hps-java/src/main/java/org/lcsim/hps/recon/ecal

diff -u -r1.15 -r1.16
--- HPSEcalRawConverterDriver.java	27 Sep 2012 01:08:12 -0000	1.15
+++ HPSEcalRawConverterDriver.java	20 Nov 2012 23:25:09 -0000	1.16
@@ -63,6 +63,10 @@

         this.applyBadCrystalMap = apply;
     }
 

+    public void setDebug(boolean debug) {
+        this.debug = debug;
+    }
+

     @Override
     public void startOfData() {
         if (ecalCollectionName == null) {

@@ -109,6 +113,9 @@

                 List<RawCalorimeterHit> hits = event.get(RawCalorimeterHit.class, rawCollectionName);
 
                 for (RawCalorimeterHit hit : hits) {

+                    if (debug) {
+                        System.out.format("old hit energy %d\n", hit.getAmplitude());
+                    }

                     CalorimeterHit newHit = converter.HitDtoA(hit, integralWindow);
                     if (newHit.getRawEnergy() > threshold) {
                         if (applyBadCrystalMap && isBadCrystal(newHit)) {

@@ -117,6 +124,9 @@

                         if (dropBadFADC && isBadFADC(newHit)) {
                             continue;
                         }

+                        if (debug) {
+                            System.out.format("new hit energy %f\n", newHit.getRawEnergy());
+                        }

                         newHits.add(newHit);
                     }
                 }

@@ -129,8 +139,14 @@

                 List<CalorimeterHit> hits = event.get(CalorimeterHit.class, ecalCollectionName);
 
                 for (CalorimeterHit hit : hits) {

+                    if (debug) {
+                        System.out.format("old hit energy %f\n", hit.getRawEnergy());
+                    }

                     RawCalorimeterHit newHit = converter.HitAtoD(hit, integralWindow);
                     if (newHit.getAmplitude() > 0) {

+                        if (debug) {
+                            System.out.format("new hit energy %d\n", newHit.getAmplitude());
+                        }

                         newHits.add(newHit);
                     }
                 }

hps-java/src/main/java/org/lcsim/hps/recon/ecal

diff -N GainCalib.java
--- GainCalib.java	9 Aug 2012 00:51:15 -0000	1.2
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,508 +0,0 @@

-package org.lcsim.hps.recon.ecal;
-
-import hep.aida.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.BufferedReader;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.*;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import org.lcsim.event.CalorimeterHit;
-import org.lcsim.event.EventHeader;
-import org.lcsim.event.Track;
-import org.lcsim.event.base.BaseLCSimEvent;
-import org.lcsim.event.base.BaseRawCalorimeterHit;
-import org.lcsim.geometry.Detector;
-import org.lcsim.hps.monitoring.AIDAFrame;
-import org.lcsim.util.aida.AIDA;
-
-/**
- *
- * @author phansson
- */
-public class GainCalib implements ActionListener {
-
-    boolean _debug = false;
-    EventHeader _event = null;
-    HPSEcalClusterer _clusterer = null;
-    private int _integralWindow = 30;
-    private double _threshold = Double.NEGATIVE_INFINITY;
-    private boolean _applyBadCrystalMap = true;
-    private Map<Long, Double> _gains = new HashMap<Long, Double>();
-    //original list
-    private Map<Integer, List<BaseRawCalorimeterHit>> _hits = new HashMap<Integer, List<BaseRawCalorimeterHit>>();
-    private Map<Integer, List<MatchedTrack>> _tracks = new HashMap<Integer, List<MatchedTrack>>();
-    private Detector _detector;
-    private String _ecalReadoutName;
-    private String _ecalTmpCollectionName = "temporaryEcalCalHits";
-    private AIDA aida = AIDA.defaultInstance();
-    private IAnalysisFactory af = aida.analysisFactory();
-    IHistogramFactory hf = aida.histogramFactory();
-    IHistogram1D pe[][] = new IHistogram1D[47][11];
-    List<PEHistograms> iterPE = new ArrayList<PEHistograms>();
-    private AIDAFrame plotFrame = new AIDAFrame();
-    private List<IPlotter> plotterList = new ArrayList<IPlotter>();
-    JComboBox xCombo = null;
-    JLabel xLabel = null;
-    Integer xList[];
-    JComboBox yCombo = null;
-    JLabel yLabel = null;
-    Integer yList[];
-
-    @Override
-    public void actionPerformed(ActionEvent ae) {
-        //if(ae == blankButton) {
-        //    //
-        //}
-        Integer x = (Integer) xCombo.getSelectedItem();
-        Integer y = (Integer) yCombo.getSelectedItem();
-        for (IPlotter p : plotterList) {
-            String title = p.title(); //("Gain iteration " + iter);
-            String v[] = title.split(" ");
-            if (v.length < 3) {
-                System.out.println("ERROR this title " + title + " doesn't have the correct syntax");
-                System.exit(1);
-            }
-            Integer iter = Integer.parseInt(v[2]);
-            for (PEHistograms peh : iterPE) {
-                if (peh._i == iter) {
-                    p.region(4).clear();
-                    p.region(4).plot(peh.pe[x + 23][y + 5]);
-                }
-            }
-
-        }
-    }
-
-    public class MatchedTrack {
-
-        long _cellid;
-        Track _track;
-
-        MatchedTrack(long id, Track trk) {
-            _cellid = id;
-            _track = trk;
-        }
-    }
-
-    class PEHistograms {
-
-        int _i;
-        IHistogram1D pe[][] = new IHistogram1D[47][11];
-
-        PEHistograms(int i) {
-            _i = i;
-        }
-    }
-
-    GainCalib() {
-        for (int irow = -5; irow <= 5; ++irow) {
-            for (int icol = -23; icol <= 23; ++icol) {
-                pe[icol + 23][irow + 5] = aida.histogram1D("(GainCalib) E over p x=" + icol + " y=" + irow, 50, 0, 3);
-            }
-        }
-
-        xList = new Integer[46];
-        yList = new Integer[10];
-        int in = 0;
-        for (int i = -5; i <= 5; ++i) {
-            if (i != 0) {
-                yList[in] = i;
-                ++in;
-            }
-        }
-        in = 0;
-        for (int i = -23; i <= 23; ++i) {
-            if (i != 0) {
-                xList[in] = i;
-                ++in;
-            }
-        }
-    }
-
-    public void setApplyBadCrystalMap(boolean d) {
-        this._applyBadCrystalMap = d;
-    }
-
-    public void setDebug(boolean d) {
-        this._debug = d;
-    }
-
-    public void setClusterer(HPSEcalClusterer clust) {
-        _clusterer = clust;
-    }
-
-    public void setOriginalHits(int evt, List<BaseRawCalorimeterHit> hits) {
-        this._hits.put(evt, hits);
-        for (BaseRawCalorimeterHit hit : hits) {
-            this._gains.put(hit.getCellID(), HPSEcalConditions.physicalToGain(hit.getCellID()));
-        }
-    }
-
-    public void setTrack(int evt, long ecalCellID, Track track) {
-        MatchedTrack mt = new MatchedTrack(ecalCellID, track);
-
-        if (!this._tracks.containsKey(evt)) {
-            this._tracks.put(evt, new ArrayList<MatchedTrack>());
-        }
-
-        List<MatchedTrack> list = this._tracks.get(evt);
-        list.add(mt);
-    }
-
-    public void setIntegralWindow(int val) {
-        _integralWindow = val;
-    }
-
-    public void setThreshold(double val) {
-        _threshold = val;
-    }
-
-    public void setEcalReadoutName(String str) {
-        this._ecalReadoutName = str;
-    }
-
-    public void setDetector(Detector det) {
-        this._detector = det;
-    }
-
-    public void runOptimization(int nIterations) {
-
-        System.out.println("Start gain calibration");
-
-        System.out.println("nIterations " + nIterations);
-
-        if (_hits == null) {
-            System.out.println("No original hits available");
-            System.exit(1);
-        }
-
-        int event;
-        int iter = 0;
-        while (iter < nIterations) {
-            System.out.println("Iteration " + iter);
-
-            Iterator it = _hits.entrySet().iterator();
-            while (it.hasNext()) {
-                event = ((Map.Entry<Integer, ArrayList<BaseRawCalorimeterHit>>) it.next()).getKey();
-                if (_debug) {
-                    System.out.println("Event " + event);
-                }
-
-                List<HPSEcalCluster> clusters = getCalibratedClusters(event);
-
-                if (_debug) {
-                    System.out.println("Found " + clusters.size() + " clusters");
-                }
-
-                for (HPSEcalCluster cluster : clusters) {
-
-                    int[] pos = new int[2];
-                    pos[0] = cluster.getSeedHit().getIdentifierFieldValue("ix");
-                    pos[1] = cluster.getSeedHit().getIdentifierFieldValue("iy");
-
-                    //find the tracks matched to those clusters
-
-                    MatchedTrack track = getTrack(event, cluster.getSeedHit().getCellID());
-
-                    if (_debug) {
-                        System.out.println("Found track with with cell id " + cluster.getSeedHit().getCellID());
-                    }
-
-                    double P = track._track.getPX() * 1000;
-                    double E = cluster.getEnergy();
-                    double samplingFraction = 0.9;
-                    double Ep = E * samplingFraction;
-                    double Eoverp = Ep / P;
-
-
-                    if (_debug) {
-                        System.out.println("P " + P + " E " + E + " Ep " + Ep + " --> E/p=" + Eoverp);
-                    }
-
-                    pe[pos[0] + 23][pos[1] + 5].fill(Eoverp);
-
-                    if (_debug) {
-                        System.out.println("Cluster icol " + pos[0] + " irow " + pos[1] + " entries " + pe[pos[0] + 23][pos[1] + 5].entries());
-                    }
-                }
-            }
-            copyPE(iter);
-            ++iter;
-        }
-    }
-
-    void copyPE(int iter) {
-
-        //copy the histograms, extract gains and reset for new iteration
-
-        IHistogram2D mpePlot = aida.histogram2D("Iter " + iter + " <E over p>", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        IHistogram2D spePlot = aida.histogram2D("Iter " + iter + " RMS(E over p)", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        IHistogram1D pePlot = hf.createCopy("Iter " + iter + " E over p", pe[0][0]);
-        IHistogram2D gainPlot = aida.histogram2D("Iter " + iter + " gain", 47, -23.5, 23.5, 11, -5.5, 5.5);
-
-
-        PEHistograms hists = new PEHistograms(iter);
-        for (int irow = -5; irow <= 5; ++irow) {
-            for (int icol = -23; icol <= 23; ++icol) {
-                hists.pe[icol + 23][irow + 5] = hf.createCopy("Iter " + iter + " E over p x=" + icol + " y=" + irow, pe[icol + 23][irow + 5]);
-                pePlot = hf.add("Iter " + iter + " E over p", pePlot, pe[icol + 23][irow + 5]);
-                if (pe[icol + 23][irow + 5].entries() > 10) {
-                    mpePlot.fill(icol, irow, pe[icol + 23][irow + 5].mean());
-                    spePlot.fill(icol, irow, pe[icol + 23][irow + 5].rms());
-                    double corr = 1.0 / pe[icol + 23][irow + 5].mean(); //Correction to get p/E==1
-                    double gain = this.getGain(icol, irow) * corr;
-                    setGain(icol, irow, gain);
-                    gain = this.getGain(icol, irow);
-                    gainPlot.fill(icol, irow, gain);
-                }
-
-            }
-        }
-        hists._i = iter;
-        iterPE.add(hists);
-
-        /*        
-        for(int irow=-5;irow<=5;++irow) {
-        for(int icol=-23;icol<=23;++icol) {
-        for(PEHistograms peh : iterPE) {
-        if(peh._i==iter) {
-        if(peh.pe[icol+23][irow+5].entries()>10) {
-        mpePlot.fill(icol,irow,peh.pe[icol+23][irow+5].mean());
-        spePlot.fill(icol,irow,peh.pe[icol+23][irow+5].rms());
-        }
-        }
-        }
-        }
-        }
-        
-         */
-
-        //Plot
-        if (xCombo == null) {
-            xCombo = new JComboBox(xList);
-            xCombo.addActionListener(this);
-            xLabel = new JLabel("x");
-            xLabel.setLabelFor(xCombo);
-            plotFrame.getControlsPanel().add(xLabel);
-            plotFrame.getControlsPanel().add(xCombo);
-            yCombo = new JComboBox(yList);
-            yCombo.addActionListener(this);
-            yLabel = new JLabel("y");
-            yLabel.setLabelFor(xCombo);
-            plotFrame.getControlsPanel().add(yLabel);
-            plotFrame.getControlsPanel().add(yCombo);
-            xCombo.setSelectedIndex(-15 + 23);
-            yCombo.setSelectedIndex(1 + 5 - 1);
-        }
-
-        IPlotter plotter = af.createPlotterFactory().create();
-        plotter.createRegions(1, 5, 0);
-        plotter.setTitle("Gain iteration " + iter);
-        //plotter.style().statisticsBoxStyle().setVisible(false);
-        plotFrame.addPlotter(plotter);
-        plotterList.add(plotter);
-
-        plotter.region(0).plot(mpePlot);
-        plotter.region(1).plot(spePlot);
-        plotter.region(2).plot(gainPlot);
-        plotter.region(3).plot(pePlot);
-        plotter.region(4).plot(hists.pe[-15 + 23][1 + 5 - 1 + 1]);
-
-        plotter.region(0).style().statisticsBoxStyle().setVisible(false);
-        plotter.region(0).style().setParameter("hist2DStyle", "colorMap");
-        plotter.region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotter.region(1).style().statisticsBoxStyle().setVisible(false);
-        plotter.region(1).style().setParameter("hist2DStyle", "colorMap");
-        plotter.region(1).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotter.region(2).style().statisticsBoxStyle().setVisible(false);
-        plotter.region(2).style().setParameter("hist2DStyle", "colorMap");
-        plotter.region(2).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-
-        //Extract gain corrections
-
-        plotFrame.pack();
-        plotFrame.setVisible(false);
-
-        //Reset basic histograms
-
-        for (int irow = -5; irow <= 5; ++irow) {
-            for (int icol = -23; icol <= 23; ++icol) {
-                pe[icol + 23][irow + 5].reset();
-            }
-        }
-    }
-
-    public void setAllGain(double g) {
-
-        for (int irow = -5; irow <= 5; ++irow) {
-            for (int icol = -23; icol <= 23; ++icol) {
-                this.setGain(icol, irow, g);
-            }
-        }
-    }
-
-    public void setAllGain() {
-        for (int irow = -5; irow <= 5; ++irow) {
-            for (int icol = -23; icol <= 23; ++icol) {
-                long cellid = HPSEcalConditions.makePhysicalID(icol, irow);
-                Double gain = HPSEcalConditions.physicalToGain(cellid);
-                if (gain != null) {
-                    this.setGain(icol, irow, gain);
-                } else {
-                    this.setGain(icol, irow, 0);
-                }
-            }
-        }
-    }
-
-    public void setAllGain(String fileName) {
-
-        FileReader fReader = null;
-        BufferedReader bReader = null;
-        try {
-            fReader = new FileReader(fileName);
-        } catch (FileNotFoundException ex) {
-            Logger.getLogger(GainCalib.class.getName()).log(Level.SEVERE, null, ex);
-        }
-        bReader = new BufferedReader(fReader);
-        String line;
-        try {
-            while ((line = bReader.readLine()) != null) {
-                if (line.contains("#")) {
-                    continue;
-                }
-                String[] vec = line.split("\\s+");
-                if (vec.length != 4) {
-                    System.out.println("Wrong format for line: " + line);
-                    throw new RuntimeException("");
-                }
-                int E = Integer.valueOf(vec[0]);
-                int x = Integer.valueOf(vec[1]);
-                int y = Integer.valueOf(vec[2]);
-                double g = Double.valueOf(vec[3]);
-                if (E == 0) {
-                    this.setGain(x, y, g);
-                }
-            }
-        } catch (IOException ex) {
-            Logger.getLogger(GainCalib.class.getName()).log(Level.SEVERE, null, ex);
-        }
-    }
-
-    public void setGain(int icol, int irow, double corr) {
-        long cellid = HPSEcalConditions.makePhysicalID(icol, irow);
-
-        //if(!this._gains.containsKey(cellid)) {
-        //    System.out.println("ERROR updating gain from icol " + icol + " irow " + irow + " this cellid " + cellid + " doesn't have a previous gain?");
-        //    System.exit(1);
-        //}
-//        double gain = corr;//this._gains.get(cellid);
-        this._gains.put(cellid, corr);
-    }
-
-    public double getGain(int icol, int irow) {
-        long cellid = HPSEcalConditions.makePhysicalID(icol, irow);
-        if (!this._gains.containsKey(cellid)) {
-            System.out.println("ERROR getting gain from icol " + icol + " irow " + irow + " this cellid " + cellid + " doesn't have a previous gain?");
-            System.exit(1);
-        }
-        return this._gains.get(cellid);
-
-    }
-
-    public MatchedTrack getTrack(int evt, long id) {
-        MatchedTrack mt = null;
-
-        if (this._tracks.containsKey(evt)) {
-            for (MatchedTrack trk : this._tracks.get(evt)) {
-                if (trk._cellid == id) {
-                    mt = trk;
-                }
-            }
-        }
-        return mt;
-
-    }
-
-    public double getGain(BaseRawCalorimeterHit hit) {
-        long id = hit.getCellID();
-        if (!this._gains.containsKey(id)) {
-            System.out.println("ERROR hit with id " + id + " doesn't exist in gain map!!!");
-        }
-        return this._gains.get(id);
-    }
-
-    public List<HPSEcalCluster> getCalibratedClusters(int eventNumber) {
-
-        if (!_hits.containsKey(eventNumber)) {
-            System.out.println("ERROR no raw hits for event " + eventNumber);
-            System.exit(1);
-        }
-
-
-        if (_hits.get(eventNumber).isEmpty()) {
-            System.out.println("empy hits for " + eventNumber);
-            System.exit(1);
-        }
-
-        if (_debug) {
-            System.out.println("Converting " + _hits.get(eventNumber).size() + " raw ecal hits");
-        }
-
-        ArrayList<CalorimeterHit> newHits = new ArrayList<CalorimeterHit>();
-
-        for (BaseRawCalorimeterHit hit : _hits.get(eventNumber)) {
-
-            if (_debug) {
-                System.out.println("Converting hit id " + hit.getCellID());
-            }
-
-            double gain = getGain(hit);
-            CalorimeterHit newHit = HPSEcalRawConverter.HitDtoA(hit, _integralWindow, gain);
-            if (_applyBadCrystalMap && HPSEcalRawConverterDriver.isBadCrystal(newHit)) {
-                continue;
-            }
-            //if(applyBadCrystalMap && HPSEcalRawConverterDriver.isBadCrystal(newHit)) continue;
-            //if (dropBadFADC && HPSEcalRawConverterDriver.isBadFADC(newHit)) continue;
-            if (newHit.getRawEnergy() > _threshold) {
-                newHits.add(newHit);
-            }
-
-            if (_debug) {
-                System.out.println("Converted hit id " + hit.getCellID() + " with gain " + gain);
-            }
-        }
-
-        if (_debug) {
-            System.out.println(newHits.size() + " calibrated calorimeter hits for event " + eventNumber);
-        }
-
-        //To be able to use decoders I need to associate with readout. Use event put to do that?! -> FIX THIS
-        BaseLCSimEvent event = new BaseLCSimEvent(999999, eventNumber, _detector.getDetectorName());
-        event.put(_ecalTmpCollectionName, newHits, CalorimeterHit.class, 0, _ecalReadoutName);
-
-
-        //Now we have a set of calibrated ecal hits
-        // Clusterize them 
-
-        // Make a hit map for quick lookup by ID.
-        Map<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
-        for (CalorimeterHit hit : newHits) {
-            hitMap.put(hit.getCellID(), hit);
-        }
-
-        List<HPSEcalCluster> clusters = _clusterer.createClusters(hitMap);
-
-        if (_debug) {
-            System.out.println(clusters.size() + " clusters found from event " + eventNumber);
-        }
-
-        return clusters;
-    }
-}

hps-java/src/main/java/org/lcsim/hps/recon/ecal

diff -N GainCalibrationDriver.java
--- GainCalibrationDriver.java	9 Aug 2012 00:51:15 -0000	1.2
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,636 +0,0 @@

-package org.lcsim.hps.recon.ecal;
-
-import hep.aida.*;
-import hep.aida.ref.plotter.PlotterRegion;
-import java.awt.Button;
-import java.awt.FlowLayout;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.io.*;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JLabel;
-import org.lcsim.event.CalorimeterHit;
-import org.lcsim.event.EventHeader;
-import org.lcsim.event.Track;
-import org.lcsim.event.base.BaseRawCalorimeterHit;
-import org.lcsim.geometry.Detector;
-import org.lcsim.geometry.IDDecoder;
-import org.lcsim.geometry.Subdetector;
-import org.lcsim.hps.monitoring.AIDAFrame;
-import org.lcsim.hps.monitoring.Redrawable;
-import org.lcsim.hps.monitoring.Resettable;
-import org.lcsim.hps.recon.tracking.EcalTrackMatch;
-import org.lcsim.util.Driver;
-import org.lcsim.util.aida.AIDA;
-
-/**
- *
- * @author phansson+
- */
-public class GainCalibrationDriver extends Driver implements Resettable, ActionListener, Redrawable {
-
-    int nevents = 0;
-    boolean debug = true;
-    protected IDDecoder dec = null;
-    protected Subdetector ecal;
-    private String ecalName = "Ecal";
-    String rawCollectionName = "EcalReadoutHits";
-    String ecalReadoutName = "EcalHits";
-    String ecalTmpCollectionName = "EcalCalHitsTmp";
-    private String trackCollectionName = "MatchedTracks";
-    private String outputPlotFileName = "test.aida";
-    private String ecalGainFileName = "";
-    private String ecalGainCalibCorrFileName = "";
-    //I would like to steel these from the converter -> FIX THIS!
-    private boolean applyBadCrystalMap = true;
-    private boolean dropBadFADC = false;
-    double threshold = Double.NEGATIVE_INFINITY;
-    private int integralWindow = 30;
-    private int _numIterations = 0;
-    HPSEcalClusterer clusterer = null;
-    EcalTrackMatch trkMatchTool = null;
-    HPSEcalRawConverter converter = null;
-    GainCalib gainCalib = new GainCalib();
-    private boolean hideFrame = false;
-    private int refreshRate = 100;
-    private AIDA aida = AIDA.defaultInstance();
-    private IAnalysisFactory af = aida.analysisFactory();
-    IHistogramFactory hf = aida.histogramFactory();
-    private AIDAFrame pePlotterFrame;
-    IPlotter plotter;
-    JComboBox xCombo;
-    JLabel xLabel;
-    JComboBox yCombo;
-    JLabel yLabel;
-    Integer xList[];
-    Integer yList[];
-    JButton blankButton;
-    boolean alive = true;
-    IHistogram1D pePlots[][][] = new IHistogram1D[47][11][5];
-    IHistogram2D mpePlot;
-    IHistogram2D spePlot;
-    IHistogram2D hitmap;
-    IHistogram1D[] h_PE_t = new IHistogram1D[5];
-    IHistogram1D[] h_PE_b = new IHistogram1D[5];
-
-    class AL extends Frame implements ActionListener, WindowListener {
-
-        Button b;
-
-        public AL(String title) {
-            super(title);
-            setLayout(new FlowLayout());
-            b = new Button("Click to stop program");
-            add(b);
-            b.addActionListener(this);
-        }
-
-        @Override
-        public void actionPerformed(ActionEvent ae) {
-            if (ae.getSource() == b) {
-                System.out.println("Clicked to exit!");
-                dispose();
-                alive = false;//System.exit(0);
-            }
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowOpened(WindowEvent we) {
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowClosing(WindowEvent we) {
-            System.out.println("windowClosing to exit!");
-            dispose();
-            alive = false;//System.exit(0);
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowClosed(WindowEvent we) {
-            System.out.println("windowClosing to exit!");
-            dispose();
-            alive = false;//System.exit(0);
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowIconified(WindowEvent we) {
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowDeiconified(WindowEvent we) {
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowActivated(WindowEvent we) {
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-
-        @Override
-        public void windowDeactivated(WindowEvent we) {
-            //throw new UnsupportedOperationException("Not supported yet.");
-        }
-    }
-
-    @Override
-    public void detectorChanged(Detector detector) {
-        // Get the Subdetector.
-        ecal = detector.getSubdetector(ecalName);
-
-        clusterer.setEcalName("Ecal");
-        clusterer.detectorChanged(detector);
-
-        // Cache ref to decoder.
-        dec = ecal.getIDDecoder();
-
-        gainCalib.setClusterer(clusterer);
-        gainCalib.setDetector(detector);
-        gainCalib.setEcalReadoutName(ecalReadoutName);
-        gainCalib.setThreshold(threshold);
-        gainCalib.setIntegralWindow(integralWindow);
-        gainCalib.setApplyBadCrystalMap(this.applyBadCrystalMap);
-
-        //Use gain calibration file
-        System.out.println("Using gain calibration file \"" + ecalGainFileName + "\"");
-        if (!"".equals(ecalGainFileName)) {
-            gainCalib.setAllGain(ecalGainFileName);
-        } else {
-            gainCalib.setAllGain();
-        }
-
-        pePlotterFrame = new AIDAFrame();
-        pePlotterFrame.setTitle("Gain Frame");
-
-        //plotterFrame = new AIDAFrame();
-        //plotterFrame.setTitle("Gain General");
-
-        IPlotterStyle style;
-
-        IPlotter plotter_hitmap_gr = af.createPlotterFactory().create();
-        plotter_hitmap_gr.createRegions(1, 3, 0);
-        plotter_hitmap_gr.setTitle("Cluster hit map");
-        plotter_hitmap_gr.style().statisticsBoxStyle().setVisible(false);
-        pePlotterFrame.addPlotter(plotter_hitmap_gr);
-
-        hitmap = aida.histogram2D("Cluster hit map", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        plotter_hitmap_gr.region(0).plot(hitmap);
-
-        style = plotter_hitmap_gr.region(0).style();
-        style.setParameter("hist2DStyle", "colorMap");
-        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        ((PlotterRegion) plotter_hitmap_gr.region(0)).getPlot().setAllowUserInteraction(true);
-        ((PlotterRegion) plotter_hitmap_gr.region(0)).getPlot().setAllowPopupMenus(true);
-
-        IPlotter[] plotter_PoverE = new IPlotter[5];
-
-        for (int iE = 0; iE <= 4; ++iE) {
-
-            String str = iE == 0 ? "" : (" iE=" + iE);
-
-            h_PE_t[iE] = aida.histogram1D("E over p top" + str, 50, 0, 2);
-            h_PE_b[iE] = aida.histogram1D("E over p bottom" + str, 50, 0, 2);
-
-            plotter_PoverE[iE] = af.createPlotterFactory().create();
-            plotter_PoverE[iE].createRegions(1, 2, 0);
-            plotter_PoverE[iE].setTitle("E over P" + str);
-            plotter_PoverE[iE].style().statisticsBoxStyle().setVisible(true);
-            pePlotterFrame.addPlotter(plotter_PoverE[iE]);
-
-            plotter_PoverE[iE].region(0).plot(h_PE_t[iE]);
-            plotter_PoverE[iE].region(1).plot(h_PE_b[iE]);
-        }
-
-        plotter = af.createPlotterFactory().create();
-        plotter.createRegions(1, 3, 0);
-        plotter.setTitle("Gain Plots");
-
-        pePlotterFrame.addPlotter(plotter);
-
-        mpePlot = aida.histogram2D("<E over p>", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        plotter.region(0).plot(mpePlot);
-        spePlot = aida.histogram2D("RMS(E over p)", 47, -23.5, 23.5, 11, -5.5, 5.5);
-        plotter.region(1).plot(spePlot);
-        plotter.region(0).style().statisticsBoxStyle().setVisible(false);
-        plotter.region(0).style().setParameter("hist2DStyle", "colorMap");
-        plotter.region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-        plotter.region(1).style().statisticsBoxStyle().setVisible(false);
-        plotter.region(1).style().setParameter("hist2DStyle", "colorMap");
-        plotter.region(1).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
-
-        for (int iE = 0; iE <= 4; ++iE) {
-            for (int irow = -5; irow <= 5; ++irow) {
-                for (int icol = -23; icol <= 23; ++icol) {
-                    if (iE == 0) {
-                        pePlots[icol + 23][irow + 5][iE] = aida.histogram1D("E over p x=" + icol + " y=" + irow, 50, 0, 2);
-                    } else {
-                        pePlots[icol + 23][irow + 5][iE] = aida.histogram1D("E over p x=" + icol + " y=" + irow + " iE=" + iE, 50, 0, 2);
-                    }
-                }
-            }
-        }
-
-        xList = new Integer[46];
-        yList = new Integer[10];
-        int in = 0;
-        for (int i = -5; i <= 5; ++i) {
-            if (i != 0) {
-                yList[in] = i;
-                ++in;
-            }
-        }
-        in = 0;
-        for (int i = -23; i <= 23; ++i) {
-            if (i != 0) {
-                xList[in] = i;
-                ++in;
-            }
-        }
-
-        xCombo = new JComboBox(xList);
-        xCombo.addActionListener(this);
-        xLabel = new JLabel("x");
-        xLabel.setLabelFor(xCombo);
-        pePlotterFrame.getControlsPanel().add(xLabel);
-        pePlotterFrame.getControlsPanel().add(xCombo);
-        yCombo = new JComboBox(yList);
-        yCombo.addActionListener(this);
-        yLabel = new JLabel("y");
-        yLabel.setLabelFor(xCombo);
-        pePlotterFrame.getControlsPanel().add(yLabel);
-        pePlotterFrame.getControlsPanel().add(yCombo);
-
-        plotter.region(2).plot(pePlots[-5 + 23][2 + 5 - 1][0]);
-        xCombo.setSelectedIndex(-5 + 23);
-        yCombo.setSelectedIndex(2 + 5 - 1);
-
-        blankButton = new JButton("Hide histogram");
-        pePlotterFrame.getControlsPanel().add(blankButton);
-        blankButton.addActionListener(this);
-
-        if (!hideFrame) {
-
-            //plotterFrame.pack();
-            //plotterFrame.setVisible(true);
-
-            pePlotterFrame.pack();
-            pePlotterFrame.setVisible(true);
-        }
-    }
-
-    public GainCalibrationDriver() {
-        converter = new HPSEcalRawConverter();
-        trkMatchTool = new EcalTrackMatch(false);
-        clusterer = new HPSEcalClusterer();
-        gainCalib = new GainCalib();
-    }
-
-    public void setNumIterations(int i) {
-        this._numIterations = i;
-    }
-
-    public void setDebug(boolean flag) {
-        this.debug = flag;
-    }
-
-    public void setOutputPlotFileName(String name) {
-        this.outputPlotFileName = name;
-    }
-
-    public void setEcalGainFileName(String name) {
-        this.ecalGainFileName = name;
-    }
-
-    public void setEcalGainCalibCorrFileName(String name) {
-        this.ecalGainCalibCorrFileName = name;
-    }
-
-    public void setHideFrame(boolean val) {
-        this.hideFrame = val;
-    }
-
-    public void process(EventHeader event) {
-        ++nevents;
-        if (debug) {
-            System.out.println("Processing event " + nevents);
-        }
-
-        if (refreshRate > 0 && nevents % refreshRate == 0) {
-            redraw();
-        }
-
-        // Find the raw hits used to build calorimeter hits
-/*
-        List<RawTrackerHit> hits = null;
-        if (event.hasCollection(RawTrackerHit.class, rawCollectionName)) {
-        hits = event.get(RawTrackerHit.class, rawCollectionName);
-        }
-        
-        if(hits==null) {
-        if(debug) System.out.println("No raw ecal hits");
-        return;
-        }
-         */
-
-        List<BaseRawCalorimeterHit> hits = null;
-        if (event.hasCollection(BaseRawCalorimeterHit.class, rawCollectionName)) {
-            hits = event.get(BaseRawCalorimeterHit.class, rawCollectionName);
-        }
-
-        if (hits == null) {
-            if (debug) {
-                System.out.println("No raw ecal hits ");
-            }
-            return;
-        }
-
-        if (debug) {
-            System.out.println(hits.size() + " raw ecal hits");
-        }
-
-        if (hits.isEmpty()) {
-            return;
-        }
-
-        ArrayList<CalorimeterHit> newHits = new ArrayList<CalorimeterHit>();
-
-        for (BaseRawCalorimeterHit hit : hits) {
-            double g = gainCalib.getGain(hit);
-            CalorimeterHit newHit = converter.HitDtoA(hit, integralWindow);
-            if (applyBadCrystalMap && HPSEcalRawConverterDriver.isBadCrystal(newHit)) {
-                continue;
-            }
-            if (dropBadFADC && HPSEcalRawConverterDriver.isBadFADC(newHit)) {
-                continue;
-            }
-            if (newHit.getRawEnergy() > threshold) {
-                newHits.add(newHit);
-            }
-        }
-
-        if (debug) {
-            System.out.println(newHits.size() + " calibrated calorimeter hits");
-        }
-
-        //To be able to use decoders I need to associate with readout. Use event put to do that?! -> FIX THIS
-        event.put(ecalTmpCollectionName, newHits, CalorimeterHit.class, 0, ecalReadoutName);
-
-        //Get the newly created hits
-
-        List<CalorimeterHit> newCalHits = null;
-        if (event.hasCollection(CalorimeterHit.class, ecalTmpCollectionName)) {
-            newCalHits = event.get(CalorimeterHit.class, ecalTmpCollectionName);
-        }
-
-        if (newCalHits == null) {
-            if (debug) {
-                System.out.println("No newCalHits ");
-            }
-            System.exit(1);
-
-        }
-
-        if (debug) {
-            System.out.println(newCalHits.size() + " newCalHits");
-        }
-
-        if (newCalHits.isEmpty()) {
-            return;
-        }
-
-        //Now we have a set of calibrated ecal hits
-        // Clusterize them to get a starting point -> copy the clusterer
-
-        // Make a hit map for quick lookup by ID.
-        Map<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
-        for (CalorimeterHit hit : newCalHits) {
-            hitMap.put(hit.getCellID(), hit);
-        }
-
-        List<HPSEcalCluster> clusters = clusterer.createClusters(hitMap);
-
-        if (debug) {
-            System.out.println(clusters.size() + " clusters found");
-        }
-
-        // Now we want to produce the corrections for each module: c = p/E
-
-        List<Track> tracks = null;
-        if (event.hasCollection(Track.class, trackCollectionName)) {
-            tracks = event.get(Track.class, trackCollectionName);
-        }
-
-        if (debug) {
-            System.out.println(tracks.size() + " tracks in this event");
-        }
-
-        if (tracks == null) {
-            return;
-        }
-
-        for (HPSEcalCluster cl : clusters) {
-
-            int[] pos = getCrystalPair(cl);
-            int side = pos[1] > 0 ? 0 : 1; //top or bottom
-
-            if (debug) {
-                System.out.println("Looking at cluster at ix=" + pos[0] + " iy=" + pos[1]);
-            }
-
-            trkMatchTool.setCluster(cl);
-            trkMatchTool.match(tracks);
-
-            if (!trkMatchTool.isMatchedY(50)) {
-                if (debug) {
-                    System.out.println("Cluster not matched to a track");
-                }
-                continue;
-            }
-
-            if (debug) {
-                System.out.println("Cluster matched to track at distance Y " + trkMatchTool.getDistanceToTrackInY() + " and X " + trkMatchTool.getDistanceToTrackInX());
-            }
-
-            double P = trkMatchTool.getMatchedTrack().getPX() * 1000;
-            double E = cl.getEnergy();
-            double samplingFraction = 0.9;
-            double Ep = E * samplingFraction;
-            double Eoverp = Ep / P;
-
-            if (debug) {
-                System.out.println("P " + P + " E " + E + " Ep " + Ep);
-            }
-
-
-            double Eseed = cl.getSeedHit().getRawEnergy();
-            double ErawSum = 0;
-            for (CalorimeterHit hit : cl.getCalorimeterHits()) {
-                ErawSum += hit.getRawEnergy();
-            }
-
-            if (Eseed / ErawSum < 0.6) {
-                continue;
-            }
-
-            int ebin = -1;
-            if (P > 500 && P <= 700) {
-                ebin = 1;
-            } else if (P > 700 && P <= 900) {
-                ebin = 2;
-            } else if (P > 900 && P <= 1100) {
-                ebin = 3;
-            } else {
-                ebin = 4;
-            }
-
-            if (side == 0) {
-                h_PE_t[0].fill(Eoverp);
-                h_PE_t[ebin].fill(Eoverp);
-
-            } else {
-                h_PE_b[0].fill(Eoverp);
-                h_PE_b[ebin].fill(Eoverp);
-            }
-
-            hitmap.fill(pos[0], pos[1]);
-
-            pePlots[pos[0] + 23][pos[1] + 5][0].fill(Eoverp);
-
-            pePlots[pos[0] + 23][pos[1] + 5][ebin].fill(Eoverp);
-
-
-            gainCalib.setOriginalHits(event.getEventNumber(), hits);
-            for (BaseRawCalorimeterHit hit : hits) {
-                gainCalib.setTrack(event.getEventNumber(), hit.getCellID(), trkMatchTool.getMatchedTrack());
-            }
-        }
-    }
-
-    public int[] getCrystalPair(HPSEcalCluster cluster) {
-        int[] pos = new int[2];
-        pos[0] = cluster.getSeedHit().getIdentifierFieldValue("ix");
-        pos[1] = cluster.getSeedHit().getIdentifierFieldValue("iy");
-
-        //System.out.println("cluster ix,iy " + pos[0] + "," + pos[1] + "    from pos  " + cluster.getSeedHit().getPositionVec().toString());
-        return pos;
-        //getCrystalPair(cluster.getPosition());
-    }
-
-    @Override
-    public void endOfData() {
-
-        redraw();
-
-        if (!"".equals(outputPlotFileName)) {
-            try {
-                aida.saveAs(outputPlotFileName);
-            } catch (IOException ex) {
-                Logger.getLogger(GainCalibrationDriver.class.getName()).log(Level.SEVERE, "Couldn't save aida plots to file " + outputPlotFileName, ex);
-            }
-        }
-        //displayFastTrackingPlots();
-
-        PrintWriter out = null;
-        try {
-            out = new PrintWriter(ecalGainCalibCorrFileName);
-        } catch (FileNotFoundException ex) {
-            Logger.getLogger(GainCalibrationDriver.class.getName()).log(Level.SEVERE, null, ex);
-        }
-        //Save a new file with corrected gains
-        for (int iE = 0; iE <= 4; ++iE) {
-            for (int irow = -5; irow <= 5; ++irow) {
-                for (int icol = -23; icol <= 23; ++icol) {
-                    IHistogram1D h = pePlots[icol + 23][irow + 5][iE];
-                    double g = gainCalib.getGain(icol, irow);
-                    int N = h.entries();
-                    if (N > 6) {
-                        double m = h.mean();
-                        double c = 1.0 / m;
-                        g = g * c;
-                        out.println(iE + " " + icol + " " + irow + " " + g);
-                    }
-
-                }
-            }
-        }
-        out.close();
-
-        //gainCalib.runOptimization(this._numIterations);
-
-        //AL alWindow = new AL("Click to quit");
-        //alWindow.setSize(350,100);
-        //alWindow.setVisible(true);
-        //while(alive) {
-        //    sleep
-        //}
-
-
-    }
-
-    @Override
-    public void reset() {
-        if (plotter != null) {
-            plotter.hide();
-            plotter.destroyRegions();
-            for (int x = -23; x <= 23; x++) { // slot
-                for (int y = -5; y <= 5; y++) { // crate  
-                    for (int iE = 0; iE <= 4; ++iE) {
-                        pePlots[x + 23][y + 5][iE].reset();
-                    }
-                }
-            }
-        }
-    }
-
-    @Override
-    public void actionPerformed(ActionEvent ae) {
-
-        if (ae.getSource() == blankButton) {
-            plotter.region(2).clear();
-        } else {
-            //get the col and row to display
-            Integer x = (Integer) xCombo.getSelectedItem();
-            Integer y = (Integer) yCombo.getSelectedItem();
-            plotter.region(2).clear();
-            plotter.region(2).plot(pePlots[x + 23][y + 5][0]);
-        }
-    }
-
-    @Override
-    public void redraw() {
-
-        //do something if needed
-        mpePlot.reset();
-        spePlot.reset();
-
-        for (int irow = -5; irow <= 5; ++irow) {
-            for (int icol = -23; icol <= 23; ++icol) {
-                //System.out.println(" redraw irow " + irow + " icol " + icol + " entries " + pePlots[icol+23][irow+5].entries());
-                if (pePlots[icol + 23][irow + 5][0].entries() > 10) {
-                    mpePlot.fill(icol, irow, pePlots[icol + 23][irow + 5][0].mean());
-                    spePlot.fill(icol, irow, pePlots[icol + 23][irow + 5][0].rms());
-
-                }
-            }
-        }
-    }
-
-    @Override
-    public void setEventRefreshRate(int eventRefreshRate) {
-        refreshRate = eventRefreshRate;
-    }
-}

hps-java/sandbox

diff -N GainCalibrationDriver.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ GainCalibrationDriver.java	20 Nov 2012 23:25:09 -0000	1.1
@@ -0,0 +1,636 @@

+package org.lcsim.hps.recon.ecal;
+
+import hep.aida.*;
+import hep.aida.ref.plotter.PlotterRegion;
+import java.awt.Button;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowEvent;
+import java.awt.event.WindowListener;
+import java.io.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import org.lcsim.event.CalorimeterHit;
+import org.lcsim.event.EventHeader;
+import org.lcsim.event.Track;
+import org.lcsim.event.base.BaseRawCalorimeterHit;
+import org.lcsim.geometry.Detector;
+import org.lcsim.geometry.IDDecoder;
+import org.lcsim.geometry.Subdetector;
+import org.lcsim.hps.monitoring.AIDAFrame;
+import org.lcsim.hps.monitoring.Redrawable;
+import org.lcsim.hps.monitoring.Resettable;
+import org.lcsim.hps.recon.tracking.EcalTrackMatch;
+import org.lcsim.util.Driver;
+import org.lcsim.util.aida.AIDA;
+
+/**
+ *
+ * @author phansson+
+ */
+public class GainCalibrationDriver extends Driver implements Resettable, ActionListener, Redrawable {
+
+    int nevents = 0;
+    boolean debug = true;
+    protected IDDecoder dec = null;
+    protected Subdetector ecal;
+    private String ecalName = "Ecal";
+    String rawCollectionName = "EcalReadoutHits";
+    String ecalReadoutName = "EcalHits";
+    String ecalTmpCollectionName = "EcalCalHitsTmp";
+    private String trackCollectionName = "MatchedTracks";
+    private String outputPlotFileName = "test.aida";
+    private String ecalGainFileName = "";
+    private String ecalGainCalibCorrFileName = "";
+    //I would like to steel these from the converter -> FIX THIS!
+    private boolean applyBadCrystalMap = true;
+    private boolean dropBadFADC = false;
+    double threshold = Double.NEGATIVE_INFINITY;
+    private int integralWindow = 30;
+    private int _numIterations = 0;
+    HPSEcalClusterer clusterer = null;
+    EcalTrackMatch trkMatchTool = null;
+    HPSEcalRawConverter converter = null;
+    GainCalib gainCalib = new GainCalib();
+    private boolean hideFrame = false;
+    private int refreshRate = 100;
+    private AIDA aida = AIDA.defaultInstance();
+    private IAnalysisFactory af = aida.analysisFactory();
+    IHistogramFactory hf = aida.histogramFactory();
+    private AIDAFrame pePlotterFrame;
+    IPlotter plotter;
+    JComboBox xCombo;
+    JLabel xLabel;
+    JComboBox yCombo;
+    JLabel yLabel;
+    Integer xList[];
+    Integer yList[];
+    JButton blankButton;
+    boolean alive = true;
+    IHistogram1D pePlots[][][] = new IHistogram1D[47][11][5];
+    IHistogram2D mpePlot;
+    IHistogram2D spePlot;
+    IHistogram2D hitmap;
+    IHistogram1D[] h_PE_t = new IHistogram1D[5];
+    IHistogram1D[] h_PE_b = new IHistogram1D[5];
+
+    class AL extends Frame implements ActionListener, WindowListener {
+
+        Button b;
+
+        public AL(String title) {
+            super(title);
+            setLayout(new FlowLayout());
+            b = new Button("Click to stop program");
+            add(b);
+            b.addActionListener(this);
+        }
+
+        @Override
+        public void actionPerformed(ActionEvent ae) {
+            if (ae.getSource() == b) {
+                System.out.println("Clicked to exit!");
+                dispose();
+                alive = false;//System.exit(0);
+            }
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowOpened(WindowEvent we) {
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowClosing(WindowEvent we) {
+            System.out.println("windowClosing to exit!");
+            dispose();
+            alive = false;//System.exit(0);
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowClosed(WindowEvent we) {
+            System.out.println("windowClosing to exit!");
+            dispose();
+            alive = false;//System.exit(0);
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowIconified(WindowEvent we) {
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowDeiconified(WindowEvent we) {
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowActivated(WindowEvent we) {
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public void windowDeactivated(WindowEvent we) {
+            //throw new UnsupportedOperationException("Not supported yet.");
+        }
+    }
+
+    @Override
+    public void detectorChanged(Detector detector) {
+        // Get the Subdetector.
+        ecal = detector.getSubdetector(ecalName);
+
+        clusterer.setEcalName("Ecal");
+        clusterer.detectorChanged(detector);
+
+        // Cache ref to decoder.
+        dec = ecal.getIDDecoder();
+
+        gainCalib.setClusterer(clusterer);
+        gainCalib.setDetector(detector);
+        gainCalib.setEcalReadoutName(ecalReadoutName);
+        gainCalib.setThreshold(threshold);
+        gainCalib.setIntegralWindow(integralWindow);
+        gainCalib.setApplyBadCrystalMap(this.applyBadCrystalMap);
+
+        //Use gain calibration file
+        System.out.println("Using gain calibration file \"" + ecalGainFileName + "\"");
+        if (!"".equals(ecalGainFileName)) {
+            gainCalib.setAllGain(ecalGainFileName);
+        } else {
+            gainCalib.setAllGain();
+        }
+
+        pePlotterFrame = new AIDAFrame();
+        pePlotterFrame.setTitle("Gain Frame");
+
+        //plotterFrame = new AIDAFrame();
+        //plotterFrame.setTitle("Gain General");
+
+        IPlotterStyle style;
+
+        IPlotter plotter_hitmap_gr = af.createPlotterFactory().create();
+        plotter_hitmap_gr.createRegions(1, 3, 0);
+        plotter_hitmap_gr.setTitle("Cluster hit map");
+        plotter_hitmap_gr.style().statisticsBoxStyle().setVisible(false);
+        pePlotterFrame.addPlotter(plotter_hitmap_gr);
+
+        hitmap = aida.histogram2D("Cluster hit map", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        plotter_hitmap_gr.region(0).plot(hitmap);
+
+        style = plotter_hitmap_gr.region(0).style();
+        style.setParameter("hist2DStyle", "colorMap");
+        style.dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        ((PlotterRegion) plotter_hitmap_gr.region(0)).getPlot().setAllowUserInteraction(true);
+        ((PlotterRegion) plotter_hitmap_gr.region(0)).getPlot().setAllowPopupMenus(true);
+
+        IPlotter[] plotter_PoverE = new IPlotter[5];
+
+        for (int iE = 0; iE <= 4; ++iE) {
+
+            String str = iE == 0 ? "" : (" iE=" + iE);
+
+            h_PE_t[iE] = aida.histogram1D("E over p top" + str, 50, 0, 2);
+            h_PE_b[iE] = aida.histogram1D("E over p bottom" + str, 50, 0, 2);
+
+            plotter_PoverE[iE] = af.createPlotterFactory().create();
+            plotter_PoverE[iE].createRegions(1, 2, 0);
+            plotter_PoverE[iE].setTitle("E over P" + str);
+            plotter_PoverE[iE].style().statisticsBoxStyle().setVisible(true);
+            pePlotterFrame.addPlotter(plotter_PoverE[iE]);
+
+            plotter_PoverE[iE].region(0).plot(h_PE_t[iE]);
+            plotter_PoverE[iE].region(1).plot(h_PE_b[iE]);
+        }
+
+        plotter = af.createPlotterFactory().create();
+        plotter.createRegions(1, 3, 0);
+        plotter.setTitle("Gain Plots");
+
+        pePlotterFrame.addPlotter(plotter);
+
+        mpePlot = aida.histogram2D("<E over p>", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        plotter.region(0).plot(mpePlot);
+        spePlot = aida.histogram2D("RMS(E over p)", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        plotter.region(1).plot(spePlot);
+        plotter.region(0).style().statisticsBoxStyle().setVisible(false);
+        plotter.region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotter.region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotter.region(1).style().statisticsBoxStyle().setVisible(false);
+        plotter.region(1).style().setParameter("hist2DStyle", "colorMap");
+        plotter.region(1).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+
+        for (int iE = 0; iE <= 4; ++iE) {
+            for (int irow = -5; irow <= 5; ++irow) {
+                for (int icol = -23; icol <= 23; ++icol) {
+                    if (iE == 0) {
+                        pePlots[icol + 23][irow + 5][iE] = aida.histogram1D("E over p x=" + icol + " y=" + irow, 50, 0, 2);
+                    } else {
+                        pePlots[icol + 23][irow + 5][iE] = aida.histogram1D("E over p x=" + icol + " y=" + irow + " iE=" + iE, 50, 0, 2);
+                    }
+                }
+            }
+        }
+
+        xList = new Integer[46];
+        yList = new Integer[10];
+        int in = 0;
+        for (int i = -5; i <= 5; ++i) {
+            if (i != 0) {
+                yList[in] = i;
+                ++in;
+            }
+        }
+        in = 0;
+        for (int i = -23; i <= 23; ++i) {
+            if (i != 0) {
+                xList[in] = i;
+                ++in;
+            }
+        }
+
+        xCombo = new JComboBox(xList);
+        xCombo.addActionListener(this);
+        xLabel = new JLabel("x");
+        xLabel.setLabelFor(xCombo);
+        pePlotterFrame.getControlsPanel().add(xLabel);
+        pePlotterFrame.getControlsPanel().add(xCombo);
+        yCombo = new JComboBox(yList);
+        yCombo.addActionListener(this);
+        yLabel = new JLabel("y");
+        yLabel.setLabelFor(xCombo);
+        pePlotterFrame.getControlsPanel().add(yLabel);
+        pePlotterFrame.getControlsPanel().add(yCombo);
+
+        plotter.region(2).plot(pePlots[-5 + 23][2 + 5 - 1][0]);
+        xCombo.setSelectedIndex(-5 + 23);
+        yCombo.setSelectedIndex(2 + 5 - 1);
+
+        blankButton = new JButton("Hide histogram");
+        pePlotterFrame.getControlsPanel().add(blankButton);
+        blankButton.addActionListener(this);
+
+        if (!hideFrame) {
+
+            //plotterFrame.pack();
+            //plotterFrame.setVisible(true);
+
+            pePlotterFrame.pack();
+            pePlotterFrame.setVisible(true);
+        }
+    }
+
+    public GainCalibrationDriver() {
+        converter = new HPSEcalRawConverter();
+        trkMatchTool = new EcalTrackMatch(false);
+        clusterer = new HPSEcalClusterer();
+        gainCalib = new GainCalib();
+    }
+
+    public void setNumIterations(int i) {
+        this._numIterations = i;
+    }
+
+    public void setDebug(boolean flag) {
+        this.debug = flag;
+    }
+
+    public void setOutputPlotFileName(String name) {
+        this.outputPlotFileName = name;
+    }
+
+    public void setEcalGainFileName(String name) {
+        this.ecalGainFileName = name;
+    }
+
+    public void setEcalGainCalibCorrFileName(String name) {
+        this.ecalGainCalibCorrFileName = name;
+    }
+
+    public void setHideFrame(boolean val) {
+        this.hideFrame = val;
+    }
+
+    public void process(EventHeader event) {
+        ++nevents;
+        if (debug) {
+            System.out.println("Processing event " + nevents);
+        }
+
+        if (refreshRate > 0 && nevents % refreshRate == 0) {
+            redraw();
+        }
+
+        // Find the raw hits used to build calorimeter hits
+/*
+        List<RawTrackerHit> hits = null;
+        if (event.hasCollection(RawTrackerHit.class, rawCollectionName)) {
+        hits = event.get(RawTrackerHit.class, rawCollectionName);
+        }
+        
+        if(hits==null) {
+        if(debug) System.out.println("No raw ecal hits");
+        return;
+        }
+         */
+
+        List<BaseRawCalorimeterHit> hits = null;
+        if (event.hasCollection(BaseRawCalorimeterHit.class, rawCollectionName)) {
+            hits = event.get(BaseRawCalorimeterHit.class, rawCollectionName);
+        }
+
+        if (hits == null) {
+            if (debug) {
+                System.out.println("No raw ecal hits ");
+            }
+            return;
+        }
+
+        if (debug) {
+            System.out.println(hits.size() + " raw ecal hits");
+        }
+
+        if (hits.isEmpty()) {
+            return;
+        }
+
+        ArrayList<CalorimeterHit> newHits = new ArrayList<CalorimeterHit>();
+
+        for (BaseRawCalorimeterHit hit : hits) {
+            double g = gainCalib.getGain(hit);
+            CalorimeterHit newHit = converter.HitDtoA(hit, integralWindow);
+            if (applyBadCrystalMap && HPSEcalRawConverterDriver.isBadCrystal(newHit)) {
+                continue;
+            }
+            if (dropBadFADC && HPSEcalRawConverterDriver.isBadFADC(newHit)) {
+                continue;
+            }
+            if (newHit.getRawEnergy() > threshold) {
+                newHits.add(newHit);
+            }
+        }
+
+        if (debug) {
+            System.out.println(newHits.size() + " calibrated calorimeter hits");
+        }
+
+        //To be able to use decoders I need to associate with readout. Use event put to do that?! -> FIX THIS
+        event.put(ecalTmpCollectionName, newHits, CalorimeterHit.class, 0, ecalReadoutName);
+
+        //Get the newly created hits
+
+        List<CalorimeterHit> newCalHits = null;
+        if (event.hasCollection(CalorimeterHit.class, ecalTmpCollectionName)) {
+            newCalHits = event.get(CalorimeterHit.class, ecalTmpCollectionName);
+        }
+
+        if (newCalHits == null) {
+            if (debug) {
+                System.out.println("No newCalHits ");
+            }
+            System.exit(1);
+
+        }
+
+        if (debug) {
+            System.out.println(newCalHits.size() + " newCalHits");
+        }
+
+        if (newCalHits.isEmpty()) {
+            return;
+        }
+
+        //Now we have a set of calibrated ecal hits
+        // Clusterize them to get a starting point -> copy the clusterer
+
+        // Make a hit map for quick lookup by ID.
+        Map<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
+        for (CalorimeterHit hit : newCalHits) {
+            hitMap.put(hit.getCellID(), hit);
+        }
+
+        List<HPSEcalCluster> clusters = clusterer.createClusters(hitMap);
+
+        if (debug) {
+            System.out.println(clusters.size() + " clusters found");
+        }
+
+        // Now we want to produce the corrections for each module: c = p/E
+
+        List<Track> tracks = null;
+        if (event.hasCollection(Track.class, trackCollectionName)) {
+            tracks = event.get(Track.class, trackCollectionName);
+        }
+
+        if (debug) {
+            System.out.println(tracks.size() + " tracks in this event");
+        }
+
+        if (tracks == null) {
+            return;
+        }
+
+        for (HPSEcalCluster cl : clusters) {
+
+            int[] pos = getCrystalPair(cl);
+            int side = pos[1] > 0 ? 0 : 1; //top or bottom
+
+            if (debug) {
+                System.out.println("Looking at cluster at ix=" + pos[0] + " iy=" + pos[1]);
+            }
+
+            trkMatchTool.setCluster(cl);
+            trkMatchTool.match(tracks);
+
+            if (!trkMatchTool.isMatchedY(50)) {
+                if (debug) {
+                    System.out.println("Cluster not matched to a track");
+                }
+                continue;
+            }
+
+            if (debug) {
+                System.out.println("Cluster matched to track at distance Y " + trkMatchTool.getDistanceToTrackInY() + " and X " + trkMatchTool.getDistanceToTrackInX());
+            }
+
+            double P = trkMatchTool.getMatchedTrack().getPX() * 1000;
+            double E = cl.getEnergy();
+            double samplingFraction = 0.9;
+            double Ep = E * samplingFraction;
+            double Eoverp = Ep / P;
+
+            if (debug) {
+                System.out.println("P " + P + " E " + E + " Ep " + Ep);
+            }
+
+
+            double Eseed = cl.getSeedHit().getRawEnergy();
+            double ErawSum = 0;
+            for (CalorimeterHit hit : cl.getCalorimeterHits()) {
+                ErawSum += hit.getRawEnergy();
+            }
+
+            if (Eseed / ErawSum < 0.6) {
+                continue;
+            }
+
+            int ebin = -1;
+            if (P > 500 && P <= 700) {
+                ebin = 1;
+            } else if (P > 700 && P <= 900) {
+                ebin = 2;
+            } else if (P > 900 && P <= 1100) {
+                ebin = 3;
+            } else {
+                ebin = 4;
+            }
+
+            if (side == 0) {
+                h_PE_t[0].fill(Eoverp);
+                h_PE_t[ebin].fill(Eoverp);
+
+            } else {
+                h_PE_b[0].fill(Eoverp);
+                h_PE_b[ebin].fill(Eoverp);
+            }
+
+            hitmap.fill(pos[0], pos[1]);
+
+            pePlots[pos[0] + 23][pos[1] + 5][0].fill(Eoverp);
+
+            pePlots[pos[0] + 23][pos[1] + 5][ebin].fill(Eoverp);
+
+
+            gainCalib.setOriginalHits(event.getEventNumber(), hits);
+            for (BaseRawCalorimeterHit hit : hits) {
+                gainCalib.setTrack(event.getEventNumber(), hit.getCellID(), trkMatchTool.getMatchedTrack());
+            }
+        }
+    }
+
+    public int[] getCrystalPair(HPSEcalCluster cluster) {
+        int[] pos = new int[2];
+        pos[0] = cluster.getSeedHit().getIdentifierFieldValue("ix");
+        pos[1] = cluster.getSeedHit().getIdentifierFieldValue("iy");
+
+        //System.out.println("cluster ix,iy " + pos[0] + "," + pos[1] + "    from pos  " + cluster.getSeedHit().getPositionVec().toString());
+        return pos;
+        //getCrystalPair(cluster.getPosition());
+    }
+
+    @Override
+    public void endOfData() {
+
+        redraw();
+
+        if (!"".equals(outputPlotFileName)) {
+            try {
+                aida.saveAs(outputPlotFileName);
+            } catch (IOException ex) {
+                Logger.getLogger(GainCalibrationDriver.class.getName()).log(Level.SEVERE, "Couldn't save aida plots to file " + outputPlotFileName, ex);
+            }
+        }
+        //displayFastTrackingPlots();
+
+        PrintWriter out = null;
+        try {
+            out = new PrintWriter(ecalGainCalibCorrFileName);
+        } catch (FileNotFoundException ex) {
+            Logger.getLogger(GainCalibrationDriver.class.getName()).log(Level.SEVERE, null, ex);
+        }
+        //Save a new file with corrected gains
+        for (int iE = 0; iE <= 4; ++iE) {
+            for (int irow = -5; irow <= 5; ++irow) {
+                for (int icol = -23; icol <= 23; ++icol) {
+                    IHistogram1D h = pePlots[icol + 23][irow + 5][iE];
+                    double g = gainCalib.getGain(icol, irow);
+                    int N = h.entries();
+                    if (N > 6) {
+                        double m = h.mean();
+                        double c = 1.0 / m;
+                        g = g * c;
+                        out.println(iE + " " + icol + " " + irow + " " + g);
+                    }
+
+                }
+            }
+        }
+        out.close();
+
+        //gainCalib.runOptimization(this._numIterations);
+
+        //AL alWindow = new AL("Click to quit");
+        //alWindow.setSize(350,100);
+        //alWindow.setVisible(true);
+        //while(alive) {
+        //    sleep
+        //}
+
+
+    }
+
+    @Override
+    public void reset() {
+        if (plotter != null) {
+            plotter.hide();
+            plotter.destroyRegions();
+            for (int x = -23; x <= 23; x++) { // slot
+                for (int y = -5; y <= 5; y++) { // crate  
+                    for (int iE = 0; iE <= 4; ++iE) {
+                        pePlots[x + 23][y + 5][iE].reset();
+                    }
+                }
+            }
+        }
+    }
+
+    @Override
+    public void actionPerformed(ActionEvent ae) {
+
+        if (ae.getSource() == blankButton) {
+            plotter.region(2).clear();
+        } else {
+            //get the col and row to display
+            Integer x = (Integer) xCombo.getSelectedItem();
+            Integer y = (Integer) yCombo.getSelectedItem();
+            plotter.region(2).clear();
+            plotter.region(2).plot(pePlots[x + 23][y + 5][0]);
+        }
+    }
+
+    @Override
+    public void redraw() {
+
+        //do something if needed
+        mpePlot.reset();
+        spePlot.reset();
+
+        for (int irow = -5; irow <= 5; ++irow) {
+            for (int icol = -23; icol <= 23; ++icol) {
+                //System.out.println(" redraw irow " + irow + " icol " + icol + " entries " + pePlots[icol+23][irow+5].entries());
+                if (pePlots[icol + 23][irow + 5][0].entries() > 10) {
+                    mpePlot.fill(icol, irow, pePlots[icol + 23][irow + 5][0].mean());
+                    spePlot.fill(icol, irow, pePlots[icol + 23][irow + 5][0].rms());
+
+                }
+            }
+        }
+    }
+
+    @Override
+    public void setEventRefreshRate(int eventRefreshRate) {
+        refreshRate = eventRefreshRate;
+    }
+}

hps-java/sandbox

diff -N GainCalib.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ GainCalib.java	20 Nov 2012 23:25:09 -0000	1.1
@@ -0,0 +1,508 @@

+package org.lcsim.hps.recon.ecal;
+
+import hep.aida.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.*;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import org.lcsim.event.CalorimeterHit;
+import org.lcsim.event.EventHeader;
+import org.lcsim.event.Track;
+import org.lcsim.event.base.BaseLCSimEvent;
+import org.lcsim.event.base.BaseRawCalorimeterHit;
+import org.lcsim.geometry.Detector;
+import org.lcsim.hps.monitoring.AIDAFrame;
+import org.lcsim.util.aida.AIDA;
+
+/**
+ *
+ * @author phansson
+ */
+public class GainCalib implements ActionListener {
+
+    boolean _debug = false;
+    EventHeader _event = null;
+    HPSEcalClusterer _clusterer = null;
+    private int _integralWindow = 30;
+    private double _threshold = Double.NEGATIVE_INFINITY;
+    private boolean _applyBadCrystalMap = true;
+    private Map<Long, Double> _gains = new HashMap<Long, Double>();
+    //original list
+    private Map<Integer, List<BaseRawCalorimeterHit>> _hits = new HashMap<Integer, List<BaseRawCalorimeterHit>>();
+    private Map<Integer, List<MatchedTrack>> _tracks = new HashMap<Integer, List<MatchedTrack>>();
+    private Detector _detector;
+    private String _ecalReadoutName;
+    private String _ecalTmpCollectionName = "temporaryEcalCalHits";
+    private AIDA aida = AIDA.defaultInstance();
+    private IAnalysisFactory af = aida.analysisFactory();
+    IHistogramFactory hf = aida.histogramFactory();
+    IHistogram1D pe[][] = new IHistogram1D[47][11];
+    List<PEHistograms> iterPE = new ArrayList<PEHistograms>();
+    private AIDAFrame plotFrame = new AIDAFrame();
+    private List<IPlotter> plotterList = new ArrayList<IPlotter>();
+    JComboBox xCombo = null;
+    JLabel xLabel = null;
+    Integer xList[];
+    JComboBox yCombo = null;
+    JLabel yLabel = null;
+    Integer yList[];
+
+    @Override
+    public void actionPerformed(ActionEvent ae) {
+        //if(ae == blankButton) {
+        //    //
+        //}
+        Integer x = (Integer) xCombo.getSelectedItem();
+        Integer y = (Integer) yCombo.getSelectedItem();
+        for (IPlotter p : plotterList) {
+            String title = p.title(); //("Gain iteration " + iter);
+            String v[] = title.split(" ");
+            if (v.length < 3) {
+                System.out.println("ERROR this title " + title + " doesn't have the correct syntax");
+                System.exit(1);
+            }
+            Integer iter = Integer.parseInt(v[2]);
+            for (PEHistograms peh : iterPE) {
+                if (peh._i == iter) {
+                    p.region(4).clear();
+                    p.region(4).plot(peh.pe[x + 23][y + 5]);
+                }
+            }
+
+        }
+    }
+
+    public class MatchedTrack {
+
+        long _cellid;
+        Track _track;
+
+        MatchedTrack(long id, Track trk) {
+            _cellid = id;
+            _track = trk;
+        }
+    }
+
+    class PEHistograms {
+
+        int _i;
+        IHistogram1D pe[][] = new IHistogram1D[47][11];
+
+        PEHistograms(int i) {
+            _i = i;
+        }
+    }
+
+    GainCalib() {
+        for (int irow = -5; irow <= 5; ++irow) {
+            for (int icol = -23; icol <= 23; ++icol) {
+                pe[icol + 23][irow + 5] = aida.histogram1D("(GainCalib) E over p x=" + icol + " y=" + irow, 50, 0, 3);
+            }
+        }
+
+        xList = new Integer[46];
+        yList = new Integer[10];
+        int in = 0;
+        for (int i = -5; i <= 5; ++i) {
+            if (i != 0) {
+                yList[in] = i;
+                ++in;
+            }
+        }
+        in = 0;
+        for (int i = -23; i <= 23; ++i) {
+            if (i != 0) {
+                xList[in] = i;
+                ++in;
+            }
+        }
+    }
+
+    public void setApplyBadCrystalMap(boolean d) {
+        this._applyBadCrystalMap = d;
+    }
+
+    public void setDebug(boolean d) {
+        this._debug = d;
+    }
+
+    public void setClusterer(HPSEcalClusterer clust) {
+        _clusterer = clust;
+    }
+
+    public void setOriginalHits(int evt, List<BaseRawCalorimeterHit> hits) {
+        this._hits.put(evt, hits);
+        for (BaseRawCalorimeterHit hit : hits) {
+            this._gains.put(hit.getCellID(), HPSEcalConditions.physicalToGain(hit.getCellID()));
+        }
+    }
+
+    public void setTrack(int evt, long ecalCellID, Track track) {
+        MatchedTrack mt = new MatchedTrack(ecalCellID, track);
+
+        if (!this._tracks.containsKey(evt)) {
+            this._tracks.put(evt, new ArrayList<MatchedTrack>());
+        }
+
+        List<MatchedTrack> list = this._tracks.get(evt);
+        list.add(mt);
+    }
+
+    public void setIntegralWindow(int val) {
+        _integralWindow = val;
+    }
+
+    public void setThreshold(double val) {
+        _threshold = val;
+    }
+
+    public void setEcalReadoutName(String str) {
+        this._ecalReadoutName = str;
+    }
+
+    public void setDetector(Detector det) {
+        this._detector = det;
+    }
+
+    public void runOptimization(int nIterations) {
+
+        System.out.println("Start gain calibration");
+
+        System.out.println("nIterations " + nIterations);
+
+        if (_hits == null) {
+            System.out.println("No original hits available");
+            System.exit(1);
+        }
+
+        int event;
+        int iter = 0;
+        while (iter < nIterations) {
+            System.out.println("Iteration " + iter);
+
+            Iterator it = _hits.entrySet().iterator();
+            while (it.hasNext()) {
+                event = ((Map.Entry<Integer, ArrayList<BaseRawCalorimeterHit>>) it.next()).getKey();
+                if (_debug) {
+                    System.out.println("Event " + event);
+                }
+
+                List<HPSEcalCluster> clusters = getCalibratedClusters(event);
+
+                if (_debug) {
+                    System.out.println("Found " + clusters.size() + " clusters");
+                }
+
+                for (HPSEcalCluster cluster : clusters) {
+
+                    int[] pos = new int[2];
+                    pos[0] = cluster.getSeedHit().getIdentifierFieldValue("ix");
+                    pos[1] = cluster.getSeedHit().getIdentifierFieldValue("iy");
+
+                    //find the tracks matched to those clusters
+
+                    MatchedTrack track = getTrack(event, cluster.getSeedHit().getCellID());
+
+                    if (_debug) {
+                        System.out.println("Found track with with cell id " + cluster.getSeedHit().getCellID());
+                    }
+
+                    double P = track._track.getPX() * 1000;
+                    double E = cluster.getEnergy();
+                    double samplingFraction = 0.9;
+                    double Ep = E * samplingFraction;
+                    double Eoverp = Ep / P;
+
+
+                    if (_debug) {
+                        System.out.println("P " + P + " E " + E + " Ep " + Ep + " --> E/p=" + Eoverp);
+                    }
+
+                    pe[pos[0] + 23][pos[1] + 5].fill(Eoverp);
+
+                    if (_debug) {
+                        System.out.println("Cluster icol " + pos[0] + " irow " + pos[1] + " entries " + pe[pos[0] + 23][pos[1] + 5].entries());
+                    }
+                }
+            }
+            copyPE(iter);
+            ++iter;
+        }
+    }
+
+    void copyPE(int iter) {
+
+        //copy the histograms, extract gains and reset for new iteration
+
+        IHistogram2D mpePlot = aida.histogram2D("Iter " + iter + " <E over p>", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        IHistogram2D spePlot = aida.histogram2D("Iter " + iter + " RMS(E over p)", 47, -23.5, 23.5, 11, -5.5, 5.5);
+        IHistogram1D pePlot = hf.createCopy("Iter " + iter + " E over p", pe[0][0]);
+        IHistogram2D gainPlot = aida.histogram2D("Iter " + iter + " gain", 47, -23.5, 23.5, 11, -5.5, 5.5);
+
+
+        PEHistograms hists = new PEHistograms(iter);
+        for (int irow = -5; irow <= 5; ++irow) {
+            for (int icol = -23; icol <= 23; ++icol) {
+                hists.pe[icol + 23][irow + 5] = hf.createCopy("Iter " + iter + " E over p x=" + icol + " y=" + irow, pe[icol + 23][irow + 5]);
+                pePlot = hf.add("Iter " + iter + " E over p", pePlot, pe[icol + 23][irow + 5]);
+                if (pe[icol + 23][irow + 5].entries() > 10) {
+                    mpePlot.fill(icol, irow, pe[icol + 23][irow + 5].mean());
+                    spePlot.fill(icol, irow, pe[icol + 23][irow + 5].rms());
+                    double corr = 1.0 / pe[icol + 23][irow + 5].mean(); //Correction to get p/E==1
+                    double gain = this.getGain(icol, irow) * corr;
+                    setGain(icol, irow, gain);
+                    gain = this.getGain(icol, irow);
+                    gainPlot.fill(icol, irow, gain);
+                }
+
+            }
+        }
+        hists._i = iter;
+        iterPE.add(hists);
+
+        /*        
+        for(int irow=-5;irow<=5;++irow) {
+        for(int icol=-23;icol<=23;++icol) {
+        for(PEHistograms peh : iterPE) {
+        if(peh._i==iter) {
+        if(peh.pe[icol+23][irow+5].entries()>10) {
+        mpePlot.fill(icol,irow,peh.pe[icol+23][irow+5].mean());
+        spePlot.fill(icol,irow,peh.pe[icol+23][irow+5].rms());
+        }
+        }
+        }
+        }
+        }
+        
+         */
+
+        //Plot
+        if (xCombo == null) {
+            xCombo = new JComboBox(xList);
+            xCombo.addActionListener(this);
+            xLabel = new JLabel("x");
+            xLabel.setLabelFor(xCombo);
+            plotFrame.getControlsPanel().add(xLabel);
+            plotFrame.getControlsPanel().add(xCombo);
+            yCombo = new JComboBox(yList);
+            yCombo.addActionListener(this);
+            yLabel = new JLabel("y");
+            yLabel.setLabelFor(xCombo);
+            plotFrame.getControlsPanel().add(yLabel);
+            plotFrame.getControlsPanel().add(yCombo);
+            xCombo.setSelectedIndex(-15 + 23);
+            yCombo.setSelectedIndex(1 + 5 - 1);
+        }
+
+        IPlotter plotter = af.createPlotterFactory().create();
+        plotter.createRegions(1, 5, 0);
+        plotter.setTitle("Gain iteration " + iter);
+        //plotter.style().statisticsBoxStyle().setVisible(false);
+        plotFrame.addPlotter(plotter);
+        plotterList.add(plotter);
+
+        plotter.region(0).plot(mpePlot);
+        plotter.region(1).plot(spePlot);
+        plotter.region(2).plot(gainPlot);
+        plotter.region(3).plot(pePlot);
+        plotter.region(4).plot(hists.pe[-15 + 23][1 + 5 - 1 + 1]);
+
+        plotter.region(0).style().statisticsBoxStyle().setVisible(false);
+        plotter.region(0).style().setParameter("hist2DStyle", "colorMap");
+        plotter.region(0).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotter.region(1).style().statisticsBoxStyle().setVisible(false);
+        plotter.region(1).style().setParameter("hist2DStyle", "colorMap");
+        plotter.region(1).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+        plotter.region(2).style().statisticsBoxStyle().setVisible(false);
+        plotter.region(2).style().setParameter("hist2DStyle", "colorMap");
+        plotter.region(2).style().dataStyle().fillStyle().setParameter("colorMapScheme", "rainbow");
+
+        //Extract gain corrections
+
+        plotFrame.pack();
+        plotFrame.setVisible(false);
+
+        //Reset basic histograms
+
+        for (int irow = -5; irow <= 5; ++irow) {
+            for (int icol = -23; icol <= 23; ++icol) {
+                pe[icol + 23][irow + 5].reset();
+            }
+        }
+    }
+
+    public void setAllGain(double g) {
+
+        for (int irow = -5; irow <= 5; ++irow) {
+            for (int icol = -23; icol <= 23; ++icol) {
+                this.setGain(icol, irow, g);
+            }
+        }
+    }
+
+    public void setAllGain() {
+        for (int irow = -5; irow <= 5; ++irow) {
+            for (int icol = -23; icol <= 23; ++icol) {
+                long cellid = HPSEcalConditions.makePhysicalID(icol, irow);
+                Double gain = HPSEcalConditions.physicalToGain(cellid);
+                if (gain != null) {
+                    this.setGain(icol, irow, gain);
+                } else {
+                    this.setGain(icol, irow, 0);
+                }
+            }
+        }
+    }
+
+    public void setAllGain(String fileName) {
+
+        FileReader fReader = null;
+        BufferedReader bReader = null;
+        try {
+            fReader = new FileReader(fileName);
+        } catch (FileNotFoundException ex) {
+            Logger.getLogger(GainCalib.class.getName()).log(Level.SEVERE, null, ex);
+        }
+        bReader = new BufferedReader(fReader);
+        String line;
+        try {
+            while ((line = bReader.readLine()) != null) {
+                if (line.contains("#")) {
+                    continue;
+                }
+                String[] vec = line.split("\\s+");
+                if (vec.length != 4) {
+                    System.out.println("Wrong format for line: " + line);
+                    throw new RuntimeException("");
+                }
+                int E = Integer.valueOf(vec[0]);
+                int x = Integer.valueOf(vec[1]);
+                int y = Integer.valueOf(vec[2]);
+                double g = Double.valueOf(vec[3]);
+                if (E == 0) {
+                    this.setGain(x, y, g);
+                }
+            }
+        } catch (IOException ex) {
+            Logger.getLogger(GainCalib.class.getName()).log(Level.SEVERE, null, ex);
+        }
+    }
+
+    public void setGain(int icol, int irow, double corr) {
+        long cellid = HPSEcalConditions.makePhysicalID(icol, irow);
+
+        //if(!this._gains.containsKey(cellid)) {
+        //    System.out.println("ERROR updating gain from icol " + icol + " irow " + irow + " this cellid " + cellid + " doesn't have a previous gain?");
+        //    System.exit(1);
+        //}
+//        double gain = corr;//this._gains.get(cellid);
+        this._gains.put(cellid, corr);
+    }
+
+    public double getGain(int icol, int irow) {
+        long cellid = HPSEcalConditions.makePhysicalID(icol, irow);
+        if (!this._gains.containsKey(cellid)) {
+            System.out.println("ERROR getting gain from icol " + icol + " irow " + irow + " this cellid " + cellid + " doesn't have a previous gain?");
+            System.exit(1);
+        }
+        return this._gains.get(cellid);
+
+    }
+
+    public MatchedTrack getTrack(int evt, long id) {
+        MatchedTrack mt = null;
+
+        if (this._tracks.containsKey(evt)) {
+            for (MatchedTrack trk : this._tracks.get(evt)) {
+                if (trk._cellid == id) {
+                    mt = trk;
+                }
+            }
+        }
+        return mt;
+
+    }
+
+    public double getGain(BaseRawCalorimeterHit hit) {
+        long id = hit.getCellID();
+        if (!this._gains.containsKey(id)) {
+            System.out.println("ERROR hit with id " + id + " doesn't exist in gain map!!!");
+        }
+        return this._gains.get(id);
+    }
+
+    public List<HPSEcalCluster> getCalibratedClusters(int eventNumber) {
+
+        if (!_hits.containsKey(eventNumber)) {
+            System.out.println("ERROR no raw hits for event " + eventNumber);
+            System.exit(1);
+        }
+
+
+        if (_hits.get(eventNumber).isEmpty()) {
+            System.out.println("empy hits for " + eventNumber);
+            System.exit(1);
+        }
+
+        if (_debug) {
+            System.out.println("Converting " + _hits.get(eventNumber).size() + " raw ecal hits");
+        }
+
+        ArrayList<CalorimeterHit> newHits = new ArrayList<CalorimeterHit>();
+
+        for (BaseRawCalorimeterHit hit : _hits.get(eventNumber)) {
+
+            if (_debug) {
+                System.out.println("Converting hit id " + hit.getCellID());
+            }
+
+            double gain = getGain(hit);
+            CalorimeterHit newHit = HPSEcalRawConverter.HitDtoA(hit, _integralWindow, gain);
+            if (_applyBadCrystalMap && HPSEcalRawConverterDriver.isBadCrystal(newHit)) {
+                continue;
+            }
+            //if(applyBadCrystalMap && HPSEcalRawConverterDriver.isBadCrystal(newHit)) continue;
+            //if (dropBadFADC && HPSEcalRawConverterDriver.isBadFADC(newHit)) continue;
+            if (newHit.getRawEnergy() > _threshold) {
+                newHits.add(newHit);
+            }
+
+            if (_debug) {
+                System.out.println("Converted hit id " + hit.getCellID() + " with gain " + gain);
+            }
+        }
+
+        if (_debug) {
+            System.out.println(newHits.size() + " calibrated calorimeter hits for event " + eventNumber);
+        }
+
+        //To be able to use decoders I need to associate with readout. Use event put to do that?! -> FIX THIS
+        BaseLCSimEvent event = new BaseLCSimEvent(999999, eventNumber, _detector.getDetectorName());
+        event.put(_ecalTmpCollectionName, newHits, CalorimeterHit.class, 0, _ecalReadoutName);
+
+
+        //Now we have a set of calibrated ecal hits
+        // Clusterize them 
+
+        // Make a hit map for quick lookup by ID.
+        Map<Long, CalorimeterHit> hitMap = new HashMap<Long, CalorimeterHit>();
+        for (CalorimeterHit hit : newHits) {
+            hitMap.put(hit.getCellID(), hit);
+        }
+
+        List<HPSEcalCluster> clusters = _clusterer.createClusters(hitMap);
+
+        if (_debug) {
+            System.out.println(clusters.size() + " clusters found from event " + eventNumber);
+        }
+
+        return clusters;
+    }
+}

hps-java/src/main/resources/org/lcsim/hps/steering

diff -u -r1.7 -r1.8
--- MultScatAna.lcsim	27 Aug 2012 18:40:10 -0000	1.7
+++ MultScatAna.lcsim	20 Nov 2012 23:25:09 -0000	1.8
@@ -48,14 +48,14 @@

 		<outputPlotFileName>/Users/phansson/work/HPS/software/reco/run/trigratefile.aida</outputPlotFileName>
 	</driver>
 

-        <driver name="GainCalibrationDriver"

+<!--        <driver name="GainCalibrationDriver"

 		type="org.lcsim.hps.recon.ecal.GainCalibrationDriver">
                 <debug>false</debug>
                 <hideFrame>true</hideFrame>
 		<outputPlotFileName>gaincalib.aida</outputPlotFileName>
                 <ecalGainFileName></ecalGainFileName>
                 <ecalGainCalibCorrFileName>gaincalibout.txt</ecalGainCalibCorrFileName>

-	</driver>

+	</driver>-->

         <driver name="EcalDaqPlots" type="org.lcsim.hps.monitoring.ecal.EcalDaqPlots">
         </driver>
         <driver name="CleanupDriver"