diff -u -r1.3 -r1.4
--- SVTHitWriter.java	2 Apr 2013 01:11:11 -0000	1.3
+++ SVTHitWriter.java	25 Apr 2013 21:33:41 -0000	1.4
@@ -1,14 +1,11 @@

 package org.lcsim.hps.evio;
 
 import java.util.ArrayList;

-import java.util.Collection;

 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import static org.lcsim.hps.evio.EventConstants.SVT_BANK_NUMBER;
 import static org.lcsim.hps.evio.EventConstants.SVT_BANK_TAG;

-import static org.lcsim.hps.evio.EventConstants.SVT_TOTAL_NUMBER_FPGAS;
-

 
 import org.jlab.coda.jevio.DataType;
 import org.jlab.coda.jevio.EventBuilder;

@@ -16,6 +13,7 @@

 import org.jlab.coda.jevio.EvioException;
 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.event.EventHeader;

+import org.lcsim.event.LCRelation;

 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.hps.recon.tracking.FpgaData;
 import org.lcsim.hps.recon.tracking.HPSSVTConstants;

@@ -26,13 +24,14 @@

 /**
  *
  * @author Sho Uemura <[log in to unmask]>

- * @version $Id: SVTHitWriter.java,v 1.3 2013/04/02 01:11:11 meeg Exp $

+ * @version $Id: SVTHitWriter.java,v 1.4 2013/04/25 21:33:41 meeg Exp $

  */
 public class SVTHitWriter implements HitWriter {
 
     boolean debug = false;
     private String hitCollectionName = "SVTRawTrackerHits";
     private String fpgaDataCollectionName = "FPGAData";

+    private String relationCollectionName = "SVTTrueHitRelations";

     String readoutName = "TrackerHits";
 
     public SVTHitWriter() {

@@ -48,14 +47,14 @@

     }
 
     //make some dummy FpgaData to use in case there isn't any real FpgaData

-    private static Map<Integer,FpgaData> makeFpgaData() {

+    private static Map<Integer, FpgaData> makeFpgaData() {

         double[] temps = new double[HPSSVTConstants.TOTAL_HYBRIDS_PER_FPGA * HPSSVTConstants.TOTAL_TEMPS_PER_HYBRID];
         for (int i = 0; i < HPSSVTConstants.TOTAL_HYBRIDS_PER_FPGA * HPSSVTConstants.TOTAL_TEMPS_PER_HYBRID; i++) {
             temps[i] = 23.0;
         }

-                Map<Integer,FpgaData> fpgaData = new HashMap<Integer, FpgaData>();

+        Map<Integer, FpgaData> fpgaData = new HashMap<>();

         for (Integer fpgaNumber : SvtUtils.getInstance().getFpgaNumbers()) {

-            fpgaData.put(fpgaNumber,new FpgaData(fpgaNumber, temps, 0));

+            fpgaData.put(fpgaNumber, new FpgaData(fpgaNumber, temps, 0));

         }
 
         return fpgaData;

@@ -65,15 +64,15 @@

     public void writeData(EventHeader event, EventBuilder builder) {
 
         List<RawTrackerHit> hits = event.get(RawTrackerHit.class, hitCollectionName);

-        Map<Integer,FpgaData> fpgaData = makeFpgaData();

+        Map<Integer, FpgaData> fpgaData = makeFpgaData();

 
         System.out.println("Writing " + hits.size() + " SVT hits");
         System.out.println("Writing " + fpgaData.size() + " FPGA data");
 

-                Map<Integer, List<int[]>> fpgaHits = new HashMap<Integer, List<int[]>>();

+        Map<Integer, List<int[]>> fpgaHits = new HashMap<>();

 
         for (Integer fpgaNumber : SvtUtils.getInstance().getFpgaNumbers()) {

-            fpgaHits.put(fpgaNumber,new ArrayList<int[]>());

+            fpgaHits.put(fpgaNumber, new ArrayList<int[]>());

         }
 
         for (RawTrackerHit hit : hits) {

@@ -143,13 +142,13 @@

     @Override
     public void writeData(EventHeader event, EventHeader toEvent) {
         List<RawTrackerHit> rawTrackerHits = event.get(RawTrackerHit.class, hitCollectionName);

-
-
-

         System.out.println("Writing " + rawTrackerHits.size() + " SVT hits");
         int flags = 1 << LCIOConstants.TRAWBIT_ID1;
         toEvent.put(hitCollectionName, rawTrackerHits, RawTrackerHit.class, flags, readoutName);
 

+        List<LCRelation> trueHitRelations = event.get(LCRelation.class, relationCollectionName);
+        toEvent.put(relationCollectionName, trueHitRelations, LCRelation.class, 0);
+

         List<FpgaData> fpgaData = new ArrayList(makeFpgaData().values());
         System.out.println("Writing " + fpgaData.size() + " FPGA data");
 

diff -u -r1.14 -r1.15
--- SimpleSvtReadout.java	24 Apr 2013 20:04:08 -0000	1.14
+++ SimpleSvtReadout.java	25 Apr 2013 21:33:41 -0000	1.15
@@ -12,8 +12,10 @@

 import org.lcsim.detector.tracker.silicon.ChargeCarrier;
 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.event.EventHeader;

+import org.lcsim.event.LCRelation;

 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.event.SimTrackerHit;

+import org.lcsim.event.base.BaseLCRelation;

 import org.lcsim.event.base.BaseRawTrackerHit;
 import org.lcsim.geometry.Detector;
 import org.lcsim.hps.readout.ecal.TriggerableDriver;

@@ -30,17 +32,19 @@

 /**
  *
  * @author Sho Uemura <[log in to unmask]>

- * @version $Id: SimpleSvtReadout.java,v 1.14 2013/04/24 20:04:08 meeg Exp $

+ * @version $Id: SimpleSvtReadout.java,v 1.15 2013/04/25 21:33:41 meeg Exp $

  */
 public class SimpleSvtReadout extends TriggerableDriver {
 
     private SimTrackerHitReadoutDriver readoutDriver = new SimTrackerHitReadoutDriver();
     private SiSensorSim siSimulation = new CDFSiSensorSim();
     private String outputCollection = "SVTRawTrackerHits";

+    private String relationCollection = "SVTTrueHitRelations";

     private Map<SiSensor, PriorityQueue<StripHit>[]> hitMap = new HashMap<>();
     //readout period time offset in ns
     private double readoutOffset = 0.0;
     private double readoutLatency = 240.0;

+    private double pileupCutoff = 300.0;

     private String readout = "TrackerHits";
     private double timeOffset = 30.0;
     private boolean noPileup = false;

@@ -129,7 +133,7 @@

                 PriorityQueue<StripHit>[] hitQueues = hitMap.get(sensor);
                 for (int i = 0; i < hitQueues.length; i++) {
                     if (hitQueues[i] != null) {

-                        while (!hitQueues[i].isEmpty() && hitQueues[i].peek().time < ClockSingleton.getTime() - 500.0) { //TODO: more intelligent time cut

+                        while (!hitQueues[i].isEmpty() && hitQueues[i].peek().time < ClockSingleton.getTime() - (readoutLatency + pileupCutoff)) {

 //                                System.out.format("Time %f: Dump stale hit with time %f\n",ClockSingleton.getTime(),hitQueues[i].peek().time);
                             hitQueues[i].poll();
                         }

@@ -288,74 +292,84 @@

 
     @Override
     protected void processTrigger(EventHeader event) {

-        if (!noPileup) {

+        if (noPileup) {
+            return;
+        }

 //            System.out.println("Got trigger");
 

-            // Create a list to hold the analog data
-            List<RawTrackerHit> hits = new ArrayList<>();
-            // Calculate time of first sample
-            double firstSample = Math.floor((ClockSingleton.getTime() - readoutLatency - readoutOffset) / Apv25Constants.SAMPLING_INTERVAL) * Apv25Constants.SAMPLING_INTERVAL + readoutOffset;

+        // Create a list to hold the analog data
+        List<RawTrackerHit> hits = new ArrayList<>();
+        List<LCRelation> trueHitRelations = new ArrayList<>();
+        // Calculate time of first sample
+        double firstSample = Math.floor((ClockSingleton.getTime() - readoutLatency - readoutOffset) / Apv25Constants.SAMPLING_INTERVAL) * Apv25Constants.SAMPLING_INTERVAL + readoutOffset;

-            for (SiSensor sensor : SvtUtils.getInstance().getSensors()) {
-                PriorityQueue<StripHit>[] hitQueues = hitMap.get(sensor);
-                for (int channel = 0; channel < hitQueues.length; channel++) {
-                    if (!addNoise && (hitQueues[channel] == null || hitQueues[channel].isEmpty())) {
-                        continue;
-                    }
-                    double[] signal = new double[6];
-                    for (int i = 0; i < 6; i++) {
-                        signal[i] = HPSSVTCalibrationConstants.getPedestal(sensor, channel);
-                    }
-                    if (addNoise) {
-                        addNoise(sensor, channel, signal);
-                    }

+        for (SiSensor sensor : SvtUtils.getInstance().getSensors()) {
+            PriorityQueue<StripHit>[] hitQueues = hitMap.get(sensor);
+            for (int channel = 0; channel < hitQueues.length; channel++) {
+                if (!addNoise && (hitQueues[channel] == null || hitQueues[channel].isEmpty())) {
+                    continue;
+                }
+                double[] signal = new double[6];
+                for (int i = 0; i < 6; i++) {
+                    signal[i] = HPSSVTCalibrationConstants.getPedestal(sensor, channel);
+                }
+                if (addNoise) {
+                    addNoise(sensor, channel, signal);
+                }

-                    List<SimTrackerHit> simHits = new ArrayList<>();

+                List<SimTrackerHit> simHits = new ArrayList<>();

-                    if (hitQueues[channel] != null) {
-                        for (StripHit hit : hitQueues[channel]) {
-                            double totalContrib = 0;
-                            for (int i = 0; i < 6; i++) {
-                                double sampleTime = firstSample + i * Apv25Constants.SAMPLING_INTERVAL;
-                                double signalAtTime = hit.amplitude * pulseAmplitude(sampleTime - hit.time, HPSSVTCalibrationConstants.getTShaping(sensor, channel));
-                                totalContrib += signalAtTime;
-                                signal[i] += signalAtTime;

+                if (hitQueues[channel] != null) {
+                    for (StripHit hit : hitQueues[channel]) {
+                        double totalContrib = 0;
+                        for (int i = 0; i < 6; i++) {
+                            double sampleTime = firstSample + i * Apv25Constants.SAMPLING_INTERVAL;
+                            double signalAtTime = hit.amplitude * pulseAmplitude(sampleTime - hit.time, HPSSVTCalibrationConstants.getTShaping(sensor, channel));
+                            totalContrib += signalAtTime;
+                            signal[i] += signalAtTime;

 //                                    System.out.format("new value of signal[%d] = %f\n", i, signal[i]);

-                                if (totalContrib > 4.0 * HPSSVTCalibrationConstants.getNoise(sensor, channel)) {
-                                    simHits.addAll(hit.simHits);
-                                }
-                            }

+                        }
+                        if (totalContrib > 4.0 * HPSSVTCalibrationConstants.getNoise(sensor, channel)) {
+//                            System.out.format("adding %d simHits\n", hit.simHits.size());
+                            simHits.addAll(hit.simHits);

                         }
                     }

+                }

-                    short[] samples = new short[6];
-                    for (int i = 0; i < 6; i++) {
-                        samples[i] = (short) Math.round(signal[i]);
-                    }

+                short[] samples = new short[6];
+                for (int i = 0; i < 6; i++) {
+                    samples[i] = (short) Math.round(signal[i]);
+                }

 //                        if (hitQueues[channel] != null && !hitQueues[channel].isEmpty()) {
 //                            for (int i = 0; i < 6; i++) {
 //                                System.out.format("samples[%d] = %d\n", i, samples[i]);
 //                            }
 //                        }

-                    long cell_id = SvtUtils.makeCellID(sensor, channel);
-                    RawTrackerHit hit = new BaseRawTrackerHit(0, cell_id, samples, simHits, sensor);
-                    if (readoutCuts(hit)) {
-                        hits.add(hit);

+                long cell_id = SvtUtils.makeCellID(sensor, channel);
+                RawTrackerHit hit = new BaseRawTrackerHit(0, cell_id, samples, simHits, sensor);
+                if (readoutCuts(hit)) {
+                    hits.add(hit);
+//                    System.out.format("simHits: %d\n", simHits.size());
+                    for (SimTrackerHit simHit : hit.getSimTrackerHits()) {
+                        LCRelation hitRelation = new BaseLCRelation(hit, simHit);
+                        trueHitRelations.add(hitRelation);

                     }
                 }
             }

+        }

-            int flags = 1 << LCIOConstants.TRAWBIT_ID1;

+        int flags = 1 << LCIOConstants.TRAWBIT_ID1;

 //            flags += 1 << LCIOConstants.RTHBIT_HITS;

-            event.put(outputCollection, hits, RawTrackerHit.class, flags, readout);
-            System.out.println("Made " + hits.size() + " RawTrackerHits");
-        }

+        event.put(outputCollection, hits, RawTrackerHit.class, flags, readout);
+        event.put(relationCollection, trueHitRelations, LCRelation.class, 0);
+        System.out.println("Made " + hits.size() + " RawTrackerHits");
+        System.out.println("Made " + trueHitRelations.size() + " LCRelations");

     }
 
     @Override
     public double readoutDeltaT() {
         double triggerTime = ClockSingleton.getTime() + triggerDelay;

-        int cycle = (int) Math.floor((triggerTime - readoutOffset + ClockSingleton.getDt()) / Apv25Constants.SAMPLING_INTERVAL);

+//        int cycle = (int) Math.floor((triggerTime - readoutOffset + ClockSingleton.getDt()) / Apv25Constants.SAMPLING_INTERVAL);

         // Calculate time of first sample
         double firstSample = Math.floor((triggerTime - readoutLatency - readoutOffset) / Apv25Constants.SAMPLING_INTERVAL) * Apv25Constants.SAMPLING_INTERVAL + readoutOffset;