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These instructions assume "hps-java.jar" is the hps-java jar file you downloaded using the instructions on Basic Use of hps-java, or compiled yourself.
The input data for this step is readout data; use either real 2012 test run data (EVIO format) or generate from simulation using the instructions in Running Readout Simulation.
Use TestRunOfflineRecon.lcsim for both test run data; substitute HPS2014OfflineRecon.lcsim for simulated 2014 data.
java -cp hps-java.jar org.lcsim.hps.evio.TestRunEvioToLcio -r -x /org/lcsim/hps/steering/recon/TestRunOfflineRecon.lcsim -d HPS-TestRun-v3 prod/hps_001351.evio.0 -DoutputFile=recon.slcio
Note: the "-d HPS-TestRun-v3" specifies the detector to be used in the reconstruction and is required. "HPS-TestRun-v3" is the latest as of this note, but make sure you ask the production manager about what detector to use for your purpose.
java -cp hps-java.jar org.lcsim.hps.evio.TestRunEvioToLcio -d HPS-TestRun-v3 prod/hps_001351.evio.0 -l raw.slcio java -jar hps-java.jar -r /org/lcsim/hps/steering/recon/TestRunOfflineRecon.lcsim -i raw.slcio -DoutputFile=recon
This is just the second half of the two-step process.
java -jar hps-java.jar -r /org/lcsim/hps/steering/recon/TestRunOfflineRecon.lcsim -i raw.slcio -DoutputFile=recon
java -jar hps-java.jar -r /org/lcsim/hps/steering/readout/HPSTrackingDefaults.lcsim -i ap2.2gev075mev_001_SLIC.slcio -DoutputFile=ap_recon.slcio