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

diff -N HPSTrackerHitDriver.java
--- HPSTrackerHitDriver.java	28 Jul 2011 23:39:57 -0000	1.3
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,277 +0,0 @@

-/*
- * TrackerHitDriver Class
- *
- */
-package org.lcsim.hps.recon.tracking;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.lcsim.detector.IDetectorElement;
-import org.lcsim.detector.tracker.silicon.SiSensor;
-import org.lcsim.detector.tracker.silicon.SiTrackerModule;
-import org.lcsim.event.EventHeader;
-import org.lcsim.event.RawTrackerHit;
-import org.lcsim.geometry.Detector;
-import org.lcsim.recon.tracking.digitization.sisim.BasicReadoutChip;
-import org.lcsim.recon.tracking.digitization.sisim.CDFSiSensorSim;
-import org.lcsim.recon.tracking.digitization.sisim.NearestNeighborRMS;
-import org.lcsim.recon.tracking.digitization.sisim.PixelHitMaker;
-import org.lcsim.recon.tracking.digitization.sisim.RawTrackerHitMaker;
-import org.lcsim.recon.tracking.digitization.sisim.SiDigitizer;
-import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHit;
-import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
-import org.lcsim.recon.tracking.digitization.sisim.StripHitMaker;
-import org.lcsim.recon.tracking.digitization.sisim.config.SimTrackerHitReadoutDriver;
-import org.lcsim.util.Driver;
-import org.lcsim.util.aida.AIDA;
-
-/**
- *
- * @author tknelson
- */
-public class HPSTrackerHitDriver extends Driver {
-
-    List<String> _readouts = new ArrayList<String>();
-    List<String> _process_paths = new ArrayList<String>();
-    List<IDetectorElement> _process_de = new ArrayList<IDetectorElement>();
-    Set<SiSensor> _process_sensors = new HashSet<SiSensor>();
-    Set<SiTrackerModule> _process_modules = new HashSet<SiTrackerModule>();
-    SiDigitizer _strip_digitizer;
-    SiDigitizer _pixel_digitizer;
-    StripHitMaker _strip_clusterer;
-    PixelHitMaker _pixel_clusterer;
-    String _digitizer_name;
-    int _nev = 0;
-    int _ngc = 0;
-    boolean _timing = true;
-    protected AIDA aida = AIDA.defaultInstance();
-
-    /**
-     * Creates a new instance of TrackerHitDriver
-     */
-    public HPSTrackerHitDriver() {
-
-        //  Instantiate the sensor simulation classes and set the thresholds
-//        SiSensorSim strip_simulation = new CDFSiSensorSim();
-        CDFSiSensorSim strip_simulation = new CDFSiSensorSim();
-
-        //  Instantiate the readout chips and set the noise parameters
-        BasicReadoutChip strip_readout = new BasicReadoutChip();
-//  ABCD -- Pristine
-/*
-        strip_readout.setNoiseIntercept(600.);
-        strip_readout.setNoiseSlope(65.);
-        strip_readout.setNoiseThreshold(4.);
-        strip_readout.setNeighborThreshold(4.);
-        strip_readout.setNbits(1);
-        strip_readout.setDynamicRange(10);
-         */
-        // APV25 -- Pristine
-
-        strip_readout.setNoiseIntercept(270.);
-        strip_readout.setNoiseSlope(36.);
-        strip_readout.setNoiseThreshold(4.);
-        strip_readout.setNeighborThreshold(4.);
-        strip_readout.setNbits(10);
-        strip_readout.setDynamicRange(40);
-
-/*
-        strip_readout.setNoiseIntercept(0.1);
-        strip_readout.setNoiseSlope(0.1);
-        strip_readout.setNoiseThreshold(4);
-        strip_readout.setNeighborThreshold(4);
-        strip_readout.setNbits(10);
-        strip_readout.setDynamicRange(40);
-*/
-
-        //set trapping to 0.2 to simulate radiation damage.
-//        strip_simulation.setTrapping(0.2);
-//                strip_simulation.setTrapping(0.12);
-
-        //  Instantiate the digitizer that produces the raw hits
-        _strip_digitizer = new RawTrackerHitMaker(strip_simulation, strip_readout);
-
-        _digitizer_name = _strip_digitizer.getName();
-
-        //  Instantiate a nearest neighbor clustering algorithm for the strips
-//        NearestNeighbor strip_clustering = new NearestNeighbor();
-//        strip_clustering.setSeedThreshold(4.);
-//        strip_clustering.setNeighborThreshold(4.);
-
-        NearestNeighborRMS strip_clustering = new NearestNeighborRMS();
-
-        strip_clustering.setSeedThreshold(4.);
-        strip_clustering.setNeighborThreshold(3.);
-        strip_clustering.setClusterThreshold(4.);
-
-
-        //  Instantiate the clusterers and set hit-making parameters
-        _strip_clusterer = new StripHitMaker(strip_simulation, strip_readout, strip_clustering);
-        _strip_clusterer.setMaxClusterSize(10);
-        _strip_clusterer.setCentralStripAveragingThreshold(4);
-        /*
-        _strip_clusterer.SetOneClusterErr(1 / Math.sqrt(12.));
-        _strip_clusterer.SetTwoClusterErr(1 / 5.0);
-        _strip_clusterer.SetThreeClusterErr(1 / 3.0);
-        _strip_clusterer.SetFourClusterErr(1 / 2.0);
-        _strip_clusterer.SetFiveClusterErr(1 / 1.0);
-         */
-        double multiplier = 1.0;
-        _strip_clusterer.SetOneClusterErr(multiplier / Math.sqrt(12.));
-        _strip_clusterer.SetTwoClusterErr(multiplier / 5.0);
-        _strip_clusterer.SetThreeClusterErr(multiplier / 3.0);
-        _strip_clusterer.SetFourClusterErr(multiplier / 2.0);
-        _strip_clusterer.SetFiveClusterErr(multiplier / 1.0);
-
-
-        //  Specify the readouts to process
-        _readouts.add("TrackerHits");
-        //  Specify the detectors to process
-        _process_paths.add("Tracker");
-    }
-
-    /**
-     * Initialize whenever we have a new detector
-     * 
-     * @param detector
-     */
-    public void detectorChanged(Detector detector) {
-        System.out.println(detector.getName());
-        super.detectorChanged(detector);
-
-        // Process detectors specified by path, otherwise process entire detector
-        IDetectorElement detector_de = detector.getDetectorElement();
-        System.out.println("detector_de Name =" + detector_de.getName());
-        for (String de_path : _process_paths) {
-            _process_de.add(detector_de.findDetectorElement(de_path));
-        }
-
-        if (_process_de.size() == 0) {
-            _process_de.add(detector_de);
-        }
-
-        for (IDetectorElement detector_element : _process_de) {
-            _process_sensors.addAll(detector_element.findDescendants(SiSensor.class));
-            _process_modules.addAll(detector_element.findDescendants(SiTrackerModule.class));
-        }
-
-    }
-
-    /**
-     * Setup readouts
-     */
-    public void startOfData() {
-        // If readouts not already set, set them up
-        if (_readouts.size() != 0) {
-            System.out.println("Adding SimTrackerHitIdentifierReadoutDriver with readouts: " + _readouts);
-            super.add(new SimTrackerHitReadoutDriver(_readouts));
-        }
-
-        super.startOfData();
-        _readouts.clear();
-        _nev = 0;
-        _ngc = 0;
-    }
-
-    /**
-     * Main digitization driver.  Creates raw hits, forms clusters, and makes
-     * tracker hits using the sisim package.
-     *
-     * @param event
-     */
-    public void process(EventHeader event) {
-        super.process(event);
-
-        //  Print out the event number
-
-        _nev++;
-        _ngc++;
-        if (_ngc == 100) {
-            System.out.println("TrackerHitDriver processing event " + _nev);
-            System.gc();
-            _ngc = 0;
-        }
-
-        long last_time = System.currentTimeMillis();
-
-
-        // Lists of hits
-        List<RawTrackerHit> raw_hits = new ArrayList<RawTrackerHit>();
-        List<SiTrackerHit> hits_strip1D = new ArrayList<SiTrackerHit>();
-        List<SiTrackerHit> hits_pixel = new ArrayList<SiTrackerHit>();
-
-        /*
-        for (SiSensor sensor : _process_sensors) {
-
-        if (sensor.hasStrips()) {
-        raw_hits.addAll(_strip_digitizer.makeHits(sensor));
-        hits_strip1D.addAll(_strip_clusterer.makeHits(sensor));
-
-        }
-
-
-        if (sensor.hasPixels()) {
-        raw_hits.addAll(_pixel_digitizer.makeHits(sensor));
-        hits_pixel.addAll(_pixel_clusterer.makeHits(sensor));
-        }
-
-        }
-
-         */
-        for (SiSensor sensor : _process_sensors) {
-            raw_hits.addAll(_strip_digitizer.makeHits(sensor));
-
-        }
-        long raw_time = System.currentTimeMillis();
-        double rtime = ((double) (raw_time - last_time)) / 1000.;
-        if (_timing) {
-            aida.cloud1D("Digitization Time").fill(rtime);
-        }
-
-
-        for (SiSensor sensor : _process_sensors) {
-            hits_strip1D.addAll(_strip_clusterer.makeHits(sensor));
-        }
-        long start_time = System.currentTimeMillis();
-        double dtime = ((double) (start_time - raw_time)) / 1000.;
-        if (_timing) {
-            aida.cloud1D("Clustering Time").fill(dtime);
-        }
-        //        int flag = (1 << LCIOConstants.RTHBIT_HITS | 1 << LCIOConstants.TRAWBIT_ID1); //correct flag for persistence
-        int flag = 0;
-        event.put(getRawHitsName(), raw_hits, RawTrackerHit.class, flag, toString());
-        event.put(getStripHits1DName(), hits_strip1D, SiTrackerHitStrip1D.class, 0, toString());
-//        event.put(getPixelHitsName(), hits_pixel, SiTrackerHitPixel.class, 0, toString());
-
-    }
-
-    /**
-     * Return the name of the raw hits collection
-     *
-     * @return name of raw hits collection
-     */
-    public String getRawHitsName() {
-        return _digitizer_name + "_RawTrackerHits";
-    }
-
-    /**
-     * Return the name of the strip hits collection
-     *
-     * @return name of strip hits collection
-     */
-    public String getStripHits1DName() {
-        return _strip_clusterer.getName() + "_SiTrackerHitStrip1D";
-    }
-
-    /**
-     * Return the name of the pixel hits collection
-     *
-     * @return name of pixel hits collection
-     */
-    public String getPixelHitsName() {
-        return _pixel_clusterer.getName() + "_SiTrackerHitPixel";
-    }
-}

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

diff -N TrackerHitDriver.java
--- TrackerHitDriver.java	27 Apr 2012 23:08:02 -0000	1.4
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,335 +0,0 @@

-package org.lcsim.hps.recon.tracking;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.lcsim.detector.IDetectorElement;
-import org.lcsim.detector.identifier.IExpandedIdentifier;
-import org.lcsim.detector.identifier.IIdentifier;
-import org.lcsim.detector.identifier.IIdentifierDictionary;
-import org.lcsim.detector.tracker.silicon.SiSensor;
-import org.lcsim.detector.tracker.silicon.SiTrackerModule;
-import org.lcsim.event.EventHeader;
-import org.lcsim.event.RawTrackerHit;
-import org.lcsim.geometry.Detector;
-import org.lcsim.recon.tracking.digitization.sisim.BasicReadoutChip;
-import org.lcsim.recon.tracking.digitization.sisim.CDFSiSensorSim;
-import org.lcsim.recon.tracking.digitization.sisim.NearestNeighborRMS;
-import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHit;
-import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
-import org.lcsim.recon.tracking.digitization.sisim.StripHitMaker;
-import org.lcsim.recon.tracking.digitization.sisim.config.SimTrackerHitReadoutDriver;
-import org.lcsim.util.Driver;
-
-/**
- * This Driver runs the tracker digitization to create raw hits and strip hits
- * from simulated data. The output can be used by a track reconstruction
- * algorithm like Seed Tracker.
- * 
- * @author jeremym
- * @version $Id: TrackerHitDriver.java,v 1.4 2012/04/27 23:08:02 meeg Exp $
- */
-public class TrackerHitDriver extends Driver {
-    
-    // Debug switch for development.
-    private boolean debug = false;
-
-    // Collection name.
-    private String readoutCollectionName = "TrackerHits";
-
-    // Subdetector name.
-    private String subdetectorName = "Tracker";
-
-    // Name of RawTrackerHit collection to be read from event.
-    private String rawTrackerHitCollectionName = "RawTrackerHitMaker_RawTrackerHits";
-
-    // Name of StripHit1D output collection.
-    private String stripHitOutputCollectionName = "StripClusterer_SiTrackerHitStrip1D";
-
-    // Readout parameters.
-    private double readoutNoiseIntercept = 270.0;
-    private double readoutNoiseSlope = 36.0;
-    private double readoutNoiseThreshold = 4.0;
-    private double readoutNeighborThreshold = 4.0;
-    private int readoutNBits = 10;
-    private int readoutDynamicRange = 40;
-
-    // Clustering parameters.
-    private double clusterSeedThreshold = 4.0;
-    private double clusterNeighborThreshold = 3.0;
-    private double clusterThreshold = 4.0;
-    private int clusterMaxSize = 10;
-    private int clusterCentralStripAveragingThreshold = 4;
-
-    // Clustering errors by number of TrackerHits.
-    private static final double clusterErrorMultiplier = 1.0;
-    private double oneClusterErr = clusterErrorMultiplier / Math.sqrt(12.);
-    private double twoClusterErr = clusterErrorMultiplier / 5.0;
-    private double threeClusterErr = clusterErrorMultiplier / 3.0;
-    private double fourClusterErr = clusterErrorMultiplier / 2.0;
-    private double fiveClusterErr = clusterErrorMultiplier / 1.0;
-
-    // Various data lists required by digitization.
-    private List<String> readouts = new ArrayList<String>();
-    private List<String> processPaths = new ArrayList<String>();
-    private List<IDetectorElement> processDEs = new ArrayList<IDetectorElement>();
-    private Set<SiSensor> processSensors = new HashSet<SiSensor>();
-    private Set<SiTrackerModule> processModules = new HashSet<SiTrackerModule>();
-
-    // Map of SiSensor objects from geometry.
-    private Map<Long, SiSensor> sensorMap = new HashMap<Long, SiSensor>();
-
-    // Digi class objects.
-    private StripHitMaker stripClusterer;
-    
-    public void setDebug(boolean debug) {
-        this.debug = debug;
-    }
-    
-    public void setRawTrackerHitCollectionName(String rawTrackerHitCollectionName) {
-        this.rawTrackerHitCollectionName = rawTrackerHitCollectionName;
-    }
-
-    public void setReadoutCollectionName(String readoutCollectionName) {
-        this.readoutCollectionName = readoutCollectionName;
-    }
-
-    public void setSubdetectorName(String subdetectorName) {
-        this.subdetectorName = subdetectorName;
-    }
-
-    public void setStripHitOutputCollectionName(
-            String stripHitOutputCollectionName) {
-        this.stripHitOutputCollectionName = stripHitOutputCollectionName;
-    }
-
-    public void setReadoutNoiseIntercept(double readoutNoiseIntercept) {
-        this.readoutNoiseIntercept = readoutNoiseIntercept;
-    }
-
-    public void setReadoutNoiseSlope(double readoutNoiseSlope) {
-        this.readoutNoiseSlope = readoutNoiseSlope;
-    }
-
-    public void setReadoutNeighborThreshold(double readoutNeighborThreshold) {
-        this.readoutNeighborThreshold = readoutNeighborThreshold;
-    }
-
-    public void setReadoutNBits(int readoutNBits) {
-        this.readoutNBits = readoutNBits;
-    }
-
-    public void setReadoutDynamicRange(int readoutDynamicRange) {
-        this.readoutDynamicRange = readoutDynamicRange;
-    }
-
-    public void setClusterSeedThreshold(double clusterSeedThreshold) {
-        this.clusterSeedThreshold = clusterSeedThreshold;
-    }
-
-    public void setClusterNeighborThreshold(double clusterNeighborThreshold) {
-        this.clusterNeighborThreshold = clusterNeighborThreshold;
-    }
-
-    public void setClusterThreshold(double clusterThreshold) {
-        this.clusterThreshold = clusterThreshold;
-    }
-
-    public void setClusterMaxSize(int clusterMaxSize) {
-        this.clusterMaxSize = clusterMaxSize;
-    }
-
-    public void setClusterCentralStripAveragingThreshold(
-            int clusterCentralStripAveragingThreshold) {
-        this.clusterCentralStripAveragingThreshold = clusterCentralStripAveragingThreshold;
-    }
-
-    public void setOneClusterErr(double oneClusterErr) {
-        this.oneClusterErr = oneClusterErr;
-    }
-
-    public void setTwoClusterErr(double twoClusterErr) {
-        this.twoClusterErr = twoClusterErr;
-    }
-
-    public void setThreeClusterErr(double threeClusterErr) {
-        this.threeClusterErr = threeClusterErr;
-    }
-
-    public void setFourClusterErr(double fourClusterErr) {
-        this.fourClusterErr = fourClusterErr;
-    }
-
-    public void setFiveClusterErr(double fiveClusterErr) {
-        this.fiveClusterErr = fiveClusterErr;
-    }
-
-    /**
-     * Creates a new instance of TrackerHitDriver.
-     */
-    public TrackerHitDriver() {
-    }
-
-    /**
-     * Initializes this Driver's objects with the job parameters.
-     */
-    private void initialize() {
-
-        // Create the sensor simulation.
-        CDFSiSensorSim stripSim = new CDFSiSensorSim();
-
-        // Create the readout chips and set the noise parameters.
-        BasicReadoutChip stripReadout = new BasicReadoutChip();
-        stripReadout.setNoiseIntercept(readoutNoiseIntercept);
-        stripReadout.setNoiseSlope(readoutNoiseSlope);
-        stripReadout.setNoiseThreshold(readoutNoiseThreshold);
-        stripReadout.setNeighborThreshold(readoutNeighborThreshold);
-        stripReadout.setNbits(readoutNBits);
-        stripReadout.setDynamicRange(readoutDynamicRange);
-
-        // Create Strip clustering algorithm.
-        NearestNeighborRMS stripClusteringAlgo = new NearestNeighborRMS();
-        stripClusteringAlgo.setSeedThreshold(clusterSeedThreshold);
-        stripClusteringAlgo.setNeighborThreshold(clusterNeighborThreshold);
-        stripClusteringAlgo.setClusterThreshold(clusterThreshold);
-
-        // Create the clusterers and set hit-making parameters.
-        stripClusterer = new StripHitMaker(stripSim, stripReadout, stripClusteringAlgo);
-        stripClusterer.setMaxClusterSize(clusterMaxSize);
-        stripClusterer.setCentralStripAveragingThreshold(clusterCentralStripAveragingThreshold);
-
-        // Set the cluster errors.
-        stripClusterer.SetOneClusterErr(oneClusterErr);
-        stripClusterer.SetTwoClusterErr(twoClusterErr);
-        stripClusterer.SetThreeClusterErr(threeClusterErr);
-        stripClusterer.SetFourClusterErr(fourClusterErr);
-        stripClusterer.SetFiveClusterErr(fiveClusterErr);
-
-        // Set the readout to process.
-        readouts.add(readoutCollectionName);
-
-        // Set the detector to process.
-        processPaths.add(subdetectorName);
-    }
-
-    /**
-     * This is executed before detectorChanged and initialization of
-     * digitization objects is done here.
-     */
-    /*
-    public void startOfData() {
-
-        System.out.println("startOfData");
-        
-    }
-    */
-
-    /**
-     * Do initialization once we get a Detector.
-     */
-    public void detectorChanged(Detector detector) {
-      
-        System.out.println(getClass().getSimpleName() + ".detectorChanged");
-        
-        // Call sub-Driver's detectorChanged methods.
-        //super.detectorChanged(detector);
-
-        // Process detectors specified by path, otherwise process entire detector.
-        IDetectorElement deDetector = detector.getDetectorElement();
-
-        for (String path : processPaths) {
-            processDEs.add(deDetector.findDetectorElement(path));
-        }
-
-        if (processDEs.size() == 0) {
-            processDEs.add(deDetector);
-        }
-
-	for (IDetectorElement detectorElement : processDEs) {
-            processSensors.addAll(detectorElement.findDescendants(SiSensor.class));
-            processModules.addAll(detectorElement.findDescendants(SiTrackerModule.class)); // FIXME Is this redundant?
-        }
-        
-        // Make sensor map.
-        for (SiSensor sensor : processSensors) {            
-            sensorMap.put(sensor.getIdentifier().getValue(), sensor);
-        }
-        
-        // Remaining lines moved from startOfData() ...
-        
-        // At start of job, setup digitization objects needed by this Driver.
-        initialize();
-
-        // If readouts not already set, set them up.
-        if (readouts.size() != 0) {
-            //System.out.println("Adding SimTrackerHitIdentifierReadoutDriver with readouts: " + readouts);
-            super.add(new SimTrackerHitReadoutDriver(readouts));
-        }
-        super.startOfData();
-        readouts.clear(); // FIXME Is this needed?
-    }
-    
-    private static IIdentifier makeSensorId(Detector detector, RawTrackerHit hit) {
-        
-        IIdentifierDictionary dict = detector.getSubdetector("Tracker").getDetectorElement().getIdentifierHelper().getIdentifierDictionary();
-        int fieldIdx = dict.getFieldIndex("side");
-        int sideIdx = dict.getFieldIndex("strip");
-
-        // The "side" and "strip" fields needs to be taken out of the ID or geometry lookup will fail.
-        IExpandedIdentifier expId = dict.unpack(hit.getIdentifier());            
-        expId.setValue(fieldIdx, 0);
-        expId.setValue(sideIdx, 0);
-        IIdentifier strippedId = dict.pack(expId);
-        
-        return strippedId;
-    }
-
-    /**
-     * Perform the digitization.
-     */
-    public void process(EventHeader event) {
-        
-        // Call sub-Driver processing.
-        super.process(event);
-
-        // Read RawTrackerHits from LCSimEvent.
-        List<RawTrackerHit> rawHits = event.get(RawTrackerHit.class, rawTrackerHitCollectionName);
-        
-        if (debug)
-            System.out.println("RawTrackerHit collection " + rawTrackerHitCollectionName + " has " + rawHits.size() + " hits.");
-               
-        // Add hits to sensors.
-        for (RawTrackerHit hit : rawHits) {            
-            IIdentifier strippedId = makeSensorId(event.getDetector(), hit);            
-            if (!sensorMap.containsKey(strippedId.getValue())) {
-                throw new RuntimeException("Missing SiSensor with id = 0x" + Long.toHexString(strippedId.getValue()));
-            }
-            SiSensor sensor = sensorMap.get(strippedId.getValue());                                
-            sensor.getReadout().addHit(hit);                                    
-        }
-
-        // Make strip hits.
-        List<SiTrackerHit> stripHits1D = new ArrayList<SiTrackerHit>();
-        for (SiSensor sensor : processSensors) {
-            if (debug)
-                System.out.println("Making TrackerHits for sensor " + sensor.getName() + " with " + sensor.getReadout().getHits(RawTrackerHit.class).size() + " hits.");
-            List<SiTrackerHit> trackerHits = stripClusterer.makeHits(sensor);
-            if (debug)
-                System.out.println("Made " + trackerHits.size() + " hits on sensor " + sensor.getName() + ".");
-            stripHits1D.addAll(trackerHits);
-        }
-
-        // Debug prints.
-        if (debug) {
-            System.out.println("TrackerHit collection " + this.stripHitOutputCollectionName + " has " + stripHits1D.size() + " hits.");
-        }
-
-        // Put output TrackerHits into event.
-        // FIXME Does this collection need a non-zero flag?
-        event.put(this.stripHitOutputCollectionName, stripHits1D, SiTrackerHitStrip1D.class, 0, toString());
-    }
-}

\ No newline at end of file

hps-java/sandbox

diff -N HeavyPhotonLLDriver_3.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ HeavyPhotonLLDriver_3.java	25 Apr 2013 21:48:17 -0000	1.1
@@ -0,0 +1,230 @@

+package org.lcsim.hps.users.mgraham.alignment;
+
+import org.lcsim.hps.users.mgraham.jlabrotation.*;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import org.lcsim.hps.event.HPSTransformations;
+import org.lcsim.hps.recon.tracking.HelicalTrackHitDriver;
+import org.lcsim.hps.recon.tracking.HPSTrackerHitDriver;
+
+//import org.lcsim.hps.recon.tracking.SiTrackerSpectrometerSensorSetup;
+import org.lcsim.recon.tracking.seedtracker.SeedStrategy;
+import org.lcsim.recon.tracking.seedtracker.SeedTracker;
+import org.lcsim.recon.tracking.seedtracker.StrategyXMLUtils;
+import org.lcsim.recon.tracking.seedtracker.diagnostic.SeedTrackerDiagnostics;
+import org.lcsim.util.Driver;
+import org.lcsim.util.loop.LCIODriver;
+
+/**
+ * Driver for track reconstruction and analysis of HPS detector.
+ *
+ * @author M. Graham
+ */
+public final class HeavyPhotonLLDriver extends Driver {
+
+    //********************
+    //   set pname to the detector you want to run...HPS1pt8 is the default test detector (uses strategy file 1.3)
+    //  see "setPName" method for list
+//    public String pName = "HPS1pt9";
+    public String pName = "HPS1pt8";
+//    JasAnalysisDriver jad;
+    DetailedAnalysisDriver dad;
+//    FastTrackAnalysisDriver ftad;
+//    KalmanFilterDriver kfd;
+    List<int[]> pairs = new ArrayList();
+    List<Integer> passLayers = new ArrayList();
+    ////   Change the prefix for your site
+//    String strategyPrefix = "/nfs/sulky21/g.ec.u12/users/mgraham/AtlasUpgrade/hps-java/src/main/resources/";
+    String strategyPrefix = "/Users/mgraham/NetBeansProjects/hps-java/src/main/resources/";
+    ////////////////////////////////////////
+    //  everything below will
+    //  get overwritten by setPName
+    int nlayers = 10;
+    int fitlayers = 10;
+    // bfield needs to be set because tracking doesn't 
+    // seme to deal with fields in the negative 
+    //  z-direction well (need to fix this)
+    double bfield = 0.5;
+    String detType = "Full";
+    String axialStrategy = "HPS-Test-1pt8.xml";
+    String finalStrategy = "HPS-Test-1pt8.xml";
+    String llStrategy = "HPS-Test-1pt8.xml";
+    public String outputFile = "foobar.slcio";
+    public String plotsFile = "myplots.aida";
+    public String outputTextName = "myevents.txt";
+    ///////////////
+
+    public HeavyPhotonLLDriver() {
+//        add(new MakeSensorsDriver());
+        add(new SiTrackerSpectrometerSensorSetup("Tracker"));
+        setPName(pName);
+
+        HPSTrackerHitDriver thd = new HPSTrackerHitDriver();
+        add(thd);
+
+        HelicalTrackHitDriver hthdriver = new HelicalTrackHitDriver();
+        hthdriver.addCollection(((HPSTrackerHitDriver) thd).getStripHits1DName());
+        hthdriver.setOutputCollectionName("HelicalTrackHits");
+        hthdriver.HitRelationName("HelicalTrackHitRelations");
+        hthdriver.MCRelationName("HelicalTrackMCRelations");
+        for (int[] pair : pairs)
+            hthdriver.setStereoPair("Tracker", pair[0], pair[1]);
+
+        if (detType.contains("Test")) {
+            System.out.println("Setting separation for a Test detector");
+            hthdriver.setMaxSeperation(10.01);
+            hthdriver.setTolerance(0.01);
+        } else {
+
+            hthdriver.setMaxSeperation(50.);
+            hthdriver.setTolerance(0.4);
+        }
+        hthdriver.setTransformToTracking(true);
+        add(hthdriver);
+
+        List<SeedStrategy> sFinallist = StrategyXMLUtils.getStrategyListFromFile(new File(strategyPrefix + finalStrategy));
+        SeedTracker stFinal = null;
+        stFinal = new SeedTracker(sFinallist);
+
+        HPSTransformations hpstrans = new HPSTransformations();
+        stFinal.setMaterialManagerTransform(hpstrans.getTransform());
+        stFinal.setInputCollectionName("RotatedHelicalTrackHits");
+
+//        stFinal.setInputCollectionName("HelicalTrackHits");
+
+        stFinal.setTrkCollectionName("MatchedTracks");
+        stFinal.setDiagnostics(new SeedTrackerDiagnostics());
+        stFinal.setBField(bfield);
+        stFinal.setSectorParams(false);
+        stFinal.setTimingPlots(true);
+
+
+
+        add(stFinal);
+
+//        MultiTrackReco trd = new MultiTrackReco(strategyPrefix, detType, bfield, axialStrategy, finalStrategy, llStrategy, pairs, passLayers);
+//        add(trd);
+
+//        dad = new DetailedAnalysisDriver(10);
+//        add(dad);
+          add(new RunAlignment(10,10,finalStrategy));
+//          kfd = new KalmanFilterDriver();
+//        add(kfd);
+//    uncomment this to look at occupancies
+        //       add(new OccupancyDriver());
+    }
+
+    public void setOutputFile(String outputFile) {
+        System.out.println("Will output events to " + outputFile);
+        add(new LCIODriver(outputFile));
+    }
+
+    public void setPlotsFile(String plotsFile) {
+        System.out.println("Will output plots to " + plotsFile);
+//        jad.setOutputPlots(plotsFile);
+    }
+
+    public void setOutputTextName(String outputTextName) {
+        System.out.println("Will output selected events to " + outputTextName);
+//        ftad.setOutputText(outputTextName);
+    }
+
+    public void setPName(String pName) {
+        System.out.println("Setting parameter set to " + pName);
+        pairs.clear();
+        if (pName.contentEquals("HPS3pt2")) {
+            detType = "Full";
+            bfield = 1.0;
+            nlayers = 12;
+            fitlayers = 10;
+            axialStrategy = "DarkPhoton-Axial-HPS3pt2.xml";
+            finalStrategy = "DarkPhoton-HPS3pt2.xml";
+            llStrategy = "DarkPhoton-HPS3pt2-LongLived.xml";
+
+            int[] p1 = {1, 2};
+            int[] p2 = {3, 4};
+            int[] p3 = {5, 6};
+            int[] p4 = {7, 8};
+            int[] p5 = {9, 10};
+            int[] p6 = {11, 12};
+            pairs.add(p1);
+            pairs.add(p2);
+            pairs.add(p3);
+            pairs.add(p4);
+            pairs.add(p5);
+            pairs.add(p6);
+            passLayers.add(11);
+        }
+        if (pName.contentEquals("HPS3pt4")) {
+            detType = "Full";
+            bfield = 0.5;
+            nlayers = 12;
+            fitlayers = 10;
+            axialStrategy = "DarkPhoton-Axial-HPS3pt2.xml";
+            finalStrategy = "DarkPhoton-HPS3pt2.xml";
+            llStrategy = "none";
+
+            int[] p1 = {1, 2};
+            int[] p2 = {3, 4};
+            int[] p3 = {5, 6};
+            int[] p4 = {7, 8};
+            int[] p5 = {9, 10};
+            int[] p6 = {11, 12};
+            pairs.add(p1);
+            pairs.add(p2);
+            pairs.add(p3);
+            pairs.add(p4);
+            pairs.add(p5);
+            pairs.add(p6);
+            passLayers.add(11);
+        }
+
+        if (pName.contentEquals("HPS1pt8")) {
+            detType = "Test";
+            nlayers = 10;
+            bfield = 0.5;
+            fitlayers = 10;
+            axialStrategy = "none";   //  don't fit tracks axially first
+            finalStrategy = "HPS-Test-1pt3.xml";
+            llStrategy = "none";//  don't fit tracks ignoring first plane
+
+            int[] p1 = {1, 2};
+            int[] p2 = {3, 4};
+            int[] p3 = {5, 6};
+            int[] p4 = {7, 8};
+            int[] p5 = {9, 10};
+
+            pairs.add(p1);
+            pairs.add(p2);
+            pairs.add(p3);
+            pairs.add(p4);
+            pairs.add(p5);
+//            passLayers.add(11);
+        }
+
+        if (pName.contentEquals("HPS1pt9")) {
+            detType = "Test";
+            nlayers = 10;
+            bfield = 0.25;
+            fitlayers = 10;
+            axialStrategy = "none";   //  don't fit tracks axially first
+            finalStrategy = "HPS-Test-1pt3.xml";
+            llStrategy = "none";//  don't fit tracks ignoring first plane
+
+            int[] p1 = {1, 2};
+            int[] p2 = {3, 4};
+            int[] p3 = {5, 6};
+            int[] p4 = {7, 8};
+            int[] p5 = {9, 10};
+
+            pairs.add(p1);
+            pairs.add(p2);
+            pairs.add(p3);
+            pairs.add(p4);
+            pairs.add(p5);
+//            passLayers.add(11);
+        }
+
+    }
+}

hps-java/sandbox

diff -N HPSTrackerHitDriver.java
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ HPSTrackerHitDriver.java	25 Apr 2013 21:48:17 -0000	1.1
@@ -0,0 +1,277 @@

+/*
+ * TrackerHitDriver Class
+ *
+ */
+package org.lcsim.hps.recon.tracking;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.lcsim.detector.IDetectorElement;
+import org.lcsim.detector.tracker.silicon.SiSensor;
+import org.lcsim.detector.tracker.silicon.SiTrackerModule;
+import org.lcsim.event.EventHeader;
+import org.lcsim.event.RawTrackerHit;
+import org.lcsim.geometry.Detector;
+import org.lcsim.recon.tracking.digitization.sisim.BasicReadoutChip;
+import org.lcsim.recon.tracking.digitization.sisim.CDFSiSensorSim;
+import org.lcsim.recon.tracking.digitization.sisim.NearestNeighborRMS;
+import org.lcsim.recon.tracking.digitization.sisim.PixelHitMaker;
+import org.lcsim.recon.tracking.digitization.sisim.RawTrackerHitMaker;
+import org.lcsim.recon.tracking.digitization.sisim.SiDigitizer;
+import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHit;
+import org.lcsim.recon.tracking.digitization.sisim.SiTrackerHitStrip1D;
+import org.lcsim.recon.tracking.digitization.sisim.StripHitMaker;
+import org.lcsim.recon.tracking.digitization.sisim.config.SimTrackerHitReadoutDriver;
+import org.lcsim.util.Driver;
+import org.lcsim.util.aida.AIDA;
+
+/**
+ *
+ * @author tknelson
+ */
+public class HPSTrackerHitDriver extends Driver {
+
+    List<String> _readouts = new ArrayList<String>();
+    List<String> _process_paths = new ArrayList<String>();
+    List<IDetectorElement> _process_de = new ArrayList<IDetectorElement>();
+    Set<SiSensor> _process_sensors = new HashSet<SiSensor>();
+    Set<SiTrackerModule> _process_modules = new HashSet<SiTrackerModule>();
+    SiDigitizer _strip_digitizer;
+    SiDigitizer _pixel_digitizer;
+    StripHitMaker _strip_clusterer;
+    PixelHitMaker _pixel_clusterer;
+    String _digitizer_name;
+    int _nev = 0;
+    int _ngc = 0;
+    boolean _timing = true;
+    protected AIDA aida = AIDA.defaultInstance();
+
+    /**
+     * Creates a new instance of TrackerHitDriver
+     */
+    public HPSTrackerHitDriver() {
+
+        //  Instantiate the sensor simulation classes and set the thresholds
+//        SiSensorSim strip_simulation = new CDFSiSensorSim();
+        CDFSiSensorSim strip_simulation = new CDFSiSensorSim();
+
+        //  Instantiate the readout chips and set the noise parameters
+        BasicReadoutChip strip_readout = new BasicReadoutChip();
+//  ABCD -- Pristine
+/*
+        strip_readout.setNoiseIntercept(600.);
+        strip_readout.setNoiseSlope(65.);
+        strip_readout.setNoiseThreshold(4.);
+        strip_readout.setNeighborThreshold(4.);
+        strip_readout.setNbits(1);
+        strip_readout.setDynamicRange(10);
+         */
+        // APV25 -- Pristine
+
+        strip_readout.setNoiseIntercept(270.);
+        strip_readout.setNoiseSlope(36.);
+        strip_readout.setNoiseThreshold(4.);
+        strip_readout.setNeighborThreshold(4.);
+        strip_readout.setNbits(10);
+        strip_readout.setDynamicRange(40);
+
+/*
+        strip_readout.setNoiseIntercept(0.1);
+        strip_readout.setNoiseSlope(0.1);
+        strip_readout.setNoiseThreshold(4);
+        strip_readout.setNeighborThreshold(4);
+        strip_readout.setNbits(10);
+        strip_readout.setDynamicRange(40);
+*/
+
+        //set trapping to 0.2 to simulate radiation damage.
+//        strip_simulation.setTrapping(0.2);
+//                strip_simulation.setTrapping(0.12);
+
+        //  Instantiate the digitizer that produces the raw hits
+        _strip_digitizer = new RawTrackerHitMaker(strip_simulation, strip_readout);
+
+        _digitizer_name = _strip_digitizer.getName();
+
+        //  Instantiate a nearest neighbor clustering algorithm for the strips
+//        NearestNeighbor strip_clustering = new NearestNeighbor();
+//        strip_clustering.setSeedThreshold(4.);
+//        strip_clustering.setNeighborThreshold(4.);
+
+        NearestNeighborRMS strip_clustering = new NearestNeighborRMS();
+
+        strip_clustering.setSeedThreshold(4.);
+        strip_clustering.setNeighborThreshold(3.);
+        strip_clustering.setClusterThreshold(4.);
+
+
+        //  Instantiate the clusterers and set hit-making parameters
+        _strip_clusterer = new StripHitMaker(strip_simulation, strip_readout, strip_clustering);
+        _strip_clusterer.setMaxClusterSize(10);
+        _strip_clusterer.setCentralStripAveragingThreshold(4);
+        /*
+        _strip_clusterer.SetOneClusterErr(1 / Math.sqrt(12.));
+        _strip_clusterer.SetTwoClusterErr(1 / 5.0);
+        _strip_clusterer.SetThreeClusterErr(1 / 3.0);
+        _strip_clusterer.SetFourClusterErr(1 / 2.0);
+        _strip_clusterer.SetFiveClusterErr(1 / 1.0);
+         */
+        double multiplier = 1.0;
+        _strip_clusterer.SetOneClusterErr(multiplier / Math.sqrt(12.));
+        _strip_clusterer.SetTwoClusterErr(multiplier / 5.0);
+        _strip_clusterer.SetThreeClusterErr(multiplier / 3.0);
+        _strip_clusterer.SetFourClusterErr(multiplier / 2.0);
+        _strip_clusterer.SetFiveClusterErr(multiplier / 1.0);
+
+
+        //  Specify the readouts to process
+        _readouts.add("TrackerHits");
+        //  Specify the detectors to process
+        _process_paths.add("Tracker");
+    }
+
+    /**
+     * Initialize whenever we have a new detector
+     * 
+     * @param detector
+     */
+    public void detectorChanged(Detector detector) {
+        System.out.println(detector.getName());
+        super.detectorChanged(detector);
+
+        // Process detectors specified by path, otherwise process entire detector
+        IDetectorElement detector_de = detector.getDetectorElement();
+        System.out.println("detector_de Name =" + detector_de.getName());
+        for (String de_path : _process_paths) {
+            _process_de.add(detector_de.findDetectorElement(de_path));
+        }
+
+        if (_process_de.size() == 0) {
+            _process_de.add(detector_de);
+        }
+
+        for (IDetectorElement detector_element : _process_de) {
+            _process_sensors.addAll(detector_element.findDescendants(SiSensor.class));
+            _process_modules.addAll(detector_element.findDescendants(SiTrackerModule.class));
+        }
+
+    }
+
+    /**
+     * Setup readouts
+     */
+    public void startOfData() {
+        // If readouts not already set, set them up
+        if (_readouts.size() != 0) {
+            System.out.println("Adding SimTrackerHitIdentifierReadoutDriver with readouts: " + _readouts);
+            super.add(new SimTrackerHitReadoutDriver(_readouts));
+        }
+
+        super.startOfData();
+        _readouts.clear();
+        _nev = 0;
+        _ngc = 0;
+    }
+
+    /**
+     * Main digitization driver.  Creates raw hits, forms clusters, and makes
+     * tracker hits using the sisim package.
+     *
+     * @param event
+     */
+    public void process(EventHeader event) {
+        super.process(event);
+
+        //  Print out the event number
+
+        _nev++;
+        _ngc++;
+        if (_ngc == 100) {
+            System.out.println("TrackerHitDriver processing event " + _nev);
+            System.gc();
+            _ngc = 0;
+        }
+
+        long last_time = System.currentTimeMillis();
+
+
+        // Lists of hits
+        List<RawTrackerHit> raw_hits = new ArrayList<RawTrackerHit>();
+        List<SiTrackerHit> hits_strip1D = new ArrayList<SiTrackerHit>();
+        List<SiTrackerHit> hits_pixel = new ArrayList<SiTrackerHit>();
+
+        /*
+        for (SiSensor sensor : _process_sensors) {
+
+        if (sensor.hasStrips()) {
+        raw_hits.addAll(_strip_digitizer.makeHits(sensor));
+        hits_strip1D.addAll(_strip_clusterer.makeHits(sensor));
+
+        }
+
+
+        if (sensor.hasPixels()) {
+        raw_hits.addAll(_pixel_digitizer.makeHits(sensor));
+        hits_pixel.addAll(_pixel_clusterer.makeHits(sensor));
+        }
+
+        }
+
+         */
+        for (SiSensor sensor : _process_sensors) {
+            raw_hits.addAll(_strip_digitizer.makeHits(sensor));
+
+        }
+        long raw_time = System.currentTimeMillis();
+        double rtime = ((double) (raw_time - last_time)) / 1000.;
+        if (_timing) {
+            aida.cloud1D("Digitization Time").fill(rtime);
+        }
+
+
+        for (SiSensor sensor : _process_sensors) {
+            hits_strip1D.addAll(_strip_clusterer.makeHits(sensor));
+        }
+        long start_time = System.currentTimeMillis();
+        double dtime = ((double) (start_time - raw_time)) / 1000.;
+        if (_timing) {
+            aida.cloud1D("Clustering Time").fill(dtime);
+        }
+        //        int flag = (1 << LCIOConstants.RTHBIT_HITS | 1 << LCIOConstants.TRAWBIT_ID1); //correct flag for persistence
+        int flag = 0;
+        event.put(getRawHitsName(), raw_hits, RawTrackerHit.class, flag, toString());
+        event.put(getStripHits1DName(), hits_strip1D, SiTrackerHitStrip1D.class, 0, toString());
+//        event.put(getPixelHitsName(), hits_pixel, SiTrackerHitPixel.class, 0, toString());
+
+    }
+
+    /**
+     * Return the name of the raw hits collection
+     *
+     * @return name of raw hits collection
+     */
+    public String getRawHitsName() {
+        return _digitizer_name + "_RawTrackerHits";
+    }
+
+    /**
+     * Return the name of the strip hits collection
+     *
+     * @return name of strip hits collection
+     */
+    public String getStripHits1DName() {
+        return _strip_clusterer.getName() + "_SiTrackerHitStrip1D";
+    }
+
+    /**
+     * Return the name of the pixel hits collection
+     *
+     * @return name of pixel hits collection
+     */
+    public String getPixelHitsName() {
+        return _pixel_clusterer.getName() + "_SiTrackerHitPixel";
+    }
+}

hps-java/src/main/java/org/lcsim/hps/users/mgraham/alignment

diff -N HeavyPhotonLLDriver.java
--- HeavyPhotonLLDriver.java	26 Nov 2012 19:27:39 -0000	1.5
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,230 +0,0 @@

-package org.lcsim.hps.users.mgraham.alignment;
-
-import org.lcsim.hps.users.mgraham.jlabrotation.*;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import org.lcsim.hps.event.HPSTransformations;
-import org.lcsim.hps.recon.tracking.HelicalTrackHitDriver;
-import org.lcsim.hps.recon.tracking.HPSTrackerHitDriver;
-
-//import org.lcsim.hps.recon.tracking.SiTrackerSpectrometerSensorSetup;
-import org.lcsim.recon.tracking.seedtracker.SeedStrategy;
-import org.lcsim.recon.tracking.seedtracker.SeedTracker;
-import org.lcsim.recon.tracking.seedtracker.StrategyXMLUtils;
-import org.lcsim.recon.tracking.seedtracker.diagnostic.SeedTrackerDiagnostics;
-import org.lcsim.util.Driver;
-import org.lcsim.util.loop.LCIODriver;
-
-/**
- * Driver for track reconstruction and analysis of HPS detector.
- *
- * @author M. Graham
- */
-public final class HeavyPhotonLLDriver extends Driver {
-
-    //********************
-    //   set pname to the detector you want to run...HPS1pt8 is the default test detector (uses strategy file 1.3)
-    //  see "setPName" method for list
-//    public String pName = "HPS1pt9";
-    public String pName = "HPS1pt8";
-//    JasAnalysisDriver jad;
-    DetailedAnalysisDriver dad;
-//    FastTrackAnalysisDriver ftad;
-//    KalmanFilterDriver kfd;
-    List<int[]> pairs = new ArrayList();
-    List<Integer> passLayers = new ArrayList();
-    ////   Change the prefix for your site
-//    String strategyPrefix = "/nfs/sulky21/g.ec.u12/users/mgraham/AtlasUpgrade/hps-java/src/main/resources/";
-    String strategyPrefix = "/Users/mgraham/NetBeansProjects/hps-java/src/main/resources/";
-    ////////////////////////////////////////
-    //  everything below will
-    //  get overwritten by setPName
-    int nlayers = 10;
-    int fitlayers = 10;
-    // bfield needs to be set because tracking doesn't 
-    // seme to deal with fields in the negative 
-    //  z-direction well (need to fix this)
-    double bfield = 0.5;
-    String detType = "Full";
-    String axialStrategy = "HPS-Test-1pt8.xml";
-    String finalStrategy = "HPS-Test-1pt8.xml";
-    String llStrategy = "HPS-Test-1pt8.xml";
-    public String outputFile = "foobar.slcio";
-    public String plotsFile = "myplots.aida";
-    public String outputTextName = "myevents.txt";
-    ///////////////
-
-    public HeavyPhotonLLDriver() {
-//        add(new MakeSensorsDriver());
-        add(new SiTrackerSpectrometerSensorSetup("Tracker"));
-        setPName(pName);
-
-        HPSTrackerHitDriver thd = new HPSTrackerHitDriver();
-        add(thd);
-
-        HelicalTrackHitDriver hthdriver = new HelicalTrackHitDriver();
-        hthdriver.addCollection(((HPSTrackerHitDriver) thd).getStripHits1DName());
-        hthdriver.setOutputCollectionName("HelicalTrackHits");
-        hthdriver.HitRelationName("HelicalTrackHitRelations");
-        hthdriver.MCRelationName("HelicalTrackMCRelations");
-        for (int[] pair : pairs)
-            hthdriver.setStereoPair("Tracker", pair[0], pair[1]);
-
-        if (detType.contains("Test")) {
-            System.out.println("Setting separation for a Test detector");
-            hthdriver.setMaxSeperation(10.01);
-            hthdriver.setTolerance(0.01);
-        } else {
-
-            hthdriver.setMaxSeperation(50.);
-            hthdriver.setTolerance(0.4);
-        }
-        hthdriver.setTransformToTracking(true);
-        add(hthdriver);
-
-        List<SeedStrategy> sFinallist = StrategyXMLUtils.getStrategyListFromFile(new File(strategyPrefix + finalStrategy));
-        SeedTracker stFinal = null;
-        stFinal = new SeedTracker(sFinallist);
-
-        HPSTransformations hpstrans = new HPSTransformations();
-        stFinal.setMaterialManagerTransform(hpstrans.getTransform());
-        stFinal.setInputCollectionName("RotatedHelicalTrackHits");
-
-//        stFinal.setInputCollectionName("HelicalTrackHits");
-
-        stFinal.setTrkCollectionName("MatchedTracks");
-        stFinal.setDiagnostics(new SeedTrackerDiagnostics());
-        stFinal.setBField(bfield);
-        stFinal.setSectorParams(false);
-        stFinal.setTimingPlots(true);
-
-
-
-        add(stFinal);
-
-//        MultiTrackReco trd = new MultiTrackReco(strategyPrefix, detType, bfield, axialStrategy, finalStrategy, llStrategy, pairs, passLayers);
-//        add(trd);
-
-//        dad = new DetailedAnalysisDriver(10);
-//        add(dad);
-          add(new RunAlignment(10,10,finalStrategy));
-//          kfd = new KalmanFilterDriver();
-//        add(kfd);
-//    uncomment this to look at occupancies
-        //       add(new OccupancyDriver());
-    }
-
-    public void setOutputFile(String outputFile) {
-        System.out.println("Will output events to " + outputFile);
-        add(new LCIODriver(outputFile));
-    }
-
-    public void setPlotsFile(String plotsFile) {
-        System.out.println("Will output plots to " + plotsFile);
-//        jad.setOutputPlots(plotsFile);
-    }
-
-    public void setOutputTextName(String outputTextName) {
-        System.out.println("Will output selected events to " + outputTextName);
-//        ftad.setOutputText(outputTextName);
-    }
-
-    public void setPName(String pName) {
-        System.out.println("Setting parameter set to " + pName);
-        pairs.clear();
-        if (pName.contentEquals("HPS3pt2")) {
-            detType = "Full";
-            bfield = 1.0;
-            nlayers = 12;
-            fitlayers = 10;
-            axialStrategy = "DarkPhoton-Axial-HPS3pt2.xml";
-            finalStrategy = "DarkPhoton-HPS3pt2.xml";
-            llStrategy = "DarkPhoton-HPS3pt2-LongLived.xml";
-
-            int[] p1 = {1, 2};
-            int[] p2 = {3, 4};
-            int[] p3 = {5, 6};
-            int[] p4 = {7, 8};
-            int[] p5 = {9, 10};
-            int[] p6 = {11, 12};
-            pairs.add(p1);
-            pairs.add(p2);
-            pairs.add(p3);
-            pairs.add(p4);
-            pairs.add(p5);
-            pairs.add(p6);
-            passLayers.add(11);
-        }
-        if (pName.contentEquals("HPS3pt4")) {
-            detType = "Full";
-            bfield = 0.5;
-            nlayers = 12;
-            fitlayers = 10;
-            axialStrategy = "DarkPhoton-Axial-HPS3pt2.xml";
-            finalStrategy = "DarkPhoton-HPS3pt2.xml";
-            llStrategy = "none";
-
-            int[] p1 = {1, 2};
-            int[] p2 = {3, 4};
-            int[] p3 = {5, 6};
-            int[] p4 = {7, 8};
-            int[] p5 = {9, 10};
-            int[] p6 = {11, 12};
-            pairs.add(p1);
-            pairs.add(p2);
-            pairs.add(p3);
-            pairs.add(p4);
-            pairs.add(p5);
-            pairs.add(p6);
-            passLayers.add(11);
-        }
-
-        if (pName.contentEquals("HPS1pt8")) {
-            detType = "Test";
-            nlayers = 10;
-            bfield = 0.5;
-            fitlayers = 10;
-            axialStrategy = "none";   //  don't fit tracks axially first
-            finalStrategy = "HPS-Test-1pt3.xml";
-            llStrategy = "none";//  don't fit tracks ignoring first plane
-
-            int[] p1 = {1, 2};
-            int[] p2 = {3, 4};
-            int[] p3 = {5, 6};
-            int[] p4 = {7, 8};
-            int[] p5 = {9, 10};
-
-            pairs.add(p1);
-            pairs.add(p2);
-            pairs.add(p3);
-            pairs.add(p4);
-            pairs.add(p5);
-//            passLayers.add(11);
-        }
-
-        if (pName.contentEquals("HPS1pt9")) {
-            detType = "Test";
-            nlayers = 10;
-            bfield = 0.25;
-            fitlayers = 10;
-            axialStrategy = "none";   //  don't fit tracks axially first
-            finalStrategy = "HPS-Test-1pt3.xml";
-            llStrategy = "none";//  don't fit tracks ignoring first plane
-
-            int[] p1 = {1, 2};
-            int[] p2 = {3, 4};
-            int[] p3 = {5, 6};
-            int[] p4 = {7, 8};
-            int[] p5 = {9, 10};
-
-            pairs.add(p1);
-            pairs.add(p2);
-            pairs.add(p3);
-            pairs.add(p4);
-            pairs.add(p5);
-//            passLayers.add(11);
-        }
-
-    }
-}