diff -u -r1.2 -r1.3
--- CCDElectronics.java	14 Dec 2010 21:42:12 -0000	1.2
+++ CCDElectronics.java	17 Dec 2010 21:48:45 -0000	1.3
@@ -33,16 +33,17 @@

    if(firstcall)
    {
     int thr = (int) (pixel_threshold * adc_scale);

-    int max = (int) (noise_level * 5);

+    int max = (int) (noise_level * 6);

     int nb = max - thr;

+    if(nb < 1) nb=1; 

     indist = new double[nb];
     double apro = 0.;
     for(int i=0; i<nb; i++)
     {

-     double bpro = erprob.getProbability(((double)(thr+i))/noise_level) 
-     - erprob.getProbability(((double)(thr+i+1))/noise_level);

+     double ipro = erprob.getProbability(((double)(thr+i))/noise_level);
+     double bpro = ipro - erprob.getProbability(((double)(thr+i+1))/noise_level);

      if(useCDS) bpro=bpro*bpro;

-     if(i==0) System.out.println("Probability of hit exceeding pixel threshold "+thr+" is "+bpro); 

+     if(i==0) System.out.println("Probability of hit exceeding pixel threshold "+thr+" is "+ipro); 

      apro+=bpro;
      indist[i]=apro; 
     }

@@ -226,7 +227,7 @@

     int inh = (int) Math.floor(enh);
     enh-= ((double) inh);
     double probe = rnd.nextDouble();

-    if(probe < enh) inh++;

+    if(probe < enh) inh++; 

     if(inh < 5)
     {
      double tprob = ((double) inh)/100.;

@@ -242,24 +243,25 @@

      double snnd = Math.sqrt((double) inh);
      double gnh = inh + snnd*rnd.nextGaussian();
      inh = (int) gnh;

-    } 

+    }
+//    System.out.println("Number of noise hits in sensor of "+np+" pixels is: "+inh);  

     for(int i=0; i<inh; i++)
     {
      int row = (int) (rnd.nextDouble() * snr);
      int col = (int) (rnd.nextDouble() * snc);
      probe = rnd.nextDouble();
      int j=0;

-     while(probe > indist[j]) j++;

+     while((probe > indist[j]) && (j<nb)) j++;

      double sig = (double) (thr+j);
      short cnt1 = (short) (Math.floor(sig/adc_scale));

-     if(cnt1 >= sens.getClusterThreshold())
-     { 

+//     if(cnt1 >= sens.getClusterThreshold())
+//     { 

       short[] adc = new short[1];
       adc[0]=cnt1;
       long cellid = sens.getCellID(row,col);
       RawTrackerHit rhit = new BaseRawTrackerHit(bc,cellid,adc,null,sens.getParent());
       sens.addRawHit(rhit);

-     }

+//     }

     }    
      
    }

diff -u -r1.1 -r1.2
--- PixilatedSensor.java	9 Dec 2008 23:36:34 -0000	1.1
+++ PixilatedSensor.java	17 Dec 2010 21:48:45 -0000	1.2
@@ -35,6 +35,7 @@

   private IPixelSensorElectronics electronics = null;
   private IReadout readout = null;
   private ErrorEstimate covm = null;

+  private Hep3Vector Lorentz_corr = new BasicHep3Vector(0.,0.,0.);

   public int nrows = 512;
   public int ncolumns = 512;
   private double x0 = 0.;

@@ -132,6 +133,8 @@

 
   public void setClusterThreshold(int t) { clust_thresh = t; }
 

+  public void setLorentzCorrection(Hep3Vector corv) { Lorentz_corr.setV(corv.x(),corv.y(),corv.z()); } 
+

   public int getClusterThreshold() { return clust_thresh; }
 
   public void setDebug(boolean yes) { debug=yes; }

@@ -602,7 +605,8 @@

     if(electronics != null) electronics.processSensor(this,bc);
     if(rawhits.size() != 0)
     {

-     if(debug) System.out.println("Number of RawTrackerHits: "+rawhits.size());

+     if(debug)
+       System.out.println("Number of RawTrackerHits: "+rawhits.size());

      if(readout != null) { for(RawTrackerHit rht:rawhits) readout.addHit(rht); }
      findClusters();
      makeTrackerHits();

@@ -641,7 +645,8 @@

     double clcc = pcl.getCenterColumn();
     double iclcc = (int) Math.floor(clcc);
     double[] locc = toLocal(clcr,clcc);

-    Hep3Vector lpos = new BasicHep3Vector(locc[0],locc[1],locc[2]);

+    Hep3Vector lposnc = new BasicHep3Vector(locc[0],locc[1],locc[2]);
+    Hep3Vector lpos = VecOp.add(lposnc,Lorentz_corr)

     Hep3Vector glpos = global.transformed(lpos);
     double[] pos = new double[3];
     pos[0]=glpos.x();

@@ -782,10 +787,14 @@

 //   if(is_endcap) System.out.println("Found "+tempcl.size()+" clusters of any ampl."); 
    for(PixCluster cl:tempcl)
    {

-    if(debug) System.out.println("Cluster ampl: "+cl.getTotalAmp()+" is valid? "+cl.isValid());

+    if(debug)
+    {
+      System.out.println("Cluster ampl: "+cl.getTotalAmp()+" is valid? "+cl.isValid());
+      System.out.println("Cluster threshold is "+clust_thresh);
+    } 

     if(cl.isValid() && (cl.getTotalAmp() >= clust_thresh)) clusters.add(cl);
    }

-//   if(is_endcap)  System.out.println("Found "+clusters.size()+" clusters above thr.");

+//   System.out.println("Found "+clusters.size()+" clusters above thr.");

    if(readout != null) { for(PixCluster pcl:clusters) readout.addHit(pcl); }
   }
 }

diff -u -r1.3 -r1.4
--- PixilatedSensorManager.java	14 Dec 2010 21:42:13 -0000	1.3
+++ PixilatedSensorManager.java	17 Dec 2010 21:48:45 -0000	1.4
@@ -14,17 +14,19 @@

 import java.text.*;
 import java.util.*;
 import org.lcsim.util.lcio.LCIOConstants;

+import org.lcsim.util.aida.AIDA;

 
 /**
  * This class are designed for creating a list of pixilated sensor
  * for each event (only sensors which have hits in them are created)
  *
  * @author Nick Sinev

- * @version $Id: PixilatedSensorManager.java,v 1.3 2010/12/14 21:42:13 sinev Exp $

+ * @version $Id: PixilatedSensorManager.java,v 1.4 2010/12/17 21:48:45 sinev Exp $

  */
 
 public class PixilatedSensorManager extends Driver
 {

+ private static boolean doHist = true;

  boolean cal_res_bar = false;
  boolean cal_res_ec = false;
  boolean read_rest_bar=true;

@@ -32,7 +34,7 @@

  boolean incl_el_noise = false;
  boolean ready = false; 
  static PixSimConstants cons = PixSimConstants.instance();

- static final int MAXHTSPEV = 10000;

+ static final int MAXHTSPEV = 100000;

  private static final double bunch_period = cons.BunchInterval;
  private static int phys_bc = 0;
  private static int cluster_thr_barr = 8;

@@ -40,6 +42,10 @@

  private static boolean firstcall = true;
  private static boolean assign_bc = true;
  private static double enoise = 50.;

+ private static long startime=0;
+ private static long endtime=0;
+ private static long proctime=0;
+ private static AIDA aida = AIDA.defaultInstance();

 
 // boolean choises for 3 sensor positions - Barrel, ECPlus and ECMinus
 

@@ -94,8 +100,8 @@

  private static boolean ec_pl_ec_mi_same_prop = true;
 
 // here we have arrays of all settable variables for different sensor options

- private static int[] opt_cluster_thr_barr = {8,8,8,1,1,1,1,1,1,8};
- private static int[] opt_cluster_thr_ec =  {8,8,8,1,1,1,1,1,1,8};

+ private static int[] opt_cluster_thr_barr = {8,1,8,1,1,1,1,1,1,8};
+ private static int[] opt_cluster_thr_ec =  {8,1,8,1,1,1,1,1,1,8};

  private static boolean[] opt_prop_tab_barrel_local = {false,false,false,true,true,true,true,true,true,true};
  private static boolean[] opt_prop_tab_ec_pl_local = {false,false,false,true,true,true,true,true,true,true};
  private static boolean[] opt_prop_tab_ec_mi_local = {false,false,false,true,true,true,true,true,true,true};

@@ -109,43 +115,44 @@

  {"CCD_20x20x20_B5_propagator.dat",
   "CCD_20x20x20_B5_propagator.dat",
   "CCD_20x20x20_B5_propagator.dat",

+  "CCD_20x20x20_B5_propagator.dat",

   "Chronopix_8x8x20hr_B5_Barr_propagator.dat",
   "Chronopix_12x12x20hr_B5_Barr_propagator.dat",
   "Chronopix_16x16x20hr_B5_Barr_propagator.dat",
   "Chronopix_8x8x12hr_B5_Barr_propagator.dat",
   "Chronopix_12x12x12hr_B5_Barr_propagator.dat",

-  "chronopix_16x16x12hr_B5_Barr_propagator.dat",
-  "mimosa18_B5_Barr_propagator.dat"

+  "chronopix_16x16x12hr_B5_Barr_propagator.dat"

  };
 
  private static String[] opt_ec_pl_prop_tname = 
  {"CCD_20x20x20_B5_EC_propagator.dat",
   "CCD_20x20x20_B5_EC_propagator.dat",
   "CCD_20x20x20_B5_EC_propagator.dat",

+  "CCD_20x20x20_B5_EC_propagator.dat",

   "Chronopix_8x8x20_B5_EC_propagator.dat",
   "Chronopix_12x12x20_B5_EC_propagator.dat",
   "Chronopix_16x16x20_B5_EC_propagator.dat",
   "Chronopix_8x8x12_B5_EC_propagator.dat",
   "Chronopix_12x12x12_B5_EC_propagator.dat",

-  "chronopix_16x16x12_hr_B5_EC_propagator.dat",
-  "mimosa18_B5_EC_propagator.dat"

+  "chronopix_16x16x12_hr_B5_EC_propagator.dat"

  };
 
  private static String[] opt_ec_mi_prop_tname = 
  {"CCD_20x20x20_B5_EC_propagator.dat",
   "CCD_20x20x20_B5_EC_propagator.dat",
   "CCD_20x20x20_B5_EC_propagator.dat",

+  "CCD_20x20x20_B5_EC_propagator.dat",

   "Chronopix_8x8x20_B5_EC_propagator.dat",
   "Chronopix_12x12x20_B5_EC_propagator.dat",
   "Chronopix_16x16x20_B5_EC_propagator.dat",
   "Chronopix_8x8x12_B5_EC_propagator.dat",
   "Chronopix_12x12x12_B5_EC_propagator.dat",

-  "chronopix_16x16x12_hr_B5_EC_propagator.dat",
-  "mimosa18_B5_EC_propagator.dat"

+  "chronopix_16x16x12_hr_B5_EC_propagator.dat"

  };
 
  private static String[] opt_rtab_name_bar = 
  {"CCD_20x20x20_B5_res_bar.dat",

+  "CCD_20x20x20_B5_res_bar.dat",

   "CPCCD_20x20x20_B5_res_bar.dat",
   "ShortColCCD_20x20x20_B5_res_bar.dat",
   "Chronopix_8x8x20hr_B5_res_bar.dat",

@@ -153,12 +160,12 @@

   "Chronopix_16x16x20hr_B5_res_bar.dat",
   "Chronopix_8x8x12hr_B5_res_bar.dat",
   "Chronopix_12x12x12hr_B5_res_barr.dat",

-  "chronopix_16x16x12hr_B5_res_barr.dat",
-  "mimosa18_B5_res_bar.dat"

+  "chronopix_16x16x12hr_B5_res_barr.dat"

  };
 
  private static String[] opt_rtab_name_ec_pl=
  {"CCD_20x20x20_B5_res_ec.dat",

+  "CCD_20x20x20_B5_res_ec.dat",

   "CPCCD_20x20x20_B5_res_ec.dat",
   "ShortColCCD_20x20x20_B5_res_ec.dat",
   "Chronopix_8x8x20hr_B5_res_ec.dat",

@@ -166,12 +173,12 @@

   "Chronopix_16x16x20hr_B5_res_ec.dat",
   "Chronopix_8x8x12hr_B5_res_ec.dat",
   "Chronopix_12x12x12hr_B5_res_ec.dat",

-  "chronopix_16x16x12hr_B5_res_ec.dat",
-  "mimosa18_B5_res_ec.dat"

+  "chronopix_16x16x12hr_B5_res_ec.dat"

  };
 
  private static String[] opt_rtab_name_ec_mi = 
  {"CCD_20x20x20_B5_res_ec.dat",

+  "CCDd_20x20x20_B5_res_ec.dat",

   "CPCCD_20x20x20_B5_res_ec.dat",
   "ShortColCCD_20x20x20_B5_res_ec.dat",
   "Chronopix_8x8x20hr_B5_res_ec.dat",

@@ -234,15 +241,15 @@

  public PixilatedSensorManager(SensorOption opt, boolean usetable)
  {
   if(opt == SensorOption.ClassicCCD) option = 0;

-  if(opt == SensorOption.CPCCD) option = 1;
-  if(opt == SensorOption.ShortColumnCCD) option = 2;
-  if(opt == SensorOption.Chrono8x8x20) option = 3;
-  if(opt == SensorOption.Chrono12x12x20) option = 4;
-  if(opt == SensorOption.Chrono16x16x20) option = 5;
-  if(opt == SensorOption.Chrono8x8x12) option = 6; 
-  if(opt == SensorOption.Chrono12x12x12) option = 7; 
-  if(opt == SensorOption.Chrono16x16x12) option = 8;
-  if(opt == SensorOption.Mimosa) option = 9;

+  if(opt == SensorOption.ClassicCCDdigit) option = 1;
+  if(opt == SensorOption.CPCCD) option = 2;
+  if(opt == SensorOption.ShortColumnCCD) option = 3;
+  if(opt == SensorOption.Chrono8x8x20) option = 4;
+  if(opt == SensorOption.Chrono12x12x20) option = 5;
+  if(opt == SensorOption.Chrono16x16x20) option = 6;
+  if(opt == SensorOption.Chrono8x8x12) option = 7; 
+  if(opt == SensorOption.Chrono12x12x12) option = 8; 
+  if(opt == SensorOption.Chrono16x16x12) option = 9;

   use_prop_tab_barrel = usetable;
   use_prop_tab_ec_pl = usetable;
   use_prop_tab_ec_mi = usetable;

@@ -276,6 +283,27 @@

     setOptionVariables();
     IPixelSensorElectronics el = new CCDElectronics();
     el.includeElectronicNoiseHits(incl_el_noise);

+    el.setADCScale(140.);
+    el.setNoiseLevel(enoise);
+    el.setADCSaturation(1);
+    el.setBunchesPerClock(30); // this is about maximum clock image speed (100 KHz) for classic CCD - asuming 50MHz speed in R register
+                              // for VXD3 CCD we would set this value to 300 (10 KHz image clock and 5 MHz R register speed)
+    el.useCorrelatedDoubleSampling(false);
+    el.setPixelThreshold(1);
+    bar_el = el;
+    ecp_el = el;
+    ecm_el = el;
+    bpcf = new PixelConfiguration();
+    bcpr = new CarrierPropagator(bpcf);
+    ecppr = new CarrierPropagator(bpcf);
+    ecmpr = ecppr;
+    ready = true;     
+   }
+   if(option == 2)
+   {
+    setOptionVariables();
+    IPixelSensorElectronics el = new CCDElectronics();
+    el.includeElectronicNoiseHits(incl_el_noise);

     el.setADCScale(25.);
     el.setNoiseLevel(enoise);
     el.setADCSaturation(255);

@@ -309,7 +337,7 @@

   cluster_thr_ec = opt_cluster_thr_ec[option];
  }
 

- public void includeElectronicsNoise(boolean yes) { incl_el_noise=yes; }

+ public void includeElectronicsNoiseHits(boolean yes) { incl_el_noise=yes; }

 
  public void setNoiseLevel(double noise) { enoise=noise; }
 

@@ -457,6 +485,7 @@

      }
     } 
    }

+

    if(use_prop_tab_ec_mi)
    {
     if(!ec_pl_ec_mi_same_prop)

@@ -569,7 +598,8 @@

    {
     PixilatedSensor pse = new PixilatedSensor(de,bcpr,false);
     pse.setElectronics(bar_el);

-    pse.setErrorEstimate(eeb); 

+    pse.setErrorEstimate(eeb);
+    pse.setClusterThreshold(cluster_thr_barr);  

     if(nbe==0 && cal_res_bar) pse.calibrateErrorEstimate(calibr_stat_b,rtab_name_bar);
     nbe++; 
     psbrl.add(pse);

@@ -585,6 +615,7 @@

     PixilatedSensor pse = new PixilatedSensor(de,ecppr,true); 
     pse.setElectronics(ecp_el);
     pse.setErrorEstimate(eeep);

+    pse.setClusterThreshold(cluster_thr_ec);  

     eeep.setTableParameters(11,11,11,0.,1.5,0.,1.5,2.2,7.2);
     if(nbc==0 && cal_res_ec) pse.calibrateErrorEstimate(calibr_stat_ep,rtab_name_ec_pl);
     nbc++; 

@@ -606,6 +637,7 @@

     PixilatedSensor pse = new PixilatedSensor(de,ecmpr,true); 
     pse.setElectronics(ecm_el);
     pse.setErrorEstimate(eeem);

+    pse.setClusterThreshold(cluster_thr_ec);  

     if(!ec_pl_ec_mi_same_prop)
     { 
      eeem.setTableParameters(11,11,11,0.,1.5,0.,1.5,2.2,7.2);

@@ -617,6 +649,7 @@

    System.out.println("Created: "+nbe+" barrel pixilated sensors and "+nbc+" EC positive and "+nbcm+" EC negative pixilated sensors");     
   } // end of if(firstcall)
   if(!ready) return;

+  if(doHist) startime =  System.currentTimeMillis();

   for(IDetectorElement de:vxbrels)
   {
    if(de.hasReadout()) { IReadout ro = de.getReadout(); ro.clear(); }

@@ -638,19 +671,19 @@

   String ehcname=null;
   if(evhits != null)
   {

-   System.out.println("Event has  "+evhits.size()+" SimTrackerHit collections: ");

+//   System.out.println("Event has  "+evhits.size()+" SimTrackerHit collections: ");

    for(List<SimTrackerHit> sdhits:evhits)
    {
     EventHeader.LCMetaData md = event.getMetaData(sdhits);
     String cname = md.getName();

-    System.out.println("Collection name: "+cname);

+//    System.out.println("Collection name: "+cname);

     if((cname.indexOf("Vtx")!=-1)||(cname.indexOf("Vertex") != -1))
     {
      if(cname.indexOf("Barrel")!=-1) bhcname=cname;
      if(cname.indexOf("Endcap")!=-1) ehcname=cname;
     }
    }

-  System.out.println("Vertex barrel sim hit collection name is: "+bhcname+" and for encap it is: "+ehcname);

+//  System.out.println("Vertex barrel sim hit collection name is: "+bhcname+" and for encap it is: "+ehcname);

   }
   int asshts = 0;
   int nprints = 0; 

@@ -659,7 +692,7 @@

    if(bhcname != null)
    {
     List<SimTrackerHit> vxbhts = event.get(SimTrackerHit.class,bhcname);

-    System.out.println("SimTrackerHit collection size for barrel: "+vxbhts.size());

+//    System.out.println("SimTrackerHit collection size for barrel: "+vxbhts.size());

     for(SimTrackerHit hit:vxbhts)
     {
      double[] hpnt = hit.getPoint();    

@@ -689,7 +722,7 @@

    if(ehcname != null)
    {
     List<SimTrackerHit> vxehts = event.get(SimTrackerHit.class,ehcname);

-    System.out.println("SimTrackerHit collection size for endcap: "+vxehts.size());

+//    System.out.println("SimTrackerHit collection size for endcap: "+vxehts.size());

     for(SimTrackerHit hit:vxehts)
     {
      double[] hpnt = hit.getPoint();    

@@ -767,12 +800,14 @@

   } // end if(evhits != null)
   List<TrackerHit> ebhits = new ArrayList<TrackerHit>();
   List<TrackerHit> eehits = new ArrayList<TrackerHit>();

-  List<RawTrackerHit> rawhits = new ArrayList<RawTrackerHit>(); 

+  List<RawTrackerHit> rawhits = new ArrayList<RawTrackerHit>();
+  int tnrawhpe = 0;  // total number of raw hirs, including noise hits 

   for(PixilatedSensor psn:psbrl)
   { 
    psn.processEvent(phys_bc);
    IDetectorElement de = psn.getParent();
    IReadout ro = de.getReadout();

+   if(doHist) tnrawhpe+=(psn.getRawHits()).size();

    List<TrackerHit> sthts = ro.getHits(TrackerHit.class);
    for(TrackerHit ht:sthts)
    {

@@ -786,6 +821,7 @@

    psn.processEvent(phys_bc);
    IDetectorElement de = psn.getParent();
    IReadout ro = de.getReadout();

+   if(doHist) tnrawhpe+=(psn.getRawHits()).size();

    List<TrackerHit> sthts = ro.getHits(TrackerHit.class);
    for(TrackerHit ht:sthts)
    {

@@ -799,6 +835,7 @@

    psn.processEvent(phys_bc);
    IDetectorElement de = psn.getParent();
    IReadout ro = de.getReadout();

+   if(doHist) tnrawhpe+=(psn.getRawHits()).size();

    List<TrackerHit> sthts = ro.getHits(TrackerHit.class);
    for(TrackerHit ht:sthts)
    {

@@ -807,12 +844,23 @@

    }
   } 
 //  System.out.println("Endcap minus hits processed!");

-  System.out.println("Adding "+ebhits.size()+" hits to RecVtxBarrHits collection");

+//  System.out.println("Adding "+ebhits.size()+" hits to RecVtxBarrHits collection");

   event.put("RecVtxBarrHits",ebhits,TrackerHit.class,0);  

-  System.out.println("Adding "+eehits.size()+" hits to RecVtxEndcapHits collection");

+//  System.out.println("Adding "+eehits.size()+" hits to RecVtxEndcapHits collection");

   event.put("RecVtxEndcapHits",eehits,TrackerHit.class,0);
   event.put("RecVtxRawHits",rawhits,RawTrackerHit.class,(1 << LCIOConstants.RTHBIT_HITS));
 //  event.put("RecVtxRawHits",rawhits,RawTrackerHit.class,0);

+  if(doHist)
+  {
+    int nrechits = 0;
+    nrechits+=ebhits.size();
+    nrechits+=eehits.size();
+    aida.cloud1D("total number of reconstructed VTX hits per event").fill(nrechits);
+    aida.cloud1D("total number of raw  VTX hits per event").fill(tnrawhpe);   
+    endtime =  System.currentTimeMillis();
+    proctime=endtime-startime; 
+    aida.cloud1D("pixsim event processing time, ms ").fill(proctime);
+  }

 
  } // end function process
 

diff -u -r1.1 -r1.2
--- SensorOption.java	9 Dec 2008 23:36:34 -0000	1.1
+++ SensorOption.java	17 Dec 2010 21:48:45 -0000	1.2
@@ -4,11 +4,11 @@

  * An enum to indicate the shape of the body.
  *
  * @author Nick Sinev

- * @version $Id: SensorOption.java,v 1.1 2008/12/09 23:36:34 jeremy Exp $

+ * @version $Id: SensorOption.java,v 1.2 2010/12/17 21:48:45 sinev Exp $

  */
 
 public enum SensorOption 
 {

-     ClassicCCD,CPCCD,ShortColumnCCD,Chrono8x8x20,Chrono12x12x20,Chrono16x16x20,Chrono8x8x12,
-     Chrono12x12x12,Chrono16x16x12,Mimosa	

+     ClassicCCD,ClassicCCDdigit,CPCCD,ShortColumnCCD,Chrono8x8x20,Chrono12x12x20,Chrono16x16x20,Chrono8x8x12,
+     Chrono12x12x12,Chrono16x16x12	

 }

\ No newline at end of file

diff -u -r1.1 -r1.2
--- TCADFieldMap.java	9 Dec 2008 23:36:34 -0000	1.1
+++ TCADFieldMap.java	17 Dec 2010 21:48:45 -0000	1.2
@@ -226,7 +226,7 @@

      {
       String rstr=null;
       BufferedReader r=null;

-      if(dbg_lvl > 0) System.out.println("Found field map file "+cache.getAbsolutePath());

+      System.out.println("Found field map file "+cache.getAbsolutePath());

       FileInputStream fins = null;
       try
       {