diff -u -r1.2 -r1.3
--- SvtQA.java	27 Jul 2012 19:02:07 -0000	1.2
+++ SvtQA.java	28 Jul 2012 01:27:49 -0000	1.3
@@ -38,7 +38,7 @@

  * SVT Quality Assurance Driver
  *  
  * @author Omar Moreno <[log in to unmask]>

- * @version $Id: SvtQA.java,v 1.2 2012/07/27 19:02:07 omoreno Exp $

+ * @version $Id: SvtQA.java,v 1.3 2012/07/28 01:27:49 omoreno Exp $

  */
 public class SvtQA extends Driver {
 	

@@ -468,50 +468,30 @@

         System.out.println("Total Bad Channels: " + HPSSVTCalibrationConstants.getTotalBadChannels() + "\n");
         
         if(enableOccupancy){

-            System.out.println("%===================================================================% \n");

             for(SiSensor sensor : SvtUtils.getInstance().getSensors()){

+                System.out.println("%===================================================================%");

                 System.out.println(SvtUtils.getInstance().getDescription(sensor) + " Bad Channels");

-                Pair<Integer, Integer> daqPair = SvtUtils.getInstance().getDaqPair(sensor);

+                System.out.println("%===================================================================%");

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

-                    double occupancy = sensorToOccupancy.get(SvtUtils.getInstance().getDescription(sensor))[index]/totalNumberEvents;
-                    double leftNeighborOccupancy = 0;
-                    double rightNeighborOccupancy = 0;
-                    double leftDiff = 0;
-                    double rightDiff = 0;
-                    if(index != 0){
-                        leftNeighborOccupancy = sensorToOccupancy.get(SvtUtils.getInstance().getDescription(sensor))[index - 1]/totalNumberEvents;
-                        leftDiff = Math.abs(leftNeighborOccupancy - occupancy)/leftNeighborOccupancy;
-                    }
-                    if(index != 639){
-                        rightNeighborOccupancy = sensorToOccupancy.get(SvtUtils.getInstance().getDescription(sensor))[index + 1]/totalNumberEvents;
-                        rightDiff = Math.abs(rightNeighborOccupancy - occupancy)/rightNeighborOccupancy;
-                    }

-                    if(occupancy > maxOccupancy){
-                        System.out.println(" Channel: " + index + "  FPGA: " + daqPair.getSecondElement() + " Hybrid: " + daqPair.getFirstElement() + " Occupancy: " + occupancy);
-                    } else if( leftDiff > maxOccupancyVariation || rightDiff > maxOccupancyVariation){
-                        System.out.println(" Channel: " + index + "  FPGA: " + daqPair.getSecondElement() + " Hybrid: " + daqPair.getFirstElement() 
-                                + " Left Difference: " + leftDiff + " Right Difference: " + rightDiff);

+                    // Check is the channel can be considered bad    
+                    this.checkChannel(sensor, index);

                     }
                 }

-            }

             System.out.println("%===================================================================% \n");
         }
         
         if(enableStereoHitOccupancy){

-            System.out.println("%===================================================================% \n");

             for(SiSensor sensor : SvtUtils.getInstance().getSensors()){

+                System.out.println("%===================================================================% \n");

                 System.out.println(SvtUtils.getInstance().getDescription(sensor) + " Bad Channels");

-                Pair<Integer, Integer> daqPair = SvtUtils.getInstance().getDaqPair(sensor);

+                System.out.println("%===================================================================% \n");

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

-                    double occupancy = sensorToStereoOccupancy.get(SvtUtils.getInstance().getDescription(sensor))[index]/totalNumberEvents;
-                    occupancy *= 1000;
-                    if(occupancy == 0){
-                        System.out.println(" Channel: " + index + "  FPGA: " + daqPair.getSecondElement() + " Hybrid: " + daqPair.getFirstElement() + " Occupancy: " + occupancy);
-                    } 

+                    // Check is the channel can be considered bad    
+                    this.checkChannel(sensor, index);

                 }

+                System.out.println("%===================================================================% \n");

             }

-            System.out.println("%===================================================================% \n");

         }
         
         if(outputFile != null){

@@ -522,4 +502,52 @@

             }
         }
     }

+    
+    public double getOccupancy(SiSensor sensor, int channel){
+        if(!enableOccupancy) throw new RuntimeException("Occupancy calculation was not enabled!"); 
+        return sensorToOccupancy.get(SvtUtils.getInstance().getDescription(sensor))[channel]/totalNumberEvents;
+    }
+    
+    public void checkChannel(SiSensor sensor, int channel){
+        if(!enableOccupancy) throw new RuntimeException("Occupancy calculation was not enabled!");
+        
+        if(HPSSVTCalibrationConstants.isBadChannel(sensor, channel)) return;
+        
+        // Find the occupancy of the current channel
+        double currentChannelOccu = this.getOccupancy(sensor, channel);
+        
+        // If the channel exceeds the maximum allowable occupancy, then it's a bad channel
+        if(currentChannelOccu > maxOccupancy){
+            System.out.println("Channel " + channel + ": Occupancy " + currentChannelOccu + " -- Exceeds maximum");
+            return;
+        }
+        
+        // Find the occupancy of the neighboring channels
+        if(channel == 0){
+            double rNeighborOccu = this.getOccupancy(sensor, channel+1);
+            if(rNeighborOccu == 0 || HPSSVTCalibrationConstants.isBadChannel(sensor, channel+1)) return; 
+            double rOccuDiff = Math.abs(rNeighborOccu - currentChannelOccu)/rNeighborOccu;
+            if(rOccuDiff >= maxOccupancyVariation)
+                System.out.println("Channel " + channel + ": Channel Variation exceeds maximum -- RVar: " + rOccuDiff);
+        } else if(channel == 638){
+            double lNeighborOccu = this.getOccupancy(sensor, channel-1);
+            if(lNeighborOccu == 0 || HPSSVTCalibrationConstants.isBadChannel(sensor, channel-1)) return;
+            double lOccuDiff = Math.abs(lNeighborOccu - currentChannelOccu)/lNeighborOccu;
+            if(lOccuDiff >= maxOccupancyVariation)
+                System.out.println("Channel " + channel + ": Channel Variation exceeds maximum -- LVar: " + lOccuDiff);
+        } else if (channel == 639){
+            return;
+        }
+        else { 
+            double rNeighborOccu = this.getOccupancy(sensor, channel+1);  
+            double lNeighborOccu = this.getOccupancy(sensor, channel-1);
+            if(rNeighborOccu == 0 || HPSSVTCalibrationConstants.isBadChannel(sensor, channel+1)
+                    || lNeighborOccu == 0 || HPSSVTCalibrationConstants.isBadChannel(sensor, channel-1)) return;
+            double rOccuDiff = Math.abs(rNeighborOccu - currentChannelOccu)/rNeighborOccu;
+            double lOccuDiff = Math.abs(lNeighborOccu - currentChannelOccu)/lNeighborOccu;
+            if(rOccuDiff >= maxOccupancyVariation && lOccuDiff >= maxOccupancyVariation){
+                System.out.println("Channel " + channel + ": Channel Variation exceeds maximum -- LVar: " + lOccuDiff + " RVar: " + rOccuDiff);
+            }
+        }
+    }

 }