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HPS-SVN  October 2015

HPS-SVN October 2015

Subject:

r3804 - /java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/

From:

[log in to unmask]

Reply-To:

Notification of commits to the hps svn repository <[log in to unmask]>

Date:

Thu, 8 Oct 2015 02:47:35 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (1111 lines)

Author: [log in to unmask]
Date: Wed Oct  7 19:47:33 2015
New Revision: 3804

Log:
Convert DQM print outs to use logger.

Modified:
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseDriver.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SVTHitMCEfficiency.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackMCEfficiency.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java
    java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseDriver.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseDriver.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseDriver.java	Wed Oct  7 19:47:33 2015
@@ -1,8 +1,8 @@
 package org.hps.analysis.dataquality;
 
-import java.sql.ResultSet;
 import java.sql.SQLException;
-import org.lcsim.conditions.ConditionsReader;
+import java.util.logging.Logger;
+
 import org.lcsim.geometry.Detector;
 import org.lcsim.util.Driver;
 
@@ -14,6 +14,8 @@
  * cribbed heavily from {@link org.hps.conditions.ConditionsDriver}
  */
 public class DQMDatabaseDriver extends Driver {
+    
+    private static Logger LOGGER = Logger.getLogger(DQMDatabaseDriver.class.getPackage().getName());
 
     // Static instance of the manager.
     static DQMDatabaseManager manager;
@@ -27,7 +29,7 @@
      * connection parameters and configuration.
      */
     public DQMDatabaseDriver() throws SQLException {
-        System.out.println("DQMDatabaseDriver.ctor");
+        LOGGER.info("DQMDatabaseDriver.ctor");
         manager = new DQMDatabaseManager();
         manager.setConnectionResource(_defaultConnectionResource);
         manager.setup();
@@ -35,7 +37,7 @@
 //       ResultSet result=manager.selectQuery("SELECT * from dqm where run=1111;");
         //      result.next();
         //      float  occ = result.getFloat(3);
-        //      System.out.println(occ);
+        //      LOGGER.info(occ);
     }
 
     /**

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DQMDatabaseManager.java	Wed Oct  7 19:47:33 2015
@@ -25,7 +25,7 @@
 
 @SuppressWarnings("rawtypes")
 public class DQMDatabaseManager {
-
+    
     int runNumber = -1;
     String detectorName;
     List<TableMetaData> tableMetaData;
@@ -45,7 +45,7 @@
      * Class constructor, which is only package accessible.
      */
     DQMDatabaseManager() {
-        System.out.println("Making the instance of DQMDatabaseManager");
+        LOGGER.info("Making the instance of DQMDatabaseManager");
 
     }
 

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java	Wed Oct  7 19:47:33 2015
@@ -23,6 +23,8 @@
  * calculateEndOfRunQuantities & printDQMData i.e. useful methods
  */
 public class DataQualityMonitor extends Driver {
+    
+    private static Logger LOGGER = Logger.getLogger(DataQualityMonitor.class.getPackage().getName());
 
     protected AIDA aida = AIDA.defaultInstance();
     protected DQMDatabaseManager manager;
@@ -89,16 +91,16 @@
         printDQMData();
         if (printDQMStrings)
             printDQMStrings();
-        System.out.println("Should I write to the database?  " + connectToDB);
+        LOGGER.info("Should I write to the database?  " + connectToDB);
         if (connectToDB) {
-            System.out.println("Connecting To Database...getting DQMDBManager");
+            LOGGER.info("Connecting To Database...getting DQMDBManager");
             manager = DQMDatabaseManager.getInstance();
             //check to see if I need to make a new db entry
             boolean entryExists = false;
             try {
                 entryExists = checkRowExists();
                 if (entryExists)
-                    System.out.println("Found an existing run/reco entry in the dqm database; overwrite = " + overwriteDB);
+                    LOGGER.info("Found an existing run/reco entry in the dqm database; overwrite = " + overwriteDB);
             } catch (SQLException ex) {
                 Logger.getLogger(DataQualityMonitor.class.getName()).log(Level.SEVERE, null, ex);
             }
@@ -111,15 +113,15 @@
     }
 
     private void makeNewRow() {
-        System.out.println("is the data base connected?  " + manager.isConnected);
+        LOGGER.info("is the data base connected?  " + manager.isConnected);
         if (manager.isConnected) {
             String ins = "insert into dqm SET runNumber=" + runNumber;
-//            System.out.println(ins);
+//            LOGGER.info(ins);
             manager.updateQuery(ins);
             ins = "update  dqm SET recoVersion='" + recoVersion + "' where runNumber=" + runNumber;
             manager.updateQuery(ins);
         }
-        System.out.println("Made a new row for runNumber=" + runNumber + "; recoVersion=" + recoVersion);
+        LOGGER.info("Made a new row for runNumber=" + runNumber + "; recoVersion=" + recoVersion);
     }
 
     private boolean checkRowExists() throws SQLException {
@@ -137,7 +139,7 @@
         double result = res.getDouble(var);
         if (res.wasNull())
             return true;
-        System.out.println("checkSelectionIsNULL::" + var + " = " + result);
+        LOGGER.info("checkSelectionIsNULL::" + var + " = " + result);
         return false;
     }
 
@@ -166,11 +168,11 @@
                 Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
             }
             if (!overwriteDB && !isnull) {
-                System.out.println("Not writing because " + name + " is already filled for this entry");
+                LOGGER.info("Not writing because " + name + " is already filled for this entry");
                 continue; //entry exists and I don't want to overwrite                
             }
             String put = "update dqm SET " + name + " = " + val + " WHERE " + getRunRecoString();
-            System.out.println(put);
+            LOGGER.info(put);
             manager.updateQuery(put);
 
         }
@@ -206,7 +208,7 @@
                         match = false;
                 }
         } else if (debug)
-            System.out.println(this.getClass().getSimpleName() + ":  No trigger bank found...running over all trigger types");
+            LOGGER.info(this.getClass().getSimpleName() + ":  No trigger bank found...running over all trigger types");
         return match;
     }
 

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/EcalMonitoring.java	Wed Oct  7 19:47:33 2015
@@ -2,8 +2,11 @@
 
 import hep.aida.IHistogram1D;
 import hep.aida.IHistogram2D;
+
 import java.util.List;
 import java.util.Map;
+import java.util.logging.Logger;
+
 import org.apache.commons.math.stat.StatUtils;
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.lcsim.event.CalorimeterHit;
@@ -21,6 +24,8 @@
  * mostly copied from online monitoring
  */
 public class EcalMonitoring extends DataQualityMonitor {
+    
+    private static Logger LOGGER = Logger.getLogger(EcalMonitoring.class.getPackage().getName());
 
     String readoutHitCollectionName = "EcalReadoutHits";//these are in ADC counts
     String calibratedHitCollectionName = "EcalCalHits";//these are in energy
@@ -91,7 +96,7 @@
 
     @Override
     protected void detectorChanged(Detector detector) {
-        System.out.println("EcalMonitoring::detectorChanged  Setting up the plotter");
+        LOGGER.info("EcalMonitoring::detectorChanged  Setting up the plotter");
         aida.tree().cd("/");
         if (fillHitPlots) {
             // Setup hit plots.
@@ -230,15 +235,15 @@
 
     @Override
     public void dumpDQMData() {
-        System.out.println("EcalMonitoring::endOfData filling DQM database");
+        LOGGER.info("EcalMonitoring::endOfData filling DQM database");
     }
 
     @Override
     public void printDQMData() {
-        System.out.println("EcalMonitoring::printDQMData");
+        LOGGER.info("EcalMonitoring::printDQMData");
         for (Map.Entry<String, Double> entry : monitoredQuantityMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
-        System.out.println("*******************************");
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        LOGGER.info("*******************************");
     }
 
     /**

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/FinalStateMonitoring.java	Wed Oct  7 19:47:33 2015
@@ -10,11 +10,13 @@
 import hep.aida.IPlotterStyle;
 import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
+
 import java.io.IOException;
 import java.util.List;
 import java.util.Map.Entry;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
@@ -40,6 +42,8 @@
  *
  */
 public class FinalStateMonitoring extends DataQualityMonitor {
+    
+    private static Logger LOGGER = Logger.getLogger(FinalStateMonitoring.class.getPackage().getName());
 
     String finalStateParticlesColName = "FinalStateParticles";
 
@@ -99,7 +103,7 @@
 
     @Override
     protected void detectorChanged(Detector detector) {
-        System.out.println("FinalStateMonitoring::detectorChanged  Setting up the plotter");
+        LOGGER.info("Setting up the plotter");
         aida.tree().cd("/");
           String trkType="SeedTrack/";
         if(isGBL)
@@ -147,7 +151,7 @@
 
         if (!event.hasCollection(ReconstructedParticle.class, finalStateParticlesColName)) {
             if (debug) {
-                System.out.println(finalStateParticlesColName + " collection not found???");
+                LOGGER.info(finalStateParticlesColName + " collection not found???");
             }
             return;
         }
@@ -165,11 +169,11 @@
         int nUnAssTracks = 0; //number of tracks w/o clusters
         List<ReconstructedParticle> finalStateParticles = event.get(ReconstructedParticle.class, finalStateParticlesColName);
         if (debug) {
-            System.out.println("This events has " + finalStateParticles.size() + " final state particles");
+            LOGGER.info("This events has " + finalStateParticles.size() + " final state particles");
         }
         for (ReconstructedParticle fsPart : finalStateParticles) {
             if (debug) {
-                System.out.println("PDGID = " + fsPart.getParticleIDUsed() + "; charge = " + fsPart.getCharge() + "; pz = " + fsPart.getMomentum().x());
+                LOGGER.info("PDGID = " + fsPart.getParticleIDUsed() + "; charge = " + fsPart.getCharge() + "; pz = " + fsPart.getMomentum().x());
             }
           if (isGBL != TrackType.isGBL(fsPart.getType()))
                 continue;
@@ -269,7 +273,7 @@
                 trackTvsECalT.fill(ClusterUtilities.getSeedHitTime(fsCluster), TrackUtils.getTrackTime(fsTrack, hitToStrips, hitToRotated));
                 timeMatchDeltaT.fill(ClusterUtilities.getSeedHitTime(fsCluster) - TrackUtils.getTrackTime(fsTrack, hitToStrips, hitToRotated));
                 //          if(dy<-20)
-                //              System.out.println("Big deltaY...")
+                //              LOGGER.info("Big deltaY...")
 
             }
             if (!hasCluster) {//if there is no cluster, can't be a track or else it wouldn't be in list
@@ -283,11 +287,11 @@
 
     @Override
     public void printDQMData() {
-        System.out.println("FinalStateMonitoring::printDQMData");
+        LOGGER.info("FinalStateMonitoring::printDQMData");
         for (Entry<String, Double> entry : monitoredQuantityMap.entrySet()) {
-            System.out.println(entry.getKey() + " = " + entry.getValue());
-        }
-        System.out.println("*******************************");
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
+        LOGGER.info("*******************************");
     }
 
     /**
@@ -302,7 +306,7 @@
         if (result != null) {
             double[] pars = result.fittedParameters();
             for (int i = 0; i < 5; i++) {
-                System.out.println("Beam Energy Peak:  " + result.fittedParameterNames()[i] + " = " + pars[i]);
+                LOGGER.info("Beam Energy Peak:  " + result.fittedParameterNames()[i] + " = " + pars[i]);
             }
             monitoredQuantityMap.put(finalStateParticlesColName + " " + triggerType + " " + fpQuantNames[7], (double) pars[1]);
             monitoredQuantityMap.put(finalStateParticlesColName + " " + triggerType + " " + fpQuantNames[8], (double) pars[2]);
@@ -336,7 +340,7 @@
     public void printDQMStrings() {
         for (int i = 0; i < 9; i++)//TODO:  do this in a smarter way...loop over the map
         {
-            System.out.println("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
         }
     }
 
@@ -350,7 +354,7 @@
         try {
             ifr = fitter.fit(h1d, "g+p1", init);
         } catch (RuntimeException ex) {
-            System.out.println(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
+            LOGGER.info(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
         }
 
         return ifr;

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/PlotAndFitUtilities.java	Wed Oct  7 19:47:33 2015
@@ -16,8 +16,10 @@
 import hep.aida.IProfile2D;
 import hep.aida.ref.plotter.style.registry.IStyleStore;
 import hep.aida.ref.plotter.style.registry.StyleRegistry;
+
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.lcsim.util.aida.AIDA;
 
 /**
@@ -26,6 +28,8 @@
  */
 public class PlotAndFitUtilities {
 
+    private static Logger LOGGER = Logger.getLogger(PlotAndFitUtilities.class.getPackage().getName());
+    
     static private AIDA aida = AIDA.defaultInstance();
 
     /*
@@ -50,7 +54,7 @@
     static void plot(IPlotter plotter, IBaseHistogram histogram, IPlotterStyle style, int region) {
         if (style == null)
             style = getPlotterStyle(histogram);
-        System.out.println("Putting plot in region " + region);
+        LOGGER.info("Putting plot in region " + region);
         plotter.region(region).plot(histogram, style);
 
     }
@@ -62,7 +66,7 @@
     static void plot(IPlotter plotter, IFunction function, IPlotterStyle style, int region) {
         if (style == null)
             style = getPlotterStyle(function);
-        System.out.println("Putting function in region " + region);
+        LOGGER.info("Putting function in region " + region);
         plotter.region(region).plot(function, style);
     }
 
@@ -125,7 +129,7 @@
         try {
             fitResult = fitter.fit(histogram, function);
         } catch (RuntimeException e) {
-            System.out.println(e.getMessage());
+            LOGGER.info(e.getMessage());
         }
         return fitResult;
     }

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SVTHitMCEfficiency.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SVTHitMCEfficiency.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SVTHitMCEfficiency.java	Wed Oct  7 19:47:33 2015
@@ -4,10 +4,13 @@
 import hep.aida.IHistogram2D;
 import hep.aida.IProfile1D;
 import hep.aida.IProfile2D;
+
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.logging.Logger;
+
 import org.hps.recon.tracking.FittedRawTrackerHit;
 import org.hps.recon.tracking.ShapeFitParameters;
 import org.lcsim.detector.tracker.silicon.SiSensor;
@@ -32,6 +35,8 @@
 // TODO: Add some quantities for DQM monitoring:  e.g. <efficiency>, probably within first 1 cm or so.   
 public class SVTHitMCEfficiency extends DataQualityMonitor {
 
+    private static Logger LOGGER = Logger.getLogger(SVTHitMCEfficiency.class.getPackage().getName());
+    
     private final String rawTrackerHitCollectionName = "SVTRawTrackerHits";
     private String helicalTrackHitCollectionName = "HelicalTrackHits";
     private final String rotatedTrackHitCollectionName = "RotatedHelicalTrackHits";
@@ -207,7 +212,7 @@
                             getLayerPlot2D(plotDir + "goodClusterFits", simhit.getLayer()).fill(ShapeFitParameters.getT0(fit), ShapeFitParameters.getAmp(fit));
                         }
                     } else {
-//                        System.out.println(clust.getRawHits().size());
+//                        LOGGER.info(clust.getRawHits().size());
                         for (RawTrackerHit rth : (List<RawTrackerHit>) clust.getRawHits()) {
                             GenericObject fit = (GenericObject) rthtofit.to(rth);
                             getLayerPlot2D(plotDir + "badClusterFits", simhit.getLayer()).fill(ShapeFitParameters.getT0(fit), ShapeFitParameters.getAmp(fit));
@@ -316,14 +321,14 @@
     @Override
     public void printDQMData() {
         for (SiSensor sensor : sensors) {
-            System.out.println(avgClusterEffNames.get(sensor.getName()) + ":  " + avgClusterEffMap.get(sensor.getName()));
+            LOGGER.info(avgClusterEffNames.get(sensor.getName()) + ":  " + avgClusterEffMap.get(sensor.getName()));
         }
     }
 
     @Override
     public void printDQMStrings() {
         for (SiSensor sensor : sensors) {
-            System.out.println("ALTER TABLE dqm ADD " + avgClusterEffNames.get(sensor.getName()) + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + avgClusterEffNames.get(sensor.getName()) + " double;");
         }
     }
 

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java	Wed Oct  7 19:47:33 2015
@@ -8,6 +8,7 @@
 import hep.aida.IHistogram2D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterStyle;
+
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.HashMap;
@@ -15,6 +16,7 @@
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.hps.recon.tracking.FittedRawTrackerHit;
 import org.hps.recon.tracking.ShapeFitParameters;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
@@ -36,6 +38,8 @@
  */
 //TODO:  add some more quantities to DQM database:  <t0> or <sigma>_t0 for intime events;  <chi^2>, <amplitude> etc
 public class SvtMonitoring extends DataQualityMonitor {
+    
+    private static Logger LOGGER = Logger.getLogger(SvtMonitoring.class.getPackage().getName());
 
     private String rawTrackerHitCollectionName = "SVTRawTrackerHits";
     private String fittedTrackerHitCollectionName = "SVTFittedRawTrackerHits";
@@ -72,7 +76,7 @@
 
     @Override
     protected void detectorChanged(Detector detector) {
-        System.out.println("SvtMonitoring::detectorChanged  Setting up the plotter");
+        LOGGER.info("Setting up the plotter");
         this.detector = detector;
         aida.tree().cd("/");
 
@@ -120,7 +124,7 @@
         Map<String, Integer> hitsPerSensor = new HashMap<String, Integer>();
 
         if (event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {
-//            System.out.println("Found a raw hit collection");
+//            LOGGER.info("Found a raw hit collection");
             List<RawTrackerHit> rawTrackerHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
             for (RawTrackerHit hit : rawTrackerHits) {
                 int[] strips = occupancyMap.get(hit.getDetectorElement().getName());
@@ -179,13 +183,13 @@
         }
 
         if (event.hasItem(trackerHitCollectionName)) {
-//            System.out.println("Found a Si cluster collection");
+//            LOGGER.info("Found a Si cluster collection");
             List<TrackerHit> siClusters = (List<TrackerHit>) event.get(trackerHitCollectionName);
             for (TrackerHit cluster : siClusters) {
                 String sensorName = getNiceSensorName((HpsSiSensor) ((RawTrackerHit) cluster.getRawHits().get(0)).getDetectorElement());
                 double t0 = cluster.getTime();
                 double dedx = cluster.getdEdx() * 1e6;
-//                System.out.println("dedx = "+dedx);
+//                LOGGER.info("dedx = "+dedx);
                 getSensorPlot(plotDir + triggerType + "/"+"t0Cluster_", sensorName).fill(t0);
                 getSensorPlot2D(plotDir + triggerType + "/"+"t0ClusterTrigTime_", sensorName).fill(t0, event.getTimeStamp() % 24);
                 getSensorPlot(plotDir + triggerType + "/"+"electrons_", sensorName).fill(dedx);
@@ -271,7 +275,7 @@
     @Override
     public void fillEndOfRunPlots() {
         // Plot strip occupancies.
-        System.out.println("SvtMonitoring::endOfData  filling occupancy plots");
+        LOGGER.info("SvtMonitoring::endOfData  filling occupancy plots");
         for (HpsSiSensor sensor : sensors) {
             Double avg = 0.0;
             //IHistogram1D sensorHist = aida.histogram1D(sensor.getName());
@@ -358,18 +362,18 @@
     @Override
     public void printDQMData() {
         for (HpsSiSensor sensor : sensors) {
-            System.out.println(avgOccupancyNames.get(sensor.getName()) + "  " +triggerType+" " + avgOccupancyMap.get(sensor.getName()));
-            System.out.println(avgt0Names.get(sensor.getName()) + "  " +triggerType+" " + avgt0Map.get(sensor.getName()));
-            System.out.println(sigt0Names.get(sensor.getName()) + "  " +triggerType+" " + sigt0Map.get(sensor.getName()));
+            LOGGER.info(avgOccupancyNames.get(sensor.getName()) + "  " +triggerType+" " + avgOccupancyMap.get(sensor.getName()));
+            LOGGER.info(avgt0Names.get(sensor.getName()) + "  " +triggerType+" " + avgt0Map.get(sensor.getName()));
+            LOGGER.info(sigt0Names.get(sensor.getName()) + "  " +triggerType+" " + sigt0Map.get(sensor.getName()));
         }
     }
 
     @Override
     public void printDQMStrings() {
         for (HpsSiSensor sensor : sensors) {
-            System.out.println("ALTER TABLE dqm ADD " + avgOccupancyNames.get(sensor.getName()) + " double;");
-            System.out.println("ALTER TABLE dqm ADD " + avgt0Names.get(sensor.getName()) + " double;");
-            System.out.println("ALTER TABLE dqm ADD " + sigt0Names.get(sensor.getName()) + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + avgOccupancyNames.get(sensor.getName()) + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + avgt0Names.get(sensor.getName()) + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + sigt0Names.get(sensor.getName()) + " double;");
         }
     }
 
@@ -388,11 +392,11 @@
             Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
         }
         if (!overwriteDB && !isnull) {
-            System.out.println("Not writing because " + name + " is already filled for this entry");
+            LOGGER.info("Not writing because " + name + " is already filled for this entry");
             return; //entry exists and I don't want to overwrite                
         }
         String put = "update dqm SET " + name + " = " + val + " WHERE " + getRunRecoString();
-        System.out.println(put);
+        LOGGER.info(put);
         manager.updateQuery(put);
     }
 }

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackMCEfficiency.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackMCEfficiency.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackMCEfficiency.java	Wed Oct  7 19:47:33 2015
@@ -5,10 +5,13 @@
 import hep.aida.IProfile1D;
 import hep.physics.vec.BasicHep3Vector;
 import hep.physics.vec.Hep3Vector;
+
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.logging.Logger;
+
 import org.hps.analysis.examples.TrackAnalysis;
 import org.hps.recon.tracking.FindableTrack;
 import org.hps.recon.tracking.FittedRawTrackerHit;
@@ -37,6 +40,8 @@
 // TODO:  Add some quantities for DQM monitoring:  e.g. <efficiency>, <eff>_findable
 public class TrackMCEfficiency extends DataQualityMonitor {
 
+    private static Logger LOGGER = Logger.getLogger(TrackMCEfficiency.class.getPackage().getName());
+    
     private String rawTrackerHitCollectionName = "SVTRawTrackerHits";
     private String trackHitCollectionName = "RotatedHelicalTrackHits";
     private String fittedSVTHitCollectionName = "SVTFittedRawTrackerHits";
@@ -118,33 +123,33 @@
         //make sure the required collections exist
         if (!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {
             if (debug)
-                System.out.println(this.getClass().getSimpleName() + ": no collection found " + rawTrackerHitCollectionName);
+                LOGGER.info(this.getClass().getSimpleName() + ": no collection found " + rawTrackerHitCollectionName);
             return;
         }
         if (!event.hasCollection(LCRelation.class, fittedSVTHitCollectionName))
             if (debug)
-                System.out.println(this.getClass().getSimpleName() + ": no collection found " + fittedSVTHitCollectionName); //mg...2/1/2015...don't return if the fitted collection isn't there...
+                LOGGER.info(this.getClass().getSimpleName() + ": no collection found " + fittedSVTHitCollectionName); //mg...2/1/2015...don't return if the fitted collection isn't there...
         //allow us to run if we simulated in "simple" mode (i.e. no time evolution)
         //            return;
         if (!event.hasCollection(Track.class, trackCollectionName)) {
             if (debug)
-                System.out.println(this.getClass().getSimpleName() + ": no collection found " + trackCollectionName);
+                LOGGER.info(this.getClass().getSimpleName() + ": no collection found " + trackCollectionName);
             return;
         }
         if (!event.hasCollection(LCRelation.class, trackHitMCRelationsCollectionName)) {
             if (debug)
-                System.out.println(this.getClass().getSimpleName() + ": no collection found " + trackHitMCRelationsCollectionName);
+                LOGGER.info(this.getClass().getSimpleName() + ": no collection found " + trackHitMCRelationsCollectionName);
             return;
         }
         if (!event.hasCollection(TrackerHit.class, siClusterCollectionName)) {
             if (debug)
-                System.out.println(this.getClass().getSimpleName() + ": no collection found " + siClusterCollectionName);
+                LOGGER.info(this.getClass().getSimpleName() + ": no collection found " + siClusterCollectionName);
             return;
         }
 
         if (!event.hasCollection(SimTrackerHit.class, trackerHitCollectionName)) {
             if (debug)
-                System.out.println(this.getClass().getSimpleName() + ": no collection found " + trackerHitCollectionName);
+                LOGGER.info(this.getClass().getSimpleName() + ": no collection found " + trackerHitCollectionName);
             return;
         }
         //
@@ -156,12 +161,12 @@
         RelationalTable hittomc = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
         List<LCRelation> mcrelations = event.get(LCRelation.class, trackHitMCRelationsCollectionName);
         if (debugTrackEfficiency)
-            System.out.println(this.getClass().getSimpleName() + ": number of MC relations = " + mcrelations.size());
+            LOGGER.info(this.getClass().getSimpleName() + ": number of MC relations = " + mcrelations.size());
         for (LCRelation relation : mcrelations)
             if (relation != null && relation.getFrom() != null && relation.getTo() != null)
                 hittomc.add(relation.getFrom(), relation.getTo());
         if (debugTrackEfficiency)
-            System.out.println(this.getClass().getSimpleName() + ": number of hittomc relations = " + hittomc.size());
+            LOGGER.info(this.getClass().getSimpleName() + ": number of hittomc relations = " + hittomc.size());
         RelationalTable mcHittomcP = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
         //  Get the collections of SimTrackerHits
         List<List<SimTrackerHit>> simcols = event.get(SimTrackerHit.class);
@@ -220,14 +225,14 @@
 
         List<Track> tracks = event.get(Track.class, trackCollectionName);
         if (debugTrackEfficiency)
-            System.out.println(this.getClass().getSimpleName() + ": nTracks = " + tracks.size());
+            LOGGER.info(this.getClass().getSimpleName() + ": nTracks = " + tracks.size());
         for (Track trk : tracks) {
             TrackAnalysis tkanal = new TrackAnalysis(trk, hittomc, rawtomc, hittostrip, hittorotated);
             tkanalMap.put(trk, tkanal);
             MCParticle mcp = tkanal.getMCParticleNew();
             if (mcp != null) {//  Create a map between the tracks found and the assigned MC particle            
                 if (debugTrackEfficiency)
-                    System.out.println(this.getClass().getSimpleName() + ": found MCP match");
+                    LOGGER.info(this.getClass().getSimpleName() + ": found MCP match");
                 trktomc.add(trk, tkanal.getMCParticleNew());
             }
         }
@@ -250,11 +255,11 @@
             double phi = Math.atan2(px, pz);
             //  Find the number of layers hit by this mc particle
             if (debugTrackEfficiency)
-                System.out.println("MC pt=" + pt);
+                LOGGER.info("MC pt=" + pt);
             int nhits = findable.LayersHit(mcp);
             boolean isFindable = findable.InnerTrackerIsFindable(mcp, nlayers - 2);
             if (debugTrackEfficiency)
-                System.out.println("nhits Findable =" + nhits + "; is findable? " + isFindable);
+                LOGGER.info("nhits Findable =" + nhits + "; is findable? " + isFindable);
             //  Calculate the helix parameters for this MC particle
             HelixParamCalculator helix = new HelixParamCalculator(mcp, bfield);
             double d0 = helix.getDCA();
@@ -299,7 +304,7 @@
                     wgt = 1.;
                 foundTracks += wgt;
                 if (debugTrackEfficiency)
-                    System.out.println("...is findable; filling plots with weight " + wgt);
+                    LOGGER.info("...is findable; filling plots with weight " + wgt);
                 peffFindable.fill(p, wgt);
                 phieffFindable.fill(phi, wgt);
                 ctheffFindable.fill(cth, wgt);
@@ -310,17 +315,17 @@
                     if (debugTrackEfficiency)
                         if (fittomc != null) {
                             Set<FittedRawTrackerHit> fitlist = fittomc.allTo(mcp);
-                            System.out.println(this.getClass().getSimpleName() + ":  Missed a findable track with MC p = " + p);
+                            LOGGER.info(this.getClass().getSimpleName() + ":  Missed a findable track with MC p = " + p);
                             if (!hasHTHInEachLayer(hitlist, fitlist))
-                                System.out.println("\t\tThis track failed becasue it's missing a helical track hit");
+                                LOGGER.info("\t\tThis track failed becasue it's missing a helical track hit");
                         }
                 }
 
             }
             if (debugTrackEfficiency){
-                System.out.println("# of mc parents " + mcp.getParents().size());
+                LOGGER.info("# of mc parents " + mcp.getParents().size());
                 if(mcp.getParents().size() > 0 )
-                    System.out.println("PDG ID of parent 0 is " + mcp.getParents().get(0).getPDGID());
+                    LOGGER.info("PDG ID of parent 0 is " + mcp.getParents().get(0).getPDGID());
             }
             if (mcp.getParents().size() == 1 && mcp.getParents().get(0).getPDGID() == 622) {
                 totelectrons++;
@@ -329,7 +334,7 @@
                 if (ntrk > 0)
                     wgt = 1.;
                 if (debugTrackEfficiency)
-                    System.out.println("...is from A'; filling plots with weight " + wgt);
+                    LOGGER.info("...is from A'; filling plots with weight " + wgt);
                 foundelectrons += wgt;
                 peffElectrons.fill(p, wgt);
                 phieffElectrons.fill(phi, wgt);
@@ -382,30 +387,30 @@
                 if (hit.Layer() == layer)
                     hasThisLayer = true;
             if (!hasThisLayer) {
-//                System.out.println("Missing reconstructed hit in layer = " + layer);
+//                LOGGER.info("Missing reconstructed hit in layer = " + layer);
                 boolean hasFitHitSL1 = false;
                 boolean hasFitHitSL2 = false;
                 FittedRawTrackerHit fitSL1 = null;
                 FittedRawTrackerHit fitSL2 = null;
-//                System.out.println("fitted hit list size = " + fitlist.size());
+//                LOGGER.info("fitted hit list size = " + fitlist.size());
                 for (FittedRawTrackerHit fit : fitlist) {
-//                    System.out.println("fitted hit layer number = " + fit.getRawTrackerHit().getLayerNumber());
+//                    LOGGER.info("fitted hit layer number = " + fit.getRawTrackerHit().getLayerNumber());
                     if (fit.getRawTrackerHit().getLayerNumber() == layer) {
                         hasFitHitSL1 = true;
                         fitSL1 = fit;
-//                        System.out.println("Found a hit in SL1 with t0 = " + fitSL1.getT0() + "; amp = " + fitSL1.getAmp() + "; chi^2 = " + fitSL1.getShapeFitParameters().getChiProb() + "; strip = " + fitSL1.getRawTrackerHit().getCellID());
+//                        LOGGER.info("Found a hit in SL1 with t0 = " + fitSL1.getT0() + "; amp = " + fitSL1.getAmp() + "; chi^2 = " + fitSL1.getShapeFitParameters().getChiProb() + "; strip = " + fitSL1.getRawTrackerHit().getCellID());
                     }
                     if (fit.getRawTrackerHit().getLayerNumber() == layer + 1) {
                         hasFitHitSL2 = true;
                         fitSL2 = fit;
-//                        System.out.println("Found a hit in SL2 with t0 = " + fitSL2.getT0() + "; amp = " + fitSL2.getAmp() + "; chi^2 = " + fitSL2.getShapeFitParameters().getChiProb() + "; strip = " + fitSL2.getRawTrackerHit().getCellID());
+//                        LOGGER.info("Found a hit in SL2 with t0 = " + fitSL2.getT0() + "; amp = " + fitSL2.getAmp() + "; chi^2 = " + fitSL2.getShapeFitParameters().getChiProb() + "; strip = " + fitSL2.getRawTrackerHit().getCellID());
 
                     }
                 }
 //                if (!hasFitHitSL1)
-//                    System.out.println("MISSING a hit in SL1!!!");
+//                    LOGGER.info("MISSING a hit in SL1!!!");
 //                if (!hasFitHitSL2)
-//                    System.out.println("MISSING a hit in SL2!!!");
+//                    LOGGER.info("MISSING a hit in SL2!!!");
 
                 return false;
             }

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java	Wed Oct  7 19:47:33 2015
@@ -8,9 +8,12 @@
 import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;
+
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.logging.Logger;
+
 import org.hps.recon.tracking.CoordinateTransformations;
 import org.hps.recon.tracking.TrackUtils;
 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
@@ -33,6 +36,8 @@
 // TODO:  Add some quantities for DQM monitoring:  e.g. <tracks>, <hits/track>, etc
 public class TrackingMonitoring extends DataQualityMonitor {
 
+    private static Logger LOGGER = Logger.getLogger(SvtMonitoring.class.getPackage().getName());
+    
     private String helicalTrackHitCollectionName = "HelicalTrackHits";
     private final String rotatedTrackHitCollectionName = "RotatedHelicalTrackHits";
     private final String helicalTrackHitRelationsCollectionName = "HelicalTrackHitRelations";
@@ -566,7 +571,7 @@
             IHistogram1D hitTimeResidual = getSensorPlot(plotDir + trackCollectionName + "/" + triggerType + "/" + timeresidDir + "hitTimeResidual_", getNiceSensorName(sensor));
             IFitResult result = fitGaussian(hitTimeResidual, fitter, "range=\"(-20.0,20.0)\"");
             if (result != null) {
-                System.out.format("%s\t%f\t%f\t%d\t%d\n", getNiceSensorName(sensor), result.fittedParameters()[1], result.fittedParameters()[2], sensor.getFebID(), sensor.getFebHybridID());
+                LOGGER.info(String.format("%s\t%f\t%f\t%d\t%d", getNiceSensorName(sensor), result.fittedParameters()[1], result.fittedParameters()[2], sensor.getFebID(), sensor.getFebHybridID()));
             }
         }
 
@@ -584,7 +589,7 @@
         try {
             ifr = fitter.fit(h1d, "g", init, range);
         } catch (RuntimeException ex) {
-            System.out.println(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
+            LOGGER.info(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
         }
         return ifr;
 //        double[] init = {20.0, 0.0, 1.0, 20, -1};
@@ -593,17 +598,16 @@
 
     @Override
     public void printDQMData() {
-        System.out.println("ReconMonitoring::printDQMData");
+        LOGGER.info("ReconMonitoring::printDQMData");
         for (Map.Entry<String, Double> entry : monitoredQuantityMap.entrySet()) {
-            System.out.println(entry.getKey() + " = " + entry.getValue());
-        }
-        System.out.println("*******************************");
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        }
     }
 
     @Override
     public void printDQMStrings() {
         for (Map.Entry<String, Double> entry : monitoredQuantityMap.entrySet()) {
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         }
     }
 

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java	Wed Oct  7 19:47:33 2015
@@ -7,12 +7,14 @@
 import hep.aida.IHistogram1D;
 import hep.aida.IPlotter;
 import hep.aida.IPlotterStyle;
+
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.hps.recon.tracking.gbl.GBLStripClusterData;
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.GenericObject;
@@ -26,6 +28,8 @@
 // TODO:  Add some quantities for DQM monitoring: 
 public class TrackingResiduals extends DataQualityMonitor {
 
+    private static Logger LOGGER = Logger.getLogger(TrackingResiduals.class.getPackage().getName());
+    
     // Collection Names
     String trackTimeDataCollectionName = "TrackTimeData";
     String trackResidualsCollectionName = "TrackResiduals";
@@ -303,52 +307,52 @@
 
     @Override
     public void printDQMData() {
-        System.out.println("TrackingResiduals::printDQMData");
+        LOGGER.info("TrackingResiduals::printDQMData");
         for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
         for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
-        System.out.println("*******************************");
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        LOGGER.info("*******************************");
     }
 
     @Override
     public void printDQMStrings() {
         for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
         for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet())
-            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + entry.getKey() + " double;");
     }
 
     private void resetOccupancyMap() {
@@ -385,7 +389,7 @@
         try {
             ifr = fitter.fit(h1d, "g", init, range);
         } catch (RuntimeException ex) {
-            System.out.println(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
+            LOGGER.info(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
         }
         return ifr;
 //        double[] init = {20.0, 0.0, 1.0, 20, -1};

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/TridentMonitoring.java	Wed Oct  7 19:47:33 2015
@@ -9,9 +9,12 @@
 import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.VecOp;
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map.Entry;
+import java.util.logging.Logger;
+
 import org.hps.recon.ecal.cluster.ClusterUtilities;
 import org.hps.recon.particle.ReconParticleDriver;
 import org.hps.recon.tracking.TrackType;
@@ -33,6 +36,8 @@
  */
 public class TridentMonitoring extends DataQualityMonitor {
 
+    private static Logger LOGGER = Logger.getLogger(TridentMonitoring.class.getPackage().getName());
+    
     private double ebeam = 1.05;
     private final BasicHep3Matrix beamAxisRotation = new BasicHep3Matrix();
     private static final int nCuts = 9;
@@ -217,7 +222,7 @@
 
     @Override
     protected void detectorChanged(Detector detector) {
-        System.out.println("TridendMonitoring::detectorChanged  Setting up the plotter");
+        LOGGER.info("TridendMonitoring::detectorChanged  Setting up the plotter");
         beamAxisRotation.setActiveEuler(Math.PI / 2, -0.0305, -Math.PI / 2);
 
         aida.tree().cd("/");
@@ -759,7 +764,8 @@
     }
 
     @Override
-    public void printDQMData() {
+    // TODO: Change from System.out to use logger instead.
+    public void printDQMData() {        
         System.out.println("TridendMonitoring::printDQMData");
         for (Entry<String, Double> entry : monitoredQuantityMap.entrySet()) {
             System.out.println(entry.getKey() + " = " + entry.getValue());
@@ -770,7 +776,7 @@
 
         System.out.println("\t\t\tTridend Selection Summary");
         System.out.println("******************************************************************************************");
-        System.out.format("Number of      V0:\t%8.0f\t%8.6f\t%8.6f\t%8.6f\n", nRecoV0, nRecoV0 / nRecoV0, nRecoV0 / nRecoV0, nRecoV0 / nEvents);
+        System.out.println(String.format("Number of      V0:\t%8.0f\t%8.6f\t%8.6f\t%8.6f\n", nRecoV0, nRecoV0 / nRecoV0, nRecoV0 / nRecoV0, nRecoV0 / nEvents));
 
         for (int i = 0; i < nCuts; i++) {
             if (i == firstVertexingCut) {
@@ -799,7 +805,7 @@
     public void printDQMStrings() {
         for (int i = 0; i < 9; i++)//TODO:  do this in a smarter way...loop over the map
         {
-            System.out.println("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
         }
     }
 

Modified: java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java
 =============================================================================
--- java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java	(original)
+++ java/trunk/analysis/src/main/java/org/hps/analysis/dataquality/V0Monitoring.java	Wed Oct  7 19:47:33 2015
@@ -11,12 +11,14 @@
 import hep.physics.vec.Hep3Vector;
 import hep.physics.vec.BasicHep3Matrix;
 import hep.physics.vec.VecOp;
+
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map.Entry;
 import java.util.logging.Level;
 import java.util.logging.Logger;
+
 import org.hps.recon.tracking.TrackType;
 import org.hps.recon.tracking.TrackUtils;
 import org.hps.recon.vertexing.BilliorTrack;
@@ -39,6 +41,8 @@
  */
 public class V0Monitoring extends DataQualityMonitor {
 
+    private static Logger LOGGER = Logger.getLogger(V0Monitoring.class.getPackage().getName());
+    
     String finalStateParticlesColName = "FinalStateParticles";
     String unconstrainedV0CandidatesColName = "UnconstrainedV0Candidates";
     String beamConV0CandidatesColName = "BeamspotConstrainedV0Candidates";
@@ -156,7 +160,7 @@
     protected void detectorChanged(Detector detector) {
         beamAxisRotation.setActiveEuler(Math.PI / 2, -0.0305, -Math.PI / 2);
 
-        System.out.println("V0Monitoring::detectorChanged  Setting up the plotter");
+        LOGGER.info("Setting up the plotter");
         aida.tree().cd("/");
         String xtra = "Extras";
         String trkType = "SeedTrack/";
@@ -381,7 +385,7 @@
         }
         List<ReconstructedParticle> finalStateParticles = event.get(ReconstructedParticle.class, finalStateParticlesColName);
         if (debug)
-            System.out.println("This events has " + finalStateParticles.size() + " final state particles");
+            LOGGER.info("This events has " + finalStateParticles.size() + " final state particles");
 
         ReconstructedParticle ele1 = null;
         ReconstructedParticle ele2 = null;
@@ -391,7 +395,7 @@
             if (isGBL != TrackType.isGBL(fsPart.getType()))
                 continue;
             if (debug)
-                System.out.println("PDGID = " + fsPart.getParticleIDUsed() + "; charge = " + fsPart.getCharge() + "; pz = " + fsPart.getMomentum().x());
+                LOGGER.info("PDGID = " + fsPart.getParticleIDUsed() + "; charge = " + fsPart.getCharge() + "; pz = " + fsPart.getMomentum().x());
             double charge = fsPart.getCharge();
             sumCharge += charge;
             if (charge != 0) {
@@ -410,8 +414,8 @@
             Hep3Vector p1 = VecOp.mult(beamAxisRotation, ele1.getMomentum());
             Hep3Vector p2 = VecOp.mult(beamAxisRotation, ele2.getMomentum());
 //            Hep3Vector beamAxis = new BasicHep3Vector(Math.sin(0.0305), 0, Math.cos(0.0305));
-//            System.out.println(p1);
-//            System.out.println(VecOp.mult(rot, p1));
+//            LOGGER.info(p1);
+//            LOGGER.info(VecOp.mult(rot, p1));
 
             double theta1 = Math.acos(p1.z() / p1.magnitude());
             double theta2 = Math.acos(p2.z() / p2.magnitude());
@@ -447,7 +451,7 @@
                 BilliorTrack btEle1 = new BilliorTrack(stEle1.getSeedCandidate().getHelix());
                 BilliorTrack btEle2 = new BilliorTrack(stEle2.getSeedCandidate().getHelix());
                 BilliorVertex bv = fitVertex(btEle1, btEle2);
-//                System.out.println("ee vertex: "+bv.toString());
+//                LOGGER.info("ee vertex: "+bv.toString());
                 mollerMass.fill(bv.getParameters().get("invMass"));
                 mollerVx.fill(bv.getPosition().x());
                 mollerVy.fill(bv.getPosition().y());
@@ -470,10 +474,10 @@
 
     @Override
     public void printDQMData() {
-        System.out.println("V0Monitoring::printDQMData");
+        LOGGER.info("V0Monitoring::printDQMData");
         for (Entry<String, Double> entry : monitoredQuantityMap.entrySet())
-            System.out.println(entry.getKey() + " = " + entry.getValue());
-        System.out.println("*******************************");
+            LOGGER.info(entry.getKey() + " = " + entry.getValue());
+        LOGGER.info("*******************************");
     }
 
     /**
@@ -498,7 +502,7 @@
             double[] parsVz = resVz.fittedParameters();
 
             for (int i = 0; i < 5; i++)
-                System.out.println("Vertex Fit Parameters:  " + resVx.fittedParameterNames()[i] + " = " + parsVx[i] + "; " + parsVy[i] + "; " + parsVz[i]);
+                LOGGER.info("Vertex Fit Parameters:  " + resVx.fittedParameterNames()[i] + " = " + parsVx[i] + "; " + parsVy[i] + "; " + parsVz[i]);
 
             IPlotter plotter = analysisFactory.createPlotterFactory().create("Vertex Position");
             plotter.createRegions(1, 3);
@@ -538,7 +542,7 @@
     @Override
     public void printDQMStrings() {
         for (int i = 0; i < 9; i++)//TODO:  do this in a smarter way...loop over the map
-            System.out.println("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
+            LOGGER.info("ALTER TABLE dqm ADD " + fpQuantNames[i] + " double;");
     }
 
     IFitResult fitVertexPosition(IHistogram1D h1d, IFitter fitter, double[] init, String range
@@ -547,7 +551,7 @@
         try {
             ifr = fitter.fit(h1d, "g+p1", init, range);
         } catch (RuntimeException ex) {
-            System.out.println(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
+            LOGGER.info(this.getClass().getSimpleName() + ":  caught exception in fitGaussian");
         }
         return ifr;
     }

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