diff -u -r1.2 -r1.3
--- DataProcessingModule.java	17 Aug 2012 01:15:34 -0000	1.2
+++ DataProcessingModule.java	28 Aug 2012 07:12:33 -0000	1.3
@@ -16,7 +16,7 @@

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

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

+ * @version $Id: DataProcessingModule.java,v 1.3 2012/08/28 07:12:33 omoreno Exp $

  */
 public class DataProcessingModule extends Driver {
 

@@ -25,127 +25,143 @@

     Map<SiSensor, Map<Integer, List<Double>>> sensorToSamplesMap 
         = new HashMap<SiSensor, Map<Integer, List<Double>>>();
     Map<SiSensor, SvtDataBlocks> sensorToDataBlocks = new HashMap<SiSensor, SvtDataBlocks>();

-    

+

     // Collection Names
     String apv25DigitalDataCollectionName = "AVP25DigitalData";
     String rawTrackerHitsCollectionName = "SVTRawTrackerHits";

-    

+

     int nSamples = 0;
     int nSamplesAboveTreshold = 3;    // Number of samples above noise threshold 
     int noiseThreshold = 3;           // Units of RMS noise

-    

+
+    boolean enableTailCut = true;
+    boolean enableThresholdCut = true;
+

     /**
      * Default Ctor
      */
     public DataProcessingModule(){};

-    

+

     /**
      * 
      */
     public void setNumberOfSamplesAboveTreshold(int nSamplesAboveThreshold){
         this.nSamplesAboveTreshold = nSamplesAboveThreshold;
     }

-    

+

     /**
      * 
      */
     public void setNoiseThreshold(int noiseThreshold){
         this.noiseThreshold = noiseThreshold;
     }

-    

+
+    /**
+     *
+     */
+    public void setEnableTailCut(boolean enableTailCut){
+        this.enableTailCut = enableTailCut;
+    }
+
+    /**
+     *
+     */
+    public void setEnableThresholdCut(boolean enableThresholdCut){
+        this.enableThresholdCut = enableThresholdCut;
+    }
+

     /**
      * 
      */
     @Override

-    public void detectorChanged(Detector detector){
-        
-        for(SiSensor sensor : SvtUtils.getInstance().getSensors()){
-            sensorToSamplesMap.put(sensor, new HashMap<Integer, List<Double>>());
-            sensorToDataBlocks.put(sensor, new SvtDataBlocks());

+        public void detectorChanged(Detector detector){
+
+            for(SiSensor sensor : SvtUtils.getInstance().getSensors()){
+                sensorToSamplesMap.put(sensor, new HashMap<Integer, List<Double>>());
+                sensorToDataBlocks.put(sensor, new SvtDataBlocks());
+            }

         }

-    }
-    

+

     private List<RawTrackerHit> findRawHits(){

-        

+

         List<RawTrackerHit> rawHits = new ArrayList<RawTrackerHit>();

-        

+

         // Loop through all blocked data
         for(Map.Entry<SiSensor, SvtDataBlocks> sensor : sensorToDataBlocks.entrySet()){

-            

+

             SvtDataBlocks blocks = sensor.getValue();

-         
-            

+

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

-            

+

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

-                

+

                 if(!this.samplesAboveThreshold(sensor.getKey(), channel, samples)) continue;

-                

+
+
+                if(enableTailCut && !this.tailCut(samples)) continue;
+

                 // Create a RawTrackerHit
                 int time = 0;
                 long cellID = sensor.getKey().makeStripId(channel, 1).getValue();
                 rawHits.add(new BaseRawTrackerHit(time, cellID, samples, null, sensor.getKey()));
             }
         }

-        

+

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

-    

+

     /**
      * 
      */
     @Override

-    protected void process(EventHeader event){
-        
-        // If the event does not contain any digital data, skip the event
-        if(!event.hasCollection(Apv25DigitalData.class, apv25DigitalDataCollectionName)) return;
-        
-        // Get the digital data from the event
-        List<Apv25DigitalData> digitalData = event.get(Apv25DigitalData.class, apv25DigitalDataCollectionName);
-        
-        // Block the data together
-        for(Apv25DigitalData digitalDatum : digitalData){
-            
-            SiSensor sensor = digitalDatum.getSensor();
-            int apvN = digitalDatum.getApv();
-            
-            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]);

+        protected void process(EventHeader event){
+
+            // If the event does not contain any digital data, skip the event
+            if(!event.hasCollection(Apv25DigitalData.class, apv25DigitalDataCollectionName)) return;
+
+            // Get the digital data from the event
+            List<Apv25DigitalData> digitalData = event.get(Apv25DigitalData.class, apv25DigitalDataCollectionName);
+
+            // Block the data together
+            for(Apv25DigitalData digitalDatum : digitalData){
+
+                SiSensor sensor = digitalDatum.getSensor();
+                int apvN = digitalDatum.getApv();
+
+                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);
+
+                    sensorToDataBlocks.get(sensor).addSample(physicalChannel, nSamples, (short) apv25DigitalOutput[channel]);
+                }
+            }
+            nSamples++;
+
+
+            // If the expected number of samples has been collected, process the data
+            if(nSamples == 6){
+
+                // Add RawTrackerHits to the event
+                event.put(rawTrackerHitsCollectionName, this.findRawHits(), RawTrackerHit.class, 0);
+                nSamples = 0;

             }
         }

-        nSamples++;
-        
-        
-        // If the expected number of samples has been collected, process the data
-        if(nSamples == 6){
-            
-            // Add RawTrackerHits to the event
-            event.put(rawTrackerHitsCollectionName, this.findRawHits(), RawTrackerHit.class, 0);
-            nSamples = 0;
-        }
-    }
-    

+

     public class SvtDataBlocks { 

-     

+

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

-        

+

         /**
          * Default Ctor
          */
         public SvtDataBlocks(){
         }

-        

+

         /**
          * 
          */

@@ -153,34 +169,44 @@

             if(!channelToSamples.containsKey(physicalChannel)) channelToSamples.put(physicalChannel, new short[6]);
             channelToSamples.get(physicalChannel)[sampleN] = value;
         }

-        

+

         /**
          * 
          */
         public short[] getSamples(int physicalChannel){
             return channelToSamples.get(physicalChannel);
         }

-        

+

     }

-    

+

     /**
      * 
      */
     private boolean samplesAboveThreshold(SiSensor sensor, int channel, short[] samples){
         // Number of samples above threshold
         int nSamplesAboveThreshold = 0;

-        

+

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

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

+
+        // Calculate the threshold
+        double threshold = Math.ceil(pedestal + noise*this.noiseThreshold); 
+

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

-        

+
+        // If the prerequiste number of samples are above threshold return true

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

-    

+
+    /**
+     *
+     */
+    private boolean tailCut(short[] sample){
+        if(sample[2] > sample[1] || sample[3] > sample[4]) return true;
+        return false; 
+    }

 }