diff -u -r1.11 -r1.12
--- SvtReadout.java	20 Dec 2012 08:25:46 -0000	1.11
+++ SvtReadout.java	25 Apr 2013 22:11:14 -0000	1.12
@@ -17,6 +17,7 @@

 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.event.EventHeader;
 import org.lcsim.geometry.Detector;

+import org.lcsim.hps.recon.tracking.HPSSVTConstants;

 import org.lcsim.recon.tracking.digitization.sisim.CDFSiSensorSim;
 import org.lcsim.recon.tracking.digitization.sisim.SiElectrodeData;
 import org.lcsim.recon.tracking.digitization.sisim.SiElectrodeDataCollection;

@@ -29,7 +30,6 @@

 import org.lcsim.hps.util.ClockSingleton;
 
 //--- Constants ---//

-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.SAMPLING_INTERVAL;

 import static org.lcsim.hps.recon.tracking.HPSSVTConstants.TOTAL_APV25_CHANNELS;
 import static org.lcsim.hps.recon.tracking.HPSSVTConstants.TOTAL_NUMBER_OF_SAMPLES;
 import static org.lcsim.hps.recon.tracking.HPSSVTConstants.TOTAL_STRIPS_PER_SENSOR;

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

diff -u -r1.1 -r1.2
--- RearTransitionModule.java	15 Mar 2013 21:05:28 -0000	1.1
+++ RearTransitionModule.java	25 Apr 2013 22:11:14 -0000	1.2
@@ -7,23 +7,19 @@

 //--- org.lcsim ---//
 import org.lcsim.event.EventHeader;
 import org.lcsim.hps.recon.tracking.HPSSVTCalibrationConstants;

+import org.lcsim.hps.recon.tracking.HPSSVTConstants;

 import org.lcsim.util.Driver;
 
 //--- hps-java ---//

-import org.lcsim.hps.recon.tracking.apv25.Apv25AnalogData;
-import org.lcsim.hps.recon.tracking.apv25.Apv25DigitalData;

 import org.lcsim.hps.util.RandomGaussian;
 
 //--- Constants ---//

-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.CHANNELS;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.MULTIPLEXER_GAIN;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.MIP;

diff -u -r1.8 -r1.9
--- Apv25Full.java	15 Sep 2012 01:28:28 -0000	1.8
+++ Apv25Full.java	25 Apr 2013 22:11:14 -0000	1.9
@@ -1,12 +1,7 @@

 package org.lcsim.hps.recon.tracking.apv25;
 
 //--- Constants ---//

-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.ANALOG_PIPELINE_LENGTH;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.FRONT_END_GAIN;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.MIP;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.SAMPLING_INTERVAL;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.MULTIPLEXER_GAIN;
-import static org.lcsim.hps.recon.tracking.apv25.Apv25Constants.CHANNELS;

+import org.lcsim.hps.recon.tracking.HPSSVTConstants;

 
 //--- hps-java ---//
 import org.lcsim.hps.util.ClockSingleton;

@@ -15,7 +10,7 @@

diff -N Apv25Constants.java
--- Apv25Constants.java	17 Aug 2012 01:17:08 -0000	1.4
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,29 +0,0 @@

diff -u -r1.6 -r1.7
--- HPSSVTConstants.java	16 Aug 2012 01:06:30 -0000	1.6
+++ HPSSVTConstants.java	25 Apr 2013 22:11:14 -0000	1.7
@@ -3,7 +3,7 @@

diff -u -r1.15 -r1.16
--- SimpleSvtReadout.java	25 Apr 2013 21:33:41 -0000	1.15
+++ SimpleSvtReadout.java	25 Apr 2013 22:11:14 -0000	1.16
@@ -19,7 +19,6 @@

 import org.lcsim.event.base.BaseRawTrackerHit;
 import org.lcsim.geometry.Detector;
 import org.lcsim.hps.readout.ecal.TriggerableDriver;

-import org.lcsim.hps.recon.tracking.apv25.Apv25Constants;

 import org.lcsim.hps.util.ClockSingleton;
 import org.lcsim.hps.util.RandomGaussian;
 import org.lcsim.recon.tracking.digitization.sisim.CDFSiSensorSim;

@@ -32,7 +31,7 @@

diff -u -r1.7 -r1.8
--- DataTrackerFakeHitDriver.java	27 Nov 2012 02:17:29 -0000	1.7
+++ DataTrackerFakeHitDriver.java	25 Apr 2013 22:11:14 -0000	1.8
@@ -41,7 +41,7 @@

  * @author phansson
  */
 public class DataTrackerFakeHitDriver extends Driver {

-    

+

     private boolean debug = false;
     TrackUtils trackUtils = new TrackUtils();
     TrackerHitUtils trackerhitutils = new TrackerHitUtils();

@@ -49,37 +49,30 @@

     SvtTrackExtrapolator extrapolator = new SvtTrackExtrapolator();
     Hep3Vector _bfield;
     TrackerHitType trackerType = new TrackerHitType(TrackerHitType.CoordinateSystem.GLOBAL, TrackerHitType.MeasurementType.STRIP_1D);

-    CoordinateSystem coordinate_system =  trackerType.getCoordinateSystem();

+    CoordinateSystem coordinate_system = trackerType.getCoordinateSystem();

     private HitIdentifier _ID = new HitIdentifier();
     private EventHeader.LCMetaData metaData = null;

-    

     private boolean _doHth = false;
     boolean createSimTrackerHits = false;

-

     // Collections

-    List<SimTrackerHit> simHits    = null;

+    List<SimTrackerHit> simHits = null;

     List<SiTrackerHit> stripHits1D = null;

-    List<HelicalTrackHit> hths     = null;

+    List<HelicalTrackHit> hths = null;

     String trackCollectionName = "MCParticle_HelicalTrackFit";
     String stripHitOutputCollectionName = "StripClusterer_SiTrackerHitStrip1D";
     String hthOutputCollectionName = "RotatedHelicalTrackHits";
     String simTrackerHitCollectionName = "FakeTrackerHits";

-   

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

-
-    

     // Various data lists required by digitization.

-    private List<String> processPaths = new ArrayList<String>();
-    private List<IDetectorElement> processDEs = new ArrayList<IDetectorElement>();
-    private Set<SiSensor> processSensors = new HashSet<SiSensor>();
-
-    

+    private List<String> processPaths = new ArrayList<>();
+    private List<IDetectorElement> processDEs = new ArrayList<>();
+    private Set<SiSensor> processSensors = new HashSet<>();

     //Visualization
     private boolean hideFrame = false;
     private AIDA aida = AIDA.defaultInstance();

-    private HashMap<SiSensor,IProfile1D> _delta_histos = new HashMap<SiSensor,IProfile1D>();
-    private HashMap<SiSensor,IHistogram1D> _delta_itercount = new HashMap<SiSensor,IHistogram1D>();

+    private HashMap<SiSensor, IProfile1D> _delta_histos;
+    private HashMap<SiSensor, IHistogram1D> _delta_itercount = new HashMap<>();

     IProfile1D _prf_final_deltas;
     IProfile1D _prf_all_deltas;
     IHistogram1D _h_nstriphits_top;

@@ -89,12 +82,8 @@

     IPlotter plotter_itercount;
     IPlotter plotter_iter_final;
     IPlotter plotter_iter_all;

-    

     IPlotter plotter_nstripclusters;
     IPlotter plotter_trackposodd;

-    
-    
-

     int[][] counts = new int[2][10];
 
     public void setDebug(boolean debug) {

@@ -104,15 +93,15 @@

     public void setHideFrame(boolean hide) {
         this.hideFrame = hide;
     }

-    

+

     public void setDoHth(boolean debug) {
         this._doHth = debug;
     }

-    

+

     /**

-     *  Enable/disable the creation of SimTrackerHits 

+     * Enable/disable the creation of SimTrackerHits

      */

-    public void setCreateSimTrackerHits(boolean createSimTrackerHits){

+    public void setCreateSimTrackerHits(boolean createSimTrackerHits) {

         this.createSimTrackerHits = createSimTrackerHits;
     }
 

@@ -126,20 +115,20 @@

     public void setStripHitOutputCollectionName(String stripHitOutputCollectionName) {
         this.stripHitOutputCollectionName = stripHitOutputCollectionName;
     }

-    

+

     public void setHthOutputCollectionName(String hthOutputCollectionName) {
         this.hthOutputCollectionName = hthOutputCollectionName;
     }

-    

+

     public void setTrackCollectionName(String trackCollectionName) {
         this.trackCollectionName = trackCollectionName;
     }
 

-    

     /**
      * Creates a new instance of TrackerHitDriver.
      */
     public DataTrackerFakeHitDriver() {

+        this._delta_histos = new HashMap<>();

     }
 
     /**

@@ -151,12 +140,12 @@

         // Call sub-Driver's detectorChanged methods.
         super.detectorChanged(detector);
 

-        

+

         Hep3Vector IP = new BasicHep3Vector(0., 0., 1.);

-        _bfield = new BasicHep3Vector(0,0,detector.getFieldMap().getField(IP).y());

+        _bfield = new BasicHep3Vector(0, 0, detector.getFieldMap().getField(IP).y());

         detToTrk = trackerhitutils.detToTrackRotationMatrix();

-        
-        

+
+

         // Process detectors specified by path, otherwise process entire
         // detector
         IDetectorElement deDetector = detector.getDetectorElement();

@@ -175,9 +164,9 @@

 
         // Set the detector to process.
         processPaths.add(subdetectorName);

-        

+

         this.makePlots();

-        

+

     }
 
     /**

@@ -188,123 +177,140 @@

 
 
         // Obtain the tracks from the event

-        if(!event.hasCollection(HpsHelicalTrackFit.class, trackCollectionName)){
-            this.printDebug("No HpsHelicalTrackFits were found, skipping event");

+        if (!event.hasCollection(HPSTrack.class, trackCollectionName)) {
+            this.printDebug("No HPSTracks were found, skipping event");

             simHits = null;
             return;
         }

-        List<HpsHelicalTrackFit> tracks = event.get(HpsHelicalTrackFit.class, trackCollectionName);
-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": found " + tracks.size() + " tracks (" + this.trackCollectionName + ")");

+        List<HPSTrack> tracks = event.get(HPSTrack.class, trackCollectionName);
+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": found " + tracks.size() + " tracks (" + this.trackCollectionName + ")");
+        }

 
         // Instantiate the list of interest 

-        if(this._doHth){

+        if (this._doHth) {

             this.printDebug("Creating HelicalTrackHits...");

-            hths = new ArrayList<HelicalTrackHit>();
-        } else if(createSimTrackerHits){

+            hths = new ArrayList<>();
+        } else if (createSimTrackerHits) {

             this.printDebug("Creating SimTrackerHits...");

-            simHits = new ArrayList<SimTrackerHit>();

+            simHits = new ArrayList<>();

             metaData = event.getMetaData(event.get(SimTrackerHit.class, "TrackerHits"));

-        } else { 

+        } else {

             // Create StripHit1Ds by default
             this.printDebug("Creating StripHit1D...");

-            stripHits1D = new ArrayList<SiTrackerHit>();

+            stripHits1D = new ArrayList<>();

         }
 

-        if(debug) System.out.println(this.getClass().getSimpleName() + ": Add hits for " + tracks.size() + " tracks (" + this.trackCollectionName + ")");
-        
-        for(HpsHelicalTrackFit helix : tracks) {
-            if(debug) System.out.println(this.getClass().getSimpleName() + ": trying to add hits for this track");

+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": Add hits for " + tracks.size() + " tracks (" + this.trackCollectionName + ")");
+        }
+
+        for (HPSTrack helix : tracks) {
+            if (debug) {
+                System.out.println(this.getClass().getSimpleName() + ": trying to add hits for this track");
+            }

 
             // Get the MC Particle associated with this track
             MCParticle mcParticle = helix.getMCParticle();

-            
-            if(debug) {

+
+            if (debug) {

                 System.out.println(this.getClass().getSimpleName() + helix.toString());
                 System.out.println(this.getClass().getSimpleName() + ": htf x0 " + helix.x0() + " y0 " + helix.y0());

-           

+

                 System.out.println(this.getClass().getSimpleName() + ": create a WTrack object");
             }
 

-            WTrack wtrack = new WTrack(helix,Math.abs(_bfield.z()),true); //remove sign from B-field (assumed to go along z-direction)

+            WTrack wtrack = new WTrack(helix, Math.abs(_bfield.z()), true); //remove sign from B-field (assumed to go along z-direction)

-            if(debug) {   

+            if (debug) {

                 System.out.println(this.getClass().getSimpleName() + ": " + wtrack.toString());
 
             }
 

-            

+

             extrapolator.setTrack(helix.parameters());

-            

+

             int n_hits_top = 0;
             int n_hits_bot = 0;
             boolean isTopTrack = false;
             boolean isBotTrack = false;

-            

+

             // Make hits if the helix passed through the sensor 
             for (SiSensor sensor : processSensors) {

-            
-                if(debug) System.out.println(this.getClass().getSimpleName() + ": add hits to sensor " + sensor.getName() + " at position " + sensor.getGeometry().getPosition().toString());
-                

+
+                if (debug) {
+                    System.out.println(this.getClass().getSimpleName() + ": add hits to sensor " + sensor.getName() + " at position " + sensor.getGeometry().getPosition().toString());
+                }
+

                 // When creating stereo hits, skip the even sensors

-                if(this._doHth && _ID.getLayer(sensor)%2==0) {
-                    if(debug) System.out.println(this.getClass().getSimpleName() + ": this was an even sensor -> skip for HTH production");

+                if (this._doHth && _ID.getLayer(sensor) % 2 == 0) {
+                    if (debug) {
+                        System.out.println(this.getClass().getSimpleName() + ": this was an even sensor -> skip for HTH production");
+                    }

                     continue;
                 }

-                

+

                 // Get the position where the sensor and track intercept (Maybe this should go 
                 // inside the method makeSimTrackerHit since it's the only method that uses it
                 Hep3Vector trackPosAtSensor = this.getHelixPlaneIntercept(sensor, wtrack);
                 this.printDebug("The track/plane intercept at " + trackPosAtSensor.toString());

-                

+

                 // Check if the track lies within the sensor

-                boolean isHit = trackUtils.sensorContainsTrack(trackPosAtSensor, sensor);
-                
-                if(isHit) {
-                    if(debug) System.out.println(this.getClass().getSimpleName() + ": make a tracker hit and add to this sensor");
-                    if(SvtUtils.getInstance().isTopLayer(sensor)) {
-                        n_hits_top++;
-                        isTopTrack=true;

+                boolean isHit = TrackUtils.sensorContainsTrack(trackPosAtSensor, sensor);
+
+                if (isHit) {
+                    if (debug) {
+                        System.out.println(this.getClass().getSimpleName() + ": make a tracker hit and add to this sensor");

                     }

-                    else {

+                    if (SvtUtils.getInstance().isTopLayer(sensor)) {
+                        n_hits_top++;
+                        isTopTrack = true;
+                    } else {

                         n_hits_bot++;

-                        isBotTrack=true;

+                        isBotTrack = true;

                     }

-                    if(this._doHth) {

+                    if (this._doHth) {

                         hths.add(this.makeHelicalTrackHit(sensor, wtrack));

-                    } else if(createSimTrackerHits){

+                    } else if (createSimTrackerHits) {

                         // Create a SimTrackerHit at the intersect between a track and a sensor
                         simHits.add(this.makeSimTrackerHit(metaData, sensor, trackPosAtSensor, mcParticle, wtrack));
                     } else {

-                        stripHits1D.add(this.makeTrackerHit(sensor, wtrack));             

+                        stripHits1D.add(this.makeTrackerHit(sensor, wtrack));

                     }
                 } else {

-                    if(debug) System.out.println(this.getClass().getSimpleName() + ": this helix didn't pass within the sensor so no hit was added");

+                    if (debug) {
+                        System.out.println(this.getClass().getSimpleName() + ": this helix didn't pass within the sensor so no hit was added");
+                    }

                 }

-                

+
+            }
+
+            if (isTopTrack) {
+                this._h_nstriphits_top.fill(n_hits_top);
+            }
+            if (isBotTrack) {
+                this._h_nstriphits_bottom.fill(n_hits_bot);

             }

-                
-            if(isTopTrack) this._h_nstriphits_top.fill(n_hits_top);
-            if(isBotTrack) this._h_nstriphits_bottom.fill(n_hits_bot);
-            if(isTopTrack && isBotTrack) {

+            if (isTopTrack && isBotTrack) {

                 System.out.println(this.getClass().getSimpleName() + ": tris track is both top and bottom??? \n" + wtrack.toString() + "\nHTF:" + helix.toString());
                 System.exit(1);
             }

-            

+

             /*

-            stripHits1D.addAll(stripHits1D_for_track);
-            hths.addAll(hths_for_track);
-            */

+             stripHits1D.addAll(stripHits1D_for_track);
+             hths.addAll(hths_for_track);
+             */

         }
 

-        
-        

+
+

         if (debug) {

-            if(stripHits1D != null){
-                System.out.println(this.getClass().getSimpleName() + ": Produced "  + stripHits1D.size() + " hits for collection " + this.stripHitOutputCollectionName);

+            if (stripHits1D != null) {
+                System.out.println(this.getClass().getSimpleName() + ": Produced " + stripHits1D.size() + " hits for collection " + this.stripHitOutputCollectionName);

             }

-            if(hths != null){
-                System.out.println(this.getClass().getSimpleName() + ": Produced "  + hths.size() + " hits for collection " + this.hthOutputCollectionName);

+            if (hths != null) {
+                System.out.println(this.getClass().getSimpleName() + ": Produced " + hths.size() + " hits for collection " + this.hthOutputCollectionName);

             }
         }
 

@@ -313,162 +319,184 @@

         //event.put(this.rawTrackerHitOutputCollectionName, rawHits, RawTrackerHit.class, flag, toString());
         // Put the collection of interest into the event
 

-       if(_doHth){
-            event.put(hthOutputCollectionName,      hths,        HelicalTrackHit.class,     0);
-       } else if(createSimTrackerHits){
-            event.put(simTrackerHitCollectionName,  simHits,     SimTrackerHit.class,       0);

+        if (_doHth) {
+            event.put(hthOutputCollectionName, hths, HelicalTrackHit.class, 0);
+        } else if (createSimTrackerHits) {
+            event.put(simTrackerHitCollectionName, simHits, SimTrackerHit.class, 0);

             this.printDebug("SimTrackerHits created: " + simHits.size());

-        } else { 

+        } else {

             event.put(stripHitOutputCollectionName, stripHits1D, SiTrackerHitStrip1D.class, 0, toString());
         }
         //event.put("RotatedHelicalTrackHits", rotatedhits, HelicalTrackHit.class, 0);

-        
-       /*
-        if (debug) {
-            if(event.hasCollection(HelicalTrackHit.class, "RotatedHelicalTrackHits")) {
-                System.out.println(this.getClass().getSimpleName() + ": has hths:");
-                for(HelicalTrackHit hth : hths) {
-                    System.out.println(this.getClass().getSimpleName() + ": " + hth.getPosition().toString());
-                }
-            } else {
-                System.out.println(this.getClass().getSimpleName() + ": has not hths!");
-            }
-        }
-        if (debug) {
-            for (int mod = 0; mod < 2; mod++) {
-                for (int layer = 0; layer < 10; layer++) {
-                    counts[mod][layer] += SvtUtils.getInstance().getSensor(mod, layer).getReadout().getHits(SiTrackerHit.class).size();
-                }
-            }
-        }*/

+
+        /*
+         if (debug) {
+         if(event.hasCollection(HelicalTrackHit.class, "RotatedHelicalTrackHits")) {
+         System.out.println(this.getClass().getSimpleName() + ": has hths:");
+         for(HelicalTrackHit hth : hths) {
+         System.out.println(this.getClass().getSimpleName() + ": " + hth.getPosition().toString());
+         }
+         } else {
+         System.out.println(this.getClass().getSimpleName() + ": has not hths!");
+         }
+         }
+         if (debug) {
+         for (int mod = 0; mod < 2; mod++) {
+         for (int layer = 0; layer < 10; layer++) {
+         counts[mod][layer] += SvtUtils.getInstance().getSensor(mod, layer).getReadout().getHits(SiTrackerHit.class).size();
+         }
+         }
+         }*/

     }

-    
-    

+

     private SiTrackerHitStrip1D makeTrackerHit(SiSensor sensor, WTrack wtrack) {

-    //private SiTrackerHitStrip1D makeTrackerHit(List<HPSFittedRawTrackerHit> cluster, SiSensorElectrodes electrodes) {

+        //private SiTrackerHitStrip1D makeTrackerHit(List<HPSFittedRawTrackerHit> cluster, SiSensorElectrodes electrodes) {

         //create fake raw tracker hit

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": makeTrackerHit");
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": makeTrackerHit");
+        }
+

         List<RawTrackerHit> rth_cluster = this.makeRawTrackerFakeHit(sensor);

-        if(rth_cluster.size()!=1) {
-            System.out.println(this.getClass().getSimpleName() + ": the fake raw tracker hit cluster is different than one!? " + rth_cluster.size() );

+        if (rth_cluster.size() != 1) {
+            System.out.println(this.getClass().getSimpleName() + ": the fake raw tracker hit cluster is different than one!? " + rth_cluster.size());

             System.exit(1);
         }

-        if(debug) System.out.println(this.getClass().getSimpleName() + ": created a fake raw tracker hit ");
-        RawTrackerHit raw_hit = rth_cluster.get(0);        

+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": created a fake raw tracker hit ");
+        }
+        RawTrackerHit raw_hit = rth_cluster.get(0);

         IIdentifier id = raw_hit.getIdentifier();
 
         //Get the electrode objects
         SiTrackerIdentifierHelper _sid_helper = (SiTrackerIdentifierHelper) sensor.getIdentifierHelper();
         ChargeCarrier carrier = ChargeCarrier.getCarrier(_sid_helper.getSideValue(id));
         SiSensorElectrodes electrodes = ((SiSensor) raw_hit.getDetectorElement()).getReadoutElectrodes(carrier);

-        
-        
-        
-        

+
+
+
+

         ITransform3D local_to_global;
         if (coordinate_system == TrackerHitType.CoordinateSystem.GLOBAL) {
             local_to_global = new Transform3D();

-        }
-        else if (coordinate_system == TrackerHitType.CoordinateSystem.SENSOR) {

+        } else if (coordinate_system == TrackerHitType.CoordinateSystem.SENSOR) {

             local_to_global = sensor.getGeometry().getLocalToGlobal();

-        }
-        else {

+        } else {

             throw new RuntimeException(this.getClass().getSimpleName() + " problem with coord system " + coordinate_system.toString());
         }

-        
-        

+
+

         ITransform3D electrodes_to_global = electrodes.getLocalToGlobal();
         ITransform3D global_to_hit = local_to_global.inverse();

-        ITransform3D electrodes_to_hit = Transform3D.multiply(global_to_hit,electrodes_to_global);
-            
-        Hep3Vector u= electrodes_to_hit.rotated(electrodes.getMeasuredCoordinate(0));
-        Hep3Vector v= electrodes_to_hit.rotated(electrodes.getUnmeasuredCoordinate(0));
-        Hep3Vector w = VecOp.cross(u, v);    

+        ITransform3D electrodes_to_hit = Transform3D.multiply(global_to_hit, electrodes_to_global);
+
+        Hep3Vector u = electrodes_to_hit.rotated(electrodes.getMeasuredCoordinate(0));
+        Hep3Vector v = electrodes_to_hit.rotated(electrodes.getUnmeasuredCoordinate(0));
+        Hep3Vector w = VecOp.cross(u, v);

         Hep3Vector _orgloc = new BasicHep3Vector(0., 0., 0.);
         electrodes_to_global.transformed(_orgloc);

-        if(debug) {

+        if (debug) {

             System.out.println(this.getClass().getSimpleName() + ": electrodes  u " + u.toString());
             System.out.println(this.getClass().getSimpleName() + ": electrodes  v " + v.toString());
             System.out.println(this.getClass().getSimpleName() + ": electrodes  w " + w.toString() + "( " + w.magnitude() + ")");
         }
 
         electrodes_to_global.getTranslation().translate(_orgloc);

-        if(debug) System.out.print(this.getClass().getSimpleName() + ": orgloc " + _orgloc.toString() + "  -> ");

+        if (debug) {
+            System.out.print(this.getClass().getSimpleName() + ": orgloc " + _orgloc.toString() + "  -> ");
+        }

         _orgloc = VecOp.mult(detToTrk, _orgloc);

-        if(debug) System.out.println(_orgloc.toString());
-        
-        
-        
-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": Try to find the interception point");
-        

+        if (debug) {
+            System.out.println(_orgloc.toString());
+        }
+
+
+
+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": Try to find the interception point");
+        }
+

         //B-field must go along Z direction

-        Hep3Vector h = new BasicHep3Vector(_bfield.x(),_bfield.y(),Math.abs(_bfield.z()));

+        Hep3Vector h = new BasicHep3Vector(_bfield.x(), _bfield.y(), Math.abs(_bfield.z()));

         h = VecOp.unit(h);
         //Rotate into tracking frame
         Hep3Vector eta = VecOp.mult(detToTrk, w);
 

-        if(debug) System.out.println(this.getClass().getSimpleName() + ": eta  " + eta.toString());
-        

+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": eta  " + eta.toString());
+        }
+

         Hep3Vector position = wtrack.getHelixAndPlaneIntercept(_orgloc, eta, h);

-                
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": found interception point at position " + position.toString());
-        
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": found interception point at position " + position.toString());
+        }
+
+

         HelicalTrackFit htf = wtrack._htf;
         List<Double> s = HelixUtils.PathToXPlane(htf, position.x(), 0, 0);
         Hep3Vector posOnHelix = HelixUtils.PointOnHelix(htf, s.get(0));
         Hep3Vector posdiff = VecOp.sub(position, posOnHelix);
         System.out.println(this.getClass().getSimpleName() + ": diffpos " + posdiff.toString() + " L " + position.toString() + " posOnHelix " + posOnHelix.toString() + " R=" + htf.R());

-        

+

         position = VecOp.mult(VecOp.inverse(detToTrk), position);

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": rotate the hit position to the global frame -> " + position.toString());
-        
-        
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": rotate the hit position to the global frame -> " + position.toString());
+        }
+
+
+

         // Need to make sure that the position is at the edge of the strip in the global frame
         // 1. Rotate to the local sensor frame

-        position = ((SiSensor)electrodes.getDetectorElement()).getGeometry().getGlobalToLocal().transformed(position);
-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": local (sensor) hit position " + position.toString());
-        

+        position = ((SiSensor) electrodes.getDetectorElement()).getGeometry().getGlobalToLocal().transformed(position);
+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": local (sensor) hit position " + position.toString());
+        }
+

         // 2. Remove the coordinate of the unmeasured direction

-        
-        position = new BasicHep3Vector(position.x(),0,position.z());
-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": fixed local (sensor) hit position " + position.toString());
-        

+
+        position = new BasicHep3Vector(position.x(), 0, position.z());
+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": fixed local (sensor) hit position " + position.toString());
+        }
+

         // 3. Transform back to global coordinates

-        

+

         position = ((SiSensor) electrodes.getDetectorElement()).getGeometry().getLocalToGlobal().transformed(position);

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": fixed global hit position " + position.toString());
-        
-        
-        
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": fixed global hit position " + position.toString());
+        }
+
+
+
+

         //Fill dummy versions
         SymmetricMatrix covariance = this.getCovariance(rth_cluster, electrodes);
         double time = this.getTime(rth_cluster);
         double energy = this.getEnergy(rth_cluster);

-        
-        

+
+

         SiTrackerHitStrip1D hit = new SiTrackerHitStrip1D(position, covariance, energy, time, rth_cluster, trackerType);

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": created SiStrip1D at " + position.toString());
-        
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": created SiStrip1D at " + position.toString());
+        }
+
+

         return hit;

-        
-       

+
+

     }

-    

+

     /**

-     * 

+     *

      * Find the unit vector of a sensor

+     *

      * @param sensor
      * @return unit vector of the plane
      */

@@ -485,29 +513,27 @@

         ITransform3D local_to_global;
         if (coordinate_system == TrackerHitType.CoordinateSystem.GLOBAL) {
             local_to_global = new Transform3D();

-        }
-        else if (coordinate_system == TrackerHitType.CoordinateSystem.SENSOR) {

+        } else if (coordinate_system == TrackerHitType.CoordinateSystem.SENSOR) {

             local_to_global = sensor.getGeometry().getLocalToGlobal();

-        }
-        else {

+        } else {

             throw new RuntimeException(this.getClass().getSimpleName() + " problem with coord system " + coordinate_system.toString());
         }
         ITransform3D electrodes_to_global = electrodes.getLocalToGlobal();
         ITransform3D global_to_hit = local_to_global.inverse();

-        ITransform3D electrodes_to_hit = Transform3D.multiply(global_to_hit,electrodes_to_global);
-            
-        Hep3Vector u= electrodes_to_hit.rotated(electrodes.getMeasuredCoordinate(0));
-        Hep3Vector v= electrodes_to_hit.rotated(electrodes.getUnmeasuredCoordinate(0));
-        Hep3Vector w = VecOp.cross(u, v);  

+        ITransform3D electrodes_to_hit = Transform3D.multiply(global_to_hit, electrodes_to_global);
+
+        Hep3Vector u = electrodes_to_hit.rotated(electrodes.getMeasuredCoordinate(0));
+        Hep3Vector v = electrodes_to_hit.rotated(electrodes.getUnmeasuredCoordinate(0));
+        Hep3Vector w = VecOp.cross(u, v);

         Hep3Vector eta = VecOp.mult(detToTrk, w);
         return eta;

-        

+

     }

-    
-    
-     /**
-     * 

+
+    /**
+     *

      * Find the origin of the sensor plane

+     *

      * @param sensor
      * @return origin position of the plane
      */

@@ -516,8 +542,8 @@

          * Weird way of getting the org location by creating a fake raw tracker hit...must be simpler way?
          */
         List<RawTrackerHit> rth_cluster = this.makeRawTrackerFakeHit(sensor);

-        if(rth_cluster.size()!=1) {
-            System.out.println(this.getClass().getSimpleName() + ": the fake raw tracker hit cluster is different than one!? " + rth_cluster.size() );

+        if (rth_cluster.size() != 1) {
+            System.out.println(this.getClass().getSimpleName() + ": the fake raw tracker hit cluster is different than one!? " + rth_cluster.size());

             System.exit(1);
         }
         //Get the electrode objects

@@ -528,33 +554,34 @@

         ITransform3D local_to_global;
         if (coordinate_system == TrackerHitType.CoordinateSystem.GLOBAL) {
             local_to_global = new Transform3D();

-        }
-        else if (coordinate_system == TrackerHitType.CoordinateSystem.SENSOR) {

+        } else if (coordinate_system == TrackerHitType.CoordinateSystem.SENSOR) {

             local_to_global = sensor.getGeometry().getLocalToGlobal();

-        }
-        else {

+        } else {

             throw new RuntimeException(this.getClass().getSimpleName() + " problem with coord system " + coordinate_system.toString());
         }
         ITransform3D electrodes_to_global = electrodes.getLocalToGlobal();
         Hep3Vector _orgloc = new BasicHep3Vector(0., 0., 0.);
         electrodes_to_global.transformed(_orgloc);
         electrodes_to_global.getTranslation().translate(_orgloc);

-        if(debug) System.out.print(this.getClass().getSimpleName() + ": orgloc " + _orgloc.toString() + "  -> ");

+        if (debug) {
+            System.out.print(this.getClass().getSimpleName() + ": orgloc " + _orgloc.toString() + "  -> ");
+        }

         _orgloc = VecOp.mult(detToTrk, _orgloc);

-        if(debug) System.out.println(_orgloc.toString());
-        

+        if (debug) {
+            System.out.println(_orgloc.toString());
+        }
+

         return _orgloc;

-        

+

     }

-    
-    

+

     private Hep3Vector getHelixPlaneIntercept(SiSensor sensor, WTrack wtrack) {

-        Hep3Vector eta = this.getPlaneUnitVector(sensor);   

+        Hep3Vector eta = this.getPlaneUnitVector(sensor);

         Hep3Vector _orgloc = this.getOrgLoc(sensor);

-        Hep3Vector h = new BasicHep3Vector(_bfield.x(),_bfield.y(),Math.abs(_bfield.z()));

+        Hep3Vector h = new BasicHep3Vector(_bfield.x(), _bfield.y(), Math.abs(_bfield.z()));

         h = VecOp.unit(h);
         Hep3Vector position = wtrack.getHelixAndPlaneIntercept(_orgloc, eta, h);

-        if(debug) {

+        if (debug) {

             HelicalTrackFit htf = wtrack._htf;
             List<Double> s = HelixUtils.PathToXPlane(htf, position.x(), 0, 0);
             Hep3Vector posOnHelix = HelixUtils.PointOnHelix(htf, s.get(0));

@@ -562,25 +589,28 @@

             System.out.println(this.getClass().getSimpleName() + ": Path length to position " + position.toString() + ": s = " + s.get(0));
             System.out.println(this.getClass().getSimpleName() + ": Difference between W and helixutils: diffpos " + posdiff.toString() + " ( " + position.toString() + " posOnHelix " + posOnHelix.toString() + " R=" + htf.R());
         }

-        
-        
-        return position;  

+
+
+        return position;

     }

-    
-    

+

     private HelicalTrackHit makeHelicalTrackHit(SiSensor sensor, WTrack wtrack) {

-    //private SiTrackerHitStrip1D makeTrackerHit(List<HPSFittedRawTrackerHit> cluster, SiSensorElectrodes electrodes) {

+        //private SiTrackerHitStrip1D makeTrackerHit(List<HPSFittedRawTrackerHit> cluster, SiSensorElectrodes electrodes) {

         //create fake raw tracker hit

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": makeTrackerHit");
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": makeTrackerHit");
+        }
+

         List<RawTrackerHit> rth_cluster = this.makeRawTrackerFakeHit(sensor);

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": Try to find the interception point");
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": Try to find the interception point");
+        }
+

         Hep3Vector position = this.getHelixPlaneIntercept(sensor, wtrack);

- 
-        

+
+

         //Fill dummy covariance matrix with minimal uncertainties
         //SymmetricMatrix covariance = this.getCovariance(rth_cluster, electrodes);
         SymmetricMatrix covariance = new SymmetricMatrix(3);

@@ -588,75 +618,79 @@

         double cov_yy = cov_xx;
         double cov_zz = cov_xx;
         covariance.setElement(0, 0, cov_xx);

-        covariance.setElement(1, 1, cov_yy); 

+        covariance.setElement(1, 1, cov_yy);

         covariance.setElement(2, 2, cov_zz);
 
         double time = this.getTime(rth_cluster);
         double energy = this.getEnergy(rth_cluster);

-        
-       

+
+

         //IDetectorElement de = sensor;
         String det = _ID.getName(sensor);
         int layer = _ID.getLayer(sensor);
         BarrelEndcapFlag beflag = _ID.getBarrelEndcapFlag(sensor);

-        
-        if(layer%2==0) {
-            if(debug) System.out.println(this.getClass().getSimpleName() + ": problem, trying to create a HTH for even layer? " + layer);

+
+        if (layer % 2 == 0) {
+            if (debug) {
+                System.out.println(this.getClass().getSimpleName() + ": problem, trying to create a HTH for even layer? " + layer);
+            }

             System.exit(1);
         }

-                
-        HelicalTrackHit hit = new HelicalTrackHit(position, covariance,0.0, time, 3,rth_cluster, det, layer, beflag);

+
+        HelicalTrackHit hit = new HelicalTrackHit(position, covariance, 0.0, time, 3, rth_cluster, det, layer, beflag);

         //SiTrackerHitStrip1D hit = new SiTrackerHitStrip1D(position, covariance, energy, time, rth_cluster, trackerType);

-        
-        if(debug) System.out.println(this.getClass().getSimpleName() + ": created HelicalTrackHit at " + position.toString() + " and layer " + hit.Layer() + "(" + layer + ")");
-                
-        

+
+        if (debug) {
+            System.out.println(this.getClass().getSimpleName() + ": created HelicalTrackHit at " + position.toString() + " and layer " + hit.Layer() + "(" + layer + ")");
+        }
+
+

         return hit;

-        
-       

+
+

     }

-    
-   

+

     /**
      * Create a SimTrackerHit and add it to the corresponding readout

-     * 

+     *

      * @param metaData : meta data associated with the SimTrackerHit collection
      * @param sensor : sensor on which the hit will be created on
      * @param trkPositionAtSensor : the position of a track at a sensor plane

-     * @param particle : MC particle associated with the track containing the hit

+     * @param particle : MC particle associated with the track containing the
+     * hit

      * @return SimTrackerHit
      */

-    private SimTrackerHit makeSimTrackerHit(EventHeader.LCMetaData metaData, SiSensor sensor, Hep3Vector trkPositionAtSensor, MCParticle particle, WTrack wtrack){

+    private SimTrackerHit makeSimTrackerHit(EventHeader.LCMetaData metaData, SiSensor sensor, Hep3Vector trkPositionAtSensor, MCParticle particle, WTrack wtrack) {

-    	// Transform the position of the SimTrackerHit to the detector coordinates
-    	// TODO: Fix the extrapolator so that it returns the position in the detector frame
-    	//Hep3Vector trkPositionAtSensorDet = VecOp.mult(VecOp.inverse(detToTrk),trkPositionAtSensor);

diff -N ParticleMaker.java
--- ParticleMaker.java	19 Jun 2012 01:44:55 -0000	1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,132 +0,0 @@

diff -N ParticleMaker.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ ParticleMaker.java	25 Apr 2013 22:11:14 -0000	1.1
@@ -0,0 +1,133 @@