diff -u -r1.1 -r1.2
--- HPSNearestNeighborRMS.java	22 Apr 2012 21:14:57 -0000	1.1
+++ HPSNearestNeighborRMS.java	24 Apr 2012 14:09:14 -0000	1.2
@@ -6,9 +6,9 @@

 
 import java.util.*;
 import org.lcsim.detector.identifier.IIdentifier;

+import org.lcsim.detector.tracker.silicon.SiSensor;

 import org.lcsim.detector.tracker.silicon.SiTrackerIdentifierHelper;

-import org.lcsim.event.RawTrackerHit;
-import org.lcsim.event.base.BaseTrackerHit;

+

 
 /**
  *

@@ -118,7 +118,8 @@

      * @param base_hits List of RawTrackerHits to be clustered
      * @return list of clusters, with a cluster being a list of RawTrackerHits
      */

-    public List<List<BaseTrackerHit>> findClusters(List<BaseTrackerHit> base_hits) {

+    @Override
+    public List<List<HPSTrackerHit>> findClusters(List<HPSTrackerHit> base_hits) {

 
         //  Check that the seed threshold is at least as large as  the neighbor threshold
         if (_seed_threshold < _neighbor_threshold) {

@@ -128,24 +129,24 @@

         //  Create maps that show the channel status and relate the channel number to the raw hit and vice versa
         int mapsize = 2 * base_hits.size();
         Map<Integer, Boolean> clusterable = new HashMap<Integer, Boolean>(mapsize);

-        Map<BaseTrackerHit, Integer> hit_to_channel = new HashMap<BaseTrackerHit, Integer>(mapsize);
-        Map<Integer, BaseTrackerHit> channel_to_hit = new HashMap<Integer, BaseTrackerHit>(mapsize);

+        Map<HPSTrackerHit, Integer> hit_to_channel = new HashMap<HPSTrackerHit, Integer>(mapsize);
+        Map<Integer, HPSTrackerHit> channel_to_hit = new HashMap<Integer, HPSTrackerHit>(mapsize);

 
         //  Create list of channel numbers to be used as cluster seeds
         List<Integer> cluster_seeds = new ArrayList<Integer>();
 
         //  Loop over the raw hits and construct the maps used to relate cells and hits, initialize the
         //  clustering status map, and create a list of possible cluster seeds

-        for (BaseTrackerHit base_hit : base_hits) {
-            RawTrackerHit raw_hit=(RawTrackerHit) base_hit.getRawHits().get(0);

+        for (HPSTrackerHit base_hit : base_hits) {
+           

             
             // get the channel number for this hit

-            SiTrackerIdentifierHelper sid_helper = (SiTrackerIdentifierHelper) raw_hit.getIdentifierHelper();
-            IIdentifier id = raw_hit.getIdentifier();

+            SiTrackerIdentifierHelper sid_helper = (SiTrackerIdentifierHelper) base_hit.getIdentifierHelper();
+            IIdentifier id = base_hit.getIdentifier();

             int channel_number = sid_helper.getElectrodeValue(id);
 
             //  Check for duplicate RawTrackerHit

-            if (hit_to_channel.containsKey(raw_hit)) {

+            if (hit_to_channel.containsKey(base_hit)) {

                 throw new RuntimeException("Duplicate hit: "+id.toString());
             }
 

@@ -159,8 +160,8 @@

             channel_to_hit.put(channel_number, base_hit);
 
             //  Get the signal from the readout chip

-            double signal = base_hit.getdEdx();
-            double noiseRMS = 666;   //need to get the noise from the calib. const. class

+            double signal = base_hit.getAmp();
+            double noiseRMS = HPSSVTCalibrationConstants.getNoise((SiSensor)base_hit.getDetectorElement(),channel_number);

 
             //  Mark this hit as available for clustering if it is above the neighbor threshold
             clusterable.put(channel_number, signal/noiseRMS >= _neighbor_threshold);

@@ -172,7 +173,7 @@

         }
 
         //  Create a list of clusters

-        List<List<BaseTrackerHit>> cluster_list = new ArrayList<List<BaseTrackerHit>>();

+        List<List<HPSTrackerHit>> cluster_list = new ArrayList<List<HPSTrackerHit>>();

 
         //  Now loop over the cluster seeds to form clusters
         for (int seed_channel : cluster_seeds) {

@@ -181,7 +182,7 @@

             if (!clusterable.get(seed_channel)) continue;
 
             //  Create a new cluster

-            List<BaseTrackerHit> cluster = new ArrayList<BaseTrackerHit>();

+            List<HPSTrackerHit> cluster = new ArrayList<HPSTrackerHit>();

             double cluster_signal = 0.;
             double cluster_noise_squared = 0.;
 

@@ -198,9 +199,9 @@

                 //  Pull the next channel off the queue and add it's hit to the cluster
                 int clustered_cell = unchecked.removeFirst();
                 cluster.add(channel_to_hit.get(clustered_cell));

-                cluster_signal += channel_to_hit.get(clustered_cell).getdEdx();
-//                cluster_noise_squared += Math.pow(readout_chip.getChannel(clustered_cell).computeNoise(electrodes.getCapacitance(clustered_cell)),2);
-                cluster_noise_squared +=0;  //need to get the noise from the calib. const. class

+                cluster_signal += channel_to_hit.get(clustered_cell).getAmp();
+                cluster_noise_squared += Math.pow(HPSSVTCalibrationConstants.getNoise((SiSensor)(channel_to_hit.get(clustered_cell)).getDetectorElement(),clustered_cell),2);
+//                cluster_noise_squared +=0;  //need to get the noise from the calib. const. class

                 //  Get the neigbor channels
 //                Set<Integer> neighbor_channels = electrodes.getNearestNeighborCells(clustered_cell);
                 Set<Integer> neighbor_channels = getNearestNeighborCells(clustered_cell);