1 /**************************************************************************
2 * Copyright(c) 1998-1999, ALICE Experiment at CERN, All rights reserved. *
4 * Author: The ALICE Off-line Project. *
5 * Contributors are mentioned in the code where appropriate. *
7 * Permission to use, copy, modify and distribute this software and its *
8 * documentation strictly for non-commercial purposes is hereby granted *
9 * without fee, provided that the above copyright notice appears in all *
10 * copies and that both the copyright notice and this permission notice *
11 * appear in the supporting documentation. The authors make no claims *
12 * about the suitability of this software for any purpose. It is *
13 * provided "as is" without express or implied warranty. *
14 **************************************************************************/
15 //_________________________________________________________________________
16 // Various utilities usefull for analysis
19 //////////////////////////////////////////////////////////////////////////////
21 #include "AliAnalysisDataContainer.h"
22 #include "AliTagAnalysis.h"
23 #include "AliEventTagCuts.h"
24 #include "AliRunTagCuts.h"
25 #include "AliXMLCollection.h"
26 #include "AliAnalysisGoodies.h"
27 #include "AliAnalysisManager.h"
28 #include "AliAnalysisTask.h"
29 //#include "AliPhotonAnalysisTask.h"
32 #include <Riostream.h>
34 #include <TAlienCollection.h>
35 #include <TGridResult.h>
38 #include <TFileMerger.h>
42 #include <TEntryList.h>
44 //______________________________________________________________________________
45 AliAnalysisGoodies::AliAnalysisGoodies() :
46 fESDTreeName("esdTree"),
54 TString token = gSystem->Getenv("GRID_TOKEN") ;
57 TGrid::Connect("alien://");
59 AliInfo("You are not connected to the GRID") ;
62 //______________________________________________________________________________
63 void AliAnalysisGoodies::Help() const
65 AliInfo("Analysis utilities:\n") ;
66 printf(" *** Alien2Local : copy files ESD files listed in an xml collection from AliEn catalog to local storage and creates a local xml collection \n") ;
67 printf(" usage: Alien2Local(in, out)\n") ;
68 printf(" in: a xml esd collection file name \n") ;
69 printf(" ou: the local directory where to save the esd root files \n") ;
70 printf(" *** Make : makes esd collection from tags \n") ;
71 printf(" usage: Make(tags, esds)\n") ;
72 printf(" tags: is either a tag root file or an xml tag collection \n") ;
73 printf(" esds: is an esd collection \n") ;
74 printf(" *** Merge : merges files listed in a xml collection \n") ;
75 printf(" usage Merge(collection, outputDile)\n") ;
76 printf(" collection: is a xml collection \n") ;
77 printf(" *** Process : process the events with an Analysis Task \n") ;
78 printf(" usage: Process(esdFile, tagCuts) \n") ;
79 printf(" esdFile: can be a root file with the ESD Tree ( ex: esd?AliESDs.root) \n") ;
80 printf(" or a root file with the Tag Tree ( ex: tag?Run100.Event0_100.ESD.tag.root) \n") ;
81 printf(" or a local or alien xml file with the ESD collection ( ex: esd?esdCollection.xml) \n") ;
82 printf(" or a local or alien xml file with the TAG collection ( ex: tag?tagCollection.xml) \n") ;
83 printf(" or a TChain of esd TTrees \n") ;
84 printf(" tagCuts: is the AliEventTagCuts (needed only for tag? cases \n") ;
85 printf(" *** Register: register files already stored in a MSS into the AliEn catalog\n") ;
86 printf(" usage: Register(lfndir, pfndir, pfnFileName) \n") ;
87 printf(" lfndir : AliEn directory ( ex: /alice/data/2006/LHC06c/PHOS_TestBeam/\n") ;
88 printf(" pfndir : MSS directory ( ex: /castor/cern.ch/alice/testbeam/phos/2006 \n") ;
89 printf(" file : text file with a list of the file names to be registered\n ") ;
93 //______________________________________________________________________
94 Bool_t AliAnalysisGoodies::Alien2Local(const TString collectionNameIn, const TString localDir)
96 // copy files ESD files listed in an xml collection from AliEn catalog to local storage and creates a local xml collection
97 // usage: Alien2Local(in, out)
98 // in: a xml esd collection file name
99 // ou: the local directory where to save the esd root files
105 AliXMLCollection * collectionIn = AliXMLCollection::Open(collectionNameIn) ;
106 collectionIn->Reset() ;
108 AliXMLCollection * collectionOu = new AliXMLCollection() ;
109 TString collectionNameOu(collectionIn->GetCollectionName()) ;
110 collectionNameOu.Append("Local") ;
111 collectionOu->SetCollectionName(collectionNameOu) ;
112 collectionOu->WriteHeader() ;
116 const char* ocwd = gSystem->WorkingDirectory();
119 while ( collectionIn->Next() ) {
120 gSystem->ChangeDirectory(localDir) ;
121 TString fileTURL = collectionIn->GetTURL("") ;
123 TString tempo(fileTURL) ;
124 tempo.Remove(tempo.Last('/'), tempo.Length()) ;
125 TString evtsNumber = tempo(tempo.Last('/')+1, tempo.Length())+"/";
126 tempo.Remove(tempo.Last('/'), tempo.Length()) ;
127 TString runNumber = tempo(tempo.Last('/')+1, tempo.Length())+"/" ;
128 TString dir = localDir + runNumber ;
131 sprintf(line, ".! mkdir -p %s", dir.Data()) ;
132 gROOT->ProcessLine(line) ;
133 printf("***************************%s\n", line) ;
134 TEntryList * list = collectionIn->GetEventList("") ;
136 list = new TEntryList() ;
138 TString filename = tempo(tempo.Last('/')+1, tempo.Length()) ;
140 AliInfo(Form("Copying %s to %s\n", fileTURL.Data(), dir.Data())) ;
141 collectionOu->WriteBody(counter, collectionIn->GetGUID(""), collectionIn->GetLFN(""), dir, list) ;
143 merger.Cp(fileTURL, dir) ;
145 collectionOu->Export() ;
146 gSystem->ChangeDirectory(ocwd) ;
154 //______________________________________________________________________
155 Bool_t AliAnalysisGoodies::Make(AliRunTagCuts *runCuts, AliEventTagCuts *evtCuts, const char * in, const char * out) const
157 // makes esd collection from tags
158 // usage Make(tags, esds)
159 // tags: is either a tag root file or an xml tag collection
160 // esds: is an esd collection
164 if ( !evtCuts && !runCuts ) {
165 AliError("No Tag cuts provided") ;
170 if ( file.Contains(".root") )
171 rv = MakeEsdCollectionFromTagFile(runCuts, evtCuts, file.Data(), out) ;
172 else if ( file.Contains(".xml") )
173 rv = MakeEsdCollectionFromTagCollection(runCuts, evtCuts, file.Data(), out) ;
175 AliError(Form("%s is not a valid file format", in)) ;
182 //______________________________________________________________________
183 Bool_t AliAnalysisGoodies::MakeEsdCollectionFromTagFile(AliRunTagCuts *runCuts, AliEventTagCuts *evtCuts, const char * in, const char * out) const
185 // Makes an esd collection from a root tag file
187 // Open the file collection
188 printf("*** Create Collection ***\n");
189 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
190 printf("*** file = |%s| \n",in);
192 AliTagAnalysis * tagAna = new AliTagAnalysis();
193 rv = tagAna->AddTagsFile(in);
197 tagAna->CreateXMLCollection(out, runCuts, evtCuts) ;
203 //______________________________________________________________________
204 Bool_t AliAnalysisGoodies::MakeEsdCollectionFromTagCollection(AliRunTagCuts * runCuts, AliEventTagCuts * evtCuts, const char * in, const char * out) const
206 // Makes an esd collection from a xml tag collection
208 // Open the file collection
209 printf("*** Create Collection ***\n");
210 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
211 printf("*** Coll = |%s| \n",in);
215 TGridCollection * collection = TAlienCollection::Open(in);
216 TGridResult* result = collection->GetGridResult("");
217 AliTagAnalysis * tagAna = new AliTagAnalysis();
218 tagAna->ChainGridTags(result);
220 tagAna->CreateXMLCollection(out, runCuts, evtCuts) ;
228 //______________________________________________________________________
229 Bool_t AliAnalysisGoodies::MakeEsdCollectionFromTagCollection(const char * runCuts, const char * evtCuts, const char * in, const char * out) const
231 // Makes an esd collection from a xml tag collection
235 // Open the file collection
236 printf("*** Create Collection ***\n");
237 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
238 printf("*** Coll = |%s| \n",in);
242 TGridCollection * collection = TAlienCollection::Open(in);
243 TGridResult* result = collection->GetGridResult("");
244 AliTagAnalysis * tagAna = new AliTagAnalysis();
245 tagAna->ChainGridTags(result);
247 tagAna->CreateXMLCollection(out, runCuts, evtCuts) ;
255 //______________________________________________________________________
256 Bool_t AliAnalysisGoodies::Merge(const char * collectionFile, const char * subFile, const char * outFile)
258 // merges files listed in a xml collection
259 // usage Merge(collection, outputFile))
260 // collection: is a xml collection
264 if ( strstr(collectionFile, ".xml") == 0 ) {
265 AliError("Input collection file must be an \".xml\" file\n") ;
271 // Open the file collection
272 printf("*** Create Collection ***\n");
273 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
274 printf("*** Coll = |%s| \n",collectionFile);
278 TGridCollection * collection = TAlienCollection::Open(collectionFile);
279 TGridResult* result = collection->GetGridResult("");
285 TString tempo(collectionFile) ;
287 tempo.ReplaceAll(".xml", subFile) ;
289 tempo.ReplaceAll(".xml", "_Merged.root") ;
290 outFile = tempo.Data() ;
292 merger.OutputFile(outFile) ;
294 while ( (turl = result->GetKey(index, "turl")) ) {
297 sprintf(file, "%s#%s", turl, subFile) ;
299 sprintf(file, "%s", turl) ;
301 printf("%s\n", file) ;
302 merger.AddFile(file) ;
309 AliInfo(Form("Files merged into %s\n", outFile)) ;
320 //______________________________________________________________________
321 Bool_t AliAnalysisGoodies::Process(TChain * chain)
323 // process events starting from a chain of esd Trees
327 rv = ProcessChain(chain) ;
335 //______________________________________________________________________
336 Bool_t AliAnalysisGoodies::Process(const char * inFile)
338 // process the events with an Analysis Task
339 // usage Process(esdFile)
340 // esdFile: is of the form opt?file_lfn
342 AliRunTagCuts * runCuts = 0x0 ;
343 AliEventTagCuts * evtCuts = 0x0 ;
345 rv = Process(inFile, runCuts, evtCuts) ;
350 //______________________________________________________________________
351 Bool_t AliAnalysisGoodies::Process(const char * inFile, AliRunTagCuts *runCuts, AliEventTagCuts * evtCuts )
353 // process the events with an Analysis Task
354 // usage Process(esdFile, runtagCuts, evtTagCuts)
355 // esdFile: is of the form opt?file_lfn
361 TString file(inFile) ;
362 if ( file.Contains("esd?") && file.Contains(".root") ) {
363 file.ReplaceAll("esd?", "") ;
364 rv = ProcessEsdFile(file.Data()) ;
366 } else if ( file.Contains("esd?") && file.Contains(".xml") ) {
367 file.ReplaceAll("esd?", "") ;
368 rv = ProcessEsdXmlCollection(file.Data()) ;
370 } else if (file.Contains("tag?") && file.Contains(".root") ) {
371 file.ReplaceAll("tag?", "") ;
372 rv = ProcessTagFile(file.Data(), runCuts, evtCuts) ;
374 } else if (file.Contains("tag?") && file.Contains(".xml") ) {
375 file.ReplaceAll("tag?", "") ;
376 rv = ProcessTagXmlCollection(file.Data(), runCuts, evtCuts) ;
379 AliError(Form("%s is not a valid file format", inFile)) ;
389 //______________________________________________________________________
390 Bool_t AliAnalysisGoodies::Process(const char * inFile, const char * runCuts, const char * evtCuts)
392 // process the events with an Analysis Task
393 // usage Process(esdFile, runtagCuts, evtTagCuts)
394 // esdFile: is of the form opt?file_lfn
400 TString file(inFile) ;
401 if ( file.Contains("esd?") && file.Contains(".root") ) {
402 file.ReplaceAll("esd?", "") ;
403 rv = ProcessEsdFile(file.Data()) ;
405 } else if ( file.Contains("esd?") && file.Contains(".xml") ) {
406 file.ReplaceAll("esd?", "") ;
407 rv = ProcessEsdXmlCollection(file.Data()) ;
409 } else if (file.Contains("tag?") && file.Contains(".root") ) {
410 file.ReplaceAll("tag?", "") ;
411 rv = ProcessTagFile(file.Data(), runCuts, evtCuts) ;
413 } else if (file.Contains("tag?") && file.Contains(".xml") ) {
414 file.ReplaceAll("tag?", "") ;
415 rv = ProcessTagXmlCollection(file.Data(), runCuts, evtCuts) ;
418 AliError(Form("%s is not a valid file format", inFile)) ;
428 //______________________________________________________________________
429 Bool_t AliAnalysisGoodies::ProcessChain(TChain * chain) const
436 AliError("No tasks defined") ;
440 // Make the analysis manager
441 AliAnalysisManager * mgr = new AliAnalysisManager("Goodies Manager", "Analysis manager created by AliAnalysisGoodies") ;
444 // The top input must be common to all top tasks
445 TClass * classIn = fTaskInType[0] ;
446 AliAnalysisDataContainer * taskInput = mgr->CreateContainer("InputContainer", classIn, AliAnalysisManager::kInputContainer) ;
448 for (index = 0; index < fnumberOfTasks; index++) {
449 AliAnalysisTask * task = fTaskList[index] ;
452 // Create containers for input/output
453 TClass * classOu = fTaskOuType[index] ;
454 AliAnalysisDataContainer * taskOutput = mgr->CreateContainer(Form("OutputContainer%d",index), classOu, AliAnalysisManager::kOutputContainer,
455 Form("%s.root",task->GetName())) ;
456 mgr->ConnectInput (task, 0, taskInput);
457 mgr->ConnectOutput(task, 0, taskOutput);
461 // taskInput->SetData(chain);
463 if (mgr->InitAnalysis()) {
465 // chain->Process(mgr);
466 mgr->StartAnalysis("local",chain);
473 //______________________________________________________________________
474 Bool_t AliAnalysisGoodies::ProcessEsdFile(const char * esdFile) const
476 // process the events in a single ESD file with an Analysis Task
477 // usage ProcessLocalEsdFile(esdFile)
478 // esdFile: is the root file (local or in alien) with the ESD Tree ( ex: AliESDs.root)
482 printf("*** Process ***\n");
483 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
484 printf("*** Coll = |%s| \n",esdFile);
486 // Makes the ESD chain
487 printf("*** Getting the Chain ***\n");
488 TChain* analysisChain = new TChain(fESDTreeName) ;
489 analysisChain->AddFile(esdFile);
491 // Process the events
492 rv = ProcessChain(analysisChain) ;
497 //______________________________________________________________________
498 Bool_t AliAnalysisGoodies::ProcessTagFile(const char * tagFile, AliRunTagCuts *runCuts, AliEventTagCuts *evtCuts) const
500 // process the events in a single Tag file with an Analysis Task
501 // usage ProcessLocalEsdFile(tagFile)
502 // tagFile: is the root file (local or in alien) with the Tag Tree (ex: Run102.Event0_100.ESD.tag.root)
506 if ( !evtCuts && !runCuts ) {
507 AliError("No Tag cuts provided") ;
511 printf("*** Process ***\n");
512 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
513 printf("*** Coll = |%s| \n",tagFile);
515 AliTagAnalysis * tagAna = new AliTagAnalysis();
516 rv = tagAna->AddTagsFile(tagFile);
520 // Query the tag file and make the analysis chain
521 TChain * analysisChain = new TChain(fESDTreeName) ;
522 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
524 // Process the events
525 rv = ProcessChain(analysisChain) ;
530 //______________________________________________________________________
531 Bool_t AliAnalysisGoodies::ProcessTagFile(const char * tagFile, const char * runCuts, const char * evtCuts) const
533 // process the events in a single Tag file with an Analysis Task
534 // usage ProcessLocalEsdFile(tagFile)
535 // tagFile: is the root file (local or in alien) with the Tag Tree (ex: Run102.Event0_100.ESD.tag.root)
540 if ( !evtCuts && !runCuts ) {
541 AliError("No Tag cuts provided") ;
545 printf("*** Process ***\n");
546 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
547 printf("*** Coll = |%s| \n",tagFile);
549 AliTagAnalysis * tagAna = new AliTagAnalysis();
550 rv = tagAna->AddTagsFile(tagFile);
554 // Query the tag file and make the analysis chain
555 TChain * analysisChain = new TChain(fESDTreeName) ;
556 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
558 // Process the events
559 rv = ProcessChain(analysisChain) ;
564 //______________________________________________________________________
565 Bool_t AliAnalysisGoodies::ProcessEsdXmlCollection(const char * xmlFile) const
567 // process the events in a xml ESD collection with an Analysis Task
568 // usage ProcessLocalEsdFile(xmlFile)
569 // xmlFile: is the local xml file with the ESD collection ( ex: esdCollection.xml)
573 printf("*** Process ***\n");
574 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
575 printf("*** Coll = |%s| \n",xmlFile);
579 TGridCollection * collection = TAlienCollection::Open(xmlFile) ;
581 AliError(Form("%s not found", xmlFile)) ;
585 TGridResult* result = collection->GetGridResult("");
586 TList* analysisfilelist = result->GetFileInfoList();
588 // Makes the ESD chain
589 printf("*** Getting the Chain ***\n");
590 TChain* analysisChain = new TChain(fESDTreeName);
591 analysisChain->AddFileInfoList(analysisfilelist);
593 // Process the events
594 rv = ProcessChain(analysisChain) ;
602 //______________________________________________________________________
603 Bool_t AliAnalysisGoodies::ProcessTagXmlCollection(const char * xmlFile, AliRunTagCuts *runCuts, AliEventTagCuts * evtCuts) const
605 // process the events in a xml ESD collection with an Analysis Task
606 // usage ProcessLocalEsdFile(xmlFile)
607 // xmlFile: is the local xml file with the tag collection ( ex: tagCollection.xml)
611 if ( !evtCuts && !runCuts ) {
612 AliError("No Tag cuts provided") ;
616 printf("*** Process ***\n");
617 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
618 printf("*** Coll = |%s| \n",xmlFile);
620 // check if file is local or alien
621 if ( gSystem->AccessPathName(xmlFile) )
622 TGrid::Connect("alien://");
626 TGridCollection * collection = TAlienCollection::Open(xmlFile) ;
628 AliError(Form("%s not found", xmlFile)) ;
632 TGridResult* result = collection->GetGridResult("");
633 AliTagAnalysis * tagAna = new AliTagAnalysis();
634 tagAna->ChainGridTags(result);
636 // Query the tag file and make the analysis chain
637 TChain * analysisChain = new TChain(fESDTreeName) ;
638 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
640 // Process the events
641 rv = ProcessChain(analysisChain) ;
649 //______________________________________________________________________
650 Bool_t AliAnalysisGoodies::ProcessTagXmlCollection(const char * xmlFile, const char * runCuts, const char * evtCuts) const
652 // process the events in a xml ESD collection with an Analysis Task
653 // usage ProcessLocalEsdFile(xmlFile)
654 // xmlFile: is the local xml file with the tag collection ( ex: tagCollection.xml)
658 if ( !evtCuts && !runCuts ) {
659 AliError("No Tag cuts provided") ;
663 printf("*** Process ***\n");
664 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
665 printf("*** Coll = |%s| \n",xmlFile);
669 // check if file is local or alien
670 if ( gSystem->AccessPathName(xmlFile) )
671 TGrid::Connect("alien://");
673 TGridCollection * collection = TAlienCollection::Open(xmlFile) ;
675 AliError(Form("%s not found", xmlFile)) ;
679 TGridResult* result = collection->GetGridResult("");
680 AliTagAnalysis * tagAna = new AliTagAnalysis();
681 tagAna->ChainGridTags(result);
683 // Query the tag file and make the analysis chain
684 TChain * analysisChain = new TChain(fESDTreeName) ;
685 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
687 // Process the events
688 rv = ProcessChain(analysisChain) ;
696 //______________________________________________________________________
697 Bool_t AliAnalysisGoodies::Register( const char * lfndir, const char * pfndir, const char * file)
699 // register files already stored in a MSS into the AliEn catalog
700 // usage: Register(lfndir, pfndir, pfnFileName)
701 // lfndir : AliEn directory ( ex: /alice/data/2006/LHC06c/PHOS_TestBeam/ )
702 // pfndir : MSS directory ( ex: /castor/cern.ch/alice/testbeam/phos/2006 )
703 // file : text file with a list of the file names to be registered
711 AliError(Form("Cannot open file %s\n", file)) ;
715 TGrid::Connect("alien://");
717 char fileName[1024] ;
725 sprintf(lfn, "%s/%s", lfndir, fileName) ;
729 sprintf(pfn, "castor://Alice::CERN::Castor2/%s/%s", pfndir, fileName) ;
731 printf("Register %s as %s\n", pfn, lfn) ;
733 gGrid->Register(lfn, pfn) ;
742 //______________________________________________________________________
743 void AliAnalysisGoodies::SetTasks(Int_t nb, AliAnalysisTask ** taskList, TClass ** inputType, TClass ** outputType)
745 // define a task with its output and input type
749 fTaskList = taskList ;
750 fTaskInType = inputType ;
751 fTaskOuType = outputType ;