--- java/trunk/users/src/main/java/org/hps/users/holly/EcalClusterIC.java	2014-04-17 16:17:49 UTC (rev 499)
+++ java/trunk/users/src/main/java/org/hps/users/holly/EcalClusterIC.java	2014-04-17 16:37:27 UTC (rev 500)
@@ -1,393 +0,0 @@

-package org.hps.users.holly;
-
-import java.io.FileWriter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.hps.recon.ecal.HPSEcalCluster;
-import org.lcsim.event.CalorimeterHit;
-import org.lcsim.event.EventHeader;
-import org.lcsim.geometry.Detector;
-import org.lcsim.geometry.subdetector.HPSEcal3;
-import org.lcsim.geometry.subdetector.HPSEcal3.NeighborMap;
-import org.lcsim.lcio.LCIOConstants;
-import org.lcsim.util.Driver;
-
-/**
- * This Driver creates clusters from the CalorimeterHits of an
- * {@link org.lcsim.geometry.subdetectur.HPSEcal3} detector.
- *
- *
- * @author Holly Szumila-Vance <[log in to unmask]>
- *
- */
-public class EcalClusterIC extends Driver {
-	FileWriter writeHits;
-    HPSEcal3 ecal;
-    String ecalCollectionName;
-    String ecalName = "Ecal";
-    String clusterCollectionName = "EcalClusters";
-    // Map of crystals to their neighbors.
-    NeighborMap neighborMap = null;
-    //Minimum energy that counts as hit (GeV)
-    double Emin = 0.0075;
-    
-
-    public EcalClusterIC() {
-    }
-
-    public void setClusterCollectionName(String clusterCollectionName) {
-        this.clusterCollectionName = clusterCollectionName;
-    }
-
-    public void setEcalCollectionName(String ecalCollectionName) {
-        this.ecalCollectionName = ecalCollectionName;
-    }
-
-    public void setEcalName(String ecalName) {
-        this.ecalName = ecalName;
-    }
-
-    public void startOfData() {
-        if (ecalCollectionName == null) {
-            throw new RuntimeException("The parameter ecalCollectionName was not set!");
-        }
-
-        if (ecalName == null) {
-            throw new RuntimeException("The parameter ecalName was not set!");
-        }
-        
-    	try{
-    		writeHits = new FileWriter("cluster-hit-IC.txt");
-    		writeHits.write("");
-    	}
-    	catch(IOException e) {};
-    }
-
-    public void detectorChanged(Detector detector) {
-        // Get the Subdetector.
-        ecal = (HPSEcal3) detector.getSubdetector(ecalName);
-
-        // Cache ref to neighbor map.
-        neighborMap = ecal.getNeighborMap();
-    }
-
-    public void process(EventHeader event) {
-	
-        if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
-            // Get the list of raw ECal hits.
-            List<CalorimeterHit> hits = event.get(CalorimeterHit.class, ecalCollectionName);
-
-            // Make a hit map for quick lookup by ID.
-            Map<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
-            
-            for (CalorimeterHit hit : hits) {
-                hitMap.put(hit.getCellID(), hit);
-            }
-            
-            System.out.println("Number of ECal hits: "+hitMap.size());
-            
-            // Put Cluster collection into event.
-            int flag = 1 << LCIOConstants.CLBIT_HITS;
-            try {
-
-            	event.put(clusterCollectionName, createClusters(hitMap), HPSEcalCluster.class, flag);
-            }
-            catch(IOException e) { }
-        }
-    }
-
-    public List<HPSEcalCluster> createClusters(Map<Long, CalorimeterHit> map) throws IOException {
-
-        // New Cluster list to be added to event.
-        List<HPSEcalCluster> clusters = new ArrayList<HPSEcalCluster>();
-             
-        //Create a Calorimeter hit list in each event, then sort with highest energy first
-        ArrayList<CalorimeterHit> chitList = new ArrayList<CalorimeterHit>(map.size());
-        for(CalorimeterHit h : map.values()) {
-        	if(h.getCorrectedEnergy()>Emin){
-        	chitList.add(h);}
-        
-        	Collections.sort(chitList, new EnergyComparator());}
-        
-        //New Seed list containing each local maximum energy hit
-        List<CalorimeterHit> seedHits = new ArrayList<CalorimeterHit>();
-
-      	//Create map to contain common hits for evaluation later, key is crystal and values are seed
-      	Map<CalorimeterHit, List<CalorimeterHit>> commonHits = new HashMap<CalorimeterHit, List<CalorimeterHit>>();
-      	
-      	//Created map to contain seeds with listed hits, key is crystal, and value is seed
-      	Map<CalorimeterHit, CalorimeterHit> clusterHits = new HashMap<CalorimeterHit, CalorimeterHit>();
-      	
-      	//Create map to contain the total energy of each cluster
-      	Map<CalorimeterHit, Double> seedEnergy = new HashMap<CalorimeterHit,Double>();
-      	
-      	//Quick Map to access hits from cell IDs
-      	Map<Long, CalorimeterHit> hitID = new HashMap<Long, CalorimeterHit>();
-      	
-      	//List to contain all hits already put into clusters
-      	List<CalorimeterHit> clusterHitList = new ArrayList<CalorimeterHit>();
-      	
-      	//List to contain hits immediately around a seed
-//      	List<CalorimeterHit> surrSeedList = new ArrayList<CalorimeterHit>();
-      	
-        //Fill Map with cell ID and hit
-      	for (CalorimeterHit hit : chitList){
-      		hitID.put(hit.getCellID(), hit);
-      	}
-        
-        for (CalorimeterHit hit : chitList) { 
-        Set<Long> neighbors = neighborMap.get(hit.getCellID()); //get all neighbors of hit
-        List<CalorimeterHit> neighborHits = new ArrayList<CalorimeterHit>();
-        for(Long neighbor : neighbors){
-        	if(hitID.containsKey(neighbor)){//map contains (neighbor's cell id, neighbor hit)
-        		neighborHits.add(hitID.get(neighbor));
-        	}
-        }
-        
-    	Collections.sort(neighborHits, new EnergyComparator());
-        
-        boolean highestE = true;
-        for(CalorimeterHit neighborHit : neighborHits){//check for seed hit
-        	if(hit.getCorrectedEnergy()>neighborHit.getCorrectedEnergy()){
-        		continue;
-        			}
-        	else {
-        		highestE = false;
-        		break;
-        	}	
-        }
-        
-        if (highestE == true){//seed hit, local maximum
-        	seedHits.add(hit);
-        	clusterHits.put(hit, hit);
-        	clusterHitList.add(hit);
-        }
-        
-        //not seed hit
-        else { 
-        	//builds immediate clusters around seed hits
-        	for(CalorimeterHit neighborHit : neighborHits){
-        		//if neighbor to seed, add to seed
-        		if (seedHits.contains(neighborHit)&&!clusterHits.containsKey(hit)){  
-					CalorimeterHit seed = clusterHits.get(neighborHit);
-        			clusterHits.put(hit, seed);
-        			clusterHitList.add(hit);
-//        			surrSeedList.add(hit);
-        		}
-        		//if neighbor to two seeds, add to common hits
-        		else if (seedHits.contains(neighborHit)&&clusterHits.containsKey(hit)){
-        			CalorimeterHit prevSeed = clusterHits.get(neighborHit);
-        			CalorimeterHit currSeed = clusterHits.get(hit);
-        			List<CalorimeterHit> commonHitList = new ArrayList<CalorimeterHit>();
-        			commonHitList.add(prevSeed);
-        			commonHitList.add(currSeed);
-        			commonHits.put(hit, commonHitList);
-        		}
-        	}
-        }
-        }
-        
-        //loop over hit list, find neighbors, compare energies, add to list 
-        for(CalorimeterHit nHit : chitList){
-        	Set<Long> neighbors2 = neighborMap.get(nHit.getCellID()); //get all neighbors of hit
-            List<CalorimeterHit> neighborHits2 = new ArrayList<CalorimeterHit>();
-            for(Long neighbor : neighbors2){
-            	if(hitID.containsKey(neighbor)){//map contains (neighbor's cell id, neighbor hit)
-            		if(!clusterHitList.contains(hitID.get(neighbor))){
-            			neighborHits2.add(hitID.get(neighbor));
-            		}
-            	}
-            }
-            
-        	Collections.sort(neighborHits2, new EnergyComparator());
-        	for(CalorimeterHit neighbor : neighborHits2){
-        		if(neighbor.getCorrectedEnergy()<nHit.getCorrectedEnergy()){
-        			CalorimeterHit seed = clusterHits.get(nHit);
-					clusterHits.put(neighbor, seed);
-					clusterHitList.add(neighbor);
-        		}
-        		else{continue;}
-        	}
-        }
-        //loop over cluster hits, compare energies of neighbors with diff seeds, if min->add to commonHits
-        for (CalorimeterHit mHit : clusterHitList){
-        	//exclude seed hits as possible common hits
-        	if(clusterHits.get(mHit) != mHit){//changed this line
-//        	if((clusterHits.get(mHit)!=mHit)&&!surrSeedList.contains(mHit)){
-        		
-        		Set<Long> neighbors3 = neighborMap.get(mHit.getCellID()); //get all neighbors of hit
-                List<CalorimeterHit> neighborHits3 = new ArrayList<CalorimeterHit>();
-                for(Long neighbor : neighbors3){
-                	if(hitID.containsKey(neighbor)){//map contains (neighbor's cell id, neighbor hit)
-                		neighborHits3.add(hitID.get(neighbor));
-                		
-                	}
-                }
-                
-            	Collections.sort(neighborHits3, new EnergyComparator());
-            	
-            	CalorimeterHit compSeed = clusterHits.get(mHit);
-            	for(CalorimeterHit neighbor : neighborHits3){
-            		if(clusterHits.get(neighbor)!=compSeed){//borders clusters
-            			if(mHit.getCorrectedEnergy() < neighbor.getCorrectedEnergy()){
-            				//add to common hits, 
-            				List<CalorimeterHit> commonHitList = new ArrayList<CalorimeterHit>();
-                			commonHitList.add(compSeed);
-                			commonHitList.add(clusterHits.get(neighbor));
-                			commonHits.put(mHit, commonHitList);
-            			}	
-            		}
-            	}	
-        	}
-        }
-        
-        //remove common hits from cluster hits list
-        for(CalorimeterHit commHit : clusterHitList){
-        	if(clusterHitList.contains(commHit)&&commonHits.containsKey(commHit)){
-        		clusterHits.remove(commHit);
-        	}
-        	else{
-        		continue;
-        	}
-        }
-        
-
-        		       	
-        //Get energy of each cluster, excluding common hits
-        for(CalorimeterHit iSeed : seedHits){
-        seedEnergy.put(iSeed, 0.0);
-        }
-        //Putting total cluster energies excluding common hit energies into map with seed keys    
-        for (Map.Entry<CalorimeterHit, CalorimeterHit> entry : clusterHits.entrySet()) {
-        	CalorimeterHit eSeed = entry.getValue();
-        	double eEnergy = seedEnergy.get(eSeed);
-        	eEnergy += entry.getKey().getCorrectedEnergy();
-        	seedEnergy.put(eSeed, eEnergy);
-        }
-        
-        //Distribute common hit energies with clusters
-        Map<CalorimeterHit, Double> seedEnergyTot = seedEnergy;
-        for (Map.Entry<CalorimeterHit, List<CalorimeterHit>> entry1 : commonHits.entrySet()) {
-        	CalorimeterHit commonCell = entry1.getKey();
-        	List<CalorimeterHit> commSeedList = entry1.getValue();
-        	CalorimeterHit seedA = commSeedList.get(0);
-        	CalorimeterHit seedB = commSeedList.get(1);
-        	double eFractionA = Math.abs(Math.log10(seedEnergy.get(seedA)))/Math.abs(Math.log10((seedEnergy.get(seedA)))+Math.abs(Math.log10(seedEnergy.get(seedB))));
-        	double eFractionB = Math.abs(Math.log10(seedEnergy.get(seedB)))/Math.abs(Math.log10((seedEnergy.get(seedA)))+Math.abs(Math.log10(seedEnergy.get(seedB))));
-//        	double eFractionA = seedEnergy.get(seedA)/(seedEnergy.get(seedA)+seedEnergy.get(seedB));
-//        	double eFractionB = seedEnergy.get(seedB)/(seedEnergy.get(seedA)+seedEnergy.get(seedB));
-        	double currEnergyA = seedEnergyTot.get(seedA);
-        	double currEnergyB = seedEnergyTot.get(seedB);
-        	currEnergyA += eFractionA*commonCell.getCorrectedEnergy();
-        	currEnergyB += eFractionB*commonCell.getCorrectedEnergy();
-        	
-        	seedEnergyTot.put(seedA, currEnergyA);
-        	seedEnergyTot.put(seedB, currEnergyB);
-        }
-        
-        //Stictly for histograms:
-//        double runSum = 0.0;
-//        for (Map.Entry<CalorimeterHit, Double> entryEnergy : seedEnergyTot.entrySet()){
-//    	  runSum = entryEnergy.getValue();	
-//        	runSum ++;
-//    	  writeHits.append("\n"+runSum);
-
-//      }
-
-
-                   
-       
-        //Do some system.out for number of crystals in each cluster, energy of each cluster
-//        for (Map.Entry<CalorimeterHit, Double> entryEnergy : seedEnergyTot.entrySet()){
-//        	System.out.println(entryEnergy.getKey().getCellID()+"\t"+entryEnergy.getKey().getCorrectedEnergy()+
-//        			"\t"+entryEnergy.getValue());
-//        }
-        
-        System.out.println("Number of clusters: "+seedHits.size());    
-
-        
-      	if (map.size()!=0){
-//          	writeHits.append("Event"+"\t"+"1"+"\n");
-          	for (CalorimeterHit n : chitList){
-//          		writeHits.append("EcalHit" + "\t" + n.getIdentifierFieldValue("ix") + "\t" + n.getIdentifierFieldValue("iy")
-//          		+ "\t" +n.getCorrectedEnergy() + "\n");
-          	}
-          	
-      		for (Map.Entry<CalorimeterHit, CalorimeterHit> entry2 : clusterHits.entrySet()){
-      			if (entry2.getKey()==entry2.getValue()){//seed
-//      				writeHits.append("Cluster" + "\t" + entry2.getKey().getIdentifierFieldValue("ix")+
-//        				"\t"+entry2.getKey().getIdentifierFieldValue("iy")+"\t"+seedEnergyTot.get(entry2.getKey())+"\n");
-      				
-//      				HPSEcalCluster cluster = new HPSEcalCluster(entry2.getKey());
- //                   cluster.addHit(entry2.getKey());
-//      				int runSum = 0;
-      				
-                    for (Map.Entry<CalorimeterHit, CalorimeterHit> entry3 : clusterHits.entrySet()){
-      					if (entry3.getValue() == entry2.getValue()){
-//      						writeHits.append("CompHit" + "\t" + entry3.getKey().getIdentifierFieldValue("ix")+ "\t"
-//      			        	+entry3.getKey().getIdentifierFieldValue("iy") + "\n");
-//      						cluster.addHit(entry3.getKey());
-//      						runSum ++;
-      					}
-      				}
-      				for (Map.Entry<CalorimeterHit, List<CalorimeterHit>> entry4 : commonHits.entrySet()){
-      					if (entry4.getValue().contains(entry2.getKey())){      						
-//      						writeHits.append("SharHit" + "\t" + entry4.getKey().getIdentifierFieldValue("ix")+ "\t"
-//      						+entry4.getKey().getIdentifierFieldValue("iy") + "\n");
-//      						cluster.addHit(entry4.getKey());
-//      						runSum ++;
-      						
-      					}
-      				}
-//                	  writeHits.append("\n"+runSum);
-
-      				
- //     				clusters.add(cluster);
-      			}
-
-      		}
-//      		writeHits.append("EndEvent\n");
-      		
-      	}
-      	
-      	 //Clear all maps for next event iteration
-        hitID.clear();
-        clusterHits.clear();
-        seedHits.clear();
-        commonHits.clear();
-        chitList.clear();
-        seedEnergy.clear();
- 
-        return clusters;
-      	
-      	
-      	
-
-      }
-    
-    public void endOfData() {
-    	try{
-    	writeHits.close();
-    	}
-    	catch (IOException e){ }
-    }
-
-    private class EnergyComparator implements Comparator<CalorimeterHit>{
-
-		@Override
-		public int compare(CalorimeterHit o1, CalorimeterHit o2) {
-			// TODO Auto-generated method stub
-			double diff = o1.getCorrectedEnergy()-o2.getCorrectedEnergy();
-			if(diff < 0) { return 1; }
-			if(diff > 0) { return -1; } 
-			else { return 0; }
-		}		
-    }   
-}