diff -N BiasSurface.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ BiasSurface.java	3 Dec 2007 23:23:30 -0000	1.1
@@ -0,0 +1,41 @@

+/*
+ * BiasSurface.java
+ *
+ * Created on November 29, 2007, 11:13 AM
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package org.lcsim.detector.tracker.silicon;
+
+import org.lcsim.detector.solids.Polygon3D;
+
+/**
+ *
+ * @author tknelson
+ */
+public class BiasSurface
+{
+    
+    Polygon3D _surface;
+    double _voltage;
+    
+    /** Creates a new instance of BiasSurface */
+    public BiasSurface(Polygon3D surface, double voltage)
+    {
+        _surface = surface;
+        _voltage = voltage;
+    }
+    
+    public Polygon3D getSurface()
+    {
+        return _surface;
+    }
+    
+    public double getVoltage()
+    {
+        return _voltage;
+    }
+    
+}

diff -u -r1.3 -r1.4
--- ChargeCarrier.java	18 May 2007 21:56:34 -0000	1.3
+++ ChargeCarrier.java	3 Dec 2007 23:23:29 -0000	1.4
@@ -55,4 +55,12 @@

     double alpha(double temperature)
     {return _alpha_factor * Math.pow( (temperature/300.0), _alpha_exponent);}
     

+    // Static
+    public static ChargeCarrier getCarrier(int charge)
+    {
+        if (charge == -1) return ChargeCarrier.ELECTRON;
+        if (charge == +1) return ChargeCarrier.HOLE;
+        else throw new RuntimeException("No ChargeCarrier for charge: "+charge);
+    }
+    

 }

diff -u -r1.1 -r1.2
--- ChargeDistribution.java	14 Oct 2007 06:13:09 -0000	1.1
+++ ChargeDistribution.java	3 Dec 2007 23:23:29 -0000	1.2
@@ -11,12 +11,13 @@

 
 import org.lcsim.detector.ITransform3D;
 import hep.physics.vec.Hep3Vector;

+import org.lcsim.detector.solids.Transformable;

 
 /**
  *
  * @author tknelson
  */

-public interface ChargeDistribution

+public interface ChargeDistribution extends Transformable

 {
     // Transform this charge distribution into new coordinates in place
     public void transform(ITransform3D transform);

diff -u -r1.16 -r1.17
--- SiSensor.java	14 Oct 2007 06:13:09 -0000	1.16
+++ SiSensor.java	3 Dec 2007 23:23:29 -0000	1.17
@@ -29,22 +29,23 @@

 import org.lcsim.detector.identifier.IIdentifierHelper;
 import org.lcsim.detector.identifier.IIdentifierDictionary.FieldNotFoundException;
 import org.lcsim.detector.identifier.IIdentifierDictionary.InvalidIndexException;

-import org.lcsim.detector.solids.Box;

+import org.lcsim.detector.solids.GeomOp3D;
+import org.lcsim.detector.solids.Point3D;
+import org.lcsim.detector.solids.Polygon3D;

 
 /**
  *
  * @author tknelson
  */

-public class SiSensor extends DetectorElement {
-

+public class SiSensor extends DetectorElement
+{
+    

     // Enumerated types
     //=================

-    public enum Orientation { PSIDE_NEGATIVE_Z, PSIDE_POSITIVE_Z };

     
     // Fields
     //=======
     // Static defaults - actual values user modifiable

-    private static Orientation _ORIENTATION_DEFAULT = Orientation.PSIDE_POSITIVE_Z;

     private static double _DEPLETION_VOLTAGE_DEFAULT = 100;// * volt;
     private static double _BIAS_VOLTAGE_DEFAULT = 110;// * volt;
     

@@ -54,13 +55,12 @@

     // Sensor ID
     private int _sensorid;
     

-    // electrodes, electrode angles and orientation of sensor

+    // biasing and electrodes
+    private Map<ChargeCarrier, Polygon3D> _bias_surfaces = new EnumMap<ChargeCarrier,Polygon3D>(ChargeCarrier.class);

     private Map<ChargeCarrier, SiSensorElectrodes> _sense_electrodes = new EnumMap<ChargeCarrier,SiSensorElectrodes>(ChargeCarrier.class);
     private Map<ChargeCarrier, SiSensorElectrodes> _readout_electrodes = new EnumMap<ChargeCarrier,SiSensorElectrodes>(ChargeCarrier.class);
     private Map<ChargeCarrier, BasicMatrix> _transfer_efficiencies = new EnumMap<ChargeCarrier,BasicMatrix>(ChargeCarrier.class);

-//    private Map<ChargeCarrier, Double> _electrode_angles = new EnumMap<ChargeCarrier,Double>(ChargeCarrier.class);
-    private Orientation _orientation;
-

+    

     // bulk - propoerties of the bulk
     private DopedSilicon _bulk;
     private double _thickness;  // accessed often, cached here for speed

@@ -69,11 +69,6 @@

     private double _depletion_voltage;
     private double _bias_voltage;
     

-    // derived properties
-    //-------------------
-    // measured coordinates in local coordinates
-//    private EnumMap<ChargeCarrier, Hep3Vector[]> _measured_coordinates = new EnumMap<ChargeCarrier,Hep3Vector[]>(ChargeCarrier.class);
-    

     // Constructors
     //=============
     

@@ -89,7 +84,6 @@

         super(name,parent,support,id);
         setSensorID(sensorid);
         setBulk(new DopedSilicon());

-        this.setOrientation(SiSensor._ORIENTATION_DEFAULT);

         setDepletionVoltage(SiSensor._DEPLETION_VOLTAGE_DEFAULT);
         setBiasVoltage(SiSensor._BIAS_VOLTAGE_DEFAULT);
     }

@@ -104,19 +98,19 @@

         _sensorid = sensorid;
     }
     

-    public void setElectrodes(ChargeCarrier carrier, SiSensorElectrodes electrodes)

+    public void setSenseElectrodes(SiSensorElectrodes sense_electrodes)

     {

-        _sense_electrodes.put(carrier,electrodes);

+        _sense_electrodes.put(sense_electrodes.getChargeCarrier(),sense_electrodes);

     }

- 
-    public void setSenseElectrodes(ChargeCarrier carrier, SiSensorElectrodes sense_electrodes)

+    
+    public void setReadoutElectrodes(SiSensorElectrodes readout_electrodes)

     {

-        _sense_electrodes.put(carrier,sense_electrodes);

+        _readout_electrodes.put(readout_electrodes.getChargeCarrier(),readout_electrodes);

     }

-
-    public void setReadoutElectrodes(ChargeCarrier carrier, SiSensorElectrodes readout_electrodes)

+    
+    public void setBiasSurface(ChargeCarrier carrier, Polygon3D bias_surface)

     {

-        _readout_electrodes.put(carrier,readout_electrodes);

+        _bias_surfaces.put(carrier,bias_surface);

     }
     
     public void setTransferEfficiencies(ChargeCarrier carrier, BasicMatrix transfer_efficiencies)

@@ -124,16 +118,6 @@

         _transfer_efficiencies.put(carrier,transfer_efficiencies);
     }
     

-//    public void setElectrodeAngle(ChargeCarrier carrier, double electrode_angle)
-//    {
-//        _electrode_angles.put(carrier,electrode_angle);
-//    }
-    
-    public void setOrientation(Orientation orientation)
-    {
-        _orientation = orientation;
-    }
-    

     public void setBulk(DopedSilicon bulk)
     {
         _bulk = bulk;

@@ -153,11 +137,6 @@

     public int getSensorID()
     {
         return _sensorid;

-    }    
-    
-    public SiSensorElectrodes getElectrodes(ChargeCarrier carrier)
-    {
-        return _sense_electrodes.get(carrier);

     }
     
     public SiSensorElectrodes getSenseElectrodes(ChargeCarrier carrier)

@@ -170,19 +149,14 @@

         return _readout_electrodes.get(carrier);
     }
     

-    public BasicMatrix getTransferEfficiencies(ChargeCarrier carrier)

+    public Polygon3D getBiasSurface(ChargeCarrier carrier)

     {

-        return _transfer_efficiencies.get(carrier);

+        return _bias_surfaces.get(carrier);

     }
     

-//    public double getElectrodeAngle(ChargeCarrier carrier)
-//    {
-//        return _electrode_angles.get(carrier);
-//    }
-    
-    public Orientation getOrientation()

+    public BasicMatrix getTransferEfficiencies(ChargeCarrier carrier)

     {

-        return _orientation;

+        return _transfer_efficiencies.get(carrier);

     }
     
     public DopedSilicon getBulk()

@@ -192,6 +166,20 @@

     
     public double getThickness()
     {

+        if (_thickness == 0)
+        {
+            
+            
+//            System.out.println("Hole plane normal: "+_bias_surfaces.get(ChargeCarrier.HOLE).getPlane().getNormal());
+//            System.out.println("Hole plane direction: "+_bias_surfaces.get(ChargeCarrier.HOLE).getPlane().getDistance());
+//
+//            System.out.println("Electron plane normal: "+_bias_surfaces.get(ChargeCarrier.ELECTRON).getPlane().getNormal());
+//            System.out.println("Electron plane direction: "+_bias_surfaces.get(ChargeCarrier.ELECTRON).getPlane().getDistance());
+            
+            _thickness = Math.abs(GeomOp3D.distanceBetween( _bias_surfaces.get(ChargeCarrier.HOLE).getPlane(), _bias_surfaces.get(ChargeCarrier.ELECTRON).getPlane()));            
+            
+//            System.out.println("Calculated thickness: "+_thickness);
+        }

         return _thickness;
     }
     

@@ -213,56 +201,24 @@

         {
             ancestor = ancestor.getParent();
         }

-        if (ancestor == null) System.out.println("WARNING: SiSensor.getBField CANNOT FIND DETECTOR!!");                
-

+        if (ancestor == null) throw new RuntimeException("SiSensor.getBField CANNOT FIND DETECTOR!!");
+        

         Hep3Vector global_position = getGeometry().getLocalToGlobal().transformed(local_position);
         Hep3Vector field_global = ((DeDetector)ancestor).getBField(global_position);

+//        Hep3Vector field_global = new BasicHep3Vector(0,0,5);

         
         return getGeometry().getGlobalToLocal().rotated(field_global);
         
     }

-        
-//    public Hep3Vector[] getMeasuredCoordinates(ChargeCarrier carrier)
-//    {
-//        return _measured_coordinates.get(carrier);
-//    }
-    

     
     // Operators
     //==========

-    public void initialize()
-    {
-
-        // Cache thickness of bulk
-        _thickness = 2.0*((Box)getGeometry().getLogicalVolume().getSolid()).getZHalfLength();
-        
-        // Store various important directions
-        for (ChargeCarrier carrier : ChargeCarrier.values())
-        {
-            if (hasElectrodesOnSide(carrier)) {  
-                
-//                // cache coordinates measured by the pattern of electrodes on each side
-//                double electrode_angle = getElectrodeAngle(carrier); 
-//                int naxes = _sense_electrodes.get(carrier).getNAxes();
-//                Hep3Vector[] measured_coordinates = new Hep3Vector[naxes];
-//                
-//                for (int iaxis = 0; iaxis < naxes ; iaxis++)
-//                {
-//                    measured_coordinates[iaxis] = measuredCoordinate(electrode_angle + iaxis*Math.PI/naxes);
-//                }
-//                _measured_coordinates.put(carrier,measured_coordinates);
-
-            
-            }
-        }
-
-    }
-    
-    private double zOfSide(ChargeCarrier carrier)
-    {   
-        if ( (carrier == ChargeCarrier.HOLE) == (_orientation == Orientation.PSIDE_POSITIVE_Z) ) return _thickness/2.0;
-        else return -_thickness/2.0;
-    }

+//    public void initialize()
+//    {
+//        // Cache thickness of bulk
+//        _thickness = Math.abs(GeomOp3D.distanceBetween( _bias_surfaces.get(ChargeCarrier.HOLE).getPlane(), _bias_surfaces.get(ChargeCarrier.HOLE).getPlane()));
+//
+//    }

     
     public boolean isACCoupled(ChargeCarrier carrier)
     {

@@ -271,8 +227,14 @@

     
     public double distanceFromSide(Hep3Vector point, ChargeCarrier carrier)
     {

-        double distance =  Math.abs(point.z() - zOfSide(carrier));
-        return distance;

+//        System.out.println("distanceFromSide: "+-GeomOp3D.distanceBetween(new Point3D(point),_bias_surfaces.get(carrier).getPlane()));
+        
+        
+        return -GeomOp3D.distanceBetween(new Point3D(point),_bias_surfaces.get(carrier).getPlane());
+//        ITransform3D electrode_transform = _sense_electrodes.get(carrier).getParentToLocal().inverse();
+//        Plane3D electrode_plane = _sense_electrodes.get(carrier).getGeometry().transformed(electrode_transform).getPlane();
+//
+//        return GeomOp3D.distanceBetween(new Point3D(point),electrode_plane);

     }
     
     public boolean hasElectrodesOnSide(ChargeCarrier carrier)

@@ -281,21 +243,43 @@

         else return true;
     }
     

-//    private Hep3Vector measuredCoordinate(double electrode_angle)
-//    {
-//        return new BasicHep3Vector(Math.cos(electrode_angle),Math.sin(electrode_angle),0.0);
-//    }
-    

     public Hep3Vector electricField(Hep3Vector position)
     {

-        Hep3Vector electric_field_direction = (this._orientation == Orientation.PSIDE_POSITIVE_Z) ?
-            new BasicHep3Vector(0.0,0.0,1.0) : new BasicHep3Vector(0.0,0.0,-1.0);

-        double electric_field_magnitude = (_bias_voltage-_depletion_voltage)/_thickness + 
-                (2.0*_depletion_voltage)/_thickness * (1.0 - this.distanceFromSide(position,ChargeCarrier.ELECTRON));

+        // See Gorelov
+        double electric_field_magnitude = (_bias_voltage-_depletion_voltage)/getThickness() +
+                (2.0*_depletion_voltage)/getThickness() * (1.0 - this.distanceFromSide(position,ChargeCarrier.ELECTRON));
+//        System.out.println("Electric field strength: "+electric_field_magnitude);
+//        System.out.println("Distance from side: "+this.distanceFromSide(position,ChargeCarrier.ELECTRON));
+//        System.out.println("Thickness: "+getThickness());
+        
+        Hep3Vector electric_field_direction = _bias_surfaces.get(ChargeCarrier.HOLE).getNormal();
+
+//        System.out.println("Electric field direction: "+electric_field_direction);

         
         return VecOp.mult(electric_field_magnitude,electric_field_direction);
         

+        
+//        Hep3Vector electric_field_direction = null;
+//        for (ChargeCarrier carrier : ChargeCarrier.values())
+//        {
+//            if (hasElectrodesOnSide(carrier))
+//            {
+//                ITransform3D electrode_transform = _sense_electrodes.get(carrier).getParentToLocal().inverse();
+//                Plane3D electrode_plane = _sense_electrodes.get(carrier).getGeometry().transformed(electrode_transform).getPlane();
+//                electric_field_direction = VecOp.mult(carrier.charge(),electrode_plane.getNormal());
+//                if (!(electric_field_direction == null)) break;
+//            }
+//        }
+//
+////        Hep3Vector electric_field_direction = (this._orientation == Orientation.PSIDE_POSITIVE_Z) ?
+////            new BasicHep3Vector(0.0,0.0,1.0) : new BasicHep3Vector(0.0,0.0,-1.0);
+//
+//        double electric_field_magnitude = (_bias_voltage-_depletion_voltage)/_thickness +
+//                (2.0*_depletion_voltage)/_thickness * (1.0 - this.distanceFromSide(position,ChargeCarrier.ELECTRON));
+//
+//        return VecOp.mult(electric_field_magnitude,electric_field_direction);
+        

     }
     
     public String toString()

@@ -308,7 +292,7 @@

     
     public IIdentifierHelper getIdentifierHelper()
     {

-        List<DeSubdetector> subdet = findAncestors(DeSubdetector.class);        

+        List<DeSubdetector> subdet = findAncestors(DeSubdetector.class);

         if ( subdet.size() == 0 )
         {
             throw new RuntimeException("Can't find DeSubdetector for SiSensor!");

@@ -318,38 +302,40 @@

     
     /**
      * Make an {@link IIdentifier} for a given strip number and side number.

-     * 

+     *

      * @param stripNumber The strip number, which should be from 1 to nstrips - 1.
      * @param sideNumber  The side number, which should be 1 or -1.
      * @return A 64-bit   A packed id for the strip.
      */
     public IIdentifier makeStripId( int stripNumber, int sideNumber )
     {

-		// Copy the DetectorElement's identifier, which will leave blank fields
-		// for side and strip.
-    	IExpandedIdentifier id = new ExpandedIdentifier(getExpandedIdentifier());
-    	
-    	// Get the helper and dictionary.
-    	IIdentifierHelper helper = getIdentifierHelper();
-		IIdentifierDictionary dict = helper.getIdentifierDictionary();
-    	
-    	try {
-    		// Fill in the side and strip numbers.
-    		id.setValue(dict.getFieldIndex("side"), sideNumber);
-    		id.setValue(dict.getFieldIndex("strip"), stripNumber);
-    	}
-    	catch (FieldNotFoundException x)
-    	{
-    		throw new RuntimeException(x);
-    	}
-    	
-    	try {
-    		// Pack and return the id.
-    		return helper.pack( id );
-    	}
-    	catch (InvalidIndexException x)
-    	{
-    		throw new RuntimeException(x);
-    	}
-    }    

+        // Copy the DetectorElement's identifier, which will leave blank fields
+        // for side and strip.
+        IExpandedIdentifier id = new ExpandedIdentifier(getExpandedIdentifier());
+        
+        // Get the helper and dictionary.
+        IIdentifierHelper helper = getIdentifierHelper();
+        IIdentifierDictionary dict = helper.getIdentifierDictionary();
+        
+        try
+        {
+            // Fill in the side and strip numbers.
+            id.setValue(dict.getFieldIndex("side"), sideNumber);
+            id.setValue(dict.getFieldIndex("strip"), stripNumber);
+        }
+        catch (FieldNotFoundException x)
+        {
+            throw new RuntimeException(x);
+        }
+        
+        try
+        {
+            // Pack and return the id.
+            return helper.pack( id );
+        }
+        catch (InvalidIndexException x)
+        {
+            throw new RuntimeException(x);
+        }
+    }

 }

\ No newline at end of file

diff -u -r1.8 -r1.9
--- SiSensorElectrodes.java	16 Nov 2007 22:47:07 -0000	1.8
+++ SiSensorElectrodes.java	3 Dec 2007 23:23:30 -0000	1.9
@@ -14,6 +14,7 @@

 import hep.physics.vec.Hep3Vector;
 import java.util.SortedMap;
 import java.util.Set;

+import org.lcsim.detector.solids.Polygon3D;

 
 /**
  *

@@ -36,6 +37,9 @@

     // Transformation from gloabl coordinates to electrode coordinates
     public ITransform3D getGlobalToLocal();
     

+    // Polygon on which electrodes are defined
+    public Polygon3D getGeometry();
+    

     // Direction of each measured coordinate
     public Hep3Vector getMeasuredCoordinate(int axis);
     

@@ -87,11 +91,13 @@

     // Location of given position within a cell
     public Hep3Vector getPositionInCell(Hep3Vector position);
     

+    // Charge carrier
+    public ChargeCarrier getChargeCarrier();
+    

     // Capacitance of electrode
     public double getCapacitance(int cell_id);
     
     // Compute Gaussian-distributed charge on electrodes
     public SortedMap<Integer,Integer> computeElectrodeData(ChargeDistribution distribution);

-//    public SortedMap<Integer,Integer> computeElectrodeData(double charge, Hep3Vector position, ErrorEllipse2D distribution);

     
 }

diff -N GeomOp2D.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ GeomOp2D.java	3 Dec 2007 23:23:30 -0000	1.1
@@ -0,0 +1,52 @@

+/*
+ * GeomOp2D.java
+ *
+ * Created on November 20, 2007, 1:28 PM
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package org.lcsim.detector.solids;
+
+import hep.physics.vec.BasicHep3Vector;
+import hep.physics.vec.Hep3Vector;
+import hep.physics.vec.VecOp;
+
+/**
+ *
+ * @author tknelson
+ */
+public class GeomOp2D
+{
+    
+    // All operations are defined on x,y plane
+    public static final Plane3D PLANE = new Plane3D(new BasicHep3Vector(0,0,1),0);
+    
+    public static final double DISTANCE_TOLERANCE = 1E-9;
+    public static final double ANGULAR_TOLERANCE = 1E-9;
+    
+    /** Creates a new instance of GeomOp2D */
+    public GeomOp2D()
+    {
+    }
+    
+    public static boolean intersects(Line3D line, LineSegment3D linesegment)
+    {
+        Hep3Vector diff_start = VecOp.sub(linesegment.getStartPoint(),line.getStartPoint());
+        Hep3Vector diff_end = VecOp.sub(linesegment.getEndPoint(),line.getStartPoint());
+        Hep3Vector start_cross = VecOp.cross(line.getDirection(),diff_start);
+        Hep3Vector end_cross = VecOp.cross(line.getDirection(),diff_end);
+        return (VecOp.dot(start_cross,end_cross) < 0);
+    }
+    
+//    public Point3D intersection(Line3D line, LineSegment3D linesegment)
+//    {
+//        
+//        
+//        
+//    }
+    
+    
+    
+}

diff -N Transformable.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ Transformable.java	3 Dec 2007 23:23:30 -0000	1.1
@@ -0,0 +1,23 @@

+/*
+ * Transformable.java
+ *
+ * Created on November 23, 2007, 4:54 AM
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package org.lcsim.detector.solids;
+
+import org.lcsim.detector.ITransform3D;
+
+/**
+ *
+ * @author tknelson
+ */
+public interface Transformable
+{
+    public void transform(ITransform3D transform);
+    
+    public Transformable transformed(ITransform3D transform);
+}

diff -N AbstractPolyhedron.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ AbstractPolyhedron.java	3 Dec 2007 23:23:30 -0000	1.1
@@ -0,0 +1,58 @@

+/*
+ * AbstractPolyhedron.java
+ *
+ * Created on November 29, 2007, 9:45 AM
+ *
+ * To change this template, choose Tools | Template Manager
+ * and open the template in the editor.
+ */
+
+package org.lcsim.detector.solids;
+
+import hep.physics.vec.Hep3Vector;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * @author tknelson
+ */
+public abstract class AbstractPolyhedron extends AbstractSolid implements IPolyhedron
+{
+    
+    /** Creates a new instance of AbstractPolyhedron */
+    public AbstractPolyhedron(String name)
+    {
+        super(name);
+    }
+    
+    public Inside inside(Hep3Vector p)
+    {
+        Point3D point = new Point3D(p);
+        
+        boolean inside = true;
+        for (Polygon3D face : getFaces())
+        {
+            if (GeomOp3D.intersects(point,face)) return Inside.SURFACE;
+            inside = inside && (GeomOp3D.distanceBetween(point,face.getPlane()) < 0);
+        }
+        
+        if (inside) return Inside.INSIDE;
+        else return Inside.OUTSIDE;
+    }
+    
+    public List<Polygon3D> getFacesNormalTo(Hep3Vector normal)
+    {
+        List<Polygon3D> faces = new ArrayList<Polygon3D>();
+      
+        for (Polygon3D face : getFaces())
+        {
+            if (GeomOp3D.isNormal(normal,face)) 
+            {
+                faces.add(face);
+            }
+        }
+        return faces;
+    }
+    
+}

diff -u -r1.1 -r1.2
--- Polygon3D.java	13 Nov 2007 21:04:50 -0000	1.1
+++ Polygon3D.java	3 Dec 2007 23:23:30 -0000	1.2
@@ -11,6 +11,7 @@

 
 import java.util.ArrayList;
 import java.util.List;

+import org.lcsim.detector.ITransform3D;

 
 /**
  *

@@ -65,4 +66,25 @@

         return edges;
     }
     

+    public void transform(ITransform3D transform)
+    {
+        for (Point3D point : _points)
+        {
+            point.transform(transform);
+        }   
+        Plane3D new_plane = new Plane3D(_points);
+        this._distance = new_plane.getDistance();
+        this._normal = new_plane.getNormal();
+    }
+    
+    public Polygon3D transformed(ITransform3D transform)
+    {
+        List<Point3D> transformed_points = new ArrayList<Point3D>();
+        for (Point3D point : _points)
+        {
+            transformed_points.add(point.transformed(transform));
+        }
+        return new Polygon3D(transformed_points);
+    }
+    

 }

diff -u -r1.1 -r1.2
--- Line3D.java	13 Nov 2007 21:04:50 -0000	1.1
+++ Line3D.java	3 Dec 2007 23:23:30 -0000	1.2
@@ -12,16 +12,17 @@

 import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;

+import org.lcsim.detector.ITransform3D;

 
 /**
  *
  * @author tknelson
  */

-public class Line3D

+public class Line3D implements Transformable

 {
     

-    private Point3D _startpoint;
-    private Hep3Vector _direction;

+    protected Point3D _startpoint;
+    protected Hep3Vector _direction;

     
     /**
      * Creates a new instance of Line3D

@@ -46,7 +47,7 @@

     public Hep3Vector getDirection()
     {
         return _direction;

-    }    

+    }

     
     public Point3D getEndPoint(double length)
     {

@@ -56,7 +57,7 @@

     public Inside inside(Hep3Vector point)
     {
         Hep3Vector v1 = VecOp.sub(point,getStartPoint());

-       

+        

         double v1mag = v1.magnitude();
         
         if ( Math.abs(VecOp.dot(v1,_direction)) - v1mag < Tolerance.TOLERANCE ) return Inside.INSIDE;

@@ -69,7 +70,7 @@

     {
         Hep3Vector normal = VecOp.cross(line.getDirection(),this.getDirection());
         Hep3Vector diff = VecOp.sub(line.getStartPoint(),this.getStartPoint());

-        return VecOp.dot(normal,diff)/normal.magnitude();       

+        return VecOp.dot(normal,diff)/normal.magnitude();

     }
     
     public double distanceTo(Point3D point)

@@ -78,5 +79,15 @@

         return Math.sqrt( diff.magnitudeSquared() - Math.pow(VecOp.dot(diff,this.getDirection()),2) );
     }
     

+    public void transform(ITransform3D transform)
+    {
+        _startpoint.transform(transform);
+        transform.rotate(_direction);
+    }
+    
+    public Line3D transformed(ITransform3D transform)
+    {
+        return new Line3D(_startpoint.transformed(transform),transform.rotated(_direction));
+    }

     
 }

diff -u -r1.1 -r1.2
--- LineSegment3D.java	13 Nov 2007 21:04:50 -0000	1.1
+++ LineSegment3D.java	3 Dec 2007 23:23:30 -0000	1.2
@@ -81,4 +81,10 @@

         return points;
     }       
     

+    public void reverse()
+    {
+        _startpoint = getEndPoint();
+        _direction = VecOp.mult(-1,getDirection());
+    }
+    

 }

diff -u -r1.2 -r1.3
--- IPolyhedron.java	14 Nov 2007 19:34:51 -0000	1.2
+++ IPolyhedron.java	3 Dec 2007 23:23:30 -0000	1.3
@@ -9,6 +9,7 @@

 
 package org.lcsim.detector.solids;
 

+import hep.physics.vec.Hep3Vector;

 import java.util.List;
 
 /**

@@ -20,5 +21,6 @@

     public List<Polygon3D> getFaces();
     public List<LineSegment3D> getEdges();
     public List<Point3D> getVertices();

+    public List<Polygon3D> getFacesNormalTo(Hep3Vector normal);

     public int[] getHepRepVertexOrdering();
 }

diff -u -r1.6 -r1.7
--- Trd.java	14 Nov 2007 19:34:51 -0000	1.6
+++ Trd.java	3 Dec 2007 23:23:30 -0000	1.7
@@ -15,10 +15,9 @@

  *
  * @author Jeremy McCormick
  * @author Tim Nelson (modified to use standard geometry objects and operations)

- * @version $Id: Trd.java,v 1.6 2007/11/14 19:34:51 tknelson Exp $

+ * @version $Id: Trd.java,v 1.7 2007/12/03 23:23:30 tknelson Exp $

  */

-public class Trd
-        extends AbstractSolid implements IPolyhedron

+public class Trd extends AbstractPolyhedron

 {
     
     private final static int[] _HEPREP_VERTEX_ORDERING = {2,3,1,0,6,7,5,4};

@@ -55,21 +54,6 @@

         return volume;
     }
     

-    public Inside inside(Hep3Vector p)
-    {
-        Point3D point = new Point3D(p);
-        
-        boolean inside = true;
-        for (Polygon3D face : getFaces())
-        {
-            if (GeomOp3D.intersects(point,face)) return Inside.SURFACE;
-            inside = inside && (GeomOp3D.distanceBetween(point,face.getPlane()) < 0);
-        }
-        
-        if (inside) return Inside.INSIDE;
-        else return Inside.OUTSIDE;
-    }
-    

     public double getXHalfLength1()
     {
         return dx1;

diff -u -r1.7 -r1.8
--- Trap.java	14 Nov 2007 19:34:51 -0000	1.7
+++ Trap.java	3 Dec 2007 23:23:30 -0000	1.8
@@ -23,11 +23,10 @@

  *
  * @author Jeremy McCormick
  * @author Tim Nelson (modified to use standard geometry objects and operations)

- * @version $Id: Trap.java,v 1.7 2007/11/14 19:34:51 tknelson Exp $

+ * @version $Id: Trap.java,v 1.8 2007/12/03 23:23:30 tknelson Exp $

  */
 

-public class Trap
-        extends AbstractSolid implements IPolyhedron

+public class Trap extends AbstractPolyhedron

 {
     
     private final static int[] _HEPREP_VERTEX_ORDERING = {2,3,1,0,6,7,5,4};

@@ -169,21 +168,6 @@

         return cubicVolume;
     }
     

-    public Inside inside(Hep3Vector p)
-    {
-        Point3D point = new Point3D(p);
-        
-        boolean inside = true;
-        for (Polygon3D face : getFaces())
-        {
-            if (GeomOp3D.intersects(point,face)) return Inside.SURFACE;
-            inside = inside && (GeomOp3D.distanceBetween(point,face.getPlane()) < 0);
-        }
-        
-        if (inside) return Inside.INSIDE;
-        else return Inside.OUTSIDE;
-    }
-    

     // Implementation of IPolyhedron
     
     public int[] getHepRepVertexOrdering()

diff -u -r1.1 -r1.2
--- Point3D.java	13 Nov 2007 21:04:50 -0000	1.1
+++ Point3D.java	3 Dec 2007 23:23:30 -0000	1.2
@@ -11,12 +11,13 @@

 
 import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;

+import org.lcsim.detector.ITransform3D;

 
 /**
  *
  * @author tknelson
  */

-public class Point3D extends BasicHep3Vector

+public class Point3D extends BasicHep3Vector implements Transformable

 {
     
     /**

@@ -41,4 +42,14 @@

         return (Hep3Vector)this;
     }
     

+    public void transform(ITransform3D transform)
+    {
+        transform.transform(this);
+    }
+    
+    public Point3D transformed(ITransform3D transform)
+    {
+        return new Point3D(transform.transformed(this));
+    }
+    

 }

diff -u -r1.1 -r1.2
--- Plane3D.java	13 Nov 2007 21:04:50 -0000	1.1
+++ Plane3D.java	3 Dec 2007 23:23:30 -0000	1.2
@@ -12,12 +12,13 @@

 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;
 import java.util.List;

+import org.lcsim.detector.ITransform3D;

 
 /**
  *
  * @author tknelson
  */

-public class Plane3D

+public class Plane3D implements Transformable

 {
     
     Hep3Vector _normal; // normal to plane

@@ -49,7 +50,7 @@

         
         // normal and distance
         _normal = VecOp.unit(VecOp.cross(v1,v2));

-        _distance = VecOp.dot(_normal,points.get(0));                

+        _distance = VecOp.dot(_normal,points.get(0));

     }
     
     public Hep3Vector getNormal()

@@ -73,5 +74,17 @@

         _distance *= -1;
     }
     

+    public void transform(ITransform3D transform)
+    {
+        Point3D closest_point = (Point3D)VecOp.mult(_distance,_normal);
+        _distance = closest_point.transformed(transform).magnitude();
+        transform.rotate(_normal);       
+    }
+    
+    public Plane3D transformed(ITransform3D transform)
+    {
+        Point3D closest_point = (Point3D)VecOp.mult(_distance,_normal);
+        return new Plane3D(transform.rotated(_normal),closest_point.transformed(transform).magnitude());
+    }

     
 }

diff -u -r1.24 -r1.25
--- SiTrackerBarrelConverter.java	14 Oct 2007 06:00:27 -0000	1.24
+++ SiTrackerBarrelConverter.java	3 Dec 2007 23:23:30 -0000	1.25
@@ -3,6 +3,8 @@

 import static java.lang.Math.cos;
 import static java.lang.Math.sin;
 import hep.physics.matrix.BasicMatrix;

+import hep.physics.vec.BasicHep3Vector;
+import hep.physics.vec.VecOp;

 
 import java.util.HashMap;
 import java.util.Iterator;

@@ -31,7 +33,10 @@

 import org.lcsim.detector.material.IMaterial;
 import org.lcsim.detector.material.MaterialStore;
 import org.lcsim.detector.solids.Box;

+import org.lcsim.detector.solids.IPolyhedron;

 import org.lcsim.detector.solids.ISolid;

+import org.lcsim.detector.solids.Point3D;
+import org.lcsim.detector.solids.Polygon3D;

 import org.lcsim.detector.solids.Tube;
 import org.lcsim.detector.tracker.silicon.ChargeCarrier;
 import org.lcsim.detector.tracker.silicon.DeSiTrackerBarrel;

@@ -40,7 +45,6 @@

 import org.lcsim.detector.tracker.silicon.SiStrips;
 import org.lcsim.detector.tracker.silicon.SiTrackerBarrelLayer;
 import org.lcsim.detector.tracker.silicon.SiTrackerBarrelModule;

-import org.lcsim.detector.tracker.silicon.SiSensor.Orientation;

 import org.lcsim.geometry.compact.Detector;
 import org.lcsim.geometry.compact.Subdetector;
 import org.lcsim.geometry.subdetector.SiTrackerBarrel;

@@ -543,22 +547,55 @@

                         SiSensor sensor = new SiSensor(sensorId,sensorName,module,sensorPath,id);
                         sensor.setIdentifier(id);
                         

-                        ITranslation3D electrodes_position = new Translation3D(0.0,0.0,sensor.getThickness()/2);
-                        IRotation3D electrodes_rotation = new RotationPassiveXYZ(0.0,0.0,0.0);

+                        // Set up SiStrips for the sensors
+                        IPolyhedron sensor_solid = (IPolyhedron)sensor.getGeometry().getLogicalVolume().getSolid();
+                        
+                        // Bias the sensor
+                        Polygon3D p_side = sensor_solid.getFacesNormalTo(new BasicHep3Vector(0,0,1)).get(0);
+//                        System.out.println("Plane of p_side polygon has... ");
+//                        System.out.println("                        normal: "+p_side.getNormal());
+//                        System.out.println("                        distance: "+p_side.getDistance());
+//                        for (Point3D point : p_side.getClosedVertices())
+//                        {
+//                            System.out.println("      Vertex: "+point);
+//                        }
+                        
+                        
+                        Polygon3D n_side = sensor_solid.getFacesNormalTo(new BasicHep3Vector(0,0,-1)).get(0);
+//                        System.out.println("Plane of n_side polygon has... ");
+//                        System.out.println("                        normal: "+n_side.getNormal());
+//                        System.out.println("                        distance: "+n_side.getDistance());
+                        
+                        sensor.setBiasSurface(ChargeCarrier.HOLE,p_side);
+                        sensor.setBiasSurface(ChargeCarrier.ELECTRON,n_side);
+                        
+                        // Add sense and readout electrodes
+                        ITranslation3D electrodes_position = new Translation3D(VecOp.mult(-p_side.getDistance(),p_side.getNormal()));  // translate to p_side
+                        IRotation3D electrodes_rotation = new RotationPassiveXYZ(0.0,0.0,0.0);                                      // no rotation (global x-y = local x-y for axial strips)

                         Transform3D electrodes_transform = new Transform3D(electrodes_position, electrodes_rotation);
                         

-                        SiSensorElectrodes sense_electrodes = new SiStrips(3679,0.025,sensor,electrodes_transform);
-                        SiSensorElectrodes readout_electrodes = new SiStrips(1840,0.050,sensor,electrodes_transform);
-                        double[][] transfer_efficiencies = { {0.986,0.419} };

+                        // Free calculation of sense electrodes, readout electrodes determined thereon
+                        SiSensorElectrodes sense_electrodes = new SiStrips(ChargeCarrier.HOLE,0.025,sensor,electrodes_transform);
+                        SiSensorElectrodes readout_electrodes = new SiStrips(ChargeCarrier.HOLE,0.050,(sense_electrodes.getNCells()+1)/2,sensor,electrodes_transform);

-                        sensor.setSenseElectrodes(ChargeCarrier.HOLE,sense_electrodes);
-                        sensor.setReadoutElectrodes(ChargeCarrier.HOLE,readout_electrodes);

+                        sensor.setSenseElectrodes(sense_electrodes);
+                        sensor.setReadoutElectrodes(readout_electrodes);
+                        
+                        double[][] transfer_efficiencies = { {0.986,0.419} };

                         sensor.setTransferEfficiencies(ChargeCarrier.HOLE,new BasicMatrix(transfer_efficiencies));

-                        sensor.setOrientation(Orientation.PSIDE_POSITIVE_Z);
-                        sensor.initialize();

                         
                         // Incremenet sensorID for double-sided.
                         ++sensorId;

+                        
+                        
+//                        SiSensorElectrodes sense_electrodes = new SiStrips(3679,0.025,sensor,electrodes_transform);
+//                        SiSensorElectrodes readout_electrodes = new SiStrips(1840,0.050,sensor,electrodes_transform);
+//
+//                        double[][] transfer_efficiencies = { {0.986,0.419} };
+//                        sensor.setSenseElectrodes(ChargeCarrier.HOLE,sense_electrodes);
+//                        sensor.setReadoutElectrodes(ChargeCarrier.HOLE,readout_electrodes);
+//                        sensor.setTransferEfficiencies(ChargeCarrier.HOLE,new BasicMatrix(transfer_efficiencies));
+                        

                     }
                 }