp.Data()));
571           }
572         }
573         if(kDeltaAODJetName.Length()>0)mgr->RegisterExtraFile(kDeltaAODJetName.Data()); 
574       }
575       if (!taskjets) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJets cannot run for this train conditions - EXCLUDED");
576    }
577
578    // Jet analysis DEV
579    if (iJETANReader) {
580       gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetsReader.C");
581       AliAnalysisTaskJetsReader *taskjets = 0;
582       
583       if(iJETANReader&1) {
584       AliAnalysisDataContainer* cont_jet1 = AddJetExchangeContainer("jets_1");
585       taskjets = AddTaskJetsReader(cont_jet1,kHighPtFilterMask);
586       } 
587       
588     if(iJETANReader&2) {
589       AliAnalysisDataContainer* cont_jet1 = AddJetExchangeContainer("jets_1");
590       taskjets = AddTaskJetsReader(cont_jet1,"AOD",kHighPtFilterMask,0.15); 
591    
592       
593       AliAnalysisDataContainer* cont_jet2 = AddJetExchangeContainer("jets_2");
594       taskjets = AddTaskJetsReader(cont_jet2,"AOD", kHighPtFilterMask,1.);
595       
596      }
597
598       taskjets->GetJetReader()->GetReaderHeader()->SetIsHighMult(kIsPbPb); 
599     
600      
601   if ( !taskjets ) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetsReader cannot run for this train conditions - EXCLUDED");
602
603    }
604
605    if (iJETANFinder && iJETANReader) {
606       gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetsFinder.C");
607       AliAnalysisTaskJetsFinder *taskjetsFinder = 0;
608       
609       if(iJETANFinder&1) {
610       taskjetsFinder = AddTaskJetsFinder(cont_jet1);
611       }
612  
613      if(iJETANFinder&2) {
614       taskjetsFinder = AddTaskJetsFinder(cont_jet1,"UA1",0.4,0);     // UA1 no bkg subtraction (reader: jet_1)
615       taskjetsFinder = AddTaskJetsFinder(cont_jet1,"FASTJET",0.4,1); // FASTJET B1             (reader: jet_1)
616      
617       taskjetsFinder = AddTaskJetsFinder(cont_jet2,"FASTJET",0.4,0); // FASTJET B0             (reader: jet_2)
618      }
619
620  if ( !taskjetsFinder || !taskjets ) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetsFinder cannot run for this train conditions - EXCLUDED"); 
621
622    }
623
624    if (iPWG4FastEmbedding && iJETAN) {
625      AliAnalysisTaskJets *taskEmbJets = AddTaskJets("AODextra", "FASTJET", 0.4, kHighPtFilterMask);
626      taskEmbJets->ReadAODFromOutput();
627      kJetSubtractBranches_extra += Form("%s ", taskEmbJets->GetNonStdBranch());
628
629      taskEmbJets = AddTaskJets("AODextraonly", "FASTJET", 0.4, kHighPtFilterMask);
630      taskEmbJets->ReadAODFromOutput();
631     
632      taskEmbJets = AddTaskJets("AODextra", "UA1", 0.4, kHighPtFilterMask,1.,0);
633      taskEmbJets->ReadAODFromOutput();
634      taskEmbJets = AddTaskJets("AODextraonly", "UA1", 0.4, kHighPtFilterMask,1.,0);
635      taskEmbJets->ReadAODFromOutput();
636      taskEmbJets = AddTaskJets("AODextra", "UA1", 0.4, kHighPtFilterMask,1.,2);
637      taskEmbJets->ReadAODFromOutput();
638    }
639
640    if(iPWG4Cluster){
641      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetCluster.C");
642      AliAnalysisTaskJetCluster *taskCl = 0;
643      Float_t fCenUp = 0;
644      Float_t fCenLo = 0;
645      if(kIsPbPb&&!kIsMC){
646        fCenLo = 0;
647        fCenUp = 80;
648      }
649      if(iPWG4Cluster&1){
650
651        if(kIsPbPb){
652          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow,0); // this one is for the background and random jets, random cones with no skip
653          taskCl->SetBackgroundCalc(kTRUE);
654          taskCl->SetNRandomCones(1);
655          //      taskCl->SetDebugLevel(11);
656          taskCl->SetCentralityCut(fCenLo,fCenUp);
657
658          taskCl->SetJetTypes(1<<0|1<<2|1<<3);
659          kDefaultJetBackgroundBranch = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
660          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
661          kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),0)));
662          kJetListSpectrum.Add(new TObjString(Form("%sRandomCone_random",taskCl->GetJetOutputBranch())));
663
664          kJetSubtractBranches += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomConeSkip00");
665          kJetSubtractBranches += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomCone_random");
666
667          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),1.0,fTrackEtaWindow,fVertexWindow,0); // this one is for the background and random jets, random cones with no skip
668          taskCl->SetNRandomCones(1);
669          taskCl->SetBackgroundCalc(kTRUE);
670          taskCl->SetCentralityCut(fCenLo,fCenUp);
671          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
672
673          taskCl->SetJetTypes(1<<0|1<<2|1<<3);
674          kDefaultJetBackgroundBranchCut1 = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
675          kJetSubtractBranchesCut1 += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomConeSkip00");
676          kJetSubtractBranchesCut1 += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomCone_random");
677          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
678          kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),0)));
679          kJetListSpectrum.Add(new TObjString(Form("%sRandomCone_random",taskCl->GetJetOutputBranch())));
680
681          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),2.0,fTrackEtaWindow,fVertexWindow,0); // this one is for the background and random jets, random cones with no skip
682          taskCl->SetNRandomCones(1);
683          taskCl->SetBackgroundCalc(kTRUE);
684          taskCl->SetCentralityCut(fCenLo,fCenUp);
685          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
686
687          taskCl->SetJetTypes(1<<0|1<<2|1<<3);
688          kDefaultJetBackgroundBranchCut2 = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
689          kJetSubtractBranchesCut2 += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomConeSkip00");
690          kJetSubtractBranchesCut2 += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomCone_random");
691          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
692          kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),0)));
693          kJetListSpectrum.Add(new TObjString(Form("%sRandomCone_random",taskCl->GetJetOutputBranch())));
694
695
696          if (iPWG4FastEmbedding) {
697            AliAnalysisTaskJetCluster *taskClEmb = 0;
698            taskClEmb = AddTaskJetCluster("AODextra","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // this one is for the background and random jets
699            taskClEmb->SetBackgroundCalc(kTRUE);
700            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
701            if(iAODanalysis==2)taskClEmb->SetAODTrackInput(kTRUE);
702            kDefaultJetBackgroundBranch_extra = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskClEmb->GetJetOutputBranch());
703
704            taskClEmb = AddTaskJetCluster("AODextraonly","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // this one is for the background and random jets
705            taskClEmb->SetBackgroundCalc(kFALSE);
706            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
707            if(iAODanalysis==2)taskClEmb->SetAODTrackInput(kTRUE);
708            
709            taskClEmb = AddTaskJetCluster("AODextra","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow);
710            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
711            taskClEmb->SetBackgroundBranch(kDefaultJetBackgroundBranch_extra.Data());
712            kJetSubtractBranches_extra += Form("%s ",taskClEmb->GetJetOutputBranch());
713            if(iAODanalysis==2)taskClEmb->SetAODTrackInput(kTRUE);
714
715            taskClEmb = AddTaskJetCluster("AODextraonly","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow);
716            taskClEmb->SetCentralityCut(fCenLo,fCenUp);
717            if(iAODanalysis==2)taskClEmb->SetAODTrackInput(kTRUE);
718          }
719
720          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.2,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow,0); // this one is for the background and random jets
721          taskCl->SetNRandomCones(1);
722          taskCl->SetBackgroundCalc(kTRUE);
723          taskCl->SetCentralityCut(fCenLo,fCenUp);
724          taskCl->SetJetTypes(1<<0|1<<2|1<<3);
725          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
726          kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),0)));
727          kJetListSpectrum.Add(new TObjString(Form("%sRandomCone_random",taskCl->GetJetOutputBranch())));
728
729
730
731          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
732        }
733        else{
734          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.6,0,1,kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // this one is for the background jets
735          taskCl->SetBackgroundCalc(kTRUE);
736          kDefaultJetBackgroundBranch = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
737          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
738          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
739
740          taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1,kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); 
741          taskCl->SetBackgroundCalc(kTRUE);
742          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
743          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
744        } 
745
746        taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // thid id sldo got the random cones but avoiding the two leading jets
747        taskCl->SetCentralityCut(fCenLo,fCenUp);
748        if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());
749        taskCl->SetNRandomCones(1);
750        if(iFilterAnalysis==2){
751          taskCl->SetJetTriggerPtCut(kJetTriggerPtCut);
752        }
753        if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
754
755        taskCl->SetJetTypes(1<<0|1<<2); // only store the RC on full event with 2 removed
756        kDefaultJetBranch = taskCl->GetJetOutputBranch();
757        kJetSubtractBranches += Form("%s ",taskCl->GetJetOutputBranch());
758        //       kJetSubtractBranches += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomConeSkip02");
759        //       kJetSubtractBranches += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomCone_random");
760        kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
761        kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),2)));
762        //       kJetListSpectrum.Add(new TObjString(Form("%sRandomCone_random",taskCl->GetJetOutputBranch())));
763
764        taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),1.0,fTrackEtaWindow,fVertexWindow);
765        taskCl->SetNRandomCones(1);
766        taskCl->SetCentralityCut(fCenLo,fCenUp);
767        if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
768        if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranchCut1.Data());
769
770        taskCl->SetJetTypes(1<<0|1<<2); // only store the RC on full event with 2 removed
771        kJetSubtractBranchesCut1 += Form("%s ",taskCl->GetJetOutputBranch());
772        kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
773        kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),2)));
774
775
776        taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1,kDeltaAODJetName.Data(),2.0,fTrackEtaWindow,fVertexWindow);
777        taskCl->SetCentralityCut(fCenLo,fCenUp);
778        taskCl->SetNRandomCones(1);
779        if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
780        if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranchCut2.Data());
781        taskCl->SetJetTypes(1<<0|1<<2); // only store the RC on full event with 2 removed
782        kJetSubtractBranchesCut2 += Form("%s ",taskCl->GetJetOutputBranch());
783        kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
784        kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),2)));
785
786        // tmp track qa...
787        /*
788        taskCl = AddTaskJetCluster("AOD","",1<<8,iPhysicsSelectionFlag,"ANTIKT",0.4,2,1,kDeltaAODJetName.Data(),2.0);
789        taskCl->SetCentralityCut(fCenLo,fCenUp);
790        taskCl->SetFilterMask(1<<4|1<<8,1);
791        */
792        taskCl = AddTaskJetCluster("AOD","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.2,0,1,kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow,2);
793        taskCl->SetCentralityCut(fCenLo,fCenUp);
794        taskCl->SetNRandomCones(1);
795        if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
796        if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());
797
798        taskCl->SetJetTypes(1<<0|1<<2); 
799        kJetSubtractBranches += Form("%s ",taskCl->GetJetOutputBranch());
800        //       kJetSubtractBranches += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomConeSkip00");
801        //       kJetSubtractBranches += Form("%s%s ",taskCl->GetJetOutputBranch(),"RandomCone_random");
802        kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
803        kJetListSpectrum.Add(new TObjString(Form("%sRandomConeSkip%02d",taskCl->GetJetOutputBranch(),2)));
804
805
806        if(kUseAODMC){
807          if(kIsPbPb){
808            taskCl = AddTaskJetCluster("AODMC","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // this one is for the background and random jets
809            taskCl->SetBackgroundCalc(kTRUE);
810            kDefaultJetBackgroundBranchMC = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
811            if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);     
812          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
813
814          taskCl = AddTaskJetCluster("AODMC2","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fVertexWindow,fVertexWindow); // this one is for the background and random jets
815            taskCl->SetBackgroundCalc(kTRUE);
816            kDefaultJetBackgroundBranchMC2 = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch()); 
817            if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
818            kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
819          }
820          else{
821            taskCl = AddTaskJetCluster("AODMC","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.6,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // this one is for the background and random jets
822            taskCl->SetBackgroundCalc(kTRUE);
823            kDefaultJetBackgroundBranchMC = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch());
824          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));       
825
826          taskCl = AddTaskJetCluster("AODMC2","",kHighPtFilterMask,iPhysicsSelectionFlag,"KT",0.6,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); // this one is for the background and random jets
827            taskCl->SetBackgroundCalc(kTRUE);
828            kDefaultJetBackgroundBranchMC2 = Form("%s_%s",AliAODJetEventBackground::StdBranchName(),taskCl->GetJetOutputBranch()); 
829            if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
830            kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
831            // pp background calcs...
832          }
833          
834          taskCl = AddTaskJetCluster("AODMC","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow); 
835          if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranchMC.Data());   
836          kDefaultJetBranchMC = taskCl->GetJetOutputBranch();
837          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
838          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
839
840          taskCl = AddTaskJetCluster("AODMC2","",kHighPtFilterMask,iPhysicsSelectionFlag,"ANTIKT",0.4,0,1, kDeltaAODJetName.Data(),0.15,fTrackEtaWindow,fVertexWindow);
841          if(kIsPbPb)taskCl->SetBackgroundBranch(kDefaultJetBackgroundBranchMC2.Data());  
842          kDefaultJetBranchMC2 = taskCl->GetJetOutputBranch();
843          if(iAODanalysis==2)taskCl->SetAODTrackInput(kTRUE);
844          kJetListSpectrum.Add(new TObjString(taskCl->GetJetOutputBranch()));
845        }
846        
847        
848        if (!taskCl) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskCluster cannot run for this train conditions - EXCLUDED");
849      }
850    }
851
852
853    if(iJETSUBTRACT&&kJetSubtractBranches.Length()){
854      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetBackgroundSubtract.C");
855      AliAnalysisTaskJetBackgroundSubtract *taskSubtract = 0;
856      if(kJetSubtractBranches.Length()){
857
858
859
860
861        for(int iB = 1;iB<3;iB++){
862          if(iB>2)continue;
863          taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranches,iB,kJetSubtractMask1.Data(),kJetSubtractMask2.Data());
864          taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranch.Data());         taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
865          if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
866          taskSubtract->SetKeepJets(kTRUE);
867          TString cTmp;       
868          TObjArray *objArr = kJetSubtractBranches.Tokenize(" ");
869          for(int iJB = 0;iJB<objArr->GetEntries();iJB++){
870            TObjString *ostr = (TObjString*)objArr->At(iJB);
871            cTmp = ostr->GetString().Data();
872            cTmp.ReplaceAll(kJetSubtractMask1.Data(),Form(kJetSubtractMask2.Data(),iB));
873            kJetListSpectrum.Add(new TObjString(cTmp.Data()));
874          }
875          
876          //     taskSubtract->SetDebugLevel(3);
877          if(iB==2){
878            if(kJetSubtractBranches.Contains(kDefaultJetBranch.Data())&&kIsPbPb){
879              kDefaultJetBranch.ReplaceAll(taskSubtract->GetToReplace(),Form(taskSubtract->GetReplacementMask(),taskSubtract->GetSubtractionMethod()));
880            }
881          }
882          
883        }
884
885        //
886        // cut1
887        Int_t iB = 2;
888        taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranchesCut1,iB,kJetSubtractMask1.Data(),kJetSubtractMask2.Data(),"Cut1000");
889        taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranchCut1.Data());               
890        taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
891        if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
892
893        objArr = kJetSubtractBranchesCut1.Tokenize(" ");
894        for(int iJB = 0;iJB<objArr->GetEntries();iJB++){
895          TObjString *ostr = (TObjString*)objArr->At(iJB);
896          cTmp = ostr->GetString().Data();
897          cTmp.ReplaceAll(kJetSubtractMask1.Data(),Form(kJetSubtractMask2.Data(),iB));
898          kJetListSpectrum.Add(new TObjString(cTmp.Data()));
899        }
900
901        taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranchesCut2,iB,kJetSubtractMask1.Data(),kJetSubtractMask2.Data(),"Cut2000");
902        taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranchCut2.Data());               
903        taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
904        if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
905
906        objArr = kJetSubtractBranchesCut2.Tokenize(" ");
907        for(int iJB = 0;iJB<objArr->GetEntries();iJB++){
908          TObjString *ostr = (TObjString*)objArr->At(iJB);
909          cTmp = ostr->GetString().Data();
910          cTmp.ReplaceAll(kJetSubtractMask1.Data(),Form(kJetSubtractMask2.Data(),iB));
911          kJetListSpectrum.Add(new TObjString(cTmp.Data()));
912        }
913
914      }
915      if(kJetSubtractBranches_extra.Length()){
916        taskSubtract = AddTaskJetBackgroundSubtract(kJetSubtractBranches_extra,2,kJetSubtractMask1.Data(),kJetSubtractMask2.Data(),"extra");
917        taskSubtract->SetBackgroundBranch(kDefaultJetBackgroundBranch_extra.Data());
918        taskSubtract->SelectCollisionCandidates(iPhysicsSelectionFlag);
919        //taskSubtract->SetDebugLevel(3);
920        if(kDeltaAODJetName.Length()>0)taskSubtract->SetNonStdOutputFile(kDeltaAODJetName.Data());
921        if(kJetSubtractBranches_extra.Contains(kDefaultJetBranch.Data())){
922          kDefaultJetBranch.ReplaceAll(taskSubtract->GetToReplace(),Form(taskSubtract->GetReplacementMask(),taskSubtract->GetSubtractionMethod()));
923        }
924      }
925      if (!taskSubtract) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetBackgroundSubtrac cannot run for this train conditions - EXCLUDED");     
926    }
927
928    if (iDIJETAN) {
929       gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskDiJets.C");
930       AliAnalysisTaskDiJets *taskdijets = 0;
931       if(iDIJETAN&1)taskdijets = AddTaskDiJets(); 
932       if (!taskdijets) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJets cannot run for this train conditions - EXCLUDED");
933       if(iDIJETAN&2){
934         taskdijets = AddTaskDiJets("jetsAOD_CDF07"); 
935         taskdijets = AddTaskDiJets("jetsAOD_DA07"); 
936         taskdijets = AddTaskDiJets("jetsAOD_FASTJET07"); 
937         taskdijets = AddTaskDiJets("jetsAOD_FASTKT07"); 
938         taskdijets = AddTaskDiJets("jetsAOD_SISCONE07"); 
939         taskdijets = AddTaskDiJets("jetsAOD_UA107");
940       }
941    }
942
943    if(iPWGPPQASym){
944      gROOT->LoadMacro("$ALICE_ROOT/PWGPP/PilotTrain/AddTaskQAsym.C");
945      AliAnalysisTaskQASym *taskQASym = AddTaskQAsym(-1);
946      if (!taskQASym) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQASym cannot run for this train conditions - EXCLUDED");
947    }
948
949
950
951    if(iPWG4TmpSourceSara){
952      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskEta.C");
953      AliAnalysisTaskEta *taskEta = AddTaskEta();
954      if (!taskEta) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskEta cannot run for this train conditions - EXCLUDED");
955    }
956
957
958    if(iPWG4JetServices){
959      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetServices.C");
960      AliAnalysisTaskJetServices *taskjetServ = 0;
961      taskjetServ = AddTaskJetServices("/Users/kleinb/Dropbox/SharedJets/Christian/Files/PWG4_JetTasksOutput_110818a.root");
962      if (!taskjetServ) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetServices cannot run for this train conditions - EXCLUDED");
963      if(kGridRunRange[0]>0)taskjetServ->SetRunRange(kGridRunRange[0],kGridRunRange[1]);
964      else taskjetServ->SetRunRange(110000,160000);
965      taskjetServ->SetMCData(kIsMC);
966      taskjetServ->SetUsePhysicsSelection((Bool_t)iPhysicsSelection);
967      taskjetServ->SetPhysicsSelectionFlag(iPhysicsSelectionFlag); // 
968      taskjetServ->SetNonStdFile(kDeltaAODJetName.Data());
969      taskjetServ->SetTrackEtaWindow(fTrackEtaWindow);
970      taskjetServ->SetZVertexCut(fVertexWindow);
971      taskjetServ->SetFilterMask(kHighPtFilterMask);
972
973      if(kIsPbPb)taskjetServ->SetCollisionType(AliAnalysisTaskJetServices::kPbPb);
974      else taskjetServ->SetCollisionType(AliAnalysisTaskJetServices::kPP);
975      if(kIsPbPb){
976        if(kDeltaAODJetName.Length()>0&&kFilterAOD)taskjetServ->SetFilterAODCollisions(kTRUE);
977        //       else if(iAODanalysis)taskjetServ->SetFilterAODCollisions(kTRUE);
978        //       taskjetServ->SetDebugLevel(3);
979      }
980      if(iAODanalysis){
981        //  
982        taskjetServ->SetAODInput(kTRUE);
983      }
984    }
985
986    if(iPWG4JetSpectrum){
987      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetSpectrum2.C");
988      AliAnalysisTaskJetSpectrum2 *taskjetSpectrum = 0;
989      TString bkgClusters = kDefaultJetBackgroundBranch.Data(); 
990      bkgClusters.ReplaceAll(Form("%s_",AliAODJetEventBackground::StdBranchName()),"");
991      Printf("############# Possible jet branches ###################");
992      for(int iJF = 0;iJF < kJetListSpectrum.GetSize();iJF++){
993        TObjString *objStr = (TObjString*)kJetListSpectrum.At(iJF);
994        Printf("%3d: %s",iJF+1,objStr->GetString().Data());
995      }
996
997      //     Printf("Type q to exit");if(getchar()=='q')return;
998      if(iPWG4JetSpectrum&1){
999        if(kIsPbPb){
1000          for(int iJF = 0;iJF < kJetListSpectrum.GetSize();iJF++){
1001            Long64_t value = kJetMapSpectrum(iJF+1);
1002            Printf("iJF: %d value: %d", iJF+1,(Int_t)value);
1003            if(value==0)continue;
1004            TObjString *objStr = (TObjString*)kJetListSpectrum.At(iJF);
1005            TString bName1 = objStr->GetString().Data();
1006            TString bName2[3];
1007            
1008            TObjString *objStrBkg = (TObjString*)kJetListSpectrum.At(iJF);
1009            TString bBkgName1(""); 
1010            TString bBkgName2[3];
1011            
1012            Long64_t valueBkg1 = kJetBackMapSpectrum(iJF+1);
1013            if(valueBkg1>0){
1014              TObjString *objStrBkg = (TObjString*)kJetListSpectrum.At(valueBkg1-1);
1015              bBkgName1 = objStrBkg->GetString().Data();
1016            }
1017            Int_t iPartner = 0;
1018            if(value>0){
1019              Int_t iJF2 = -1; 
1020              for(int i = 0;i<3;i++){
1021                iJF2 = value/kJetMapOffset[i]-1;
1022                value = value%kJetMapOffset[i];
1023                Printf("%d %d", iJF2+1,(Int_t)value);
1024                if(iJF2>=0&&iJF2<kJetListSpectrum.GetSize()){
1025                  TObjString *objStr2 = (TObjString*)kJetListSpectrum.At(iJF2);
1026                  bName2[iPartner] = objStr2->GetString().Data();
1027                  Long64_t valueBkg2 = kJetBackMapSpectrum(iJF2+1);
1028                  if(valueBkg2>0){
1029                    TObjString *objStrBkg2 = (TObjString*)kJetListSpectrum.At(valueBkg2-1);
1030                    bBkgName2[iPartner] = objStrBkg2->GetString().Data();
1031                  }
1032                  iPartner++;
1033                }
1034              }
1035            }
1036            
1037            
1038            // loop over all centralities
1039            for(int ic = 0;ic<5;ic++){
1040              if(ic!=0)continue;
1041              Bool_t bDone = kFALSE;
1042              for(int i = 0;i<TMath::Max(iPartner,1);i++){
1043                if(bName2[i].Length()){
1044                  taskjetSpectrum = AddTaskJetSpectrum2(bName1.Data(),bName2[i].Data(),kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,ic);
1045                  bDone = kTRUE; 
1046                }
1047                else{
1048                  if(!bDone){
1049                    taskjetSpectrum = AddTaskJetSpectrum2(bName1.Data(),bName2[i].Data(),kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,ic);
1050                    bDone = kTRUE; 
1051                  }
1052                  else{
1053                    continue;
1054                  }
1055                }
1056                Printf("%s/%s %s/%s",bName1.Data(),bBkgName1.Data(),bName2[i].Data(),bBkgName2[i].Data());
1057
1058                // setting all the other things...
1059                taskjetSpectrum->SetTrackEtaWindow(fTrackEtaWindow);
1060                taskjetSpectrum->SetJetEtaWindow(fJetEtaWindow);
1061
1062                // negative values do not fill the track histos
1063                taskjetSpectrum->SetFlagJetType(AliAnalysisTaskJetSpectrum2::kJetGenFull,-1);
1064                taskjetSpectrum->SetFlagJetType(AliAnalysisTaskJetSpectrum2::kJetGen,-1);              
1065                if(!bName1.Contains("ANTIKT")||bName1.Contains("Cone")){
1066                  taskjetSpectrum->SetFlagJetType(AliAnalysisTaskJetSpectrum2::kJetRecFull,-1);
1067                  taskjetSpectrum->SetFlagJetType(AliAnalysisTaskJetSpectrum2::kJetRec,-1);            
1068                }
1069
1070
1071                if(bName2[i].Length()==0){
1072                  taskjetSpectrum->SetFlagJetType(AliAnalysisTaskJetSpectrum2::kJetGenFull,0);
1073                  taskjetSpectrum->SetFlagJetType(AliAnalysisTaskJetSpectrum2::kJetGen,0);
1074                }
1075                if(iAODanalysis==1){
1076                  taskjetSpectrum->SetAODJetInput(kTRUE);
1077                  taskjetSpectrum->SetAODTrackInput(kTRUE);
1078                }
1079                else if (iAODanalysis==2){
1080                  taskjetSpectrum->SetAODTrackInput(kTRUE);
1081                  taskjetSpectrum->SetAODJetInput(kFALSE);
1082                }
1083                //              taskjetSpectrum->SetDebugLevel(11);
1084                taskjetSpectrum->SetBranchBkgRec(bBkgName1.Data());
1085                taskjetSpectrum->SetBranchBkgGen(bBkgName2[i].Data());
1086              } 
1087            }
1088          }
1089        }
1090        else{ // ! PbPb
1091          Int_t i = 0;
1092
1093          taskjetSpectrum = AddTaskJetSpectrum2(kDefaultJetBranch.Data(),
1094                                                "",kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,i);
1095          
1096
1097          
1098          if(kDefaultJetBranchMC.Length()){
1099            taskjetSpectrum = AddTaskJetSpectrum2(kDefaultJetBranch.Data(),
1100                                                kDefaultJetBranchMC.Data(),kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,i);
1101            //      taskjetSpectrum->SetMinJetPt(10);
1102            taskjetSpectrum->SetTrackEtaWindow(fTrackEtaWindow);
1103            taskjetSpectrum->SetJetEtaWindow(fJetEtaWindow);
1104            taskjetSpectrum->SetBranchBkgRec(bkgClusters.Data());
1105            taskjetSpectrum->SetBranchBkgGen(bkgClusters.Data());
1106            if(iAODanalysis)SetAODInput(taskjetSpectrum);
1107          }
1108          if(kDefaultJetBranchMC2.Length()){
1109            taskjetSpectrum = AddTaskJetSpectrum2(kDefaultJetBranch.Data(),
1110                                                  kDefaultJetBranchMC2.Data(),kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,i);
1111            //      taskjetSpectrum->SetMinJetPt(10);
1112            taskjetSpectrum->SetTrackEtaWindow(fTrackEtaWindow);
1113            taskjetSpectrum->SetJetEtaWindow(fJetEtaWindow);
1114            taskjetSpectrum->SetBranchBkgRec(bkgClusters.Data());
1115            taskjetSpectrum->SetBranchBkgGen(bkgClusters.Data());
1116            if(iAODanalysis)SetAODInput(taskjetSpectrum);
1117          }
1118
1119          /*
1120          TString tmp2(kDefaultJetBranch.Data());
1121          tmp2.ReplaceAll(Form(kJetSubtractMask2.Data(),0),Form(kJetSubtractMask2.Data(),2));
1122          taskjetSpectrum = AddTaskJetSpectrum2(tmp2.Data(),kDefaultJetBranch.Data(),kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,i);
1123          //      taskjetSpectrum->SetDebugLevel(3);
1124          //        taskjetSpectrum->SetMinJetPt(10);
1125          taskjetSpectrum->SetBranchBkgRec(bkgClusters.Data());
1126          taskjetSpectrum->SetBranchBkgGen(bkgClusters.Data());
1127          taskjetSpectrum->SetTrackEtaWindow(0.8);
1128          taskjetSpectrum->SetJetEtaWindow(0.4);
1129
1130          // check the old subtracted vs. the new subtracted
1131          TString tmp3(kDefaultJetBranch.Data());
1132          tmp3.ReplaceAll(Form(kJetSubtractMask2.Data(),0),Form(kJetSubtractMask2.Data(),3));
1133          taskjetSpectrum = AddTaskJetSpectrum2(tmp3.Data(),kDefaultJetBranch.Data(),kDeltaAODJetName.Data(),kHighPtFilterMask,AliVEvent::kMB,0,i);
1134          //      taskjetSpectrum->SetDebugLevel(3);
1135          //        taskjetSpectrum->SetMinJetPt(10);
1136          taskjetSpectrum->SetBranchBkgRec(bkgClusters.Data());
1137          taskjetSpectrum->SetBranchBkgGen(bkgClusters.Data());
1138          taskjetSpectrum->SetTrackEtaWindow(0.8);
1139          taskjetSpectrum->SetJetEtaWindow(0.4);
1140          if(iAODanalysis)SetAODInput(taskjetSpectrum);
1141          */
1142        }
1143        if (!taskjetSpectrum) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetSpectrum2 cannot run for this train conditions - EXCLUDED");
1144      }
1145    }
1146    AliAnalysisManager::SetCommonFileName("PWG4_Fragmentation.root");
1147    if(iPWG4Fragmentation){
1148      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskFragmentationFunction.C");
1149        AliAnalysisTaskFragmentationFunction *taskFrag = 0;
1150        if(kUseAODMC){
1151
1152        }
1153        else{
1154
1155
1156          for(int ic = 1;ic < 5;ic++){
1157            // Anti-kT
1158            taskFrag = AddTaskFragmentationFunction(1<<23,kHighPtFilterMask, ic);
1159            if(kDeltaAODJetName.Length()>0)taskFrag->SetNonStdFile(kDeltaAODJetName.Data());
1160            if(iAODanalysis==2)taskFrag->UseAODInputJets(kFALSE);
1161
1162            // UA1
1163            taskFrag = AddTaskFragmentationFunction(1<<0,kHighPtFilterMask, ic); 
1164            if(kDeltaAODJetName.Length()>0)taskFrag->SetNonStdFile(kDeltaAODJetName.Data());
1165            if(iAODanalysis==2)taskFrag->UseAODInputJets(kFALSE);
1166
1167          // SISCONE 
1168            if(ic==1){
1169              /*
1170                taskFrag = AddTaskFragmentationFunction(1<<28,kHighPtFilterMask, ic);
1171                taskFrag = AddTaskFragmentationFunction(1<<29,kHighPtFilterMask, ic);
1172                taskFrag = AddTaskFragmentationFunction(1<<30,kHighPtFilterMask, ic);
1173              */
1174
1175
1176
1177              // Anti-kT B2 - B3
1178              if(!iAODanalysis==1){
1179                taskFrag = AddTaskFragmentationFunction(1<<26,kHighPtFilterMask, ic);
1180                if(kDeltaAODJetName.Length()>0)taskFrag->SetNonStdFile(kDeltaAODJetName.Data());
1181                if(iAODanalysis==2)taskFrag->UseAODInputJets(kFALSE);
1182                
1183                taskFrag = AddTaskFragmentationFunction(1<<27,kHighPtFilterMask, ic);
1184                if(kDeltaAODJetName.Length()>0)taskFrag->SetNonStdFile(kDeltaAODJetName.Data());
1185                if(iAODanalysis==2)taskFrag->UseAODInputJets(kFALSE);
1186              }
1187            }
1188
1189          } 
1190
1191
1192        }
1193        if (!taskFrag) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskFragmentationFunction cannot run for this train conditions - EXCLUDED");
1194    }
1195
1196    if(iPWG4JetChem){
1197      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetChem.C");
1198      AliAnalysisTask *taskChem = AddTaskJetChem(kHighPtFilterMask);
1199      if (!taskChem) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetChem cannot run for this train conditions - EXCLUDED");
1200    }
1201
1202    if (iPWG4JetResponse) {
1203      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJetResponse.C");
1204      AliAnalysisTask *taskJetResponse = 0;
1205
1206      if(iJETAN){
1207         taskJetResponse = AddTaskJetResponse("jets", "FASTJET", 0.4, kHighPtFilterMask, 0.15, 0);
1208         taskJetResponse = AddTaskJetResponse("jets", "FASTJET", 0.4, kHighPtFilterMask, 0.15, 1);
1209
1210         taskJetResponse = AddTaskJetResponse("jets", "UA1", 0.4, kHighPtFilterMask, 1., 0);
1211         taskJetResponse = AddTaskJetResponse("jets", "UA1", 0.4, kHighPtFilterMask, 1., 2);
1212      }
1213      if(iPWG4Cluster){
1214         taskJetResponse = AddTaskJetResponse("clusters", "ANTIKT", 0.4, kHighPtFilterMask, 0.15, 0);
1215         taskJetResponse = AddTaskJetResponse("clusters", "ANTIKT", 0.4, kHighPtFilterMask, 0.15, 1);
1216      }
1217      if (!taskJetResponse) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskJetResponse cannot run for this train conditions - EXCLUDED");
1218
1219    }
1220
1221    if(iPWG4JCORRAN){
1222      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskJCORRANTask.C");
1223      AliJCORRANTask* corran = AddTaskJCORRAN(kDeltaAODJCORRANName.Data(),0);
1224      if(!corran)::Warning("AnalysisTrainPWG4Jets", "AliJCORRANTask cannot run for this train conditions - EXCLUDED");
1225      else{
1226        if(kDeltaAODJCORRANName.Length()>0)mgr->RegisterExtraFile(kDeltaAODJCORRANName.Data()); 
1227      }
1228    }
1229
1230    if(iPWG4UE){
1231      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskUE.C");
1232      AliAnalysisTaskUE *taskUE = 0;
1233      if(iPWG4UE&1)taskUE = AddTaskUE(); 
1234      if(iPWG4UE&2){
1235        taskUE  =AddTaskUE("jetsAOD_CDF04","CDF", "LJ", "TRANSV","MSP"); //finder not yet in train
1236        //       taskUE  =AddTaskUE("jetsAOD_CDF07","CDF", "LJ", "TRANSV","MSP");
1237        taskUE  =AddTaskUE("jetsAOD_SISCONE04","CDF", "LJ", "TRANSV","MSP");
1238        //       taskUE  =AddTaskUE("jetsAOD_SISCONE07","CDF", "LJ", "TRANSV","MSP"); //finder not yet in train
1239        taskUE  =AddTaskUE("jetsAOD_ICDF","CDF","LJ","TRANSV","MSP");
1240        taskUE  =AddTaskUE("jetsAOD_FASTKT04","CDF", "LJ", "TRANSV","MSP");
1241        //       taskUE  =AddTaskUE("jetsAOD_FASTKT07","CDF", "LJ", "TRANSV","MSP"); //finder not yet in train
1242        taskUE  =AddTaskUE("jetsAOD_NONE","CDF", "MP_eta05", "TRANSV","MSP");
1243        taskUE  =AddTaskUE("jetsAOD_NONE","CDF", "MP_eta09", "TRANSV","MSP");
1244      }
1245
1246      if (!taskUE) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskUE cannot run for this train conditions - EXCLUDED");
1247    }
1248
1249    if(iPWG4LeadingUE){
1250      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskLeadingTrackUE.C");
1251      AliAnalysisTaskLeadingTrackUE *taskLeadingUE = AddTaskLeadingTrackUE(kUseMC);
1252      if (!taskLeadingUE) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTasLeadingTrackkUE cannot run for this train conditions - EXCLUDED");
1253      //     taskLeadingUE->SetFilterBit(64);
1254    }
1255
1256
1257    if(iPWG4CorrectionsUE){
1258      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskCorrectionsUE.C");
1259      AliAnalysisTaskCorrectionsUE *taskCorrectionsUE = 0;
1260      if(iPWG4CorrectionsUE&1)taskCorrectionsUE = AddTaskCorrectionsUE("jetsAOD_NONE","CDF","MP_eta05","TRANSV","MSP",kFALSE);
1261      if (!taskCorrectionsUE) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskCorrectionsUE cannot run for this train conditions - EXCLUDED");
1262    }
1263
1264    if(iPWG4ThreeJets){
1265      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskThreeJets.C");
1266      AliAnalysisTaskThreeJets *taskThree = AddTaskThreeJets();
1267      if(!taskThree)::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskThreets cannot run for this train conditions - EXCLUDED");
1268    }
1269    if(iPWG4QGSep){
1270      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskQGSep.C");
1271      AliAnalysisTaskQGSep *taskQGSep = AddTaskQGSep(kUseMC,iAODanalysis);
1272      if(!taskQGSep)::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQGSep cannot run for this train conditions - EXCLUDED");
1273    }
1274   
1275
1276    if(iPWG4Minijet){
1277      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskMinijet.C");
1278      AliAnalysisTaskMinijet *taskMini = AddTaskMinijet(-1,"esd",kUseMC,kGridDataSet);
1279      // if we ha highmult trigger add another task
1280      if(!taskMini)::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskMinjet cannot run for this train conditions - EXCLUDED");
1281    }
1282
1283    AliAnalysisManager::SetCommonFileName("PWG4_HighPtQA.root");
1284    if(iPWG4PtQAMC){
1285      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskPWG4HighPtQAMC.C");
1286      AliPWG4HighPtQAMC *taskQAMC = 0;
1287      if(kUseMC){
1288        if(iPWG4PtQAMC&1){
1289          taskQAMC = AddTaskPWG4HighPtQAMCAll(kGridDataSet.Data());
1290        }
1291      }
1292      if (!taskQAMC) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQAMC cannot run for this train conditions - EXCLUDED");
1293    }
1294
1295    if(iPWG4PtTrackQA){
1296      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskPWG4HighPtTrackQA.C");
1297      if(iPWG4PtTrackQA&2)AddTaskPWG4HighPtTrackQAAll(kGridDataSet.Data(),kIsPbPb,iAODanalysis);
1298      else AddTaskPWG4HighPtTrackQAAllReduced(kGridDataSet.Data(),kIsPbPb,iAODanalysis);
1299    }
1300
1301    if(iPWG4PtQATPC){
1302      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskPWG4HighPtQATPConly.C");
1303      AliPWG4HighPtQATPConly *taskQATPC = 0;
1304      if(iPWG4PtQATPC&1)taskQATPC = AddTaskPWG4HighPtQATPConly(kGridDataSet.Data(),1);
1305      if(iPWG4PtQATPC&2)taskQATPC = AddTaskPWG4HighPtQATPConly(kGridDataSet.Data(),2);
1306
1307  if (!taskQATPC) ::Warning("AnalysisTrainPWG4Jets", "AliAnalysisTaskQATPC cannot run for this train conditions - EXCLUDED");
1308    }
1309
1310    if(iPWG4Cosmics){
1311      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskPWG4CosmicCandidates.C");
1312
1313      AliPWG4CosmicCandidates *taskPWG4CosmicCandidates = AddTaskPWG4CosmicCandidates(0);
1314      taskPWG4CosmicCandidates = AddTaskPWG4CosmicCandidates(1);
1315
1316      if (!taskPWG4CosmicCandidates) ::Warning("AnalysisTrainPWG4Jets", "AddTaskPWG4CosmicCandidates cannot run for this train conditions - EXCLUDED");
1317    }
1318
1319
1320    if(iPWG4PtSpectra){
1321      gROOT->LoadMacro("$ALICE_ROOT/PWGJE/macros/AddTaskPWG4HighPtSpectra.C");
1322      AddTaskPWG4HighPtSpectraAll(kGridDataSet.Data(),kIsPbPb,iAODanalysis);
1323    }
1324    
1325    //==========================================================================
1326    // FOR THE REST OF THE TASKS THE MACRO AddTaskXXX() is not yet implemented/
1327    // Run the analysis
1328    //    
1329    if (kPluginUse) {
1330       AliAnalysisGrid *alienHandler = CreateAlienHandler(plugin_mode);
1331       AliAnalysisManager::GetAnalysisManager()->SetGridHandler(alienHandler);
1332    }
1333    
1334    if (mgr->InitAnalysis()) {
1335      mgr->PrintStatus();
1336      // if (kSaveTrain || strlen(config_file)) gSystem->ChangeDirectory(kTrainName);
1337      if (!strcmp(plugin_mode,"submit")&&smode=="GRID"){
1338        TString alien_workdir = gGrid->GetHomeDirectory();
1339        if (iAODanalysis) alien_workdir += "analysisAOD";
1340        else              alien_workdir += "analysisESD";
1341        if(kGridDataSet.Length()>0)alien_workdir += Form("/%s%s",kGridDataSet.Data(),kGridExtraAliendirLevel.Data());
1342        AliAnalysisAlien *gridhandler = (AliAnalysisAlien*)mgr->GetGridHandler();
1343        printf("=== AnalysisTrainPWG4Jets:: Registering jdl in the work directory alien://%s/%s, should be done by the manager! ===\n",
1344               alien_workdir.Data(),gridhandler->GetGridOutputDir());
1345
1346        TString dest;
1347        dest = Form("%s/%s/%s.jdl",alien_workdir.Data(),gridhandler->GetGridOutputDir(),kTrainName.Data());
1348        if(AliAnalysisAlien::FileExists(dest.Data())){
1349          Printf("%s exist on grid removing...",dest.Data());
1350          gGrid->Rm(dest.Data());
1351        }
1352        Printf("%s copy ...",dest.Data());
1353        TFile::Cp(Form("file:%s.jdl",kTrainName.Data()),Form("alien://%s",dest.Data()));
1354
1355
1356        TString dest;
1357        dest = Form("%s/%s/%s_merge.jdl",alien_workdir.Data(),gridhandler->GetGridOutputDir(),kTrainName.Data());
1358        if(AliAnalysisAlien::FileExists(dest.Data())){
1359          Printf("%s exist on grid removing...",dest.Data());
1360          gGrid->Rm(dest.Data());
1361        }
1362        Printf("%s copy ...",dest.Data());
1363        TFile::Cp(Form("file:%s_merge.jdl",kTrainName.Data()),Form("alien://%s",dest.Data()));
1364        
1365        dest = Form("%s/%s/%s_merge_final.jdl",alien_workdir.Data(),gridhandler->GetGridOutputDir(),kTrainName.Data());
1366        if(AliAnalysisAlien::FileExists(dest.Data())){
1367          Printf("%s exist on grid removing...",dest.Data());
1368          gGrid->Rm(dest.Data());
1369        }
1370        Printf("%s copy ...",dest.Data());
1371        TFile::Cp(Form("file:%s_merge.jdl",kTrainName.Data()),Form("alien://%s",dest.Data()));
1372      }
1373      AliLog::SetGlobalLogLevel(AliLog::kError);
1374      if((kUseSysInfo>0&&smode=="LOCAL")||!strcmp(plugin_mode, "test")){
1375        TFile * fM = TFile::Open("manager_local.root","RECREATE");
1376        mgr->Write();
1377        fM->Close();
1378      }
1379      
1380      // grmpf, aliroot error handler overwrites root
1381      gErrorIgnoreLevel = kErrorIgnoreLevel;
1382      if(gErrorIgnoreLevel>3000) AliLog::SetGlobalLogLevel(AliLog::kFatal);
1383      StartAnalysis(smode, chain);
1384      if((kUseSysInfo>0&&smode=="LOCAL")||!strcmp(plugin_mode, "test")){
1385        for(int i = 0;i < mgr->GetTopTasks()->GetEntries();i++){
1386          mgr->ProfileTask(i);
1387        }
1388      }
1389      if (!strcmp(plugin_mode, "offline")&&smode=="GRID"){
1390        // Offline mode path files
1391        //       PatchJDL();
1392        //       PatchAnalysisMacro();
1393      }
1394
1395      if (kSaveTrain && smode=="GRID") {
1396        AliAnalysisAlien *gridhandler = (AliAnalysisAlien*)mgr->GetGridHandler();
1397        TString alien_workdir = gGrid->GetHomeDirectory();
1398        if (iAODanalysis) alien_workdir += "analysisAOD";
1399        else              alien_workdir += "analysisESD";
1400        if(kGridDataSet.Length()>0)alien_workdir += Form("/%s%s",kGridDataSet.Data(),kGridExtraAliendirLevel.Data());
1401        //     kGridOutdir = gridhandler->GetGridOutputDir();
1402        printf("=== Registering ConfigTrain.C in the work directory <%s> ===\n",
1403                 alien_workdir.Data());
1404        if (AliAnalysisAlien::FileExists(Form("%s/%sConfig.C", alien_workdir.Data(), kTrainName.Data())))
1405          gGrid->Rm(Form("%s/%sConfig.C", alien_workdir.Data(), kTrainName.Data()));
1406        if (strcmp(plugin_mode, "test"))
1407          TFile::Cp(Form("file:%sConfig.C",kTrainName.Data()), Form("alien://%s/%sConfig.C", alien_workdir.Data(), kTrainName.Data()));
1408      }
1409    }
1410 }
1411
1412 //______________________________________________________________________________
1413 void StartAnalysis(const char *mode, TChain *chain) {
1414 // Start analysis.
1415    Int_t imode = -1;
1416    AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
1417    if (!strcmp(mode, "LOCAL")) imode = 0;
1418    if (!strcmp(mode, "PROOF")) imode = 1;
1419    if (!strcmp(mode, "GRID"))  imode = 2;
1420    switch (imode) {
1421       case 0:
1422          if (!chain) {
1423             ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "Cannot create the chain");
1424             return;
1425          }   
1426          mgr->StartAnalysis(mode, chain,kNumberOfEvents);
1427          return;
1428       case 1:
1429          if (!kProofDataSet.Length()) {
1430             ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "kProofDataSet is empty");
1431             return;
1432          }   
1433          mgr->StartAnalysis(mode, kProofDataSet, kProofEvents,kProofOffset);
1434          return;
1435       case 2:
1436          if (kPluginUse) {
1437             if (!mgr->GetGridHandler()) {
1438                ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "Grid plugin not initialized");
1439                return;
1440             }   
1441             mgr->StartAnalysis("grid",chain,kNumberOfEvents);
1442          } else {
1443             if (!chain) {
1444                ::Error("AnalysisTrainPWG4Jets.C::StartAnalysis", "Cannot create the chain");
1445                return;
1446             }   
1447             //            mgr->StartAnalysis(mode, chain);
1448             mgr->StartAnalysis(mode, chain,kNumberOfEvents);
1449          }   
1450          return;
1451    }      
1452 }          
1453     
1454 //______________________________________________________________________________
1455 void CheckModuleFlags(const char *mode) {
1456 // Checks selected modules and insure compatibility
1457    Int_t imode = -1;
1458    if (!strcmp(mode, "LOCAL")) imode = 0;
1459    if (!strcmp(mode, "PROOF")) imode = 1;
1460    if (!strcmp(mode, "GRID"))  imode = 2;
1461
1462
1463    if (kUseCPAR) {
1464      kPluginAliRootVersion    = ""; // NO aliroot if we use CPAR
1465    }
1466
1467    if (imode==1) {
1468       if (!kUsePAR) {
1469          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PAR files enabled due to PROOF analysis");
1470          kUsePAR = kTRUE;
1471       }   
1472    }  
1473    if (imode != 2) {
1474       ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "AliEn plugin disabled since not in GRID mode");
1475       kPluginUse = kFALSE; 
1476    }   
1477
1478
1479    if(!kIsMC){
1480      // switch off anthin related to MC
1481      kUseMC = 0;
1482      kUseAODMC = 0;
1483      kUseTR = kFALSE;
1484    }
1485
1486    // Decide if we have PbPb
1487    if(kGridDataSet.CompareTo("LHC10h")==0||kGridDataSet.Contains("LHC10h")) {
1488      Printf("Using settings for Pb+Pb");
1489      kIsPbPb = true;
1490    }
1491
1492    
1493
1494    if (iAODanalysis) {
1495    // AOD analysis
1496       if (kUseMC)
1497          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "MC usage disabled in analysis on AOD's");
1498       if (kUseAODTags)
1499          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "AOD tags usage disabled in analysis on AOD's");
1500       kUseMC = kFALSE;
1501       kUseTR = kFALSE;
1502       kUseAODTags = kFALSE;
1503       if (iESDfilter)
1504          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "ESD filter disabled in analysis on AOD's");
1505       iESDfilter   = 0;
1506       if (iPhysicsSelection)
1507          ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "Physics Selection disabled in analysis on AOD's");
1508       iPhysicsSelection   = 0;
1509       if (!iAODhandler) {
1510          if (iJETAN || iJETANReader || iJETANFinder) 
1511             ::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "JETAN disabled in analysis on AOD's without AOD handler");
1512          iJETAN = 0;
1513          iJETANReader=0;
1514          iJETANFinder=0;
1515          iDIJETAN = 0;
1516       }
1517       // Disable tasks that do not work yet on AOD data
1518       if(iPWG4JCORRAN)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 JCORRAN disabled in analysis on AOD's");
1519       iPWG4JCORRAN = 0;
1520       if( iPWG4PtQAMC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtQAMC disabled in analysis on AOD's");
1521       iPWG4PtQAMC        = 0;
1522       if( iPWG4PtQATPC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtTPC disabled in analysis on AOD's");
1523       iPWG4PtQATPC        = 0;
1524       if( iPWG4Cosmics)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 Comics disabled in analysis on AOD's");
1525       iPWG4Cosmics        = 0;
1526
1527       if(iPWG4KMeans)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4KMeans disabled on AOD's");
1528       iPWG4KMeans       = 0;
1529       if (iPWG4JetCorr)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4Jetcorr disabled on AOD's");
1530       iPWG4JetCorr = 0;
1531       if (iPWG4PartCorr)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4partcorr disabled on AOD's");
1532       iPWG4PartCorr = 0;
1533       if (iPWG4CaloQA)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4CaloQA disabled on AOD's");
1534       iPWG4CaloQA = 0;
1535       if (iPWG4Tagged)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4tagged disabled on AOD's");
1536       iPWG4Tagged = 0;
1537       if (iPWG4omega3pi)
1538         ::Info("AnalysisTrainNew.C::CheckModuleFlags", "PWG4omega3pi disabled on AOD's");
1539       iPWG4omega3pi = 0;
1540       if(iPWGPPQASym)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWGPP QA Sym disabled in analysis on AOD's");
1541       if (iPWG4GammaConv)::Info("AnalysisPWG4Jets.C::CheckModuleFlags", "PWG4gammaconv disabled on AOD's");
1542       iPWG4GammaConv = 0;   
1543       iPWGPPQASym     = 0;
1544       iCentralitySelection = 0;
1545    } else {   
1546    // ESD analysis
1547
1548      if(kIsPbPb){
1549        iCentralitySelection = 1;
1550      }
1551
1552      if (!kUseMC){
1553        kUseTR = kFALSE;
1554        
1555        if(kUseKinefilter)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 Kine Filter disabled in analysis without MC");
1556        kUseKinefilter = kFALSE;
1557        if( iPWG4PtQAMC)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 PtQAMC disabled in analysis without MC");
1558        iPWG4PtQAMC        = 0;
1559        if( iPWG4CorrectionsUE)::Info("AnalysisTrainPWG4Jets.C::CheckModuleFlags", "PWG4 CorrectionsUE disabled in analysis without MC");
1560        iPWG4CorrectionsUE = 0;
1561      }
1562       if (!iESDfilter){
1563         kUseKinefilter = kFALSE;
1564         kUseMuonfilter = kFALSE;
1565       }
1566       if(!iJETAN ||iJETANReader || iJETANFinder){
1567         iPWG4JetSpectrum = iPWG4UE =  iPWG4CorrectionsUE = iPWG4ThreeJets = iPWG4QGSep = iDIJETAN = 0;
1568       }
1569    }
1570    iPWG4JetTasks = iPWG4JetServices||iPWG4JetSpectrum||iPWG4UE||iPWG4LeadingUE||iPWG4PtQAMC||iPWG4PtTrackQA||iPWG4PtSpectra||iPWG4PtQATPC||iPWG4Cosmics||iPWG4ThreeJets||iPWG4QGSep||iPWG4JetChem||iPWG4Minijet||iPWG4Fragmentation;
1571    iPWG4PartCorrLibs = iPWG4PartCorr||iPWG4Tagged||iPWG4CaloQA;
1572    iPWG4GammaConvLib = iPWG4GammaConv||iPWG4CaloConv;
1573
1574
1575    iEMCUtilLibs = iPWG4JetTasks||iPWG4PartCorrLibs||iPWG4JCORRAN||iPWG4GammaConvLib||iJETAN||iJETANReader||iJETANFinder;
1576    iJETANLib = (iPWG4JetTasks||iJETAN||iDIJETAN) && !(iJETANReader||iJETANFinder) ;
1577    iJETANdevLib = (iPWG4JetTasks||iJETANReader||iJETANFinder||iDIJETAN) && !iJETAN ;
1578
1579    if (iESDfilter) {iAODhandler=1;}
1580    if (kUseKinefilter && !kUseMC) kUseKinefilter = kFALSE;
1581    if (kUseAODTags && !iAODhandler) kUseAODTags = kFALSE;
1582
1583
1584    
1585 }
1586
1587 //______________________________________________________________________________
1588 Bool_t Connect(const char *mode) {
1589 // Connect <username> to the back-end system.
1590    Int_t imode = -1;
1591    if (!strcmp(mode, "LOCAL")) imode = 0;
1592    if (!strcmp(mode, "PROOF")) imode = 1;
1593    if (!strcmp(mode, "GRID"))  imode = 2;
1594    TString username = gSystem->Getenv("alien_API_USER");
1595    switch (imode) {
1596       case 0:
1597          break;
1598       case 1:
1599          if  (!username.Length()) {
1600             ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), "Make sure you:\n \
1601                            1. Have called: alien-token-init <username>\n \
1602                            2. Have called: >source /tmp/gclient_env_$UID");
1603             return kFALSE;
1604          }
1605          ::Info("AnalysisTrainPWG4Jets.C::Connect", "Connecting user <%s> to PROOF cluster <%s>", 
1606                 username.Data(), kProofCluster.Data());
1607          gEnv->SetValue("XSec.GSI.DelegProxy", "2");
1608 //         TProof::Open(Form("%s@%s:31093", username.Data(), kProofCluster.Data()));       
1609          TProof::Open(Form("%s@%s", username.Data(), kProofCluster.Data()));       
1610          if (!gProof) {
1611             if (strcmp(gSystem->Getenv("XrdSecGSISRVNAMES"), "lxfsrd0506.cern.ch"))
1612                ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), "Environment XrdSecGSISRVNAMES different from lxfsrd0506.cern.ch");
1613             return kFALSE;
1614          }
1615          if(kProofClearPackages)gProof->ClearPackages();
1616
1617          if(kProofSaveToAlien){
1618            TGrid::Connect("alien://");
1619            if (gGrid) {
1620              TString homedir = gGrid->GetHomeDirectory();
1621              TString workdir = homedir + kTrainName;
1622              if (!gGrid->Cd(workdir)) {
1623                gGrid->Cd(homedir);
1624                if (gGrid->Mkdir(workdir)) {
1625                  gGrid->Cd(kTrainName);
1626                  ::Info("AnalysisTrainPWG4Jets::Connect()", "Directory %s created", gGrid->Pwd());
1627                }
1628              }
1629              gGrid->Mkdir("proof_output");
1630              gGrid->Cd("proof_output");
1631              kProofOutdir = Form("alien://%s", gGrid->Pwd());
1632            }   
1633          }
1634          break;
1635       case 2:      
1636          if  (!username.Length()) {
1637             ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), "Make sure you:\n \
1638                            1. Have called: alien-token-init <username>\n \
1639                            2. Have called: >source /tmp/gclient_env_$UID");
1640             return kFALSE;
1641          }
1642          if (kPluginUse && !gSystem->Getenv("alien_CLOSE_SE")) {
1643             ::Error(Form("AnalysisTrainPWG4Jets.C::Connect <%s>", mode), 
1644                            "When using the AliEn plugin it is preferable to define the \
1645                            variable alien_CLOSE_SE in your environment.");
1646             return kFALSE;
1647          }
1648          ::Info("AnalysisTrainPWG4Jets.C::Connect", "Connecting user <%s> to AliEn ...", 
1649                 username.Data());
1650          TGrid::Connect("alien://");
1651          if (!gGrid || !gGrid->IsConnected()) return kFALSE;
1652          break;
1653       default:
1654          ::Error("AnalysisTrainPWG4Jets.C::Connect", "Unknown run mode: %s", mode);
1655          return kFALSE;
1656    }
1657    ::Info("AnalysisTrainPWG4Jets.C::Connect","Connected in %s mode", mode);
1658    return kTRUE;
1659 }
1660
1661 //______________________________________________________________________________
1662 Bool_t LoadCommonLibraries(const char *mode)
1663 {
1664    if (!gSystem->Getenv("ALICE_ROOT")) {
1665       ::Error("AnalysisTrainPWG4Jets.C", "Analysis train requires that ALICE_ROOT is set to pick up Configurations"); 
1666       return kFALSE;
1667    }   
1668    
1669    // Load common analysis libraries.
1670    Int_t imode = -1;
1671    if (!strcmp(mode, "LOCAL")) imode = 0;
1672    if (!strcmp(mode, "PROOF")) imode = 1;
1673    if (!strcmp(mode, "GRID"))  imode = 2;
1674    Bool_t success = kTRUE;
1675    // ROOT libraries
1676    gSystem->Load("libTree.so");
1677    gSystem->Load("libGeom.so");
1678    gSystem->Load("libVMC.so");
1679    gSystem->Load("libPhysics.so");
1680    gSystem->Load("libMinuit.so");
1681    
1682    // Load framework classes. Par option ignored here.
1683    switch (imode) {
1684       case 0:
1685       case 2:
1686          if (kUseCPAR) {
1687             success &= LoadLibrary("STEERBase", mode, kTRUE);
1688             success &= LoadLibrary("ESD", mode, kTRUE);
1689             success &= LoadLibrary("AOD", mode, kTRUE);
1690             success &= LoadLibrary("ANALYSIS", mode, kTRUE);
1691             success &= LoadLibrary("OADB", mode, kTRUE);
1692             success &= LoadLibrary("ANALYSISalice", mode, kTRUE);
1693             success &= LoadLibrary("ROOTFILES", mode, kTRUE);
1694             //            success &= LoadLibrary("EventMixing", mode,kTRUE);
1695             success &= LoadLibrary("CORRFW", mode, kTRUE);
1696          } else {   
1697             success &= LoadLibrary("libSTEERBase.so", mode);
1698             success &= LoadLibrary("libESD.so", mode);
1699             success &= LoadLibrary("libAOD.so", mode);
1700             success &= LoadLibrary("libANALYSIS.so", mode);
1701             success &= LoadLibrary("libOADB.so", mode, kTRUE);
1702             success &= LoadLibrary("libANALYSISalice.so", mode);
1703             //            success &= LoadLibrary("libEventMixing.so", mode);
1704             success &= LoadLibrary("libCORRFW.so", mode);
1705             gROOT->ProcessLine(".include $ALICE_ROOT/include");
1706          }   
1707          break;
1708       case 1:
1709          Int_t ires = -1;
1710          if (kProofUseAFPAR && !gSystem->AccessPathName(kProofAFversion)) ires = gProof->UploadPackage(kProofAFversion);
1711          if (ires < 0) {
1712             success &= LoadLibrary("STEERBase", mode);
1713             success &= LoadLibrary("ESD", mode);
1714             success &= LoadLibrary("AOD", mode);
1715             success &= LoadLibrary("ANALYSIS", mode);
1716             success &= LoadLibrary("ANALYSISalice", mode);
1717             success &= LoadLibrary("EventMixing", mode);
1718             success &= LoadLibrary("CORRFW", mode);
1719          } else { 
1720             ires = gProof->EnablePackage(kProofAFversion);
1721             if (ires<0) success = kFALSE;
1722             success &= LoadLibrary("CORRFW", mode);
1723          }
1724          break;         
1725       default:
1726          ::Error("AnalysisTrainPWG4Jets.C::LoadCommonLibraries", "Unknown run mode: %s", mode);
1727          return kFALSE;
1728    }
1729    if (success) {
1730       ::Info("AnalysisTrainPWG4Jets.C::LoadCommodLibraries", "Load common libraries:    SUCCESS");
1731       ::Info("AnalysisTrainPWG4Jets.C::LoadCommodLibraries", "Include path for Aclic compilation:\n%s",
1732               gSystem->GetIncludePath());
1733    } else {           
1734       ::Info("AnalysisTrainPWG4Jets.C::LoadCommodLibraries", "Load common libraries:    FAILED");
1735    }   
1736       
1737    return success;
1738 }
1739
1740 //______________________________________________________________________________
1741 Bool_t LoadAnalysisLibraries(const char *mode)
1742 {
1743 // Load common analysis libraries.
1744   Bool_t success = kTRUE;
1745   if (useTender) {
1746       if (!LoadLibrary("TENDER", mode, kTRUE) ||
1747           !LoadLibrary("TENDERSupplies", mode, kTRUE)) return kFALSE;
1748    }
1749    if (iESDfilter) {
1750      /*
1751       if (!LoadLibrary("PWG3base", mode, kTRUE) ||
1752           !LoadLibrary("PWG3muon", mode, kTRUE)) return kFALSE;
1753      */
1754    }   
1755    // JETAN
1756    if (iJETANLib) {
1757      // this part needs some rework in case we do not need the fastjed finders for processing
1758      if(iEMCUtilLibs){
1759        if (!LoadLibrary("EMCALUtils", mode, kTRUE) ||
1760            !LoadLibrary("PHOSUtils", mode, kTRUE)) return kFALSE;
1761      }
1762      if (!LoadLibrary("JETAN", mode, kTRUE)) return kFALSE;
1763      if (!strcmp(mode, "PROOF")){
1764        gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libCGAL.so\"\)", kTRUE); 
1765        gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libfastjet.so\"\)", kTRUE); 
1766        // problem when loading siscone copiled with different gcc version??
1767        // gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libsiscone.so\"\)", kTRUE); 
1768        gProof->Exec("gSystem->Load\(\"/afs/cern.ch/user/d/dperrino/public/libSISConePlugin.so\"\)", kTRUE);      
1769      }
1770      if(!kUsePAR){ 
1771        if (!LoadLibrary("CGAL", mode, kTRUE)) return kFALSE;
1772        if (!LoadLibrary("fastjet", mode, kTRUE)) return kFALSE;
1773        if (!LoadLibrary("siscone", mode, kTRUE)) return kFALSE;
1774        if (!LoadLibrary("SISConePlugin", mode, kTRUE)) return kFALSE;
1775      }
1776      else{
1777        // par files plus FASTJET needs some extra work... need to change
1778        // the loading sequence in the auto generated .C file
1779        if (!LoadLibrary("libCGAL.so", mode, kTRUE)) return kFALSE;
1780        if (!LoadLibrary("libfastjet.so", mode, kTRUE)) return kFALSE;
1781        if (!LoadLibrary("libsiscone.so", mode, kTRUE)) return kFALSE;
1782        if (!LoadLibrary("libSISConePlugin.so", mode, kTRUE)) return kFALSE;
1783      }
1784      if (!LoadLibrary("FASTJETAN", mode, kTRUE)) return kFALSE;
1785    }
1786
1787    // JETANdev
1788    if (iJETANdevLib) {
1789      // this part needs some rework in case we do not need the fastjed finders for processing
1790      if(iEMCUtilLibs){
1791        if (!LoadLibrary("EMCALUtils", mode, kTRUE) &&
1792            !LoadLibrary("PHOSUtils", mode, kTRUE)) return kFALSE;
1793      }
1794      if (!LoadLibrary("JETANdev", mode, kTRUE)) return kFALSE;
1795      if (!strcmp(mode, "PROOF")){
1796      if (!LoadLibrary("FASTJET", mode, kTRUE)) return kFALSE;  
1797      }
1798      if(!kUsePAR){ 
1799        if (!LoadLibrary("CGAL", mode, kTRUE)) return kFALSE;
1800        if (!LoadLibrary("fastjet", mode, kTRUE)) return kFALSE;
1801        if (!LoadLibrary("siscone", mode, kTRUE)) return kFALSE;
1802        if (!LoadLibrary("SISConePlugin", mode, kTRUE)) return kFALSE;
1803      }
1804      else{
1805        // par files plus FASTJET needs some extra work... need to change
1806        // the loading sequence in the auto generated .C file
1807        if (!LoadLibrary("libCGAL.so", mode, kTRUE)) return kFALSE;
1808        if (!LoadLibrary("libfastjet.so", mode, kTRUE)) return kFALSE;
1809        if (!LoadLibrary("libsiscone.so", mode, kTRUE)) return kFALSE;
1810        if (!LoadLibrary("libSISConePlugin.so", mode, kTRUE)) return kFALSE;
1811      }
1812      if (!LoadLibrary("FASTJETANdev", mode, kTRUE)) return kFALSE;
1813    }
1814
1815    if(iPWG4JetTasks){
1816      if (!LoadLibrary("PWGBase", mode, kTRUE)) return kFALSE;
1817      if (!LoadLibrary("PWGJE", mode, kTRUE)) return kFALSE;
1818    }
1819
1820    if(iPWGPPQASym){
1821      if (!LoadSource(Form("%s/PWGPP/AliAnalysisTaskQASym.cxx",gSystem->ExpandPathName("$ALICE_ROOT")), mode, kTRUE))return kFALSE;
1822    }
1823    if(iPWG4TmpSourceSara){
1824      if(!kUsePAR)gSystem->AddIncludePath("-I$ALICE_ROOT/include/JetTasks"); // ugly hack!!
1825      if(!LoadSource(Form("%s/PWG4/JetTasks/AliAnalysisTaskEta.cxx",gSystem->ExpandPathName("$ALICE_ROOT")), mode, kTRUE))return kFALSE;
1826    }
1827
1828    if (iPWG4PartCorrLibs) {   
1829       if (!LoadLibrary("PWG4PartCorrBase", mode, kTRUE) ||
1830           !LoadLibrary("PWG4PartCorrDep", mode, kTRUE)) return kFALSE;
1831    }
1832    if(iPWG4JCORRAN){
1833      // PWG4 particle correlations
1834      if(!LoadLibrary("PWG4JCORRAN",mode,kTRUE))return kFALSE;
1835    }
1836    if (iPWG4JetCorr) { 
1837      if (!LoadLibrary("PWG4JetCorrel", mode, kTRUE)) return kFALSE;
1838    }  
1839    if (iPWG4omega3pi) {
1840      if (!LoadLibrary("PWG4omega3pi", mode, kTRUE)) return kFALSE;
1841    }
1842    if (iPWG4GammaConvLib) {
1843       if (!LoadLibrary("PWG4GammaConv", mode, kTRUE)) return kFALSE;
1844    }      
1845
1846    ::Info("AnalysisTrainPWG4Jets.C::LoadAnalysisLibraries", "Load other libraries:   SUCCESS");
1847    return kTRUE;
1848 }
1849
1850 //______________________________________________________________________________
1851 Bool_t LoadLibrary(const char *module, const char *mode, Bool_t rec=kFALSE)
1852 {
1853 // Load a module library in a given mode. Reports success.
1854    Int_t imode = -1;
1855    Int_t result;
1856    TString smodule(module);
1857    if (!strcmp(mode, "LOCAL")) imode = 0;
1858    if (!strcmp(mode, "PROOF")) imode = 1;
1859    if (!strcmp(mode, "GRID"))  imode = 2;
1860    TString mod(module);
1861    if (!mod.Length()) {
1862       ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Empty module name");
1863       return kFALSE;
1864    }   
1865    // If a library is specified, just load it
1866    if (smodule.EndsWith(".so")) {
1867       mod.Remove(mod.Index(".so"));
1868       result = gSystem->Load(mod);
1869       if (result < 0) {
1870          ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Could not load library %s", module);
1871          return kFALSE;
1872       }
1873       if (rec) anaLibs += Form("%s.so ",mod.Data()); 
1874       if (rec) anaLibsExtra += Form("%s.so ",mod.Data()); 
1875       return kTRUE;
1876    } 
1877    // Check if the library is already loaded
1878    if (strlen(gSystem->GetLibraries(Form("%s.so", module), "", kFALSE)) > 0)
1879       return kTRUE;    
1880    switch (imode) {
1881       case 0:
1882       case 2:
1883          if (kUsePAR) {
1884             result = SetupPar(module);
1885             if (rec) anaPars += Form("%s.par ", module);
1886          } else {
1887             result = gSystem->Load(Form("lib%s.so", module));
1888             if (rec) anaLibs += Form("lib%s.so ", module);
1889          }   
1890          break;
1891       case 1:
1892         if(!gSystem->AccessPathName(module)){
1893           ::Info("AnalysisTrainPWG4Jets.C::LoadLibrary", "Removing directory %s",module);
1894           gSystem->Exec(Form("rm -rf %s",module));
1895         }
1896          result = gProof->UploadPackage(module);
1897          if (result<0) {
1898             result = gProof->UploadPackage(gSystem->ExpandPathName(Form("$ALICE_ROOT/%s.par", module)));
1899             if (result<0) {
1900                ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Could not find module %s.par in current directory nor in $ALICE_ROOT", module);
1901                return kFALSE;
1902             }
1903          }   
1904          result = gProof->EnablePackage(module);
1905          break;
1906       default:
1907          return kFALSE;
1908    }         
1909    if (result < 0) {
1910       ::Error("AnalysisTrainPWG4Jets.C::LoadLibrary", "Could not load module %s", module);
1911       return kFALSE;
1912    }
1913    return kTRUE;
1914 }           
1915
1916
1917
1918 //______________________________________________________________________________
1919 Bool_t LoadSource(const char *source, const char *mode, Bool_t rec=kFALSE)
1920 {
1921 // Load a module library in a given mode. Reports success.
1922    Int_t imode = -1;
1923    Int_t result = -1;
1924    if (!strcmp(mode, "LOCAL")) imode = 0;
1925    if (!strcmp(mode, "PROOF")) imode = 1;
1926    if (!strcmp(mode, "GRID"))  imode = 2;
1927    TString ssource(source);
1928    TString basename = gSystem->BaseName(ssource.Data());
1929    if (!ssource.Length()) {
1930       ::Error("AnalysisTrainPWG4Jets.C::LoadSource", "Empty task name");
1931       return kFALSE;
1932    }   
1933    // we have a source code so compile it
1934    if (ssource.EndsWith(".cxx")) {
1935      // need to copy it here other wise the path is also used on grid...
1936      ssource.Remove(ssource.Index(".cxx"));
1937      basename.Remove(basename.Index(".cxx"));
1938      Printf("LoadSources:: Copying...  path %s{cxx,h}",ssource.Data());
1939      gSystem->Exec(Form("cp %s.cxx . ",ssource.Data()));
1940      gSystem->Exec(Form("cp %s.h . ",ssource.Data()));
1941      // Path to code
1942      // only needed for local compilation, in grid and proof mode 
1943      // the task headers are uploaded 
1944      //     path.Remove(path.Index(gSystem->BaseName(path.Data())));
1945      // Printf("LoadSources:: Including path %s",path.Data());
1946      //  if(path.Length()>0)gROOT->ProcessLine(Form(".include %s",path.Data()));
1947      Printf("LoadSources:: Loading...  path %s",basename.Data());
1948      switch (imode) {
1949      case 0:
1950        result = gROOT->LoadMacro(Form("%s.cxx++g",basename.Data()));
1951        break;
1952      case 1:
1953        result = gProof->LoadMacro(Form("%s.cxx++g",basename.Data()));
1954        break;
1955      case 2:
1956        result = gROOT->LoadMacro(Form("%s.cxx++g",basename.Data()));
1957        if (rec){
1958          // what we want to compile
1959          anaSources += Form("%s.cxx ",basename.Data()); 
1960          // what we need as input...
1961          anaLibs += Form("%s.cxx %s.h ",basename.Data(),basename.Data()); 
1962        }
1963        break;
1964      default:
1965        return kFALSE;
1966      }
1967    } 
1968    if (result < 0) {
1969       ::Error("AnalysisTrainPWG4Jets.C::LoadSources", "Could not load source %s", source);
1970       return kFALSE;
1971    }
1972    return kTRUE;
1973 }           
1974
1975
1976 //______________________________________________________________________________
1977 TChain *CreateChain(const char *mode, const char *plugin_mode)
1978 {
1979 // Create the input chain
1980    Int_t imode = -1;
1981    if (!strcmp(mode, "LOCAL")) imode = 0;
1982    if (!strcmp(mode, "PROOF")) imode = 1;
1983    if (!strcmp(mode, "GRID"))  imode = 2;
1984    TChain *chain = NULL;
1985    // Local chain
1986    switch (imode) {
1987       case 0:
1988          if (iAODanalysis) {
1989             if (!kLocalXMLDataset.Length()) {
1990                // Local AOD
1991                chain = new TChain("aodTree");
1992                TString line;
1993                ifstream in;
1994                in.open(kLocalDataList.Data());
1995                Int_t ic = 0;
1996                while (in.good()) {
1997                  in >> line;
1998                  if (line.Length() == 0) continue;
1999                  Printf("%d adding %s",ic,line.Data());
2000                  chain->Add(line.Data());
2001                  ic++;
2002                }       
2003             } else {
2004                // Interactive AOD
2005                chain = CreateChainSingle(kLocalXMLDataset, "aodTree");
2006             }
2007          } else {      
2008            if (!kLocalXMLDataset.Length()) {
2009              // Local ESD
2010              chain = new TChain("esdTree");
2011              TString line;
2012              ifstream in;
2013              in.open(kLocalDataList.Data());
2014              while (in.good()) {
2015                in >> line;
2016                if (line.Length() == 0) continue;
2017                cout << " line = " << line << endl;
2018                chain->Add(line.Data());
2019              }       
2020            } else {
2021              // Interactive ESD
2022                chain = CreateChainSingle(kLocalXMLDataset, "esdTree");
2023            }   
2024          }
2025          break;
2026       case 1:
2027          break;
2028       case 2:
2029          if (kPluginUse) {
2030 //            AliAnalysisGrid *alienHandler = CreateAlienHandler(plugin_mode);
2031 //            AliAnalysisManager::GetAnalysisManager()->SetGridHandler(alienHandler);
2032          } else {
2033             TString           treeName = "esdTree";
2034             if (iAODanalysis) treeName = "aodTree";
2035             chain = CreateChainSingle("wn.xml", treeName);
2036          }
2037          break;      
2038       default:   
2039    }
2040    if (chain && chain->GetNtrees()) return chain;
2041    return NULL;
2042 }   
2043
2044 //______________________________________________________________________________
2045 TChain* CreateChainSingle(const char* xmlfile, const char *treeName)
2046 {
2047    printf("*******************************\n");
2048    printf("*** Getting the ESD Chain   ***\n");
2049    printf("*******************************\n");
2050    TAlienCollection * myCollection  = TAlienCollection::Open(xmlfile);
2051
2052    if (!myCollection) {
2053       ::Error("AnalysisTrainPWG4Jets.C::CreateChainSingle", "Cannot create an AliEn collection from %s", xmlfile) ;
2054       return NULL ;
2055    }
2056
2057    TChain* chain = new TChain(treeName);
2058    myCollection->Reset() ;
2059    while ( myCollection->Next() ) chain->Add(myCollection->GetTURL("")) ;
2060    chain->ls();
2061    return chain;
2062 }
2063
2064 //______________________________________________________________________________
2065 Int_t SetupPar(char* pararchivename)
2066 {
2067    if (!pararchivename || !strlen(pararchivename)) return -1;
2068    char processline[1024];
2069    if (gSystem->AccessPathName(Form("%s.par", pararchivename))) {
2070       if (!gSystem->AccessPathName(Form("%s/%s.par", gSystem->Getenv("ALICE_ROOT"),pararchivename))) {
2071          ::Info("AnalysisTrainPWG4Jets.C::SetupPar", "Getting %s.par from $ALICE_ROOT", pararchivename);
2072         TFile::Cp(gSystem->ExpandPathName(Form("$ALICE_ROOT/%s.par", pararchivename)), 
2073                   Form("%s.par",pararchivename));
2074       } else {
2075          ::Error("AnalysisTrainPWG4Jets.C::SetupPar", "Cannot find %s.par", pararchivename);
2076          return -1;
2077       }   
2078    }
2079    if (kPluginUse && kSaveTrain) gSystem->Exec(Form("ln -s ../%s.par %s",pararchivename, kTrainName.Data()));
2080    gSystem->Exec(Form("tar xvzf %s.par", pararchivename));
2081
2082    TString ocwd = gSystem->WorkingDirectory();
2083    if (!gSystem->ChangeDirectory(pararchivename)) return -1;
2084         
2085    // check for BUILD.sh and execute
2086    if (!gSystem->AccessPathName("PROOF-INF/BUILD.sh")) {
2087       printf("*******************************\n");
2088       printf("*** Building PAR archive    ***\n");
2089       printf("*******************************\n");          
2090       if (gSystem->Exec("PROOF-INF/BUILD.sh")) {
2091          Error("runProcess","Cannot Build the PAR Archive! - Abort!");
2092          return -1;
2093       }
2094    }
2095
2096         // check for SETUP.C and execute
2097         if (!gSystem->AccessPathName("PROOF-INF/SETUP.C")) {
2098             printf("*******************************\n");
2099             printf("*** Setup PAR archive       ***\n");
2100             printf("*******************************\n");
2101             gROOT->Macro("PROOF-INF/SETUP.C");
2102         }       
2103         if (!gSystem->ChangeDirectory(ocwd.Data())){
2104           Error("Change back directory",Form("Cannot change to %s",ocwd.Data()));
2105           return -1;
2106         }
2107    return 0;
2108 }
2109
2110 //______________________________________________________________________________
2111 AliAnalysisAlien* CreateAlienHandler(const char *plugin_mode)
2112 {
2113 // Check if user has a valid token, otherwise make one. This has limitations.
2114 // One can always follow the standard procedure of calling alien-token-init then
2115 //   source /tmp/gclient_env_$UID in the current shell.
2116 //   if (!AliAnalysisGrid::CreateToken()) return NULL;
2117    AliAnalysisAlien *plugin = new AliAnalysisAlien();
2118 // Set the run mode (can be "full", "test", "offline", "submit" or "terminate")
2119    plugin->SetRunMode(plugin_mode);
2120    plugin->SetCheckCopy(kFALSE); 
2121    if (kPluginUseProductionMode) plugin->SetProductionMode();
2122    plugin->SetJobTag(kJobTag);
2123    plugin->SetNtestFiles(1);
2124 //   plugin->SetPreferedSE("ALICE::NIHAM::File");
2125 // Set versions of used packages
2126    plugin->SetAPIVersion("V1.1x");
2127    //   plugin->SetAPIVersion("V1.0x");
2128 //   plugin->SetAPIVersion("V2.4");
2129    plugin->SetROOTVersion(kPluginRootVersion);
2130    plugin->SetAliROOTVersion(kPluginAliRootVersion);
2131 // Declare input data to be processed.
2132 // Method 1: Create automatically XML collections using alien 'find' command.
2133 // Define production directory LFN
2134    plugin->SetGridDataDir(kGridDatadir.Data());
2135 // Set data search pattern
2136    if (iAODanalysis) plugin->SetDataPattern(Form(" %s/*/*AliAOD.root",kGridPassPattern.Data()));
2137    else              plugin->SetDataPattern(Form(" %s/*/*AliESDs.root",kGridPassPattern.Data()));
2138 // ...then add run numbers to be considered
2139 //   plugin->SetRunRange(kGridRunRange[0], kGridRunRange[1]);
2140    for (Int_t i=kGridRunRange[0]; i<=kGridRunRange[1]; i++) {
2141      Printf("AnalysisTrainPWG4Jets Adding run number %s", Form(kGridRunPattern.Data(),i));
2142      plugin->AddRunNumber(Form(kGridRunPattern.Data(),i));
2143    }   
2144
2145    if(kGridLocalRunList.Length()>0){
2146      ifstream in1;
2147      in1.open(kGridLocalRunList.Data());
2148      int iRun = 0;
2149      int icount = 0;
2150      Int_t nRun = 0;
2151      // just use run numbers, negatives will be excluded
2152      while(in1>>iRun){
2153        if(iRun>=0){
2154          if(iRun>=0&&nRun>=kGridOffsetRunFromList&&(nRun<kGridMaxRunsFromList)){
2155            Printf("AnalysisTrainPWG4Jets Adding run number from File %d: %s",nRun,Form(kGridRunPattern.Data(),iRun));
2156            plugin->AddRunNumber(Form(kGridRunPattern.Data(),iRun));
2157
2158          }
2159          else{
2160            Printf("AnalysisTrainPWG4Jets Skipping run number from File %d: %d",nRun, iRun);
2161          }
2162          nRun++;
2163        }
2164        else{
2165          Printf("AnalysisTrainPWG4Jets Skipping run number from File %d: %d",nRun, iRun);
2166        }
2167      }
2168    }
2169 // Method 2: Declare existing data files (raw collections, xml collections, root file)
2170 // If no path mentioned data is supposed to be in the work directory (see SetGridWorkingDir())
2171 // XML collections added via this method can be combined with the first method if
2172 // the content is compatible (using or not tags)
2173 //   plugin->AddDataFile("tag.xml");
2174 //   plugin->AddDataFile("/alice/data/2008/LHC08c/000057657/raw/Run57657.Merged.RAW.tag.root");
2175 // Define alien work directory where all files will be copied. Relative to alien $HOME.
2176    TString alien_workdir = "";
2177    
2178    if (iAODanalysis)  alien_workdir += "analysisAOD";
2179    else               alien_workdir += "analysisESD";    
2180        if(kGridDataSet.Length()>0)alien_workdir += Form("/%s%s",kGridDataSet.Data(),kGridExtraAliendirLevel.Data());
2181    plugin->SetGridWorkingDir(alien_workdir.Data());
2182
2183    // Declare alien output directory. Relative to working directory.
2184    if (!kGridOutdir.Length()) kGridOutdir = Form("output_%s",kTrainName.Data());
2185    plugin->SetGridOutputDir(kGridOutdir);
2186
2187    // Add external packages
2188    plugin->AddExternalPackage("boost::v1_43_0");
2189    plugin->AddExternalPackage("cgal::v3.6");
2190    plugin->AddExternalPackage("fastjet::v2.4.2");
2191
2192
2193    // set extra libs before par file compilation
2194    anaLibs += kGridExtraFiles;
2195    anaLibs     = anaLibs.Strip();   
2196    Printf("anaLibs %s",anaLibs.Data());
2197    Printf("anaLibsExtra %s",anaLibsExtra.Data());
2198
2199    if (anaLibs.Length())          plugin->SetAdditionalLibs(anaLibs.Data());
2200    if (anaLibsExtra.Length())     plugin->SetAdditionalRootLibs(anaLibsExtra.Data());
2201
2202    TString ana_sources = "";
2203    TString ana_add = "";
2204    if (kUsePAR && anaPars.Length()) {
2205       printf("%s\n", anaPars.Data());
2206       TObjArray *arr;
2207       TObjString *objstr;
2208       arr = anaPars.Tokenize(" ");
2209       TIter next(arr);
2210       while ((objstr=(TObjString*)next())) plugin->EnablePackage(objstr->GetString());
2211       delete arr;
2212    } 
2213    
2214 // Declare the analysis source files names separated by blancs. To be compiled runtime
2215 // using ACLiC on the worker nodes.
2216    ana_sources = anaSources.Strip();
2217 // Declare all libraries (other than the default ones for the framework. These will be
2218 // loaded by the generated analysis macro. Add all extra files (task .cxx/.h) here.
2219
2220    if (ana_sources.Length()) plugin->SetAnalysisSource(ana_sources);
2221    plugin->SetExecutableCommand(kPluginExecutableCommand.Data());  
2222    // Declare the output file names separated by blancs.
2223    // (can be like: file.root or file.root@ALICE::Niham::File)
2224    plugin->SetMergeExcludes(kGridMergeExclude);
2225    plugin->SetMaxMergeFiles(kGridMaxMergeFiles);
2226    plugin->SetNrunsPerMaster(kGridRunsPerMaster);
2227    plugin->SetMergeViaJDL(kPluginMergeViaJDL);
2228    // Use fastread option
2229    plugin->SetFastReadOption(kPluginFastReadOption);
2230    // UseOverwrite mode
2231    plugin->SetOverwriteMode(kPluginOverwriteMode); 
2232    // Optionally define the files to be archived.
2233    //   plugin->SetOutputArchive("log_archive.zip:stdout,stderr@ALICE::NIHAM::File root_archive.zip:AliAOD.root,AOD.tag.root@ALICE::NIHAM::File");
2234    plugin->SetOutputToRunNo(kPluginOutputToRunNumber);     // write the output to subdirs named after run number
2235    
2236    // Put default output files to archive
2237    TString listhists = "";
2238    TString listaods  = "";
2239    AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2240    TIter next(mgr->GetOutputs());
2241    AliAnalysisDataContainer *output;
2242    while ((output=(AliAnalysisDataContainer*)next())) {
2243       const char *filename = output->GetFileName();
2244       if (!(strcmp(filename, "default"))) {
2245         if (!mgr->GetOutputEventHandler()) continue;
2246          filename = mgr->GetOutputEventHandler()->GetOutputFileName();
2247          if (listaods.Length()) listaods += " ";
2248          listaods += filename;
2249       } else {
2250         if(!listhists.Contains(filename)){
2251           if (listhists.Length()) listhists += " ";
2252           listhists += filename;
2253         }
2254       }
2255    }
2256
2257    if (mgr->GetExtraFiles().Length()) {
2258      if (listaods.Length()) listaods += " ";
2259      listaods += mgr->GetExtraFiles();
2260    }
2261
2262    // if we do not fill the aod we do not need to store it
2263    //   kGridMergeExclude = listaods;
2264    
2265    if(kSaveAOD>=0){
2266      TString outputFiles =  "";
2267      outputFiles += mgr->GetExtraFiles();
2268      if (listhists.Length()) outputFiles += " ";
2269      outputFiles += listhists;
2270      plugin->SetDefaultOutputs(kFALSE);
2271      Printf("%s:%d Starting with the files %s",(char*)__FILE__,__LINE__,outputFiles.Data());
2272      // remove
2273      // no harm done when we try to remove something that is not there :)
2274      if(!(kSaveAOD&(1<<0))){
2275        outputFiles.ReplaceAll("AliAOD.root ","");
2276        listaods.ReplaceAll("AliAOD.root ","");
2277      }
2278      if(!(kSaveAOD&(1<<1))){
2279        if(kDeltaAODJetName.Length())outputFiles.ReplaceAll(kDeltaAODJetName.Data(),"");
2280        if(kDeltaAODJetName.Length())listaods.ReplaceAll(kDeltaAODJetName.Data(),"");
2281        
2282      }
2283      if(!(kSaveAOD&(1<<2))){
2284        if(kDeltaAODPartCorrName.Length())outputFiles.ReplaceAll(kDeltaAODPartCorrName.Data(),"");
2285        if(kDeltaAODPartCorrName.Length())listaods.ReplaceAll(kDeltaAODPartCorrName.Data(),"");
2286      }
2287      if(!(kSaveAOD&(1<<3))){
2288        if(kDeltaAODJCORRANName.Length())outputFiles.ReplaceAll(kDeltaAODJCORRANName.Data(),"");
2289        if(kDeltaAODJCORRANName.Length())listaods.ReplaceAll(kDeltaAODJCORRANName.Data(),"");
2290      }
2291      
2292      // 
2293      plugin->SetDefaultOutputs(kFALSE);
2294      Printf("%s:%d Saving the files %s",(char*)__FILE__,__LINE__,outputFiles.Data());
2295      plugin->SetOutputFiles(outputFiles.Data());
2296    }
2297
2298    TString outputArchive;
2299    outputArchive = Form("log_archive.zip:std*@%s","disk=1");
2300    listaods.ReplaceAll(" ", ",");
2301    listhists.ReplaceAll(" ", ",");
2302    if (listhists.Length()){
2303      outputArchive += " ";
2304      outputArchive += "root_archive.zip:";
2305      outputArchive += listhists;
2306      if (listaods.Length()){
2307        outputArchive += ",";
2308        outputArchive += listaods;
2309      }
2310      outputArchive += Form("@%s", kGridOutputStorages.Data());
2311    }
2312    else{
2313      
2314      if (listaods.Length()){
2315        // we have only aod'ish output
2316        outputArchive += " ";
2317        outputArchive += "root_archive.zip:";
2318        outputArchive += listaods;
2319        outputArchive += Form("@%s", kGridOutputStorages.Data());
2320      }
2321      else{
2322        // no other outputs than std..
2323       ::Fatal("AnalysisTrainPWG4Jets", "No task output !");
2324      }
2325    }
2326
2327    plugin->SetDefaultOutputs(kFALSE);
2328    plugin->SetOutputArchive(outputArchive);
2329
2330
2331    // Optionally set a name for the generated analysis macro (default MyAnalysis.C)
2332    plugin->SetAnalysisMacro(Form("%s.C", kTrainName.Data()));
2333    // Optionally set maximum number of input files/subjob (default 100, put 0 to ignore)
2334    plugin->SetSplitMaxInputFileNumber(kGridFilesPerJob);
2335    // Optionally set number of failed jobs that will trigger killing waiting sub-jobs.
2336    //   plugin->SetMaxInitFailed(5);
2337    // Optionally resubmit threshold.
2338    // plugin->SetMasterResubmitThreshold(90);
2339    // Optionally set time to live (default 30000 sec)
2340    plugin->SetTTL(80000); // 22h...
2341    // Optionally set input format (default xml-single)
2342    plugin->SetInputFormat("xml-single");
2343    // Optionally modify the name of the generated JDL (default analysis.jdl)
2344    plugin->SetJDLName(Form("%s.jdl", kTrainName.Data()));
2345    // Optionally modify the executable name (default analysis.sh)
2346    plugin->SetExecutable(Form("%s.sh", kTrainName.Data()));
2347    // Optionally modify job price (default 1)
2348    plugin->SetPrice(1);      
2349    // Optionally modify split mode (default 'se')    
2350    plugin->SetSplitMode("se");
2351    return plugin;
2352 }
2353
2354 //______________________________________________________________________________
2355 void WriteConfig()
2356 {
2357 // Write train configuration in a file. The file name has the format:
2358 // train_[trainName]_ddMonthyyyy_time.C
2359    if (kUseDate) {
2360       gSystem->Exec("date +%d%b%Y_%Hh%M > date.tmp");
2361       ifstream fdate("date.tmp");
2362       if (!fdate.is_open()) {
2363          ::Error("AnalysisTrainPWG4Jets.C::Export","Could not generate file name");
2364          return;
2365       }
2366       const char date[64];
2367       fdate.getline(date,64);
2368       fdate.close();
2369       gSystem->Exec("rm date.tmp");
2370       kTrainName = Form("train_%s_%s", kTrainName.Data(), date);
2371    } else {
2372       kTrainName = Form("train_%s", kTrainName.Data());
2373    }   
2374    TString cdir = gSystem->WorkingDirectory();
2375    gSystem->MakeDirectory(kTrainName);
2376    gSystem->ChangeDirectory(kTrainName);
2377    ofstream out;
2378    out.open(Form("%sConfig.C",kTrainName.Data()), ios::out); 
2379    if (out.bad()) {
2380       ::Error("AnalysisTrainPWG4Jets.C::Export", "Cannot open ConfigTrain.C for writing");
2381       return;
2382    }
2383    out << "{" << endl;
2384    out << "   kTrainName      = " << "\"" << kTrainName.Data() << "\";" << endl;
2385    out << "   kProofCluster   = " << "\"" << kProofCluster.Data() << "\";" << endl;
2386    out << "   kProofUseAFPAR        = " << kProofUseAFPAR << ";" << endl;
2387    if (kProofUseAFPAR) 
2388       out << "   kProofAFversion       = " << kProofAFversion.Data() << ";" << endl;
2389    out << "   kProofDataSet   = " << "\"" << kProofDataSet.Data() << "\";" << endl;
2390    out << "   kPluginUse       = " << kPluginUse << ";" << endl;
2391    out << "   kUsePAR          = " << kUsePAR << ";" << endl;
2392    out << "   kUseCPAR         = " << kUseCPAR << ";" << endl;
2393    out << "   kPluginRootVersion    = " << "\"" << kPluginRootVersion.Data() << "\";" << endl;
2394    out << "   kPluginAliRootVersion = " << "\"" << kPluginAliRootVersion.Data() << "\";" << endl;
2395    out << "   kGridDatadir   = " << "\"" << kGridDatadir.Data() << "\";" << endl;
2396    if (!kGridOutdir.Length()) kGridOutdir = Form("output_%s",kTrainName.Data());
2397    out << "   kGridOutdir    = " << "\"" << kGridOutdir.Data() << "\";" << endl;
2398    out << "   kGridMaxMergeFiles   = " << kGridMaxMergeFiles << ";" << endl;
2399    out << "   kGridMergeExclude    = " << "\"" << kGridMergeExclude.Data() << "\";" << endl;
2400    out << "   kGridRunsPerMaster  = " << kGridRunsPerMaster << ";" << endl;
2401    out << "   kGridFilesPerJob    = " << kGridFilesPerJob << ";" << endl;
2402    out << "   kGridRunRange[0]    = " << kGridRunRange[0] << ";" << endl;
2403    out << "   kGridRunRange[1]    = " << kGridRunRange[1] << ";" << endl;
2404    out << "   kUseDebug          = " << kUseDebug << ";" << endl;
2405    out << "   kUseMC           = " << kUseMC << ";" << endl;
2406    out << "   kUseESDTags         = " << kUseESDTags << ";" << endl;
2407    out << "   kUseKinefilter      = " << kUseKinefilter << ";" << endl;
2408    out << "   kUseTR           = " << kUseTR << ";" << endl;
2409    out << "   kUseAODTags      = " << kUseAODTags << ";" << endl;
2410    out << "   kSaveTrain       = " << "kFALSE;" << endl << endl;
2411    out << "   // Analysis modules" << endl;
2412    out << "   iAODanalysis    = " << iAODanalysis << ";" << endl;
2413    out << "   iAODhandler     = " << iAODhandler << ";" << endl;
2414    out << "   iESDfilter      = " << iESDfilter << ";" << endl;
2415    out << "   iJETAN          = " << iJETAN << ";" << endl;
2416    out << "// Configuration fot the wagons" << endl;
2417    out << "}" << endl;
2418    ::Info("AnalysisTrainPWG4Jets.C::WriteConfig", "Train configuration wrote to file %s", Form("config_%s.C", kTrainName.Data()));
2419    gSystem->ChangeDirectory(cdir);
2420 }   
2421
2422 //______________________________________________________________________________
2423 Bool_t LoadConfig(const char *filename)
2424 {
2425 // Read train configuration from file
2426    if (gSystem->AccessPathName(filename)) {
2427       ::Error("AnalysisTrainPWG4Jets.C::LoadConfig", "Config file name not found");
2428       return kFALSE;
2429    }   
2430    gROOT->ProcessLine(Form(".x %s", filename));
2431    ::Info("AnalysisTrainPWG4Jets.C::LoadConfig", "Train configuration loaded from file %s", filename);
2432    return kTRUE;
2433 }
2434
2435 Bool_t PatchJDL(){
2436   Printf(">>> Patching JDL");
2437   AliAnalysisManager *mgr = AliAnalysisManager::GetAnalysisManager();
2438   AliAnalysisAlien*    gridHandler = (AliAnalysisAlien*)mgr->GetGridHandler();
2439   TGridJDL *jdl = gridHandler->GetGridJDL();
2440   if(iJETAN)jdl->AddToPackages("fastjet","v2.4.0");
2441   gridHandler->WriteJDL(kFALSE);
2442   Printf("<<<  Patching JDL");
2443   return kTRUE;
2444 }
2445
2446 Bool_t PatchAnalysisMacro(){
2447   Printf(">>> Patching AnalysisMacro");
2448   gSystem->Exec(Form("mv %s.C %s.C_tmp",kTrainName.Data(),kTrainName.Data()));
2449
2450   ifstream in1; 
2451   in1.open(Form("%s.C_tmp", kTrainName.Data()));
2452   char cLine[250];
2453   TString st;
2454   while(in1.getline(cLine,250)){
2455     st += cLine;
2456     st += "\n";
2457   }
2458   Int_t index= -1;
2459   index = st.Index("gSystem->Load(\"libPhysics\");");
2460   index += strlen("gSystem->Load(\"libPhysics\");");
2461   /*
2462     TObjArray *arr;
2463     TObjString *objstr;
2464     arr = anaLibs.Tokenize(" ");
2465     TIter next(arr);
2466
2467     add += "\n\n // added by CKB \n";
2468     while ((objstr=(TObjString*)next())){
2469       if(objstr->GetString().Contains("PWG3"))continue;
2470       if(objstr->GetString().EndsWith(".so"))add += Form("gSystem->Load(\"%s\");\n",objstr->GetString().Data());
2471     }
2472     delete arr; 
2473     */
2474     //    add += Form("AliLog::SetGlobalLogLevel(%d);\n",AliLog::GetGlobalLogLevel());
2475   TString add = "";
2476
2477   if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2478   add += "\n\n // added by CKB \n";
2479   if(kErrorIgnoreLevel>0)add += Form("gErrorIgnoreLevel = %d;\n",kErrorIgnoreLevel);
2480   add += "\n gSystem->AddIncludePath(\"./\"); \n";
2481   add += "\n gSystem->SetFPEMask(); \n";
2482
2483
2484   if(gGrid&&kPluginAliRootVersion.Length()==0){
2485     /*
2486     add += "\n // Dirty hack for TRD reference data \n";
2487     add += "\n gSystem->Setenv(\"ALICE_ROOT\",\"";
2488     add += Form("alien://%s/rootfiles/",gGrid->GetHomeDirectory());
2489     add += "\"); \n";
2490     */
2491   }
2492
2493   add += "// BKC \n\n";
2494   st.Insert(index,add.Data());
2495
2496   if(kUseDebug){
2497     //    st.Insert(index,"\n gROOT->ProcessLine(\".trace\"); // CKB \n");
2498   }
2499
2500   if(kUseCPAR&&kPluginAliRootVersion.Length()==0){
2501     index = st.Index("gSystem->AddIncludePath(\"-I$"); // uncommen $ALICE_ROOT include for par files
2502     if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2503     st.Insert(index,"// CKB comment out whehn no aliroot is provided \n //");
2504   }
2505
2506   if(AliLog::GetGlobalLogLevel()==AliLog::kFatal){
2507     index = st.Index("AliLog::SetGlobal"); // ncomment setting of log level, do my own
2508     if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2509     st.Insert(index,"AliLog::SetGlobalLogLevel(AliLog::kFatal);// CKB \n  // CKB comment out for own setting \n  //");
2510   }
2511
2512   ofstream out;
2513   out.open(Form("%s.C", kTrainName.Data()));
2514   if (out.bad()) {
2515     return kFALSE;
2516   }
2517   out << st << endl;
2518   Printf("<<< Patching AnalysisMacro");
2519
2520
2521
2522
2523
2524   Printf(">>> Patching Merge Macro");
2525   gSystem->Exec(Form("mv %s_merge.C %s_merge.C_tmp",kTrainName.Data(),kTrainName.Data()));
2526
2527   ifstream in2; 
2528   in2.open(Form("%s_merge.C_tmp", kTrainName.Data()));
2529   TString st2;
2530   while(in2.getline(cLine,250)){
2531     st2 += cLine;
2532     st2 += "\n";
2533   }
2534   index = st2.Index("gSystem->Load(\"libPhysics\");");
2535   index += strlen("gSystem->Load(\"libPhysics\");");
2536   TString add2 = "";
2537   add2 += "\n gSystem->AddIncludePath(\"./\"); \n";
2538   if(gGrid&&kPluginAliRootVersion.Length()==0){
2539     /*
2540     add2 += "\n // Dirty hack for TRD reference data \n";
2541     add2 += "\n gSystem->Setenv(\"ALICE_ROOT\",\"";
2542     add2 += Form("alien://%s/rootfiles/",gGrid->GetHomeDirectory());
2543     add2 += "\"); \n";
2544     */
2545   }
2546   add2 += "// BKC \n\n";
2547   if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2548   st2.Insert(index,add.Data());
2549
2550
2551   if(kUseDebug){
2552     //    st2.Insert(index,"\n gROOT->ProcessLine(\".trace\"); // CKB \n");
2553   }
2554
2555   if(kUseCPAR&&kPluginAliRootVersion.Length()==0){
2556     index = st2.Index("gSystem->AddIncludePath(\"-I$"); // uncomment $ALICE_ROOT include for par files
2557     if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2558     st2.Insert(index,"// CKB comment out whehn no aliroot is provided \n //");
2559   }
2560
2561   // do not exclude the extra files from merign, this is done explicitly in this train script
2562   //  index = st2.Index("mergeExcludes +="); // uncommen $ALICE_ROOT include for par files
2563   //  if(index<0)Printf("%s:%d index out of bounds",(char*)__FILE__,__LINE__);
2564   // st2.Insert(index,"// CKB comment out, handled explicitly by the train macro \n //");
2565
2566
2567   ofstream out2;
2568   out2.open(Form("%s_merge.C", kTrainName.Data()));
2569   if (out2.bad()) {
2570     return kFALSE;
2571   }
2572   out2 << st2 << endl;
2573   Printf("<<< Patching Merging Macro");
2574
2575
2576
2577   return kTRUE;
2578
2579 }