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+{{indexmenu_n>5}}
+[[:|<< back to HepSim manual]]
+====== Analysis of LCIO files  ======
+Currently, the Geant4-based detector simulation can be done using the SLIC software. You will need to convert ProMC files to LCIO files and
+use these files for the "slic" Geant4-based program.
+To process SLCIO files, you will need [[http://atlaswww.hep.anl.gov/asc/jas4pp/|Jas4pp]]  program.
+The files with full simulations are located under the "rfullNNN" tags ("NNN" is a number)
+Here how you can find all samples that have "rfull" tag for download. Click here: [[https://atlaswww.hep.anl.gov/hepsim/list.php?find=rfull]].
+The description of the detector tags is given in [[:hepsim:usage_detectors|Detector description]].
+ If you need to find all  files
+for a give tag, say rfull005, use this command:
+<code bash>
+hs-find tev10mumu%rfull005
+</code>
+which searches for all samples with the dataset name "tev10mumu" (mu+mu-, 40 TeV samples).
+Then download a selected sample as:
+<code bash>
+hs-get tev10mumu_pythia6_zprime10tev_qqbar%rfull005
+</code>
+The [[https://atlaswww.hep.anl.gov/hepsim/soft/detectors/| detector repository]] contains the description of available detectors.
+Each "rfullNNN" tag corresponds to the  detector given in the  [[https://atlaswww.hep.anl.gov/hepsim/soft/detectors/| detector repository]].
+The physics performance studies based on full simulation files from HepSim
+are  [[fcs:start|listed here]].
+====== Processing LCIO files  ======
+To perform data analysis using LCIO files, use the [[https://atlaswww.hep.anl.gov/asc/jas4pp/|Jas4pp]] data-analysis package.
+The installation does not have external dependencies besides Java. Make sure Java7 and above is installed.
+Then run these commands to install the package using Linux/Mac with the "bash" shell:
+<code bash>
+wget https://atlaswww.hep.anl.gov/asc/jas4pp/download/current.php -O jas4pp.tgz
+tar -zvxf jas4pp.tgz
+cd jas4pp
+source ./setup.sh # takes 5 sec for first-time optimization
+</code>
+The last command optimizes Java packages for the Python language.
+Now you are ready to run over  any file with truth-level and datector-simulation files, such as LCIO and ProMC. This program can be used for:
+  * Downloading and searching HepSim data
+  * Processing ProMC files from HepSim
+  * Running over SLCIO files with Geant4 simulated / reconstructed events.
+  * Data analysis (jets, physics vectors, histogram packages)
+  * Visualisation of reconstructed events using Wired4 display
+You can find more details in [[hepsim:jas4pp|Jas4pp manual]]. The examples showing how to run over SLCIO files using [[https://atlaswww.hep.anl.gov/asc/jas4pp/|Jas4pp]] are located in the "examples/slic" directory of the Jas4pp package.
+The standard set of containers is available from the LCIO files posted on HepSim. Read [[http://lcio.desy.de/v02-04-03/doc/manual_html/manual.html|Manual]]. The API is described in [[http://lcio.desy.de/v02-04-03/doc/api/| LCIO Java API description]].
+Look the Java API definition of the needed objects in [[http://www.lcsim.org/sites/lcsim/apidocs/org/lcsim/lcio/package-summary.html|org.lcsim.lcio]]. The data containers are shown below:
+<hidden>
+<code>
+BeamCalHits
+CalorimeterHitRelations
+EM_BARREL
+EM_ENDCAP
+EcalBarrelHits
+EcalEndcapHits
+HAD_BARREL
+HAD_ENDCAP
+HcalBarrelHits
+HcalEndcapHits
+HelicalTrackHitRelations
+HelicalTrackHits
+HelicalTrackMCRelations
+LumiCalHits
+MCParticle
+MUON_BARREL
+MUON_ENDCAP
+MuonBarrelHits
+MuonEndcapHits
+PandoraPFOCollection
+ReconClusters
+SiTrackerBarrelHits
+SiTrackerEndcapHits
+SiTrackerForwardHits
+SiVertexBarrelHits
+SiVertexEndcapHits
+StateAtECal
+StateAtEnd
+StateAtStart
+TKR_RawTrackerHits
+TKR_TrackerHits
+Tracks
+VXD_RawTrackerHits
+VXD_TrackerHits
+</code>
+</hidden>
+====== Using C++/ROOT with LCIO ======
+If you need to read LCIO files in C++ code with ROOT/FastJet, use the example package [[https://github.com/chekanov/HepSim]].
+<code bash>
+git clone https://github.com/chekanov/HepSim
+cd HepSim/analysis/cpp_lcio
+</code>
+Look at README file to see how to install the "LCIO" package required by this example.  Your LCIO" files from HepSim should be in the directory "data".
+Generally, you program to read SLCIO files can look as this:
+<hidden Click here to show the code example>
+<code cpp>
+string input="data.slcio";
+LCReader* lcReader = LCFactory::getInstance()->createLCReader() ;
+lcReader->open( infile1.c_str() ) ;
+LCEvent*  evt;
+int nEvents=0;
+while( (evt = lcReader->readNextEvent()) != 0 ) {
+      if (nEvents==0) UTIL::LCTOOLS::dumpEvent( evt ) ;
+           cout << "  Run : " << evt->getRunNumber() << " Detector: "      << evt->getDetectorName() <<  endl ;
+           // print stored EVGEN parameters
+           const LCParameters& params=evt->getParameters();
+           StringVec floatKeys ;
+           int nFloatParameters = params.getFloatKeys( floatKeys ).size() ;
+           for(int i=0; i< nFloatParameters ; i++ ){
+              FloatVec floatVec ;
+              params.getFloatVals(  floatKeys[i], floatVec ) ;
+              int nFloat  = floatVec.size()  ;
+              cout << " parameter " << floatKeys[i] << " [float]: " ;
+              for(int j=0; j< nFloat ; j++ ){
+                    cout << floatVec[j] << ", " ;
+                }
+               cout << endl ;
+               }
+  // extract PFA objects
+  IMPL::LCCollectionVec* col = (IMPL::LCCollectionVec*) evt->getCollection( "PandoraPFOCollection"  ) ;
+  int nPFO = col->getNumberOfElements() ;
+  for(int i=0 ; i<nPFO ; ++i){
+      EVENT::ReconstructedParticle* mcp =  (EVENT::ReconstructedParticle*) col->getElementAt(i) ;
+      double px = mcp->getMomentum()[0];
+      double py = mcp->getMomentum()[1];
+      double pz = mcp->getMomentum()[2];
+     }
+  // look at tracks
+  IMPL::LCCollectionVec* col3 = (IMPL::LCCollectionVec*) evt->getCollection( "Tracks"  ) ;
+  int nTRK = col3->getNumberOfElements() ;
+    for(int i=0 ; i<nTRK ; ++i){
+      EVENT::Track* mcp =  (EVENT::Track*) col3->getElementAt(i) ;
+  }
+   nEvents ++ ;
+   }
+  lcReader->close() ;
+</code>
+</hidden>
+This code example shows how to print float parameters from the EVGEN level (copied from the input ProMC).
+Here is the example of all parameters (float, integers, strings):
+<hidden>
+<code cpp>
+ parameter EVGEN:Code [int]: 10,
+ parameter EVGEN:DIS:ISR [int]: 0,
+ parameter EVGEN:ID1 [int]: 11,
+ parameter EVGEN:ID2 [int]: 2212,
+ parameter EVGEN:ProcessID [int]: 10,
+ parameter EVGEN:AlphaQCD [float]: 0.00255778,
+ parameter EVGEN:AlphaQED [float]: 0.243193,
+ parameter EVGEN:DIS:Q2 [float]: 12.4407,
+ parameter EVGEN:DIS:W [float]: 69.6586,
+ parameter EVGEN:DIS:XBJ [float]: 0.00255778,
+ parameter EVGEN:DIS:YBJ [float]: 0.243193,
+ parameter EVGEN:EventsRequested [float]: 50000,
+ parameter EVGEN:PDF1 [float]: 0,
+ parameter EVGEN:PDF2 [float]: 0,
+ parameter EVGEN:Scale [float]: 69.6586,
+ parameter EVGEN:ScalePDF [float]: 12.4407,
+ parameter EVGEN:SigmaErrorPB [float]: 737.376,
+ parameter EVGEN:SigmaPB [float]: 164882,
+ parameter EVGEN:Weight [float]: 1,
+ parameter EVGEN:X1 [float]: 0.00255778,
+ parameter EVGEN:X2 [float]: 0.243193,
+ parameter EVGEN:eCM [float]: 141,
+ parameter _weight [float]: 1,
+ parameter EVGEN:Process [string]: e-p,
+ parameter GEANT4_VERSION [string]: 10.2.0,
+ parameter HepSim [string]: 1.1,
+ parameter ProcessID [string]: -1,
+ parameter SLIC_VERSION [string]: 5.0.0,
+</code>
+</hidden>
+Note that SLCIO files have two records representing truth level MC: MCParticle and MCInfo. MCInfo includes information on generated events.
+See the example how this record was created in [[https://github.com/Argonne-National-Laboratory/ProMC/blob/master/examples/promc2lcio/promc2lcio.java|promc2lcio.java]].
+ --- //[[[email protected]|Sergei Chekanov]] 2016/09/19 07:06//
+====== Visualizing events with Jas+Wired ======
+You can run Jas+Wired to visualize the simulated events.  The Wired program is included in Jas4pp, so you simply run it as:
+<code bash>
+./jaspp
+</code>
+This will start a Jas3-like environment  with all needed plugins.
+Then copy the detector geometry file from the [[http://atlaswww.hep.anl.gov/hepsim/soft/detectors/| detector repository]].
+<code bash>
+wget http://atlaswww.hep.anl.gov/hepsim/soft/detectors/sidloi3.tgz -O - | tar -xz;
+</code>
+This will create a directory "sidloi3". This detector corresponds to "rfull001" tag used for the reconstruction of pythia6_zpole_ee (Z->e+e-).
+Now we can visualize the detector as **[File]-[Open data source]-[HepRep]** XML and select the file "sidloi3.heprep" from sidloi3.tgz:
+This is how to do this using the command line:
+<code bash>
+./jaspp  sidloi3.heprep
+</code>
+You will see the detector layout:
+{{:fcs:detector.png?400|Whired4 event display}}
+Now, we will read the event: Open any *.slcio file you copied from HepSim as
+**[File]-[Open data source]-[LCIO]** file.  Then click a small button [Go] (top menu bar). It will process
+ events.  Then select again **[File]-[New]-[Wired 4 view]**.  You will get an image in the Wired4 display.
+Now press [Go] again to look at next event.
+ If you want to see how data records are organized inside the slcio file,
+do this **[File]-[New]-[LCSim Event browser]**
+Generally, when you open a SLCIO file from the HepSim, you do not need to load the geometry file. The geometry file will be downloaded automatically from HepSim and will be put to ".lcsim/cache/" inside your home directory.
+====== Visualizing geometry using ROOT ======
+(contribution from N.Nikiforou):
+You can also visualize the detector using ROOT. Here are a few steps:
+Locate the file detector.gdml inside the file detector.zip (where "detector" shows the name of the detector).
+<hidden show more details here>
+This file is created using this command during the detector design stage
+<code>
+slic -g detector.lcdd -G detector.gdml
+</code>
+</hidden>
+Once you have the GDML file, you can use ROOT to visualize it. You just
+need to make sure the ROOT installation has openGL/GDML support (CERN
+AFS installations have it for sure). At the ROOT prompt do:
+<code cpp>
+TGeoManager::Import("detector.gdml");
+gGeoManager->GetTopVolume()->Draw("ogl");
+</code>
+This should popup an OpenGL display with the detector which you can clip, pan, rotate etc. You will the image as shown here:
+{{:hepsim:detector_jas4pp.png?400|}}
+====== People ======
+  * S.Chekanov (ANL, main developer)
+  * E.May (ANL, debugging, Wired4)
+====== Additional help ======
+  * [[http://jas.freehep.org/jas3/]] - JAS3
+  * [[http://java.freehep.org/]] - FreeHep
+  * [[http://jwork.org/dmelt]] - DMelt
+  * [[https://confluence.slac.stanford.edu/display/ilc/ILC+Detector+Simulation+FAQ]] - SLIC
+  * [[https://confluence.slac.stanford.edu/display/ilc/LCSim+Tutorials]] - SLIC
+  * [[https://atlaswww.hep.anl.gov/asc/promc/]] ProMC file format
+  * [[http://lcio.desy.de/]] LCIO file format
+ --- //[[[email protected]|Sergei Chekanov]] 2016/03/23 21:53//