diff -u -r1.6 -r1.7
--- HPSNearestNeighborRMS.java	17 May 2012 18:24:10 -0000	1.6
+++ HPSNearestNeighborRMS.java	30 Jul 2012 22:27:09 -0000	1.7
@@ -6,18 +6,17 @@

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

-

 /**
  *
  * @author mgraham
  */
 public class HPSNearestNeighborRMS implements HPSClusteringAlgorithm {

-  

+

     private static String _NAME = "NearestNeighborRMS";
     private double _seed_threshold;
     private double _neighbor_threshold;

-    private double _cluster_threshold; 
-    private double _meanTime=24;

+    private double _cluster_threshold;
+    private double _meanTime = 24;

     private double _timeWindow = 48;
     private double _maxChisq = 10.0;
 

@@ -28,14 +27,14 @@

      * Cluster threshold is minimum charge of the entire cluster.
      * All thresholds are in units of RMS noise of the channel(s).
      *

-     * @param seed_threshold seed threshhold

+     * @param seed_threshold seed threshold

      * @param neighbor_threshold neighbor threshold
      * @param cluster_threshold cluster threshold
      */
     public HPSNearestNeighborRMS(double seed_threshold, double neighbor_threshold, double cluster_threshold) {
         _seed_threshold = seed_threshold;
         _neighbor_threshold = neighbor_threshold;

-        _cluster_threshold = cluster_threshold;       

+        _cluster_threshold = cluster_threshold;

     }
 
     /**

@@ -77,42 +76,6 @@

     }
 
     /**

-     * Return the seed threshold.  Units are RMS noise.
-     *
-     * @return seed threshold
-     */
-    public double getSeedThreshold() {
-        return _seed_threshold;
-    }
-
-    /**
-     * Return the neighbor threshold.  Units are RMS noise.
-     *
-     * @return neighbor threshold
-     */
-    public double getNeighborThreshold() {
-        return _neighbor_threshold;
-    }
-
-    /**
-     * Return the cluster threshold.  Units are RMS noise.
-     *
-     * @return cluster threshold
-     */
-    public double getClusterThreshold() {
-        return _cluster_threshold;
-    }
-
-    /**
-     * Return the name of the clustering algorithm.
-     * 
-     * @return _name clusting algorithm name
-     */
-    public String getName() {
-        return _NAME;
-    }
-
-    /**

      * Find clusters using the nearest neighbor algorithm.
      *    
      * @param base_hits List of RawTrackerHits to be clustered

@@ -138,8 +101,8 @@

         //  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 (HPSFittedRawTrackerHit base_hit : base_hits) {

-           
-            RawTrackerHit rth=base_hit.getRawTrackerHit();

+
+            RawTrackerHit rth = base_hit.getRawTrackerHit();

             // get the channel number for this hit
             SiTrackerIdentifierHelper sid_helper = (SiTrackerIdentifierHelper) rth.getIdentifierHelper();
             IIdentifier id = rth.getIdentifier();

@@ -147,13 +110,13 @@

 
             //  Check for duplicate RawTrackerHit
             if (hit_to_channel.containsKey(base_hit)) {

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

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

             }
 
             //  Check for duplicate RawTrackerHits or channel numbers
             if (channel_to_hit.containsKey(channel_number)) {
 //                throw new RuntimeException("Duplicate channel number: "+channel_number);

-                System.out.println("Duplicate channel number: "+channel_number);

+                System.out.println("Duplicate channel number: " + channel_number);

             }
 
             //  Add this hit to the maps that relate channels and hits

@@ -162,13 +125,13 @@

 
             //  Get the signal from the readout chip
             double signal = base_hit.getAmp();

-            double noiseRMS = HPSSVTCalibrationConstants.getNoise((SiSensor)rth.getDetectorElement(),channel_number);
-            double time=base_hit.getT0();

+            double noiseRMS = HPSSVTCalibrationConstants.getNoise((SiSensor) rth.getDetectorElement(), channel_number);
+            double time = base_hit.getT0();

             //  Mark this hit as available for clustering if it is above the neighbor threshold

-            clusterable.put(channel_number, signal/noiseRMS >= _neighbor_threshold);

+            clusterable.put(channel_number, signal / noiseRMS >= _neighbor_threshold);

 
             //  Add this hit to the list of seeds if it is above the seed threshold

-            if (signal/noiseRMS >= _seed_threshold&&passTimingCut(base_hit) && passChisqCut(base_hit)) {

+            if (signal / noiseRMS >= _seed_threshold && passTimingCut(base_hit) && passChisqCut(base_hit)) {

                 cluster_seeds.add(channel_number);
             }
         }

@@ -180,7 +143,9 @@

         for (int seed_channel : cluster_seeds) {
 
             //  First check if this hit is still available for clustering

-            if (!clusterable.get(seed_channel)) continue;

+            if (!clusterable.get(seed_channel)) {
+                continue;
+            }

 
             //  Create a new cluster
             List<HPSFittedRawTrackerHit> cluster = new ArrayList<HPSFittedRawTrackerHit>();

@@ -201,7 +166,7 @@

                 int clustered_cell = unchecked.removeFirst();
                 cluster.add(channel_to_hit.get(clustered_cell));
                 cluster_signal += channel_to_hit.get(clustered_cell).getAmp();

-                cluster_noise_squared += Math.pow(HPSSVTCalibrationConstants.getNoise((SiSensor)(channel_to_hit.get(clustered_cell)).getRawTrackerHit().getDetectorElement(),clustered_cell),2);

+                cluster_noise_squared += Math.pow(HPSSVTCalibrationConstants.getNoise((SiSensor) (channel_to_hit.get(clustered_cell)).getRawTrackerHit().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);

@@ -214,10 +179,14 @@

                     Boolean addhit = clusterable.get(channel);
 
                     //  If the map entry is null, there is no raw hit for this channel

-                    if (addhit == null) continue;

+                    if (addhit == null) {
+                        continue;
+                    }

 
                     //  Check if this neighbor channel is still available for clustering

-                    if (!addhit) continue;

+                    if (!addhit) {
+                        continue;
+                    }

 
                     //  Add channel to the list of unchecked clustered channels
                     //  and mark it unavailable for clustering

@@ -228,9 +197,8 @@

             }  // end of loop over unchecked cells
 
             //  Finished with this cluster, check cluster threshold and add it to the list of clusters

-            if (cluster.size() > 0 &&
-                cluster_signal/Math.sqrt(cluster_noise_squared) > _cluster_threshold)
-            {

+            if (cluster.size() > 0
+                    && cluster_signal / Math.sqrt(cluster_noise_squared) > _cluster_threshold) {

                 cluster_list.add(cluster);
             }
 

@@ -238,43 +206,44 @@

 
         //  Finished finding clusters
         return cluster_list;

-    }  
-    
-    private boolean passTimingCut(HPSFittedRawTrackerHit hit){
-        
-        boolean pass=false;
-        double time=hit.getT0();
-        if(Math.abs(time-_meanTime)<_timeWindow)

+    }
+
+    private boolean passTimingCut(HPSFittedRawTrackerHit hit) {
+
+        boolean pass = false;
+        double time = hit.getT0();
+        if (Math.abs(time - _meanTime) < _timeWindow) {

             pass = true;

-        

+        }
+

         return pass;
     }

-    
-    private boolean passChisqCut(HPSFittedRawTrackerHit hit){

+
+    private boolean passChisqCut(HPSFittedRawTrackerHit hit) {

         return hit.getShapeFitParameters().getChiSq() < _maxChisq;
     }

-    
-    public int getNeighborCell(int cell, int ncells_0, int ncells_1)
-    {

+
+    public int getNeighborCell(int cell, int ncells_0, int ncells_1) {

         int neighbor_cell = cell + ncells_0;

-        if (isValidCell(neighbor_cell)) return neighbor_cell;
-        else return -1;

+        if (isValidCell(neighbor_cell)) {
+            return neighbor_cell;
+        } else {
+            return -1;
+        }

     }

-    
-    public Set<Integer> getNearestNeighborCells(int cell)
-    {

+
+    public Set<Integer> getNearestNeighborCells(int cell) {

         Set<Integer> neighbors = new HashSet<Integer>();

-        for (int ineigh = -1 ; ineigh <= 1; ineigh=ineigh+2)
-        {
-            int neighbor_cell = getNeighborCell(cell,ineigh,0);
-            if (isValidCell(neighbor_cell)) neighbors.add(neighbor_cell);

+        for (int ineigh = -1; ineigh <= 1; ineigh = ineigh + 2) {
+            int neighbor_cell = getNeighborCell(cell, ineigh, 0);
+            if (isValidCell(neighbor_cell)) {
+                neighbors.add(neighbor_cell);
+            }

         }
         return neighbors;
     }

-    
-    
-    public boolean isValidCell(int cell)
-    {

+
+    public boolean isValidCell(int cell) {

         return (cell >= 0 && cell < HPSSVTConstants.TOTAL_STRIPS_PER_SENSOR);
     }
 }

diff -u -r1.8 -r1.9
--- HPSHelicalTrackHitDriver.java	24 May 2012 17:29:38 -0000	1.8
+++ HPSHelicalTrackHitDriver.java	30 Jul 2012 22:27:09 -0000	1.9
@@ -62,7 +62,7 @@

 //    private StereoHitMaker _crosser = new StereoHitMaker(2., 10.);
 
     private boolean _debug = false;

-    private StereoHitMaker _crosser = new StereoHitMaker(0.0, 10.);

+    private StereoHitMaker _crosser = new StereoHitMaker(0.01, 10.01);

     private HitIdentifier _ID = new HitIdentifier();
     private String _outname = "HelicalTrackHits";
     private String _hitrelname = "HelicalTrackHitRelations";

@@ -70,8 +70,6 @@

     private List<String> _colnames = new ArrayList<String>();
     private Map<String, String> _stereomap = new HashMap<String, String>();
     private Hep3Vector _orgloc = new BasicHep3Vector(0., 0., 0.);

-    private double _eps = 1.0e-6;
-    private SymmetricMatrix _covTrkSystem;

     private boolean _doTranformToTracking = true;
     private HPSTransformations _detToTrk;
     String subdetectorName = "Tracker";

@@ -83,8 +81,6 @@

 //        setDetToTrkMatrix();
         _detToTrk = new HPSTransformations();
         _colnames.add("StripClusterer_SiTrackerHitStrip1D");

-        _crosser.setMaxSeparation(10.01);
-        _crosser.setTolerance(0.01); // user parameter?

     }
 
     public void setSubdetectorName(String subdetectorName) {

@@ -217,15 +213,6 @@

                 System.out.println("Number of stereo hits = " + stereohits.size());
             }
 

-            for (HelicalTrackCross htc : stereohits) {
-                double ypos = htc.x();
-                double zpos = htc.z();
-                List<HelicalTrackStrip> htstrips = htc.getStrips();
-                for (HelicalTrackStrip hts : htstrips) {
-                }
-            }
-
-

             //  Add the stereo hits to our list of HelicalTrackHits
             helhits.addAll(stereohits);
             //mg...6/24/11  add new set of helical track hits that are rotated to from jlab to tracking frame

diff -u -r1.4 -r1.5
--- DataTrackerHitDriver.java	4 May 2012 14:06:37 -0000	1.4
+++ DataTrackerHitDriver.java	30 Jul 2012 22:27:09 -0000	1.5
@@ -24,7 +24,7 @@

     private boolean debug = false;
 
     // Collection name.

-    private String readoutCollectionName = "TrackerHits";

+//    private String readoutCollectionName = "TrackerHits";

 
     // Subdetector name.
     private String subdetectorName = "Tracker";

@@ -66,9 +66,9 @@

         this.debug = true;
     }
 

-    public void setReadoutCollectionName(String readoutCollectionName) {
-        this.readoutCollectionName = readoutCollectionName;
-    }

+//    public void setReadoutCollectionName(String readoutCollectionName) {
+//        this.readoutCollectionName = readoutCollectionName;
+//    }

 
     public void setSubdetectorName(String subdetectorName) {
         this.subdetectorName = subdetectorName;

@@ -126,26 +126,6 @@

     }
 
     /**

-     * Initializes this Driver's objects with the job parameters.
-     */
-    private void initialize() {
-                     
-     
-                       
-    }
-
-    /**
-     * This is executed before detectorChanged and initialization of
-     * digitization objects is done here.
-     */
-    public void startOfData() {
-
-        // At start of job, setup digitization objects needed by this Driver.
-        initialize();
-      
-    }
-
-    /**

      * Do initialization once we get a Detector.
      */
     public void detectorChanged(Detector detector) {