diff -u -r1.12 -r1.13
--- MuonFinder.java	20 Oct 2008 19:02:40 -0000	1.12
+++ MuonFinder.java	21 Oct 2008 22:44:34 -0000	1.13
@@ -44,7 +44,7 @@

     EventHeader m_event;
 
     protected HelixExtrapolator m_findCluster = new org.lcsim.recon.pfa.identifier.LocalHelixExtrapolator();

-    protected boolean useMuonhits = true;

+    protected boolean useMuonHitsForDebug = false;

 
     public MuonFinder(String tracklist, String inCal, String inMu, String outMap, String outMapTrackToClusters){
         _inCal = inCal;

@@ -71,7 +71,7 @@

         Set<CalorimeterHit> mudethits = new HashSet<CalorimeterHit>(); 
 
 

-        if(useMuonhits){

+        if(useMuonHitsForDebug){

             List<CalorimeterHit> allHitsEcalBarrel = event.get(CalorimeterHit.class, "EcalBarrDigiHits");
             List<CalorimeterHit> allHitsEcalEndcap = event.get(CalorimeterHit.class, "EcalEndcapDigiHits");
             List<CalorimeterHit> allHitsHcalBarrel = event.get(CalorimeterHit.class, "HcalBarrDigiHits");

@@ -263,6 +263,10 @@

                     //This helps remove pion which is showering in CAL and also take the MIP which is contaminated by
                     //other shower so it stopped in the middle of CAL.
                     if(!(muon || (isolated > 6) )) continue;

+		    if (!muon) { 
+			// Skip these cases to avoid pion contamination.
+			continue; 
+		    }

                     Hep3Vector link = VecOp.sub(muonpos0, lastpoint);
                     Hep3Vector linkUnit = VecOp.unit(link);
                     double cos0 = VecOp.dot(lastUnit, MuonUnit);