From 83909585d405870300cf4a53068a80cd6e238466 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Thu, 26 Nov 2020 00:43:43 -0600
Subject: [PATCH 01/11] First version of signal overlay driver

---
 .../org/hps/util/SignalOverlayDriver.java     | 130 ++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100644 util/src/main/java/org/hps/util/SignalOverlayDriver.java

diff --git a/util/src/main/java/org/hps/util/SignalOverlayDriver.java b/util/src/main/java/org/hps/util/SignalOverlayDriver.java
new file mode 100644
index 0000000000..185c50d831
--- /dev/null
+++ b/util/src/main/java/org/hps/util/SignalOverlayDriver.java
@@ -0,0 +1,130 @@
+package org.hps.util;
+
+import java.io.EOFException;
+import java.io.File;
+import java.io.IOException;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Queue;
+import java.util.Set;
+import java.util.logging.Logger;
+
+import org.lcsim.event.EventHeader;
+import org.lcsim.event.EventHeader.LCMetaData;
+import org.lcsim.lcio.LCIOReader;
+import org.lcsim.util.Driver;
+
+/**
+ * Overlay signal collections from a side event stream every N events.
+ */
+public class SignalOverlayDriver extends Driver {
+
+    private static Logger LOGGER = Logger.getLogger(SignalOverlayDriver.class.getPackage().getName());
+
+    private Queue<String> signalFileNames = new LinkedList<String>();
+    private int eventSpacing = 250;
+    private int sequence = 0;
+    LCIOReader reader = null;
+
+    class EndOfDataException extends Exception {
+        private static final long serialVersionUID = 1L;
+    }
+
+    public void setSignalFile(String signalFileName) {
+        this.signalFileNames.add(signalFileName);
+    }
+
+    public void setEventSpacing(int eventSpacing) {
+        if (eventSpacing <= 0) {
+            throw new IllegalArgumentException("Bad value for event spacing: " + eventSpacing);
+        }
+        this.eventSpacing = eventSpacing;
+    }
+
+    @Override
+    protected void startOfData() {
+        if (this.signalFileNames.size() == 0) {
+            throw new RuntimeException("No signal files were provided!");
+        }
+        String filePath = this.signalFileNames.remove();
+        try {
+            LOGGER.info("Opening signal file: " + filePath);
+            File file = new File(filePath);
+            if (!file.exists()) {
+                throw new RuntimeException("File does not exist: " + file.getName());
+            }
+            reader = new LCIOReader(file);
+        } catch (IOException e) {
+            LOGGER.severe("Failed to read from: " + filePath);
+            throw new RuntimeException(e);
+        }
+    }
+
+    private void openNextFile() throws EndOfDataException {
+        try {
+            LOGGER.info("Closing previous reader...");
+            reader.close();
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+        if (signalFileNames.size() == 0) {
+            throw new EndOfDataException();
+        }
+        String path = signalFileNames.remove();
+        LOGGER.info("Opening next file: " + path);
+        try {
+            reader = new LCIOReader(new File(path));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    private EventHeader readNextEvent() throws EndOfDataException {
+        EventHeader event = null;
+        try {
+            LOGGER.info("Reading next event...");
+            event = this.reader.read();
+        } catch (EOFException eof) {
+            openNextFile();
+            try {
+                LOGGER.info("Reading first event in new file...");
+                event = this.reader.read();
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        } catch (IOException ioe) {
+            ioe.printStackTrace();
+        } finally {
+            if (event == null) {
+                throw new RuntimeException("Failed to read next event.");
+            }
+        }
+        return event;
+    }
+
+    @Override
+    protected void process(EventHeader event) {
+        try {
+            LOGGER.fine("Processing background event: " + event.getEventNumber());
+            if (this.sequence % this.eventSpacing == 0) {
+                EventHeader signalEvent = this.readNextEvent();
+                LOGGER.fine("Read signal event: " + signalEvent.getEventNumber());
+                Set<List> lists = signalEvent.getLists();
+                for (List list : lists) {
+                    LCMetaData meta = signalEvent.getMetaData(list);
+                    String collName = meta.getName();
+                    if (!event.hasItem(collName)) {
+                        event.put(collName, list, meta.getType(), meta.getFlags());
+                    } else {
+                        event.get(meta.getClass(), collName).addAll(list);
+                    }
+                    LOGGER.info("Added " + list.size() + " objects to collection: " + collName);
+                }
+            }
+            ++this.sequence;
+        } catch (EndOfDataException e) {
+            throw new RuntimeException("Ran out of signal events!");
+        }
+    }
+}
+

From 2c2fd05507f895b32e76b60abc0c3486e7073a60 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 14:28:07 -0600
Subject: [PATCH 02/11] Update signal overlay driver

---
 .../org/hps/util/SignalOverlayDriver.java     | 140 +++++++++++++++---
 1 file changed, 119 insertions(+), 21 deletions(-)

diff --git a/util/src/main/java/org/hps/util/SignalOverlayDriver.java b/util/src/main/java/org/hps/util/SignalOverlayDriver.java
index 185c50d831..d67b48f60e 100644
--- a/util/src/main/java/org/hps/util/SignalOverlayDriver.java
+++ b/util/src/main/java/org/hps/util/SignalOverlayDriver.java
@@ -3,6 +3,7 @@
 import java.io.EOFException;
 import java.io.File;
 import java.io.IOException;
+import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Queue;
@@ -11,25 +12,90 @@
 
 import org.lcsim.event.EventHeader;
 import org.lcsim.event.EventHeader.LCMetaData;
+import org.lcsim.event.SimCalorimeterHit;
+import org.lcsim.event.SimTrackerHit;
 import org.lcsim.lcio.LCIOReader;
 import org.lcsim.util.Driver;
 
 /**
- * Overlay signal collections from a side event stream every N events.
+ * Overlay signal collections from a side event stream every N events,
+ * applying optional event filters to reject events.
  */
 public class SignalOverlayDriver extends Driver {
 
-    private static Logger LOGGER = Logger.getLogger(SignalOverlayDriver.class.getPackage().getName());
-
+    private static Logger LOGGER =
+            Logger.getLogger(SignalOverlayDriver.class.getCanonicalName());
     private Queue<String> signalFileNames = new LinkedList<String>();
     private int eventSpacing = 250;
     private int sequence = 0;
+    private int nRejected = 0;
+    private int nSignal = 0;
+    private String ecalHitCollection = "EcalHits";
+    private String hodoHitCollection = "HodoscopeHits";
+
     LCIOReader reader = null;
 
+    interface EventFilter {
+        public boolean accept(EventHeader event);
+    }
+
+    class EcalEnergyFilter implements EventFilter {
+
+        double eCut = 0;
+
+        public EcalEnergyFilter(double eCut) {
+            this.eCut = eCut;
+        }
+
+        public boolean accept(EventHeader event) {
+            List<SimCalorimeterHit> ecalHits = event.get(SimCalorimeterHit.class,
+                    SignalOverlayDriver.this.ecalHitCollection);
+            double totalE = 0;
+            for (SimCalorimeterHit hit : ecalHits) {
+                totalE += hit.getRawEnergy();
+            }
+            System.out.println("totalE = " + totalE);
+            return totalE > eCut;
+        }
+    }
+
+    class HodoHitFilter implements EventFilter {
+
+        int nHits = 0;
+
+        public HodoHitFilter(int nHits) {
+            this.nHits = nHits;
+        }
+
+        public boolean accept(EventHeader event) {
+            List<SimTrackerHit> hodoHits = event.get(SimTrackerHit.class,
+                    SignalOverlayDriver.this.hodoHitCollection);
+            return hodoHits.size() >= nHits;
+        }
+    }
+
+    private Set<EventFilter> eventFilters = new HashSet<EventFilter>();
+
     class EndOfDataException extends Exception {
         private static final long serialVersionUID = 1L;
     }
 
+    public void setMinHodoHits(int nHits) {
+        eventFilters.add(new HodoHitFilter(nHits));
+    }
+
+    public void setHodoHitCollection(String hodoHitCollection) {
+        this.hodoHitCollection = hodoHitCollection;
+    }
+
+    public void setEcalEnergyCut(double eCut) {
+        eventFilters.add(new EcalEnergyFilter(eCut));
+    }
+
+    public void setEcalHitCollection(String ecalHitCollection) {
+        this.ecalHitCollection = ecalHitCollection;
+    }
+
     public void setSignalFile(String signalFileName) {
         this.signalFileNames.add(signalFileName);
     }
@@ -102,29 +168,61 @@ private EventHeader readNextEvent() throws EndOfDataException {
         return event;
     }
 
+    private boolean accept(EventHeader event) {
+        for (EventFilter filter : eventFilters) {
+            if (!filter.accept(event)) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    @SuppressWarnings({ "rawtypes", "unchecked" })
     @Override
     protected void process(EventHeader event) {
-        try {
-            LOGGER.fine("Processing background event: " + event.getEventNumber());
-            if (this.sequence % this.eventSpacing == 0) {
-                EventHeader signalEvent = this.readNextEvent();
-                LOGGER.fine("Read signal event: " + signalEvent.getEventNumber());
-                Set<List> lists = signalEvent.getLists();
-                for (List list : lists) {
-                    LCMetaData meta = signalEvent.getMetaData(list);
-                    String collName = meta.getName();
-                    if (!event.hasItem(collName)) {
-                        event.put(collName, list, meta.getType(), meta.getFlags());
-                    } else {
-                        event.get(meta.getClass(), collName).addAll(list);
-                    }
-                    LOGGER.info("Added " + list.size() + " objects to collection: " + collName);
+        LOGGER.fine("Processing background event: " + event.getEventNumber());
+
+        // Overlay signal event
+        if (this.sequence % this.eventSpacing == 0) {
+
+            // Find the next acceptable signal event
+            EventHeader signalEvent = null;
+            try {
+                signalEvent = this.readNextEvent();
+                while (true) {
+                    if (accept(signalEvent)) break;
+                    LOGGER.fine("Rejected signal event: " + signalEvent.getEventNumber());
+                    nRejected += 1;
+                    signalEvent = this.readNextEvent();
+                }
+            } catch (EndOfDataException e) {
+                throw new RuntimeException("Ran out of signal events!", e);
+            }
+            LOGGER.fine("Read signal event: " + signalEvent.getEventNumber());
+
+            // Overlay signal collections onto background event
+            Set<List> lists = signalEvent.getLists();
+            for (List list : lists) {
+                LCMetaData meta = signalEvent.getMetaData(list);
+                String collName = meta.getName();
+                if (!event.hasItem(collName)) {
+                    event.put(collName, list, meta.getType(), meta.getFlags());
+                } else {
+                    event.get(meta.getClass(), collName).addAll(list);
                 }
+                LOGGER.info("Added " + list.size() + " objects to collection: " + collName);
             }
-            ++this.sequence;
-        } catch (EndOfDataException e) {
-            throw new RuntimeException("Ran out of signal events!");
+
+            ++nSignal;
         }
+
+        ++this.sequence;
+    }
+
+    protected void endOfData() {
+        System.out.println("End event sequence: " + this.sequence);
+        System.out.println("Signal events rejected: " + nRejected);
+        System.out.println("Signal events overlaid: " + nSignal);
     }
 }
 

From b8b08468945bd0d008209180087f7a8411cb84f3 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 14:34:47 -0600
Subject: [PATCH 03/11] Add example steering file for signal overlay

---
 .../readout/SignalOverlayExample.lcsim        | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim

diff --git a/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim b/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim
new file mode 100644
index 0000000000..e28c9da300
--- /dev/null
+++ b/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim
@@ -0,0 +1,26 @@
+<lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
+        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
+    <inputFiles>
+        <file>${beamFile}</file>
+    </inputFiles>
+<!--
+    <control>
+        <numberOfEvents>25000</numberOfEvents>
+    </control>
+-->
+    <execute>
+        <driver name="SignalOverlayDriver"/>
+        <driver name="LCIOWriter"/>
+    </execute>
+    <drivers>
+        <driver name="SignalOverlayDriver" type="org.hps.readout.SignalOverlayDriver">
+            <eventSpacing>250</eventSpacing>
+            <ecalEnergyCut>0.04</ecalEnergyCut>
+<!--            <minHodoHits>1</minHodoHits> -->
+            <signalFile>${signalFile}</signalFile>
+        </driver>
+        <driver name="LCIOWriter" type="org.lcsim.util.loop.LCIODriver">
+            <outputFilePath>${outputFile}.slcio</outputFilePath>
+        </driver>
+    </drivers>
+</lcsim>

From 2906f03b278675cb37d570a1aeddc8b00e5b69ee Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 14:35:14 -0600
Subject: [PATCH 04/11] Rename file

---
 .../src/main/java/org/hps/readout}/SignalOverlayDriver.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)
 rename {util/src/main/java/org/hps/util => ecal-readout-sim/src/main/java/org/hps/readout}/SignalOverlayDriver.java (98%)

diff --git a/util/src/main/java/org/hps/util/SignalOverlayDriver.java b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
similarity index 98%
rename from util/src/main/java/org/hps/util/SignalOverlayDriver.java
rename to ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
index d67b48f60e..a0c23ab3d0 100644
--- a/util/src/main/java/org/hps/util/SignalOverlayDriver.java
+++ b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
@@ -1,4 +1,4 @@
-package org.hps.util;
+package org.hps.readout;
 
 import java.io.EOFException;
 import java.io.File;
@@ -148,12 +148,12 @@ private void openNextFile() throws EndOfDataException {
     private EventHeader readNextEvent() throws EndOfDataException {
         EventHeader event = null;
         try {
-            LOGGER.info("Reading next event...");
+            LOGGER.fine("Reading next event...");
             event = this.reader.read();
         } catch (EOFException eof) {
             openNextFile();
             try {
-                LOGGER.info("Reading first event in new file...");
+                LOGGER.fine("Reading first event in new file...");
                 event = this.reader.read();
             } catch (IOException e) {
                 e.printStackTrace();

From 03b85478bbf2bfe1b23e39b3431aac369fe0e173 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 15:04:33 -0600
Subject: [PATCH 05/11] Use logger for debug printout

---
 .../src/main/java/org/hps/readout/SignalOverlayDriver.java      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
index a0c23ab3d0..67e795680c 100644
--- a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
+++ b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
@@ -54,7 +54,7 @@ public boolean accept(EventHeader event) {
             for (SimCalorimeterHit hit : ecalHits) {
                 totalE += hit.getRawEnergy();
             }
-            System.out.println("totalE = " + totalE);
+            LOGGER.fine("ECAL totalE = " + totalE);
             return totalE > eCut;
         }
     }

From b5d78ed0e4004ff5f7d3a4b07155dc850e9937a8 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 17:14:48 -0600
Subject: [PATCH 06/11] Minor cleanup

---
 .../java/org/hps/readout/SignalOverlayDriver.java |  6 +++---
 .../steering/readout/SignalOverlayExample.lcsim   | 15 +++++++++------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
index 67e795680c..7f61781013 100644
--- a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
+++ b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
@@ -18,13 +18,13 @@
 import org.lcsim.util.Driver;
 
 /**
- * Overlay signal collections from a side event stream every N events,
- * applying optional event filters to reject events.
+ * Overlay signal event collections every N events, applying optional
+ * filters to reject unwanted events.
  */
 public class SignalOverlayDriver extends Driver {
 
     private static Logger LOGGER =
-            Logger.getLogger(SignalOverlayDriver.class.getCanonicalName());
+            Logger.getLogger(SignalOverlayDriver.class.getPackageName());
     private Queue<String> signalFileNames = new LinkedList<String>();
     private int eventSpacing = 250;
     private int sequence = 0;
diff --git a/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim b/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim
index e28c9da300..ecc16a75d4 100644
--- a/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim
+++ b/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayExample.lcsim
@@ -1,13 +1,15 @@
+<!--
+    Overlay signal file onto beam background
+
+    Beam file is specified using '-DbeamFile=beam.slcio'
+    and signal with '-DsignalFile=signal.slcio'
+-->
+
 <lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
         xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
     <inputFiles>
         <file>${beamFile}</file>
     </inputFiles>
-<!--
-    <control>
-        <numberOfEvents>25000</numberOfEvents>
-    </control>
--->
     <execute>
         <driver name="SignalOverlayDriver"/>
         <driver name="LCIOWriter"/>
@@ -16,7 +18,8 @@
         <driver name="SignalOverlayDriver" type="org.hps.readout.SignalOverlayDriver">
             <eventSpacing>250</eventSpacing>
             <ecalEnergyCut>0.04</ecalEnergyCut>
-<!--            <minHodoHits>1</minHodoHits> -->
+            <!-- uncomment this for 2019 data to filter on number of Hodoscope hits -->
+            <!-- <minHodoHits>1</minHodoHits> -->
             <signalFile>${signalFile}</signalFile>
         </driver>
         <driver name="LCIOWriter" type="org.lcsim.util.loop.LCIODriver">

From 7dd449324b4dcaf8fc85cf5834c2126ba471f669 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 17:57:50 -0600
Subject: [PATCH 07/11] Add copy of 2016 readout with signal overlay

---
 ...2016TrigPairs1_NoTruth_SignalOverlay.lcsim | 283 ++++++++++++++++++
 1 file changed, 283 insertions(+)
 create mode 100644 steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim

diff --git a/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim b/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim
new file mode 100644
index 0000000000..86948f951b
--- /dev/null
+++ b/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim
@@ -0,0 +1,283 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
+    <execute>
+
+        <!-- overlay signal onto the beam events -->
+        <driver name="SignalOverlayDriver"/>
+
+        <!-- SLiC Data Readout Drivers -->
+        <driver name="EcalHitsOutputDriver"/>
+        <driver name="MCParticleOutputDriver"/>
+        <driver name="TrackerHitsSVTOutputDriver"/>
+        <driver name="TrackerHitsEcalOutputDriver"/>
+        
+        <!-- SVT Readout Drivers -->
+        <driver name="SVTReadoutDriver" />
+        <driver name="InactiveTrackerHitsOutputDriver"/>
+        
+        <!-- Readout Simulation Drivers -->
+        <driver name="EcalDigitizationDriver"/>
+        <driver name="EcalRawConverterDriver"/>
+        <driver name="GTPReadoutDriver"/>
+        <driver name="Pair1TriggerDriver"/>
+        
+        <!-- LCIO Output and Data Management Driver -->
+        <driver name="ReadoutManagerDriver"/>
+        
+        <driver name="CleanupDriver" />
+    </execute> 
+    
+    <drivers>
+
+        <driver name="SignalOverlayDriver" type="org.hps.readout.SignalOverlayDriver">
+            <eventSpacing>250</eventSpacing>
+            <ecalEnergyCut>0.04</ecalEnergyCut>
+<!--            <minHodoHits>1</minHodoHits> -->
+            <signalFile>${signalFile}</signalFile>
+        </driver>  
+
+        <!--
+             Truth handler drivers load truth information from the input SLIC file
+             and pass them off to the readout data manager, where they may be
+             accessed by other readout drivers.
+             
+             It is required that these drivers specify the name of the collection
+             that they manage, and be of the appropriate handler type that matches
+             the object type of the collection. They may also, optionally, specify
+             whether the truth collection managed by the driver should be output
+             into the readout file, and if so, over what time range.
+             
+             By default, SLIC truth data is not written out. If no output window is
+             specified, and truth is written, the output window will be derived
+             from the readout window and trigger offset parameters of the readout
+             data manager.
+             
+             In general, calorimeter truth information (and the related particles
+             data) are best handled by including truth readout in the calorimeter
+             simulation. This will automatically include all calorimeter truth hits
+             and related MC particles in the readout file.
+          -->
+        <driver name="EcalHitsOutputDriver" type="org.hps.readout.SimCalorimeterHitReadoutDriver">
+            <collectionName>EcalHits</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="MCParticleOutputDriver" type="org.hps.readout.MCParticleReadoutDriver">
+            <collectionName>MCParticle</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>32.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="TrackerHitsSVTOutputDriver" type="org.hps.readout.svt.SVTTrackerHitReadoutDriver">
+            <collectionName>TrackerHits</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="InactiveTrackerHitsOutputDriver" type="org.hps.readout.SimTrackerHitReadoutDriver">
+            <collectionName>TrackerHits_Inactive</collectionName>
+           
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="TrackerHitsEcalOutputDriver" type="org.hps.readout.SimTrackerHitReadoutDriver">
+            <collectionName>TrackerHitsECal</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        
+        <!--
+            The SVT driver. Works just like before. Documentation is left to
+            the SVT group.
+        -->
+        <driver name="SVTReadoutDriver" type="org.hps.readout.svt.SVTReadoutDriver">
+            <enablePileupCut>false</enablePileupCut>
+            <useTimingConditions>true</useTimingConditions>
+            <addNoise>true</addNoise>
+        </driver>
+        
+        <!--
+             The calorimeter readout driver handles conversion of SLIC truth
+             hits into voltage pulses and ultimately into ADC counts every 4 ns
+             sample. These samples are then integrated and output as hits which
+             are used internally by the readout simulation in the collection
+             set by variable "outputHitCollectionName".
+             
+             When a trigger occurs, the ADC buffer is used to generate readout
+             hits. The exact form these take differs based on the mode that is
+             simulated, but they are always output to the collection defined by
+             variable "readoutHitCollectionName".
+             
+             If truth information is enabled, then a set of truth relations are
+             output as well that link each readout hit to all of the truth hits
+             that are associated with it. Additionally, all truth hits as well
+             as the particle (and its parents) that generated that truth hit
+             are written out to ensure that they are available post-readout.
+             The additional truth information is automatically written to the
+             same collection name as the input truth data. If a truth handler
+             driver also outputs data into this collection, the two will merge.
+          -->
+        <driver name="EcalDigitizationDriver" type="org.hps.readout.ecal.updated.EcalDigitizationReadoutDriver">
+            <!-- LCIO Collection Names -->
+            <inputHitCollectionName>EcalHits</inputHitCollectionName>
+            <outputHitCollectionName>EcalRawHits</outputHitCollectionName>
+            <readoutHitCollectionName>EcalReadoutHits</readoutHitCollectionName>
+            <truthRelationsCollectionName>EcalTruthRelations</truthRelationsCollectionName>
+            <triggerPathTruthRelationsCollectionName>TriggerPathTruthRelations</triggerPathTruthRelationsCollectionName>
+            
+            <!-- Driver Parameters -->
+            <mode>1</mode>                                  <!-- Allowed values: 1, 3, or 7. -->
+            <addNoise>true</addNoise>
+            <!-- 
+                 Readout offset is not the same as the old system - it measures
+                 amount of samples that are included before the trigger time in
+                 the ADC readout window. The old version can be converted by
+                 selecting a readout window equal to (readoutLatency - 64).
+              -->
+            <readoutOffset>13</readoutOffset>               <!-- Units of 4 ns clock-cycles. -->
+            <readoutWindow>50</readoutWindow>               <!-- Units of 4 ns clock-cycles. -->
+            <numberSamplesAfter>25</numberSamplesAfter>     <!-- Units of 4 ns clock-cycles. -->
+            <numberSamplesBefore>5</numberSamplesBefore>    <!-- Units of 4 ns clock-cycles. -->
+            <integrationThreshold>18</integrationThreshold> <!-- Units of ADC. -->
+            
+            <!--
+                The digitization driver produces as output a list of ADC values
+                within a specified window, in emulation of Mode-1 data. This
+                removes the truth information that is otherwise present in the
+                original SLiC output. Setting this option to true creates new
+                LCRelation objects that link the ADC list to the truth hits that
+                created it and stores this in readout. For production running,
+                this should generally be off to save space. Truth hits will be
+                included in readout automatically - the truth hit driver above
+                does not need to be persistent.
+            -->
+            <writeTruth>false</writeTruth>
+            
+            <!--
+                As above, except that truth relations are persisted for the
+                readout hits that are seen by the clusterer and trigger. This
+                is useful if some analysis needs to be performed at the readout
+                level. Otherwise, this should be left off.
+            -->
+            <writeTriggerPathTruth>false</writeTriggerPathTruth>
+        </driver>
+        
+        <!--
+             The raw converter handles the conversion of simulated ADC pulses from
+             the calorimeter readout driver into proper hits that can be used for
+             triggering.
+             
+             Note that it allows for these hits to be written to LCIO if desired,
+             though by default they are not persisted. This is generally unneeded,
+             since the clusterer will automatically output the hits which appear in
+             GTP clusters if cluster output is enabled.
+          -->
+        <driver name="EcalRawConverterDriver" type="org.hps.readout.ecal.updated.EcalRawConverterReadoutDriver">
+            <!--
+                NSA and NSB must match the digitization driver settings.
+            -->
+            <numberSamplesAfter>25</numberSamplesAfter>     <!-- Units of 4 ns clock-cycles. -->
+            <numberSamplesBefore>5</numberSamplesBefore>    <!-- Units of 4 ns clock-cycles. -->
+            
+            <!--
+                Outputs all the trigger-level hits within the readout window.
+                This is not generally necessary outside of specialized
+                circumstances. Note that all readout hits associated with GTP
+                clusters will automatically be included if GTP clusters are
+                persisted.
+            -->
+            <persistent>false</persistent>
+        </driver>
+        
+        <!--
+             The GTP clusterer creates clusters from converted calorimeter hits
+             for use in the trigger. It take two parametesr: the clustering
+             window, which specifies the number of clock-cycles in which a seed
+             hit candidate must be a spatiotemporal maximum, and seed energy
+             threshold, which specifies how much energy a seed hit candidate
+             must have in order to be used.
+             
+             The GTP clusterer is able to be persisted into LCIO. If persisted,
+             it will output all of the clusters in the readout window range
+             (either specified manually as with the truth drivers or using the
+             default readout window and trigger offset of the manager). It will
+             also output all of the hits contained in each cluster into the
+             output file as well.
+          -->
+        <driver name="GTPReadoutDriver" type="org.hps.readout.ecal.updated.GTPClusterReadoutDriver">
+            <!-- Units of 4 ns clock-cycles. -->
+            <clusterWindow>4</clusterWindow>
+            <!-- Units of GeV. -->
+            <seedEnergyThreshold>0.100</seedEnergyThreshold>
+            
+            <!--
+                Specifies whether GTP clusters should be persisted in the
+                output LCIO data. This should generally be false for production
+                running to save space, but can be useful for some analyses, as
+                the exact trigger-time clusters are not otherwise recoverable
+                after readout.
+            -->
+            <persistent>false</persistent>
+        </driver>
+        
+        <!--
+            The production pair trigger. This trigger allows the user to
+            specify the trigger deadtime (how much time must pass before a new
+            trigger can occur after a previous trigger has been created) and
+            the values of all the trigger cuts.
+        -->
+        <driver name="Pair1TriggerDriver" type="org.hps.readout.trigger.PairTriggerReadoutDriver">
+            <inputCollectionName>EcalClustersGTP</inputCollectionName>
+            
+            <!-- Units of 2 ns beam bunches. -->
+            <deadTime>15</deadTime>
+            
+            <!-- Units of GeV. -->
+            <seedEnergyLow>0.100</seedEnergyLow>
+            <!-- Units of cluster hits. -->
+            <minHitCount>2</minHitCount>
+            <!-- Units of 4 ns clock-cycles. -->
+            <pairCoincidence>3</pairCoincidence>
+            <!-- Units of GeV. -->
+            <clusterEnergyLow>0.150</clusterEnergyLow>
+            <!-- Units of GeV. -->
+            <clusterEnergyHigh>1.400</clusterEnergyHigh>
+            <!-- Units of GeV. -->
+            <energySumLow>0.600</energySumLow>
+            <!-- Units of GeV. -->
+            <energySumHigh>2.000</energySumHigh>
+            <!-- Units of GeV. -->
+            <energyDifferenceHigh>1.1</energyDifferenceHigh>
+            <!-- Units of degrees. -->
+            <coplanarityHigh>35</coplanarityHigh>
+            <!-- Units of GeV / mm. -->
+            <energySlopeParamF>0.0055</energySlopeParamF>
+            <!-- Units of GeV. -->
+            <energySlopeLow>0.700</energySlopeLow>
+        </driver>
+        
+        <driver name="ReadoutManagerDriver" type="org.hps.readout.ReadoutDataManager">
+            <readoutWindow>200</readoutWindow>
+            <outputFile>${outputFile}.slcio</outputFile>
+        </driver>
+        
+        <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver" />
+    </drivers>
+</lcsim>

From 9d3fa634b9354380500a26873fad82676d04d061 Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Fri, 27 Nov 2020 19:08:54 -0600
Subject: [PATCH 08/11] Cleanup steering file (dos2unix)

---
 ...2016TrigPairs1_NoTruth_SignalOverlay.lcsim | 566 +++++++++---------
 1 file changed, 283 insertions(+), 283 deletions(-)

diff --git a/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim b/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim
index 86948f951b..82ce88d11d 100644
--- a/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim
+++ b/steering-files/src/main/resources/org/hps/steering/readout/PhysicsRun2016TrigPairs1_NoTruth_SignalOverlay.lcsim
@@ -1,283 +1,283 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
-    <execute>
-
-        <!-- overlay signal onto the beam events -->
-        <driver name="SignalOverlayDriver"/>
-
-        <!-- SLiC Data Readout Drivers -->
-        <driver name="EcalHitsOutputDriver"/>
-        <driver name="MCParticleOutputDriver"/>
-        <driver name="TrackerHitsSVTOutputDriver"/>
-        <driver name="TrackerHitsEcalOutputDriver"/>
-        
-        <!-- SVT Readout Drivers -->
-        <driver name="SVTReadoutDriver" />
-        <driver name="InactiveTrackerHitsOutputDriver"/>
-        
-        <!-- Readout Simulation Drivers -->
-        <driver name="EcalDigitizationDriver"/>
-        <driver name="EcalRawConverterDriver"/>
-        <driver name="GTPReadoutDriver"/>
-        <driver name="Pair1TriggerDriver"/>
-        
-        <!-- LCIO Output and Data Management Driver -->
-        <driver name="ReadoutManagerDriver"/>
-        
-        <driver name="CleanupDriver" />
-    </execute> 
-    
-    <drivers>
-
-        <driver name="SignalOverlayDriver" type="org.hps.readout.SignalOverlayDriver">
-            <eventSpacing>250</eventSpacing>
-            <ecalEnergyCut>0.04</ecalEnergyCut>
-<!--            <minHodoHits>1</minHodoHits> -->
-            <signalFile>${signalFile}</signalFile>
-        </driver>  
-
-        <!--
-             Truth handler drivers load truth information from the input SLIC file
-             and pass them off to the readout data manager, where they may be
-             accessed by other readout drivers.
-             
-             It is required that these drivers specify the name of the collection
-             that they manage, and be of the appropriate handler type that matches
-             the object type of the collection. They may also, optionally, specify
-             whether the truth collection managed by the driver should be output
-             into the readout file, and if so, over what time range.
-             
-             By default, SLIC truth data is not written out. If no output window is
-             specified, and truth is written, the output window will be derived
-             from the readout window and trigger offset parameters of the readout
-             data manager.
-             
-             In general, calorimeter truth information (and the related particles
-             data) are best handled by including truth readout in the calorimeter
-             simulation. This will automatically include all calorimeter truth hits
-             and related MC particles in the readout file.
-          -->
-        <driver name="EcalHitsOutputDriver" type="org.hps.readout.SimCalorimeterHitReadoutDriver">
-            <collectionName>EcalHits</collectionName>
-            
-            <!-- Units of ns. -->
-            <readoutWindowBefore>8.0</readoutWindowBefore>
-            <readoutWindowAfter>32.0</readoutWindowAfter>
-            <persistent>false</persistent>
-        </driver>
-        
-        <driver name="MCParticleOutputDriver" type="org.hps.readout.MCParticleReadoutDriver">
-            <collectionName>MCParticle</collectionName>
-            
-            <!-- Units of ns. -->
-            <readoutWindowBefore>32.0</readoutWindowBefore>
-            <readoutWindowAfter>32.0</readoutWindowAfter>
-            <persistent>false</persistent>
-        </driver>
-        
-        <driver name="TrackerHitsSVTOutputDriver" type="org.hps.readout.svt.SVTTrackerHitReadoutDriver">
-            <collectionName>TrackerHits</collectionName>
-            
-            <!-- Units of ns. -->
-            <readoutWindowBefore>8.0</readoutWindowBefore>
-            <readoutWindowAfter>32.0</readoutWindowAfter>
-            <persistent>false</persistent>
-        </driver>
-        
-        <driver name="InactiveTrackerHitsOutputDriver" type="org.hps.readout.SimTrackerHitReadoutDriver">
-            <collectionName>TrackerHits_Inactive</collectionName>
-           
-            <!-- Units of ns. -->
-            <readoutWindowBefore>8.0</readoutWindowBefore>
-            <readoutWindowAfter>32.0</readoutWindowAfter>
-            <persistent>false</persistent>
-        </driver>
-        
-        <driver name="TrackerHitsEcalOutputDriver" type="org.hps.readout.SimTrackerHitReadoutDriver">
-            <collectionName>TrackerHitsECal</collectionName>
-            
-            <!-- Units of ns. -->
-            <readoutWindowBefore>8.0</readoutWindowBefore>
-            <readoutWindowAfter>32.0</readoutWindowAfter>
-            <persistent>false</persistent>
-        </driver>
-        
-        
-        <!--
-            The SVT driver. Works just like before. Documentation is left to
-            the SVT group.
-        -->
-        <driver name="SVTReadoutDriver" type="org.hps.readout.svt.SVTReadoutDriver">
-            <enablePileupCut>false</enablePileupCut>
-            <useTimingConditions>true</useTimingConditions>
-            <addNoise>true</addNoise>
-        </driver>
-        
-        <!--
-             The calorimeter readout driver handles conversion of SLIC truth
-             hits into voltage pulses and ultimately into ADC counts every 4 ns
-             sample. These samples are then integrated and output as hits which
-             are used internally by the readout simulation in the collection
-             set by variable "outputHitCollectionName".
-             
-             When a trigger occurs, the ADC buffer is used to generate readout
-             hits. The exact form these take differs based on the mode that is
-             simulated, but they are always output to the collection defined by
-             variable "readoutHitCollectionName".
-             
-             If truth information is enabled, then a set of truth relations are
-             output as well that link each readout hit to all of the truth hits
-             that are associated with it. Additionally, all truth hits as well
-             as the particle (and its parents) that generated that truth hit
-             are written out to ensure that they are available post-readout.
-             The additional truth information is automatically written to the
-             same collection name as the input truth data. If a truth handler
-             driver also outputs data into this collection, the two will merge.
-          -->
-        <driver name="EcalDigitizationDriver" type="org.hps.readout.ecal.updated.EcalDigitizationReadoutDriver">
-            <!-- LCIO Collection Names -->
-            <inputHitCollectionName>EcalHits</inputHitCollectionName>
-            <outputHitCollectionName>EcalRawHits</outputHitCollectionName>
-            <readoutHitCollectionName>EcalReadoutHits</readoutHitCollectionName>
-            <truthRelationsCollectionName>EcalTruthRelations</truthRelationsCollectionName>
-            <triggerPathTruthRelationsCollectionName>TriggerPathTruthRelations</triggerPathTruthRelationsCollectionName>
-            
-            <!-- Driver Parameters -->
-            <mode>1</mode>                                  <!-- Allowed values: 1, 3, or 7. -->
-            <addNoise>true</addNoise>
-            <!-- 
-                 Readout offset is not the same as the old system - it measures
-                 amount of samples that are included before the trigger time in
-                 the ADC readout window. The old version can be converted by
-                 selecting a readout window equal to (readoutLatency - 64).
-              -->
-            <readoutOffset>13</readoutOffset>               <!-- Units of 4 ns clock-cycles. -->
-            <readoutWindow>50</readoutWindow>               <!-- Units of 4 ns clock-cycles. -->
-            <numberSamplesAfter>25</numberSamplesAfter>     <!-- Units of 4 ns clock-cycles. -->
-            <numberSamplesBefore>5</numberSamplesBefore>    <!-- Units of 4 ns clock-cycles. -->
-            <integrationThreshold>18</integrationThreshold> <!-- Units of ADC. -->
-            
-            <!--
-                The digitization driver produces as output a list of ADC values
-                within a specified window, in emulation of Mode-1 data. This
-                removes the truth information that is otherwise present in the
-                original SLiC output. Setting this option to true creates new
-                LCRelation objects that link the ADC list to the truth hits that
-                created it and stores this in readout. For production running,
-                this should generally be off to save space. Truth hits will be
-                included in readout automatically - the truth hit driver above
-                does not need to be persistent.
-            -->
-            <writeTruth>false</writeTruth>
-            
-            <!--
-                As above, except that truth relations are persisted for the
-                readout hits that are seen by the clusterer and trigger. This
-                is useful if some analysis needs to be performed at the readout
-                level. Otherwise, this should be left off.
-            -->
-            <writeTriggerPathTruth>false</writeTriggerPathTruth>
-        </driver>
-        
-        <!--
-             The raw converter handles the conversion of simulated ADC pulses from
-             the calorimeter readout driver into proper hits that can be used for
-             triggering.
-             
-             Note that it allows for these hits to be written to LCIO if desired,
-             though by default they are not persisted. This is generally unneeded,
-             since the clusterer will automatically output the hits which appear in
-             GTP clusters if cluster output is enabled.
-          -->
-        <driver name="EcalRawConverterDriver" type="org.hps.readout.ecal.updated.EcalRawConverterReadoutDriver">
-            <!--
-                NSA and NSB must match the digitization driver settings.
-            -->
-            <numberSamplesAfter>25</numberSamplesAfter>     <!-- Units of 4 ns clock-cycles. -->
-            <numberSamplesBefore>5</numberSamplesBefore>    <!-- Units of 4 ns clock-cycles. -->
-            
-            <!--
-                Outputs all the trigger-level hits within the readout window.
-                This is not generally necessary outside of specialized
-                circumstances. Note that all readout hits associated with GTP
-                clusters will automatically be included if GTP clusters are
-                persisted.
-            -->
-            <persistent>false</persistent>
-        </driver>
-        
-        <!--
-             The GTP clusterer creates clusters from converted calorimeter hits
-             for use in the trigger. It take two parametesr: the clustering
-             window, which specifies the number of clock-cycles in which a seed
-             hit candidate must be a spatiotemporal maximum, and seed energy
-             threshold, which specifies how much energy a seed hit candidate
-             must have in order to be used.
-             
-             The GTP clusterer is able to be persisted into LCIO. If persisted,
-             it will output all of the clusters in the readout window range
-             (either specified manually as with the truth drivers or using the
-             default readout window and trigger offset of the manager). It will
-             also output all of the hits contained in each cluster into the
-             output file as well.
-          -->
-        <driver name="GTPReadoutDriver" type="org.hps.readout.ecal.updated.GTPClusterReadoutDriver">
-            <!-- Units of 4 ns clock-cycles. -->
-            <clusterWindow>4</clusterWindow>
-            <!-- Units of GeV. -->
-            <seedEnergyThreshold>0.100</seedEnergyThreshold>
-            
-            <!--
-                Specifies whether GTP clusters should be persisted in the
-                output LCIO data. This should generally be false for production
-                running to save space, but can be useful for some analyses, as
-                the exact trigger-time clusters are not otherwise recoverable
-                after readout.
-            -->
-            <persistent>false</persistent>
-        </driver>
-        
-        <!--
-            The production pair trigger. This trigger allows the user to
-            specify the trigger deadtime (how much time must pass before a new
-            trigger can occur after a previous trigger has been created) and
-            the values of all the trigger cuts.
-        -->
-        <driver name="Pair1TriggerDriver" type="org.hps.readout.trigger.PairTriggerReadoutDriver">
-            <inputCollectionName>EcalClustersGTP</inputCollectionName>
-            
-            <!-- Units of 2 ns beam bunches. -->
-            <deadTime>15</deadTime>
-            
-            <!-- Units of GeV. -->
-            <seedEnergyLow>0.100</seedEnergyLow>
-            <!-- Units of cluster hits. -->
-            <minHitCount>2</minHitCount>
-            <!-- Units of 4 ns clock-cycles. -->
-            <pairCoincidence>3</pairCoincidence>
-            <!-- Units of GeV. -->
-            <clusterEnergyLow>0.150</clusterEnergyLow>
-            <!-- Units of GeV. -->
-            <clusterEnergyHigh>1.400</clusterEnergyHigh>
-            <!-- Units of GeV. -->
-            <energySumLow>0.600</energySumLow>
-            <!-- Units of GeV. -->
-            <energySumHigh>2.000</energySumHigh>
-            <!-- Units of GeV. -->
-            <energyDifferenceHigh>1.1</energyDifferenceHigh>
-            <!-- Units of degrees. -->
-            <coplanarityHigh>35</coplanarityHigh>
-            <!-- Units of GeV / mm. -->
-            <energySlopeParamF>0.0055</energySlopeParamF>
-            <!-- Units of GeV. -->
-            <energySlopeLow>0.700</energySlopeLow>
-        </driver>
-        
-        <driver name="ReadoutManagerDriver" type="org.hps.readout.ReadoutDataManager">
-            <readoutWindow>200</readoutWindow>
-            <outputFile>${outputFile}.slcio</outputFile>
-        </driver>
-        
-        <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver" />
-    </drivers>
-</lcsim>
+<?xml version="1.0" encoding="UTF-8"?>
+<lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
+    <execute>
+
+        <!-- overlay signal onto the beam events -->
+        <driver name="SignalOverlayDriver"/>
+
+        <!-- SLiC Data Readout Drivers -->
+        <driver name="EcalHitsOutputDriver"/>
+        <driver name="MCParticleOutputDriver"/>
+        <driver name="TrackerHitsSVTOutputDriver"/>
+        <driver name="TrackerHitsEcalOutputDriver"/>
+        
+        <!-- SVT Readout Drivers -->
+        <driver name="SVTReadoutDriver" />
+        <driver name="InactiveTrackerHitsOutputDriver"/>
+        
+        <!-- Readout Simulation Drivers -->
+        <driver name="EcalDigitizationDriver"/>
+        <driver name="EcalRawConverterDriver"/>
+        <driver name="GTPReadoutDriver"/>
+        <driver name="Pair1TriggerDriver"/>
+        
+        <!-- LCIO Output and Data Management Driver -->
+        <driver name="ReadoutManagerDriver"/>
+        
+        <driver name="CleanupDriver" />
+    </execute> 
+    
+    <drivers>
+
+        <driver name="SignalOverlayDriver" type="org.hps.readout.SignalOverlayDriver">
+            <eventSpacing>250</eventSpacing>
+            <ecalEnergyCut>0.04</ecalEnergyCut>
+<!--            <minHodoHits>1</minHodoHits> -->
+            <signalFile>${signalFile}</signalFile>
+        </driver>  
+
+        <!--
+             Truth handler drivers load truth information from the input SLIC file
+             and pass them off to the readout data manager, where they may be
+             accessed by other readout drivers.
+             
+             It is required that these drivers specify the name of the collection
+             that they manage, and be of the appropriate handler type that matches
+             the object type of the collection. They may also, optionally, specify
+             whether the truth collection managed by the driver should be output
+             into the readout file, and if so, over what time range.
+             
+             By default, SLIC truth data is not written out. If no output window is
+             specified, and truth is written, the output window will be derived
+             from the readout window and trigger offset parameters of the readout
+             data manager.
+             
+             In general, calorimeter truth information (and the related particles
+             data) are best handled by including truth readout in the calorimeter
+             simulation. This will automatically include all calorimeter truth hits
+             and related MC particles in the readout file.
+          -->
+        <driver name="EcalHitsOutputDriver" type="org.hps.readout.SimCalorimeterHitReadoutDriver">
+            <collectionName>EcalHits</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="MCParticleOutputDriver" type="org.hps.readout.MCParticleReadoutDriver">
+            <collectionName>MCParticle</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>32.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="TrackerHitsSVTOutputDriver" type="org.hps.readout.svt.SVTTrackerHitReadoutDriver">
+            <collectionName>TrackerHits</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="InactiveTrackerHitsOutputDriver" type="org.hps.readout.SimTrackerHitReadoutDriver">
+            <collectionName>TrackerHits_Inactive</collectionName>
+           
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        <driver name="TrackerHitsEcalOutputDriver" type="org.hps.readout.SimTrackerHitReadoutDriver">
+            <collectionName>TrackerHitsECal</collectionName>
+            
+            <!-- Units of ns. -->
+            <readoutWindowBefore>8.0</readoutWindowBefore>
+            <readoutWindowAfter>32.0</readoutWindowAfter>
+            <persistent>false</persistent>
+        </driver>
+        
+        
+        <!--
+            The SVT driver. Works just like before. Documentation is left to
+            the SVT group.
+        -->
+        <driver name="SVTReadoutDriver" type="org.hps.readout.svt.SVTReadoutDriver">
+            <enablePileupCut>false</enablePileupCut>
+            <useTimingConditions>true</useTimingConditions>
+            <addNoise>true</addNoise>
+        </driver>
+        
+        <!--
+             The calorimeter readout driver handles conversion of SLIC truth
+             hits into voltage pulses and ultimately into ADC counts every 4 ns
+             sample. These samples are then integrated and output as hits which
+             are used internally by the readout simulation in the collection
+             set by variable "outputHitCollectionName".
+             
+             When a trigger occurs, the ADC buffer is used to generate readout
+             hits. The exact form these take differs based on the mode that is
+             simulated, but they are always output to the collection defined by
+             variable "readoutHitCollectionName".
+             
+             If truth information is enabled, then a set of truth relations are
+             output as well that link each readout hit to all of the truth hits
+             that are associated with it. Additionally, all truth hits as well
+             as the particle (and its parents) that generated that truth hit
+             are written out to ensure that they are available post-readout.
+             The additional truth information is automatically written to the
+             same collection name as the input truth data. If a truth handler
+             driver also outputs data into this collection, the two will merge.
+          -->
+        <driver name="EcalDigitizationDriver" type="org.hps.readout.ecal.updated.EcalDigitizationReadoutDriver">
+            <!-- LCIO Collection Names -->
+            <inputHitCollectionName>EcalHits</inputHitCollectionName>
+            <outputHitCollectionName>EcalRawHits</outputHitCollectionName>
+            <readoutHitCollectionName>EcalReadoutHits</readoutHitCollectionName>
+            <truthRelationsCollectionName>EcalTruthRelations</truthRelationsCollectionName>
+            <triggerPathTruthRelationsCollectionName>TriggerPathTruthRelations</triggerPathTruthRelationsCollectionName>
+            
+            <!-- Driver Parameters -->
+            <mode>1</mode>                                  <!-- Allowed values: 1, 3, or 7. -->
+            <addNoise>true</addNoise>
+            <!-- 
+                 Readout offset is not the same as the old system - it measures
+                 amount of samples that are included before the trigger time in
+                 the ADC readout window. The old version can be converted by
+                 selecting a readout window equal to (readoutLatency - 64).
+              -->
+            <readoutOffset>13</readoutOffset>               <!-- Units of 4 ns clock-cycles. -->
+            <readoutWindow>50</readoutWindow>               <!-- Units of 4 ns clock-cycles. -->
+            <numberSamplesAfter>25</numberSamplesAfter>     <!-- Units of 4 ns clock-cycles. -->
+            <numberSamplesBefore>5</numberSamplesBefore>    <!-- Units of 4 ns clock-cycles. -->
+            <integrationThreshold>18</integrationThreshold> <!-- Units of ADC. -->
+            
+            <!--
+                The digitization driver produces as output a list of ADC values
+                within a specified window, in emulation of Mode-1 data. This
+                removes the truth information that is otherwise present in the
+                original SLiC output. Setting this option to true creates new
+                LCRelation objects that link the ADC list to the truth hits that
+                created it and stores this in readout. For production running,
+                this should generally be off to save space. Truth hits will be
+                included in readout automatically - the truth hit driver above
+                does not need to be persistent.
+            -->
+            <writeTruth>false</writeTruth>
+            
+            <!--
+                As above, except that truth relations are persisted for the
+                readout hits that are seen by the clusterer and trigger. This
+                is useful if some analysis needs to be performed at the readout
+                level. Otherwise, this should be left off.
+            -->
+            <writeTriggerPathTruth>false</writeTriggerPathTruth>
+        </driver>
+        
+        <!--
+             The raw converter handles the conversion of simulated ADC pulses from
+             the calorimeter readout driver into proper hits that can be used for
+             triggering.
+             
+             Note that it allows for these hits to be written to LCIO if desired,
+             though by default they are not persisted. This is generally unneeded,
+             since the clusterer will automatically output the hits which appear in
+             GTP clusters if cluster output is enabled.
+          -->
+        <driver name="EcalRawConverterDriver" type="org.hps.readout.ecal.updated.EcalRawConverterReadoutDriver">
+            <!--
+                NSA and NSB must match the digitization driver settings.
+            -->
+            <numberSamplesAfter>25</numberSamplesAfter>     <!-- Units of 4 ns clock-cycles. -->
+            <numberSamplesBefore>5</numberSamplesBefore>    <!-- Units of 4 ns clock-cycles. -->
+            
+            <!--
+                Outputs all the trigger-level hits within the readout window.
+                This is not generally necessary outside of specialized
+                circumstances. Note that all readout hits associated with GTP
+                clusters will automatically be included if GTP clusters are
+                persisted.
+            -->
+            <persistent>false</persistent>
+        </driver>
+        
+        <!--
+             The GTP clusterer creates clusters from converted calorimeter hits
+             for use in the trigger. It take two parametesr: the clustering
+             window, which specifies the number of clock-cycles in which a seed
+             hit candidate must be a spatiotemporal maximum, and seed energy
+             threshold, which specifies how much energy a seed hit candidate
+             must have in order to be used.
+             
+             The GTP clusterer is able to be persisted into LCIO. If persisted,
+             it will output all of the clusters in the readout window range
+             (either specified manually as with the truth drivers or using the
+             default readout window and trigger offset of the manager). It will
+             also output all of the hits contained in each cluster into the
+             output file as well.
+          -->
+        <driver name="GTPReadoutDriver" type="org.hps.readout.ecal.updated.GTPClusterReadoutDriver">
+            <!-- Units of 4 ns clock-cycles. -->
+            <clusterWindow>4</clusterWindow>
+            <!-- Units of GeV. -->
+            <seedEnergyThreshold>0.100</seedEnergyThreshold>
+            
+            <!--
+                Specifies whether GTP clusters should be persisted in the
+                output LCIO data. This should generally be false for production
+                running to save space, but can be useful for some analyses, as
+                the exact trigger-time clusters are not otherwise recoverable
+                after readout.
+            -->
+            <persistent>false</persistent>
+        </driver>
+        
+        <!--
+            The production pair trigger. This trigger allows the user to
+            specify the trigger deadtime (how much time must pass before a new
+            trigger can occur after a previous trigger has been created) and
+            the values of all the trigger cuts.
+        -->
+        <driver name="Pair1TriggerDriver" type="org.hps.readout.trigger.PairTriggerReadoutDriver">
+            <inputCollectionName>EcalClustersGTP</inputCollectionName>
+            
+            <!-- Units of 2 ns beam bunches. -->
+            <deadTime>15</deadTime>
+            
+            <!-- Units of GeV. -->
+            <seedEnergyLow>0.100</seedEnergyLow>
+            <!-- Units of cluster hits. -->
+            <minHitCount>2</minHitCount>
+            <!-- Units of 4 ns clock-cycles. -->
+            <pairCoincidence>3</pairCoincidence>
+            <!-- Units of GeV. -->
+            <clusterEnergyLow>0.150</clusterEnergyLow>
+            <!-- Units of GeV. -->
+            <clusterEnergyHigh>1.400</clusterEnergyHigh>
+            <!-- Units of GeV. -->
+            <energySumLow>0.600</energySumLow>
+            <!-- Units of GeV. -->
+            <energySumHigh>2.000</energySumHigh>
+            <!-- Units of GeV. -->
+            <energyDifferenceHigh>1.1</energyDifferenceHigh>
+            <!-- Units of degrees. -->
+            <coplanarityHigh>35</coplanarityHigh>
+            <!-- Units of GeV / mm. -->
+            <energySlopeParamF>0.0055</energySlopeParamF>
+            <!-- Units of GeV. -->
+            <energySlopeLow>0.700</energySlopeLow>
+        </driver>
+        
+        <driver name="ReadoutManagerDriver" type="org.hps.readout.ReadoutDataManager">
+            <readoutWindow>200</readoutWindow>
+            <outputFile>${outputFile}.slcio</outputFile>
+        </driver>
+        
+        <driver name="CleanupDriver" type="org.lcsim.recon.tracking.digitization.sisim.config.ReadoutCleanupDriver" />
+    </drivers>
+</lcsim>

From 832e44ec80bee166d8910ad4ea4535eb8b6fef0e Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Sun, 29 Nov 2020 18:25:53 -0600
Subject: [PATCH 09/11] Add method to read signal files from list in a text
 file

---
 .../org/hps/readout/SignalOverlayDriver.java  | 21 +++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
index 7f61781013..a5511b49ba 100644
--- a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
+++ b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
@@ -1,7 +1,9 @@
 package org.hps.readout;
 
+import java.io.BufferedReader;
 import java.io.EOFException;
 import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 import java.util.HashSet;
 import java.util.LinkedList;
@@ -24,7 +26,7 @@
 public class SignalOverlayDriver extends Driver {
 
     private static Logger LOGGER =
-            Logger.getLogger(SignalOverlayDriver.class.getPackageName());
+            Logger.getLogger(SignalOverlayDriver.class.getPackage().getName());
     private Queue<String> signalFileNames = new LinkedList<String>();
     private int eventSpacing = 250;
     private int sequence = 0;
@@ -100,6 +102,21 @@ public void setSignalFile(String signalFileName) {
         this.signalFileNames.add(signalFileName);
     }
 
+    public void setSignalFileList(String signalFileList) {
+        BufferedReader reader;
+        try {
+            reader = new BufferedReader(new FileReader(signalFileList));
+            String line = reader.readLine();
+            while (line != null) {
+                line = reader.readLine();
+                signalFileNames.add(line);
+            }
+            reader.close();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
     public void setEventSpacing(int eventSpacing) {
         if (eventSpacing <= 0) {
             throw new IllegalArgumentException("Bad value for event spacing: " + eventSpacing);
@@ -210,7 +227,7 @@ protected void process(EventHeader event) {
                 } else {
                     event.get(meta.getClass(), collName).addAll(list);
                 }
-                LOGGER.info("Added " + list.size() + " objects to collection: " + collName);
+                LOGGER.finer("Added " + list.size() + " objects to collection: " + collName);
             }
 
             ++nSignal;

From e49447af1b77ef8be7c63b298c81e9fca96fd42b Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Sun, 29 Nov 2020 18:26:45 -0600
Subject: [PATCH 10/11] Add example steering reading signal files from a list

---
 .../readout/SignalOverlayListExample.lcsim    | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayListExample.lcsim

diff --git a/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayListExample.lcsim b/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayListExample.lcsim
new file mode 100644
index 0000000000..7676309eb9
--- /dev/null
+++ b/steering-files/src/main/resources/org/hps/steering/readout/SignalOverlayListExample.lcsim
@@ -0,0 +1,29 @@
+<!--
+    Overlay signal file onto beam background
+
+    Beam file is specified using '-DbeamFile=beam.slcio'
+    and signal with '-DsignalFile=signal.slcio'
+-->
+
+<lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
+        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
+    <inputFiles>
+        <fileList>beam_files.txt</fileList>
+    </inputFiles>
+    <execute>
+        <driver name="SignalOverlayDriver"/>
+        <driver name="LCIOWriter"/>
+    </execute>
+    <drivers>
+        <driver name="SignalOverlayDriver" type="org.hps.readout.SignalOverlayDriver">
+            <eventSpacing>250</eventSpacing>
+            <ecalEnergyCut>0.04</ecalEnergyCut>
+            <!-- uncomment this for 2019 data to filter on number of Hodoscope hits -->
+            <!-- <minHodoHits>1</minHodoHits> -->
+            <signalFileList>signal_files.txt</signalFileList>
+        </driver>
+        <driver name="LCIOWriter" type="org.lcsim.util.loop.LCIODriver">
+            <outputFilePath>${outputFile}.slcio</outputFilePath>
+        </driver>
+    </drivers>
+</lcsim>

From 17f6a6859b3017bea63e7aa73386b9fc9a2158da Mon Sep 17 00:00:00 2001
From: Jeremy McCormick <jermccormick@gmail.com>
Date: Tue, 1 Dec 2020 13:39:09 -0600
Subject: [PATCH 11/11] Add ecal pair event filter

---
 .../org/hps/readout/SignalOverlayDriver.java  | 32 +++++++++++++++++--
 1 file changed, 29 insertions(+), 3 deletions(-)

diff --git a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
index a5511b49ba..e96c402128 100644
--- a/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
+++ b/ecal-readout-sim/src/main/java/org/hps/readout/SignalOverlayDriver.java
@@ -34,8 +34,8 @@ public class SignalOverlayDriver extends Driver {
     private int nSignal = 0;
     private String ecalHitCollection = "EcalHits";
     private String hodoHitCollection = "HodoscopeHits";
-
-    LCIOReader reader = null;
+    private LCIOReader reader = null;
+    private Set<EventFilter> eventFilters = new HashSet<EventFilter>();
 
     interface EventFilter {
         public boolean accept(EventHeader event);
@@ -76,7 +76,29 @@ public boolean accept(EventHeader event) {
         }
     }
 
-    private Set<EventFilter> eventFilters = new HashSet<EventFilter>();
+    class EcalPairFilter implements EventFilter {
+
+        double eCut;
+
+        public EcalPairFilter(double eCut) {
+            this.eCut = eCut;
+        }
+
+        @Override
+        public boolean accept(EventHeader event)  {
+            List<SimCalorimeterHit> ecalHits = event.get(SimCalorimeterHit.class,
+                    SignalOverlayDriver.this.ecalHitCollection);
+            double topE = 0, botE = 0;
+            for (SimCalorimeterHit hit : ecalHits) {
+                if (hit.getIdentifierFieldValue("iy") > 0) {
+                    topE += hit.getRawEnergy();
+                } else {
+                    botE += hit.getRawEnergy();
+                }
+            }
+            return (topE > eCut && botE > eCut);
+        }
+    }
 
     class EndOfDataException extends Exception {
         private static final long serialVersionUID = 1L;
@@ -98,6 +120,10 @@ public void setEcalHitCollection(String ecalHitCollection) {
         this.ecalHitCollection = ecalHitCollection;
     }
 
+    public void setEcalPairEnergyCut(double eCut) {
+        eventFilters.add(new EcalPairFilter(eCut));
+    }
+
     public void setSignalFile(String signalFileName) {
         this.signalFileNames.add(signalFileName);
     }