diff -N MergeMCBunches.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ MergeMCBunches.java	6 Nov 2012 00:10:30 -0000	1.1
@@ -0,0 +1,192 @@

+package org.lcsim.hps.users.meeg;
+
+import hep.physics.event.generator.MCEvent;
+import java.io.*;
+
+import java.util.ArrayList;
+import java.util.List;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+import org.lcsim.event.EventHeader;
+import org.lcsim.event.MCParticle;
+import org.lcsim.event.SimCalorimeterHit;
+import org.lcsim.event.SimTrackerHit;
+import org.lcsim.event.base.BaseLCSimEvent;
+import org.lcsim.util.lcio.LCIOReader;
+import org.lcsim.util.lcio.LCIOWriter;
+
+/**
+ * Selects LCIO events passing a cut; spaces out these events with blank events.
+ * Intended use is to clean up a photon-run MC file before running trigger and readout sim.
+ * Can also be used to chain multiple LCIO files together.
+ *
+ * @author Sho Uemura <[log in to unmask]>
+ * @version $Id: MergeMCBunches.java,v 1.1 2012/11/06 00:10:30 meeg Exp $
+ */
+public class MergeMCBunches {
+
+    /**
+     * Defines command line options for this program.
+     *
+     * @return The command line options.
+     */
+    private static Options createCommandLineOptions() {
+        Options options = new Options();
+        options.addOption(new Option("f", true, "Number of bunches merged for front SVT layers (default 4)"));
+        options.addOption(new Option("r", true, "Number of bunches merged for rear SVT layers (default 8)"));
+        options.addOption(new Option("s", true, "LCIO file containing signal events"));
+        options.addOption(new Option("n", true, "Number of events to read"));
+        return options;
+    }
+
+    public static void main(String[] args) {
+        // Set up command line parsing.
+        Options options = createCommandLineOptions();
+        CommandLineParser parser = new PosixParser();
+
+        // Parse command line arguments.
+        CommandLine cl = null;
+        try {
+            cl = parser.parse(options, args);
+        } catch (ParseException e) {
+            throw new RuntimeException("Problem parsing command line options.", e);
+        }
+
+        String[] parsedArgs = cl.getArgs();
+
+        if (parsedArgs.length < 2) {
+            System.out.println("FilterMCBunches <input files> <output file>");
+            HelpFormatter help = new HelpFormatter();
+            help.printHelp(" ", options);
+            System.exit(1);
+        }
+
+        String outFileName = parsedArgs[parsedArgs.length - 1];
+
+        LCIOWriter writer = null;
+        try {
+            writer = new LCIOWriter(new File(outFileName));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+
+        int nEvents = -1;
+        if (cl.hasOption("n")) {
+            nEvents = Integer.valueOf(cl.getOptionValue("n"));
+        }
+        int readEvents = 0;
+        int writtenEvents = 0;
+
+        int mergeN = 8;
+        if (cl.hasOption("r")) {
+            mergeN = Integer.valueOf(cl.getOptionValue("r"));
+        }
+        int mergeFront = 4;
+        if (cl.hasOption("f")) {
+            mergeFront = Integer.valueOf(cl.getOptionValue("f"));
+        }
+        int frontLayers = 6;
+
+        LCIOReader signalReader = null;
+        if (cl.hasOption("s")) {
+            try {
+                signalReader = new LCIOReader(new File(cl.getOptionValue("s")));
+                System.out.println("Opened input file " + cl.getOptionValue("s"));
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+
+        String detectorName = null;
+
+        List<MCParticle> mcParticles = new ArrayList<MCParticle>();
+        List<SimTrackerHit> trackerHits = new ArrayList<SimTrackerHit>();
+        List<SimCalorimeterHit> ecalHits = new ArrayList<SimCalorimeterHit>();
+
+        fileLoop:
+        for (int fileNumber = 0; fileNumber < parsedArgs.length - 1; fileNumber++) {
+            LCIOReader reader = null;
+            String inFileName = parsedArgs[fileNumber];
+            try {
+                reader = new LCIOReader(new File(inFileName));
+                System.out.println("Opened input file " + inFileName);
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+
+            eventLoop:
+            while (true) {
+                if (nEvents != -1 && readEvents == nEvents) {
+                    break fileLoop;
+                }
+                EventHeader event;
+                try {
+                    event = reader.read();
+                } catch (IOException e) {
+                    break eventLoop;
+                }
+                readEvents++;
+                mcParticles.addAll(event.get(MCParticle.class, MCEvent.MC_PARTICLES));
+                ecalHits.addAll(event.get(SimCalorimeterHit.class, "EcalHits"));
+//                trackerHits.addAll(event.get(SimTrackerHit.class, "TrackerHits"));
+                for (SimTrackerHit hit : event.get(SimTrackerHit.class, "TrackerHits")) {
+                    if (hit.getLayer() < frontLayers) {
+                        if (readEvents % mergeN < mergeFront) {
+                            trackerHits.add(hit);
+                        }
+                    } else {
+                        trackerHits.add(hit);
+                    }
+                }
+
+                if (detectorName == null) {
+                    detectorName = event.getDetectorName();
+                }
+
+                if (readEvents % mergeN == 0) {
+                    EventHeader newEvent = new BaseLCSimEvent(event.getRunNumber(), event.getEventNumber(), detectorName);
+                    if (cl.hasOption("s")) {
+                        EventHeader signalEvent = null;
+                        try {
+                            signalEvent = signalReader.read();
+                        } catch (IOException e) {
+                            break fileLoop;
+                        }
+                        mcParticles.addAll(signalEvent.get(MCParticle.class, MCEvent.MC_PARTICLES));
+                        ecalHits.addAll(signalEvent.get(SimCalorimeterHit.class, "EcalHits"));
+                        trackerHits.addAll(signalEvent.get(SimTrackerHit.class, "TrackerHits"));
+                    }
+                    newEvent.put(MCEvent.MC_PARTICLES, mcParticles);
+                    newEvent.put("EcalHits", ecalHits);
+                    newEvent.put("TrackerHits", trackerHits);
+                    try {
+                        writer.write(newEvent);
+                    } catch (IOException e) {
+                        throw new RuntimeException(e);
+                    }
+                    writtenEvents++;
+                    mcParticles.clear();
+                    ecalHits.clear();
+                    trackerHits.clear();
+                }
+            }
+            try {
+                reader.close();
+            } catch (IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+
+        System.out.format("Read %d events, wrote %d\n", readEvents, writtenEvents);
+        try {
+            writer.close();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+}

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