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>
37 #include <TFileMerger.h>
41 #include <TEntryList.h>
43 //______________________________________________________________________________
44 AliAnalysisGoodies::AliAnalysisGoodies() :
45 fESDTreeName("esdTree"),
53 TString token = gSystem->Getenv("GRID_TOKEN") ;
56 TGrid::Connect("alien://");
58 AliInfo("You are not connected to the GRID") ;
61 //______________________________________________________________________________
62 void AliAnalysisGoodies::Help() const
64 AliInfo("Analysis utilities:\n") ;
65 printf(" *** Alien2Local : copy files ESD files listed in an xml collection from AliEn catalog to local storage and creates a local xml collection \n") ;
66 printf(" usage: Alien2Local(in, out)\n") ;
67 printf(" in: a xml esd collection file name \n") ;
68 printf(" ou: the local directory where to save the esd root files \n") ;
69 printf(" *** Make : makes esd collection from tags \n") ;
70 printf(" usage: Make(tags, esds)\n") ;
71 printf(" tags: is either a tag root file or an xml tag collection \n") ;
72 printf(" esds: is an esd collection \n") ;
73 printf(" *** Merge : merges files listed in a xml collection \n") ;
74 printf(" usage Merge(collection, outputDile)\n") ;
75 printf(" collection: is a xml collection \n") ;
76 printf(" *** Process : process the events with an Analysis Task \n") ;
77 printf(" usage: Process(esdFile, tagCuts) \n") ;
78 printf(" esdFile: can be a root file with the ESD Tree ( ex: esd?AliESDs.root) \n") ;
79 printf(" or a root file with the Tag Tree ( ex: tag?Run100.Event0_100.ESD.tag.root) \n") ;
80 printf(" or a local or alien xml file with the ESD collection ( ex: esd?esdCollection.xml) \n") ;
81 printf(" or a local or alien xml file with the TAG collection ( ex: tag?tagCollection.xml) \n") ;
82 printf(" or a TChain of esd TTrees \n") ;
83 printf(" tagCuts: is the AliEventTagCuts (needed only for tag? cases \n") ;
84 printf(" *** Register: register files already stored in a MSS into the AliEn catalog\n") ;
85 printf(" usage: Register(lfndir, pfndir, pfnFileName) \n") ;
86 printf(" lfndir : AliEn directory ( ex: /alice/data/2006/LHC06c/PHOS_TestBeam/\n") ;
87 printf(" pfndir : MSS directory ( ex: /castor/cern.ch/alice/testbeam/phos/2006 \n") ;
88 printf(" file : text file with a list of the file names to be registered\n ") ;
92 //______________________________________________________________________
93 const Bool_t AliAnalysisGoodies::Alien2Local(const TString collectionNameIn, const TString localDir)
95 // copy files ESD files listed in an xml collection from AliEn catalog to local storage and creates a local xml collection
96 // usage: Alien2Local(in, out)
97 // in: a xml esd collection file name
98 // ou: the local directory where to save the esd root files
104 AliXMLCollection * collectionIn = AliXMLCollection::Open(collectionNameIn) ;
105 collectionIn->Reset() ;
107 AliXMLCollection * collectionOu = new AliXMLCollection() ;
108 TString collectionNameOu(collectionIn->GetCollectionName()) ;
109 collectionNameOu.Append("Local") ;
110 collectionOu->SetCollectionName(collectionNameOu) ;
111 collectionOu->WriteHeader() ;
115 const char* ocwd = gSystem->WorkingDirectory();
118 while ( collectionIn->Next() ) {
119 gSystem->ChangeDirectory(localDir) ;
120 TString fileTURL = collectionIn->GetTURL("") ;
122 TString tempo(fileTURL) ;
123 tempo.Remove(tempo.Last('/'), tempo.Length()) ;
124 TString evtsNumber = tempo(tempo.Last('/')+1, tempo.Length())+"/";
125 tempo.Remove(tempo.Last('/'), tempo.Length()) ;
126 TString runNumber = tempo(tempo.Last('/')+1, tempo.Length())+"/" ;
127 TString dir = localDir + runNumber ;
130 sprintf(line, ".! mkdir -p %s", dir.Data()) ;
131 gROOT->ProcessLine(line) ;
132 printf("***************************%s\n", line) ;
133 TEntryList * list = collectionIn->GetEventList("") ;
135 list = new TEntryList() ;
137 TString filename = tempo(tempo.Last('/')+1, tempo.Length()) ;
139 AliInfo(Form("Copying %s to %s\n", fileTURL.Data(), dir.Data())) ;
140 collectionOu->WriteBody(counter, collectionIn->GetGUID(""), collectionIn->GetLFN(""), dir, list) ;
142 merger.Cp(fileTURL, dir) ;
144 collectionOu->Export() ;
145 gSystem->ChangeDirectory(ocwd) ;
153 //______________________________________________________________________
154 const Bool_t AliAnalysisGoodies::Make(AliRunTagCuts *runCuts, AliEventTagCuts *evtCuts, const char * in, const char * out) const
156 // makes esd collection from tags
157 // usage Make(tags, esds)
158 // tags: is either a tag root file or an xml tag collection
159 // esds: is an esd collection
163 if ( !evtCuts && !runCuts ) {
164 AliError("No Tag cuts provided") ;
169 if ( file.Contains(".root") )
170 rv = MakeEsdCollectionFromTagFile(runCuts, evtCuts, file.Data(), out) ;
171 else if ( file.Contains(".xml") )
172 rv = MakeEsdCollectionFromTagCollection(runCuts, evtCuts, file.Data(), out) ;
174 AliError(Form("%s is not a valid file format", in)) ;
181 //______________________________________________________________________
182 const Bool_t AliAnalysisGoodies::MakeEsdCollectionFromTagFile(AliRunTagCuts *runCuts, AliEventTagCuts *evtCuts, const char * in, const char * out) const
184 // Makes an esd collection from a root tag file
186 // Open the file collection
187 printf("*** Create Collection ***\n");
188 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
189 printf("*** file = |%s| \n",in);
191 AliTagAnalysis * tagAna = new AliTagAnalysis();
192 rv = tagAna->AddTagsFile(in);
196 tagAna->CreateXMLCollection(out, runCuts, evtCuts) ;
202 //______________________________________________________________________
203 const Bool_t AliAnalysisGoodies::MakeEsdCollectionFromTagCollection(AliRunTagCuts * runCuts, AliEventTagCuts * evtCuts, const char * in, const char * out) const
205 // Makes an esd collection from a xml tag collection
207 // Open the file collection
208 printf("*** Create Collection ***\n");
209 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
210 printf("*** Coll = |%s| \n",in);
214 TAlienCollection * collection = TAlienCollection::Open(in);
215 TGridResult* result = collection->GetGridResult("");
216 AliTagAnalysis * tagAna = new AliTagAnalysis();
217 tagAna->ChainGridTags(result);
219 tagAna->CreateXMLCollection(out, runCuts, evtCuts) ;
227 //______________________________________________________________________
228 const Bool_t AliAnalysisGoodies::MakeEsdCollectionFromTagCollection(const char * runCuts, const char * evtCuts, const char * in, const char * out) const
230 // Makes an esd collection from a xml tag collection
234 // Open the file collection
235 printf("*** Create Collection ***\n");
236 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
237 printf("*** Coll = |%s| \n",in);
241 TAlienCollection * collection = TAlienCollection::Open(in);
242 TGridResult* result = collection->GetGridResult("");
243 AliTagAnalysis * tagAna = new AliTagAnalysis();
244 tagAna->ChainGridTags(result);
246 tagAna->CreateXMLCollection(out, runCuts, evtCuts) ;
254 //______________________________________________________________________
255 const Bool_t AliAnalysisGoodies::Merge(const char * collectionFile, const char * subFile, const char * outFile)
257 // merges files listed in a xml collection
258 // usage Merge(collection, outputFile))
259 // collection: is a xml collection
263 if ( strstr(collectionFile, ".xml") == 0 ) {
264 AliError("Input collection file must be an \".xml\" file\n") ;
270 // Open the file collection
271 printf("*** Create Collection ***\n");
272 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
273 printf("*** Coll = |%s| \n",collectionFile);
277 TAlienCollection * collection = TAlienCollection::Open(collectionFile);
278 TGridResult* result = collection->GetGridResult("");
284 TString tempo(collectionFile) ;
286 tempo.ReplaceAll(".xml", subFile) ;
288 tempo.ReplaceAll(".xml", "_Merged.root") ;
289 outFile = tempo.Data() ;
291 merger.OutputFile(outFile) ;
293 while ( (turl = result->GetKey(index, "turl")) ) {
296 sprintf(file, "%s#%s", turl, subFile) ;
298 sprintf(file, "%s", turl) ;
300 printf("%s\n", file) ;
301 merger.AddFile(file) ;
308 AliInfo(Form("Files merged into %s\n", outFile)) ;
319 //______________________________________________________________________
320 const Bool_t AliAnalysisGoodies::Process(TChain * chain)
322 // process events starting from a chain of esd Trees
327 rv = ProcessChain(chain) ;
335 //______________________________________________________________________
336 const 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 const 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 const 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 const Bool_t AliAnalysisGoodies::ProcessChain(TChain * chain) const
436 AliError("No tasks defined") ;
440 // Make the analysis manager
441 AliAnalysisManager * mgr = new AliAnalysisManager() ;
444 // The top input must be common to all top tasks
445 TClass * classIn = fTaskInType[0] ;
446 AliAnalysisDataContainer * taskInput = mgr->CreateContainer("Input Container", 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("Output Container", classOu, AliAnalysisManager::kOutputContainer) ;
455 mgr->ConnectInput (task, 0, taskInput);
456 mgr->ConnectOutput(task, 0, taskOutput);
460 taskInput->SetData(chain);
462 if (mgr->InitAnalysis()) {
471 //______________________________________________________________________
472 const Bool_t AliAnalysisGoodies::ProcessEsdFile(const char * esdFile) const
474 // process the events in a single ESD file with an Analysis Task
475 // usage ProcessLocalEsdFile(esdFile)
476 // esdFile: is the root file (local or in alien) with the ESD Tree ( ex: AliESDs.root)
480 printf("*** Process ***\n");
481 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
482 printf("*** Coll = |%s| \n",esdFile);
484 // Makes the ESD chain
485 printf("*** Getting the Chain ***\n");
486 TChain* analysisChain = new TChain(fESDTreeName) ;
487 analysisChain->AddFile(esdFile);
489 // Process the events
490 rv = ProcessChain(analysisChain) ;
495 //______________________________________________________________________
496 const Bool_t AliAnalysisGoodies::ProcessTagFile(const char * tagFile, AliRunTagCuts *runCuts, AliEventTagCuts *evtCuts) const
498 // process the events in a single Tag file with an Analysis Task
499 // usage ProcessLocalEsdFile(tagFile)
500 // tagFile: is the root file (local or in alien) with the Tag Tree (ex: Run102.Event0_100.ESD.tag.root)
504 if ( !evtCuts && !runCuts ) {
505 AliError("No Tag cuts provided") ;
509 printf("*** Process ***\n");
510 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
511 printf("*** Coll = |%s| \n",tagFile);
513 AliTagAnalysis * tagAna = new AliTagAnalysis();
514 rv = tagAna->AddTagsFile(tagFile);
518 // Query the tag file and make the analysis chain
519 TChain * analysisChain = new TChain(fESDTreeName) ;
520 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
522 // Process the events
523 rv = ProcessChain(analysisChain) ;
528 //______________________________________________________________________
529 const Bool_t AliAnalysisGoodies::ProcessTagFile(const char * tagFile, const char * runCuts, const char * evtCuts) const
531 // process the events in a single Tag file with an Analysis Task
532 // usage ProcessLocalEsdFile(tagFile)
533 // tagFile: is the root file (local or in alien) with the Tag Tree (ex: Run102.Event0_100.ESD.tag.root)
538 if ( !evtCuts && !runCuts ) {
539 AliError("No Tag cuts provided") ;
543 printf("*** Process ***\n");
544 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
545 printf("*** Coll = |%s| \n",tagFile);
547 AliTagAnalysis * tagAna = new AliTagAnalysis();
548 rv = tagAna->AddTagsFile(tagFile);
552 // Query the tag file and make the analysis chain
553 TChain * analysisChain = new TChain(fESDTreeName) ;
554 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
556 // Process the events
557 rv = ProcessChain(analysisChain) ;
562 //______________________________________________________________________
563 const Bool_t AliAnalysisGoodies::ProcessEsdXmlCollection(const char * xmlFile) const
565 // process the events in a xml ESD collection with an Analysis Task
566 // usage ProcessLocalEsdFile(xmlFile)
567 // xmlFile: is the local xml file with the ESD collection ( ex: esdCollection.xml)
571 printf("*** Process ***\n");
572 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
573 printf("*** Coll = |%s| \n",xmlFile);
577 TAlienCollection * collection = TAlienCollection::Open(xmlFile) ;
579 AliError(Form("%s not found", xmlFile)) ;
583 TGridResult* result = collection->GetGridResult("");
584 TList* analysisfilelist = result->GetFileInfoList();
586 // Makes the ESD chain
587 printf("*** Getting the Chain ***\n");
588 TChain* analysisChain = new TChain(fESDTreeName);
589 analysisChain->AddFileInfoList(analysisfilelist);
591 // Process the events
592 rv = ProcessChain(analysisChain) ;
600 //______________________________________________________________________
601 const Bool_t AliAnalysisGoodies::ProcessTagXmlCollection(const char * xmlFile, AliRunTagCuts *runCuts, AliEventTagCuts * evtCuts) const
603 // process the events in a xml ESD collection with an Analysis Task
604 // usage ProcessLocalEsdFile(xmlFile)
605 // xmlFile: is the local xml file with the tag collection ( ex: tagCollection.xml)
609 if ( !evtCuts && !runCuts ) {
610 AliError("No Tag cuts provided") ;
614 printf("*** Process ***\n");
615 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
616 printf("*** Coll = |%s| \n",xmlFile);
618 // check if file is local or alien
619 if ( gSystem->AccessPathName(xmlFile) )
620 TGrid::Connect("alien://");
624 TAlienCollection * collection = TAlienCollection::Open(xmlFile) ;
626 AliError(Form("%s not found", xmlFile)) ;
630 TGridResult* result = collection->GetGridResult("");
631 AliTagAnalysis * tagAna = new AliTagAnalysis();
632 tagAna->ChainGridTags(result);
634 // Query the tag file and make the analysis chain
635 TChain * analysisChain = new TChain(fESDTreeName) ;
636 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
638 // Process the events
639 rv = ProcessChain(analysisChain) ;
647 //______________________________________________________________________
648 const Bool_t AliAnalysisGoodies::ProcessTagXmlCollection(const char * xmlFile, const char * runCuts, const char * evtCuts) const
650 // process the events in a xml ESD collection with an Analysis Task
651 // usage ProcessLocalEsdFile(xmlFile)
652 // xmlFile: is the local xml file with the tag collection ( ex: tagCollection.xml)
656 if ( !evtCuts && !runCuts ) {
657 AliError("No Tag cuts provided") ;
661 printf("*** Process ***\n");
662 printf("*** Wk-Dir = |%s| \n",gSystem->WorkingDirectory());
663 printf("*** Coll = |%s| \n",xmlFile);
667 // check if file is local or alien
668 if ( gSystem->AccessPathName(xmlFile) )
669 TGrid::Connect("alien://");
671 TAlienCollection * collection = TAlienCollection::Open(xmlFile) ;
673 AliError(Form("%s not found", xmlFile)) ;
677 TGridResult* result = collection->GetGridResult("");
678 AliTagAnalysis * tagAna = new AliTagAnalysis();
679 tagAna->ChainGridTags(result);
681 // Query the tag file and make the analysis chain
682 TChain * analysisChain = new TChain(fESDTreeName) ;
683 analysisChain = tagAna->QueryTags(runCuts, evtCuts);
685 // Process the events
686 rv = ProcessChain(analysisChain) ;
694 //______________________________________________________________________
695 const Bool_t AliAnalysisGoodies::Register( const char * lfndir, const char * pfndir, const char * file)
697 // register files already stored in a MSS into the AliEn catalog
698 // usage: Register(lfndir, pfndir, pfnFileName)
699 // lfndir : AliEn directory ( ex: /alice/data/2006/LHC06c/PHOS_TestBeam/ )
700 // pfndir : MSS directory ( ex: /castor/cern.ch/alice/testbeam/phos/2006 )
701 // file : text file with a list of the file names to be registered
709 AliError(Form("Cannot open file %s\n", file)) ;
713 TGrid::Connect("alien://");
715 char fileName[1024] ;
723 sprintf(lfn, "%s/%s", lfndir, fileName) ;
727 sprintf(pfn, "castor://Alice::CERN::Castor2/%s/%s", pfndir, fileName) ;
729 printf("Register %s as %s\n", pfn, lfn) ;
731 gGrid->Register(lfn, pfn) ;
740 //______________________________________________________________________
741 void AliAnalysisGoodies::SetTasks(Int_t nb, AliAnalysisTask ** taskList, TClass ** inputType, TClass ** outputType)
743 // define a task with its output and input type
747 fTaskList = taskList ;
748 fTaskInType = inputType ;
749 fTaskOuType = outputType ;