hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N PolarCount.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ PolarCount.java	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,69 @@

+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.lcsim.hps.users.phansson;
+
+
+import hep.aida.IHistogram1D;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * @author phansson
+ */
+public class PolarCount {
+    
+    private String run;
+    private String name;
+    private double val;
+    private Count count;
+    
+    
+    PolarCount(String n, String r, double v, Count c) {
+        this.name = n;
+        this.run = r;
+        this.val = v;
+        this.count = c;
+    }
+    
+    PolarCount(PolarCount c) {
+        this.name = c.name();
+        this.run = c.run();
+        this.val = c.val;
+        this.count = c.count();
+    }
+        
+    
+    public String name() {
+        return this.name;
+    }
+
+    public void setName(String str) {
+        this.name = str;
+    }
+
+    public void setCount(Count c) {
+        this.count = c;
+    }
+    
+    public String run() {
+        return this.run;
+    }
+
+    public double val() {
+        return this.val;
+    }
+
+    public void addSimple(PolarCount l) {
+        this.count.addSimple(l.count().n(), l.count().en());
+    }
+    
+    public Count count() {
+        return this.count;
+    }
+    
+
+    
+}

hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N TrigRateAna.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ TrigRateAna.java	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,1275 @@

+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.lcsim.hps.users.phansson;
+
+import hep.aida.*;
+import hep.aida.ref.plotter.PlotterRegion;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.lcsim.util.aida.AIDA;
+
+
+
+/**
+ *
+ * @author phansson
+ */
+
+
+
+
+
+public class TrigRateAna {
+    
+    private AIDA aida = AIDA.defaultInstance();
+    private IAnalysisFactory af = aida.analysisFactory();
+    IHistogramFactory hf = aida.histogramFactory();
+//    ITree tree = aida.tree();//(ITreeFactory) af.createTreeFactory().create();
+    
+    private int _bkgRunNr1 = -1;
+    private int _bkgRunNr2 = -1;
+    
+    private boolean _saveFiles = false;
+    private boolean _hide = false;
+    private String _addOn = "";
+    
+    double _C_ep = 1;
+    
+    ECalHitMapPlots util = new ECalHitMapPlots();
+    
+    List<Count> _countList = new ArrayList<Count>();
+
+    HashMap<String,Integer> _counts = new HashMap<String,Integer>();
+    HashMap<String,Integer> _counts_merged = new HashMap<String,Integer>();
+    HashMap<String,Double> _counts_merged_norm = new HashMap<String,Double>();
+    HashMap<String,Double> _counts_merged_norm_subtr = new HashMap<String,Double>();
+    HashMap<String,Double> _counts_merged_norm_subtr_qscaled = new HashMap<String,Double>();
+    HashMap<String,Double> _counts_merged_norm_subtr_qscaled_daqscaled = new HashMap<String,Double>();
+    
+    HashMap<String,Double> _ratio = new HashMap<String,Double>();
+
+    List<PolarCount> _polarCountList = new ArrayList<PolarCount>();
+    
+    List<BeamCurrentData> _beamCurrent = new ArrayList<BeamCurrentData>();
+    List<DAQDeadTimeData> _deadTime = new ArrayList<DAQDeadTimeData>();
+    HashMap<Integer,Double> _thicknessMap = new HashMap<Integer,Double>();
+
+  
+    double _chargeScale = 1.0;
+    
+    
+    public void saveFiles(boolean v) {
+        _saveFiles = v;
+    }
+    
+    public void addOn(String s) {
+        _addOn = s;
+    }
+    
+    public void hidePlots(boolean h) {
+        this._hide = h;
+        this.util.hidePlots(this._hide);
+    }
+    
+    public TrigRateAna() {
+        
+        //System.out.println("Constructor ECalHitMapPlots");
+        
+    }
+    
+    public void setChargeNormalization(double q) {
+        _chargeScale = q;
+    }
+   
+    public void setBackgroundRunNrs(int nr1, int nr2) {
+        _bkgRunNr1 = nr1;
+        _bkgRunNr2 = nr2;
+        
+    }
+    
+    
+    public void getGainCalibration(ITree tree,String side) {
+        
+        IHistogram1D h = (IHistogram1D)tree.find("Cluster E>600GeV Eoverp good region " + side);
+        
+        util.plotBasic1D(h,"Eoverp good region E>600MeV", "E/p","Arbitrary Units","green",_saveFiles);
+        
+        double max = -1;
+        int bin_max = -1;
+        for(int bin=1;bin<h.axis().bins();++bin) {
+            if(h.binEntries(bin)>max) {
+                max=h.binEntries(bin);
+                bin_max = bin;
+            }
+        }
+        
+        System.out.println("Maximum E/p: " + h.axis().binCenter(bin_max));
+        _C_ep = h.axis().binCenter(bin_max);
+        System.out.println("Gain calibration: " + _C_ep);
+        
+        return;
+        
+//        IHistogram2D hm = (IHistogram2D)tree.find("Cluster hit map all");        
+//        plotBasic2D(hm,"Cluster Hit Map", "Horizontal Crystal Index","Vertical Crystal Index");
+//        
+//        IHistogram1D hAmp = (IHistogram1D)tree.find("Cluster size all");
+//        plotBasic1D(hAmp,"Cluster Size", "Cluster Size","Arbitrary Units","green");
+
+        
+        
+
+
+    
+        
+    }
+    
+    
+    private int findCount(List<Count> list, String r,String n) {
+        //System.out.println("Looking for run " + r + " for type " + n + " among " + list.size() + "count objects");
+        for(int i=0;i<list.size();++i) {
+            System.out.println(i +": " + list.get(i).run() + " " + list.get(i).name());
+            if(list.get(i).name().equals(n)) {
+                if(list.get(i).run().equals(r)) {
+                    //System.out.println("Found it! " + i);
+                    return i;
+                }
+            }
+        }
+        return -1;
+    }
+    
+    private int findPolarCount(List<PolarCount> list, String r, double v, String n) {
+        //System.out.println("Looking for run " + r + " for type " + n + " and val " + v + " among " + list.size() + " polar count objects");
+        for(int i=0;i<list.size();++i) {
+            //System.out.println(i +": " + list.get(i).run() + " " + list.get(i).name() + " " + list.get(i).val());
+            if(list.get(i).name().equals(n)) {
+                if(list.get(i).run().equals(r)) {
+                    if(Double.compare(list.get(i).val(),v)==0) {
+                        //System.out.println("Found it! " + i);
+                        return i;
+                    }
+                }
+            }
+        }
+        return -1;
+    }
+    
+    private List<Count> findCount(String name) {
+        List<Count> list = new ArrayList<Count>();
+        for(Count c :_countList) {
+            if(c.name().equals(name)) list.add(c);
+        }
+        return list;
+    }
+
+    private List<PolarCount> findPolarCount(String name) {
+        List<PolarCount> list = new ArrayList<PolarCount>();
+        for(PolarCount c :_polarCountList) {
+            if(c.name().equals(name)) list.add(c);
+        }
+        return list;
+    }
+
+    
+    public void mergeCounts() {
+//        HashMap<String,Integer> m = _counts_merged;
+//        for (Map.Entry<String, Integer> e : _counts.entrySet()) {
+//            String k = e.getKey();
+//            Integer n = e.getValue();
+//            if(k.contains("_")) {
+//                int idx = k.indexOf("_");
+//                String str = k.substring(0, idx);
+//                k = str;
+//            }
+//            if(m.containsKey(k)) {
+//                n += m.get(k);
+//            }
+//            m.put(k, n);
+//        }
+//        
+        List<Count> list = new ArrayList<Count>();
+        
+        for(Count c : _countList) {
+            String run = c.run();
+            String name = "merged"; //c.name();
+            if(run.contains("_")) {
+                int idx = run.indexOf("_");
+                String str = run.substring(0, idx);
+                run = str;
+            }
+            int idx = findCount(list,run,name);
+            if(idx<0) {
+                Count c_new = new Count(name,run,c.n(),c.en());
+                list.add(c_new);
+            } else {
+                list.get(idx).addSimple(c.n(),c.en());
+            }
+            
+        }
+        _countList.addAll(list);
+        
+        
+        
+        
+        List<PolarCount> list2 = new ArrayList<PolarCount>();
+        
+        for(PolarCount c : _polarCountList) {
+            String run = c.run();
+            String name = "merged"; //c.name();
+            if(run.contains("_")) {
+                int idx = run.indexOf("_");
+                String str = run.substring(0, idx);
+                run = str;
+            }
+            int idx = findPolarCount(list2,run,c.val(),name);
+            if(idx<0) {
+                PolarCount c_new = new PolarCount(name,run,c.val(),c.count());
+                
+                list2.add(c_new);
+            } else {
+                list2.get(idx).addSimple(c);
+            }
+            
+        }
+        _polarCountList.addAll(list2);
+        
+        
+        
+        
+    }
+    
+    public boolean isBackgroundRun(int nr) {
+        if(_bkgRunNr1==nr) return true;
+        if(_bkgRunNr2==nr) return true;
+        return false;
+        
+    }
+    
+    
+    public BeamCurrentData getBCD(String run_str) {
+        for(BeamCurrentData b : _beamCurrent) {
+            if(b.getRun()==Integer.parseInt(run_str)) return b;
+        }
+        return null;
+    }
+    
+    
+    
+    public void normalize() {
+        
+//        HashMap<String,Double> m = _counts_merged_norm;
+//        
+//        for (Map.Entry<String, Integer> e : _counts_merged.entrySet()) {
+//            String k = e.getKey();
+//            Integer n = e.getValue();
+//            //get the integrated beam current
+//            BeamCurrentData bcd = getBCD(k);
+//            if(bcd==null) {
+//                System.out.println("Error run " + k + " is not in beam current list!");
+//                System.exit(1);
+//            }
+//            
+//            double current = bcd.getIntCurrent();
+//            double n_norm = n/current; // unit is [/nC]
+//            m.put(k, n_norm);
+//            
+//        }
+//        
+        
+        List<Count> list = new ArrayList<Count>();
+        for(Count c : _countList) {
+            if(c.name()!="merged") continue;
+            String run = c.run();
+            String name = "normalized"; //c.name();
+            BeamCurrentData bcd = getBCD(run);
+            if(bcd==null) {
+                System.out.println("Error run " + run + " is not in beam current list!");
+                System.exit(1);
+            }
+            double current = bcd.getIntCurrent();
+            double ecurrent = bcd.getIntCurrentError();
+            double n = c.n();
+            double en = c.en();
+            double n_norm = n/current;
+            double en_norm = Math.sqrt((en/current)*(en/current) + (n/(current*current)*ecurrent)*(n/(current*current)*ecurrent));
+            
+            Count c_new = new Count(name,run,n_norm,en_norm);
+            list.add(c_new);
+            
+        }
+        _countList.addAll(list);
+        
+        
+        List<PolarCount> polarlist = new ArrayList<PolarCount>();
+        for(PolarCount c : _polarCountList) {
+            if(c.name()!="merged") continue;
+            String run = c.run();
+            String name = "normalized"; //c.name();
+            BeamCurrentData bcd = getBCD(run);
+            if(bcd==null) {
+                System.out.println("Error run " + run + " is not in beam current list!");
+                System.exit(1);
+            }
+            double current = bcd.getIntCurrent();
+            double ecurrent = bcd.getIntCurrentError();
+            double n = c.count().n();
+            double en = c.count().en();
+            double n_norm = n/current;
+            double en_norm = Math.sqrt((en/current)*(en/current) + (n/(current*current)*ecurrent)*(n/(current*current)*ecurrent));
+            
+            PolarCount c_new = new PolarCount(name,run,c.val(),new Count(name,run,n_norm,en_norm));
+            polarlist.add(c_new);
+            
+        }
+        _polarCountList.addAll(polarlist);
+        
+        
+        
+        
+    }
+    
+    
+      
+    public void subtractBackground() {
+       
+//        double bkg1 = _counts_merged_norm.get(String.valueOf(this._bkgRunNr1));
+//        double bkg2 = _counts_merged_norm.get(String.valueOf(this._bkgRunNr2));
+//        for (Map.Entry<String, Double> e : _counts_merged_norm.entrySet()) {
+//            String k = e.getKey();
+//            double n = e.getValue();
+//            int k_int = Integer.parseInt(k);
+//            if(k_int == this._bkgRunNr1) continue;
+//            if(k_int == this._bkgRunNr2) continue;
+//            
+//            double ns = k_int<1360 ? (n-bkg1) : (n-bkg2);
+//                
+//            _counts_merged_norm_subtr.put(k, ns);
+//        }
+//        
+        
+        int idx_bkg1 = findCount(this._countList,String.valueOf(this._bkgRunNr1),"normalized");
+        int idx_bkg2 = findCount(this._countList,String.valueOf(this._bkgRunNr2),"normalized");
+        
+        double bkg1 = _countList.get(idx_bkg1).n();
+        double bkg2 = _countList.get(idx_bkg2).n();
+        
+        System.out.println("bkg1 " + bkg1 + " bkg2 " + bkg2);
+        
+        double ebkg1 = _countList.get(idx_bkg1).en();
+        double ebkg2 = _countList.get(idx_bkg2).en();
+        
+        List<Count> list = new ArrayList<Count>();
+        for(Count c: _countList) {
+            if(!c.name().equals("normalized")) continue;
+            String name = "bkgsubtr";
+            String run = c.run();
+            int run_int = Integer.parseInt(run);
+            if(this.isBackgroundRun(run_int)) continue;
+            double b = run_int<1360 ? bkg1 : bkg2;
+            double eb = run_int<1360 ? ebkg1 : ebkg2;
+            double n = c.n()-b;
+            double en = Math.sqrt(c.en()*c.en() + eb*eb);
+            
+            Count c_new = new Count(name,run,n,en);
+            list.add(c_new);
+        }
+        _countList.addAll(list);
+        
+        
+        
+        List<PolarCount> polarList = new ArrayList<PolarCount>();
+        for(PolarCount c: _polarCountList) {
+            if(!c.name().equals("normalized")) continue;
+            String name = "bkgsubtr";
+            String run = c.run();
+            int run_int = Integer.parseInt(run);
+            if(this.isBackgroundRun(run_int)) continue;
+            
+            idx_bkg1 = findPolarCount(this._polarCountList,String.valueOf(this._bkgRunNr1),c.val(),"normalized");
+            idx_bkg2 = findPolarCount(this._polarCountList,String.valueOf(this._bkgRunNr2),c.val(),"normalized");
+            bkg1 = _polarCountList.get(idx_bkg1).count().n();
+            bkg2 = _polarCountList.get(idx_bkg2).count().n();
+        
+            System.out.println("polar " + c.val() + " bkg1 " + bkg1 + " bkg2 " + bkg2);
+        
+            ebkg1 = _polarCountList.get(idx_bkg1).count().en();
+            ebkg2 = _polarCountList.get(idx_bkg2).count().en();
+            
+            double b = run_int<1360 ? bkg1 : bkg2;
+            double eb = run_int<1360 ? ebkg1 : ebkg2;
+            double n = c.count().n()-b;
+            double en = Math.sqrt(c.count().en()*c.count().en() + eb*eb);
+            
+            PolarCount c_new = new PolarCount(name,run,c.val(),new Count(name,run,n,en));
+            polarList.add(c_new);
+        }
+        _polarCountList.addAll(polarList);
+        
+        
+    }
+    
+    
+    
+        
+    public void scaleToRndCharge() {
+
+        System.out.println("Scaling to " + _chargeScale + " nC  from nC");
+        
+        
+//        for (Map.Entry<String, Double> e : this._counts_merged_norm_subtr.entrySet()) {
+//            String k = e.getKey();
+//            double n = e.getValue();
+//            int k_int = Integer.parseInt(k);
+//            
+//            double ns = n*_chargeScale;
+//            
+//            _counts_merged_norm_subtr_qscaled.put(k, ns);
+//        }
+        
+        List<Count> list = new ArrayList<Count>();
+        for(Count c : _countList) {
+            if(!c.name().equals("bkgsubtr")) continue;
+            String name = "q-scaled";
+            String run  = c.run();
+            double ns = c.n()*_chargeScale;
+            double ens = c.en()*_chargeScale;
+            Count c_new = new Count(name,run,ns,ens);
+            list.add(c_new);
+            
+        }
+        _countList.addAll(list);
+        
+        
+        List<PolarCount> polarList = new ArrayList<PolarCount>();
+        for(PolarCount c : _polarCountList) {
+            if(!c.name().equals("bkgsubtr")) continue;
+            String name = "q-scaled";
+            String run  = c.run();
+            double ns = c.count().n()*_chargeScale;
+            double ens = c.count().en()*_chargeScale;
+            PolarCount c_new = new PolarCount(name,run,c.val(),new Count(name,run,ns,ens));
+            polarList.add(c_new);
+            
+        }
+        _polarCountList.addAll(polarList);
+        
+        
+        
+        
+    }
+    
+    
+     public DAQDeadTimeData getDTD(String run_str) {
+        for(DAQDeadTimeData b : _deadTime) {
+            if(b.getRun()==Integer.parseInt(run_str)) return b;
+        }
+        return null;
+    }
+    
+     public void scaleDAQDeadTime() {
+
+        System.out.println("Scaling DAQ dead time");
+        
+        
+//        for (Map.Entry<String, Double> e : this._counts_merged_norm_subtr_qscaled.entrySet()) {
+//            String k = e.getKey();
+//            double n = e.getValue();
+//            DAQDeadTimeData dtd = getDTD(k);
+//            if(dtd==null) {
+//                System.out.println("Error run " + k + " is not in daq dead time map");
+//                System.exit(1);
+//            }
+//            
+//            double ns = n/dtd.getDAQLiveTimeFraction();
+//            
+//            _counts_merged_norm_subtr_qscaled_daqscaled.put(k, ns);
+//        }
+        
+        
+        List<Count> list = new ArrayList<Count>();
+        for(Count c : _countList) {
+            if(!c.name().equals("q-scaled")) continue;
+            String name = "daq-scaled";
+            String run  = c.run();
+            DAQDeadTimeData dtd = getDTD(run);
+            if(dtd==null) {
+                System.out.println("Error run " + run + " is not in daq dead time map");
+                System.exit(1);
+            }
+            double a = c.n();
+            double b = dtd.getDAQLiveTimeFraction();
+            double ea = c.en();
+            double eb = dtd.getDAQLiveTimeFractionError();
+            double ns = a/b;
+            double ens = Math.sqrt((ea/b)*(ea/b) + (eb*a/(b*b))*(eb*a/(b*b)));
+            Count c_new = new Count(name,run,ns,ens);
+            list.add(c_new);
+            
+        }
+        
+        _countList.addAll(list);
+        
+        
+         List<PolarCount> polarList = new ArrayList<PolarCount>();
+        for(PolarCount c : _polarCountList) {
+            if(!c.name().equals("q-scaled")) continue;
+            String name = "daq-scaled";
+            String run  = c.run();
+            DAQDeadTimeData dtd = getDTD(run);
+            if(dtd==null) {
+                System.out.println("Error run " + run + " is not in daq dead time map");
+                System.exit(1);
+            }
+            double a = c.count().n();
+            double b = dtd.getDAQLiveTimeFraction();
+            double ea = c.count().en();
+            double eb = dtd.getDAQLiveTimeFractionError();
+            double ns = a/b;
+            double ens = Math.sqrt((ea/b)*(ea/b) + (eb*a/(b*b))*(eb*a/(b*b)));
+            PolarCount c_new = new PolarCount(name,run,c.val(),new Count(name,run,ns,ens));
+            polarList.add(c_new);
+            
+        }
+        
+        _polarCountList.addAll(polarList);
+        
+        
+    }
+    
+    
+     public double thickness(String run) {
+         if(run.contains("_")) {
+             run = run.split("_")[0];
+         }
+         int run_int = Integer.parseInt(run);
+         if(!_thicknessMap.containsKey(run_int)) {
+             System.out.println("thickness map do not contain " + run_int);
+             System.exit(1);
+         }
+         return _thicknessMap.get(run_int);
+         
+     }
+     
+     
+    public void prettyPrintCount() {
+        System.out.println("== Raw counts ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        
+        for (Map.Entry<String, Integer> e : _counts.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10d\n", e.getKey(),thickness(e.getKey()),e.getValue());
+        }
+        
+        System.out.println("== Merged ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Map.Entry<String, Integer> e : _counts_merged.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10d\n", e.getKey(),thickness(e.getKey()),e.getValue());
+        }
+        System.out.println("== Merged and normalized ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Map.Entry<String, Double> e : _counts_merged_norm.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10.2f [/nC]\n", e.getKey(),thickness(e.getKey()),e.getValue());
+        }
+        System.out.println("== Merged, normalized and subtracted ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Map.Entry<String, Double> e : _counts_merged_norm_subtr.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10.2f [/nC]\n", e.getKey(),thickness(e.getKey()),e.getValue());
+        }
+        System.out.println("== Merged, normalized, subtracted ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Map.Entry<String, Double> e : _counts_merged_norm_subtr_qscaled.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10.2f [/%.1fnC]\n", e.getKey(),thickness(e.getKey()),e.getValue(),_chargeScale);
+        }
+        System.out.println("== Merged, normalized, subtracted and corrected for DAQ dead time ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Map.Entry<String, Double> e : _counts_merged_norm_subtr_qscaled_daqscaled.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10.2f [/%.1fnC]\n", e.getKey(),thickness(e.getKey()),e.getValue(),_chargeScale);
+        }
+
+        System.out.println("== Ratio w.r.t. 0.18% thickness ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","N[thickness]/N[0.18%]");
+        for (Map.Entry<String, Double> e : _ratio.entrySet()) {
+            System.out.printf("%10s\t%17.2f\t%10.2f\n", e.getKey(),thickness(e.getKey()),e.getValue());
+        }
+
+        
+        
+        System.out.println("\n\n== Integrated beam currents ==");
+        System.out.printf("%10s\t%8s\t%8s\t%8s\n","run","start","stop","Int. I [nC]\n");
+        for(BeamCurrentData b: _beamCurrent) {
+            System.out.printf("%s\n",b.toString());
+        }
+        
+        System.out.println("\n\n== DAQ Dead Time ==");
+        for(DAQDeadTimeData b: _deadTime) {
+            System.out.printf("%s\n",b.toString());
+        }
+        
+        
+        
+        
+        
+    }
+    
+    
+    
+    
+    public void prettyPrintCountList() {
+        System.out.println("== Raw counts ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        List<Count> list = findCount("raw");
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f\n", e.run(),thickness(e.run()),e.n(),e.en());
+        }
+        System.out.println("== Merged ==");
+        list = findCount("merged");        
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f\n", e.run(),thickness(e.run()),e.n(),e.en());
+        }
+
+        System.out.println("== Merged and normalized ==");
+        list = findCount("normalized");        
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f\n", e.run(),thickness(e.run()),e.n(),e.en());
+        }
+
+        System.out.println("== Merged, normalized and subtracted ==");
+        list = findCount("bkgsubtr");        
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f\n", e.run(),thickness(e.run()),e.n(),e.en());
+        }
+       
+        System.out.println("== Merged, normalized, subtracted, q-scaled ==");
+        list = findCount("q-scaled");        
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f [/%.1fnC]\n", e.run(),thickness(e.run()),e.n(),e.en(),_chargeScale);
+        }
+        
+        System.out.println("== Merged, normalized, subtracted and corrected for DAQ dead time ==");
+        list = findCount("daq-scaled");        
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","Counts");
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f [/%.1fnC]\n", e.run(),thickness(e.run()),e.n(),e.en(),_chargeScale);
+        }
+
+        System.out.println("== Ratio w.r.t. 0.18% thickness ==");
+        System.out.printf("%10s\t%17s\t%10s\n","run","Target thickn. [% r.l.]","N[thickness]/N[0.18%]");
+        list = findCount("ratio0.18");        
+        for (Count e : list) {
+            System.out.printf("%10s\t%17.2f\t%10.2f+-%.3f [/%.1fnC]\n", e.run(),thickness(e.run()),e.n(),e.en(),_chargeScale);
+        }
+
+        
+       
+        System.out.println("== Polar: Merged, normalized, subtracted and corrected for DAQ dead time ==");
+        List<PolarCount> polarList = findPolarCount("daq-scaled");        
+        List<String> listRun = new ArrayList<String>();
+        for(PolarCount c : polarList) {
+            if(listRun.contains(c.run())) continue;
+            listRun.add(c.run());
+        }
+        System.out.printf("%10s\t%17s\t%10s\t%10s\n","run","Target thickn. [% r.l.]","Polar \"Y\"","Counts");
+        for(String r : listRun) {
+            for (PolarCount e : polarList) {
+                if(!e.run().equals(r)) continue;
+                System.out.printf("%10s\t%17.2f\t%10.1f\t%10.2f+-%.3f [/%.1fnC]\n", e.run(),thickness(e.run()),e.val(),e.count().n(),e.count().en(),_chargeScale);
+            }
+        }
+        
+        
+        
+        
+        
+        
+        
+        System.out.println("\n\n== Integrated beam currents ==");
+        System.out.printf("%10s\t%8s\t%8s\t%8s\n","run","start","stop","Int. I [nC]\n");
+        for(BeamCurrentData b: _beamCurrent) {
+            System.out.printf("%s\n",b.toString());
+        }
+        
+        System.out.println("\n\n== DAQ Dead Time ==");
+        for(DAQDeadTimeData b: _deadTime) {
+            System.out.printf("%s\n",b.toString());
+        }
+        
+        
+        
+        
+        
+    }
+    
+    
+    
+    
+    
+    public void plotCount() {
+        plotCount("raw");
+        plotCount("merged");
+        plotCount("normalized");
+        plotCount("bkgsubtr");
+        plotCount("q-scaled");
+        plotCount("daq-scaled");
+        
+        plotPolarCount("raw");
+        plotPolarCount("merged");
+        plotPolarCount("normalized");
+        plotPolarCount("bkgsubtr");
+        plotPolarCount("q-scaled");
+        plotPolarCount("daq-scaled");
+
+/*
+        plotCount(this._counts,"Counts raw");
+        plotCount(this._counts_merged,"Counts merged");
+        plotCountD(this._counts_merged_norm,"Counts merged normalized");
+        plotCountD(this._counts_merged_norm,"Counts merged background subtracted");
+        plotCountD(this._counts_merged_norm_subtr_qscaled,"Counts merged normalized q-norm");
+        plotCountD(this._counts_merged_norm_subtr_qscaled_daqscaled,"Counts merged normalized q-norm");
+        */
+    }
+
+//    public void plotCount(Map<String,Integer> map, String name) {
+//        HashMap<String,Double> m = new HashMap<String,Double>();
+//        for(Map.Entry<String,Integer> e : map.entrySet()) {
+//            m.put(e.getKey(), e.getValue().doubleValue());
+//        }
+//        plotCountD(m,name);
+//    }
+//    
+    public void plotCount(String name) {
+
+      //IDataPointSetFactory dpsf = af.createDataPointSetFactory();
+      
+      // Create a one dimensional IDataPointSet.
+      IDataPointSet dps = af.createDataPointSetFactory(af.createTreeFactory().createTree()).create("dps1D",name,2);
+      String xtitle = "Target thickness [% rad. len.]";
+      for (Count e : _countList) {
+          if(!e.name().equals(name)) continue;
+            dps.addPoint();
+            dps.point(dps.size()-1).coordinate(0).setValue(this.thickness(e.run()));
+            dps.point(dps.size()-1).coordinate(0).setErrorPlus(0);
+            dps.point(dps.size()-1).coordinate(1).setValue(e.n());
+            dps.point(dps.size()-1).coordinate(1).setErrorPlus(e.en());
+            //xtitle += " " + e.getKey();
+            
+      }
+      IPlotter plotter_hm = af.createPlotterFactory().create();
+      plotter_hm.setTitle("Counts");
+      plotter_hm.currentRegion().plot(dps);
+        
+      ((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xtitle);
+        
+        
+        //if(fillColor=="") fillColor="yellow";
+        //plotter_hm.createRegion(10.0,20.0, 460.0,100.0);
+        //plotter_hm.createRegion(d, d1, d2, d3)
+//        plotter_hm.createRegions(1,1);//.plot(hm);
+//        plotter_hm.region(0).plot(h);
+//        plotter_hm.region(1).plot(h2);
+//        plotter_hm.region(2).plot(h);
+//        plotter_hm.region(2).plot(h2,"mode=overlay");
+        plotter_hm.style().statisticsBoxStyle().setVisible(false);
+        //plotter_hm.style().dataStyle().fillStyle().setColor(fillColor);
+        //((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xTitle);
+        //((PlotterRegion) plotter_hm.region(0)).getPlot().getYAxis().setLabel(yTitle);          
+        if(!this._hide) plotter_hm.show();
+        
+        
+        if(_saveFiles) {
+            try {
+                plotter_hm.writeToFile(name + "_" + _addOn +".png", "png");
+            } catch(IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+        
+        
+        
+    }
+    
+    public void plotPolarCount(String name) {
+
+      IPlotter plotter_hm = af.createPlotterFactory().create();
+      plotter_hm.setTitle("Polar Angle Counts");
+      
+      int nregions;
+      List<String> runs = new ArrayList<String>();
+      for (PolarCount e : _polarCountList) {
+          if(!e.name().equals(name)) continue;
+          if(runs.contains(e.run())) continue;
+          runs.add(e.run());
+      }
+      
+      System.out.println("Found " + runs.size() + " runs for " + name);
+      boolean first = true;
+      for(String run : runs) {
+        //IDataPointSetFactory dpsf = af.createDataPointSetFactory();
+      
+        // Create a one dimensional IDataPointSet.
+        IDataPointSet dps = af.createDataPointSetFactory(af.createTreeFactory().createTree()).create("dps1D",name,2);
+        String xtitle = "Polar Hit Count";//Target thickness [% rad. len.]";
+        for (PolarCount e : _polarCountList) {
+            if(!e.name().equals(name)) continue;
+            if(!e.run().equals(run)) continue;
+                dps.addPoint();
+//                dps.point(dps.size()-1).coordinate(0).setValue(this.thickness(e.run()));
+                dps.point(dps.size()-1).coordinate(0).setValue(e.val());
+                dps.point(dps.size()-1).coordinate(0).setErrorPlus(0);
+                dps.point(dps.size()-1).coordinate(1).setValue(e.count().n());
+                dps.point(dps.size()-1).coordinate(1).setErrorPlus(e.count().en());
+                //xtitle += " " + e.getKey();
+                
+        }
+      
+        if(first) plotter_hm.currentRegion().plot(dps);
+        else {
+           plotter_hm.currentRegion().plot(dps,"mode=overlay"); 
+        }
+        
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xtitle);
+      }
+        
+        //if(fillColor=="") fillColor="yellow";
+        //plotter_hm.createRegion(10.0,20.0, 460.0,100.0);
+        //plotter_hm.createRegion(d, d1, d2, d3)
+//        plotter_hm.createRegions(1,1);//.plot(hm);
+//        plotter_hm.region(0).plot(h);
+//        plotter_hm.region(1).plot(h2);
+//        plotter_hm.region(2).plot(h);
+//        plotter_hm.region(2).plot(h2,"mode=overlay");
+        plotter_hm.style().statisticsBoxStyle().setVisible(false);
+        //plotter_hm.style().dataStyle().fillStyle().setColor(fillColor);
+        //((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xTitle);
+        //((PlotterRegion) plotter_hm.region(0)).getPlot().getYAxis().setLabel(yTitle);          
+        if(!this._hide) plotter_hm.show();
+        
+        
+        if(_saveFiles) {
+            try {
+                plotter_hm.writeToFile(name + "_" + _addOn +".png", "png");
+            } catch(IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+        
+        
+        
+    }
+
+    
+      public void makeRatio(double denominator_name, String name) {
+
+           //Find the denominator
+          double den = -1;
+          double eden = 0;
+//          for (Map.Entry<String, Double> e : this._counts_merged_norm_subtr.entrySet()) {
+//              if(isBackgroundRun(Integer.parseInt(e.getKey()))) continue;
+//              double t = this.thickness(e.getKey());
+//              if(t == denominator_name) {
+//                  den = e.getValue();
+//                  break;
+//              }
+//          }
+//          
+//          System.out.println("Den " + den + " (" + denominator_name + ")");
+//          if(den<0) {
+//              System.exit(1);
+//          }
+//          
+//        
+//        for (Map.Entry<String, Double> e : this._counts_merged_norm_subtr.entrySet()) {
+//        
+//          double n =  e.getValue();
+//          double ratio = n/den;
+//          double t = this.thickness(e.getKey());
+//          _ratio.put(e.getKey(), ratio);
+//          //System.out.println(e.getKey() + " t " + t + " n " + n + " ratio " + ratio);
+//
+//            
+//        }
+//        
+        
+        
+        for(Count c : _countList) {
+            if(c.name()!="bkgsubtr") continue;
+            if(isBackgroundRun(Integer.parseInt(c.run()))) continue;
+            double t = this.thickness(c.run());
+              if(t == denominator_name) {
+                  den = c.n();
+                  eden = c.en();
+                  break;
+              }
+        }
+        List<Count> list = new ArrayList<Count>();
+        for(Count c : _countList) {
+            if(c.name()!="bkgsubtr") continue;
+            String name_new = "ratio0.18";
+            double a = c.n();
+            double ea = c.en();
+            double b = den;
+            double eb = eden;
+            double r = a/b;
+            double er = Math.sqrt((ea/b)*(ea/b) + (eb*a/(b*b))*(eb*a/(b*b)));
+            Count c_new = new Count(name_new,c.run(),r,er);
+            list.add(c_new);
+            
+            
+        }
+        _countList.addAll(list);
+        
+        
+        
+        
+      }
+    
+    
+    
+    
+     public void plotRatio(String name) {
+     
+     
+         
+          
+      // Create a one dimensional IDataPointSet.
+      IDataPointSet dps = af.createDataPointSetFactory(af.createTreeFactory().createTree()).create("dps2D",name,2);
+      String xtitle = " Converter thickness (% r.l.)";
+      //for (Map.Entry<String, Double> e : this._ratio.entrySet()) {
+      for (Count e : this._countList) {
+          if(!e.name().equals("ratio0.18")) continue;
+          dps.addPoint();
+          double t = this.thickness(e.run());
+          dps.point(dps.size()-1).coordinate(0).setValue(t);
+          dps.point(dps.size()-1).coordinate(0).setErrorPlus(0);
+          dps.point(dps.size()-1).coordinate(1).setValue(e.n());
+          dps.point(dps.size()-1).coordinate(1).setErrorPlus(e.en());
+          //xtitle += " " + e.getKey();
+          
+            
+      }
+      
+        IPlotter plotter_hm = af.createPlotterFactory().create();
+        plotter_hm.style().dataStyle().lineStyle().setVisible(false);
+        plotter_hm.setTitle("Ratio " + name);
+        plotter_hm.currentRegion().plot(dps);
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xtitle);
+        
+        
+        //if(fillColor=="") fillColor="yellow";
+        //plotter_hm.createRegion(10.0,20.0, 460.0,100.0);
+        //plotter_hm.createRegion(d, d1, d2, d3)
+//        plotter_hm.createRegions(1,1);//.plot(hm);
+//        plotter_hm.region(0).plot(h);
+//        plotter_hm.region(1).plot(h2);
+//        plotter_hm.region(2).plot(h);
+//        plotter_hm.region(2).plot(h2,"mode=overlay");
+        plotter_hm.style().statisticsBoxStyle().setVisible(false);
+        //plotter_hm.style().dataStyle().fillStyle().setColor(fillColor);
+        //((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xTitle);
+        //((PlotterRegion) plotter_hm.region(0)).getPlot().getYAxis().setLabel(yTitle);          
+        if(!this._hide) plotter_hm.show();
+        if(_saveFiles) {
+            try {
+                plotter_hm.writeToFile(name + "_" + _addOn + ".png", "png");
+            } catch(IOException e) {
+                throw new RuntimeException(e);
+            }
+        }
+        
+        
+        
+    }
+    
+    
+    public void addCount(ITree tree,String hname, String name) {

[truncated at 1000 lines; 279 more skipped]

hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N Count.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ Count.java	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,47 @@

+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.lcsim.hps.users.phansson;
+
+/**
+ *
+ * @author phansson
+ */
+public class Count {
+    
+    private String run;
+    private String name;
+    private double n;
+    private double en;
+    
+    Count(String n, String r, double N, double err) {
+        this.name = n;
+        this.run = r;
+        this.n = N;
+        this.en = err;
+    }
+    
+    public String name() {
+        return this.name;
+    }
+
+    public String run() {
+        return this.run;
+    }
+
+    public double n() {
+        return this.n;
+    }
+
+    public double en() {
+        return this.en;
+    }
+    public void addSimple(double N,double eN) {
+        //Assume these are just counts so simply add up
+        this.n = this.n + N;
+        this.en = this.en + eN;
+    }
+
+    
+}

hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N BeamCurrentData.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ BeamCurrentData.java	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,49 @@

+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.lcsim.hps.users.phansson;
+
+/**
+ *
+ * @author phansson
+ */
+public class BeamCurrentData {
+    
+    private double _int_current;
+    private int _start_time;
+    private int _stop_time;
+    private int _run_nr;
+    
+    public BeamCurrentData(int run,int start,int stop,double int_cur) {
+        _run_nr = run;
+        _start_time = start;
+        _stop_time = stop;
+        _int_current = int_cur;
+        
+    }
+    
+    public int getRun() {
+        return this._run_nr;
+    }
+    public int getStartTime() {
+        return this._start_time;
+    }
+    public int getStopTime() {
+        return this._stop_time;
+    }
+    public double getIntCurrent() {
+        return this._int_current;
+    }
+    public double getIntCurrentError() {
+        return this._int_current*0.0; //0.05;
+    }
+    
+    public String toString() {
+         String str = String.format("%10s\t%8d\t%8d\t%8.2f+-%.2f",getRun(),getStartTime(),getStopTime(),getIntCurrent(),getIntCurrentError());
+         return str;
+    }
+    
+    
+    
+}

hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N DAQDeadTimeData.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ DAQDeadTimeData.java	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,41 @@

+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.lcsim.hps.users.phansson;
+
+/**
+ *
+ * @author phansson
+ */
+public class DAQDeadTimeData {
+    
+    private double _daq_rate;
+    private double _trigger_rate;
+    private int _run_nr;
+    
+    public DAQDeadTimeData(int run,double trig, double daq) {
+        _run_nr = run;
+        _trigger_rate = trig;
+        _daq_rate = daq;
+        
+    }
+    
+    public int getRun() {
+        return this._run_nr;
+    }
+    public double getDAQLiveTimeFraction() {
+        return this._daq_rate/this._trigger_rate;
+    }
+    public double getDAQLiveTimeFractionError() {
+        return this._daq_rate/this._trigger_rate*0.0;//0.05;
+    }
+    
+    public String toString() {
+        String str = String.format("%10s\tDAQ rate %8.1f Hz\tTrigger rate%8.2f Hz -> livetime %8.2f +- %.2f",getRun(),_daq_rate,_trigger_rate,this.getDAQLiveTimeFraction(),this.getDAQLiveTimeFractionError());
+         return str;
+    }
+    
+    
+    
+}

hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N residualLimits.txt
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ residualLimits.txt	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,21 @@

+#ap.setResLimits(top/bottom layer direction: u/v/w  min  max);
+0 1 0 -0.3 0.3
+0 2 0 -0.3 0.3
+0 3 0 -0.4 0.1
+0 4 0 -0.2 0.3
+0 5 0 -0.1 0.4
+0 6 0 -0.3 0.1
+0 7 0 -0.4 0.45
+0 8 0 -0.5 0.3
+0 9 0 -1 1
+0 10 0 -1 1
+1 1 0 -0.2 0.2
+1 2 0 -0.2 0.2
+1 3 0 -0.2 0.2
+1 4 0 -0.3 0.3
+1 5 0 -0.2 0.4
+1 6 0 -0.5 0.
+1 7 0 -0.7 0.15
+1 8 0 -0.1 0.7
+1 9 0 -1 0.7
+1 10 0 -0.5 1

hps-java/src/main/java/org/lcsim/hps/users/phansson

diff -N ECalHitMapPlots.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ ECalHitMapPlots.java	22 Jun 2012 22:57:31 -0000	1.1
@@ -0,0 +1,288 @@

+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package org.lcsim.hps.users.phansson;
+
+import hep.aida.*;
+import hep.aida.IHistogram2D;
+import hep.aida.IPlotter;
+import hep.aida.ITree;
+import hep.aida.ref.plotter.PlotterRegion;
+import java.io.IOException;
+import org.lcsim.util.aida.AIDA;
+
+/**
+ *
+ * @author phansson
+ */
+public class ECalHitMapPlots {
+    
+    private AIDA aida = AIDA.defaultInstance();
+    private IAnalysisFactory af = aida.analysisFactory();
+    IHistogramFactory hf = aida.histogramFactory();
+//    ITree tree = aida.tree();//(ITreeFactory) af.createTreeFactory().create();
+
+    private boolean hide = false;
+    
+    
+    public ECalHitMapPlots() {
+        
+    }
+    
+    public ECalHitMapPlots(boolean h) {
+        this.hide = h;
+        //System.out.println("Constructor ECalHitMapPlots");
+        
+    }
+    
+    public void hidePlots(boolean h) {
+        this.hide = h;
+    }
+    
+    public void default2DStyle(IPlotterStyle s) {
+        s.statisticsBoxStyle().setVisible(false);
+        s.setParameter("hist2DStyle","colorMap");
+        s.dataStyle().fillStyle().setParameter("colorMapScheme","rainbow");
+        
+    }
+
+    public void plotBasic2DMap(IHistogram2D h, String title, String xTitle, String yTitle,boolean writeToFile) {
+        plotBasic2D(h, title, xTitle, yTitle, 1500, 300,writeToFile);
+        
+    }
+    public void plotBasic2D(IHistogram2D h, String title, String xTitle, String yTitle, int width, int height,boolean writeToFile) {
+        IPlotter plotter_hm = af.createPlotterFactory().create();
+        plotter_hm.setTitle(title);
+        h.setTitle(title);
+        plotter_hm.setParameter("plotterWidth","1500");
+        plotter_hm.setParameter("plotterHeight","300");
+        
+        //plotter_hm.createRegion(10.0,20.0, 460.0,100.0);
+        //plotter_hm.createRegion(d, d1, d2, d3)
+        //plotter_hm.createRegions(1,1);//.plot(hm);
+        plotter_hm.region(0).plot(h);
+        //default2DStyle(plotter_hm.region(0).style());
+        plotter_hm.style().statisticsBoxStyle().setVisible(false);
+        plotter_hm.style().setParameter("hist2DStyle","colorMap");
+        plotter_hm.style().dataStyle().fillStyle().setParameter("colorMapScheme","rainbow");
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xTitle);
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getYAxis().setLabel(yTitle);          
+        if (!hide) plotter_hm.show();
+        if(writeToFile) {
+        try {
+            plotter_hm.writeToFile(title+".png", "png");
+        } catch(IOException e) {
+            throw new RuntimeException(e);
+        }
+        }
+    }
+    
+     public void plotBasic1D(IHistogram1D h, String title, String xTitle, String yTitle, String fillColor,boolean writeToFile) {
+        IPlotter plotter_hm = af.createPlotterFactory().create();
+        plotter_hm.setTitle(title);
+        if(fillColor=="") fillColor="yellow";
+        //plotter_hm.createRegion(10.0,20.0, 460.0,100.0);
+        //plotter_hm.createRegion(d, d1, d2, d3)
+        plotter_hm.createRegions(1,1);//.plot(hm);
+        plotter_hm.region(0).plot(h);
+        plotter_hm.style().statisticsBoxStyle().setVisible(true);
+        plotter_hm.style().dataStyle().fillStyle().setColor(fillColor);
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xTitle);
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getYAxis().setLabel(yTitle);          
+        if(!hide) plotter_hm.show();
+        if(writeToFile) {
+        try {
+            plotter_hm.writeToFile(title+".png", "png");
+        } catch(IOException e) {
+            throw new RuntimeException(e);
+        }
+        }
+        
+    }
+
+     
+     
+    public void plotBasic1D(IHistogram1D h, IHistogram1D h2, String title, String xTitle, String yTitle, String fillColor,boolean writeToFile) {
+        IPlotter plotter_hm = af.createPlotterFactory().create();
+        plotter_hm.setTitle(title);
+        //if(fillColor=="") fillColor="yellow";
+        //plotter_hm.createRegion(10.0,20.0, 460.0,100.0);
+        //plotter_hm.createRegion(d, d1, d2, d3)
+        plotter_hm.createRegions(1,3);//.plot(hm);
+        plotter_hm.region(0).plot(h);
+        plotter_hm.region(1).plot(h2);
+        plotter_hm.region(2).plot(h);
+        plotter_hm.region(2).plot(h2,"mode=overlay");
+        plotter_hm.style().statisticsBoxStyle().setVisible(true);
+        //plotter_hm.style().dataStyle().fillStyle().setColor(fillColor);
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getXAxis().setLabel(xTitle);
+        ((PlotterRegion) plotter_hm.region(0)).getPlot().getYAxis().setLabel(yTitle);          
+        if(!hide) plotter_hm.show();
+        if(writeToFile) {
+        try {
+            plotter_hm.writeToFile(title+".png", "png");
+        } catch(IOException e) {
+            throw new RuntimeException(e);
+        }
+        }
+        
+    }
+
+
+    
+    
+    public void plotMultScatAna(ITree tree) {
+
+        boolean save =true;
+        
+        IHistogram2D hm = (IHistogram2D)tree.find("Cluster hit map all");        
+        plotBasic2DMap(hm,"Cluster Hit Map", "Horizontal Crystal Index","Vertical Crystal Index",save);
+        
+        IHistogram1D hAmp = (IHistogram1D)tree.find("Cluster size all");
+        plotBasic1D(hAmp,"Cluster Size", "Cluster Size","Arbitrary Units","green",save);
+
+        IHistogram1D hAmp2 = (IHistogram1D)tree.find("Cluster energy all");
+        plotBasic1D(hAmp2,"Cluster Energy", "Cluster Energy","Arbitrary Units","green",save);
+
+        IHistogram1D hAmp3 = (IHistogram1D)tree.find("toptrig_cl_ecal_e_bottom");
+        plotBasic1D(hAmp3,"Cluster Energy Bottom Unbiased", "Cluster Energy","Arbitrary Units","green",save);
+
+        IHistogram2D hcrhm = (IHistogram2D)tree.find("Crystal hit map all");        
+        plotBasic2DMap(hcrhm,"Crystal Hit Map", "Horizontal Crystal Index","Vertical Crystal Index",save);
+
+        IHistogram1D hEP_t = (IHistogram1D)tree.find("allcl_clEoverP_top");
+        plotBasic1D(hEP_t,"E over P Top", "E over P","Arbitrary Units","green",save);
+
+        IHistogram1D hdx_t = (IHistogram1D)tree.find("allcl_cltrkdx_all");
+        plotBasic1D(hdx_t,"Track Matching", "Cluster X - Track X [mm]","Arbitrary Units","blue",save);
+
+        IHistogram1D hdy_t = (IHistogram1D)tree.find("allcl_cltrkdy_all");
+        plotBasic1D(hdy_t,"Track Matching", "Cluster Y - Track Y [mm]","Arbitrary Units","green",save);
+
+        
+        
+
+
+    
+        
+    }
+    
+    
+    
+    public void plotEcalFilter(ITree tree) {
+
+        boolean save = true;
+       
+        IHistogram2D hAmpMap = (IHistogram2D)tree.find("HPS-TestRun-v2 : EcalCalHits : Mean (Amplitude)");        
+        plotBasic2DMap(hAmpMap,"Average Crystal Amplitude", "Horizontal Crystal Index","Vertical Crystal Index",save);
+
+        
+        IHistogram1D hAmp = (IHistogram1D)tree.find("HPS-TestRun-v2 : EcalCalHits : <Mean> (Amplitude) Filter");        
+        plotBasic1D(hAmp,"Average Crystal Amplitude", "Average Crystal Amplitude","Arbitrary Units","",save);
+
+        IHistogram1D hAmp2 = (IHistogram1D)tree.find("/HPS-TestRun-v2 : EcalCalHits : <Mean> (Amplitude) Bottom Trig Filter");
+        plotBasic1D(hAmp2,"Average Crystal Amplitude unbiased", "Average Crystal Amplitude","Arbitrary Units","",save);
+
+        
+        IHistogram1D hAmpSingle = (IHistogram1D)tree.find("ECAL Amplitudes: x=21; y=-1");        
+        plotBasic1D(hAmpSingle,"Single Crystal Amplitude (21,-1)", "Single Crystal Amplitude","Arbitrary Units","",save);
+        
+        IHistogram1D hAmpSingle2 = (IHistogram1D)tree.find("Top ECAL Amplitudes: x=21; y=-1");        
+        plotBasic1D(hAmpSingle2,"Single Crystal Amplitude unbiased (21,-1)", "Single Crystal Amplitude","Arbitrary Units","",save);
+        
+        
+    }
+
+   
+    
+    public void overLayUpStrBkg(ITree tree_empty, ITree tree) {
+        
+        boolean save = true;
+        
+        IHistogram1D hYp_t = (IHistogram1D)tree.find("Top track q>0 Y @ -67cm");        
+        IHistogram1D hYn_t = (IHistogram1D)tree.find("Top track q<0 Y @ -67cm");                
+        IHistogram1D heYp_t = (IHistogram1D)tree_empty.find("Top track q>0 Y @ -67cm");
+        IHistogram1D heYn_t = (IHistogram1D)tree_empty.find("Top track q<0 Y @ -67cm");        
+
+        IHistogram1D hYp_b = (IHistogram1D)tree.find("Bottom track q>0 Y @ -67cm");        
+        IHistogram1D hYn_b = (IHistogram1D)tree.find("Bottom track q<0 Y @ -67cm");                
+        IHistogram1D heYp_b = (IHistogram1D)tree_empty.find("Bottom track q>0 Y @ -67cm");        
+        IHistogram1D heYn_b = (IHistogram1D)tree_empty.find("Bottom track q<0 Y @ -67cm");        
+
+        
+        double r_t = 1933.479;
+        double r_b = 1933.479;
+        double re_t = 309.785;
+        double re_b = 309.785;
+        
+        double c_t = re_t/r_t;
+        double c_b = re_b/r_b;
+
+        //plotBasic1D(hYp_t,"Top track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue");
+        //plotBasic1D(heYp_t,"Top track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","red");
+        //plotBasic1D(hYp_t,heYp_t,"Top track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue");
+        //plotBasic1D(hYn_t,heYn_t,"Top track q<0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue");
+
+        //plotBasic1D(hYp_b,heYp_b,"Bottom track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue");
+        //plotBasic1D(hYn_b,heYn_b,"Bottom track q<0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue");
+
+        
+        heYp_t.scale(hYp_t.entries()/heYp_t.entries()*c_t);
+        heYn_t.scale(hYn_t.entries()/heYn_t.entries()*c_t);
+
+        heYp_b.scale(hYp_b.entries()/heYp_b.entries()*c_b);
+        heYn_b.scale(hYn_b.entries()/heYn_b.entries()*c_b);
+
+        plotBasic1D(hYp_t,heYp_t,"(norm) Top track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+        plotBasic1D(hYn_t,heYn_t,"(norm) Top track q<0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+
+        plotBasic1D(hYp_b,heYp_b,"(norm) Bottom track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+        plotBasic1D(hYn_b,heYn_b,"(norm) Bottom track q<0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+
+        
+        IHistogram1D hsYn_t = hf.subtract("(subtr) Top track q<0 Y @ -67cm", hYn_t, heYn_t);
+        IHistogram1D hsYp_t = hf.subtract("(subtr) Top track q>0 Y @ -67cm", hYp_t, heYp_t);
+
+        IHistogram1D hsYn_b = hf.subtract("(subtr) Bottom track q<0 Y @ -67cm", hYn_b, heYn_b);
+        IHistogram1D hsYp_b = hf.subtract("(subtr) Bottom track q>0 Y @ -67cm", hYp_b, heYp_b);
+
+        plotBasic1D(hsYp_t,"(subtr) Top track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+        plotBasic1D(hsYn_t,"(subtr) Top track q<0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+        plotBasic1D(hsYp_b,"(subtr) Bottom track q>0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+        plotBasic1D(hsYn_b,"(subtr) Bottom track q<0 Y @ -67cm", "Track Y @ -67cm [mm]","Arbitrary Units","blue",save);
+        
+        
+        
+        
+    }
+    
+    
+
+/*    
+    public void plotAveAmpMap(ITree tree) {
+
+        System.out.println("plotAveAmp with tree " + tree.name());
+
+        IHistogram2D hm = (IHistogram2D)tree.find("Cluster hit map all");
+        
+        
+        IPlotter plotter_hm = af.createPlotterFactory().create();
+        plotter_hm.setTitle("Cluster Hit Map");
+        plotter_hm.createRegion().plot(hm);
+        plotter_hm.show();
+        default2DStyle(plotter_hm.region(0).style());
+        plotter_hm.style().statisticsBoxStyle().setVisible(false);
+        plotter_hm.style().setParameter("hist2DStyle","colorMap");
+        plotter_hm.style().dataStyle().fillStyle().setParameter("colorMapScheme","rainbow");
+              //((PlotterRegion) plotter_trig_other.region(i)).getPlot().setAllowPopupMenus(true);
+        
+        
+        
+        
+    }
+
+    */
+    
+    
+}