diff -N SeedTrackerDiagnostics.java
--- SeedTrackerDiagnostics.java	10 Dec 2008 22:03:06 -0000	1.1.1.1
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,249 +0,0 @@

-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
-
-package org.lcsim.contrib.Partridge.TrackingTest;
-
-import hep.physics.vec.Hep3Vector;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import org.lcsim.recon.tracking.seedtracker.ConfirmerExtender.Task;
-import org.lcsim.recon.tracking.seedtracker.diagnostic.EmptySeedTrackerDiagnostics;
-import org.lcsim.recon.tracking.seedtracker.diagnostic.FindableTracks;
-import org.lcsim.recon.tracking.seedtracker.diagnostic.ISeedTrackerDiagnostics;
-import org.lcsim.recon.tracking.seedtracker.diagnostic.SeedValidator;
-import org.lcsim.event.MCParticle;
-import org.lcsim.fit.helicaltrack.HelicalTrackHit;
-import org.lcsim.math.chisq.ChisqProb;
-import org.lcsim.recon.tracking.seedtracker.HelixFitter;
-import org.lcsim.recon.tracking.seedtracker.SeedCandidate;
-import org.lcsim.recon.tracking.seedtracker.SeedStrategy;
-import org.lcsim.util.aida.AIDA;
-
-/**
- *
- * @author cozzy
- */
-public class SeedTrackerDiagnostics extends EmptySeedTrackerDiagnostics implements ISeedTrackerDiagnostics{
-
-    AIDA aida = AIDA.defaultInstance();
-     
-    private double purity_cutoff = 0.0; 
-    private String prefix = ""; 
-    private boolean debugOut = true; 
-    
-    public SeedTrackerDiagnostics(){
-
-    }
-    
-    /**
-     * Generates diagnostic plots given a list of seed candidates and a strategy.
-     * @param seedlist
-     * @param strategy
-     */
-    @Override
-    public void fireFinalDiagnostics(List<SeedCandidate> seedlist){
-        
-        System.out.println(" After merging: "+seedlist.size());
-        Map<SeedCandidate,SeedValidator> vmap = generateValidators(seedlist);
-        makePurityPlots(vmap);        
-        Set<MCParticle> likelyMCs = generateLikelyMCSet(vmap);
-        makeEfficiencyPlots(likelyMCs,currentStrategy);
-    }
-    
-   /**
-    * Sets the purity cutoff for a track's MC to be considered found when 
-    * calculating efficiency. Default is 0.0. 
-    * @param new_purity_cutoff
-    */
-    public void setPurityCutoff(double new_purity_cutoff){
-        purity_cutoff = new_purity_cutoff; 
-    }
-    
-    /**
-     * Sets the prefix to be appended to the beginning of each plot (for example, a strategy name
-     * @param str the new prefix
-     */
-    public void setPrefix(String str){
-        this.prefix = str; 
-    }
-    
-    
-    @Override
-    public void fireStrategyChanged(SeedStrategy strategy) {
-        setPrefix("chisq cut = "+strategy.getMaxChisq()+"/");
-        super.fireStrategyChanged(strategy);
-    }
-
-
-    @Override
-    public void fireMergeIsBetterDiagnostics(SeedCandidate newSeed, SeedCandidate oldSeed, boolean returnValue) {
-        if (returnValue){
-            
-            SeedValidator oldV = new SeedValidator(oldSeed);
-            SeedValidator newV = new SeedValidator(newSeed);
-
-                if (oldV.getPurity() > newV.getPurity()){
-                     makeBadDecisionPlots(newSeed,oldSeed, oldV,newV);
-                }
-        }
-    }
-
-    @Override
-    public void fireFinderDone(int maxseeds, int nseed, int nfit, int nconfirm, List<SeedCandidate> confirmedSeeds) {
-//        System.out.println("Possible seeds: "+maxseeds);
-//        System.out.print(" Trial seeds: "+nseed);
-//        System.out.println(" Fitted seeds: "+nfit);
-//        System.out.println(" Confirmed seeds: "+nconfirm);
-//        System.out.println(" Confirmed seed candidates: "+confirmedSeeds.size());
-    }
-    
-    @Override
-    public void fireConfirmerExtenderWorkingSeedInfo(Task task, SeedCandidate seed, List<HelicalTrackHit> hitlist) {
-        if (debugOut) {
-            System.out.println("Oldcirclechisq: "+seed.getHelix().chisq()[0]);
-            System.out.println("Oldchisq: "+seed.getHelix().chisqtot());
-            System.out.println("Oldhits: "+seed.getHits().size());
-            System.out.println("Old Helix: "+seed.getHelix().toString()); 
-        }
-        return;
-    }
-
-    @Override
-    public void fireConfirmerExtenderFitNoSuccess(Task task, SeedCandidate Seed, HelicalTrackHit hit, HelixFitter fitter,  boolean optimize) {
-        if (debugOut) System.out.println("Circlechissq" + fitter.getCircleFit().chisq());
-    }
-
-    @Override
-   public void fireConfirmerExtenderFitSuccess(Task task, SeedCandidate Seed, HelicalTrackHit hit, HelixFitter fitter, double chisqbest, boolean optimize) {
-        if (debugOut) {
-            System.out.println("Good fit");
-            System.out.println("Chisq: "+fitter.getHelix().chisqtot());
-            System.out.println("Circle Chisq: "+fitter.getHelix().chisq()[0]);
-            System.out.println("New Helix: "+fitter.getHelix().toString());
-        }
-    }
-
-    @Override
-    public void fireConfirmerExtenderLayerDone(Task task, int numSeeds, List<SeedCandidate> seedlist) {
-        if (debugOut){
-            System.out.println(" "+task.toString()+" seeds: "+numSeeds);
-            System.out.println(" "+task.toString()+" seed candidates: "+seedlist.size());
-        }
-    }
-    
-        private void makeBadDecisionPlots(SeedCandidate newseed, SeedCandidate seed, SeedValidator oldV, SeedValidator newV) {
-
-        aida.cloud1D(prefix+"Bad Decision newseed chisq").fill(newseed.getHelix().chisqtot());
-        aida.cloud1D(prefix+"Bad Decision oldseed chisq").fill(seed.getHelix().chisqtot());
-        aida.cloud2D(prefix+"Bad Decision newseed vs. oldseed chisq").fill(newseed.getHelix().chisqtot(), seed.getHelix().chisqtot());
-        aida.cloud1D(prefix+"Bad Decision old seedpurity").fill(oldV.getPurity());
-        aida.cloud1D(prefix+"Bad Decision new seedpurity").fill(newV.getPurity());
-        
-        
-        if(oldV.getVerdict().isGoodValue()){
-            Hep3Vector p = oldV.getLikelyMC().getMomentum();
-            double pt = Math.sqrt(p.x() * p.x() + p.y() * p.y());
-            aida.cloud1D(prefix+"Bad Decision real particle transverse momentum").fill(pt);
-        
-            Hep3Vector r = oldV.getLikelyMC().getOrigin();
-            double rc = Math.sqrt(r.x()*r.x()+r.y()*r.y()); 
-            aida.cloud1D(prefix + "Bad Decision real particle start radius (cylindrical)").fill(rc);
-        }
-        
-    }
-
- 
-    //makes purity plots
-    private void makePurityPlots(Map<SeedCandidate, SeedValidator> vmap) {
-        
-        for (SeedCandidate s : vmap.keySet()) {
-
-            SeedValidator v = vmap.get(s);
-   
-            if (v.getVerdict().isGoodValue()) {
-                aida.cloud1D(prefix+"Good seeds chisq").fill(s.getHelix().chisqtot());
-                aida.cloud1D(prefix+"Good seeds numhits").fill(s.getHits().size());
-                aida.cloud1D(prefix+"Good seeds pt").fill(s.getHelix().pT(5.0));
-            } else {
-                aida.cloud1D(prefix+"Bad seeds chisq").fill(s.getHelix().chisqtot());
-                aida.cloud1D(prefix+"Bad seeds numhits").fill(s.getHits().size());
-                aida.cloud1D(prefix+"Bad seeds pt").fill(s.getHelix().pT(5.0));
-            }
-            
-            aida.cloud1D(prefix+"purity").fill(v.getPurity());
-            aida.cloud2D(prefix+"purity vs. numHits").fill(v.getPurity(), s.getHits().size());
-            aida.cloud2D(prefix+"purity vs. pt").fill(v.getPurity(), s.getHelix().pT(5.0));
-            aida.cloud2D(prefix+"purity vs. cth").fill(v.getPurity(), s.getHelix().cth());
-            aida.cloud2D(prefix+"purity vs. chisq").fill(v.getPurity(), s.getHelix().chisqtot());
-            
-            double chisqdof = ChisqProb.gammq(s.getHelix().chisqtot(), s.getHits().size()-1); 
-            
-            aida.cloud2D(prefix+"purity vs. (1 - chisq_cdf(chisq,ndof)").fill(v.getPurity(), chisqdof);
-            aida.cloud2D(prefix+"purity cs. dca").fill(v.getPurity(), s.getHelix().dca());
-        }
-    }
-    
-    private void makeEfficiencyPlots(Set<MCParticle> likelyMCs, SeedStrategy strat){
-        
-        FindableTracks findable = new FindableTracks(strat, hitManager);
-        findable.setBField(bField);
-        
-        List<MCParticle> MCs = new ArrayList<MCParticle>(); 
-        MCs.addAll(event.getMCParticles());
-        
-        Iterator iter = MCs.iterator();
-
-            //remove all none findable MCs
-            while(iter.hasNext()){
-                if(!findable.isFindable((MCParticle)iter.next()))
-                    iter.remove();
-            }
-
-            int numFindable = MCs.size(); 
-            aida.cloud1D(prefix+"Number findable").fill(numFindable);
-
-            
-            // remove all the MC's we've found... this gives us findable - found
-            MCs.removeAll(likelyMCs);
-
-            int numFound = numFindable - MCs.size(); // findable - (findable - found) = found 
-            
-            aida.cloud1D(prefix+"Num found (purity cutoff="+purity_cutoff+") ").fill(numFound);
-            
-            if(numFindable > 0){
-                double eff = (double) numFound / (double) numFindable;
-                aida.cloud1D(prefix+"Efficiency").fill(eff);
-            }
-        
-    }
-    
-    
-    private Map<SeedCandidate,SeedValidator> generateValidators(List<SeedCandidate> seedlist) {
-        
-        Map<SeedCandidate,SeedValidator> ret = new HashMap<SeedCandidate,SeedValidator>(); 
-        for (SeedCandidate s : seedlist) {
-            ret.put(s, new SeedValidator(s));
-        }
-        
-        return ret;
-    }
-    
-    private Set<MCParticle> generateLikelyMCSet(Map<SeedCandidate, SeedValidator> vmap) {
-        
-        Set<MCParticle> set = new HashSet<MCParticle>(); 
-        
-        for (SeedValidator v : vmap.values()) {
-            if(v.getPurity()<purity_cutoff) continue; 
-            set.add(v.getLikelyMC());
-        }
-        return set; 
-    }   
-}
-    

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