--- projects/lcsim/trunk/detector-framework/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014GeomDef.java	2014-07-17 19:54:09 UTC (rev 3193)
+++ projects/lcsim/trunk/detector-framework/src/main/java/org/lcsim/geometry/compact/converter/lcdd/HPSTestRunTracker2014GeomDef.java	2014-07-17 20:16:38 UTC (rev 3194)
@@ -20,6 +20,10 @@

  * @author Per Hansson Adrian <[log in to unmask]>
  *
  */

+/**
+ * @author phansson
+ *
+ */

 public final class HPSTestRunTracker2014GeomDef {
 	
 		//General

@@ -31,11 +35,19 @@

 		private static final double target_pos_wrt_base_plate_z = 926.59; //from Marco's 3D model
 		protected static final double PS_vac_box_inner_height = 7.0*inch;
 		

-		protected static class BaseGeom {

+		
+		
+		/**
+		 * 
+		 * Base geometry class for generating volumes based on survey information. 
+		 * 
+		 */
+		protected static abstract class BaseGeom {

 			private String name;
 			private BaseGeom mother;

-			// If the survey positions are referenced to an intermediate coordinate system
-			// normally this is null.

+			// The reference geometry is used when the survey points are w.r.t. to 
+			// a different/intermediate coord system. So that transformation has to be used when 
+			// transforming to the mother system

 			private BaseGeom referenceGeom;
 			private Coord coord;
 			protected  Hep3Vector ballPos;

@@ -45,16 +57,30 @@

 			private Hep3Vector boxDim;
 			
 			public BaseGeom(String name, BaseGeom m) {

+				setName(name);

 				setMother(m);
 				setReferenceGeom(null);

-				coord = null;
-				ballPos = null;
-				veePos = null;
-				flatPos = null;
-				setCenter(null);
-				setBoxDim(null);

+			}
+			public BaseGeom(String name, BaseGeom m, BaseGeom ref) {

 				setName(name);

+				setMother(m);
+				setReferenceGeom(ref);

 			}

+			
+			protected abstract void setPos();
+			protected abstract void setCoord();
+			protected abstract void setCenter();
+			protected abstract void setBoxDim();
+
+			/**
+			 * Initialize the survey constants, volume positions and dimensions
+			 */
+			protected void init() {
+				setPos();
+				setCoord();
+				setCenter();
+				setBoxDim();
+			}

 			public  void setBallPos(double x, double y, double z) {
 				ballPos = new BasicHep3Vector(x,y,z);
 			}

@@ -73,9 +99,6 @@

 			public  Hep3Vector getFlatPos() {
 				return flatPos;
 			}

-			public void setCoord() {
-				setCoord(null);
-			}			

 			public void setCoord(Hep3Vector origin) {
 				if(ballPos==null || veePos==null || flatPos==null) {
 					throw new RuntimeException("Need to set ball, vee and flat before building coord system!");

@@ -110,9 +133,6 @@

 			public Hep3Vector getBoxDim() {
 				return boxDim;
 			}

-			public void setBoxDim(Hep3Vector boxDim) {
-				this.boxDim = boxDim;
-			}

 			public void setBoxDim(double x, double y, double z) {
 				this.boxDim = new BasicHep3Vector(x,y,z);
 			}

@@ -138,15 +158,31 @@

 		}
 	
 		

+		/**
+		 * Tracking volume geometry definition. 
+		 */

 		public static class TrackingBase extends BaseGeom {
 			public TrackingBase(String name, BaseGeom mother) {
 				super(name,mother);

+				init();
+			}
+			protected void setPos() {
+				// Dummy survey positions to setup a coordinate system

 				ballPos = new BasicHep3Vector(1,0,0);
 				veePos = new BasicHep3Vector(0,1,0);
 				flatPos = new BasicHep3Vector(0,0,1);

+			}
+			protected void setCoord() {
+				// at the origin

 				setCoord(new BasicHep3Vector(0,0,0));

+			}
+			protected void setCenter() {
+				// at the origin

 				setCenter(new BasicHep3Vector(0,0,0));
 			}

+			protected void setBoxDim() {
+				// do nothing since we are not building a tracking volume
+			}

 		}
 
 		public static class Base extends BaseGeom {

@@ -158,6 +194,9 @@

 			
 			public Base(String name, BaseGeom mother) {
 				super(name,mother);

+				init();
+			}
+			protected void setPos() {

 				final double ball_pos_base_x = -1.0*target_pos_wrt_base_plate_x;
 				final double ball_pos_base_y = -1.0*target_pos_wrt_base_plate_y;
 				final double ball_pos_base_z = target_pos_wrt_base_plate_z;		

@@ -170,10 +209,16 @@

 				setBallPos(ball_pos_base_x,ball_pos_base_y,ball_pos_base_z);
 				setVeePos(vee_pos_base_x,vee_pos_base_y,vee_pos_base_z);
 				setFlatPos(flat_pos_base_x, flat_pos_base_y, flat_pos_base_z);

-				setCoord();
-				setBoxDim(base_width,base_length,base_height);

+			}
+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {

 				setCenter(base_width/2.0, base_length/2.0, base_height/2.0 - BasePlate.base_plate_thickness);
 			}

+			protected void setBoxDim() {
+				setBoxDim(base_width,base_length,base_height);
+			}

 		}
 
 		

@@ -185,23 +230,40 @@

 			protected static final double base_plate_length = 1216.00;
 			//height from vacuum chamber surface
 			protected static final double base_plate_offset_height = 2.0; //from Marco's 3D model

-			
-			

 			public BasePlate(String name, BaseGeom mother) {
 				super(name,mother);

-				ballPos = new BasicHep3Vector(0,0,0);

+				init();
+			}
+			protected void setPos() {
+				setBallPos(0,0,0);

 				setVeePos(base_plate_width,ballPos.y(),ballPos.z());
 				setFlatPos(ballPos.x(),base_plate_length,ballPos.z());

-				setCoord();
-				setBoxDim(base_plate_width,base_plate_length, base_plate_thickness);

+			}
+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {

 				setCenter(base_plate_width/2.0, base_plate_length/2.0, -base_plate_thickness/2.0);
 			}

+			protected void setBoxDim() {
+				setBoxDim(base_plate_width,base_plate_length, base_plate_thickness);
+			}

 		}
 		
 		
 
 
 		public static class CSupport extends BaseGeom {

+			// This is the sequence of locating the support plate positions:
+			// The c-support pin positions are found
+			// the points on the axis of rotation are used as references for building the box surrounding the support plates (incl sensors).
+			// this should make it more straightforward when applying a tilt angle
+			// c-support:
+			// ball position is C-support pin position on electron side on the base plate surface
+			// vee position is C-support pin position on positron side on the base plate surface
+			// flat position is a randomly chosen point perpendicular to ball to vee vector and offset 10mm along the plate. 
+			// Note that the flat here sets the tilt angle of the support plates.
+			

 			// c-support references
 			// pin position on base plate surface
 			private static final double ball_pos_csup_pin_bottom_x = 51.15;

@@ -214,10 +276,7 @@

 			
 			public CSupport(String name, BaseGeom mother) {
 				super(name,mother);

-				setBallPos(ball_pos_csup_pin_bottom_x,ball_pos_csup_pin_bottom_y,ball_pos_csup_pin_bottom_z);
-				setVeePos(vee_pos_csup_pin_bottom_x,vee_pos_csup_pin_bottom_y,vee_pos_csup_pin_bottom_z);
-				calcAndSetFlatPos();
-				setCoord();

+				init();

 			}			
 			private void calcAndSetFlatPos() {
 				// find the rotation to place the flat point

@@ -235,6 +294,20 @@

 				double flat_pos_csup_pin_bottom_z = ball_pos_csup_pin_bottom_z + flat_pos_csup_pin_bottom_3D_rot.getZ();
 				setFlatPos(flat_pos_csup_pin_bottom_x,flat_pos_csup_pin_bottom_y,flat_pos_csup_pin_bottom_z);
 			}

+			protected void setPos() {
+				setBallPos(ball_pos_csup_pin_bottom_x,ball_pos_csup_pin_bottom_y,ball_pos_csup_pin_bottom_z);
+				setVeePos(vee_pos_csup_pin_bottom_x,vee_pos_csup_pin_bottom_y,vee_pos_csup_pin_bottom_z);
+				calcAndSetFlatPos();
+			}
+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {
+				// this is never used since it's only a reference volume
+				setCenter(null);
+			}
+			protected void setBoxDim() {
+			}

 			
 		}
 	

@@ -244,57 +317,41 @@

 		public static class SupportTop extends BaseGeom {
 			// Top only needs a vertical offset to be specified
 			private static final double ball_pos_csup_bearings_top_z = 146.4;

-

 			//these are for the box surrounding the whole support including modules
 			protected static final double support_top_length = SupportBottom.support_bottom_length;
 			protected static final double support_top_width = SupportBottom.support_bottom_width;
 			protected static final double support_top_height = SupportBottom.support_bottom_height;

-			

-			
-			

 			public SupportTop(String name, BaseGeom mother) {
 				super(name,mother);

-				setPos();
-				setCoord();
-				setBoxDim(support_top_width,support_top_length,support_top_height);
-				setCenter(support_top_width/2.0+1.0, support_top_length/2.0 + (17.00-10.50/2.0), -1.0 * (support_top_height/2.0 - (12.70-6.66-1.34)));

+				init();

 			}
 			public SupportTop(String name, BaseGeom mother, BaseGeom referenceGeom) {

-				super(name,mother);
-				setReferenceGeom(referenceGeom);
-				setPos();
-				setCoord();
-				setBoxDim(support_top_width,support_top_length,support_top_height);
-				setCenter(support_top_width/2.0+1.0, support_top_length/2.0 + (17.00-10.50/2.0), -1.0 * (support_top_height/2.0 - (12.70-6.66-1.34)));

+				super(name,mother,referenceGeom);
+				init();

 			}
 

-			private void setPos() {
-				

+			protected void setPos() {

 				System.out.printf("setPos support top\n");

-				
-				

 				// the top has the same bearing positions as the bottom c-support except for the offset vertically from base plate
 				// the tilt angle is independent though.

-				

 				setBallPos(SupportBottom.ball_pos_csup_bearings_bottom_x, SupportBottom.ball_pos_csup_bearings_bottom_y, ball_pos_csup_bearings_top_z);
 				setVeePos(SupportBottom.vee_pos_csup_bearings_bottom_x, SupportBottom.vee_pos_csup_bearings_bottom_y, ball_pos_csup_bearings_top_z);

-				
-				

 				// build the rotation to find the proper location of the flat
 				org.apache.commons.math3.geometry.euclidean.threed.Rotation rot_csup_top = 
 						new org.apache.commons.math3.geometry.euclidean.threed.Rotation(org.apache.commons.math3.geometry.euclidean.threed.RotationOrder.XYZ, 
 								SupportPlateTop.support_plate_top_tilt_angle, 0.0, 0.0 );

+				

 				// apply to flat local position (as for bottom it is arbitrary offset)
 				org.apache.commons.math3.geometry.euclidean.threed.Vector3D flat_pos_csup_bearings_top_3D_rot = 
 						rot_csup_top.applyTo(new org.apache.commons.math3.geometry.euclidean.threed.Vector3D(0.0,10.0,0.0));

+				

 				// translate the flat position
 				final double flat_pos_csup_bearings_top_x = getBallPos().x() + flat_pos_csup_bearings_top_3D_rot.getX();
 				final double flat_pos_csup_bearings_top_y = getBallPos().y() + flat_pos_csup_bearings_top_3D_rot.getY();
 				final double flat_pos_csup_bearings_top_z = getBallPos().z() + flat_pos_csup_bearings_top_3D_rot.getZ();
 				setFlatPos(flat_pos_csup_bearings_top_x,flat_pos_csup_bearings_top_y,flat_pos_csup_bearings_top_z);
 

-				

 				// since we don't care (no volume is built) about the local position of the bearings in the pin coord system we'll get rid of it
 				// and find the bearings position in the base coordinate system directly
 				BaseGeom ref = getReferenceGeom();

@@ -313,16 +370,22 @@

 				
 				System.out.printf("after ref %s transform\n",ref.getName());
 				printSurveyPos();

-				
-				

 			}

-		

+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {
+				setCenter(support_top_width/2.0+1.0, support_top_length/2.0 + (17.00-10.50/2.0), -1.0 * (support_top_height/2.0 - (12.70-6.66-1.34)));
+			}
+			protected void setBoxDim() {
+				setBoxDim(support_top_width,support_top_length,support_top_height);
+			}

 		}
 	
 		
 		
 		public static class SupportBottom extends BaseGeom {

-			// point on axis of rotation on the inside of the c-support frame where the insert get's attached

+			// "bearings" are points on axis of rotation on the inside of the c-support frame where the insert get's attached

 			// this is referenced to the pin position of the c-support
 			private static final double ball_pos_csup_bearings_bottom_x = 240.0 - 265.0 + 14.0;
 			private static final double ball_pos_csup_bearings_bottom_y = (-6.0 + 22.0);

@@ -337,23 +400,12 @@

 			protected static final double support_bottom_height = SupportPlateBottom.support_plate_bottom_height - SupportPlateBottom.support_plate_pocket_depth + TestRunModuleL13.module_box_L13_width + SupportPlateBottom.pedestal_height_L1;
 			
 			

-			public SupportBottom(String name, BaseGeom mother) {
-				super(name,mother);
-				setPos();
-				setCoord();
-				setBoxDim(support_bottom_width,support_bottom_length,support_bottom_height);
-				setCenter(support_bottom_width/2.0+1.0, support_bottom_length/2.0 + (17.00-10.50/2.0), support_bottom_height/2.0 - (12.70-6.66-1.34));
-			}			

 			public SupportBottom(String name, BaseGeom mother, BaseGeom referenceGeom) {

-				super(name,mother);
-				setReferenceGeom(referenceGeom);
-				setPos();
-				setCoord();
-				setBoxDim(support_bottom_width,support_bottom_length,support_bottom_height);
-				setCenter(support_bottom_width/2.0+1.0, support_bottom_length/2.0 + (17.00-10.50/2.0), support_bottom_height/2.0 - (12.70-6.66-1.34));

+				super(name,mother,referenceGeom);
+				init();

 			}
 			

-			private void setPos() {

+			protected void setPos() {

 				
 				System.out.printf("setPos support bottom\n");
 				

@@ -401,11 +453,20 @@

 				printSurveyPos();
 			
 			}

+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {
+				setCenter(support_bottom_width/2.0+1.0, support_bottom_length/2.0 + (17.00-10.50/2.0), support_bottom_height/2.0 - (12.70-6.66-1.34));
+			}
+			protected void setBoxDim() {
+				setBoxDim(support_bottom_width,support_bottom_length,support_bottom_height);
+			}

 			
 		}
 	
 		

-		protected static class SupportPlate extends BaseGeom {

+		protected static abstract class SupportPlate extends BaseGeom {

 			protected static final double support_plate_pocket_depth = 6.65; // Tim's sketchup, drawing says 6.66mm?
 			protected static final double pedestal_height_L1 = 11.00;
 			protected static final double pedestal_height_L2 = 9.50;

@@ -429,17 +490,26 @@

 			protected static final double support_plate_bottom_height = 12.7;
 			protected static final double support_plate_bottom_length = 736.1;
 			protected static final double support_plate_bottom_width = 120.0;

-			

 
 			public SupportPlateBottom(String name, BaseGeom mother) {
 				super(mother,name);

+				init();
+			}
+			protected void setPos() {

 				ballPos = new BasicHep3Vector(1.0, (17.0-5.0), 6.66+1.34); 
 				veePos = new BasicHep3Vector(ballPos.x() + support_plate_bottom_length, ballPos.y(),ballPos.z());
 				flatPos = new BasicHep3Vector(ballPos.x(), ballPos.y() + support_plate_bottom_length,ballPos.z());

-				setCoord();
-				setBoxDim(support_plate_bottom_width,support_plate_bottom_length,support_plate_bottom_height);

+			}
+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {

 				setCenter(support_plate_bottom_width/2.0, support_plate_bottom_length/2.0, -1.0 * support_plate_bottom_height/2.0);
 			}

+			@Override
+			protected void setBoxDim() {
+				setBoxDim(support_plate_bottom_width,support_plate_bottom_length,support_plate_bottom_height);
+			}

 		}
 		
 		

@@ -453,14 +523,23 @@

 			
 			public SupportPlateTop(String name, BaseGeom mother) {
 				super(mother,name);

+				init();
+			}
+			protected void setPos() {

 				ballPos = new BasicHep3Vector(1.0, (17.0-5.0), -1.0 * (6.66+1.34)); 
 				veePos = new BasicHep3Vector(ballPos.x() + support_plate_top_width, ballPos.y(),ballPos.z());
 				flatPos = new BasicHep3Vector(ballPos.x(), ballPos.y() + support_plate_top_length,ballPos.z());

-				setCoord();
-				setBoxDim(support_plate_top_width, support_plate_top_length, support_plate_top_height);

+			}
+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {

 				setCenter(support_plate_top_width/2.0, support_plate_top_length/2.0,  support_plate_top_height/2.0);

-

 			}

+			@Override
+			protected void setBoxDim() {
+				setBoxDim(support_plate_top_width, support_plate_top_length, support_plate_top_height);
+			}

 		}
 		
 		

@@ -525,27 +604,17 @@

 			protected double get_dist_lower_sensor_edge_to_cold_block_mounting_surface() {
 				return dist_lower_sensor_edge_to_cold_block_mounting_surface;
 			}

-			
-			
-			

 		}
 		
 			
 		public static abstract class TestRunModule extends BaseModule {
 			public TestRunModule(String name, BaseGeom mother, int layer, String half) {
 				super(name, mother,layer,half);

-				setPos();
-				setCoord();
-				setBoxDim();
-				setCenter();

+				init();

 			}			

-			public TestRunModule(String name, BaseGeom mother, BaseGeom reference, int layer, String half) {
-				super(name, mother,layer,half);
-				setReferenceGeom(reference);
-				setPos();
-				setCoord();
-				setBoxDim();
-				setCenter();

+			public TestRunModule(String name, BaseGeom mother, BaseGeom ref, int layer, String half) {
+				super(name, mother,ref,layer,half);
+				init();

 			}			
 			protected abstract double getColdBlockThickness();
 			protected abstract double getModuleBoxLength();

@@ -554,14 +623,14 @@

 			protected abstract double get_dist_lower_sensor_edge_to_cold_block_mounting_surface();
 			
 			protected void setBoxDim() {

-				//TODO why is this not: width,length,height as for the other volumes!?
-				setBoxDim(new BasicHep3Vector(getModuleBoxLength(),getModuleBoxHeight(),getModuleBoxWidth()));

+				setBoxDim(getModuleBoxLength(),getModuleBoxHeight(),getModuleBoxWidth());

 			}

-			

+			protected void setCoord() {
+				setCoord(null);
+			}

 			protected void setCenter() {
 				setCenter(getModuleBoxLength()/2.0-5.0, 0.0, getModuleBoxWidth()/2.0); 

-			}
-			

+			}			

 			protected void setPos() {
 				// bottom
 				if(isBottom()) {

@@ -662,25 +731,31 @@

 		}
 		
 		

-		public static class BaseModule extends BaseGeom {

+		public static abstract class BaseModule extends BaseGeom {

 			private int layer;
 			private String half;
 			
 			public BaseModule(String name, BaseGeom mother, int layer, String half) {
 				super(name, mother);

+				setLayer(layer);
+				setHalf(half);
+				isValid();
+			}
+			public BaseModule(String name, BaseGeom mother, BaseGeom ref, int layer, String half) {
+				super(name, mother,ref);
+				setLayer(layer);
+				setHalf(half);
+				isValid();
+			}
+			private void isValid() {

 				if(half!="bottom" && half!="top") {

-					System.out.printf("ERROR invalid half %s\n",half);

+					System.out.printf("ERROR invalid half %s for BaseModule\n",half);

 					System.exit(1);
 				}

-				setLayer(layer);
-				setHalf(half);

 			}

-			
-			

 			public int getLayer() {
 				return layer;
 			}

-

 			public void setLayer(int layer) {
 				this.layer = layer;
 			}

@@ -713,33 +788,31 @@

 			// Distance from screw hole to edge of cold block: 33.75mm
 			// Distance from edge of cold block to hole/ball position: 5mm
 			protected static final double dist_sensor_center_to_coldblock_hole_vdir = (180.0 - 30.0 + (33.75 - 5.0)) - Sensor.sensor_length/2.0;	

-			protected static final double half_module_thickness = HPSTestRunTracker2014GeomDef.TestRunHalfModule.getHybridThickness() + HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFThickness() + HalfModuleLamination.getThickness();

+			protected static final double half_module_thickness = HPSTestRunTracker2014GeomDef.TestRunHalfModule.getHybridThickness() + HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFThickness() + HalfModuleLamination.kapton_thickness;

 			protected static final double half_module_length = HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFLength();
 			protected static final double half_module_width = 6.83 + HPSTestRunTracker2014GeomDef.Sensor.getSensorWidth();
 			
 			
 			public TestRunHalfModule(String name, BaseGeom mother, int layer, String half) {
 				super(name,mother, layer, half);

-				setPos();
-				setCoord();
-				setBoxDim(getLength(), getThickness(), getWidth());
-				setCenter();
-				

 			}

-			
-			protected abstract void setPos();
-			
-			private void setCenter() {

+						
+			protected void setCenter() {

 				// Find distance to center in the local coordinate system 
 				// Note that this can be different between axial and stereo since the survey positions determine the local coordinate 
 				// system now.
 				// I'm not sure this feels good but this has to be done somewhere
 				double box_center_local_x =  HPSTestRunTracker2014GeomDef.TestRunHalfModule.getLength()/2.0 - ( (170.00 + 10.00) - HPSTestRunTracker2014GeomDef.Sensor.getSensorLength()/2.0); 

-				double box_center_local_y = -1.0*HPSTestRunTracker2014GeomDef.TestRunHalfModule.getThickness()/2.0 + (HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFThickness() + HalfModuleLamination.getThickness() + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0);

+				double box_center_local_y = -1.0*HPSTestRunTracker2014GeomDef.TestRunHalfModule.getThickness()/2.0 + (HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFThickness() + HalfModuleLamination.kapton_thickness + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0);

 				double box_center_local_z = HPSTestRunTracker2014GeomDef.TestRunHalfModule.getWidth()/2.0 - ( 12.66 - (8.83 -3.00) + HPSTestRunTracker2014GeomDef.Sensor.getSensorWidth()/2.0 ); 
 				setCenter(box_center_local_x, box_center_local_y, box_center_local_z); 
 			}

-			

+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setBoxDim() {
+				setBoxDim(getLength(), getThickness(), getWidth());
+			}

 			public static double getCFThickness() {
 				return CarbonFiber.cf_thickness;
 			}

@@ -776,6 +849,7 @@

 
 			public TestRunHalfModuleAxial(String name, BaseGeom mother, int layer, String half) {
 				super(name, mother, layer, half);

+				init();

 			}
 			
 			protected void setPos() {

@@ -783,7 +857,7 @@

 				final double dist_lower_sensor_edge_to_cold_block_mounting_surface = getLayer() <=3 ? TestRunModuleL13.dist_lower_sensor_edge_to_cold_block_mounting_surface : TestRunModuleL45.dist_lower_sensor_edge_to_cold_block_mounting_surface;
 				
 				final double ball_pos_halfmod_axial_local_x =  dist_sensor_center_to_coldblock_hole_vdir;

-				final double ball_pos_halfmod_axial_local_y =  -1.0* (coldBlockThick/2.0 + TestRunHalfModule.getCFThickness() + HalfModuleLamination.getThickness() + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0);

+				final double ball_pos_halfmod_axial_local_y =  -1.0* (coldBlockThick/2.0 + TestRunHalfModule.getCFThickness() + HalfModuleLamination.kapton_thickness + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0);

 				final double ball_pos_halfmod_axial_local_z =  dist_lower_sensor_edge_to_cold_block_mounting_surface + Sensor.getSensorWidth()/2.0;
 				final double vee_pos_halfmod_axial_local_x =  ball_pos_halfmod_axial_local_x + Sensor.getSensorLength()/2.0;
 				final double vee_pos_halfmod_axial_local_y =  ball_pos_halfmod_axial_local_y;

@@ -796,7 +870,6 @@

 				flatPos = new BasicHep3Vector(flat_pos_halfmod_axial_local_x, flat_pos_halfmod_axial_local_y,flat_pos_halfmod_axial_local_z);
 
 			}

-			

 		}
 		
 		

@@ -804,6 +877,7 @@

 
 			public TestRunHalfModuleStereo(String name, BaseGeom mother, int layer, String half) {
 				super(name, mother, layer, half);

+				init();

 			}
 			
 			protected void setPos() {

@@ -815,7 +889,7 @@

 				
 				final double ball_pos_halfmod_axial_local_x =  dist_sensor_center_to_coldblock_hole_vdir;
 				// note minus sign to separate from axial

-				final double ball_pos_halfmod_axial_local_y =  -1.0 * (-1.0* (coldBlockThick/2.0 + TestRunHalfModule.getCFThickness() + HalfModuleLamination.getThickness() + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0));

+				final double ball_pos_halfmod_axial_local_y =  -1.0 * (-1.0* (coldBlockThick/2.0 + TestRunHalfModule.getCFThickness() + HalfModuleLamination.kapton_thickness + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0));

 				final double ball_pos_halfmod_axial_local_z =  dist_lower_sensor_edge_to_cold_block_mounting_surface + Sensor.getSensorWidth()/2.0;
 				final double vee_pos_halfmod_axial_local_x =  ball_pos_halfmod_axial_local_x + Sensor.getSensorLength()/2.0;
 				final double vee_pos_halfmod_axial_local_y =  ball_pos_halfmod_axial_local_y;

@@ -833,11 +907,8 @@

 			private int layer;
 			public TestRunColdBlock(String name, BaseGeom mother, int layer) {
 				super(name, mother);

-				this.layer = layer;
-				setPos();
-				setCoord();
-				setBoxDim(getLength(), getHeight(), getWidth());
-				setCenter(getLength()/2.0, 0.0, getWidth()/2.0); 

+				setLayer(layer);
+				init();

 			}
 			protected abstract double getWidth();
 			protected abstract double getLength();

@@ -848,7 +919,13 @@

 			public void setLayer(int layer) {
 				this.layer = layer;
 			}

-			private void setPos() {

+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {
+				setCenter(getLength()/2.0, 0.0, getWidth()/2.0); 
+			}
+			protected void setPos() {

 				// cold block position w.r.t. module box coordinate system
 				// this is a dummy coordinate system, make it simple
 				// edge of cold block on the mounting surface

@@ -861,12 +938,13 @@

 				final double flat_pos_coldblock_local_x =  ball_pos_coldblock_local_x;  
 				final double flat_pos_coldblock_local_y =  ball_pos_coldblock_local_y + 1.0;  //arbitrary distance 
 				final double flat_pos_coldblock_local_z =  ball_pos_coldblock_local_z;  

-				

 				setBallPos(ball_pos_coldblock_local_x, ball_pos_coldblock_local_y, ball_pos_coldblock_local_z);
 				setVeePos(vee_pos_coldblock_local_x, vee_pos_coldblock_local_y,vee_pos_coldblock_local_z);
 				setFlatPos(flat_pos_coldblock_local_x, flat_pos_coldblock_local_y,flat_pos_coldblock_local_z);

-

 			}

+			protected void setBoxDim() {
+				setBoxDim(getLength(), getHeight(), getWidth());
+			}

 		}
 		
 		public static class TestRunColdBlockL13 extends TestRunColdBlock {			

@@ -922,10 +1000,7 @@

 			public Sensor(String name, BaseGeom m, int id) {
 				super(name, m);
 				this.id = id;

-				setPos();	
-				setCoord();
-				setCenter(0,0,0);
-				setBoxDim(getSensorLength(),getSensorThickness(),getSensorWidth());

+				init();

 			}			
 			public static double getSensorLength() {
 				return sensor_length;

@@ -939,19 +1014,26 @@

 			public static double getSensorThickness() {
 				return getSensorHeight();
 			}

-			private void setPos() {

+			protected void setPos() {

 				setBallPos(0,0,0);

-				setVeePos(ballPos.x() + HPSTestRunTracker2014GeomDef.Sensor.getSensorLength()/2.0, ballPos.y(), ballPos.z());
-				setFlatPos(ballPos.x(),ballPos.y() + HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0, ballPos.z());

+				setVeePos(ballPos.x() + getSensorLength()/2.0, ballPos.y(), ballPos.z());
+				setFlatPos(ballPos.x(),ballPos.y() + getSensorThickness()/2.0, ballPos.z());

 			}

+			protected void setCoord() {
+				setCoord(null);
+			}

 			public int getId() {
 				return id;
 			}
 			public void setId(int id) {
 				this.id = id;
 			}

-			
-

+			protected void setCenter() {
+				setCenter(0,0,0);
+			}
+			protected void setBoxDim() {
+				setBoxDim(getSensorLength(),getSensorThickness(),getSensorWidth());
+			}			

 		}
 		
 		public static class ActiveSensor extends BaseGeom {

@@ -960,10 +1042,7 @@

 			private static final double sensor_active_thickness = Sensor.sensor_thickness;
 			public ActiveSensor(String name, BaseGeom m) {
 				super(name, m);

-				setPos();	
-				setCoord();
-				setCenter(0,0,0);
-				setBoxDim(getActiveSensorLength(),getActiveSensorThickness(),getActiveSensorWidth());

+				init();

 			}
 			public static double getActiveSensorLength() {
 				return sensor_active_length;

@@ -977,49 +1056,53 @@

 			public static double getActiveSensorThickness() {
 				return getActiveSensorHeight();
 			}

-			private void setPos() {

+			protected void setPos() {

 				ballPos = new BasicHep3Vector(0,0,0);
 				veePos = new BasicHep3Vector(getActiveSensorWidth()/2.0,0,0);
 				flatPos = new BasicHep3Vector(0,getActiveSensorLength()/2.0,0);

-				

 			}

+			protected void setCoord() {
+				setCoord(null);
+			}
+			protected void setCenter() {
+				setCenter(0,0,0);
+			}
+			@Override
+			protected void setBoxDim() {
+				setBoxDim(getActiveSensorLength(),getActiveSensorThickness(),getActiveSensorWidth());
+			}

 		}
 		
 		public static abstract class HalfModuleComponent extends BaseGeom {
 			public HalfModuleComponent(String name, BaseGeom m) {
 				super(name, m);

-				setPos();
-				setCoord();

 			}

-			protected abstract void setPos();

 			protected abstract double getThickness();
 			protected abstract double getHeigth();
 			protected abstract double getWidth();
 			protected abstract double getLength();

-			
-			
-		}
-		
-		public static class HalfModuleLamination extends BaseGeom {

+			protected void setCoord() {
+				setCoord(null);
+			}
+		}		
+
+		public static class HalfModuleLamination extends HalfModuleComponent {

 			protected static final double kapton_length = 184.0;
 			protected static final double kapton_width = 40.0;
 			protected static final double kapton_thickness = 0.050;
 			public HalfModuleLamination(String name, BaseGeom m) {
 				super(name, m);

-				setPos();	
-				setCoord();
-				setCenter(getLength()/2.0, 0.0, getWidth()/2.0);
-				setBoxDim(getLength(),getThickness(),getWidth());

+				init();

 			}

-			private void setPos() {

+			protected void setPos() {

 				final double ball_pos_kapton_local_x =  -1 * (180.0 - HPSTestRunTracker2014GeomDef.Sensor.getSensorLength()/2.0) + 8.5;

-				final double ball_pos_kapton_local_y =  (HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0 + HalfModuleLamination.getThickness()/2.0);

+				final double ball_pos_kapton_local_y =  (HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0 + HalfModuleLamination.kapton_thickness/2.0);

 				final double ball_pos_kapton_local_z = -1 * (HPSTestRunTracker2014GeomDef.Sensor.getSensorWidth()/2.0 + 12.66) + 8.83 - 3.00 + 6.00 ;
 				final double vee_pos_kapton_local_x =  ball_pos_kapton_local_x + 1.0; // arbitrary distance
 				final double vee_pos_kapton_local_y =  ball_pos_kapton_local_y;
 				final double vee_pos_kapton_local_z =  ball_pos_kapton_local_z;
 				final double flat_pos_kapton_local_x =  ball_pos_kapton_local_x;

-				final double flat_pos_kapton_local_y =  ball_pos_kapton_local_y + HalfModuleLamination.getThickness()/2.0; // arbitrary distance

+				final double flat_pos_kapton_local_y =  ball_pos_kapton_local_y + HalfModuleLamination.kapton_thickness/2.0; // arbitrary distance

 				final double flat_pos_kapton_local_z =  ball_pos_kapton_local_z;
 				
 				ballPos = new BasicHep3Vector(ball_pos_kapton_local_x,ball_pos_kapton_local_y,ball_pos_kapton_local_z);

@@ -1027,18 +1110,24 @@

 				flatPos = new BasicHep3Vector(flat_pos_kapton_local_x,flat_pos_kapton_local_y,flat_pos_kapton_local_z);
 				
 			}

-			public static double getThickness() {

+			protected void setCenter() {
+				setCenter(getLength()/2.0, 0.0, getWidth()/2.0);
+			}
+			protected  double getThickness() {

 				return kapton_thickness;
 			}

-			public static double getHeight() {

+			protected  double getHeigth() {

 				return getThickness();
 			}

-			public static double getWidth() {

+			protected  double getWidth() {

 				return kapton_width;
 			}

-			public static double getLength() {

+			protected  double getLength() {

 				return kapton_length;
 			}

+			protected void setBoxDim() {
+				setBoxDim(getLength(),getThickness(),getWidth());
+			}

 		}
 		
 		public static class CarbonFiber extends HalfModuleComponent {

@@ -1047,12 +1136,11 @@

 			protected static  final double cf_thickness = 0.250;
 			public CarbonFiber(String name, BaseGeom m) {
 				super(name, m);

-				setCenter(getLength()/2.0, 0.0, getWidth()/2.0);
-				setBoxDim(getLength(),getThickness(),getWidth());

+				init();

 			}
 			protected void setPos() {
 				final double ball_pos_cf_local_x =  -1 * (180.0 - HPSTestRunTracker2014GeomDef.Sensor.getSensorLength()/2.0);

-				final double ball_pos_cf_local_y =  (HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0 + HPSTestRunTracker2014GeomDef.HalfModuleLamination.getThickness() + HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFThickness()/2.0);

+				final double ball_pos_cf_local_y =  (HPSTestRunTracker2014GeomDef.Sensor.getSensorThickness()/2.0 + HPSTestRunTracker2014GeomDef.HalfModuleLamination.kapton_thickness + HPSTestRunTracker2014GeomDef.TestRunHalfModule.getCFThickness()/2.0);

 				final double ball_pos_cf_local_z = -1 * (HPSTestRunTracker2014GeomDef.Sensor.getSensorWidth()/2.0 + 12.66) + 8.83 - 3.00;
 				final double vee_pos_cf_local_x =  ball_pos_cf_local_x + 1.0; // arbitrary distance
 				final double vee_pos_cf_local_y =  ball_pos_cf_local_y;

@@ -1063,8 +1151,10 @@

 				setBallPos(ball_pos_cf_local_x,ball_pos_cf_local_y,ball_pos_cf_local_z);
 				setVeePos(vee_pos_cf_local_x,vee_pos_cf_local_y,vee_pos_cf_local_z);
 				setFlatPos(flat_pos_cf_local_x,flat_pos_cf_local_y,flat_pos_cf_local_z);

-				

 			}

+			protected void setCenter() {
+				setCenter(getLength()/2.0, 0.0, getWidth()/2.0);
+			}

 			protected double getThickness() {
 				return cf_thickness;
 			}

@@ -1077,6 +1167,9 @@

 			protected double getHeigth() {
 				return getThickness();
 			}

+			protected void setBoxDim() {
+				setBoxDim(getLength(),getThickness(),getWidth());
+			}

 		}
 		
 		

@@ -1086,9 +1179,7 @@

 			protected static final double hybrid_thickness = 4.0/64.0*inch;
 			public Hybrid(String name, BaseGeom m) {
 				super(name, m);

-				setCenter(getLength()/2.0, 0.0, getWidth()/2.0);
-				setBoxDim(getLength(),getThickness(), getWidth());
-				

+				init();

 			}
 			protected void setPos() {
 				final double ball_pos_hybrid_local_x =  -1 * (170.0 - HPSTestRunTracker2014GeomDef.Sensor.getSensorLength()/2.0);

@@ -1105,6 +1196,9 @@

 				setFlatPos(flat_pos_hybrid_local_x,flat_pos_hybrid_local_y,flat_pos_hybrid_local_z);
 				
 			}

+			protected void setCenter() {
+				setCenter(getLength()/2.0, 0.0, getWidth()/2.0);
+			}

 			protected double getThickness() {
 				return hybrid_thickness;
 			}

@@ -1117,8 +1211,20 @@

 			protected double getLength() {
 				return hybrid_length;
 			}

+			protected void setBoxDim() {
+				setBoxDim(getLength(),getThickness(), getWidth());
+			}

 		}
 		

+		
+		
+		
+		
+		/**
+		 * 
+		 * Class that keeps tracks of unit vectors and origin for a 3D coordinate system.
+		 *
+		 */

 		public static class Coord {
 			private Hep3Vector origin;
 			private Hep3Vector u;

@@ -1134,8 +1240,7 @@

 
 			private void check() {
 				if(u.magnitude()-1>0.00001 || v.magnitude()-1>0.00001 || v.magnitude()-1>0.00001) {

-					System.out.printf("Error: this coordinate system is ill-defined\n%s\n",this.toString());
-					System.exit(1);

+					throw new RuntimeException("Error: this coordinate system is ill-defined " + toString());

 				}
 			}
 			

@@ -1146,6 +1251,7 @@

 				Hep3Vector ball_to_flat = VecOp.sub(flat, ball);
 				w = VecOp.unit(VecOp.cross(ball_to_vee,ball_to_flat));
 				v = VecOp.cross(w, u);

+				check();

 			}
 	/*
 			public void rotate(Hep3Vector euler_angles) {