diff -u -r1.20 -r1.21
--- HPSSVTCalibrationConstants.java	21 Sep 2012 23:22:17 -0000	1.20
+++ HPSSVTCalibrationConstants.java	21 Nov 2012 08:33:18 -0000	1.21
@@ -14,18 +14,18 @@

 /**
  *
  * @author Mathew Graham <[log in to unmask]>

- * $Id: HPSSVTCalibrationConstants.java,v 1.20 2012/09/21 23:22:17 meeg Exp $

+ * $Id: HPSSVTCalibrationConstants.java,v 1.21 2012/11/21 08:33:18 omoreno Exp $

  */
 public class HPSSVTCalibrationConstants {
 

-    // TODO: Change all pairs such that FPGA is the fist value

     // TODO: Change all map keys to type SiSensor?

-    private static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, double[] /* constants */> noiseMap = new HashMap<Pair<Integer, Integer>, double[]>();
-    private static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, double[] /* constants */> pedestalMap = new HashMap<Pair<Integer, Integer>, double[]>();
-    private static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, double[] /* constants */> tpMap = new HashMap<Pair<Integer, Integer>, double[]>();
-    private static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, Set<Integer> /* Bad channels */> badChannelMap = new HashMap<Pair<Integer, Integer>, Set<Integer>>();
-    private static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, List<Double> /* channels */> gainMap = new HashMap<Pair<Integer, Integer>, List<Double>>();
-    private static Map<Pair<Integer /* Hybrid */, Integer /* FPGA */>, List<Double> /* channels */> offsetMap = new HashMap<Pair<Integer, Integer>, List<Double>>();

+    // TODO: Update everything to make it compatible new version of SVT Utils
+    private static Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, double[] /* constants */> noiseMap = new HashMap<Pair<Integer, Integer>, double[]>();
+    private static Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, double[] /* constants */> pedestalMap = new HashMap<Pair<Integer, Integer>, double[]>();
+    private static Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, double[] /* constants */> tpMap = new HashMap<Pair<Integer, Integer>, double[]>();
+    private static Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, Set<Integer> /* Bad channels */> badChannelMap = new HashMap<Pair<Integer, Integer>, Set<Integer>>();
+    private static Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, List<Double> /* channels */> gainMap = new HashMap<Pair<Integer, Integer>, List<Double>>();
+    private static Map<Pair<Integer /* FPGA */, Integer /* Hybrid */>, List<Double> /* channels */> offsetMap = new HashMap<Pair<Integer, Integer>, List<Double>>();

     private static boolean pedestalLoaded = false;
     private static boolean tpLoaded = false;
     private static int totalBadChannels = 0;

@@ -36,10 +36,6 @@

     private HPSSVTCalibrationConstants() {
     }
 

-//    public static void loadCalibrationConstants() {
-//        loadCalibrationConstants(-1);
-//    }
-//

     public static void loadCalibration(int runNumber) {
         loadCalibrationConstants(runNumber);
         loadBadChannels(runNumber);

@@ -109,7 +105,7 @@

                     double pedestal = Double.valueOf(lineTok.nextToken());
                     double noise = Double.valueOf(lineTok.nextToken());
 

-                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);

+                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(fpga, hybrid);

 
                     double[] pedestals = pedestalMap.get(daqPair);
                     if (pedestals == null) {

@@ -165,7 +161,7 @@

                     double tp = Double.valueOf(lineTok.nextToken()) * 24.0 / 25.0; //FIXME: this is a hack to compensate for the calibrations we have that assumed 25 ns APV clock
                     double chisq = Double.valueOf(lineTok.nextToken());
 

-                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);

+                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(fpga, hybrid);

 
                     double[] tps = tpMap.get(daqPair);
                     if (tps == null) {

@@ -243,7 +239,7 @@

                     int badChannel = Integer.valueOf(stringTok.nextToken());
                     int fpga = Integer.valueOf(stringTok.nextToken());
                     int hybrid = Integer.valueOf(stringTok.nextToken());

-                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);

+                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(fpga, hybrid);

                     if (!badChannelMap.containsKey(daqPair)) {
                         badChannelMap.put(daqPair, new HashSet<Integer>());
                     }

@@ -281,7 +277,7 @@

                     int channel = Integer.valueOf(stringTok.nextToken());
                     double gain = Double.valueOf(stringTok.nextToken());
                     double offset = Double.valueOf(stringTok.nextToken());

-                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(hybrid, fpga);

+                    Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(fpga, hybrid);

                     if (!gainMap.containsKey(daqPair)) {
                         gainMap.put(daqPair, new ArrayList<Double>());
                     }

@@ -455,7 +451,7 @@

     /**
      * Checks if a channel has been tagged as bad
      * 

-     * @param daqPair : a Hybrid/FPGA pair defining which sensor the 

+     * @param daqPair : a FPGA/Hybrid pair defining which sensor the 

      * 					channels in located on
      * @param channel : The channel to be checked
      * @return true if the channel is bad, false otherwise

diff -u -r1.1 -r1.2
--- SVTEvioReader_RTH.java	14 Aug 2012 00:58:03 -0000	1.1
+++ SVTEvioReader_RTH.java	21 Nov 2012 08:33:18 -0000	1.2
@@ -30,7 +30,7 @@

 /**
  *
  * @author Omar Moreno <[log in to unmask]>

- * @version $Id: SVTEvioReader_RTH.java,v 1.1 2012/08/14 00:58:03 meeg Exp $

+ * @version $Id: SVTEvioReader_RTH.java,v 1.2 2012/11/21 08:33:18 omoreno Exp $

  */
 public class SVTEvioReader_RTH extends EvioReader {
 

@@ -152,7 +152,7 @@

 
     private static RawTrackerHit makeHit(int[] data) {
         int hitTime = 0;

-        Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(HPSSVTData.getHybridNumber(data), HPSSVTData.getFPGAAddress(data));

+        Pair<Integer, Integer> daqPair = new Pair<Integer, Integer>(HPSSVTData.getFPGAAddress(data), HPSSVTData.getHybridNumber(data));

         SiSensor sensor = SvtUtils.getInstance().getSensor(daqPair);
 
         // Find the side number (is 1)

diff -u -r1.6 -r1.7
--- SvtTrackRecoEfficiency.java	18 Oct 2012 02:43:31 -0000	1.6
+++ SvtTrackRecoEfficiency.java	21 Nov 2012 08:33:18 -0000	1.7
@@ -51,7 +51,7 @@

 /**
  * 
  * @author Omar Moreno <[log in to unmask]>

- * @version $Id: SvtTrackRecoEfficiency.java,v 1.6 2012/10/18 02:43:31 omoreno Exp $ 

+ * @version $Id: SvtTrackRecoEfficiency.java,v 1.7 2012/11/21 08:33:18 omoreno Exp $ 

  */
 public class SvtTrackRecoEfficiency extends Driver {
 

@@ -260,9 +260,9 @@

         	this.printDebug("Event " + eventNumber + " contains " + simTrackerHits.size() + " SimTrackerHits");
 
         // Add the SimTrackerHits to its respective sensor readout

-        for(SimTrackerHit simHitTrackerHit : simTrackerHits){

+        /*for(SimTrackerHit simHitTrackerHit : simTrackerHits){

             ((SiSensor) simHitTrackerHit.getDetectorElement()).getReadout().addHit(simHitTrackerHit);

-        }

+        }*/

 
         // Get the list of RawTrackerHits and add them to the sensor readout
         List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);

@@ -360,6 +360,12 @@

                 Set<SimTrackerHit> simHits = findable.getSimTrackerHits(mcParticle);
                 boolean[] planesHit = new boolean[10];
                 

+                // Clear the sensor readout's and then add the SimTrackerHits from  the MC particles to them
+                for(SiSensor sensor : SvtUtils.getInstance().getSensors()) sensor.getReadout().clear();
+                for(SimTrackerHit simHitTrackerHit : simHits){
+                    ((SiSensor) simHitTrackerHit.getDetectorElement()).getReadout().addHit(simHitTrackerHit);
+                }
+                

                 // Clear all previously stored simTrackerHits
                 for(int index = 0; index < 10; index++){
                     topSimTrackerHitsList.get(index+1).clear();

@@ -412,8 +418,20 @@

                 String title = null;
                 for(int index = 0; index < layerHit.length; index++){
                     if(isTopTrack){

-                        axialSensor = SvtUtils.getInstance().getTopSensor(2*index + 1);
-                        stereoSensor = SvtUtils.getInstance().getTopSensor(2*index + 2);

+                        axialSensor = SvtUtils.getInstance().getTopSensor(2*index + 1, 0);
+                        stereoSensor = SvtUtils.getInstance().getTopSensor(2*index + 2, 0);
+                        
+                        if(axialSensor.getReadout().getHits(SimTrackerHit.class).isEmpty() 
+                                || stereoSensor.getReadout().getHits(SimTrackerHit.class).isEmpty()){
+                            this.printDebug("One of the sensors does not have a SimTrackerHit associated with it; moving on to next layer");
+                            continue;
+                        }
+                        
+                        this.printDebug(SvtUtils.getInstance().getDescription(axialSensor) + ": SimTrackerHit: " + axialSensor.getReadout().getHits(SimTrackerHit.class).size());
+                        this.printDebug(SvtUtils.getInstance().getDescription(stereoSensor) + ": SimTrackerHit: " + stereoSensor.getReadout().getHits(SimTrackerHit.class).size());
+                        if(layerHit[index]){
+                            this.printDebug("Top Layer " + (index+1) + " was hit");
+                        }

                         
                         for(SimTrackerHit simHit : axialSensor.getReadout().getHits(SimTrackerHit.class)){
                             if(layerHit[index] && !topStereoLayerHit[index]){

@@ -455,9 +473,21 @@

                         }
                         
                     } else {

-                        axialSensor = SvtUtils.getInstance().getBottomSensor(2*index + 2);
-                        stereoSensor = SvtUtils.getInstance().getBottomSensor(2*index + 1);

+                        axialSensor = SvtUtils.getInstance().getBottomSensor(2*index + 2, 0);
+                        stereoSensor = SvtUtils.getInstance().getBottomSensor(2*index + 1, 0);
+                        
+                        if(axialSensor.getReadout().getHits(SimTrackerHit.class).isEmpty() 
+                                || stereoSensor.getReadout().getHits(SimTrackerHit.class).isEmpty()){
+                            this.printDebug("One of the sensors does not have a SimTrackerHit associated with it; moving on to next layer");
+                            continue;
+                        }

+                        this.printDebug(SvtUtils.getInstance().getDescription(axialSensor) + ": SimTrackerHit: " + axialSensor.getReadout().getHits(SimTrackerHit.class).size());
+                        this.printDebug(SvtUtils.getInstance().getDescription(stereoSensor) + ": SimTrackerHit: " + stereoSensor.getReadout().getHits(SimTrackerHit.class).size());
+                        if(layerHit[index]){
+                            this.printDebug("Bottom Layer " + (index+1) + " was hit");
+                        }
+                        

                         for(SimTrackerHit simHit : axialSensor.getReadout().getHits(SimTrackerHit.class)){
                             if(debug)
                                 this.printDebug(SvtUtils.getInstance().getDescription(axialSensor) + ": Position: " + simHit.getPositionVec().toString());