diff -u -r1.3 -r1.4
--- Apv25Full.java	15 Aug 2012 02:52:59 -0000	1.3
+++ Apv25Full.java	16 Aug 2012 01:11:50 -0000	1.4
@@ -13,7 +13,7 @@

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

- * @version $Id: Apv25Full.java,v 1.3 2012/08/15 02:52:59 omoreno Exp $

+ * @version $Id: Apv25Full.java,v 1.4 2012/08/16 01:11:50 omoreno Exp $

  */
 public class Apv25Full {
     

@@ -49,15 +49,11 @@

      */
     public void injectCharge(int channel, double charge) {
         

-        // Only inject charge if the channel isn't bad
-        if(!this.getChannel(channel).isBadChannel()){
-        

         	// Shape the injected charge
             this.getChannel(channel).shapeSignal(charge);
 
             // Sample the resulting shaper signal
             this.getChannel(channel).sampleShaperSignal();

-        }

     }
     
     /**

@@ -176,7 +172,7 @@

                 double sample = shaperSignal.getAmplitudeAtTime(sampleTime, shapingTime);
                 
                 // Add the value to the pipeline

-                pipeline.addToCell(cell, sample);

+                if(sample > .001) pipeline.addToCell(cell, sample);

             }
         }
     }

@@ -190,17 +186,19 @@

         
         // Note: ptr gives the position of the trigger pointer
         

-        private int triggerLatency = (int) Math.floor(200 /* ns */ / SAMPLING_INTERVAL);

+        private int triggerLatency = (int) Math.floor(100 /* ns */ / SAMPLING_INTERVAL);

         private int writerPointer = 0;
         
         /**
          * Constructor
          */
         public Apv25Pipeline(){

-            

+             

             // Initialize the pipeline to the APV25 pipeline length
             super(ANALOG_PIPELINE_LENGTH);
             

+            System.out.println("Trigger Latency: " + triggerLatency);
+            

             // Initialize the position of the trigger pointer to a random position
             this.ptr = (int) (Math.random()*ANALOG_PIPELINE_LENGTH);
             

@@ -220,8 +218,9 @@

          */
         @Override
         public void addToCell(int position, double element){

-            if((writerPointer + position)%ANALOG_PIPELINE_LENGTH == this.ptr) return;
-            super.addToCell(position, element);

+            int writePosition = (writerPointer + position)%ANALOG_PIPELINE_LENGTH;
+            if(writePosition == this.ptr) return;
+            array[writePosition] += element;

         }
         
         /**

@@ -281,6 +280,7 @@

         Apv25ShaperSignal(double charge) {
             // Find the maximum amplitude of the shaper signal
             maxAmp = (charge/MIP)*FRONT_END_GAIN;  // mV

+            System.out.println(this.getClass().getSimpleName()+ ": Maximum shaper signal: " + maxAmp);

         }
 
         /**

diff -u -r1.3 -r1.4
--- SvtReadout.java	15 Aug 2012 02:52:59 -0000	1.3
+++ SvtReadout.java	16 Aug 2012 01:11:50 -0000	1.4
@@ -2,6 +2,7 @@

 
 //--- java ---//
 import java.util.ArrayList;

+import java.util.HashMap;

 import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;

@@ -36,7 +37,7 @@

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

- * @version $Id: SvtReadout.java,v 1.3 2012/08/15 02:52:59 omoreno Exp $

+ * @version $Id: SvtReadout.java,v 1.4 2012/08/16 01:11:50 omoreno Exp $

  */
 public class SvtReadout extends Driver {
 

@@ -46,11 +47,13 @@

     // FIFO queue to store "local" triggers by time
     private Queue<Double> triggerQueue = new LinkedList<Double>();
     List<String> readouts = new ArrayList<String>();

+    Map<SiSensor, List<Integer>> sensorToChannel = new HashMap<SiSensor, List<Integer>>();

     
     double readoutDeadTime = 24; // ns
     double lastTriggerTime = 0;
     
     boolean debug = false;

+    boolean timingIn = false;

     
     public SvtReadout(){
     	// Load the driver which transfers SimTrackerHits to their 

@@ -69,6 +72,13 @@

     /**
      * 
      */

+    public void setTimingIn(boolean timingIn){
+        this.timingIn = timingIn;
+    }
+    
+    /**
+     * 
+     */

     @Override
     public void detectorChanged(Detector detector){
         super.detectorChanged(detector);

@@ -177,18 +187,39 @@

                 // Loop over all sensor channels
                 for(Integer physicalChannel : electrodeDataCol.keySet()){
                     

+                    // find the APV channel number from the physical channel
+                    int channel = physicalChannel - TOTAL_STRIPS_PER_SENSOR
+                            + halfModule.getAPV25Number(physicalChannel)*TOTAL_APV25_CHANNELS + (TOTAL_APV25_CHANNELS - 1); 
+                    
+                    // Only inject charge if the channels isn't considered bad
+                    if(halfModule.getAPV25(physicalChannel).getChannel(channel).isBadChannel()) continue;
+                    

                     // Get the electrode data for this channel
                     SiElectrodeData electrodeData = electrodeDataCol.get(physicalChannel);
                     
                     // Get the charge in units of electrons
                     double charge = electrodeData.getCharge();
                     

-                    // find the APV channel number from the physical channel
-                    int channel = physicalChannel - TOTAL_STRIPS_PER_SENSOR
-    						+ halfModule.getAPV25Number(physicalChannel)*TOTAL_APV25_CHANNELS + (TOTAL_APV25_CHANNELS - 1); 

+                    if(debug){
+                        if(charge > 0) System.out.println(this.getClass().getSimpleName() + ": Injecting charge " + charge + " into channel " + physicalChannel);
+                    }
+                    
+                    if(timingIn){
+                        if(charge > 0){
+                            if(!sensorToChannel.containsKey(halfModule.getSensor())){
+                                sensorToChannel.put(halfModule.getSensor(), new ArrayList<Integer>());
+                            }
+                            sensorToChannel.get(halfModule.getSensor()).add(physicalChannel);
+                        }
+                    }

                     
                     // Inject the charge into the APV25 amplifier chain
                     halfModule.getAPV25(physicalChannel).injectCharge(channel, charge);

+                    
+                    if(debug){
+                            System.out.println(this.getClass().getSimpleName() + ": Writer pointer value: " + halfModule.getAPV25(physicalChannel).getChannel(channel).getPipeline().getWriterPointerValue());
+                            System.out.println(this.getClass().getSimpleName() + ": Channel " + physicalChannel + " pipeline: " + halfModule.getAPV25(physicalChannel).getChannel(channel).getPipeline().toString() );
+                    }

                 }
             }
         }

@@ -210,6 +241,19 @@

             // Get the sensor associated with this half-module
             SiSensor sensor = halfModule.getSensor();
             

+            if(timingIn && sensorToChannel.containsKey(sensor)){
+                for(Integer physicalChannel = 0; physicalChannel < 640; physicalChannel++){
+                    if(sensorToChannel.get(sensor).contains(physicalChannel)){
+                        // find the APV channel number from the physical channel
+                        int channel = physicalChannel - TOTAL_STRIPS_PER_SENSOR
+                                + halfModule.getAPV25Number(physicalChannel)*TOTAL_APV25_CHANNELS + (TOTAL_APV25_CHANNELS - 1); 
+                        System.out.println(this.getClass().getSimpleName() + ": Channel " + physicalChannel + " pipeline: " + halfModule.getAPV25(physicalChannel).getChannel(channel).getPipeline().toString() );
+                    }
+                
+                    sensorToChannel.get(sensor).remove(physicalChannel);
+                }
+            }
+            

             // Get all of the APVs associated with the sensor
             Apv25Full[] apv25 = halfModule.getAllApv25s();