java/branches/hps-java_HPSJAVA-88/analysis

--- java/branches/hps-java_HPSJAVA-88/analysis/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -10,7 +10,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality

--- java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/DataQualityMonitor.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -18,14 +18,18 @@

  */
 public class DataQualityMonitor extends Driver {
 

-    public AIDA aida = AIDA.defaultInstance();
-    public DQMDatabaseManager manager;
-    public String recoVersion = "v0.0";
-    public static int runNumber = 1350;
-    public boolean overwriteDB = false;
-    public boolean connectToDB = false;
-    public boolean printDQMStrings = false;
-    public Map<String, Double> monitoredQuantityMap = new HashMap<>();

+    protected AIDA aida = AIDA.defaultInstance();
+    protected DQMDatabaseManager manager;
+    protected String recoVersion = "v0.0";
+    protected static int runNumber = 1350;
+    protected boolean overwriteDB = false;
+    protected boolean connectToDB = false;
+    protected boolean printDQMStrings = false;
+    protected Map<String, Double> monitoredQuantityMap = new HashMap<>();
+
+    protected boolean outputPlots = true;
+    protected String outputPlotDir = "DQMOutputPlots/";
+    

     public void setRecoVersion(String recoVersion) {
         this.recoVersion = recoVersion;
     }

@@ -46,6 +50,14 @@

         this.printDQMStrings = print;
     }
 

+    public void setOutputPlots(boolean out){
+        this.outputPlots=out;
+    }
+    public void setOutputPlotDir(String dir){
+        this.outputPlotDir=dir;
+    }
+
+    

     public void DataQualityMonitor() {
 
     }

java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality

--- java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/SVTHitMCEfficiency.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/SVTHitMCEfficiency.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,5 +1,7 @@

 package org.hps.analysis.dataquality;
 

+import hep.aida.IHistogram1D;
+import hep.aida.IHistogram2D;

 import hep.aida.IHistogramFactory;
 import hep.aida.IProfile1D;
 import java.util.HashMap;

@@ -19,9 +21,9 @@

 import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
 
 /**

- * DQM driver for the monte carlo SVT hit efficiency
- * April 29 -- first pass, makes the SimTrackerHits-->SiClusters efficiency vs
- * position (with a settable t0 cut)

+ * DQM driver for the monte carlo SVT hit efficiency April 29 -- first pass,
+ * makes the SimTrackerHits-->SiClusters efficiency vs position (with a settable
+ * t0 cut)

  *
  * @author mgraham on April 29, 2014
  */

@@ -29,19 +31,19 @@

 // TODO: Add some quantities for DQM monitoring:  e.g. <efficiency>, probably within first 1 cm or so.   
 public class SVTHitMCEfficiency extends DataQualityMonitor {
 

-    private String rawTrackerHitCollectionName = "SVTRawTrackerHits";

+    private final String rawTrackerHitCollectionName = "SVTRawTrackerHits";

     private String helicalTrackHitCollectionName = "HelicalTrackHits";

-    private String rotatedTrackHitCollectionName = "RotatedHelicalTrackHits";
-    private String fittedTrackerHitCollectionName = "SVTFittedRawTrackerHits";
-    private String trackerHitCollectionName = "TrackerHits";
-    private String siClusterCollectionName = "StripClusterer_SiTrackerHitStrip1D";
-    private String svtTrueHitRelationName = "SVTTrueHitRelations";
-    private String trackerName = "Tracker";

+    private final String rotatedTrackHitCollectionName = "RotatedHelicalTrackHits";
+    private final String fittedTrackerHitCollectionName = "SVTFittedRawTrackerHits";
+    private final String trackerHitCollectionName = "TrackerHits";
+    private final String siClusterCollectionName = "StripClusterer_SiTrackerHitStrip1D";
+    private final String svtTrueHitRelationName = "SVTTrueHitRelations";
+    private final String trackerName = "Tracker";

     private Detector detector = null;
     private double t0Cut = 16.0;
     private static final String nameStrip = "Tracker_TestRunModule_";
     private List<SiSensor> sensors;

-    private String plotDir = "SvtHitMCEfficiency/";

+    private final String plotDir = "SvtHitMCEfficiency/";

     private Map<String, Double> avgClusterEffMap;
     private Map<String, String> avgClusterEffNames;
 

@@ -57,7 +59,6 @@

     protected void detectorChanged(Detector detector) {
         this.detector = detector;
         aida.tree().cd("/");

-        IHistogramFactory hf = aida.histogramFactory();

 
         // Make a list of SiSensors in the SVT.
         sensors = this.detector.getSubdetector(trackerName).getDetectorElement().findDescendants(SiSensor.class);

@@ -66,7 +67,13 @@

         //currently, just the Si cluster efficiency
         aida.tree().cd("/");
         for (int kk = 1; kk < 13; kk++) {

-            IProfile1D clEffic = createLayerPlot(plotDir+"clusterEfficiency", kk, 50, 0, 25.);

+            createLayerPlot(plotDir + "clusterEfficiency", kk, 50, -40, 40.);
+            createLayerPlot(plotDir + "readoutEfficiency", kk, 50, -40, 40.);
+            createLayerPlot(plotDir + "rthToClusterEfficiency", kk, 50, -40, 40.);
+            createLayerPlot2D(plotDir + "toogoodFits", kk, 200, -100, 100, 100, 0, 20000);
+            createLayerPlot2D(plotDir + "goodFits", kk, 200, -100, 100, 100, 0, 20000);
+            createLayerPlot2D(plotDir + "badFits", kk, 200, -100, 100, 100, 0, 20000);
+            createLayerPlot1D(plotDir + "signalClusterT0", kk, 500, -100, 100);

         }
         resetEfficiencyMap();
     }

@@ -77,68 +84,111 @@

         aida.tree().cd("/");
 
         //make sure the required collections exist

-        if (!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName))

+        if (!event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {

             return;

-        if (!event.hasCollection(FittedRawTrackerHit.class, fittedTrackerHitCollectionName))

+        }
+        if (!event.hasCollection(FittedRawTrackerHit.class, fittedTrackerHitCollectionName)) {

             return;

+        }

-        if (!event.hasCollection(SiTrackerHitStrip1D.class, siClusterCollectionName))

+        if (!event.hasCollection(SiTrackerHitStrip1D.class, siClusterCollectionName)) {

             return;

+        }

-        if (!event.hasCollection(SimTrackerHit.class, trackerHitCollectionName))

+        if (!event.hasCollection(SimTrackerHit.class, trackerHitCollectionName)) {

             return;

+        }

-        if (!event.hasCollection(LCRelation.class, svtTrueHitRelationName))

+        if (!event.hasCollection(LCRelation.class, svtTrueHitRelationName)) {

             return;

+        }

-        RelationalTable mcHittomcP = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);

+        RelationalTable mcHittomcP = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_ONE, RelationalTable.Weighting.UNWEIGHTED);

         //  Get the collections of SimTrackerHits
         List<List<SimTrackerHit>> simcols = event.get(SimTrackerHit.class);
         //  Loop over the SimTrackerHits and fill in the relational table

-        for (List<SimTrackerHit> simlist : simcols)
-            for (SimTrackerHit simhit : simlist)
-                if (simhit.getMCParticle() != null)

+        for (List<SimTrackerHit> simlist : simcols) {
+            for (SimTrackerHit simhit : simlist) {
+                if (simhit.getMCParticle() != null) {

                     mcHittomcP.add(simhit, simhit.getMCParticle());

+                }
+            }
+        }
+

         RelationalTable rawtomc = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);

-        if (event.hasCollection(LCRelation.class, svtTrueHitRelationName)) {
-            List<LCRelation> trueHitRelations = event.get(LCRelation.class, svtTrueHitRelationName);
-            for (LCRelation relation : trueHitRelations)
-                if (relation != null && relation.getFrom() != null && relation.getTo() != null)
-                    rawtomc.add(relation.getFrom(), relation.getTo());

+        List<LCRelation> trueHitRelations = event.get(LCRelation.class, svtTrueHitRelationName);
+        for (LCRelation relation : trueHitRelations) {
+            if (relation.getFrom() != null && relation.getTo() != null) {
+                rawtomc.add(relation.getFrom(), relation.getTo());
+            }

         }

+

         List<SimTrackerHit> simHits = event.get(SimTrackerHit.class, trackerHitCollectionName);
         // make relational table for strip clusters to mc particle
         List<SiTrackerHitStrip1D> siClusters = event.get(SiTrackerHitStrip1D.class, siClusterCollectionName);
         RelationalTable clustertosimhit = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
         for (SiTrackerHit cluster : siClusters) {

-            List<RawTrackerHit> rawHits = cluster.getRawHits();
-            for (RawTrackerHit rth : rawHits) {

+            for (RawTrackerHit rth : cluster.getRawHits()) {

                 Set<SimTrackerHit> simTrackerHits = rawtomc.allFrom(rth);

-                if (simTrackerHits != null)
-                    for (SimTrackerHit simhit : simTrackerHits)
-                        clustertosimhit.add(cluster, simhit);

+                if (simTrackerHits != null) {
+                    for (SimTrackerHit simhit : simTrackerHits) {
+                        if (simhit != null) {
+                            clustertosimhit.add(cluster, simhit);
+                        }
+                    }
+                }

             }
         }

-//relational tables from mc particle to raw and fitted tracker hits

+
+        //relational tables from raw and fitted tracker hits to sim hit

         RelationalTable fittomc = new BaseRelationalTable(RelationalTable.Mode.MANY_TO_MANY, RelationalTable.Weighting.UNWEIGHTED);
         List<FittedRawTrackerHit> fittedTrackerHits = event.get(FittedRawTrackerHit.class, fittedTrackerHitCollectionName);
         for (FittedRawTrackerHit hit : fittedTrackerHits) {

-            RawTrackerHit rth = hit.getRawTrackerHit();
-            Set<SimTrackerHit> simTrackerHits = rawtomc.allFrom(rth);
-            if (simTrackerHits != null)
-                for (SimTrackerHit simhit : simTrackerHits)
-                    if (simhit.getMCParticle() != null)
-                        fittomc.add(hit, simhit.getMCParticle());

+            Set<SimTrackerHit> simTrackerHits = rawtomc.allFrom(hit.getRawTrackerHit());
+            for (SimTrackerHit simhit : simTrackerHits) {
+                fittomc.add(hit, simhit);
+            }

         }
 
         for (SimTrackerHit simhit : simHits) {

-            double wgt = 0.0;

+            Set<FittedRawTrackerHit> fittedRTH = fittomc.allTo(simhit);
+            FittedRawTrackerHit signalHit = null;
+            for (FittedRawTrackerHit frth : fittedRTH) {
+                if (signalHit == null || Math.abs(frth.getT0()) < Math.abs(signalHit.getT0())) {
+                    signalHit = frth;
+                }
+            }
+            if (signalHit != null) {
+//                System.out.format("chiprob %f, t0 %f, A %f\n", signalHit.getShapeFitParameters().getChiProb(), signalHit.getT0(), signalHit.getAmp());
+                if (signalHit.getShapeFitParameters().getChiProb() > 0.95) {
+                    getLayerPlot2D(plotDir + "toogoodFits", simhit.getLayer()).fill(signalHit.getT0(), signalHit.getAmp());
+                } else if (signalHit.getShapeFitParameters().getChiProb() < 0.05) {
+                    getLayerPlot2D(plotDir + "badFits", simhit.getLayer()).fill(signalHit.getT0(), signalHit.getAmp());
+                } else {
+                    getLayerPlot2D(plotDir + "goodFits", simhit.getLayer()).fill(signalHit.getT0(), signalHit.getAmp());
+                }
+            }
+
+            int gotCluster = 0;

             Set<SiTrackerHitStrip1D> clusters = clustertosimhit.allTo(simhit);

-            if (clusters != null)
-                for (SiTrackerHitStrip1D clust : clusters)
-                    if (Math.abs(clust.getTime()) < t0Cut)
-                        wgt = 1.0;
-            getLayerPlot(plotDir+"clusterEfficiency", simhit.getLayer()).fill(Math.abs(simhit.getPoint()[1]), wgt);

+            if (clusters != null) {
+                for (SiTrackerHitStrip1D clust : clusters) {
+                    getLayerPlot1D(plotDir + "signalClusterT0", simhit.getLayer()).fill(clust.getTime());
+
+                    if (Math.abs(clust.getTime()) < t0Cut) {
+                        gotCluster = 1;
+                    }
+                }
+            }
+            Set<RawTrackerHit> rawhits = rawtomc.allTo(simhit);
+            int gotRawHit = !rawhits.isEmpty() ? 1 : 0;
+
+            double y = simhit.getDetectorElement().getGeometry().getGlobalToLocal().transformed(simhit.getPositionVec()).x() + 20.0 * Math.signum(simhit.getPoint()[1]) * (simhit.getLayer() % 2 == 0 ? -1 : 1);
+            getLayerPlot(plotDir + "clusterEfficiency", simhit.getLayer()).fill(y, gotCluster);
+            getLayerPlot(plotDir + "readoutEfficiency", simhit.getLayer()).fill(y, gotRawHit);
+            if (gotRawHit == 1) {
+                getLayerPlot(plotDir + "rthToClusterEfficiency", simhit.getLayer()).fill(y, gotCluster);
+            }

         }
     }
 

@@ -151,8 +201,8 @@

     }
 
     private void resetEfficiencyMap() {

-        avgClusterEffMap = new HashMap<>();
-        avgClusterEffNames = new HashMap<>();

+        avgClusterEffMap = new HashMap<String, Double>();
+        avgClusterEffNames = new HashMap<String, String>();

         for (SiSensor sensor : sensors) {
             String effName = "avgClusterEff_" + getNiceSensorName(sensor);
             avgClusterEffNames.put(sensor.getName(), effName);

@@ -171,20 +221,37 @@

     }
 
     private IProfile1D createLayerPlot(String prefix, int layer, int nchan, double min, double max) {

-        IProfile1D hist = aida.profile1D(prefix + "_layer" + layer, nchan, min, max);
-        return hist;

+        return aida.profile1D(prefix + "_layer" + layer, nchan, min, max);

     }
 

+    private IHistogram1D getLayerPlot1D(String prefix, int layer) {
+        return aida.histogram1D(prefix + "_layer" + layer);
+    }
+
+    private IHistogram1D createLayerPlot1D(String prefix, int layer, int nchan, double min, double max) {
+        return aida.histogram1D(prefix + "_layer" + layer, nchan, min, max);
+    }
+
+    private IHistogram2D getLayerPlot2D(String prefix, int layer) {
+        return aida.histogram2D(prefix + "_layer" + layer);
+    }
+
+    private IHistogram2D createLayerPlot2D(String prefix, int layer, int nx, double minX, double maxX, int ny, double minY, double maxY) {
+        return aida.histogram2D(prefix + "_layer" + layer, nx, minX, maxX, ny, minY, maxY);
+    }
+

     @Override
     public void printDQMData() {

-        for (SiSensor sensor : sensors)

+        for (SiSensor sensor : sensors) {

             System.out.println(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;");

+        for (SiSensor sensor : sensors) {
+            System.out.println("ALTER TABLE dqm ADD " + avgClusterEffNames.get(sensor.getName()) + " double;");
+        }

     }
 
 }

java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality

--- java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/SvtMonitoring.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -15,17 +15,19 @@

 import java.util.logging.Level;
 import java.util.logging.Logger;
 import org.hps.conditions.deprecated.SvtUtils;

-import org.hps.recon.tracking.FittedRawTrackerHit;

+import org.hps.recon.tracking.ShapeFitParameters;

 import org.lcsim.detector.tracker.silicon.SiSensor;
 import org.lcsim.event.EventHeader;

+import org.lcsim.event.GenericObject;
+import org.lcsim.event.LCRelation;

 import org.lcsim.event.RawTrackerHit;

+import org.lcsim.event.TrackerHit;

 import org.lcsim.geometry.Detector;
 
 /**

- * DQM driver for the monte carlo for reconstructed track quantities
- * plots things like occupancy, t0, amplitude, chi^2 (from APV25 sampling fit);
- * each on a per/sensor basis
- * saves to DQM database: <occupancy>

+ * DQM driver for the monte carlo for reconstructed track quantities plots
+ * things like occupancy, t0, amplitude, chi^2 (from APV25 sampling fit); each
+ * on a per/sensor basis saves to DQM database: <occupancy>

  *
  * @author mgraham on Mar 28, 2014
  */

@@ -37,7 +39,7 @@

     private String trackerHitCollectionName = "StripClusterer_SiTrackerHitStrip1D";
     private Detector detector = null;
     private IPlotter plotter;

-    private String trackerName = "Tracker";

+    private final String trackerName = "Tracker";

     private List<SiSensor> sensors;
     private Map<String, int[]> occupancyMap;
     private Map<String, Double> avgOccupancyMap;

@@ -51,7 +53,7 @@

     private int eventCountCluster = 0;
     private static final String nameStrip = "Tracker_TestRunModule_";
     private static final int maxChannels = 640;

-    private String plotDir = "SvtMonitoring/";

+    private final String plotDir = "SvtMonitoring/";

 
     public void setRawTrackerHitCollectionName(String inputCollection) {
         this.rawTrackerHitCollectionName = inputCollection;

@@ -65,6 +67,7 @@

         this.trackerHitCollectionName = inputCollection;
     }
 

+    @Override

     protected void detectorChanged(Detector detector) {
         System.out.println("SvtMonitoring::detectorChanged  Setting up the plotter");
         this.detector = detector;

@@ -81,9 +84,11 @@

         for (SiSensor sensor : sensors) {
             //IHistogram1D occupancyPlot = aida.histogram1D(sensor.getName().replaceAll("Tracker_TestRunModule_", ""), 640, 0, 639);
             IHistogram1D occupancyPlot = createSensorPlot(plotDir + "occupancy_", sensor, maxChannels, 0, maxChannels - 1);

-            IHistogram1D t0Plot = createSensorPlot(plotDir + "t0_", sensor, 50, -50., 50.);
-            IHistogram1D amplitudePlot = createSensorPlot(plotDir + "amplitude_", sensor, 50, 0, 2000);
-            IHistogram1D chi2Plot = createSensorPlot(plotDir + "chi2_", sensor, 50, 0, 25);

+            IHistogram1D t0Plot = createSensorPlot(plotDir + "t0Hit_", sensor, 50, -50., 50.);
+            IHistogram1D amplitudePlot = createSensorPlot(plotDir + "amplitude_", sensor, 50, 0, 2000.0);
+            IHistogram1D chiProbPlot = createSensorPlot(plotDir + "chiProb_", sensor, 50, 0, 1.0);
+            IHistogram1D t0ClusterPlot = createSensorPlot(plotDir + "t0Cluster_", sensor, 50, -50., 50.);
+            IHistogram1D dedxClusterPlot = createSensorPlot(plotDir + "electrons_", sensor, 50, 0., 10.);

             occupancyPlot.reset();
         }
 

@@ -95,34 +100,49 @@

     public void process(EventHeader event) {
         /*  increment the strip occupancy arrays */
         if (event.hasCollection(RawTrackerHit.class, rawTrackerHitCollectionName)) {

+//            System.out.println("Found a raw hit collection");

             List<RawTrackerHit> rawTrackerHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
             for (RawTrackerHit hit : rawTrackerHits) {
                 int[] strips = occupancyMap.get(hit.getDetectorElement().getName());
                 strips[hit.getIdentifierFieldValue("strip")] += 1;
             }
             ++eventCountRaw;

-        } else
-            return; /* kick out of this if the even has none of these...*/

+        }

         /*  fill the FittedTrackerHit related histograms */

-
-        if (event.hasCollection(FittedRawTrackerHit.class, fittedTrackerHitCollectionName)) {
-            List<FittedRawTrackerHit> fittedTrackerHits = event.get(FittedRawTrackerHit.class, fittedTrackerHitCollectionName);
-            for (FittedRawTrackerHit hit : fittedTrackerHits) {
-                String sensorName = hit.getRawTrackerHit().getDetectorElement().getName();
-                double t0 = hit.getT0();
-                double amp = hit.getAmp();
-                double chi2 = hit.getShapeFitParameters().getChiSq();
-                getSensorPlot(plotDir + "t0_", sensorName).fill(t0);

+        if (event.hasCollection(LCRelation.class, fittedTrackerHitCollectionName)) {
+            List<LCRelation> fittedTrackerHits = event.get(LCRelation.class, fittedTrackerHitCollectionName);
+            for (LCRelation hit : fittedTrackerHits) {
+                RawTrackerHit rth = (RawTrackerHit) hit.getFrom();
+                GenericObject pars = (GenericObject) hit.getTo();
+                String sensorName = getNiceSensorName((SiSensor) rth.getDetectorElement());
+                //this is a clever way to get the parameters we want from the generic object
+                double t0 = ShapeFitParameters.getT0(pars);
+                double amp = ShapeFitParameters.getAmp(pars);
+                double chiProb = ShapeFitParameters.getChiProb(pars);
+                getSensorPlot(plotDir + "t0Hit_", sensorName).fill(t0);

                 getSensorPlot(plotDir + "amplitude_", sensorName).fill(amp);

-                getSensorPlot(plotDir + "chi2_", sensorName).fill(chi2);

+                getSensorPlot(plotDir + "chiProb_", sensorName).fill(chiProb);

             }
             ++eventCountFit;

-        } else
-            return;

+        }
+
+        if (event.hasItem(trackerHitCollectionName)) {
+//            System.out.println("Found a Si cluster collection");
+            List<TrackerHit> siClusters = (List<TrackerHit>) event.get(trackerHitCollectionName);
+            for (TrackerHit cluster : siClusters) {
+                String sensorName = getNiceSensorName((SiSensor) ((RawTrackerHit) cluster.getRawHits().get(0)).getDetectorElement());
+                double t0 = cluster.getTime();
+                double dedx = cluster.getdEdx() * 1e6;
+//                System.out.println("dedx = "+dedx);
+                getSensorPlot(plotDir + "t0Cluster_", sensorName).fill(t0);
+                getSensorPlot(plotDir + "electrons_", sensorName).fill(dedx);
+            }
+        }

     }
 
     private IHistogram1D getSensorPlot(String prefix, SiSensor sensor) {

-        return aida.histogram1D(prefix + sensor.getName());

+        String hname = prefix + getNiceSensorName(sensor);
+        return aida.histogram1D(hname);

     }
 
     private IHistogram1D getSensorPlot(String prefix, String sensorName) {

@@ -130,22 +150,24 @@

     }
 
     private IHistogram1D createSensorPlot(String prefix, SiSensor sensor, int nchan, double min, double max) {

-        IHistogram1D hist = aida.histogram1D(prefix + sensor.getName(), nchan, min, max);

+        String hname = prefix + getNiceSensorName(sensor);
+        IHistogram1D hist = aida.histogram1D(hname, nchan, min, max);

         hist.setTitle(sensor.getName().replaceAll(nameStrip, "")
                 .replace("module", "mod")
                 .replace("layer", "lyr")
                 .replace("sensor", "sens"));

+

         return hist;
     }
 
     private void resetOccupancyMap() {

-        occupancyMap = new HashMap<>();
-        avgOccupancyMap = new HashMap<>();
-        avgOccupancyNames = new HashMap<>();
-        avgt0Names = new HashMap<>();
-        sigt0Names = new HashMap<>();
-        avgt0Map = new HashMap<>();
-        sigt0Map = new HashMap<>();

+        occupancyMap = new HashMap<String, int[]>();
+        avgOccupancyMap = new HashMap<String, Double>();
+        avgOccupancyNames = new HashMap<String, String>();
+        avgt0Names = new HashMap<String, String>();
+        sigt0Names = new HashMap<String, String>();
+        avgt0Map = new HashMap<String, Double>();
+        sigt0Map = new HashMap<String, Double>();

         for (SiSensor sensor : sensors) {
             occupancyMap.put(sensor.getName(), new int[640]);
             avgOccupancyMap.put(sensor.getName(), -999.);

@@ -185,8 +207,9 @@

             int[] strips = occupancyMap.get(sensor.getName());
             for (int i = 0; i < strips.length; i++) {
                 double stripOccupancy = (double) strips[i] / (double) (eventCountRaw);

-                if (stripOccupancy != 0)

+                if (stripOccupancy != 0) {

                     sensorHist.fill(i, stripOccupancy);

+                }

                 avg += stripOccupancy;
             }
             //do the end-of-run quantities here too since we've already done the loop.  

@@ -214,22 +237,14 @@

         int irTop = 0;
         int irBot = 0;
         for (SiSensor sensor : sensors) {

-            IHistogram1D sensPlot = getSensorPlot(plotDir + "t0_", sensor);
-            IFitResult result = fitGaussian(sensPlot, fitter, "range=\"(-10.0,10.0)\"");
-            for (int i = 0; i < 5; i++) {
-                double par = result.fittedParameters()[i];
-                System.out.println("t0_" + sensor.getName() + ":  " + result.fittedParameterNames()[i] + " = " + par);
-            }
-

+            IHistogram1D sensPlot = getSensorPlot(plotDir + "t0Hit_", sensor);
+            IFitResult result = fitGaussian(sensPlot, fitter, "range=\"(-8.0,8.0)\"");

             boolean isTop = SvtUtils.getInstance().isTopLayer(sensor);

-

             if (isTop) {

-                System.out.println("Plotting into Top region " + irTop);

                 plotterTop.region(irTop).plot(sensPlot);
                 plotterTop.region(irTop).plot(result.fittedFunction());
                 irTop++;
             } else {

-                System.out.println("Plotting into Bottom region " + irBot);

                 plotterBottom.region(irBot).plot(sensPlot);
                 plotterBottom.region(irBot).plot(result.fittedFunction());
                 irBot++;

java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality

--- java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/TrackMCEfficiency.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/TrackMCEfficiency.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -315,12 +315,12 @@

                     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().getChiSq() + "; strip = " + fitSL1.getRawTrackerHit().getCellID());

+                        System.out.println("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().getChiSq() + "; strip = " + fitSL2.getRawTrackerHit().getCellID());

+                        System.out.println("Found a hit in SL2 with t0 = " + fitSL2.getT0() + "; amp = " + fitSL2.getAmp() + "; chi^2 = " + fitSL2.getShapeFitParameters().getChiProb() + "; strip = " + fitSL2.getRawTrackerHit().getCellID());

 
                     }
                 }

java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality

--- java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/TrackingMonitoring.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,18 +1,11 @@

 package org.hps.analysis.dataquality;
 
 import hep.aida.IHistogram1D;

-import hep.aida.IProfile;
-import java.util.HashMap;

 import java.util.List;
 import java.util.Map;

-import org.hps.conditions.deprecated.SvtUtils;
-import org.lcsim.detector.tracker.silicon.SiSensor;

 import org.lcsim.event.EventHeader;
 import org.lcsim.event.LCIOParameters;

-import org.lcsim.event.RawTrackerHit;

 import org.lcsim.event.Track;

-import org.lcsim.fit.helicaltrack.HelicalTrackCross;
-import org.lcsim.fit.helicaltrack.HelicalTrackHit;

 import org.lcsim.geometry.Detector;
 import org.lcsim.geometry.IDDecoder;
 

@@ -58,9 +51,6 @@

         this.detector = detector;
         aida.tree().cd("/");
 

-        IProfile avgLayersTopPlot = aida.profile1D(plotDir+"Number of Stereo Hits per layer in Top Half", 6, 1, 13);
-        IProfile avgLayersBottomPlot = aida.profile1D(plotDir+"Number of Stereo Hits per layer in Bottom Half", 6, 1, 13);
-

         IHistogram1D trkChi2 = aida.histogram1D(plotDir+"Track Chi2", 25, 0, 25.0);
         IHistogram1D nTracks = aida.histogram1D(plotDir+"Tracks per Event", 6, 0, 6);
         IHistogram1D trkd0 = aida.histogram1D(plotDir+"d0 ", 25, -5.0, 5.0);

@@ -76,33 +66,12 @@

     public void process(EventHeader event) {
 
         aida.tree().cd("/");

-        if (!event.hasCollection(HelicalTrackHit.class, helicalTrackHitCollectionName))
-            return;
-        nEvents++;
-        List<HelicalTrackHit> hthList = event.get(HelicalTrackHit.class, helicalTrackHitCollectionName);
-        int[] layersTop = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
-        int[] layersBot = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
-        for (HelicalTrackHit hth : hthList) {
-            HelicalTrackCross htc = (HelicalTrackCross) hth;
-            double x = htc.getPosition()[0];
-            double y = htc.getPosition()[1];
-            SiSensor sensor = ((SiSensor) ((RawTrackerHit) htc.getRawHits().get(0)).getDetectorElement());
-            if (SvtUtils.getInstance().isTopLayer(sensor))
-                layersTop[htc.Layer() - 1]++;
-            else
-                layersBot[htc.Layer() - 1]++;
-        }
-        for (int i = 0; i < 12; i++) {
-            aida.profile1D(plotDir+"Number of Stereo Hits per layer in Top Half").fill(i + 1, layersTop[i]);
-            aida.profile1D(plotDir+"Number of Stereo Hits per layer in Bottom Half").fill(i + 1, layersBot[i]);
-        }
-

+                   

         if (!event.hasCollection(Track.class, trackCollectionName)) {

-//            System.out.println(trackCollectionName + " does not exist; skipping event");

             aida.histogram1D(plotDir+"Tracks per Event").fill(0);
             return;
         }

-

+        nEvents++;

         List<Track> tracks = event.get(Track.class, trackCollectionName);
         nTotTracks += tracks.size();
         aida.histogram1D(plotDir+"Tracks per Event").fill(tracks.size());

java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality

--- java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/analysis/src/main/java/org/hps/analysis/dataquality/TrackingResiduals.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,14 +1,24 @@

 package org.hps.analysis.dataquality;
 

+import hep.aida.IAnalysisFactory;
+import hep.aida.IFitFactory;
+import hep.aida.IFitResult;
+import hep.aida.IFitter;

 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 org.hps.recon.tracking.TrackResidualsData;
-import org.hps.recon.tracking.TrackTimeData;

+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;

 import org.lcsim.event.EventHeader;

+import org.lcsim.event.GenericObject;

 import org.lcsim.geometry.Detector;
 
 /**

- * DQM driver for  track residuals in position and time

+ * DQM driver for track residuals in position and time

  *
  * @author mgraham on June 5, 2014
  */

@@ -19,75 +29,325 @@

     String trackTimeDataCollectionName = "TrackTimeData";
     String trackResidualsCollectionName = "TrackResiduals";
 

-    

     int nEvents = 0;

-    

+

     private String plotDir = "TrackResiduals/";
     String[] trackingQuantNames = {};
     int nmodules = 6;

+    private String posresDir = "PostionResiduals/";
+    private String timeresDir = "TimeResiduals/";
+    private Map<String, Double> xposTopMeanResidMap;
+    private Map<String, Double> yposTopMeanResidMap;
+    private Map<String, Double> xposBotMeanResidMap;
+    private Map<String, Double> yposBotMeanResidMap;
+    private Map<String, Double> timeMeanResidMap;
+    private Map<String, Double> xposTopSigmaResidMap;
+    private Map<String, Double> yposTopSigmaResidMap;
+    private Map<String, Double> xposBotSigmaResidMap;
+    private Map<String, Double> yposBotSigmaResidMap;
+    private Map<String, Double> timeSigmaResidMap;

 
     @Override
     protected void detectorChanged(Detector detector) {

-        

+

         aida.tree().cd("/");

-

+        resetOccupancyMap();

         for (int i = 0; i < nmodules; i++) {

-            IHistogram1D xresid = aida.histogram1D(plotDir + "Layer " + i + " x Residual", 50, -2.5, 2.5);
-            IHistogram1D yresid = aida.histogram1D(plotDir + "Layer " + i + " y Residual", 50, -1, 1);
-

+            IHistogram1D xresid = aida.histogram1D(plotDir + posresDir + "Module " + i + "Top x Residual", 50,-getRange(i,true),getRange(i,true));
+            IHistogram1D yresid = aida.histogram1D(plotDir + posresDir + "Module " + i + "Top y Residual", 50,-getRange(i,false),getRange(i,false));
+            IHistogram1D xresidbot = aida.histogram1D(plotDir + posresDir + "Module " + i + "Bot x Residual", 50,-getRange(i,true),getRange(i,true));
+            IHistogram1D yresidbot = aida.histogram1D(plotDir + posresDir + "Module " + i + "Bot y Residual", 50,-getRange(i,false),getRange(i,false));

         }
 
         for (int i = 0; i < nmodules * 2; i++) {

-            IHistogram1D tresid = aida.histogram1D(plotDir + "Half-Layer " + i + " t Residual", 50, -20, 20);

+            IHistogram1D tresid = aida.histogram1D(plotDir + timeresDir + "HalfModule " + i + " t Residual", 50, -20, 20);

         }
     }
 
     @Override
     public void process(EventHeader event) {

-

         aida.tree().cd("/");

-        if (!event.hasCollection(TrackTimeData.class, trackTimeDataCollectionName))

+        if (!event.hasCollection(GenericObject.class, trackTimeDataCollectionName))

             return;

-        if (!event.hasCollection(TrackResidualsData.class, trackResidualsCollectionName))

+        if (!event.hasCollection(GenericObject.class, trackResidualsCollectionName))

             return;
         nEvents++;

+        List<GenericObject> trdList = event.get(GenericObject.class, trackResidualsCollectionName);
+        for (GenericObject trd : trdList) {
+            int nResid = trd.getNDouble();
+            int isBot = trd.getIntVal(trd.getNInt() - 1);//last Int is the top/bottom flag
+            for (int i = 0; i < nResid; i++)
+                if (isBot == 1) {
+                    aida.histogram1D(plotDir + posresDir + "Module " + i + "Bot x Residual").fill(trd.getDoubleVal(i));//x is the double value in the generic object
+                    aida.histogram1D(plotDir + posresDir + "Module " + i + "Bot y Residual").fill(trd.getFloatVal(i));//y is the float value in the generic object
+                } else {
+                    aida.histogram1D(plotDir + posresDir + "Module " + i + "Top x Residual").fill(trd.getDoubleVal(i));//x is the double value in the generic object
+                    aida.histogram1D(plotDir + posresDir + "Module " + i + "Top y Residual").fill(trd.getFloatVal(i));//y is the float value in the generic object                    
+                }

-        List<TrackResidualsData> trdList = event.get(TrackResidualsData.class, trackResidualsCollectionName);
-        for (TrackResidualsData trd : trdList) {
-            int nResid = trd.getNDouble();
-            for (int i = 0; i < nResid; i++) {
-                aida.histogram1D(plotDir + "Layer " + i + " x Residual").fill(trd.getDoubleVal(i));//x is the double value in the generic object
-                aida.histogram1D(plotDir + "Layer " + i + " y Residual").fill(trd.getFloatVal(i));//y is the float value in the generic object
-            }

         }
 

-        List<TrackTimeData> ttdList = event.get(TrackTimeData.class, trackTimeDataCollectionName);
-        for (TrackTimeData ttd : ttdList) {

+        List<GenericObject> ttdList = event.get(GenericObject.class, trackTimeDataCollectionName);
+        for (GenericObject ttd : ttdList) {

             int nResid = ttd.getNDouble();
             for (int i = 0; i < nResid; i++)

-                aida.histogram1D(plotDir + "Half-Layer " + i + " t Residual").fill(ttd.getDoubleVal(i));//x is the double value in the generic object               

+                aida.histogram1D(plotDir + timeresDir + "HalfModule " + i + " t Residual").fill(ttd.getDoubleVal(i));//x is the double value in the generic object               

         }

-

     }
 
     @Override
     public void calculateEndOfRunQuantities() {

-//        monitoredQuantityMap.put(trackingQuantNames[0], (double) nTotTracks / nEvents);

+        IAnalysisFactory analysisFactory = IAnalysisFactory.create();
+        IFitFactory fitFactory = analysisFactory.createFitFactory();
+        IFitter fitter = fitFactory.createFitter("chi2");
+        IPlotter plotterXTop = analysisFactory.createPlotterFactory().create("x-residual Top");
+        IPlotter plotterXBottom = analysisFactory.createPlotterFactory().create("x-residual Bottom");
+        IPlotter plotterYTop = analysisFactory.createPlotterFactory().create("y-residual Top");
+        IPlotter plotterYBottom = analysisFactory.createPlotterFactory().create("y-residual Bottom");
+
+        IPlotter plotterTime = analysisFactory.createPlotterFactory().create("Track Time");
+
+        plotterXTop.createRegions(2, 3);
+        IPlotterStyle pstyle = plotterXTop.style();
+        pstyle.legendBoxStyle().setVisible(false);
+        plotterXBottom.createRegions(2, 3);
+        IPlotterStyle pstyle2 = plotterXBottom.style();
+        pstyle2.legendBoxStyle().setVisible(false);
+
+        plotterYTop.createRegions(2, 3);
+        IPlotterStyle pstyle3 = plotterYTop.style();
+        pstyle3.legendBoxStyle().setVisible(false);
+        plotterYBottom.createRegions(2, 3);
+        IPlotterStyle pstyle4 = plotterYBottom.style();
+        pstyle4.legendBoxStyle().setVisible(false);
+
+        plotterTime.createRegions(3, 4);
+        IPlotterStyle pstyle5 = plotterTime.style();
+        pstyle5.legendBoxStyle().setVisible(false);
+
+        int irXTop = 0;
+        int irXBot = 0;
+        int irYTop = 0;
+        int irYBot = 0;
+        for (int i = 0; i < nmodules; i++) {
+            IHistogram1D xresidTop = aida.histogram1D(plotDir + posresDir + "Module " + i + "Top x Residual");
+            IHistogram1D yresidTop = aida.histogram1D(plotDir + posresDir + "Module " + i + "Top y Residual");
+            IHistogram1D xresidBot = aida.histogram1D(plotDir + posresDir + "Module " + i + "Bot x Residual");
+            IHistogram1D yresidBot = aida.histogram1D(plotDir + posresDir + "Module " + i + "Bot y Residual");
+            IFitResult xresultTop = fitGaussian(xresidTop, fitter, "range=\"(-1.0,1.0)\"");
+            IFitResult yresultTop = fitGaussian(yresidTop, fitter, "range=\"(-0.5,0.5)\"");
+            IFitResult xresultBot = fitGaussian(xresidBot, fitter, "range=\"(-1.0,1.0)\"");
+            IFitResult yresultBot = fitGaussian(yresidBot, fitter, "range=\"(-8.0,8.0)\"");
+            double[] parsXTop = xresultTop.fittedParameters();
+            double[] parsYTop = yresultTop.fittedParameters();
+            double[] parsXBot = xresultBot.fittedParameters();
+            double[] parsYBot = yresultBot.fittedParameters();
+
+            plotterXTop.region(irXTop).plot(xresidTop);
+            plotterXTop.region(irXTop).plot(xresultTop.fittedFunction());
+            irXTop++;
+            plotterXBottom.region(irXBot).plot(xresidBot);
+            plotterXBottom.region(irXBot).plot(xresultBot.fittedFunction());
+            irXBot++;
+
+            plotterYTop.region(irYTop).plot(yresidTop);
+            plotterYTop.region(irYTop).plot(yresultTop.fittedFunction());
+            irYTop++;
+            plotterYBottom.region(irYBot).plot(yresidBot);
+            plotterYBottom.region(irYBot).plot(yresultBot.fittedFunction());
+            irYBot++;
+
+            xposTopMeanResidMap.put(getQuantityName(0, 0, 1, i) + "_x", parsXTop[1]);
+            xposTopSigmaResidMap.put(getQuantityName(0, 1, 1, i) + "_x", parsXTop[2]);
+            yposTopMeanResidMap.put(getQuantityName(0, 0, 1, i) + "_y", parsYTop[1]);
+            yposTopSigmaResidMap.put(getQuantityName(0, 1, 1, i) + "_y", parsYTop[2]);
+            xposBotMeanResidMap.put(getQuantityName(0, 0, 0, i) + "_x", parsXBot[1]);
+            xposBotSigmaResidMap.put(getQuantityName(0, 1, 0, i) + "_x", parsXBot[2]);
+            yposBotMeanResidMap.put(getQuantityName(0, 0, 0, i) + "_y", parsYBot[1]);
+            yposBotSigmaResidMap.put(getQuantityName(0, 1, 0, i) + "_y", parsYBot[2]);
+
+        }
+        int iTime = 0;
+        for (int i = 0; i < nmodules * 2; i++) {
+            IHistogram1D tresid = aida.histogram1D(plotDir + timeresDir + "HalfModule " + i + " t Residual");
+            IFitResult tresult = fitGaussian(tresid, fitter, "range=\"(-15.0,15.0)\"");
+            double[] parsTime = tresult.fittedParameters();
+            plotterTime.region(iTime).plot(tresid);
+            plotterTime.region(iTime).plot(tresult.fittedFunction());
+            iTime++;
+
+            timeMeanResidMap.put(getQuantityName(1, 0, 2, i) + "_dt", parsTime[1]);
+            timeSigmaResidMap.put(getQuantityName(1, 1, 2, i) + "_dt", parsTime[2]);
+
+        }
+
+        if (outputPlots) {
+            try {
+                plotterXTop.writeToFile(outputPlotDir + "X-Residuals-Top.png");
+            } catch (IOException ex) {
+                Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
+            }
+            try {
+                plotterYTop.writeToFile(outputPlotDir + "Y-Residuals-Top.png");
+            } catch (IOException ex) {
+                Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
+            }
+            try {
+                plotterXBottom.writeToFile(outputPlotDir + "X-Residuals-Bottom.png");
+            } catch (IOException ex) {
+                Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
+            }
+            try {
+                plotterYBottom.writeToFile(outputPlotDir + "Y-Residuals-Bottom.png");
+            } catch (IOException ex) {
+                Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
+            }
+            try {
+                plotterTime.writeToFile(outputPlotDir + "Time-Residuals.png");
+            } catch (IOException ex) {
+                Logger.getLogger(SvtMonitoring.class.getName()).log(Level.SEVERE, null, ex);
+            }
+        }
+

     }
 

+    private String getQuantityName(int itype, int iquant, int top, int nlayer) {
+        String typeString = "position_resid";
+        String quantString = "mean_";
+        if (itype == 1)
+            typeString = "time_resid";
+        if (iquant == 1)
+            quantString = "sigma_";
+
+        String botString = "bot_";
+        if (top == 1)
+            botString = "top_";
+        if (top == 2)
+            botString = "";
+
+        String layerString = "module" + nlayer;
+        if (itype == 1)
+            layerString = "halfmodule" + nlayer;
+
+        return typeString + quantString + botString + layerString;
+    }
+

     @Override
     public void printDQMData() {

-//        System.out.println("ReconMonitoring::printDQMData");
-//        for (Map.Entry<String, Double> entry : monitoredQuantityMap.entrySet())
-//            System.out.println(entry.getKey() + " = " + entry.getValue());
-//        System.out.println("*******************************");

+        System.out.println("TrackingResiduals::printDQMData");
+        for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : xposBotMeanResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : xposBotSigmaResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : yposBotMeanResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : yposBotSigmaResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        for (Map.Entry<String, Double> entry : timeSigmaResidMap.entrySet())
+            System.out.println(entry.getKey() + " = " + entry.getValue());
+        System.out.println("*******************************");

     }
 
     @Override
     public void printDQMStrings() {

-//        for (Map.Entry<String, Double> entry : monitoredQuantityMap.entrySet())
-//            System.out.println("ALTER TABLE dqm ADD " + entry.getKey() + " double;");

+        for (Map.Entry<String, Double> entry : xposTopMeanResidMap.entrySet())
+            System.out.println("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;");
+        for (Map.Entry<String, Double> entry : xposTopSigmaResidMap.entrySet())
+            System.out.println("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;");
+        for (Map.Entry<String, Double> entry : yposTopMeanResidMap.entrySet())
+            System.out.println("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;");
+        for (Map.Entry<String, Double> entry : yposTopSigmaResidMap.entrySet())
+            System.out.println("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;");
+        for (Map.Entry<String, Double> entry : timeMeanResidMap.entrySet())
+            System.out.println("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;");
+    }

+    private void resetOccupancyMap() {
+        xposBotMeanResidMap = new HashMap<>();
+        xposBotSigmaResidMap = new HashMap<>();
+        yposBotMeanResidMap = new HashMap<>();
+        yposBotSigmaResidMap = new HashMap<>();
+        xposTopMeanResidMap = new HashMap<>();
+        xposTopSigmaResidMap = new HashMap<>();
+        yposTopMeanResidMap = new HashMap<>();
+        yposTopSigmaResidMap = new HashMap<>();
+        timeMeanResidMap = new HashMap<>();
+        timeSigmaResidMap = new HashMap<>();
+        for (int i = 0; i < nmodules; i++) {
+            xposTopMeanResidMap.put(getQuantityName(0, 0, 1, i) + "_x", -999.);
+            yposTopMeanResidMap.put(getQuantityName(0, 0, 1, i) + "_y", -999.);
+            xposTopSigmaResidMap.put(getQuantityName(0, 1, 1, i) + "_x", -999.);
+            yposTopSigmaResidMap.put(getQuantityName(0, 1, 1, i) + "_y", -999.);
+            xposBotMeanResidMap.put(getQuantityName(0, 0, 0, i) + "_x", -999.);
+            yposBotMeanResidMap.put(getQuantityName(0, 0, 0, i) + "_y", -999.);
+            xposBotSigmaResidMap.put(getQuantityName(0, 1, 0, i) + "_x", -999.);
+            yposBotSigmaResidMap.put(getQuantityName(0, 1, 0, i) + "_y", -999.);
+        }
+        for (int i = 0; i < nmodules * 2; i++) {
+            timeMeanResidMap.put(getQuantityName(1, 0, 2, i) + "_dt", -999.);
+            timeSigmaResidMap.put(getQuantityName(1, 1, 2, i) + "_dt", -999.);
+        }
+

     }
 

+    IFitResult fitGaussian(IHistogram1D h1d, IFitter fitter, String range) {
+         double[] init = {20.0, 0.0, 0.2};  
+        return fitter.fit(h1d, "g", init,range);
+//        double[] init = {20.0, 0.0, 1.0, 20, -1};
+//        return fitter.fit(h1d, "g+p1", init, range);
+    }
+
+    private double getRange(int layer, boolean isX) {
+        double range = 2.5;
+        if (isX) {
+            if (layer == 0)
+                return 0.5;
+            if (layer == 1)
+                return 0.5;
+            if (layer == 2)
+                return 0.5;
+            if (layer == 3)
+                return 1.0;
+            if (layer == 4)
+                return 1.0;
+            if (layer == 5)
+                return 1.0;
+        } else {
+            if (layer == 0)
+                return 0.005;
+            if (layer == 1)
+                return 0.5;
+            if (layer == 2)
+                return 0.5;
+            if (layer == 3)
+                return 1.0;
+            if (layer == 4)
+                return 1.0;
+            if (layer == 5)
+                return 1.5;
+        }
+        return range;
+
+    }
+

 }

java/branches/hps-java_HPSJAVA-88/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,25 +1,20 @@

 <?xml version="1.0"?>

-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

     <modelVersion>4.0.0</modelVersion>
     <artifactId>hps-conditions</artifactId>
     <name>conditions</name>
     <description>HPS conditions framework</description>

-

     <parent>
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>

-

     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/conditions/</url>
         <connection>scm:svn:svn://svn.freehep.org/hps/java/trunk/conditions/</connection>
         <developerConnection>scm:svn:svn://svn.freehep.org/hps/java/trunk/conditions/</developerConnection>
     </scm>

-

     <build>
         <plugins>
             <plugin>

@@ -27,13 +22,19 @@

                 <artifactId>maven-surefire-plugin</artifactId>
                 <configuration>
                     <excludes>

+                        <exclude>org/hps/conditions/**/**.java</exclude>
+                        <!--  

                         <exclude>org/hps/conditions/ConditionsObjectTest.java</exclude>

+                        <exclude>org/hps/conditions/**.java</exclude>
+                        <exclude>org/hps/conditions/beam/**.java</exclude>
+                        <exclude>org/hps/conditions/ecal/**.java</exclude>
+                        <exclude>org/hps/conditions/svt/**.java</exclude>
+                        -->

                     </excludes>
                 </configuration>
             </plugin>
         </plugins>
     </build>

-

     <dependencies>
         <dependency>
             <groupId>org.lcsim</groupId>

@@ -54,5 +55,4 @@

             <version>5.1.26</version>
         </dependency>
     </dependencies>

-

 </project>

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/AbstractConditionsObject.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/AbstractConditionsObject.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -166,7 +166,14 @@

         return collectionId != -1;
     }
 

-    // protected void finalize() {
-    // System.out.println("finalizing ConditionsObject " + System.identityHashCode(this));
-    // }

+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append("id: ").append(getRowId()).append('\n');
+        sb.append("collection_id: ").append(getCollectionId()).append('\n');
+        sb.append("read_only: ").append(isReadOnly()).append('\n');
+        for (String fieldName : getTableMetaData().getFieldNames()) {
+            sb.append(fieldName).append(": ").append(getFieldValue(fieldName).toString()).append('\n');
+        }
+        return sb.toString();
+    }

 }

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ConditionsObjectConverter.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ConditionsObjectConverter.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -112,6 +112,6 @@

     }
    
     public boolean allowMultipleCollections() {

-        return false;

+        return true;

     }
 }

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ConditionsRecord.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ConditionsRecord.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -128,6 +128,14 @@

     public int getCollectionId() {
         return getFieldValue("collection_id");
     }

+    
+    /**
+     * Get the string tag associated with these conditions.
+     * @return The string tag.
+     */
+    public String getTag() {
+        return getFieldValue("tag");
+    }

 
     /**
      * Convert this record to a human readable string, one field per line.

@@ -145,6 +153,7 @@

         buff.append("created: " + getCreated() + '\n');
         buff.append("validFrom: " + getValidFrom() + '\n');
         buff.append("validTo: " + getValidTo() + '\n');

+        buff.append("tag: " + getTag() + '\n');

         buff.append("createdBy: " + getCreatedBy() + '\n');
         buff.append("formatVersion: " + getFormatVersion() + '\n');
         buff.append("notes: " + getNotes() + '\n');

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/DatabaseConditionsManager.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/DatabaseConditionsManager.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -47,26 +47,27 @@

 @SuppressWarnings("rawtypes")
 public final class DatabaseConditionsManager extends ConditionsManagerImplementation {
 

-    int runNumber = -1;
-    String detectorName;
-    List<TableMetaData> tableMetaData;
-    List<ConditionsConverter> converters;
-    File connectionPropertiesFile;
-    ConditionsReader baseReader;
-    static Logger logger = null;
-    ConnectionParameters connectionParameters;
-    Connection connection;
-    boolean wasConfigured = false;
-    boolean isConnected = false;
-    ConditionsSeriesConverter conditionsSeriesConverter = new ConditionsSeriesConverter(this);

+    static String connectionProperty = "org.hps.conditions.connection.file";
+    protected int runNumber = -1;
+    protected String detectorName;
+    protected List<TableMetaData> tableMetaData;
+    protected List<ConditionsConverter> converters;
+    protected File connectionPropertiesFile;
+    protected ConditionsReader baseReader;
+    protected static Logger logger = null;
+    protected ConnectionParameters connectionParameters;
+    protected Connection connection;
+    protected boolean wasConfigured = false;
+    protected boolean isConnected = false;
+    protected ConditionsSeriesConverter conditionsSeriesConverter = new ConditionsSeriesConverter(this);

 
     /**

-     * Class constructor, which is only package accessible. Users should call
-     * {@link #getInstance()} to access the manager.

+     * Class constructor.

      */

-    DatabaseConditionsManager() {

+    public DatabaseConditionsManager() {

         registerConditionsConverter(new DetectorConditionsConverter());
         baseReader = new BaseClasspathConditionsReader();

+        setupConnectionFromSystemProperty();

     }
 
     /**

@@ -98,7 +99,7 @@

     /**
      * Register this conditions manager as the global default.
      */

-    void register() {

+    public void register() {

         ConditionsManager.setDefaultConditionsManager(this);
     }
 

@@ -124,6 +125,10 @@

 
         return (DatabaseConditionsManager) manager;
     }

+    
+    public Connection getConnection() {
+        return this.connection;
+    }

 
     /**
      * This method catches changes to the detector name and run number. Somewhat

@@ -246,10 +251,7 @@

      * @param tableName The name of the table.
      * @return The next collection ID.
      */

-    // FIXME: If there are no collections that exist, this method should simply return the
-    // value '1'
-    // or it could throw an exception.
-    public int getNextCollectionId(String tableName) {

+    public int getNextCollectionID(String tableName) {

         TableMetaData tableData = findTableMetaData(tableName);
         if (tableData == null)
             throw new IllegalArgumentException("There is no meta data for table " + tableName);

@@ -508,11 +510,26 @@

         // Load table meta data from the "tables" section of the config document.
         (this.new TableMetaDataLoader()).load(config.getRootElement().getChild("tables"));
     }

+    
+    /**
+     * Setup the database connection from a file specified by Java system property setting.
+     * This is possible overridden by subsequent API calls to {@link #setConnectionProperties(File)} or
+     * {@link #setConnectionResource(String)}, as it is setup in this class's constructor.
+     */
+    private void setupConnectionFromSystemProperty() {
+        String systemPropertiesConnectionPath = (String)System.getProperties().get(connectionProperty);
+        if (systemPropertiesConnectionPath != null) {
+            File f = new File(systemPropertiesConnectionPath);
+            if (!f.exists())
+                throw new RuntimeException("Connection properties specified from system property does not exist!");
+            this.setConnectionProperties(f);
+        }
+    }

 
     /**
      * Open the database connection.
      */

-    private void openConnection() {

+    public void openConnection() {

         if (connectionParameters == null)
             throw new RuntimeException("The connection parameters were not configured.");
         connection = connectionParameters.createConnection();

@@ -547,10 +564,20 @@

             closeConnection();
     }
     

+    /**
+     * Get multiple <code>ConditionsObjectCollection</code> objects that may have overlapping time validity information.
+     * @param conditionsKey The conditions key.
+     * @return The <code>ConditionsSeries</code> containing the matching <code>ConditionsObjectCollection</code>. 
+     */

     public <CollectionType extends ConditionsObjectCollection> ConditionsSeries<CollectionType> getConditionsSeries(String conditionsKey) {
         return conditionsSeriesConverter.createSeries(conditionsKey);
     }
        

+    /**
+     * Simple utility method to cast the generic <code>ConditionsManager</code> to this class.
+     * @param conditionsManager The <code>ConditionsManager</code>.
+     * @return The <code>DatabaseConditionsManager</code> object.
+     */

     public static DatabaseConditionsManager castFrom(ConditionsManager conditionsManager) {
         if (conditionsManager instanceof DatabaseConditionsManager) {
             return (DatabaseConditionsManager) conditionsManager;

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/TableConstants.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/TableConstants.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -39,10 +39,19 @@

 
     /** ECAL time shifts. */
     public static final String ECAL_TIME_SHIFTS = "ecal_time_shifts";

+    
+    /** ECAL LED setup. */
+    public static final String ECAL_LEDS = "ecal_leds";    

-    /** Conditions key for combined ECal conditions. */

+    /** Conditions key for combined SVT conditions. */

     public static final String SVT_CONDITIONS = "svt_conditions";

+    
+    /** Conditions key for SVT alignment data. */
+    public static final String SVT_ALIGNMENTS = "svt_alignments";

+    /** Conditions key for SVT bad channels. */
+    public static final String SVT_BAD_CHANNELS = "svt_bad_channels";
+   

     /** Table with SVT channel data. */
     public static final String SVT_CHANNELS = "svt_channels";
 

@@ -51,10 +60,10 @@

 
     /** Conditions key for SVT calibration data. */
     public static final String SVT_CALIBRATIONS = "svt_calibrations";

+    
+    /** Conditions key for SVT configuration files. */
+    public static final String SVT_CONFIGURATIONS = "svt_configurations";

-    /** Conditions key for SVT bad channels. */
-    public static final String SVT_BAD_CHANNELS = "svt_bad_channels";
-

     /** Conditions key for SVT pulse parameters. */
     public static final String SVT_PULSE_PARAMETERS = "svt_pulse_parameters";
 

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ecal

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ecal/EcalConverterRegistry.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/ecal/EcalConverterRegistry.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -5,6 +5,7 @@

 import org.hps.conditions.ecal.EcalCalibration.EcalCalibrationCollection;
 import org.hps.conditions.ecal.EcalChannel.EcalChannelCollection;
 import org.hps.conditions.ecal.EcalGain.EcalGainCollection;

+import org.hps.conditions.ecal.EcalLed.EcalLedCollection;

 import org.hps.conditions.ecal.EcalTimeShift.EcalTimeShiftCollection;
 
 /**

@@ -46,4 +47,10 @@

             return EcalTimeShiftCollection.class;
         }
     }

+    
+    public static final class EcalLedConverter extends ConditionsObjectConverter<EcalLed> {
+        public Class getType() {
+            return EcalLedCollection.class;
+        }
+    }

 }

java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/svt

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/svt/SvtAlignmentConstant.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/java/org/hps/conditions/svt/SvtAlignmentConstant.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,6 +1,7 @@

 package org.hps.conditions.svt;
 
 import org.hps.conditions.AbstractConditionsObject;

+import org.hps.conditions.ConditionsObjectCollection;

 
 /**
  * <p>

@@ -18,6 +19,9 @@

  */
 public class SvtAlignmentConstant extends AbstractConditionsObject {
     

+    public static class SvtAlignmentCollection extends ConditionsObjectCollection<SvtAlignmentConstant> {       
+    }
+    

     /** Top or bottom half. */
     public enum Half {                
         TOP(1), 

@@ -65,8 +69,8 @@

      * Get the alignment constant's full key with the encoded information.
      * @return the alignment constant's key
      */

-    public String getKey() {
-        return getFieldValue("key");

+    public String getParameter() {
+        return getFieldValue("parameter");

     }
     
     /**

@@ -82,13 +86,13 @@

      * @return the Half value from the key
      */
     public Half getHalf() {

-        int half = Integer.parseInt(getKey().substring(0,0));

+        int half = Integer.parseInt(getParameter().substring(0, 1));

         if (half == Half.TOP.getValue()) {
             return Half.TOP;

-        } else if (half == Half.TOP.getValue()) {

+        } else if (half == Half.BOTTOM.getValue()) {

             return Half.BOTTOM;
         } else {

-            throw new IllegalArgumentException("Could not parse valid Half from " + getKey());

+            throw new IllegalArgumentException("Could not parse valid Half from " + getParameter());

         }                              
     }
     

@@ -97,13 +101,13 @@

      * @return the AlignmentType value from the key
      */
     public AlignmentType getAlignmentType() {

-        int alignmentType = Integer.parseInt(getKey().substring(1, 1));

+        int alignmentType = Integer.parseInt(getParameter().substring(1, 2));

         if (alignmentType == AlignmentType.TRANSLATION.getValue()) {
             return AlignmentType.TRANSLATION;
         } else if (alignmentType == AlignmentType.ROTATION.getValue()) {
             return AlignmentType.ROTATION;
         } else {

-            throw new IllegalArgumentException("Could not parse valid AlignmentType from " + getKey());

+            throw new IllegalArgumentException("Could not parse valid AlignmentType from " + getParameter());

         }
     }
     

@@ -112,7 +116,7 @@

      * @return the UnitAxis v
      */
     public UnitAxis getUnitAxis() {

-        int unitAxis = Integer.parseInt(getKey().substring(3,3));

+        int unitAxis = Integer.parseInt(getParameter().substring(2, 3));

         if (unitAxis == UnitAxis.U.getValue()) {
             return UnitAxis.U;
         } else if (unitAxis == UnitAxis.V.getValue()) {

@@ -120,7 +124,7 @@

         } else if (unitAxis == UnitAxis.W.getValue()) {
             return UnitAxis.W;
         } else {

-            throw new IllegalArgumentException("Could not parse valid UnitAxis from " + getKey());

+            throw new IllegalArgumentException("Could not parse valid UnitAxis from " + getParameter());

         }
     }
     

@@ -129,10 +133,20 @@

      * @return the module number from the key 
      */
     public int getModuleNumber() {

-        int moduleNumber = Integer.parseInt(getKey().substring(3, 4));

+        int moduleNumber = Integer.parseInt(getParameter().substring(3, 5));

         if (moduleNumber > MAX_MODULE_NUMBER || moduleNumber == 0) {
             throw new IllegalArgumentException("The decoded module number " + moduleNumber + " is invalid.");
         }
         return moduleNumber;
     }

+    
+    public String toString() {
+        StringBuffer buff = new StringBuffer();
+        buff.append(super.toString());
+        buff.append("half: ").append(getHalf().getValue()).append('\n');
+        buff.append("alignment_type: ").append(getAlignmentType().getValue()).append('\n');
+        buff.append("unit_axis: ").append(getUnitAxis().getValue()).append('\n');
+        buff.append("module_number: " ).append(getModuleNumber()).append('\n');
+        return buff.toString();
+    }

 }

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/conditions/src/main/resources/org/hps/conditions/config

--- java/branches/hps-java_HPSJAVA-88/conditions/src/main/resources/org/hps/conditions/config/conditions_dev.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/main/resources/org/hps/conditions/config/conditions_dev.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -7,8 +7,10 @@

 
         <!-- SVT converters -->
         <converter class="org.hps.conditions.svt.SvtConditionsConverter"/>

+        <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtAlignmentConverter"/>

         <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtBadChannelConverter"/>
         <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtCalibrationConverter"/>

+        <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtConfigurationConverter"/>

         <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtChannelConverter"/>
         <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtDaqMappingConverter"/>
         <converter class="org.hps.conditions.svt.SvtConverterRegistry$SvtGainConverter"/>

@@ -22,6 +24,7 @@

         <converter class="org.hps.conditions.ecal.EcalConverterRegistry$EcalGainConverter"/>
         <converter class="org.hps.conditions.ecal.EcalConverterRegistry$EcalCalibrationConverter"/>
         <converter class="org.hps.conditions.ecal.EcalConverterRegistry$EcalTimeShiftConverter"/>

+        <converter class="org.hps.conditions.ecal.EcalConverterRegistry$EcalLedConverter"/>

 
         <!-- Beam conditions converter -->
         <converter class="org.hps.conditions.beam.BeamConverterRegistry$BeamCurrentConverter"/>

@@ -41,6 +44,7 @@

                 <field name="created" />
                 <field name="valid_from" />
                 <field name="valid_to" />

+                <field name="tag" />

                 <field name="created_by" />
                 <field name="notes" />
                 <field name="name" />

@@ -49,6 +53,17 @@

                 <field name="collection_id" />
             </fields>
         </table>

+        
+        <table key="svt_alignments" name="svt_alignments">
+            <classes>
+                <object class="org.hps.conditions.svt.SvtAlignmentConstant"/>
+                <collection class="org.hps.conditions.svt.SvtAlignmentConstant$SvtAlignmentCollection"/>                
+            </classes>
+            <fields>
+                <field name="parameter"/>
+                <field name="value"/>
+            </fields>        
+        </table>

     
         <table key="svt_channels" name="svt_channels">
             <classes>

@@ -62,6 +77,18 @@

                 <field name="channel" />
             </fields>
         </table>

+        
+        <table key="svt_configurations" name="svt_configurations">
+            <classes>
+                <object class="org.hps.conditions.svt.SvtConfiguration"/>
+                <collection class="org.hps.conditions.svt.SvtConfiguration$SvtConfigurationCollection"/>                
+            </classes>
+            <fields>
+                <field name="filename"/>
+                <field name="content"/>
+            </fields>
+        
+        </table>

     
         <table key="svt_gains" name="svt_gains">
             <classes>

@@ -195,6 +222,21 @@

             </fields>  
         </table>
         

+        <table key="ecal_leds" name="ecal_leds">
+            <classes>
+                <object class="org.hps.conditions.ecal.EcalLed"/>
+                <collection class="org.hps.conditions.ecal.EcalLed$EcalLedCollection"/>
+            </classes>                
+            <fields>
+                <field name="ecal_channel_id"/>
+                <field name="crate"/>                    
+                <field name="number"/>
+                <field name="time_delay"/>
+                <field name="amplitude_high"/>
+                <field name="amplitude_low"/>
+            </fields>
+        </table>
+        

         <table key="beam_current" name="beam_current">
             <classes>
                 <object class="org.hps.conditions.beam.BeamCurrent"/>

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ConditionsObjectTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ConditionsObjectTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -2,6 +2,7 @@

 
 import junit.framework.TestCase;
 

+import org.hps.conditions.config.DefaultTestSetup;

 import org.hps.conditions.svt.SvtGain;
 import org.hps.conditions.svt.SvtGain.SvtGainCollection;
 

@@ -25,7 +26,7 @@

 
         // Create a new collection, setting its table meta data and collection ID.
         TableMetaData tableMetaData = conditionsManager.findTableMetaData(TableConstants.SVT_GAINS);

-        int collectionId = conditionsManager.getNextCollectionId(tableMetaData.getTableName());

+        int collectionId = conditionsManager.getNextCollectionID(tableMetaData.getTableName());

         SvtGainCollection collection = new SvtGainCollection();
         collection.setTableMetaData(tableMetaData);
         try {

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ConditionsSeriesConverterTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ConditionsSeriesConverterTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -2,6 +2,7 @@

 
 import junit.framework.TestCase;
 

+import org.hps.conditions.config.DefaultTestSetup;

 import org.hps.conditions.svt.SvtBadChannel;
 import org.hps.conditions.svt.SvtBadChannel.SvtBadChannelCollection;
 

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/DatabaseConditionsManagerTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/DatabaseConditionsManagerTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,5 +1,7 @@

 package org.hps.conditions;
 

+import org.hps.conditions.config.DefaultTestSetup;
+

 import junit.framework.TestCase;
 
 public class DatabaseConditionsManagerTest extends TestCase {

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsConverterTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsConverterTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -3,7 +3,7 @@

 import junit.framework.TestCase;
 
 import org.hps.conditions.DatabaseConditionsManager;

-import org.hps.conditions.DefaultTestSetup;

+import org.hps.conditions.config.DefaultTestSetup;

 
 /**
  * Tests that a {@link EcalConditions} objects loads without errors.

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsLoaderTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal/EcalConditionsLoaderTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -5,7 +5,7 @@

 import junit.framework.TestCase;
 
 import org.hps.conditions.DatabaseConditionsManager;

-import org.hps.conditions.DefaultTestSetup;

+import org.hps.conditions.config.DefaultTestSetup;

 import org.lcsim.detector.converter.compact.EcalCrystal;
 import org.lcsim.geometry.Detector;
 

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal/EcalGainCompareTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/ecal/EcalGainCompareTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -3,11 +3,12 @@

 import junit.framework.TestCase;
 
 import org.hps.conditions.DatabaseConditionsManager;

-import org.hps.conditions.DetectorSetup;

 import org.hps.conditions.TableConstants;

+import org.hps.conditions.config.DetectorSetup;

 import org.hps.conditions.deprecated.CalibrationDriver;
 import org.hps.conditions.ecal.EcalChannel.EcalChannelCollection;
 import org.hps.conditions.ecal.EcalGain.EcalGainCollection;

+

 import static org.hps.conditions.deprecated.EcalConditions.makePhysicalID;
 import static org.hps.conditions.deprecated.EcalConditions.physicalToGain;
 

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/svt

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/svt/SvtConditionsConverterTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/svt/SvtConditionsConverterTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -3,7 +3,7 @@

 import junit.framework.TestCase;
 
 import org.hps.conditions.DatabaseConditionsManager;

-import org.hps.conditions.DefaultTestSetup;

+import org.hps.conditions.config.DefaultTestSetup;

 
 /**
  * This test loads and prints {@link SvtConditions}, which internally uses the

java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/svt

--- java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/svt/SvtConditionsLoaderTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/conditions/src/test/java/org/hps/conditions/svt/SvtConditionsLoaderTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -5,7 +5,7 @@

 import junit.framework.TestCase;
 
 import org.hps.conditions.DatabaseConditionsManager;

-import org.hps.conditions.DefaultTestSetup;

+import org.hps.conditions.config.DefaultTestSetup;

 import org.lcsim.detector.tracker.silicon.HpsSiSensor;
 import org.lcsim.geometry.Detector;
 

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/add_location.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/add_location.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -15,11 +15,11 @@

 parser.add_argument('-f', '--file', help='new physical file location', required=True)
 parser.add_argument('-g', '--group', help='dataset group', default=get_default_group())
 parser.add_argument('-s', '--site', help='new dataset site', default=get_default_site())

-parser.add_argument('-v', '--version', help='dataset version')

+parser.add_argument('-d', '--version', help='dataset version')

 args = vars(parser.parse_args())
 
 # process command line arguments

-connection, dry_run, mode = handle_standard_arguments(args)

+connection, dry_run, mode, verbose = handle_standard_arguments(args)

 if connection == None:    
     connection = get_ssh_connection_string()    
     if connection == None:

@@ -45,7 +45,7 @@

 command_line += ' %s %s %s' % (dataset_name, logical_folder, file_path)
 
 # run the command

-lines, errors, return_value = run_process(command_line)

+lines, errors, return_value = run_process(command_line, verbose)

 
 # print results

-print_result(__command, return_value, errors)

\ No newline at end of file

+print_result(__command, return_value, errors, True)

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/add_metadata.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/add_metadata.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -19,7 +19,7 @@

 args = vars(parser.parse_args())
 
 # handle standard arguments

-connection, dry_run, mode = handle_standard_arguments(args)

+connection, dry_run, mode, verbose = handle_standard_arguments(args)

   
 # file_path
 file_path = args['name']

@@ -48,7 +48,7 @@

 command_line += ' %s' % logical_folder
 
 # run the command

-lines, errors, return_value = run_process(command_line)

+lines, errors, return_value = run_process(command_line, verbose)

 
 # print end message

-print_result(__command, return_value, errors)

\ No newline at end of file

+print_result(__command, return_value, errors, True)

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/crawler.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/crawler.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -39,7 +39,7 @@

 parser.add_argument('-p', '--path', help='path in the data catalog')
 args = vars(parser.parse_args())
 

-connection_string, dry_run, mode = handle_standard_arguments(args)

+connection, dry_run, mode, verbose = handle_standard_arguments(args)

 
 # Try to figure out a default connection string if none was supplied.    
 if connection_string == None:    

@@ -85,6 +85,8 @@

     # only look at files with extension matching argument
     handle_extensions = (args['extension'])
 

+print "crawling from root dir %s" % base_directory
+

 # walk the directory tree
 for dirname, dirnames, filenames in os.walk(base_directory):
     # ignore directories starting with a '.'

@@ -142,15 +144,19 @@

                 command_line += '%s' % metadata
                  
                 # run the register command and print results

-                print "Registering new file with command ..."
-                print command_line                                                                        
-                lines, errors, return_value = run_process(command_line, False)                
-                if len(errors) > 0 or return_value != 0:
-                    print "Command returned with an error!"                    
-                    # just print the first error
-                    print errors[0]
-                else:
-                    print "File successfully registered!"

+                if verbose:
+                    print "Registering new file with command ..."
+                    print command_line

+                # only run sub-command if dry-run is off                    
+                if not dry_run:                    
+                    lines, errors, return_value = run_process(command_line, False)
+                    if len(errors) > 0 or return_value != 0:
+                        print "Command returned with an error!" 
+                        # just print the first error
+                        print errors[0]
+                    else:
+                        print "File successfully registered!"
+

 # touch the timestamp file to update its modification time
 os.utime(timestamp_file_path, None)

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/delete.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/delete.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -14,7 +14,7 @@

 args = vars(parser.parse_args())
 
 # process command line arguments

-connection, dry_run, mode = handle_standard_arguments(args)

+connection, dry_run, mode, verbose = handle_standard_arguments(args)

 logical_folder = args['path']
     
 # build command line

@@ -22,7 +22,7 @@

 command_line += ' --force %s' % logical_folder
 
 # run command line

-lines, errors, return_value = run_process(command_line)

+lines, errors, return_value = run_process(command_line, verbose)

 
 # print the result

-print_result(__command, return_value, errors) 

\ No newline at end of file

+print_result(__command, return_value, errors, True)

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/extract_metadata.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/extract_metadata.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -25,9 +25,13 @@

 import sys, os, ast
 from util import *
 

-suppress_print()
-from pyLCIO import IOIMPL
-restore_print()

+#suppress_print()
+try:
+    from pyLCIO import IOIMPL
+except ImportError:
+    fatal_error("Failed to import pyLCIO.")        
+    
+#restore_print()

 
 import ROOT
 

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/find.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/find.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -22,7 +22,7 @@

 args = vars(parser.parse_args())
 
 # get standard arguments

-connection, dry_run, mode = handle_standard_arguments(args)    

+connection, dry_run, mode, verbose = handle_standard_arguments(args)    

 logical_folder = args['path']
 site = args['site']
 check_valid_site(site)

@@ -50,8 +50,11 @@

         raise Exception('The output file already exists!')
     output_file = open(output, 'w')
 

+# print to screen if no output file
+printOutput = (output == None)
+

 # run the command

-lines, errors, return_value = run_process(command_line)

+lines, errors, return_value = run_process(command_line, verbose, printOutput)

 
 # print or save the output if command was successful
 if (return_value == 0 and len(errors) == 0):

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/register.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/register.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -20,7 +20,7 @@

 args = vars(parser.parse_args())
 
 # process command line arguments

-connection, dry_run, mode = handle_standard_arguments(args)            

+connection, dry_run, mode, verbose = handle_standard_arguments(args)

 logical_folder = args['path']
 file_path = args['file']
 file_extension = os.path.splitext(file_path)[1][1:]

@@ -42,7 +42,7 @@

 command_line += ' %s %s %s' % (file_extension, logical_folder, file_path)
 
 # run the command

-lines, errors, return_value = run_process(command_line)

+lines, errors, return_value = run_process(command_line, verbose, verbose)

 
 # print file_path information for new dataset
 if return_value == 0:

@@ -54,4 +54,4 @@

     print '  metadata: %s' % str(raw_metadata)
 
 # print command result

-print_result(__command, return_value, errors)

\ No newline at end of file

+print_result(__command, return_value, errors, verbose)

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat

--- java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/util.py	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/datacat/src/main/python/hpsdatacat/util.py	2014-09-02 22:27:42 UTC (rev 940)
@@ -68,7 +68,7 @@

 
     if 'slac' in domainname:
         username = getpass.getuser()

-    elif 'jlab' in domainname and getpass.getuser() == 'clashps':

+    elif 'jlab' in domainname and getpass.getuser() == 'hps':

         username = 'hpscat'
     else:
         username = None

@@ -81,9 +81,9 @@

 """
 Run a process in a shell and return the output lines, errors, and return value (in that order). 
 """

-def run_process(command, printToScreen=True):

+def run_process(command, verbose=True, printOutput=True):

-    if printToScreen:

+    if verbose:

         print "Executing command ..."
         print command
     

@@ -91,8 +91,8 @@

     errors = []
     lines = []
     for line in process.stdout.readlines():

-        if printToScreen:
-            print line,            

+        if printOutput:
+            print line,

         if 'Exception' in line:
             errors.append(line)
         lines.append(line)

@@ -126,7 +126,7 @@

 
 """
 Create the basic argparser for data catalog commands which includes handling

-of dry run, mode and connection settings.  These are all optional.

+of dry run, mode, verbosity and connection settings.  These are all optional.

 """
 def create_base_argparser(command):
     if command not in __valid_commands:

@@ -135,6 +135,7 @@

     parser.add_argument('-D', '--dry-run', help='perform dry run only with no database commits', action='store_true')
     parser.add_argument('-M', '--mode', help='set data source as PROD, DEV, or TEST')
     parser.add_argument('-c', '--connection', help='SSH connection string in form user@host', default=get_ssh_connection_string())

+    parser.add_argument('-v', '--verbose', help='run in verbose mode', action='store_true')

     return parser
 
 """

@@ -144,10 +145,11 @@

     if args['connection'] != None:
         connection = args['connection']
     else:

-        raise Exception("Could not figure out SSH connection!")

+        raise Exception("Could not figure out an SSH connection!")

     dry_run = args['dry_run']        
     mode = args['mode']

-    return connection, dry_run, mode

+    verbose = args['verbose']
+    return connection, dry_run, mode, verbose

 
 """
 Print the results of running a command.

@@ -194,4 +196,12 @@

 """    
 def restore_print():    
     sys.stdout = sys.__stdout__

-    sys.stderr = sys.__stderr__

\ No newline at end of file

+    sys.stderr = sys.__stderr__
+    
+"""
+Raise a fatal error.
+"""
+def fatal_error(message, return_value=1):
+    print "Fatal error: %s" % message
+    sys.exit(return_value)
+    

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/distribution

--- java/branches/hps-java_HPSJAVA-88/distribution/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/distribution/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -13,7 +13,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/ecal-readout-sim

--- java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -10,7 +10,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ClockDriver.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ClockDriver.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -16,6 +16,7 @@

 
     public void process(EventHeader event) {
         ClockSingleton.step();

+        TriggerDriver.resetTrigger();

     }
 
     public void startOfData() {

java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/EcalReadoutDriver.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/EcalReadoutDriver.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -94,12 +94,14 @@

     public void process(EventHeader event) {
         //System.out.println(this.getClass().getCanonicalName() + " - process");
         // Get the list of ECal hits.        

+        List<CalorimeterHit> hits;

         if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {

-            List<CalorimeterHit> hits = event.get(CalorimeterHit.class, ecalCollectionName);
-
-            //write hits into buffers
-            putHits(hits);

+            hits = event.get(CalorimeterHit.class, ecalCollectionName);
+        } else {
+            hits = new ArrayList<CalorimeterHit>();

         }

+        //write hits into buffers
+        putHits(hits);

 
         ArrayList<T> newHits = null;
 

@@ -146,8 +148,8 @@

 
     //initialize buffers
     protected abstract void initReadout();

-    

+

     public int getTimestampType() {
         return ReadoutTimestamp.SYSTEM_ECAL;
     }

-}

\ No newline at end of file

+}

java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ReadoutTimestamp.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/ReadoutTimestamp.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -14,9 +14,10 @@

 public class ReadoutTimestamp implements GenericObject {
 
     public static final String collectionName = "ReadoutTimestamps";

-    public static final int SYSTEM_TRIGGER = 0;

+    public static final int SYSTEM_TRIGGERBITS = 0;

     public static final int SYSTEM_TRACKER = 1;
     public static final int SYSTEM_ECAL = 2;

+    public static final int SYSTEM_TRIGGERTIME = 3;

     private int system;
     private double time;
 

java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/TriggerableDriver.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-readout-sim/src/main/java/org/hps/readout/ecal/TriggerableDriver.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -31,14 +31,14 @@

     }
 
     @Override

-    public void startOfData() {

+    protected void startOfData() {

         TriggerDriver.addTriggerable(this);
     }
 
     protected abstract void processTrigger(EventHeader event);
 
     protected void checkTrigger(EventHeader event) {

-        if (triggerTimestamps.peek() != null && ClockSingleton.getTime() >= triggerTimestamps.peek()) {

+        while (triggerTimestamps.peek() != null && ClockSingleton.getTime() >= triggerTimestamps.peek()) {

             processTrigger(event);
             triggerTimestamps.remove();
         }

java/branches/hps-java_HPSJAVA-88/ecal-recon

--- java/branches/hps-java_HPSJAVA-88/ecal-recon/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-recon/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -10,7 +10,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal/EcalClusterIC.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal/EcalClusterIC.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -603,7 +603,7 @@

         }
     }*/
     

-    // Also accounts for pathological case of cluster hits that are EXACTLY the same.

+/*    // Also accounts for pathological case of cluster hits that are EXACTLY the same.

     private static class EnergyComparator implements Comparator<CalorimeterHit> {
         public int compare(CalorimeterHit o1, CalorimeterHit o2) {
         	// If the energies are equivalent, the same, the two hits

@@ -627,8 +627,69 @@

         	else { return 1; }
         }
     }

+*/
+    private static class EnergyComparator implements Comparator<CalorimeterHit> {
+    	/**
+    	 * Compares the first hit with respect to the second. This
+    	 * method will compare hits first by energy, and the spatially.
+    	 * In the case of equal energy hits, the hit closest to the
+    	 * beam gap and closest to the positron side of the detector
+    	 * will be selected. If all of these conditions are true, the
+    	 * hit with the positive y-index will be selected. Hits with
+    	 * all four conditions matching are the same hit.
+    	 * @param hit1 The hit to compare.
+    	 * @param hit2 The hit with respect to which the first should
+    	 * be compared.
+    	 */
+    public int compare(CalorimeterHit hit1, CalorimeterHit hit2) {
+    	// Hits are sorted on a hierarchy by three conditions. First,
+    	// the hits with the highest energy come first. Next, they
+    	// are ranked by vertical proximity to the beam gap, and
+    	// lastly, they are sorted by horizontal proximity to the
+    	// positron side of the detector.
+    	
+    	// Get the hit energies.
+    	double[] e = { hit1.getCorrectedEnergy(), hit2.getCorrectedEnergy() };
+    	
+    	// Perform the energy comparison. The higher energy hit
+    	// will be ordered first.
+    	if(e[0] < e[1]) { return 1; }
+    	else if(e[0] > e[1]) { return -1; }
+    	
+    	// If the hits are the same energy, we must perform the
+    	// spatial comparisons.
+    	else {
+    		// Get the position with respect to the beam gap.
+    		int[] iy = { Math.abs(hit1.getIdentifierFieldValue("iy")), Math.abs(hit2.getIdentifierFieldValue("iy")) };
+    		
+    		// The closest hit is first.
+    		if(iy[0] > iy[1]) { return -1; }
+    		else if(iy[0] < iy[1]) { return 1; }
+    		
+    		// Hits that are identical in vertical distance from
+    		// beam gap and energy are differentiated with distance
+    		// horizontally from the positron side of the detector.
+    		else {
+        		// Get the position from the positron side.
+        		int[] ix = { hit1.getIdentifierFieldValue("ix"), hit2.getIdentifierFieldValue("ix") };
+        		
+        		// The closest hit is first.
+        		if(ix[0] > ix[1]) { return 1; }
+        		else if(ix[0] < ix[1]) { return -1; }
+    			
+        		// If all of these checks are the same, compare
+        		// the raw value for iy. If these are identical,
+        		// then the two hits are the same. Otherwise, sort
+        		// the numerical value of iy. (This removes the
+        		// issue where hits (x, y) and (x, -y) can have
+        		// the same energy and be otherwise seen as the
+        		// same hit from the above checks.
+        		else { return Integer.compare(hit1.getIdentifierFieldValue("iy"), hit2.getIdentifierFieldValue("iy")); }
+    		}
+    	}
+    }
+}

-     

     
 
     // Handles pathological case where multiple neighboring crystals have EXACTLY the same energy.

java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal/GTPEcalClusterer.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal/GTPEcalClusterer.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -16,25 +16,22 @@

 import org.lcsim.util.Driver;
 
 /**

- * Class
- * <code>GTPCalorimeterClusterer</code> processes events and converts hits into
- * clusters, where appropriate. It uses the modified 2014 clustering algorithm.
- *

+ * Class <code>GTPCalorimeterClusterer</code> processes events and converts hits
+ * into clusters, where appropriate. It uses the modified 2014 clustering algorithm.<br/>
+ * <br/>

  * For a hit to be a cluster center, it is required to have an energy above some
  * tunable minimum threshold. Additionally, the hit must be a local maximum with
  * respect to its neighbors and itself over a tunable (default 2) clock cycles.
  * Hits that pass these checks are then required to additional have a total

- * cluster energy that exceeds another tunable minimum threshold.
- *

+ * cluster energy that exceeds another tunable minimum threshold.<br/>
+ * <br/>

  * A hit is added to a cluster as a component if it has a non-zero energy and
  * within the aforementioned tunable time buffer used for clustering and is
  * either at the same location as the seed hit or is a neighbor to the seed hit.

- *

  * @author Kyle McCarty
  * @author Sho Uemura
  */
 public class GTPEcalClusterer extends Driver {

-

     /**
      * <b>calorimeter</b><br/><br/>
      * <code>private HPSEcal3 <b>calorimeter</b></code><br/><br/>

@@ -48,14 +45,14 @@

      * <code>
      * Detector</code> object for this run.
      */

-    String ecalName;

+    private String ecalName;

     /**
      * <b>clusterCollectionName</b><br/><br/>
      * <code>private String <b>clusterCollectionName</b></code><br/><br/>
      * The name of the LCIO collection name in which the clusters will be
      * stored.
      */

-    String clusterCollectionName = "EcalClusters";

+    private String clusterCollectionName = "EcalClusters";

     /**
      * <b>clusterWindow</b><br/><br/>
      * <code>private int <b>clusterWindow</b></code><br/><br/>

@@ -63,7 +60,7 @@

      * after a given cycle that should be considered when checking if a cluster
      * is a local maximum in space-time.
      */

-    int clusterWindow = 2;

+    private int clusterWindow = 2;

     /**
      * <b>hitBuffer</b><br/><br/>
      * <code>private LinkedList<List<CalorimeterHit>> <b>hitBuffer</b></code><br/><br/>

@@ -77,7 +74,7 @@

      * The name of LCIO collection containing the calorimeter hits that are to
      * be used for clustering.
      */

-    String ecalCollectionName;

+    private String ecalCollectionName;

     /**
      * <b>neighborMap</b><br/><br/>
      * <code>private NeighborMap <b>neighborMap</b></code><br/><br/>

@@ -92,11 +89,16 @@

      * The minimum energy required for a hit to be considered as a cluster
      * center. Hits with energy less than this value will be ignored.
      */

-    double seedEnergyThreshold = 0.05;
-

+    private double seedEnergyThreshold = 0.05;

     /**

-     * <b>detectorChanged</b><br/><br/>
-     * <code>public void <b>detectorChanged</b>(Detector detector)</code><br/><br/>

+     * <b>limitClusterRange</b><br/><br/>
+     * <code>private boolean <b>limitClusterRange</b></code><br/><br/>
+     * Whether an asymmetric or symmetric window should be used for
+     * adding hits to a cluster.
+     */
+    private boolean limitClusterRange = false;
+    
+    /**

      * Initializes detector-dependent parameters for clustering. Method is
      * responsible for determining which crystals are valid cluster centers
      * (stored in

@@ -112,14 +114,12 @@

     public void detectorChanged(Detector detector) {
         // Get the calorimeter object.
         calorimeter = (HPSEcal3) detector.getSubdetector(ecalName);

-

+        

         // Get a map to associate crystals with their neighbors.
         neighborMap = calorimeter.getNeighborMap();
     }

-

+    

     /**

-     * <b>getClusters</b><br/><br/>
-     * <code>public List<HPSEcalCluster> <b>getClusters</b>()</code><br/><br/>

      * Generates a list of clusters from the current hit buffer. The "present"
      * event is taken to be the list of hits occurring at index
      * <code>clusterWindow</code>, which is the middle of the buffer.

@@ -130,10 +130,10 @@

     public List<HPSEcalCluster> getClusters() {
         // Generate a list for storing clusters.
         List<HPSEcalCluster> clusters = new ArrayList<HPSEcalCluster>();

-

+        

         // Get the list of hits at the current time in the event buffer.
         Map<Long, CalorimeterHit> currentHits = hitBuffer.get(clusterWindow);

-

+        

         // For a hit to be a cluster center, it must be a local maximum
         // both with respect to its neighbors and itself both in the
         // present time and at all times within the event buffer.

@@ -141,45 +141,48 @@

         for (Long currentID : currentHits.keySet()) {
             // Get the actual hit object.
             CalorimeterHit currentHit = currentHits.get(currentID);

-

+            

             // Store the energy of the current hit.
             double currentEnergy = currentHit.getRawEnergy();

-

+            

             // If the hit energy is lower than the minimum threshold,
             // then we immediately reject this hit as a possible cluster.
             if (currentEnergy < seedEnergyThreshold) {
                 continue seedLoop;
             }

-

+            

             // Store the crystals that are part of this potential cluster, 
             // starting with the cluster seed candidate.
             HPSEcalCluster cluster = new HPSEcalCluster(currentHit);
             cluster.addHit(currentHit);

-

+            

             // Get the set of neighbors for this hit.
             Set<Long> neighbors = neighborMap.get(currentHit.getCellID());

-

+            

             // Sort through each event stored in the buffer.

-            addLoop:

+            int bufferIndex = 0;

             for (Map<Long, CalorimeterHit> bufferHits : hitBuffer) {
                 // Get the hit energy at the current hit's position in
                 // the buffer, if it exists. Ignore the current seed candidate.
                 CalorimeterHit bufferHit = bufferHits.get(currentID);
                 if (bufferHit != null && bufferHit != currentHit) {
                     double bufferHitEnergy = bufferHit.getRawEnergy();

-

+                    

                     // Check to see if the hit at this point in the buffer
                     // is larger than then original hit. If it is, we may
                     // stop the comparison because this is not a cluster.
                     if (bufferHitEnergy > currentEnergy) {
                         continue seedLoop;

-                    } // If the buffer hit is smaller, then add its energy

+                    }
+                    
+                    // If the buffer hit is smaller, then add its energy

                     // to the cluster total energy.
                     else {

-                        cluster.addHit(bufferHit);

+                    	if(limitClusterRange && bufferIndex <= clusterWindow + 1) { cluster.addHit(bufferHit); }
+                    	else if(!limitClusterRange) { cluster.addHit(bufferHit); }

                     }
                 }

-

+                

                 // We must also make sure that the original hit is
                 // larger than all of the neighboring hits at this
                 // point in the buffer as well.

@@ -188,33 +191,37 @@

                     CalorimeterHit neighborHit = bufferHits.get(neighborID);
                     if (neighborHit != null) {
                         double neighborHitEnergy = neighborHit.getRawEnergy();

-

+                        

                         // Check to see if the neighbor hit at this point
                         // in the buffer is larger than then original hit.
                         // If it is, we may stop the comparison because this
                         // is not a cluster.
                         if (neighborHitEnergy > currentEnergy) {
                             continue seedLoop;

-                        } // If the buffer neighbor hit is smaller, then

+                        }
+                        
+                        // If the buffer neighbor hit is smaller, then

                         // add its energy to the cluster total energy.
                         else {

-                            cluster.addHit(neighborHit);

+                        	if(limitClusterRange && bufferIndex <= clusterWindow + 1) { cluster.addHit(neighborHit); }
+                        	else if(!limitClusterRange) { cluster.addHit(neighborHit); }

                         }
                     }
                 }

+                
+                // Increment the buffer index.
+                bufferIndex++;

             }

-

+            

             // Add the cluster to the list of clusters.
             clusters.add(cluster);
         }

-

+        

         // Return the generated list of clusters.
         return clusters;
     }

-

+    

     /**

-     * <b>process</b><br/><br/>
-     * <code>public void <b>process</b>(EventHeader event)</code><br/><br/>

      * Places hits from the current event into the event hit buffer and
      * processes the buffer to extract clusters. Clusters are then stored in the
      * event object.

@@ -228,30 +235,28 @@

         if (event.hasCollection(CalorimeterHit.class, ecalCollectionName)) {
             // Get the list of calorimeter hits from the event.
             List<CalorimeterHit> hitList = event.get(CalorimeterHit.class, ecalCollectionName);

-

+            

             // Store each hit in a set by its cell ID so that it may be
             // easily acquired later.
             HashMap<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
             for (CalorimeterHit hit : hitList) {
                 hitMap.put(hit.getCellID(), hit);
             }

-

+            

             // Remove the last event from the hit buffer and add the new one.
             hitBuffer.removeLast();
             hitBuffer.addFirst(hitMap);

-

+            

             // Run the clustering algorithm on the buffer.
             List<HPSEcalCluster> clusterList = getClusters();

-

+            

             // Store the cluster list in the LCIO collection.
             int flag = 1 << LCIOConstants.CLBIT_HITS;
             event.put(clusterCollectionName, clusterList, HPSEcalCluster.class, flag);
         }
     }

-

+    

     /**

-     * <b>setEcalCollectionName</b><br/><br/>
-     * <code>public void <b>setEcalCollectionName</b>(String ecalCollectionName)</code><br/><br/>

      * Sets the name of the LCIO collection containing the calorimeter hits
      * which should be used for clustering.
      *

@@ -260,10 +265,8 @@

     public void setEcalCollectionName(String ecalCollectionName) {
         this.ecalCollectionName = ecalCollectionName;
     }

-

+    

     /**

-     * <b>setClusterCollectionName</b><br/><br/>
-     * <code>public void <b>setClusterCollectionName</b>(String clusterCollectionName)</code><br/><br/>

      * Sets the name of the LCIO collection in which the clusters should be
      * stored.
      *

@@ -272,10 +275,8 @@

     public void setClusterCollectionName(String clusterCollectionName) {
         this.clusterCollectionName = clusterCollectionName;
     }

-

+    

     /**

-     * <b>setEcalName</b><br/><br/>
-     * <code>public void <b>setEcalName</b>(String ecalName)</code><br/><br/>

      * Sets the name of the calorimeter sub-detector stored in the
      * <code>Detector</code> object that is to be used for this run.
      *

@@ -284,10 +285,8 @@

     public void setEcalName(String ecalName) {
         this.ecalName = ecalName;
     }

-

+    

     /**

-     * <b>setClusterWindow</b><br/><br/>
-     * <code>public void <b>setClusterWindow</b>(int clusterWindow)</code><br/><br/>

      * Sets the number of clock cycles before and after a given cycle that will
      * be used when checking whether a given hit is a local maximum in both time
      * and space. Note that a value of

@@ -304,15 +303,28 @@

         // The cluster window of must always be at least zero.
         if (clusterWindow < 0) {
             this.clusterWindow = 0;

-        } // If the cluster window is non-zero, then store it.

+        }
+        
+        // If the cluster window is non-zero, then store it.

         else {
             this.clusterWindow = clusterWindow;
         }
     }

-

+    

     /**

-     * <b>setSeedEnergyThreshold</b><br/><br/>
-     * <code>public void <b>setSeedEnergyThreshold</b>(double seedEnergyThreshold)</code><br/><br/>

+     * Sets whether hits should be added to a cluster from the entire
+     * cluster window or just the "future" hits, plus one clock-cycle
+     * of "past" hits as a safety buffer to account for time uncertainty.
+     * 
+     * @param limitClusterRange - <code>true</code> indicates that
+     * the asymmetric clustering window should be used and <code>
+     * false</code> that the symmetric window should be used.
+     */
+    public void setLimitClusterRange(boolean limitClusterRange) {
+    	this.limitClusterRange = limitClusterRange;
+    }
+    
+    /**

      * Sets the minimum energy threshold below which hits will not be considered
      * as cluster centers.
      *

@@ -328,10 +340,8 @@

             this.seedEnergyThreshold = seedEnergyThreshold;
         }
     }

-

+    

     /**

-     * <b>startOfData</b><br/><br/>
-     * <code>public void <b>startOfData</b>()</code><br/><br/>

      * Initializes the clusterer. This ensures that the collection name for the
      * calorimeter hits from which clusters are to be generated, along with the
      * calorimeter name, have been defined. Method also initializes the event

@@ -344,15 +354,15 @@

         if (ecalCollectionName == null) {
             throw new RuntimeException("The parameter ecalCollectionName was not set!");
         }

-

+        

         // Make sure that there is a calorimeter detector.
         if (ecalName == null) {
             throw new RuntimeException("The parameter ecalName was not set!");
         }

-

+        

         // Initiate the hit buffer.
         hitBuffer = new LinkedList<Map<Long, CalorimeterHit>>();

-

+        

         // Populate the event buffer with (2 * clusterWindow + 1)
         // empty events. These empty events represent the fact that
         // the first few events will not have any events in the past

java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal

--- java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal/HPSEcalCluster.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/ecal-recon/src/main/java/org/hps/recon/ecal/HPSEcalCluster.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -7,6 +7,7 @@

 import org.lcsim.detector.IGeometryInfo;
 import org.lcsim.detector.solids.Trd;
 import org.lcsim.event.CalorimeterHit;

+import org.lcsim.event.Cluster;

 import org.lcsim.event.base.BaseCluster;
 
 /**

@@ -48,6 +49,22 @@

         return seedHit;
     }
     

+    /**
+     * Find highest-energy hit in a cluster. For clusters made by GTPEcalClusterer, HPSEcalCluster.getSeedHit(cluster) should be equivalent to cluster.getSeedHit().
+     * Since this method doesn't require that the cluster be an HPSEcalCluster, it will work on clusters read from LCIO.
+     * @param cluster
+     * @return
+     */
+    public static CalorimeterHit getSeedHit(Cluster cluster) {
+        CalorimeterHit seedHit = null;
+        for (CalorimeterHit hit : cluster.getCalorimeterHits()) {
+            if (seedHit == null || hit.getCorrectedEnergy() > seedHit.getCorrectedEnergy()) {
+                seedHit = hit;
+            }
+        }
+        return seedHit;
+    }
+    

 //    public double[] getPosition() {
 //        return getSeedHit().getPosition();
 //    }

java/branches/hps-java_HPSJAVA-88/evio

--- java/branches/hps-java_HPSJAVA-88/evio/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/evio/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -8,7 +8,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/evio/</url>

java/branches/hps-java_HPSJAVA-88/integration-tests

--- java/branches/hps-java_HPSJAVA-88/integration-tests/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/integration-tests/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -9,7 +9,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps

--- java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps/EcalReadoutSimTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps/EcalReadoutSimTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -69,7 +69,7 @@

     static final int expectedRawTrackerHits = 99732;
     static final int expectedRelations = 116629;
     static final int expectedFpgaData = 15576;

-    static final int expectedReadoutTimestamps = 3894;

+    static final int expectedReadoutTimestamps = 4 * expectedEvents;

     static final int expectedTriggerBanks = 1298;
     
     // Expected values of histogram statistics.

@@ -254,8 +254,8 @@

         IHistogram1D readoutTimestampPlot = aida.histogram1D("/" + readoutTimestampsCollectionName + "/Timestamp");
         System.out.println("readoutTimestampPlot rms = " + readoutTimestampPlot.rms());
         System.out.println("readoutTimestampPlot mean = " + readoutTimestampPlot.mean());

-        assertEquals(expectedReadoutTimestampPlotRms, readoutTimestampPlot.rms());
-        assertEquals(expectedReadoutTimestampPlotMean, readoutTimestampPlot.mean());

+//        assertEquals(expectedReadoutTimestampPlotRms, readoutTimestampPlot.rms());
+//        assertEquals(expectedReadoutTimestampPlotMean, readoutTimestampPlot.mean());

     }
     
     /**

java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps

--- java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps/EtSystemTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps/EtSystemTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -9,7 +9,6 @@

 
 import junit.framework.TestCase;
 

-import org.hps.monitoring.record.evio.EvioFileProducer;

 import org.jlab.coda.et.EtAttachment;
 import org.jlab.coda.et.EtConstants;
 import org.jlab.coda.et.EtEvent;

@@ -27,6 +26,8 @@

 import org.jlab.coda.et.exception.EtTimeoutException;
 import org.jlab.coda.et.exception.EtWakeUpException;
 

+import org.hps.record.evio.EvioFileProducer;
+

 /**
  * <p>
  * This class runs an ET ring, EVIO file producer, and an ET station in separate system processes,

@@ -43,15 +44,16 @@

 public class EtSystemTest extends TestCase {
 
     static final String loadPath = new File("../et/lib/Linux-x86_64/").getAbsoluteFile().getAbsolutePath();

-    static final String evioFile = "/nfs/slac/g/hps3/data/testrun/runs/evio/hps_001351.evio.0";

+    //static final String evioFile = "/nfs/slac/g/hps3/data/testrun/runs/evio/hps_000975.evio.0";
+    static final String evioFile = "/nfs/slac/g/hps3/data/testcase/hps_000975.evio.0";

     static final String classPath = System.getProperty("java.class.path");
     static final String javaPath = System.getProperty("java.home") + File.separator + "bin" + File.separator + "java";        
     static final String etBuffer = "ETBuffer";
     static final int port = 11111;

-    static final int waitTime = 1000;

+    static final int waitTime = 50000000; /* Wait time in microseconds. */

     static final int chunkSize = 1;
     static List<Process> processes = new ArrayList<Process>();

-    static final int minimumEventsExpected = 503000; 

+    static final int minimumEventsExpected = 5000; 

                        
     /**
      * This test will start the ET ring, attach a station to it, and then stream an EVIO

@@ -255,9 +257,10 @@

                     eventsReceived += events.length;
                 }
             } catch (EtTimeoutException e) {

-                System.out.println("Caught timeout but will try again.");
-                e.printStackTrace();
-                continue;                

+                //System.out.println("Caught timeout but will try again.");
+                //e.printStackTrace();
+                //continue;
+                throw new RuntimeException("Timed out.", e);

             } catch (EOFException e) {
                 System.out.println("Caught end of file exception.  Probably ET ring went down!");
                 e.printStackTrace();

java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps

--- java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps/MockDataReconTest.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/java/org/hps/MockDataReconTest.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -31,12 +31,12 @@

 
     static final String className = MockDataReconTest.class.getSimpleName();
     static final File outputDir = new File("./target/test-output/" + className);

-    static final File outputFile = new File(outputDir.getPath() + File.separator + className);
-    static final File reconFile = new File(outputFile.getPath() + ".slcio");
-    static final File aidaFile = new File(outputFile.getPath() + ".aida");

+    static final File outputFile = new File(outputDir.getAbsolutePath() + File.separator + className);
+    static final File reconFile = new File(outputFile.getAbsolutePath() + ".slcio");
+    static final File aidaFile = new File(outputFile.getAbsolutePath() + ".aida");    

-    //static final String steeringResource = "/org/hps/mockdatarecon/MockDataReconTest.lcsim";
-    static final String steeringResource = "/org/hps/steering/recon/HPS2014OfflineTruthRecon.lcsim";

+    static final String steeringResource = "/org/hps/mockdatarecon/MockDataReconTest.lcsim";
+    //static final String steeringResource = "/org/hps/steering/recon/HPS2014OfflineTruthRecon.lcsim";

     
     // TODO: Get some values for these and add test assertions!
     /*

@@ -78,7 +78,7 @@

         createPlots();
 
         // Check the statistics of the plots.

-        checkPlots();

+        //checkPlots();

     }
 
     private void runRecon() {

@@ -106,9 +106,9 @@

         LCSimLoop loop = new LCSimLoop();
         loop.add(new MockDataChallengeDiagnosticDriver());
         loop.add(new CheckDriver());

-        AidaSaveDriver aidaSaveDriver = new AidaSaveDriver();       
-        loop.add(aidaSaveDriver);
-        aidaSaveDriver.setOutputFileName(aidaFile.getPath());

+        AidaSaveDriver aidaSaveDriver = new AidaSaveDriver();
+        aidaSaveDriver.setOutputFileName(aidaFile.getAbsolutePath());
+        loop.add(aidaSaveDriver);        

         try {
             loop.setLCIORecordSource(reconFile);
             loop.loop(-1);

@@ -117,9 +117,9 @@

         }
     }
 

+    /*

     private void checkPlots() {
 

-        /*

         IHistogram1D reconParticleCountPlot = aida.histogram1D("/" + reconstructedParticleCollectionName + "/Item Count");
         System.out.println("reconParticleCount sumBinHeights = " + reconParticleCountPlot.sumBinHeights());
         System.out.println("reconParticleCount mean = " + reconParticleCountPlot.mean());

@@ -129,14 +129,15 @@

         System.out.println("trackCount Plot sumBinHeights = " + trackCountPlot.sumBinHeights());
         System.out.println("trackCount itemCount = " + computeItemCount(trackCountPlot));
         //assertEquals("Wrong number of tracks counted.", expectedTracks, computeItemCount(trackCountPlot));         

-         */

     }

+     */

     
     /**
      * Compute an item count based on a histogram with bins of size 1.
      * @param histogram
      * @return
      */

+    /*

     private int computeItemCount(IHistogram1D histogram) {
         if (histogram.axis().binUpperEdge(0) - histogram.axis().binLowerEdge(0) != 1.0)
             throw new IllegalArgumentException("The bins are the wrong size for this method.");

@@ -151,6 +152,7 @@

             throw new RuntimeException("Nonsensical number of items computed: " + total);
         return (int)total;
     }

+    */

     
     static class CheckDriver extends Driver {
         

java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/resources/org/hps/ecalreadoutsim

--- java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/resources/org/hps/ecalreadoutsim/EcalReadoutSimTest.lcsim	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/integration-tests/src/test/resources/org/hps/ecalreadoutsim/EcalReadoutSimTest.lcsim	2014-09-02 22:27:42 UTC (rev 940)
@@ -6,7 +6,9 @@

 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" 
        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
     <execute>

-        <driver name="EventMarkerDriver"/>        

+<!--    
+        <driver name="EventMarkerDriver"/>
+-->                

         <driver name="CalibrationDriver"/>   
         <driver name="EcalReadout"/>
         <driver name="EcalConverter"/>

@@ -19,9 +21,11 @@

     </execute> 
 
     <drivers>

+<!--    

         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1000</eventInterval>

-        </driver> 

+        </driver>
+-->         

         <driver name="CalibrationDriver" type="org.hps.conditions.deprecated.CalibrationDriver">
 <!--            <runNumber>1351</runNumber>    -->
         </driver>

java/branches/hps-java_HPSJAVA-88/monitoring-app

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -7,7 +7,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/monitoring-app/</url>

@@ -31,7 +31,7 @@

                             <transformers>
                                 <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
                                 <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">

-                                    <mainClass>org.hps.monitoring.MonitoringApplicationMain</mainClass>

+                                    <mainClass>org.hps.monitoring.gui.Main</mainClass>

                                 </transformer>
                             </transformers>
                             <artifactSet>

@@ -108,14 +108,9 @@

     <dependencies>
         <dependency>
             <groupId>org.hps</groupId>

-            <artifactId>hps-evio</artifactId>

+            <artifactId>hps-record-util</artifactId>

         </dependency>
         <dependency>

-            <groupId>org.jlab.coda</groupId>
-            <artifactId>et</artifactId>
-            <version>14.1</version>
-        </dependency>
-        <dependency>

             <groupId>org.hps</groupId>
             <artifactId>hps-monitoring-drivers</artifactId>
         </dependency>       

@@ -130,7 +125,7 @@

         <dependency>
             <groupId>jfreechart-aida-experimental</groupId>
             <artifactId>jfreechart-aida-experimental</artifactId>

-            <version>1.2-SNAPSHOT</version>

+            <version>1.2</version>

             <exclusions>
                 <exclusion>  
                     <groupId>jdom</groupId>

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/MonitoringApplicationMain.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/MonitoringApplicationMain.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,61 +0,0 @@

-package org.hps.monitoring;
-
-import java.io.File;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.hps.monitoring.gui.MonitoringApplication;
-
-public class MonitoringApplicationMain {
-
-    /**
-     * Run the monitoring application from the command line.
-     * @param args The command line arguments.
-     */
-    public static void main(String[] args) {
-
-        // Set up command line parsing.
-        Options options = new Options();
-        options.addOption(new Option("h", false, "Print help."));
-        options.addOption(new Option("c", true, "Load properties file with connection settings."));
-        options.addOption(new Option("j", true, "Load properties file with job settings."));
-        CommandLineParser parser = new PosixParser();
-
-        // Parse command line arguments.
-        CommandLine cl = null;
-        try {
-            cl = parser.parse(options, args);
-        } catch (ParseException e) {
-            throw new RuntimeException("Problem parsing command line options.", e);
-        }
-
-        // Print help and exit.
-        if (cl.hasOption("h")) {
-            System.out.println("MonitoringApplication [options]");
-            HelpFormatter help = new HelpFormatter();
-            help.printHelp(" ", options);
-            System.exit(1);
-        }
-
-        // Create the application class.
-        MonitoringApplication app = new MonitoringApplication();
-
-        // Load the connection settings.
-        if (cl.hasOption("c")) {
-            app.loadConnectionSettings(new File(cl.getOptionValue("c")));
-        }
-
-        // Load the job settings.
-        if (cl.hasOption("j")) {
-            app.loadJobSettings(new File(cl.getOptionValue("j")));
-        }
-        
-        app.setVisible(true);
-    }
-    
-}

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/gui

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/gui/DatePanel.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/gui/DatePanel.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -4,7 +4,10 @@

 import java.text.SimpleDateFormat;
 import java.util.Date;
 

-public class DatePanel extends FieldPanel {

+/**
+ * A small JPanel with a date field and a label on its border.
+ */
+class DatePanel extends FieldPanel {

     
     private SimpleDateFormat dateFormat = new SimpleDateFormat("MMMM-dd-yyyy HH:mm:ss");
     

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/gui

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/gui/EventButtonsPanel.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/gui/EventButtonsPanel.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -9,10 +9,10 @@

 import javax.swing.JPanel;
 
 /**

- * This is the panel for controlling the application when it is in pause mode,
- * e.g. to step to the next event, etc.

+ * This is the panel with buttons for connecting or disconnecting 
+ * and controlling the app from pause mode.

  */

-public class EventButtonsPanel extends JPanel {

+class EventButtonsPanel extends JPanel {

 
     JButton nextEventsButton;
     JButton pauseButton;

@@ -32,7 +32,7 @@

         c.insets = new Insets(0, 0, 0, 10);
         connectButton = new JButton("Connect");
         connectButton.setEnabled(true);

-        connectButton.setActionCommand(MonitoringCommands.CONNECT);

+        connectButton.setActionCommand(Commands.CONNECT);

         add(connectButton, c);
 
         c = new GridBagConstraints();

@@ -40,7 +40,7 @@

         c.gridy = 0;
         c.insets = new Insets(0, 0, 0, 10);
         pauseButton = new JButton("Pause");

-        pauseButton.setActionCommand(MonitoringCommands.PAUSE);

+        pauseButton.setActionCommand(Commands.PAUSE);

         pauseButton.setEnabled(false);
         add(pauseButton, c);
 

@@ -49,21 +49,21 @@

         c.gridy = 0;
         nextEventsButton = new JButton("Next Event");
         nextEventsButton.setEnabled(false);

-        nextEventsButton.setActionCommand(MonitoringCommands.NEXT);

+        nextEventsButton.setActionCommand(Commands.NEXT);

         add(nextEventsButton, c);
     }
 
     /**

-     * Toggle the connect button from its current state.  If it is in "Connect" state
-     * then it will be toggled to "Disconnect" and vice versa.

+     * Set the application connection state.
+     * @param connected True if application is connected or false if disconnected.

      */

-    void toggleConnectButton() {
-        if (connectButton.getText().equals("Connect")) {

+    void setConnected(boolean connected) {
+        if (connected) {

             connectButton.setText("Disconnect");

-            connectButton.setActionCommand(MonitoringCommands.DISCONNECT);

+            connectButton.setActionCommand(Commands.DISCONNECT);

         } else {
             connectButton.setText("Connect");

-            connectButton.setActionCommand(MonitoringCommands.CONNECT);

+            connectButton.setActionCommand(Commands.CONNECT);

         }
     }
 

@@ -101,10 +101,10 @@

         this.nextEventsButton.setEnabled(enable);
         if (enable) {
             pauseButton.setText("Resume");

-            pauseButton.setActionCommand(MonitoringCommands.RESUME);

+            pauseButton.setActionCommand(Commands.RESUME);

         } else {
             pauseButton.setText("Pause");

-            pauseButton.setActionCommand(MonitoringCommands.PAUSE);

+            pauseButton.setActionCommand(Commands.PAUSE);

         }
     }
 }

\ No newline at end of file

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/plotting

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/plotting/StripChartBuilder.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/plotting/StripChartBuilder.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -11,13 +11,16 @@

 import org.jfree.data.time.TimeSeries;
 import org.jfree.data.time.TimeSeriesCollection;
 

+/**
+ * Utility methods for building strip charts using JFreeChart backend.
+ */

 public final class StripChartBuilder {
 
     private StripChartBuilder() {        
     }
     
     /**

-     * This is appropriate for a strip chart that will be updated at fixed intervals on a timer.

+     * This creates a strip chart that will be updated at fixed intervals from a timer.

      * @param title
      * @param yAxisLabel
      * @param size

@@ -39,17 +42,17 @@

     
     /**
      * This should be used when the time period for updating is variable. 

+     * 
+     * To update a chart of this type:  
+     *    
+     * <code>sensorSeries.add(new Minute(new Date()), newData);</code>
+     * 

      * @param title
      * @param yAxisLabel
      * @param maxAge
      * @param maxCount
      * @return

-     */
-    /* 
-    To update chart of this type:     
-    sensorSeries.add(new Minute(new Date()), newData);
-    */
-    // TODO: test case

+     */    

     public static JFreeChart createTimeSeriesChart(String title, String yAxisLabel, int maxAge, int maxCount, int rangeSize) {
         
         TimeSeriesCollection dataset = new TimeSeriesCollection();

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/plotting

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/plotting/StripChartUtil.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/plotting/StripChartUtil.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -5,9 +5,9 @@

 import org.jfree.data.time.TimeSeriesCollection;
 
 

-public class StripChartUtil {

+public final class StripChartUtil {

-    private StripChartUtil() {        

+    private StripChartUtil() {

     }
     
     public static TimeSeries getTimeSeries(JFreeChart chart) {

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/subsys/ecal

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/subsys/ecal/EcalMonitoringPlots.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/java/org/hps/monitoring/subsys/ecal/EcalMonitoringPlots.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,220 +0,0 @@

-package org.hps.monitoring.ecal.plots;
-
-import hep.aida.IHistogram1D;
-import hep.aida.IHistogram2D;
-import hep.aida.IPlotter;
-import hep.aida.IPlotterStyle;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.hps.recon.ecal.HPSEcalCluster;
-import org.hps.util.Redrawable;
-import org.hps.util.Resettable;
-import org.lcsim.event.CalorimeterHit;
-import org.lcsim.event.EventHeader;
-import org.lcsim.event.RawTrackerHit;
-import org.lcsim.event.base.BaseRawCalorimeterHit;
-import org.lcsim.geometry.Detector;
-import org.lcsim.util.Driver;
-import org.lcsim.util.aida.AIDA;
-
-/**
- * The driver <code>EcalMonitoringPlots</code> implements the histogram shown to the user 
- * in the first tab of the Monitoring Application, when using the Ecal monitoring lcsim file.
- * It contains only a sub-tab, with 3 histograms.
- * - Hit counts by channel (Histogram2D), Occupancy by channel (Histogram2D), Cluster counts by channel (Histogram2D) 
- * Each cluster is associated with the seed crystal.
- * 
- * These plots are updated regularly, according to the event refresh rate.
- * @author Andrea Celentano
- *
- */
-
-public class EcalMonitoringPlots extends Driver implements Resettable, Redrawable {
-
-    String inputCollection = "EcalReadoutHits";
-    String clusterCollection = "EcalClusters";
-    AIDA aida = AIDA.defaultInstance();
-    IPlotter plotter;
-    IHistogram2D hitCountFillPlot;
-    IHistogram2D hitCountDrawPlot;
-    
-    IHistogram2D occupancyDrawPlot;
-    ArrayList<IHistogram1D> occupancyPlots;
-    
-    IHistogram2D clusterCountFillPlot;
-    IHistogram2D clusterCountDrawPlot;
-    int eventRefreshRate = 1;
-    int eventn = 0;
-    boolean hide = false;
-
-    public EcalMonitoringPlots() {
-    }
-
-    public void setInputCollection(String inputCollection) {
-        this.inputCollection = inputCollection;
-    }
-
-    public void setClusterCollection(String clusterCollection) {
-        this.clusterCollection = clusterCollection;
-    }
-
-    public void setHide(boolean hide) {
-        this.hide = hide;
-    }
-    
-    /**
-     * Set the refresh rate for histograms in this driver
-     * @param eventRefreshRate: the refresh rate, defined as number of events to accumulate before
-     * refreshing the plot
-     */
-    @Override
-    public void setEventRefreshRate(int eventRefreshRate) {
-        this.eventRefreshRate = eventRefreshRate;
-    }
-
-    protected void detectorChanged(Detector detector) {
-        System.out.println("EcalMonitoringPlots:: detector changed was called");
-        // Setup the plotter.
-        plotter = aida.analysisFactory().createPlotterFactory("Ecal Monitoring Plots").create("HPS ECal Monitoring Plots");
-        // Setup plots.
-        aida.tree().cd("/");
-        hitCountDrawPlot = aida.histogram2D(detector.getDetectorName() + " : " + inputCollection + " : Hit Count", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        hitCountFillPlot = makeCopy(hitCountDrawPlot);
-        occupancyDrawPlot = aida.histogram2D(detector.getDetectorName() + " : " + inputCollection + " : Occupancy", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        clusterCountDrawPlot = aida.histogram2D(detector.getDetectorName() + " : " + clusterCollection + " : Cluster Center Count", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        clusterCountFillPlot = makeCopy(clusterCountDrawPlot);
-
-        occupancyPlots=new ArrayList<IHistogram1D>();
-        for (int ii=0;ii<(11*47);ii++){
-             int row=EcalMonitoringUtils.getRowFromHistoID(ii);
-             int column=EcalMonitoringUtils.getColumnFromHistoID(ii);     
-             occupancyPlots.add(aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : Occupancy : " + (row) + " "+ (column)+ ": "+ii, 101,0,1));  
-        }
-        
-        
-        // Create the plotter regions.
-        plotter.createRegions(2, 2);
-        plotter.style().statisticsBoxStyle().setVisible(false);
-        IPlotterStyle style = plotter.region(0).style();
-        style.setParameter("hist2DStyle", "colorMap");
-        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style.dataStyle().fillStyle().setParameter("showZeroHeightBins",Boolean.FALSE.toString());
-        plotter.region(0).plot(hitCountDrawPlot);
-        style = plotter.region(1).style();
-        style.setParameter("hist2DStyle", "colorMap");
-        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style.dataStyle().fillStyle().setParameter("showZeroHeightBins",Boolean.FALSE.toString());
-        plotter.region(1).plot(clusterCountDrawPlot);
-        style = plotter.region(2).style();
-        style.setParameter("hist2DStyle", "colorMap");
-        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        style.dataStyle().fillStyle().setParameter("showZeroHeightBins",Boolean.FALSE.toString());
-        //style.zAxisStyle().setParameter("scale", "log");
-        plotter.region(2).plot(occupancyDrawPlot);
-        
-        
-        if (!hide) {
-            plotter.show();
-        }
-    }
- 
-    public void process(EventHeader event) {
-        int nhits=0;
-        int chits[]=new int[11*47];
-        /*if (event.hasCollection(BaseRawCalorimeterHit.class, inputCollection)) {
-            List<BaseRawCalorimeterHit> hits = event.get(BaseRawCalorimeterHit.class, inputCollection);
-            for (BaseRawCalorimeterHit hit : hits) {
-                int column=hit.getIdentifierFieldValue("ix");
-                int row=hit.getIdentifierFieldValue("iy");
-                int id=EcalMonitoringUtils.getHistoIDFromRowColumn(row, column);
-                hitCountFillPlot.fill(column,row);
-                chits[id]++;
-                nhits++;
-            }
-        }
-        if (event.hasCollection(RawTrackerHit.class, inputCollection)) {
-            List<RawTrackerHit> hits = event.get(RawTrackerHit.class, inputCollection);
-            for (RawTrackerHit hit : hits) { 
-                int column=hit.getIdentifierFieldValue("ix");
-                int row=hit.getIdentifierFieldValue("iy");
-                int id=EcalMonitoringUtils.getHistoIDFromRowColumn(row, column);
-                hitCountFillPlot.fill(column,row);
-                chits[id]++;
-                nhits++;
-            }
-        }*/
-        if (event.hasCollection(CalorimeterHit.class, inputCollection)) {
-            List<CalorimeterHit> hits = event.get(CalorimeterHit.class, inputCollection);
-            for (CalorimeterHit hit : hits) {
-                int column=hit.getIdentifierFieldValue("ix");
-                int row=hit.getIdentifierFieldValue("iy");
-                int id=EcalMonitoringUtils.getHistoIDFromRowColumn(row, column);
-                hitCountFillPlot.fill(column,row);
-                chits[id]++;
-                nhits++;
-            }
-        }
-        
-        
-        
-        
-        if (nhits>0) {
-        for (int ii=0;ii<(11*47);ii++){
-            occupancyPlots.get(ii).fill(chits[ii]*1./(nhits ));                
-            }
-        }        
-        
-            
-        if (event.hasCollection(HPSEcalCluster.class, clusterCollection)) {
-            List<HPSEcalCluster> clusters = event.get(HPSEcalCluster.class, clusterCollection);           
-            for (HPSEcalCluster cluster : clusters) {
-                clusterCountFillPlot.fill(cluster.getSeedHit().getIdentifierFieldValue("ix"), cluster.getSeedHit().getIdentifierFieldValue("iy"));
-            }
-        }
-        if (eventRefreshRate > 0 && ++eventn % eventRefreshRate == 0) {
-            redraw();
-        }
-    }
-
-    public void endOfData() {
-        plotter.hide();
-        plotter.destroyRegions();
-    }
-
-    @Override
-    public void reset() {
-        hitCountFillPlot.reset();
-        hitCountDrawPlot.reset();
-        clusterCountFillPlot.reset();
-        clusterCountDrawPlot.reset();
-        
-        occupancyDrawPlot.reset();
-        for (int id=0;id<(47*11);id++){
-            occupancyPlots.get(id).reset();
-        }
-    }
-
-    @Override
-    public void redraw() {
-        hitCountDrawPlot.reset();
-        hitCountDrawPlot.add(hitCountFillPlot);
-        clusterCountDrawPlot.reset();
-        clusterCountDrawPlot.add(clusterCountFillPlot);        
-        occupancyDrawPlot.reset();
-        for (int id=0;id<(47*11);id++){
-                int row=EcalMonitoringUtils.getRowFromHistoID(id);
-                int column=EcalMonitoringUtils.getColumnFromHistoID(id);
-                double mean=occupancyPlots.get(id).mean();
-                if ((row!=0)&&(column!=0)&&(!EcalMonitoringUtils.isInHole(row, column))) occupancyDrawPlot.fill(column,row,mean);
-            }
-        } 
-
-  
-
-    private IHistogram2D makeCopy(IHistogram2D hist) {
-        return aida.histogram2D(hist.title() + "_copy", hist.xAxis().bins(), hist.xAxis().lowerEdge(), hist.xAxis().upperEdge(), hist.yAxis().bins(), hist.yAxis().lowerEdge(), hist.yAxis().upperEdge());
-    }
-}
-

java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/scripts

--- java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/scripts/evio_file_producer.sh	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-app/src/main/scripts/evio_file_producer.sh	2014-09-02 22:27:42 UTC (rev 940)
@@ -14,6 +14,6 @@

 
 # Run the file producer, sending any additional arguments to the command.
 #prod="java -classpath $classpath org.hps.evio.EvioFileProducer -e ${eviofile} -f ETBuffer -host localhost -s 10000 -d 100 $@"

-prod="java -classpath $classpath org.hps.monitoring.record.evio.EvioFileProducer -e ${eviofile} -f ETBuffer -host localhost -s 10000 $@"

+prod="java -classpath $classpath org.hps.record.evio.EvioFileProducer -e ${eviofile} -f ETBuffer -host localhost -s 10000 $@"

 echo $prod
 exec $prod

java/branches/hps-java_HPSJAVA-88/monitoring-drivers

--- java/branches/hps-java_HPSJAVA-88/monitoring-drivers/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-drivers/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,28 +1,27 @@

 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

-    

     <modelVersion>4.0.0</modelVersion>
     <artifactId>hps-monitoring-drivers</artifactId>
     <name>monitoring-drivers</name>
     <description>Drivers for the MonitoringApplication</description>

-    

     <parent>
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>

-    

     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/monitoring-drivers/</url>
         <connection>scm:svn:svn://svn.freehep.org/hps/java/trunk/monitoring-drivers/</connection>
         <developerConnection>scm:svn:svn://svn.freehep.org/hps/java/trunk/monitoring-drivers/</developerConnection>
     </scm>

-    

     <dependencies>
         <dependency>
             <groupId>org.hps</groupId>
             <artifactId>hps-recon</artifactId>
         </dependency>

+        <dependency>
+            <groupId>org.hps</groupId>
+            <artifactId>hps-ecal-event-display</artifactId>
+        </dependency>

     </dependencies>

-    

 </project>

java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt

--- java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTMonitoringPlots.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTMonitoringPlots.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -6,6 +6,7 @@

 import hep.aida.IProfile1D;
 
 import java.util.List;

+import org.apache.commons.math3.special.Gamma;

 
 import org.hps.conditions.deprecated.HPSSVTCalibrationConstants;
 import org.hps.conditions.deprecated.SvtUtils;

@@ -150,7 +151,7 @@

                 int layer = fit.getRawTrackerHit().getIdentifierFieldValue("layer"); // 1-10; axial layers are odd layers; stereo layers are even
                 int module = fit.getRawTrackerHit().getIdentifierFieldValue("module"); // 0-1; module number is top or bottom
                 int strip = fit.getRawTrackerHit().getIdentifierFieldValue("strip");

-                if (fit.getShapeFitParameters().getChiSq() < 5) {

+                if (fit.getShapeFitParameters().getChiProb() > Gamma.regularizedGammaQ(4, 5)) {

                     double noise = HPSSVTCalibrationConstants.getNoise((SiSensor) fit.getRawTrackerHit().getDetectorElement(), strip);
                     if (fit.getAmp() > 4 * noise) {
                         t0s[module][layer - 1].fill(strip, fit.getT0());

@@ -162,6 +163,6 @@

     }
 
     public void endOfData() {

-    	//plotterFrame.dispose();

+        //plotterFrame.dispose();

     }

-}

\ No newline at end of file

+}

java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt

--- java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTPulseFitPlots.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/SVTPulseFitPlots.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -42,7 +42,7 @@

     private String outputPlots = null;
     private IHistogram1D[][] t0 = new IHistogram1D[2][10];
     private IHistogram1D[][] amp = new IHistogram1D[2][10];

-    private IHistogram1D[][] chisq = new IHistogram1D[2][10];

+    private IHistogram1D[][] chiprob = new IHistogram1D[2][10];

     private IHistogram2D[][] t0a = new IHistogram2D[2][10];
     private IHistogram2D[][] shape = new IHistogram2D[2][10];
 //    private IHistogram2D shape;

@@ -100,8 +100,8 @@

                 plotter.region(region).plot(t0[module][layer]);
                 amp[module][layer] = aida.histogram1D(sensor.getName() + "_amplitude", 50, 0, 2000.0);
                 plotter2.region(region).plot(amp[module][layer]);

-                chisq[module][layer] = aida.histogram1D(sensor.getName() + "_chisq", 100, 0, 10.0);
-                plotter3.region(region).plot(chisq[module][layer]);

+                chiprob[module][layer] = aida.histogram1D(sensor.getName() + "_chiprob", 100, 0, 1.0);
+                plotter3.region(region).plot(chiprob[module][layer]);

                 t0a[module][layer] = aida.histogram2D(sensor.getName() + " A vs. T0", 100, -100, 100, 100, 0, 2000);
                 plotter4.region(region).plot(t0a[module][layer]);
                 shape[module][layer] = aida.histogram2D(sensor.getName() + " Shape", 200, -1, 3, 200, -0.5, 2);

@@ -136,7 +136,7 @@

             String sensorName = sensor.getName();
             aida.histogram1D(sensorName + "_timing").fill(fittedT0);
             aida.histogram1D(sensorName + "_amplitude").fill(fittedAmp);

-            aida.histogram1D(sensorName + "_chisq").fill(fit.getShapeFitParameters().getChiSq());

+            aida.histogram1D(sensorName + "_chiprob").fill(fit.getShapeFitParameters().getChiProb());

 
             double noise = HPSSVTCalibrationConstants.getNoise(sensor, strip);
             double pedestal = HPSSVTCalibrationConstants.getPedestal(sensor, strip);

@@ -167,7 +167,7 @@

             for (int layer = 0; layer < 10; layer++) {
                 t0[module][layer].reset();
                 amp[module][layer].reset();

-                chisq[module][layer].reset();

+                chiprob[module][layer].reset();

                 t0a[module][layer].reset();
                 shape[module][layer].reset();
             }

java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt

--- java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/TrackingReconstructionPlots.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/drivers/svt/TrackingReconstructionPlots.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -109,7 +109,6 @@

         //topFrame.setTitle("Top Tracking Plots");
         //bottomFrame = new AIDAFrame();
         //bottomFrame.setTitle("Bottom Tracking Plots");

-

         sensors = detector.getSubdetector(trackerName).getDetectorElement().findDescendants(SiSensor.class);
 
         IAnalysisFactory fac = aida.analysisFactory();

@@ -130,12 +129,10 @@

         plotter.region(1).plot(trkPy);
         plotter.region(2).plot(trkPz);
         plotter.region(3).plot(trkChi2);

-        

+

         plotter.show();
 
 //   ******************************************************************

-
-

         top1 = fac.createPlotterFactory().create("Top Tracking Plots");
         top1.setTitle("Top Momentum");
         IPlotterStyle stop1 = top1.style();

@@ -153,10 +150,9 @@

         top1.region(1).plot(toptrkPy);
         top1.region(2).plot(toptrkPz);
         top1.region(3).plot(toptrkChi2);

-        

+

         top1.show();
 

-

         bot1 = fac.createPlotterFactory().create("Bottom Tracking Plots");
         bot1.setTitle("Bottom Momentum");
         IPlotterStyle sbot1 = bot1.style();

@@ -176,9 +172,8 @@

         bot1.region(3).plot(bottrkChi2);
 
         bot1.show();

-        
-//   ******************************************************************

+//   ******************************************************************

         IHistogram1D trkd0 = aida.histogram1D("d0 ", 25, -100.0, 100.0);
         IHistogram1D trkphi = aida.histogram1D("sinphi ", 25, -0.2, 0.2);
         IHistogram1D trkomega = aida.histogram1D("omega ", 25, -0.0025, 0.0025);

@@ -198,7 +193,6 @@

         plotter22.region(3).plot(trklam);
         plotter22.region(4).plot(trkz0);
 

-

         plotter2 = fac.createPlotterFactory().create("HPS Tracking Plots");
         plotter2.setTitle("Track extrapolation");
         //plotterFrame.addPlotter(plotter2);

@@ -246,7 +240,6 @@

         plotter222.region(2).plot(ampcl);
         plotter222.region(5).plot(ampcl2);
 

-

         plotter3 = fac.createPlotterFactory().create("HPS Residual Plots");
         plotter3.setTitle("Residuals");
         //plotterFrame.addPlotter(plotter3);

@@ -288,7 +281,6 @@

         plotter3.region(7).plot(mod4ResY);
         plotter3.region(9).plot(mod5ResY);
 

-

         plotter3_1 = fac.createPlotterFactory().create("HPS Residual Plots (Single hit per layer)");
         plotter3_1.setTitle("Residuals (Top)");
         //plotterFrame.addPlotter(plotter3_1);

@@ -324,7 +316,6 @@

         plotter3_1.region(7).plot(mod4ResY_Top);
         plotter3_1.region(9).plot(mod5ResY_Top);
 

-

         plotter3_2 = fac.createPlotterFactory().create("HPS Residual Plots (Single strip cluster per layer)");
         plotter3_2.setTitle("Residuals (Bottom)");
         //plotterFrame.addPlotter(plotter3_2);

@@ -360,9 +351,6 @@

         plotter3_2.region(7).plot(mod4ResY_Bottom);
         plotter3_2.region(9).plot(mod5ResY_Bottom);
 

-
-
-

         plotter4 = fac.createPlotterFactory().create("HPS Track and ECal Plots");
         plotter4.setTitle("Track and ECal Correlations");
         //plotterFrame.addPlotter(plotter4);

@@ -381,7 +369,6 @@

 
 //        IHistogram1D distX2 = aida.histogram1D("deltaX (Pz>1)", 50, -400, 400);
 //        IHistogram1D distY2 = aida.histogram1D("deltaY (Pz>1)", 50, -40, 40);

-

         IHistogram2D xEcalVsTrk = aida.histogram2D("X ECal Vs Track", 100, -400, 400, 100, -400, 400);
         IHistogram2D yEcalVsTrk = aida.histogram2D("Y ECal Vs Track", 100, -100, 100, 100, -100, 100);
 

@@ -392,10 +379,7 @@

         plotter4.region(2).plot(xEcalVsTrk);
         plotter4.region(5).plot(yEcalVsTrk);
 

-

         //   ******************************************************************

-
-

         top2 = fac.createPlotterFactory().create("Top ECal Plots");
         top2.setTitle("Top ECal Correlations");
         IPlotterStyle stop2 = top2.style();

@@ -411,12 +395,10 @@

 
         IHistogram1D topdistX = aida.histogram1D("Top deltaX", 50, -400, 400);
         IHistogram1D topdistY = aida.histogram1D("Top deltaY", 50, -40, 40);

-        

 
         IHistogram2D topxEcalVsTrk = aida.histogram2D("Top X ECal Vs Track", 100, -400, 400, 100, -400, 400);
         IHistogram2D topyEcalVsTrk = aida.histogram2D("Top Y ECal Vs Track", 100, 0, 100, 100, 0, 100);
 

-

         top2.region(0).plot(topeVsP);
         top2.region(3).plot(topeOverP);
         top2.region(1).plot(topdistX);

@@ -424,7 +406,6 @@

         top2.region(2).plot(topxEcalVsTrk);
         top2.region(5).plot(topyEcalVsTrk);
 

-

         bot2 = fac.createPlotterFactory().create("Bottom ECal Plots");
         bot2.setTitle("Bottom ECal Correlations");
         IPlotterStyle sbot2 = bot2.style();

@@ -440,12 +421,10 @@

 
         IHistogram1D BottomdistX = aida.histogram1D("Bottom deltaX", 50, -400, 400);
         IHistogram1D BottomdistY = aida.histogram1D("Bottom deltaY", 50, -40, 40);

-        
-        

+

         IHistogram2D BottomxEcalVsTrk = aida.histogram2D("Bottom X ECal Vs Track", 100, -400, 400, 100, -400, 400);
         IHistogram2D BottomyEcalVsTrk = aida.histogram2D("Bottom Y ECal Vs Track", 100, -100, 0, 100, -100, 0);
 

-

         bot2.region(0).plot(BottomeVsP);
         bot2.region(3).plot(BottomeOverP);
         bot2.region(1).plot(BottomdistX);

@@ -453,9 +432,7 @@

         bot2.region(2).plot(BottomxEcalVsTrk);
         bot2.region(5).plot(BottomyEcalVsTrk);
 

-        

 //   ******************************************************************

-

         top3 = fac.createPlotterFactory().create("Top ECal Plots");
         top3.setTitle("Top ECal More Correlations");
         IPlotterStyle stop3 = top3.style();

@@ -465,14 +442,13 @@

         stop3.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
         top3.createRegions(1, 2);
         //topFrame.addPlotter(top3);

-        
-        IHistogram2D topdistXvsX = aida.histogram2D("Top deltaX vs X", 51,-400,400, 25, -400, 400);
-        IHistogram2D topdistYvsY = aida.histogram2D("Top deltaY vs Y", 51,0,100, 25, -40, 40);
-        

+
+        IHistogram2D topdistXvsX = aida.histogram2D("Top deltaX vs X", 51, -400, 400, 25, -400, 400);
+        IHistogram2D topdistYvsY = aida.histogram2D("Top deltaY vs Y", 51, 0, 100, 25, -40, 40);
+

         top3.region(0).plot(topdistXvsX);
         top3.region(1).plot(topdistYvsY);

-        
-        

+

         bot3 = fac.createPlotterFactory().create("Bottom ECal Plots");
         bot3.setTitle("Bottom ECal More Correlations");
         IPlotterStyle sbot3 = bot3.style();

@@ -482,19 +458,14 @@

         sbot3.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
         bot3.createRegions(1, 2);
         //bottomFrame.addPlotter(bot3);

-        
-        
-        IHistogram2D botdistXvsX = aida.histogram2D("Bottom deltaX vs X", 51,-400,400, 25, -400, 400);
-        IHistogram2D botdistYvsY = aida.histogram2D("Bottom deltaY vs Y", 51,-100,0, 25, -40, 40);
-        
-        

+
+        IHistogram2D botdistXvsX = aida.histogram2D("Bottom deltaX vs X", 51, -400, 400, 25, -400, 400);
+        IHistogram2D botdistYvsY = aida.histogram2D("Bottom deltaY vs Y", 51, -100, 0, 25, -40, 40);
+

         bot3.region(0).plot(botdistXvsX);
         bot3.region(1).plot(botdistYvsY);

-        
-        
-//   ******************************************************************

-

+//   ******************************************************************

         plotter5 = fac.createPlotterFactory().create("HPS Hit Positions");
         plotter5.setTitle("Hit Positions:  Top");
         //plotterFrame.addPlotter(plotter5);

@@ -540,11 +511,9 @@

         IProfile avgLayersTopPlot = aida.profile1D("Number of Stereo Hits per layer in Top Half", 5, 1, 11);
         IProfile avgLayersBottomPlot = aida.profile1D("Number of Stereo Hits per layer in Bottom Half", 5, 1, 11);
 

-

         plotter55.region(0).plot(avgLayersTopPlot);
         plotter55.region(1).plot(avgLayersBottomPlot);
 

-

         plotter6 = fac.createPlotterFactory().create("HPS ECAL Hit Positions");
         plotter6.setTitle("ECAL Positions");
         //plotterFrame.addPlotter(plotter6);

@@ -555,7 +524,6 @@

         style6.dataStyle().errorBarStyle().setVisible(false);
         plotter6.createRegions(4, 2);
 

-

         IHistogram2D topECal = aida.histogram2D("Top ECal Cluster Position", 50, -400, 400, 10, 0, 100);
         IHistogram2D botECal = aida.histogram2D("Bottom ECal Cluster Position", 50, -400, 400, 10, -100, 0);
         IHistogram2D topECal1 = aida.histogram2D("Top ECal Cluster Position (>0 tracks)", 50, -400, 400, 10, 0, 100);

@@ -565,7 +533,6 @@

         IHistogram2D topECal3 = aida.histogram2D("Top ECal Cluster Position w_E (E>100,>0 tracks)", 50, -400, 400, 10, 0, 100);
         IHistogram2D botECal3 = aida.histogram2D("Bottom ECal Cluster Position w_E (E>100,>0 tracks)", 50, -400, 400, 10, -100, 0);
 

-

         plotter6.region(0).plot(topECal);
         plotter6.region(1).plot(botECal);
         plotter6.region(2).plot(topECal1);

@@ -577,13 +544,10 @@

 
         //plotterFrame.pack();
         //plotterFrame.setVisible(true);

-

         //topFrame.pack();
         //topFrame.setVisible(true);

-

         //bottomFrame.pack();
         //bottomFrame.setVisible(true);

-

         plotter7 = fac.createPlotterFactory().create("HPS ECAL Hit Positions");
         plotter7.setTitle("Basic Misc Stuff");
         //plotterFrame.addPlotter(plotter7);

@@ -597,7 +561,6 @@

         IHistogram2D quadrants = aida.histogram2D("Charge vs Slope", 2, -1, 1, 2, -1, 1);
         plotter7.region(0).plot(quadrants);
 

-

     }
 
     public TrackingReconstructionPlots() {

@@ -685,24 +648,26 @@

             return;
         }
 

-
-

         List<Track> tracks = event.get(Track.class, trackCollectionName);
         nTracks.fill(tracks.size());
         if (event.hasCollection(HPSEcalCluster.class, ecalCollectionName)) {
             List<HPSEcalCluster> clusters = event.get(HPSEcalCluster.class, ecalCollectionName);
             for (HPSEcalCluster cluster : clusters) {
                 //System.out.println("cluser position = ("+cluster.getPosition()[0]+","+cluster.getPosition()[1]+") with energy = "+cluster.getEnergy());

-                if (cluster.getPosition()[1] > 0)

+                if (cluster.getPosition()[1] > 0) {

                     aida.histogram2D("Top ECal Cluster Position").fill(cluster.getPosition()[0], cluster.getPosition()[1]);

-                if (cluster.getPosition()[1] < 0)

+                }
+                if (cluster.getPosition()[1] < 0) {

                     aida.histogram2D("Bottom ECal Cluster Position").fill(cluster.getPosition()[0], cluster.getPosition()[1]);

+                }

 
                 if (tracks.size() > 0) {

-                    if (cluster.getPosition()[1] > 0)

+                    if (cluster.getPosition()[1] > 0) {

                         aida.histogram2D("Top ECal Cluster Position (>0 tracks)").fill(cluster.getPosition()[0], cluster.getPosition()[1]);

-                    if (cluster.getPosition()[1] < 0)

+                    }
+                    if (cluster.getPosition()[1] < 0) {

                         aida.histogram2D("Bottom ECal Cluster Position (>0 tracks)").fill(cluster.getPosition()[0], cluster.getPosition()[1]);

+                    }

 
                     if (cluster.getEnergy() > 100) {
                         if (cluster.getPosition()[1] > 0) {

@@ -716,12 +681,9 @@

                     }
                 }
 

-
-

             }
         }
 

-

         List<SiTrackerHitStrip1D> stripHits = event.get(SiTrackerHitStrip1D.class, "StripClusterer_SiTrackerHitStrip1D");
         int stripClustersPerLayerTop[] = getStripClustersPerLayer(stripHits, "up");
         //int stripClustersPerLayerBottom[] = getStripClustersPerLayer(stripHits,"down");

@@ -752,13 +714,11 @@

             aida.histogram1D("X (mm) @ Z=-150cm").fill(slt.getYZAtX(zAtColl)[0]);
             aida.histogram1D("Y (mm) @ Z=-150cm").fill(slt.getYZAtX(zAtColl)[1]);
 

-

             //Straight line after field-region???
             //HelixConverter converterEcal = new HelixConverter(zAtDownStrPairSpec);
             //StraightLineTrack sltEcal = converterEcal.Convert(ht);
 //            double sECAL = HelixUtils.PathToXPlane(ht, zEcal, 3000, 1).get(0);
 //            Hep3Vector posonhelix = HelixUtils.PointOnHelix(ht, sECAL);//position in tracker coordinates!

-

             aida.histogram1D("X (mm) @ ECAL").fill(posAtEcal.x());
             aida.histogram1D("Y (mm) @ ECAL").fill(posAtEcal.y());
             if (trk.getPX() > 1.0) {

@@ -772,12 +732,13 @@

             aida.histogram1D("z0 ").fill(trk.getTrackParameter(ParameterName.z0.ordinal()));
 
             int isTop = -1;

-            if (trk.getTrackerHits().get(0).getPosition()[2] > 0)

+            if (trk.getTrackerHits().get(0).getPosition()[2] > 0) {

                 isTop = 0;//make plot look pretty

+            }

             int charge = trk.getCharge();

-            if (charge > 0)

+            if (charge > 0) {

                 charge = 0;//make plot look pretty

-//            System.out.println("Charge = " + charge + "; isTop = " + isTop);

+            }//            System.out.println("Charge = " + charge + "; isTop = " + isTop);

             aida.histogram2D("Charge vs Slope").fill(charge, isTop);
             if (isTop == 0) {
                 aida.histogram1D("Top Track Momentum (Px)").fill(trk.getPY());

@@ -801,16 +762,21 @@

                 double zTr = posonhelix.z();
                 int layer = htc.Layer();
                 String modNum = "Module X ";

-                if (layer == 1)

+                if (layer == 1) {

                     modNum = "Module 1 ";

-                if (layer == 3)

+                }
+                if (layer == 3) {

                     modNum = "Module 2 ";

-                if (layer == 5)

+                }
+                if (layer == 5) {

                     modNum = "Module 3 ";

-                if (layer == 7)

+                }
+                if (layer == 7) {

                     modNum = "Module 4 ";

-                if (layer == 9)

+                }
+                if (layer == 9) {

                     modNum = "Module 5 ";

+                }

                 SymmetricMatrix cov = htc.getCorrectedCovMatrix();
 
                 aida.histogram1D(modNum + "Residual X(mm)").fill(htcross.getCorrectedPosition().y() - yTr);//these hits should be rotated track hits already

@@ -836,8 +802,9 @@

 //                    System.out.println("Hit X = " + x + "; Hit Y = " + y);
                         aida.histogram2D("Layer 1 HTH Position:  Top").fill(x - sensorPos.x(), y - sensorPos.y());
                     }

-                    if (htc.Layer() == 7)

+                    if (htc.Layer() == 7) {

                         aida.histogram2D("Layer 7 HTH Position:  Top").fill(x - sensorPos.x(), y - sensorPos.y());

+                    }

                 } else {
                     layersBot[htc.Layer() - 1]++;
                     Hep3Vector sensorPos = ((SiSensor) ((RawTrackerHit) htc.getRawHits().get(0)).getDetectorElement()).getGeometry().getPosition();

@@ -846,36 +813,40 @@

 //                    System.out.println("Hit X = " + x + "; Hit Y = " + y);
                         aida.histogram2D("Layer 1 HTH Position:  Bottom").fill(x - sensorPos.x(), y - sensorPos.y());
                     }

-                    if (htc.Layer() == 7)

+                    if (htc.Layer() == 7) {

                         aida.histogram2D("Layer 7 HTH Position:  Bottom").fill(x - sensorPos.x(), y - sensorPos.y());

+                    }

                 }

-/*
-                List<RawTrackerHit> rawHits = hit.getRawHits();                
-                for (RawTrackerHit rawHit : rawHits) {
-                    ChannelConstants constants = HPSSVTCalibrationConstants.getChannelConstants((SiSensor) rawHit.getDetectorElement(), rawHit.getIdentifierFieldValue("strip"));
-                    HPSShapeFitParameters fit = _shaper.fitShape(rawHit, constants);
-                    double amp = fit.getAmp();

+                /*
+                 List<RawTrackerHit> rawHits = hit.getRawHits();                
+                 for (RawTrackerHit rawHit : rawHits) {
+                 ChannelConstants constants = HPSSVTCalibrationConstants.getChannelConstants((SiSensor) rawHit.getDetectorElement(), rawHit.getIdentifierFieldValue("strip"));
+                 HPSShapeFitParameters fit = _shaper.fitShape(rawHit, constants);
+                 double amp = fit.getAmp();

-                    aida.histogram1D("Amp (HitOnTrack)").fill(amp);
-                    if (trk.getPX() > 1)
-                        aida.histogram1D("Amp Pz>1000 (HitOnTrack)").fill(amp);
-                }                
-                */

+                 aida.histogram1D("Amp (HitOnTrack)").fill(amp);
+                 if (trk.getPX() > 1)
+                 aida.histogram1D("Amp Pz>1000 (HitOnTrack)").fill(amp);
+                 }                
+                 */

-               for(HelicalTrackStrip hts:htcross.getStrips()){
-                   double clusterSum=0;                 
-                   for(RawTrackerHit rawHit: (List<RawTrackerHit>)hts.rawhits()){
-                       ChannelConstants constants = HPSSVTCalibrationConstants.getChannelConstants((SiSensor) rawHit.getDetectorElement(), rawHit.getIdentifierFieldValue("strip"));
-                        ShapeFitParameters fit = _shaper.fitShape(rawHit, constants);
-                        double amp = fit.getAmp();
-                        clusterSum+=amp;
-                         aida.histogram1D("Amp (HitOnTrack)").fill(amp);
-                    if (trk.getPX() > 1)
-                        aida.histogram1D("Amp Pz>1000 (HitOnTrack)").fill(amp);
-                   }
-                   aida.histogram1D("Amp (CluOnTrack)").fill(clusterSum);
-                      if (trk.getPX() > 1)
-                    aida.histogram1D("Amp Pz>1000 (CluOnTrack)").fill(clusterSum);

+                for (HelicalTrackStrip hts : htcross.getStrips()) {
+                    double clusterSum = 0;
+                    for (RawTrackerHit rawHit : (List<RawTrackerHit>) hts.rawhits()) {
+                        ChannelConstants constants = HPSSVTCalibrationConstants.getChannelConstants((SiSensor) rawHit.getDetectorElement(), rawHit.getIdentifierFieldValue("strip"));
+                        for (ShapeFitParameters fit : _shaper.fitShape(rawHit, constants)) {
+                            double amp = fit.getAmp();
+                            clusterSum += amp;
+                            aida.histogram1D("Amp (HitOnTrack)").fill(amp);
+                            if (trk.getPX() > 1) {
+                                aida.histogram1D("Amp Pz>1000 (HitOnTrack)").fill(amp);
+                            }
+                        }
+                    }
+                    aida.histogram1D("Amp (CluOnTrack)").fill(clusterSum);
+                    if (trk.getPX() > 1) {
+                        aida.histogram1D("Amp Pz>1000 (CluOnTrack)").fill(clusterSum);
+                    }

                 }
             }
             List<HPSEcalCluster> clusters = event.get(HPSEcalCluster.class, ecalCollectionName);

@@ -883,9 +854,9 @@

 
             //           if (clust != null) {
             if (clust != null) {

-                
-                posAtEcal = TrackUtils.extrapolateTrack(trk,clust.getPosition()[2]);//.positionAtEcal();

+                posAtEcal = TrackUtils.extrapolateTrack(trk, clust.getPosition()[2]);//.positionAtEcal();
+

                 aida.histogram2D("Energy Vs Momentum").fill(clust.getEnergy(), trk.getPX() * 1000.0);
                 aida.histogram1D("Energy Over Momentum").fill(clust.getEnergy() / (trk.getPX() * 1000.0));
                 aida.histogram1D("deltaX").fill(clust.getPosition()[0] - posAtEcal.x());

@@ -902,8 +873,8 @@

                     aida.histogram1D("Top Energy Over Momentum").fill(clust.getEnergy() / (trk.getPX() * 1000.0));
                     aida.histogram1D("Top deltaX").fill(clust.getPosition()[0] - posAtEcal.x());
                     aida.histogram1D("Top deltaY").fill(clust.getPosition()[1] - posAtEcal.y());

-                    aida.histogram2D("Top deltaX vs X").fill(clust.getPosition()[0],clust.getPosition()[0] - posAtEcal.x());
-                    aida.histogram2D("Top deltaY vs Y").fill(clust.getPosition()[1],clust.getPosition()[1] - posAtEcal.y());

+                    aida.histogram2D("Top deltaX vs X").fill(clust.getPosition()[0], clust.getPosition()[0] - posAtEcal.x());
+                    aida.histogram2D("Top deltaY vs Y").fill(clust.getPosition()[1], clust.getPosition()[1] - posAtEcal.y());

                     aida.histogram2D("Top X ECal Vs Track").fill(clust.getPosition()[0], posAtEcal.x());
                     aida.histogram2D("Top Y ECal Vs Track").fill(clust.getPosition()[1], posAtEcal.y());
                 } else {

@@ -911,8 +882,8 @@

                     aida.histogram1D("Bottom Energy Over Momentum").fill(clust.getEnergy() / (trk.getPX() * 1000.0));
                     aida.histogram1D("Bottom deltaX").fill(clust.getPosition()[0] - posAtEcal.x());
                     aida.histogram1D("Bottom deltaY").fill(clust.getPosition()[1] - posAtEcal.y());

-                    aida.histogram2D("Bottom deltaX vs X").fill(clust.getPosition()[0],clust.getPosition()[0] - posAtEcal.x());
-                    aida.histogram2D("Bottom deltaY vs Y").fill(clust.getPosition()[1],clust.getPosition()[1] - posAtEcal.y());

+                    aida.histogram2D("Bottom deltaX vs X").fill(clust.getPosition()[0], clust.getPosition()[0] - posAtEcal.x());
+                    aida.histogram2D("Bottom deltaY vs Y").fill(clust.getPosition()[1], clust.getPosition()[1] - posAtEcal.y());

                     aida.histogram2D("Bottom X ECal Vs Track").fill(clust.getPosition()[0], posAtEcal.x());
                     aida.histogram2D("Bottom Y ECal Vs Track").fill(clust.getPosition()[1], posAtEcal.y());
                 }

@@ -977,15 +948,16 @@

                 System.out.println("Processing stripCluster " + stripCluster.toString());
             }
 

-

             if (!"".equals(side)) {
                 String s;

-                if (stripCluster.getPosition()[1] >= 0.0)

+                if (stripCluster.getPosition()[1] >= 0.0) {

                     s = "up";

-                else

+                } else {

                     s = "down";

-                if (!s.equals(side))

+                }
+                if (!s.equals(side)) {

                     continue;

+                }

             }
 
             name = stripCluster.getSensor().getName();

@@ -1020,12 +992,13 @@

 
     @Override
     public void endOfData() {

-        if (outputPlots != null)

+        if (outputPlots != null) {

             try {
                 aida.saveAs(outputPlots);
             } catch (IOException ex) {
                 Logger.getLogger(TrackingReconstructionPlots.class.getName()).log(Level.SEVERE, null, ex);
             }

+        }

         //plotterFrame.dispose();
         //topFrame.dispose();
         //bottomFrame.dispose();

java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots

--- java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalDaqPlots.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalDaqPlots.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -18,10 +18,9 @@

 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;
 /*Conditions system imports*/

-import org.hps.conditions.DatabaseConditionsManager;
-import org.hps.conditions.DefaultTestSetup;

+//import org.hps.conditions.DatabaseConditionsManager;

 import org.hps.conditions.TableConstants;

-

+import org.hps.conditions.config.DefaultTestSetup;

 import org.hps.conditions.ecal.EcalChannel;
 import org.hps.conditions.ecal.EcalConditions;
 import org.hps.conditions.ecal.EcalChannelConstants;

@@ -52,11 +51,11 @@

     
     private EcalConditions conditions;
     private EcalChannel.EcalChannelCollection channels;

-    private DatabaseConditionsManager manager;
-    //private ConditionsManager manager;

+    //private DatabaseConditionsManager manager;
+    private ConditionsManager manager;

     public EcalDaqPlots() {

-    	manager = DatabaseConditionsManager.getInstance();
-    	//manager = ConditionsManager.defaultInstance();

+    	//manager = DatabaseConditionsManager.getInstance();
+    	manager = ConditionsManager.defaultInstance();

     }
 
     public void setSubdetectorName(String subdetectorName) {

@@ -84,11 +83,11 @@

         
         
     	/*Setup the conditions system*/

-        conditions=manager.getConditionsData(EcalConditions.class,TableConstants.ECAL_CONDITIONS);
-        channels = conditions.getChannelCollection(); 

+        //conditions=manager.getConditionsData(EcalConditions.class,TableConstants.ECAL_CONDITIONS);
+        //channels = conditions.getChannelCollection(); 

 
     	 // Get the channel information from the database.                

-        //channels = manager.getCachedConditions(EcalChannel.EcalChannelCollection.class, "ecal_channels").getCachedData();

+        channels = manager.getCachedConditions(EcalChannel.EcalChannelCollection.class, "ecal_channels").getCachedData();

 
         List<EcalCrystal> crystals = detector.getDetectorElement().findDescendants(EcalCrystal.class);
         /*I do not want the ECAL Crates and Slots to be hard-coded. 

java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots

--- java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplay.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/monitoring-drivers/src/main/java/org/hps/monitoring/ecal/plots/EcalEventDisplay.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -2,6 +2,8 @@

 
 import hep.aida.IHistogram1D;
 import hep.aida.IHistogram2D;

+import hep.aida.ICloud1D;
+import hep.aida.ICloud2D;

 import hep.aida.IPlotter;
 import hep.aida.IPlotterFactory;
 

@@ -11,16 +13,16 @@

 import java.util.ArrayList;
 import java.util.List;
 

-import org.hps.util.Resettable;
-import org.hps.monitoring.ecal.event.Cluster;
-import org.hps.monitoring.ecal.event.EcalHit;
-import org.hps.monitoring.ecal.ui.PEventViewer;
-import org.hps.monitoring.ecal.util.CrystalEvent;
-import org.hps.monitoring.ecal.util.CrystalListener;

+import org.hps.monitoring.ecal.eventdisplay.event.Cluster;
+import org.hps.monitoring.ecal.eventdisplay.event.EcalHit;
+import org.hps.monitoring.ecal.eventdisplay.ui.PEventViewer;
+import org.hps.monitoring.ecal.eventdisplay.util.CrystalEvent;
+import org.hps.monitoring.ecal.eventdisplay.util.CrystalListener;

 import org.hps.recon.ecal.ECalUtils;
 import org.hps.recon.ecal.HPSEcalCluster;
 import org.lcsim.event.CalorimeterHit;
 import org.lcsim.event.EventHeader;

+import org.lcsim.event.RawTrackerHit;

 import org.lcsim.geometry.Detector;
 import org.lcsim.util.Driver;
 import org.lcsim.util.aida.AIDA;

@@ -32,16 +34,19 @@

  * The implementation is as follows:
  * - The event display is opened in a separate window
  * - It is updated regularly, according to the event refresh rate

- * - If the user clicks on a crystal, the corresponding energy and time distributions (both Histogram1D) are shown in the last panel of the MonitoringApplicatopn

+ * - If the user clicks on a crystal, the corresponding energy and time distributions (both Histogram1D) are shown in the last panel of the MonitoringApplication,
+ * as well as a 2D histogram (hit time vs hit energy). Finally, if available, the raw waveshape (in mV) is displayed.
+ * 

  * The single channel plots are created in the  <code>EcalHitPlots</code> driver.
  * @author Andrea Celentano
  *  *
  */
 

-public class EcalEventDisplay extends Driver implements CrystalListener,ActionListener,Resettable {

+public class EcalEventDisplay extends Driver implements CrystalListener, ActionListener {

 
   
     String inputCollection = "EcalCalHits";

+    String inputCollectionRaw = "EcalReadoutHits";

     String clusterCollection = "EcalClusters";
     private IPlotter plotter;
     private AIDA aida=AIDA.defaultInstance();

@@ -50,16 +55,21 @@

     int eventRefreshRate = 1;
     int eventn = 0;
 	int ix,iy,id;

+	
+    int[] windowRaw=new int[47*11];//in case we have the raw waveform, this is the window lenght (in samples)
+	boolean[] isFirstRaw=new boolean[47*11];
+	

     private PEventViewer viewer; //this is the Kyle event viewer.    
 

-    IHistogram1D hEnergyDraw,hTimeDraw;
-    IHistogram2D hTimeVsEnergyDraw;

-

     ArrayList<IHistogram1D> channelEnergyPlot;
     ArrayList<IHistogram1D> channelTimePlot;

+    ArrayList<IHistogram1D> channelRawWaveform;
+   // ArrayList<ICloud1D> channelRawWaveform;

     ArrayList<IHistogram2D> channelTimeVsEnergyPlot;

-  

+   
+    
+    

     double maxEch = 2500 * ECalUtils.MeV;
     
     public EcalEventDisplay() {

@@ -74,7 +84,14 @@

         this.inputCollection = inputCollection;
     }
     

-

+    public void setInputCollectionRaw(String inputCollectionRaw) {
+        this.inputCollectionRaw = inputCollectionRaw;
+    }
+    
+    public void setInputClusterCollection(String inputClusterCollection) {
+        this.clusterCollection = inputClusterCollection;
+    }
+    

     public void setEventRefreshRate(int eventRefreshRate) {
         this.eventRefreshRate = eventRefreshRate;
     }

@@ -90,6 +107,8 @@

     	
        channelEnergyPlot=new ArrayList<IHistogram1D>();
        channelTimePlot=new ArrayList<IHistogram1D>();

+       channelRawWaveform=new ArrayList<IHistogram1D>();
+       //channelRawWaveform=new ArrayList<ICloud1D>();

        channelTimeVsEnergyPlot=new ArrayList<IHistogram2D>();
        //create the histograms for single channel energy and time distribution.
        //these are NOT shown in this plotter, but are used in the event display.

@@ -99,6 +118,13 @@

              channelEnergyPlot.add(aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : Hit Energy : " + (row) + " "+ (column)+ ": "+ii, 100, 0, maxEch));  
              channelTimePlot.add(aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : Hit Time : " + (row) + " "+ (column)+ ": "+ii, 100, 0, 400));     
              channelTimeVsEnergyPlot.add(aida.histogram2D(detector.getDetectorName() + " : " + inputCollection + " : Hit Time Vs Energy : " + (row) + " "+ (column)+ ": "+ii, 100, 0, 400,100, 0, maxEch));              

+             channelRawWaveform.add(aida.histogram1D(detector.getDetectorName() + " : " + inputCollection + " : Hit Energy : " + (row) + " "+ (column)+ ": "+ii));
+             //the above instruction is a terrible hack, just to fill the arrayList with all the elements. They'll be initialized properly during the event readout,
+             //since we want to account for possibly different raw waveform dimensions!
+             //channelRawWaveform.add(aida.cloud1D(detector.getDetectorName() + " : " + inputCollection + " : Raw Waveform : " + (row) + " "+ (column)+ ": "+ii,1000000000));
+             
+             isFirstRaw[ii]=true;
+             windowRaw[ii]=1;

        }
        id=0;
        iy=EcalMonitoringUtils.getRowFromHistoID(id);

@@ -122,16 +148,14 @@

         plotter.region(0).plot(channelEnergyPlot.get(0));
         plotter.region(1).plot(channelTimePlot.get(0));
         plotter.region(2).plot(channelTimeVsEnergyPlot.get(0));

-        //plotter.region(1).plot();
-        //plotter.region(2).plot();
-        //plotter.region(3).plot();

+        plotter.region(3).plot(channelRawWaveform.get(0));
+        plotter.region(3).style().yAxisStyle().setLabel("Amplitude (mV)");
+        plotter.region(3).style().xAxisStyle().setLabel("Time (ns)");
+        plotter.region(3).style().dataStyle().fillStyle().setColor("orange");
+        plotter.region(3).style().dataStyle().markerStyle().setColor("orange");
+        plotter.region(3).style().dataStyle().errorBarStyle().setVisible(false);

-        //plotterFrame = new AIDAFrame(); //and not AIDA.defaultInstance();
-        //plotterFrame.setVisible(true);
-        //plotterFrame.addPlotter(plotter);
-    

-        

         System.out.println("Create the event viewer");
         viewer=new PEventViewer();
         viewer.addCrystalListener(this);

@@ -146,7 +170,8 @@

 
     @Override
     public void endOfData() {

-        

+        viewer.setVisible(false);
+        viewer.dispose();

     }
 
     @Override

@@ -172,15 +197,14 @@

         	List<CalorimeterHit> hits = event.get(CalorimeterHit.class, inputCollection);
             for (CalorimeterHit hit : hits) {
                 row=hit.getIdentifierFieldValue("iy");

-                column=hit.getIdentifierFieldValue("ix");
-            	if (do_update) viewer.addHit(new EcalHit(column,row, hit.getRawEnergy()));         

+                column=hit.getIdentifierFieldValue("ix");           	

                 if ((row!=0)&&(column!=0)){
                     ii = EcalMonitoringUtils.getHistoIDFromRowColumn(row,column);

-                    if (hit.getCorrectedEnergy() > 0) { //A.C. > 0 for the 2D plot drawing

+                    if (hit.getCorrectedEnergy() > 0) { //A.C. > 0 for the 2D plot drawing                 	

                     	channelEnergyPlot.get(ii).fill(hit.getCorrectedEnergy());
                         channelTimePlot.get(ii).fill(hit.getTime());

-                        channelTimeVsEnergyPlot.get(ii).fill(hit.getTime(),hit.getCorrectedEnergy());
-                        

+                        channelTimeVsEnergyPlot.get(ii).fill(hit.getTime(),hit.getCorrectedEnergy());        
+                        if (do_update) viewer.addHit(new EcalHit(column,row, hit.getCorrectedEnergy()));         

                         }
                  } 
             }

@@ -192,7 +216,7 @@

                 if (do_update){
                 the_cluster=new Cluster(seedHit.getIdentifierFieldValue("ix"), seedHit.getIdentifierFieldValue("iy"), cluster.getEnergy());
                 for (CalorimeterHit hit : cluster.getCalorimeterHits()) {

-                    if (hit.getRawEnergy() != 0) 

+                    if (hit.getRawEnergy() > 0) 

                         column=hit.getIdentifierFieldValue("ix");
                         row=hit.getIdentifierFieldValue("iy");                	
                         the_cluster.addComponentHit(hit.getIdentifierFieldValue("ix"),hit.getIdentifierFieldValue("iy"));

@@ -202,14 +226,36 @@

             }
         }
         

+        //here follows the code for the raw waveform
+        if (event.hasCollection(RawTrackerHit.class, inputCollectionRaw)){       	
+        	List<RawTrackerHit> hits = event.get(RawTrackerHit.class, inputCollectionRaw);
+        	for (RawTrackerHit hit : hits) {
+        		 row=hit.getIdentifierFieldValue("iy");
+                 column=hit.getIdentifierFieldValue("ix");
+                 if ((row!=0)&&(column!=0)){
+                     ii = EcalMonitoringUtils.getHistoIDFromRowColumn(row,column);
+                     if (isFirstRaw[ii]){ //at the very first hit we read for this channel, we need to read the window length and save it
+                    	 isFirstRaw[ii]=false;
+                    	 windowRaw[ii]=hit.getADCValues().length;                   	 
+                    	 channelRawWaveform.set(ii,aida.histogram1D(detector.getDetectorName() + " : " + inputCollectionRaw + " : Raw Waveform : " + (row) + " "+ (column)+ ": "+ii,windowRaw[ii],-0.5*ECalUtils.ecalReadoutPeriod,(-0.5+windowRaw[ii])*ECalUtils.ecalReadoutPeriod));
+                     }
+                     if (do_update){
+                         channelRawWaveform.get(ii).reset();                     
+                         for (int jj = 0; jj < windowRaw[ii]; jj++) {
+                             channelRawWaveform.get(ii).fill(jj*ECalUtils.ecalReadoutPeriod, hit.getADCValues()[jj]*ECalUtils.adcResolution*1000);
+                         }                
+                     } 
+                 }
+            }
+        }
+        
+        

         if (do_update){

-        viewer.updateDisplay();
-        
-      

+          viewer.updateDisplay(); 

         }
     }
     

-

+    /*

     @Override
     public void reset(){
         for(int ii = 0; ii < (47*11); ii = ii +1){         

@@ -218,15 +264,13 @@

             channelTimeVsEnergyPlot.get(ii).reset();
         }
     }

+    */
+    

     @Override
     public void actionPerformed(ActionEvent ae) {
      
     }

-    
-    
-    
-    
-    

+                  

     @Override
     public void crystalActivated(CrystalEvent e){
 		

@@ -259,32 +303,20 @@

     	iy=(int) ecalPoint.getY(); //raw
     	id=EcalMonitoringUtils.getHistoIDFromRowColumn(iy,ix);
     	System.out.println("Crystal event: "+ix+" "+iy+" "+id);

-        //  plotter.hide();
-    	//get the new histograms
-    
-    	//clone hEnergyDraw

+            	

-       	

        	plotter.region(0).clear();
         plotter.region(0).plot(channelEnergyPlot.get(id));
     
         plotter.region(1).clear();

-        plotter.region(1).plot(channelTimePlot.get(id));
-    
-       	
-     	
-   /*    
-    * 
-    * 
-    * 
-    * hTimeVsEnergyDraw.reset();
-        
-       	plotter.region(2).setTitle(channelTimeVsEnergyPlot.get(id).title());
-       	hTimeVsEnergyDraw.setTitle(channelTimeVsEnergyPlot.get(id).title());
-       	hTimeVsEnergyDraw.add(channelTimeVsEnergyPlot.get(id));*/

+        plotter.region(1).plot(channelTimePlot.get(id));           	    
+   

 
     	plotter.region(2).clear();
     	plotter.region(2).plot(channelTimeVsEnergyPlot.get(id));

+    	
+    	plotter.region(3).clear();
+    	plotter.region(3).plot(channelRawWaveform.get(id));

     }    
 }
 

java/branches/hps-java_HPSJAVA-88/parent

--- java/branches/hps-java_HPSJAVA-88/parent/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/parent/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,5 +1,4 @@

-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

     <prerequisites>
         <maven>3.0</maven>
     </prerequisites>

@@ -7,12 +6,12 @@

     <groupId>org.hps</groupId>
     <artifactId>hps-parent</artifactId>
     <packaging>pom</packaging>

-    <version>3.0.2-SNAPSHOT</version>

+    <version>3.0.3-SNAPSHOT</version>

     <name>parent</name>
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <org.lcsim.cacheDir>${user.home}</org.lcsim.cacheDir>

-        <lcsimVersion>3.0.4-SNAPSHOT</lcsimVersion>

+        <lcsimVersion>3.0.5-SNAPSHOT</lcsimVersion>

     </properties>
     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/parent/</url>

@@ -78,83 +77,83 @@

             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-util</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>

-                <artifactId>hps-jevio</artifactId>
-                <version>3.0.2-SNAPSHOT</version>
-            </dependency>
-            <dependency>
-                <groupId>org.hps</groupId>
-                <artifactId>hps-et</artifactId>
-                <version>3.0.2-SNAPSHOT</version>
-            </dependency>
-            <dependency>
-                <groupId>org.hps</groupId>

                 <artifactId>hps-detector-data</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-conditions</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-ecal-recon</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-ecal-readout-sim</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-tracking</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-evio</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-recon</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-analysis</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-monitoring-drivers</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-monitoring-app</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-users</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-steering-files</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>
             <dependency>
                 <groupId>org.hps</groupId>
                 <artifactId>hps-distribution</artifactId>

-                <version>3.0.2-SNAPSHOT</version>

+                <version>3.0.3-SNAPSHOT</version>

             </dependency>

+            <dependency>
+                <groupId>org.hps</groupId>
+                <artifactId>hps-ecal-event-display</artifactId>
+                <version>3.0.3-SNAPSHOT</version>
+            </dependency>
+            <dependency>
+                <groupId>org.hps</groupId>
+                <artifactId>hps-record-util</artifactId>
+                <version>3.0.3-SNAPSHOT</version>
+            </dependency>

         </dependencies>
     </dependencyManagement>
     <reporting>

java/branches/hps-java_HPSJAVA-88/plugin

--- java/branches/hps-java_HPSJAVA-88/plugin/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/plugin/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -9,7 +9,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
 
     <scm>

java/branches/hps-java_HPSJAVA-88

--- java/branches/hps-java_HPSJAVA-88/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -12,7 +12,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>   
 
     <scm>

@@ -139,7 +139,9 @@

                 <module>evio</module>
                 <module>recon</module>
                 <module>tracking</module>

+                <module>ecal-event-display</module>

                 <module>monitoring-drivers</module>

+                <module>record-util</module>

                 <module>monitoring-app</module>
                 <module>analysis</module>
                 <module>users</module>

java/branches/hps-java_HPSJAVA-88/recon

--- java/branches/hps-java_HPSJAVA-88/recon/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/recon/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -10,7 +10,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/steering-files

--- java/branches/hps-java_HPSJAVA-88/steering-files/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/steering-files/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -10,7 +10,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/monitoring

--- java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/monitoring/ECalBasicMonitoring.lcsim	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/monitoring/ECalBasicMonitoring.lcsim	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,34 +1,26 @@

 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" 

-       xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">       
-    

+       xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">           

     <execute>
         <driver name="EventMarkerDriver"/>
         <driver name="CalibrationDriver"/>
         <driver name="EcalRawConverter"/>
         <driver name="EcalClusterer"/>
         <driver name="EcalMonitoringPlots"/>

-    </execute>    
-    

+    </execute>        

     <drivers>

-

         <driver name="EventMarkerDriver"
                 type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1</eventInterval>
         </driver>

-

         <driver name="CalibrationDriver" type="org.hps.conditions.deprecated.CalibrationDriver"/> 

-

         <driver name="EcalRawConverter" type="org.hps.recon.ecal.EcalRawConverterDriver">
             <applyBadCrystalMap>false</applyBadCrystalMap>
             <use2014Gain>false</use2014Gain>

-        </driver>
-        

+        </driver>        

         <driver name="EcalClusterer" type="org.hps.recon.ecal.EcalClusterer">
             <ecalName>Ecal</ecalName>
             <ecalCollectionName>EcalCalHits</ecalCollectionName>

-        </driver>
-        
-        <driver name="EcalMonitoringPlots" type="org.hps.monitoring.drivers.ecal.BasicMonitoringPlotsDriver"/>
-

+        </driver>        
+        <driver name="EcalMonitoringPlots" type="org.hps.monitoring.ecal.plots.BasicMonitoringPlotsDriver"/>

     </drivers>
 </lcsim>

java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/monitoring

--- java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringFinal.lcsim	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/monitoring/EcalMonitoringFinal.lcsim	2014-09-02 22:27:42 UTC (rev 940)
@@ -57,7 +57,7 @@

         </driver>
         
         <driver name="EcalMonitoringPlots" type="org.hps.monitoring.ecal.plots.EcalMonitoringPlots">

-            <inputCollection>EcalCalHits</inputCollection>

+            <inputCollection>EcalCalHits</inputCollection>         

             <eventRefreshRate>100</eventRefreshRate>
         </driver>
         

@@ -77,6 +77,8 @@

        
         <driver name="EcalEventDisplay" type="org.hps.monitoring.ecal.plots.EcalEventDisplay">
             <inputCollection>EcalCalHits</inputCollection>

+            <inputCollectionRaw>EcalReadoutHits</inputCollectionRaw>
+            <inputClusterCollection>EcalClusters</inputClusterCollection>

             <maxEch>2.0</maxEch>
             <eventRefreshRate>100</eventRefreshRate>
         </driver>

java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/recon

--- java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/recon/TestRunOfflineRecon.lcsim	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/recon/TestRunOfflineRecon.lcsim	2014-09-02 22:27:42 UTC (rev 940)
@@ -7,7 +7,8 @@

        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
     <execute>
         <driver name="EventMarkerDriver"/>

-        <driver name="CalibrationDriver"/>

+        <driver name="ConditionsDriver" />
+        <!-- <driver name="CalibrationDriver"/> -->

         <driver name="RawTrackerHitSensorSetup"/>
         <driver name="BadChannelFilter" />
         <driver name="RawTrackerHitFitterDriver" />

@@ -22,9 +23,10 @@

         <driver name="CleanupDriver"/>
     </execute>    
     <drivers>    

-        <driver name="CalibrationDriver" type="org.hps.conditions.deprecated.CalibrationDriver">

+        <driver name="ConditionsDriver" type="org.hps.conditions.ConditionsDriver" />
+        <!-- <driver name="CalibrationDriver" type="org.hps.conditions.deprecated.CalibrationDriver">

             <runNumber>${runNumber}</runNumber>

-        </driver>   

+        </driver> -->   

         <driver name="EventMarkerDriver" type="org.lcsim.job.EventMarkerDriver">
             <eventInterval>1000</eventInterval>
         </driver>        

java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/users/mgraham

--- java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/users/mgraham/DataQualityMonitor.lcsim	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/steering-files/src/main/resources/org/hps/steering/users/mgraham/DataQualityMonitor.lcsim	2014-09-02 22:27:42 UTC (rev 940)
@@ -7,24 +7,24 @@

     <execute>
         <driver name="EventMarkerDriver"/>
         <driver name="DQMDatabaseDriver"/>  

-        <driver name="CalibrationDriver"/>
-        <driver name="RawTrackerHitSensorSetup"/>

+        <driver name="CalibrationDriver"/> 
+         <driver name="RawTrackerHitSensorSetup"/>

         <driver name="BadChannelFilter" /> 

-        <driver name="RawTrackerHitFitterDriver" />
-        <driver name="TrackerHitDriver"/>
-        <driver name="HelicalTrackHitDriver"/>
-        <driver name="TrackerReconDriver"/>
-         <driver name="TrackDataDriver"/>

+         <driver name="RawTrackerHitFitterDriver" />
+         <driver name="TrackerHitDriver"/>
+         <driver name="HelicalTrackHitDriver"/>
+         <driver name="TrackerReconDriver"/>
+          <driver name="TrackDataDriver"/>

         <driver name="EcalRawConverter" />

-        <driver name="EcalClusterer" />
-        <driver name="ReconParticle" />      

+         <driver name="EcalClusterer" />
+          <driver name="ReconParticle" />      

         <driver name="SVTMonitoring"/>  

-        <driver name="SVTHitMCEfficiency"/>  
-        <driver name="TrackingMonitoring"/>  
-        <driver name="TrackingResiduals"/>  
-        <driver name="TrackMCEfficiency"/> 

+       <driver name="SVTHitMCEfficiency"/>  
+        <driver name="TrackingMonitoring"/> 
+        <driver name="TrackingResiduals"/> 
+        <driver name="TrackMCEfficiency"/>

         <driver name="FinalStateMonitoring"/>  

-        <driver name="V0Monitoring"/>          

+        <driver name="V0Monitoring"/>         

         <driver name="AidaSaveDriver"/>
         <driver name="CleanupDriver"/>
     </execute>    

java/branches/hps-java_HPSJAVA-88/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -10,7 +10,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>

@@ -27,6 +27,9 @@

                 <configuration>
                     <excludes>
                         <exclude>org/hps/recon/tracking/TruthResidualTest.java</exclude>

+                        <!-- Test input LCIO file is missing for next two. -->
+                        <exclude>org/hps/recon/tracking/TestRunTrackReconTest.java</exclude>
+                        <exclude>org/hps/recon/tracking/HelicalTrackHitDriverTest.java</exclude>

                     </excludes>
                 </configuration>
             </plugin>

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/DumbShaperFit.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/DumbShaperFit.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,10 +1,12 @@

 package org.hps.recon.tracking;
 

+import java.util.ArrayList;
+import java.util.Collection;

 import org.hps.conditions.deprecated.HPSSVTCalibrationConstants.ChannelConstants;
 import org.lcsim.event.RawTrackerHit;
 
 /**

- * 

+ *

  * @author Matt Graham
  */
 // FIXME: Is there some other description besides "dumb" that could be used in this class name?

@@ -12,18 +14,24 @@

 // TODO: Add class documentation.
 public class DumbShaperFit implements ShaperFitAlgorithm {
 

+    private boolean debug = false;
+

     public DumbShaperFit() {
     }
 

+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
+

     @Override

-    public ShapeFitParameters fitShape(RawTrackerHit rth, ChannelConstants constants) {

+    public Collection<ShapeFitParameters> fitShape(RawTrackerHit rth, ChannelConstants constants) {

         short[] adcVals = rth.getADCValues();
         return this.fitShape(adcVals, constants);
     }
 

-    public ShapeFitParameters fitShape(short[] adcVals, ChannelConstants constants) {

+    public Collection<ShapeFitParameters> fitShape(short[] adcVals, ChannelConstants constants) {

         ShapeFitParameters fitresults = new ShapeFitParameters();

-        double[] pedSub = { -99.0, -99.0, -99.0, -99.0, -99.0, -99.0 };

+        double[] pedSub = {-99.0, -99.0, -99.0, -99.0, -99.0, -99.0};

         double maxADC = -99999;
         int iMax = -1;
         double t0 = -999;

@@ -44,22 +52,27 @@

 
         // mg...put in a cut here to make sure pulse shape is reasonable
         // if not, set t0 to -99 (which will fail the later t0>0 cut

-        if (iMax == 0 || iMax == 5)

+        if (iMax == 0 || iMax == 5) {

             t0 = -99;

+        }

         // make sure it goes up below iMax
         for (int i = 0; i < iMax; i++) {

-            if (pedSub[i + 1] < pedSub[i])

+            if (pedSub[i + 1] < pedSub[i]) {

                 t0 = -99;

+            }

         }
         // ...and down below iMax
         for (int i = iMax; i < 5; i++) {

-            if (pedSub[i + 1] > pedSub[i])

+            if (pedSub[i + 1] > pedSub[i]) {

                 t0 = -99;

+            }

         }
 
         fitresults.setAmp(maxADC);
         fitresults.setT0(t0);
 

-        return fitresults;

+        ArrayList<ShapeFitParameters> fits = new ArrayList<ShapeFitParameters>();
+        fits.add(fitresults);
+        return fits;

     }
 }

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/RawTrackerHitFitterDriver.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/RawTrackerHitFitterDriver.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -20,7 +20,7 @@

  */
 // TODO: Add class documentation.
 public class RawTrackerHitFitterDriver extends Driver {

-    

+

     private boolean debug = false;
     private ShaperFitAlgorithm _shaper = new DumbShaperFit();
     private String rawHitCollectionName = "SVTRawTrackerHits";

@@ -41,57 +41,64 @@

     public void setUseTruthTime(boolean useTruthTime) {
         this.useTruthTime = useTruthTime;
     }

-    

+

     public void setDebug(boolean debug) {
         this.debug = debug;
     }

-    

+

     public void setCorrectT0Shift(boolean correctT0Shift) {
         this.correctT0Shift = correctT0Shift;
     }

-    

+

     public void setUseTimestamps(boolean useTimestamps) {
         this.useTimestamps = useTimestamps;
     }

-    

+

     public void setSubtractTOF(boolean subtractTOF) {
         this.subtractTOF = subtractTOF;
     }

-    

+

     public void setFitAlgorithm(String fitAlgorithm) {
         if (fitAlgorithm.equals("Analytic")) {
             _shaper = new ShaperAnalyticFitAlgorithm();

+        } else if (fitAlgorithm.equals("Linear")) {
+            _shaper = new ShaperLinearFitAlgorithm(1);
+        } else if (fitAlgorithm.equals("PileupAlways")) {
+            _shaper = new ShaperPileupFitAlgorithm(1.0);
+        } else if (fitAlgorithm.equals("Pileup")) {
+            _shaper = new ShaperPileupFitAlgorithm();

         } else {
             throw new RuntimeException("Unrecognized fitAlgorithm: " + fitAlgorithm);
         }
     }

-    

+

     public void setFitCollectionName(String fitCollectionName) {
         this.fitCollectionName = fitCollectionName;
     }

-    

+

     public void setFittedHitCollectionName(String fittedHitCollectionName) {
         this.fittedHitCollectionName = fittedHitCollectionName;
     }

-    

+

     public void setRawHitCollectionName(String rawHitCollectionName) {
         this.rawHitCollectionName = rawHitCollectionName;
     }

-    

+

     @Override
     public void startOfData() {

+        _shaper.setDebug(debug);

         if (rawHitCollectionName == null) {
             throw new RuntimeException("The parameter ecalCollectionName was not set!");
         }
     }

-    

+

     @Override
     public void process(EventHeader event) {
         if (!event.hasCollection(RawTrackerHit.class, rawHitCollectionName)) {
             // System.out.println(rawHitCollectionName + " does not exist; skipping event");
             return;
         }

-        

+

         List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawHitCollectionName);
         if (rawHits == null) {
             throw new RuntimeException("Event is missing SVT hits collection!");

@@ -103,37 +110,38 @@

         for (RawTrackerHit hit : rawHits) {
             int strip = hit.getIdentifierFieldValue("strip");
             ChannelConstants constants = HPSSVTCalibrationConstants.getChannelConstants((SiSensor) hit.getDetectorElement(), strip);

-            ShapeFitParameters fit = _shaper.fitShape(hit, constants);
-            if (correctT0Shift) {
-                fit.setT0(fit.getT0() - constants.getT0Shift());

+            for (ShapeFitParameters fit : _shaper.fitShape(hit, constants)) {
+                if (correctT0Shift) {
+                    fit.setT0(fit.getT0() - constants.getT0Shift());
+                }
+                if (subtractTOF) {
+                    double tof = hit.getDetectorElement().getGeometry().getPosition().magnitude() / (Const.SPEED_OF_LIGHT * Const.nanosecond);
+                    fit.setT0(fit.getT0() - tof);
+                }
+                if (useTimestamps) {
+                    double t0Svt = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRACKER, event);
+                    double t0Trig = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRIGGERBITS, event);
+                    double corMod = (t0Svt - t0Trig) + 200.0;
+                    fit.setT0(fit.getT0() + corMod);
+                }
+                if (useTruthTime) {
+                    double t0Svt = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRACKER, event);
+                    double absoluteHitTime = fit.getT0() + t0Svt;
+                    double relativeHitTime = ((absoluteHitTime + 250.0) % 500.0) - 250.0;
+
+                    fit.setT0(relativeHitTime);
+                }
+                if (debug) {
+                    System.out.println(fit);
+                }
+                fits.add(fit);
+                FittedRawTrackerHit hth = new FittedRawTrackerHit(hit, fit);
+                hits.add(hth);
+                if (strip == HPSSVTConstants.TOTAL_STRIPS_PER_SENSOR) { // drop unbonded channel
+                    continue;
+                }
+                hit.getDetectorElement().getReadout().addHit(hth);

             }

-            if (subtractTOF) {
-                double tof = hit.getDetectorElement().getGeometry().getPosition().magnitude() / (Const.SPEED_OF_LIGHT * Const.nanosecond);
-                fit.setT0(fit.getT0() - tof);
-            }
-            if (useTimestamps) {
-                double t0Svt = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRACKER, event);
-                double t0Trig = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRIGGER, event);
-                double corMod = (t0Svt - t0Trig) + 200.0;
-                fit.setT0(fit.getT0() + corMod);
-            }
-            if (useTruthTime) {
-                double t0Svt = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRACKER, event);
-                double absoluteHitTime = fit.getT0() + t0Svt;
-                double relativeHitTime = ((absoluteHitTime + 250.0) % 500.0) - 250.0;
-                
-                fit.setT0(relativeHitTime);
-            }
-            if (debug) {
-                System.out.println(fit);
-            }
-            fits.add(fit);
-            FittedRawTrackerHit hth = new FittedRawTrackerHit(hit, fit);
-            hits.add(hth);
-            if (strip == HPSSVTConstants.TOTAL_STRIPS_PER_SENSOR) { // drop unbonded channel
-                continue;
-            }
-            hit.getDetectorElement().getReadout().addHit(hth);

         }
         event.put(fitCollectionName, fits, ShapeFitParameters.class, genericObjectFlags);
         event.put(fittedHitCollectionName, hits, FittedRawTrackerHit.class, relationFlags);

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/ShapeFitParameters.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/ShapeFitParameters.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,13 +1,9 @@

-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */

 package org.hps.recon.tracking;
 
 import org.lcsim.event.GenericObject;
 
 /**

- * 

+ *

  * @author Matt Graham
  */
 public class ShapeFitParameters implements GenericObject {

@@ -16,9 +12,9 @@

     private double _t0Err = Double.NaN;
     private double _amp = Double.NaN;
     private double _ampErr = Double.NaN;

-    private double _tp = Double.NaN;
-    private double _tpErr = Double.NaN;
-    private double _chiSq = Double.NaN;

+//    private double _tp = Double.NaN;
+//    private double _tpErr = Double.NaN;
+    private double _chiProb = Double.NaN;

 
     public ShapeFitParameters() {
     }

@@ -36,9 +32,9 @@

         _amp = amp;
     }
 

-    public void setTp(double tp) {
-        _tp = tp;
-    }

+//    public void setTp(double tp) {
+//        _tp = tp;
+//    }

 
     public void setAmpErr(double _ampErr) {
         this._ampErr = _ampErr;

@@ -48,12 +44,12 @@

         this._t0Err = _t0Err;
     }
 

-    public void setTpErr(double _tpErr) {
-        this._tpErr = _tpErr;
-    }

+//    public void setTpErr(double _tpErr) {
+//        this._tpErr = _tpErr;
+//    }

-    public void setChiSq(double _chiSq) {
-        this._chiSq = _chiSq;

+    public void setChiProb(double _chiProb) {
+        this._chiProb = _chiProb;

     }
 
     public double getT0() {

@@ -64,9 +60,9 @@

         return _amp;
     }
 

-    public double getTp() {
-        return _tp;
-    }

+//    public double getTp() {
+//        return _tp;
+//    }

 
     public double getT0Err() {
         return _t0Err;

@@ -76,14 +72,42 @@

         return _ampErr;
     }
 

-    public double getTpErr() {
-        return _tpErr;

+//    public double getTpErr() {
+//        return _tpErr;
+//    }
+
+    public double getChiProb() {
+        return _chiProb;

     }
 

-    public double getChiSq() {
-        return _chiSq;

+    public static double getT0(GenericObject object) {
+        return object.getDoubleVal(0);

     }
 

+    public static double getT0Err(GenericObject object) {
+        return object.getDoubleVal(1);
+    }
+
+    public static double getAmp(GenericObject object) {
+        return object.getDoubleVal(2);
+    }
+
+    public static double getAmpErr(GenericObject object) {
+        return object.getDoubleVal(3);
+    }
+
+//    public static double getTp(GenericObject object) {
+//        return object.getDoubleVal(4);
+//    }
+//
+//    public static double getTpErr(GenericObject object) {
+//        return object.getDoubleVal(5);
+//    }
+
+    public static double getChiProb(GenericObject object) {
+        return object.getDoubleVal(4);
+    }
+

     @Override
     public int getNInt() {
         return 0;

@@ -96,7 +120,7 @@

 
     @Override
     public int getNDouble() {

-        return 7;

+        return 5;

     }
 
     @Override

@@ -120,14 +144,14 @@

                 return _amp;
             case 3:
                 return _ampErr;

+//            case 4:
+//                return _tp;
+//            case 5:
+//                return _tpErr;

             case 4:

-                return _tp;
-            case 5:
-                return _tpErr;
-            case 6:
-                return _chiSq;

+                return _chiProb;

             default:

-                throw new UnsupportedOperationException("Only 7 double values in " + this.getClass().getSimpleName());

+                throw new UnsupportedOperationException("Only 5 double values in " + this.getClass().getSimpleName());

         }
 
     }

@@ -139,6 +163,6 @@

 
     @Override
     public String toString() {

-        return String.format("chisq=%f\tA=%f\tAerr=%f\tT0=%f\tT0err=%f", _chiSq, _amp, _ampErr, _t0, _t0Err);

+        return String.format("chiprob=%f\tA=%f\tAerr=%f\tT0=%f\tT0err=%f", _chiProb, _amp, _ampErr, _t0, _t0Err);

     }
 }

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/ShaperAnalyticFitAlgorithm.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/ShaperAnalyticFitAlgorithm.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,25 +1,32 @@

 package org.hps.recon.tracking;
 

+import java.util.ArrayList;
+import java.util.Collection;
+import org.apache.commons.math3.special.Gamma;

 import org.hps.conditions.deprecated.HPSSVTCalibrationConstants.ChannelConstants;
 import org.hps.conditions.deprecated.HPSSVTConstants;
 import org.lcsim.event.RawTrackerHit;

-//import org.lcsim.math.chisq.ChisqProb;

 
 /**

- * Fast fitter; currently only fits single hits. Uses Tp from ChannelConstants; fits values and
- * errors for T0 and amplitude.
- * 

+ * Fast fitter; currently only fits single hits. Uses Tp from ChannelConstants;
+ * fits values and errors for T0 and amplitude.
+ *

  * @author Sho Uemura
  */
 public class ShaperAnalyticFitAlgorithm implements ShaperFitAlgorithm {
 

+    private boolean debug = false;
+
+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
+

     @Override

-    public ShapeFitParameters fitShape(RawTrackerHit rth, ChannelConstants constants) {
-        short[] samples = rth.getADCValues();
-        return this.fitShape(samples, constants);

+    public Collection<ShapeFitParameters> fitShape(RawTrackerHit rth, ChannelConstants constants) {
+        return this.fitShape(rth.getADCValues(), constants);

     }
 

-    public ShapeFitParameters fitShape(short[] samples, ChannelConstants constants) {

+    public Collection<ShapeFitParameters> fitShape(short[] samples, ChannelConstants constants) {

         double minChisq = Double.POSITIVE_INFINITY;
         int bestStart = 0;
         ShapeFitParameters fit = new ShapeFitParameters();

@@ -37,7 +44,9 @@

         // constants.getPedestal(), samples[4] - constants.getPedestal(), samples[5] -
         // constants.getPedestal());
         // System.out.println("start = " + bestStart + ", " + fit);

-        return fit;

+        ArrayList<ShapeFitParameters> fits = new ArrayList<ShapeFitParameters>();
+        fits.add(fit);
+        return fits;

     }
 
     private double fitSection(short[] samples, ChannelConstants constants, ShapeFitParameters fit, int start) {

@@ -87,7 +96,6 @@

         fit.setAmpErr(Math.sqrt(height_var));
         fit.setT0(t0);
         fit.setT0Err(Math.sqrt(time_var));

-        fit.setTp(constants.getTp());

 
         double chisq = 0;
         for (int i = 0; i < samples.length; i++) {

@@ -95,10 +103,10 @@

             double fit_y = A * (Math.max(0, (ti - t0)) / constants.getTp()) * Math.exp(1 - (ti - t0) / constants.getTp()) + constants.getPedestal();
             chisq += Math.pow((fit_y - samples[i]) / constants.getNoise(), 2);
         }

-        fit.setChiSq(chisq);

-        if (A > 0) {

+        if (A > 0 && chisq < Double.POSITIVE_INFINITY) {

             // return ChisqProb.gammp(samples.length - 2, chisq);

+            fit.setChiProb(Gamma.regularizedGammaQ(samples.length - 2, chisq));

             return chisq / (samples.length - 2);
         } else {
             return Double.POSITIVE_INFINITY;

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/ShaperFitAlgorithm.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/ShaperFitAlgorithm.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,15 +1,17 @@

 package org.hps.recon.tracking;
 

+import java.util.Collection;

 import org.hps.conditions.deprecated.HPSSVTCalibrationConstants.ChannelConstants;
 import org.lcsim.event.RawTrackerHit;
 
 /**

- * 

+ *

  * @author Matt Graham
  */
 // TODO: Add class documentation.
 public interface ShaperFitAlgorithm {
 

-    public ShapeFitParameters fitShape(RawTrackerHit rth, ChannelConstants constants);

+    public Collection<ShapeFitParameters> fitShape(RawTrackerHit rth, ChannelConstants constants);

+    public void setDebug(boolean debug);

 }

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/StripMaker.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/StripMaker.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -273,19 +273,21 @@

     }
 
     private double getTime(List<FittedRawTrackerHit> cluster) {

-        int time_sum = 0;
-        int signal_sum = 0;

+        double time_sum = 0;
+        double signal_sum = 0;

+//        System.out.format("Hits:\n");

         for (FittedRawTrackerHit hit : cluster) {
 
             double signal = hit.getAmp();
             double time = hit.getT0();

+//        System.out.format("t0=%f\tA=%f\n",hit.getT0(),hit.getAmp());

 
             time_sum += time * signal;
             signal_sum += signal;
 
         }

-        return (double) time_sum / (double) signal_sum;

+        return time_sum / signal_sum;

     }
 
     private SymmetricMatrix getCovariance(List<FittedRawTrackerHit> cluster, SiSensorElectrodes electrodes) {

java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking

--- java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/TrackerReconDriver.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/tracking/src/main/java/org/hps/recon/tracking/TrackerReconDriver.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -6,6 +6,7 @@

 
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.Track;

+import org.lcsim.event.base.BaseTrack;

 import org.lcsim.fit.helicaltrack.HelicalTrackHit;
 import org.lcsim.geometry.Detector;
 import org.lcsim.recon.tracking.seedtracker.SeedStrategy;

@@ -173,6 +174,10 @@

                 System.out.println(this.getClass().getSimpleName() + ": chi2 = " + track.getChi2());
             }
         }

+        
+        // Set the type of track to indicate B-field in Y e.g. for swimming in Wired.
+        List<Track> tracks = event.get(Track.class, trackCollectionName);
+        setTrackType(tracks);

 
         // Increment number of events.
         ++nevents;

@@ -180,6 +185,16 @@

         // Add to tracks found.
         ntracks += event.get(Track.class, trackCollectionName).size();
     }

+    
+    /**
+     * Set the track type to Y_FIELD so swimming is done correctly in Wired.
+     * @param tracks The list of <code>Track</code> objects.
+     */
+    private void setTrackType(List<Track> tracks) {
+        for (Track track : tracks) {
+            ((BaseTrack)track).setTrackType(BaseTrack.TrackType.Y_FIELD.ordinal());
+        }
+    }

 
     @Override
     public void endOfData() {

java/branches/hps-java_HPSJAVA-88/users

--- java/branches/hps-java_HPSJAVA-88/users/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,30 +1,25 @@

 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

-    

     <modelVersion>4.0.0</modelVersion>
     <artifactId>hps-users</artifactId>
     <name>users</name>
     <description>user code packages</description>

-    

     <parent>
         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>

-    

     <scm>
         <url>http://java.freehep.org/svn/repos/hps/list/java/trunk/users/</url>
         <connection>scm:svn:svn://svn.freehep.org/hps/java/trunk/users/</connection>
         <developerConnection>scm:svn:svn://svn.freehep.org/hps/java/trunk/users/</developerConnection>
     </scm>

-    

     <dependencies>
         <dependency>
             <groupId>org.hps</groupId>
             <artifactId>hps-analysis</artifactId>
         </dependency> 
     </dependencies>

-    

     <build>
         <plugins>
             <plugin>

@@ -33,10 +28,10 @@

                 <configuration>
                     <excludes>
                         <exclude>org/hps/users/jeremym/MockDataChallengeDiagnosticDriverTest.java</exclude>

+                        <exclude>org/hps/users/ngraf/NearestNeighborClusterDriverTest.java</exclude>

                     </excludes>
                 </configuration>
             </plugin>
         </plugins>
     </build>

-        

 </project>

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/jeremym

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/jeremym/MockDataChallengeDiagnosticDriver.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/jeremym/MockDataChallengeDiagnosticDriver.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -76,7 +76,8 @@

             }
         }
     }

-     

+    
+    /*

     @Override
     protected void endOfData() {
         try {

@@ -85,6 +86,7 @@

             throw new RuntimeException(e);
         }
     }

+    */

         
     @Override
     public void process(EventHeader event) {

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/luca

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/luca/CalibTest2.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/luca/CalibTest2.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -83,7 +83,7 @@

       eneMCallPlot.fill(particle.getEnergy());
       if(particle.getPDGID()==11)
       {eneEminusPlot.fill(particle.getEnergy());}

-      if(particle.getPDGID()==1 && particle.getEnergy()>2.150)

+      if(particle.getPDGID()==11 && particle.getEnergy()>2.150)

       {eneCoulombEPlot.fill(particle.getEnergy());}
     
       

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/luca

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/luca/mycluster3.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/luca/mycluster3.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -20,17 +20,17 @@

 
 import org.hps.recon.ecal.ECalUtils;
 import org.hps.recon.ecal.HPSEcalCluster;

-import org.lcsim.event.Cluster;

+

 import org.lcsim.event.EventHeader;
 import org.lcsim.geometry.Detector;
 import org.lcsim.util.aida.AIDA;
 import org.lcsim.util.Driver;
 import hep.aida.*;

-import hep.aida.IHistogram3D;

+

 import java.io.FileWriter;
 import org.lcsim.event.CalorimeterHit;

-import org.lcsim.event.MCParticle;

+

 /**
  * 
  * @author Luca Colaneri 

@@ -46,12 +46,15 @@

     private LinkedList<ArrayList<HPSEcalCluster>> clusterBuffer;
     protected String clusterCollectionName = "EcalClusters";
     

- 
- 

+ AIDA aida = AIDA.defaultInstance();
+ IHistogram1D clusterEne=aida.histogram1D("Clusters energy with Luca's trigger",300, 0, 3);
+// ArrayList<IHistogram1D> SeedHistograms = new ArrayList<IHistogram1D>(442);
+  //  ArrayList<IHistogram1D> ClustHistograms = new ArrayList<IHistogram1D>(442);
+ //    ArrayList<IHistogram1D> HitHistograms = new ArrayList<IHistogram1D>(442);

     private FileWriter writer;

-    //private FileWriter writer2;
-    String outputFileName = "ClusterInfonew.txt";
-   // String outputFileName2 = "ClusterEnePos2.txt";

+    private FileWriter writer2;
+    String outputFileName = "LucaTriggerFEE.txt";
+    String outputFileName2 = "LucaTriggerHits.txt";

@@ -71,6 +74,9 @@

    public void setOutputFileName(String outputFileName){
 this.outputFileName = outputFileName;
 }

+   public void setOutputFileName2(String outputFileName2){
+this.outputFileName2 = outputFileName2;
+   }

    public void settimeDifference(double time){
    this.timeDifference=time;
    

@@ -99,10 +105,26 @@

     try{
     //initialize the writers
     writer=new FileWriter(outputFileName);

- //   writer2=new FileWriter(outputFileName2);

+    writer2=new FileWriter(outputFileName2);

     //Clear the files
     writer.write("");

-  //  writer2.write("");

+    writer2.write("");
+    
+     //initialize histograms  
+  /*  for(int t=0; t<442; t++){
+      String cristallo=String.valueOf(t);  
+      String seedhistogram="SeedHit_" + String.valueOf(t);
+      String Clushistogram="Clusters_" + String.valueOf(t);
+      String HitHistogram="Hits_" + String.valueOf(t);
+      
+      IHistogram1D seedhisto=aida.histogram1D(seedhistogram, 150, 0.0,3.0);
+      IHistogram1D clushisto=aida.histogram1D(Clushistogram, 150, 0.0,3.0);
+      IHistogram1D hitshisto=aida.histogram1D(HitHistogram,150,0.0,3.0);
+    SeedHistograms.add(seedhisto);
+    ClustHistograms.add(clushisto);
+    HitHistograms.add(hitshisto);
+    }*/
+    

 }
 catch(IOException e ){
 System.err.println("Error initializing output file for event display.");

@@ -116,7 +138,7 @@

     try{
 //close the file writer.
     writer.close();

-   // writer2.close();

+    writer2.close();

     }
 catch(IOException e){
     System.err.println("Error closing utput file for event display.");

@@ -131,6 +153,7 @@

            
      
      //get the clusters from the event

+    if(TriggerDriver.triggerBit()){ //if they have triggered!

      if(event.hasCollection(HPSEcalCluster.class, "EcalClusters")) {
         List<HPSEcalCluster> clusterList =event.get(HPSEcalCluster.class,clusterCollectionName );    
              

@@ -138,6 +161,7 @@

      
      ArrayList<HPSEcalCluster> clusterSet = new ArrayList<HPSEcalCluster>(); 
      for(HPSEcalCluster cluster : clusterList){

+         clusterEne.fill(cluster.getEnergy());

          TotalCluster++;
          clusterSet.add(cluster);
      }

@@ -147,6 +171,21 @@

     //Run the sorting algorithm;
      ClusterAnalyzer();
      }

+     
+      //get the hits from the event
+     if(event.hasCollection(CalorimeterHit.class,"EcalCorrectedHits")){
+     List<CalorimeterHit> hits =event.get(CalorimeterHit.class,"EcalCorrectedHits");
+     
+        for(CalorimeterHit hit : hits){
+            int id=getCrystal(hit)-1;
+          //  HitHistograms.get(id).fill(hit.getRawEnergy());
+                try{    writer2.append(id + " " + hit.getRawEnergy()+ "\n");}
+                catch(IOException e ){System.err.println("Error writing to output for event display");} 
+        }//end of for cycle
+     }
+     
+    }
+     

 }
 
  

@@ -174,15 +213,16 @@

             Clustercount++;
            id=getCrystal(cluster);
            try{

-     writer.append(id + " " + cluster.getSeedHit().getTime() + " " + cluster.getEnergy()+ " " + cluster.getSize() + " " + cluster.getSeedHit().getRawEnergy() + " ");

+     writer.append(id + " " + cluster.getEnergy()+ " " + cluster.getSize() + " " + cluster.getSeedHit().getRawEnergy() + " " + cluster.getSeedHit().getIdentifierFieldValue("ix")+" " +cluster.getSeedHit().getIdentifierFieldValue("iy"));

      /*for(CalorimeterHit hit : cluster.getCalorimeterHits())
      {writer.append(hit.getRawEnergy()+ " ");
        }*/
      writer.append("\n");

-    

+  //  SeedHistograms.get(id-1).fill(cluster.getSeedHit().getRawEnergy());
+  //   ClustHistograms.get(id-1).fill(cluster.getEnergy());

      }
      

-   catch(IOException e ){System.err.println("Error writing tooutput for event display");}   

+   catch(IOException e ){System.err.println("Error writing to output for event display");}   

            
            }
       }

@@ -218,7 +258,7 @@

          for(HPSEcalCluster currentcluster : currentList){
            if(currentcluster!= cluster){
              //if there is a cluster in the buffer that is in the considered radius in a time window lower than expected, the loop is brocken and the analyzed cluster is not good

-         if(!((currentcluster.getSeedHit().getIdentifierFieldValue("ix")< posx-radius || currentcluster.getSeedHit().getIdentifierFieldValue("ix")> posx+radius)&& (currentcluster.getSeedHit().getIdentifierFieldValue("iy")< posy-radius || currentcluster.getSeedHit().getIdentifierFieldValue("iy")> posy+radius))&& Math.abs(cluster.getSeedHit().getTime()-currentcluster.getSeedHit().getTime())<timeDifference){

+         if(!((currentcluster.getSeedHit().getIdentifierFieldValue("ix") < posx-radius || currentcluster.getSeedHit().getIdentifierFieldValue("ix")> posx+radius)&& (currentcluster.getSeedHit().getIdentifierFieldValue("iy")< posy-radius || currentcluster.getSeedHit().getIdentifierFieldValue("iy")> posy+radius))&& Math.abs(cluster.getSeedHit().getTime()-currentcluster.getSeedHit().getTime())<timeDifference){

          check=false;
          break loops;
          }

@@ -277,7 +317,7 @@

      if(x>0){
   id=-x+245;}
  else if(x==-1 )id=245;

- else if(x<-1){id=-x+257;}}

+ else if(x<-1){id=-x+235;}}

  
  
  else if(y==-2)

@@ -304,7 +344,71 @@

  
  }
  

+ public int getCrystal (CalorimeterHit hit){
+ int x,y,id=0;
+ x= (-1)*hit.getIdentifierFieldValue("ix");
+ y= hit.getIdentifierFieldValue("iy");

+ if(y==5){
+ if(x<0)
+ {id=x+24;}
+ else id= x+23;
+ }
+ 
+ else if(y==4)
+ {if(x<0){
+  id=x+70;}
+ else id=x+69;}
+ 
+ else if(y==3)
+ {if(x<0){
+  id=x+116;}
+ else id=x+115;}
+ 
+ else if(y==2)
+ {if(x<0){
+  id=x+162;}
+ else id=x+161;}
+ 
+ else if(y==1)
+ {x=-x;
+     if(x>0){
+  id=-x+208;}
+ else if(x==-1){id=208;}
+ else if(x<-1) id=-x+198;}
+ 
+  else if(y==-1)
+ {x=-x;
+     if(x>0){
+  id=-x+245;}
+ else if(x==-1 )id=245;
+ else if(x<-1){id=-x+235;}}
+ 
+ 
+ else if(y==-2)
+ {if(x<0){
+  id=x+282;}
+ else id=x+281;}
+ 
+  else if(y==-3)
+ {if(x<0){
+  id=x+328;}
+ else id=x+327;}
+ 
+ else if(y==-4)
+ {if(x<0){
+  id=x+374;}
+ else id=x+373;}
+ 
+ else if(y==-5)
+ {if(x<0){
+  id=x+420;}
+ else id=x+419;}
+ 
+ return id;
+ 
+ }
+ 

  } //chiusura driver  
     
     

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/mgraham

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/mgraham/HitTimePlotter.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/mgraham/HitTimePlotter.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -203,7 +203,7 @@

 //                + ", Trigger timestamp " + ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRIGGER, event));
         double t0Ecal = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_ECAL, event);
         double t0Svt = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRACKER, event);

-        double t0Trig = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRIGGER, event);

+        double t0Trig = ReadoutTimestamp.getTimestamp(ReadoutTimestamp.SYSTEM_TRIGGERBITS, event);

         for (CalorimeterHit hit : ecalHits) {
             double cor = hit.getTime() + (t0Ecal - t0Trig);
             aida.histogram1D("ECAL Hit Time").fill(hit.getTime());

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno/PlotUtils.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno/PlotUtils.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -1,6 +1,8 @@

 package org.hps.users.omoreno;
 
 import hep.aida.ICloud2D;

+import hep.aida.IFitResult;
+import hep.aida.IFitter;

 //--- hep ---//
 import hep.aida.IHistogram1D;
 import hep.aida.IHistogram2D;

@@ -99,5 +101,37 @@

         int region = ix * 4 + iy;
         return region;
     }

+   
+    public static IHistogram1D getYProjection(int binX, IHistogram2D histogram){
+    	int binsY = histogram.yAxis().bins();
+    	double yMin = histogram.yAxis().lowerEdge();
+    	double yMax = histogram.yAxis().upperEdge(); 
+    	
+    	IHistogram1D projection 
+    		= AIDA.defaultInstance().histogram1D(histogram.title() + "_" + binX, binsY, yMin, yMax);
+    	projection.reset();
+    	
+    	double dataY = 0; 
+    	for(int binY = 0; binY < binsY; binY++){
+    		dataY = histogram.binEntries(binX, binY);
+    		projection.fill(yMin, dataY);
+    		yMin++;
+    	}
+    	
+    	return projection; 
+    }

+    public static double[] fitToGuassian(IHistogram1D histogram){
+    	
+    	double[] fitParameters = {0, 0};
+    	IFitter fitter = AIDA.defaultInstance().analysisFactory().createFitFactory().createFitter();
+    	IFitResult fitResult = fitter.fit(histogram, "g");
+    	int meanIndex  = fitResult.fittedFunction().indexOfParameter("mean");
+    	fitParameters[0] = fitResult.fittedParameters()[meanIndex];
+
+    	int sigmaIndex  = fitResult.fittedFunction().indexOfParameter("sigma");
+    	fitParameters[1] = fitResult.fittedParameters()[sigmaIndex];
+    	
+		return fitParameters;
+    }

 }

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno/SvtPerformance.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno/SvtPerformance.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -375,14 +375,14 @@

                             }
                         }
                         

-                        constants = HPSSVTCalibrationConstants.getChannelConstants(sensor, channel);
-                        fit = shaperFitter.fitShape(rawHit, constants);

+                        //constants = HPSSVTCalibrationConstants.getChannelConstants(sensor, channel);
+                       // fit = shaperFitter.fitShape(rawHit);

                         if (fit.getAmp() > maxClusterAmplitude) {
                             maxClusterChannel = channel;
                             maxClusterAmplitude = fit.getAmp();
                         }
                         if(stripHit.rawhits().size() == 1){

-                        	chiSquared = fit.getChiSq();

+                       // 	chiSquared = fit.getChiSq();

                         }
                         noise += Math.pow(sensor.getNoise(channel), 2);
                         clusterAmplitude += fit.getAmp();

java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno

--- java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno/SvtQA.java	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/users/src/main/java/org/hps/users/omoreno/SvtQA.java	2014-09-02 22:27:42 UTC (rev 940)
@@ -466,10 +466,10 @@

             int apv = this.getAPVNumber(channel);
 
             // Get the constants associated with this channel

-            constants = HPSSVTCalibrationConstants.getChannelConstants(sensor, channel);

+            //constants = HPSSVTCalibrationConstants.getChannelConstants(sensor, channel);

 
             // Fit the samples associated with the RawTrackerHit

-            fit = shaperFitter.fitShape(rawHit, constants);

+            //fit = shaperFitter.fitShape(rawHit);

 
             // Fill the occupancy plots
             if(enableOccupancy){

@@ -553,7 +553,7 @@

             // Fill Chi Squared vs Channel # plots
             if(enableChiSquaredvsChannel && SvtUtils.getInstance().getDescription(sensor).equals(sensorName)){
                 title = sensorName + " - Chi Squared vs Channel #";

-                aida.histogram2D(title).fill(channel, fittedHit.getShapeFitParameters().getChiSq());

+                //aida.histogram2D(title).fill(channel, fittedHit.getShapeFitParameters().getChiSq());

             }
         }
 

@@ -580,10 +580,10 @@

                 int channel = rawHit.getIdentifierFieldValue("strip");
 
                 // Get the constants associated with this channel

-                constants = HPSSVTCalibrationConstants.getChannelConstants(sensor, channel);

+                //constants = HPSSVTCalibrationConstants.getChannelConstants(sensor, channel);

 
                 // Fit the samples associated with the RawTrackerHit

-                fit = shaperFitter.fitShape(rawHit, constants);

+                //fit = shaperFitter.fitShape(rawHit);

 
                 // Get the shaper signal samples
                 short[] samples = rawHit.getADCValues();

java/branches/hps-java_HPSJAVA-88/util

--- java/branches/hps-java_HPSJAVA-88/util/pom.xml	2014-09-02 21:58:56 UTC (rev 939)
+++ java/branches/hps-java_HPSJAVA-88/util/pom.xml	2014-09-02 22:27:42 UTC (rev 940)
@@ -9,7 +9,7 @@

         <groupId>org.hps</groupId>
         <artifactId>hps-parent</artifactId>
         <relativePath>../parent/pom.xml</relativePath>

-        <version>3.0.2-SNAPSHOT</version>

+        <version>3.0.3-SNAPSHOT</version>

     </parent>
     
     <scm>