diff -u -r1.2 -r1.3
--- RearTransitionModule.java	13 Aug 2012 23:08:12 -0000	1.2
+++ RearTransitionModule.java	17 Aug 2012 01:15:34 -0000	1.3
@@ -13,10 +13,13 @@

 import org.lcsim.hps.recon.tracking.apv25.Apv25AnalogData;
 import org.lcsim.hps.recon.tracking.apv25.Apv25DigitalData;
 

+//--- Constants ---//
+import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.CHANNELS;
+

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

- * @version $Id: RearTransitionModule.java,v 1.2 2012/08/13 23:08:12 omoreno Exp $

+ * @version $Id: RearTransitionModule.java,v 1.3 2012/08/17 01:15:34 omoreno Exp $

  */
 public class RearTransitionModule extends Driver {
 

@@ -79,7 +82,7 @@

         
         // If the event does not contain any analog data that needs to be digitized, skip the event
         if(!event.hasCollection(Apv25AnalogData.class, apv25AnalogDataCollectionName)) return;

-    

+        

         // Get the analog data from the event
         List<Apv25AnalogData> analogData = event.get(Apv25AnalogData.class, apv25AnalogDataCollectionName);
         

@@ -106,8 +109,14 @@

                 apv25Output[index] = Math.floor((apv25Output[index] - adcVLowRef)/adcVoltageResolution);
             }
             

+            // Add pedestal and noise
+            for(int channel = 0; channel < CHANNELS; channel++){
+                int physicalChannel = 639 - (analogDatum.getApvNumber()*128 + 127 - channel);
+                apv25Output[channel + 12] += HPSSVTCalibrationConstants.getPedestal(analogDatum.getSensor(), physicalChannel);
+            }
+            

             // Add the digital data to the list

-            digitalData.add(new Apv25DigitalData(analogDatum.getSensor(), analogDatum.getApv(), apv25Output));

+            digitalData.add(new Apv25DigitalData(analogDatum.getSensor(), analogDatum.getApvNumber(), apv25Output));

         }
     
         event.put(apv25DigitalDataCollectionName, digitalData, Apv25DigitalData.class, 0);

diff -u -r1.1 -r1.2
--- DataProcessingModule.java	13 Aug 2012 23:08:12 -0000	1.1
+++ DataProcessingModule.java	17 Aug 2012 01:15:34 -0000	1.2
@@ -16,7 +16,7 @@

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

- * @version $Id: DataProcessingModule.java,v 1.1 2012/08/13 23:08:12 omoreno Exp $

+ * @version $Id: DataProcessingModule.java,v 1.2 2012/08/17 01:15:34 omoreno Exp $

  */
 public class DataProcessingModule extends Driver {
 

@@ -73,10 +73,12 @@

         for(Map.Entry<SiSensor, SvtDataBlocks> sensor : sensorToDataBlocks.entrySet()){
             
             SvtDataBlocks blocks = sensor.getValue();

+         

             
             for(int channel = 0; channel < 640; channel++){

-                short[] samples = blocks.getSamples(channel);            

+                short[] samples = blocks.getSamples(channel);  
+                

                 if(!this.samplesAboveThreshold(sensor.getKey(), channel, samples)) continue;
                 
                 // Create a RawTrackerHit

@@ -86,6 +88,7 @@

             }
         }
         

+        System.out.println(this.getClass().getSimpleName() + ": Number of RawTrackerHits created: " + rawHits.size());

         return rawHits;
     }
     

@@ -107,14 +110,17 @@

             SiSensor sensor = digitalDatum.getSensor();
             int apvN = digitalDatum.getApv();
             

-            double[] apv25DigitalOutput = new double[140];
-            System.arraycopy(digitalDatum.getApv25DigitalOutput(), 0, apv25DigitalOutput, 0, apv25DigitalOutput.length);

+            double[] apv25DigitalOutput = new double[128];
+            System.arraycopy(digitalDatum.getSamples(), 0, apv25DigitalOutput, 0, apv25DigitalOutput.length);

         
             for(int channel = 0; channel < apv25DigitalOutput.length; channel++){
                 
                 // Calculate the physical number
                 int physicalChannel = 639 - (apvN*128 + 127 - channel);
                 

+        //        if(apv25DigitalOutput[channel] > 3276)
+          //          System.out.println(this.getClass().getSimpleName() + ": Channel " + channel + " Sample " + apv25DigitalOutput[channel]);
+                

                 sensorToDataBlocks.get(sensor).addSample(physicalChannel, nSamples, (short) apv25DigitalOutput[channel]);
             }
         }

@@ -126,12 +132,13 @@

             
             // Add RawTrackerHits to the event
             event.put(rawTrackerHitsCollectionName, this.findRawHits(), RawTrackerHit.class, 0);

+            nSamples = 0;

         }
     }
     
     public class SvtDataBlocks { 
      

-        List<short[]> samples = new ArrayList<short[]>();

+        Map<Integer, short[]> channelToSamples = new HashMap<Integer, short[]>();

         
         /**
          * Default Ctor

@@ -142,16 +149,16 @@

         /**
          * 
          */

-        public void addSample(int physicalChannel, int sampleN, short value){
-            if(samples.get(physicalChannel) == null) samples.add(physicalChannel, new short[6]);
-            samples.get(physicalChannel)[sampleN] = value;

+        public void addSample(Integer physicalChannel, int sampleN, short value){
+            if(!channelToSamples.containsKey(physicalChannel)) channelToSamples.put(physicalChannel, new short[6]);
+            channelToSamples.get(physicalChannel)[sampleN] = value;

         }
         
         /**
          * 
          */
         public short[] getSamples(int physicalChannel){

-            return samples.get(physicalChannel);

+            return channelToSamples.get(physicalChannel);

         }
         
     }

@@ -166,13 +173,13 @@

         // Get the pedestal and noise for this channel
         double pedestal = HPSSVTCalibrationConstants.getPedestal(sensor, channel);
         double noise = HPSSVTCalibrationConstants.getNoise(sensor, channel);

-        double threshold = pedestal + noise*this.noiseThreshold;

+        double threshold = 3276 + pedestal + noise*this.noiseThreshold;

         
         for(short sample : samples){
             if(sample > threshold) nSamplesAboveThreshold++;
         }
         

-        if(nSamplesAboveThreshold == this.nSamplesAboveTreshold) return true;

+        if(nSamplesAboveThreshold >= this.nSamplesAboveTreshold) return true;

         return false;
     }