Merge branch 'master' of github.com:JeffersonLab/hps-java into saveRory

Getting things done.

.gitignore

@@ -51,3 +51,6 @@ target/
 
 # ignore user VS Code settings
 .vscode
+
+# ignore local user documentation
+html/

detector-data/detectors/HPS_Run2021Pass1_v4/README

@@ -0,0 +1,12 @@
+Start at HPS_Run2021Pass1_v1
+L6Ssp80
+L7Ssp140
+L7SsRwp2
+L6SsRwp1
+L7SsRwm1
+This gets the top slot side looking a lot better
+
+Now focusing on Top hole side
+L7ShTum130 gets a large number of hits on track and significant improve to neg track chi2 in top
+
+shift stereo sensor du in bottom to move x hits so x at ecal is shifted by 5 mm

detector-data/detectors/HPS_Run2021Pass1_v4/SamplingFractions/Ecal.properties

@@ -0,0 +1 @@
+samplingFraction: 1.0

detector-data/detectors/HPS_Run2021Pass1_v4/SamplingFractions/Hodoscope.properties

@@ -0,0 +1 @@
+samplingFraction: 1.0

detector-data/detectors/HPS_Run2021Pass1_v4/detector.properties

@@ -0,0 +1 @@
+name: HPS_Run2021Pass1_v4

detector-data/detectors/HPS_Run2021Pass1_v4_1pt92GeV/README

@@ -0,0 +1,12 @@
+Start at HPS_Run2021Pass1_v1
+L6Ssp80
+L7Ssp140
+L7SsRwp2
+L6SsRwp1
+L7SsRwm1
+This gets the top slot side looking a lot better
+
+Now focusing on Top hole side
+L7ShTum130 gets a large number of hits on track and significant improve to neg track chi2 in top
+
+shift stereo sensor du in bottom to move x hits so x at ecal is shifted by 5 mm

detector-data/detectors/HPS_Run2021Pass1_v4_1pt92GeV/SamplingFractions/Ecal.properties

@@ -0,0 +1 @@
+samplingFraction: 1.0

detector-data/detectors/HPS_Run2021Pass1_v4_1pt92GeV/SamplingFractions/Hodoscope.properties

@@ -0,0 +1 @@
+samplingFraction: 1.0

detector-data/detectors/HPS_Run2021Pass1_v4_1pt92GeV/detector.properties

@@ -0,0 +1 @@
+name: HPS_Run2021Pass1_v4_1pt92GeV

detector-data/detectors/HPS_Run2021Pass1_v5/README

@@ -0,0 +1,20 @@
+Start at HPS_Run2021Pass1_v1
+L6Ssp80
+L7Ssp140
+L7SsRwp2
+L6SsRwp1
+L7SsRwm1
+This gets the top slot side looking a lot better
+
+Now focusing on Top hole side
+L7ShTum130 gets a large number of hits on track and significant improve to neg track chi2 in top
+
+shift stereo sensor du in bottom to move x hits so x at ecal is shifted by 5 mm
+
+use physics run 14770 and do kf based momentum constraint freeing L5 and L6 top sensors in Tu and Rw
+
+use physics run 14770 and do kf based momentum constraint freeing L6 tu and L7 turw top slot sensors
+
+use fee skim of run 14770 and do kf based momentum constraint free L5 6 7 tu top slot sensors
+
+use fee skim of run 14770, remove layer 7 top hits, and do kf based momentum constraint free L5 6 tu top slot/hole sensors and L6 top slot rw

detector-data/detectors/HPS_Run2021Pass1_v5_1pt92GeV/README

@@ -0,0 +1,20 @@
+Start at HPS_Run2021Pass1_v1
+L6Ssp80
+L7Ssp140
+L7SsRwp2
+L6SsRwp1
+L7SsRwm1
+This gets the top slot side looking a lot better
+
+Now focusing on Top hole side
+L7ShTum130 gets a large number of hits on track and significant improve to neg track chi2 in top
+
+shift stereo sensor du in bottom to move x hits so x at ecal is shifted by 5 mm
+
+use physics run 14770 and do kf based momentum constraint freeing L5 and L6 top sensors in Tu and Rw
+
+use physics run 14770 and do kf based momentum constraint freeing L6 tu and L7 turw top slot sensors
+
+use fee skim of run 14770 and do kf based momentum constraint free L5 6 7 tu top slot sensors
+
+use fee skim of run 14770, remove layer 7 top hits, and do kf based momentum constraint free L5 6 tu top slot/hole sensors and L6 top slot rw

detector-data/detectors/HPS_Run2021Pass1_v5_1pt92GeV/SamplingFractions/Ecal.properties

@@ -0,0 +1 @@
+samplingFraction: 1.0

detector-data/detectors/HPS_Run2021Pass1_v5_1pt92GeV/SamplingFractions/Hodoscope.properties

@@ -0,0 +1 @@
+samplingFraction: 1.0

detector-data/detectors/HPS_Run2021Pass1_v5_1pt92GeV/detector.properties

@@ -0,0 +1 @@
+name: HPS_Run2021Pass1_v5_1pt92GeV

digi/src/main/java/org/hps/digi/DigitizationWithPulserDataMergingReadoutDriver.java

@@ -504,13 +504,7 @@ public void process(EventHeader event) {
                 // If noise should be added, calculate a random value for
                 // the noise and add it to the truth energy deposition.
                 if(addNoise) {
-                    // Calculate a randomized noise value.
-                    double noiseSigma = Math.sqrt(Math.pow(getNoiseConditions(hitCellID) * getGainConditions(hitCellID) * EcalUtils.MeV, 2)
-                            + hit.getRawEnergy() * EcalUtils.MeV / pePerMeV);
-                    double noise = RandomGaussian.getGaussian(0, noiseSigma);
-
-                    // Increment the truth energy deposition by this amount.
-                    energyAmplitude += noise;
+                    energyAmplitude += getAmplitudeFluctuation(hit);
                 }
 
                 // Simulate the pulse for each position in the preamp
@@ -531,6 +525,13 @@ public void process(EventHeader event) {
                     // a value of maxVolt.
                     double currentValue = voltageBuffer.getValue(i) * ((Math.pow(2, nBit) - 1) / maxVolt);
 
+                    // If noise should be added, calculate a random value for
+                    // the noise and add it to the ADC value. 
+                    if(addNoise) {
+                        double sigma = getNoiseConditions(hitCellID);
+                        currentValue += RandomGaussian.getGaussian(0, sigma);
+                    }
+
                     // An ADC value is not allowed to exceed 4095. If a
                     // larger value is observed, 4096 (overflow) is given
                     // instead. (This corresponds to >2 Volts.)
@@ -1026,6 +1027,16 @@ private static final void addDaughtersToSet(MCParticle particle, Set<MCParticle>
      */
     protected abstract int getTimestampFlag();
 
+    /**
+     * Generate photoelectron/amplification noise for a pulse's amplitude.
+     * @param hit - The hit for which to generate a fluctuation.
+     * @return Returns a fluctuation in units GeV. 
+     */
+    protected double getAmplitudeFluctuation(CalorimeterHit hit) {
+        double sigma = Math.sqrt(hit.getRawEnergy() * EcalUtils.MeV / pePerMeV);
+        return RandomGaussian.getGaussian(0, sigma);
+    }
+
     @Override
     protected Collection<TriggeredLCIOData<?>> getOnTriggerData(double triggerTime) {
         // Create a list to store the extra collections.

digi/src/main/java/org/hps/digi/EcalDigitizationWithPulserDataMergingReadoutDriver.java

@@ -8,6 +8,7 @@
 import org.hps.conditions.ecal.EcalChannelConstants;
 import org.hps.conditions.ecal.EcalConditions;
 import org.hps.readout.ReadoutTimestamp;
+import org.hps.recon.ecal.EcalUtils;
 import org.lcsim.event.RawTrackerHit;
 import org.lcsim.geometry.Detector;
 import org.lcsim.geometry.subdetector.HPSEcal3;
@@ -50,7 +51,7 @@ public EcalDigitizationWithPulserDataMergingReadoutDriver() {
         setTriggerPathTruthRelationsCollectionName("TriggerPathTruthRelations");
         setReadoutHitCollectionName("EcalReadoutHits");
 
-        setPhotoelectronsPerMeV(32.8);
+        setPhotoelectronsPerMeV(EcalUtils.photoelectronsPerMeV);
         setPulseTimeParameter(9.6);
     }
 
@@ -81,7 +82,6 @@ public void actionPerformed(ActionEvent e) {
                     // Get the FADC configuration.
                     config = daq.getEcalFADCConfig();
                     configStat = true;
-                    integrationThreshold = config.getThreshold((int)10);
                 }
             });
         }

digi/src/main/java/org/hps/digi/HodoscopeDigitizationWithPulserDataMergingReadoutDriver.java

@@ -77,6 +77,8 @@ public HodoscopeDigitizationWithPulserDataMergingReadoutDriver() {
         setNumberSamplesBefore(6);
         setPulseTimeParameter(4.0);
         setPhotoelectronsPerMeV(10.0);
+
+        setIntegrationThreshold(12);
     }
 
     /**
@@ -106,7 +108,6 @@ public void actionPerformed(ActionEvent e) {
                     // Get the FADC configuration.
                     config = daq.getHodoFADCConfig();
                     configStat = true;
-                    integrationThreshold = config.getThreshold((int)10);
                 }
             });
         }

ecal-readout-sim/src/main/java/org/hps/readout/DigitizationReadoutDriver.java

@@ -354,7 +354,7 @@ public void detectorChanged(Detector detector) {
         // Reinstantiate the buffers.
         resetBuffers();
     }
-    
+
     @Override
     public void process(EventHeader event) {                  
         /*
@@ -390,15 +390,10 @@ public void process(EventHeader event) {
 
             // If noise should be added, calculate a random value for
             // the noise and add it to the truth energy deposition.
+
             if(addNoise) {
-                // Calculate a randomized noise value.
-                double noiseSigma = Math.sqrt(Math.pow(getNoiseConditions(hit.getCellID()) * getGainConditions(hit.getCellID()) * EcalUtils.MeV, 2)
-                        + hit.getRawEnergy() * EcalUtils.MeV / pePerMeV);
-                double noise = RandomGaussian.getGaussian(0, noiseSigma);
-
-                // Increment the truth energy deposition by this amount.
-                energyAmplitude += noise;
-            }
+                energyAmplitude += getAmplitudeFluctuation(hit);
+            }            
 
             // Check to see if the hit time seems valid. This is done
             // by calculating the time of the next readout cycle in
@@ -414,11 +409,12 @@ public void process(EventHeader event) {
             // pulse buffer for the subdetector channel on which the
             // hit occurred.
             for(int i = 0; i < BUFFER_LENGTH; i++) {
+
                 // Calculate the voltage deposition for the current
                 // buffer time.
                 double voltageDeposition = energyAmplitude * pulseAmplitude((i + 1) * READOUT_PERIOD + readoutTime()
                         - (ReadoutDataManager.getCurrentTime() + hit.getTime()) - getTimeShiftConditions(hit.getCellID()), hit.getCellID());
-                
+
                 // Increase the current buffer time's voltage value
                 // by the calculated amount.
                 voltageBuffer.addToCell(i, voltageDeposition);
@@ -464,9 +460,16 @@ private void readHits(List<RawCalorimeterHit> newHits, List<LCRelation> newTruth
             // a value of maxVolt.
             double currentValue = voltageBuffer.getValue() * ((Math.pow(2, nBit) - 1) / maxVolt);
 
-            // Get the pedestal for the channel.
-            int pedestal = (int) Math.round(getPedestalConditions(cellID));            
+            // If noise should be added, calculate a random value for
+            // the noise and add it to the ADC value. 
+            if(addNoise) {
+                double sigma = getNoiseConditions(cellID);
+                currentValue += RandomGaussian.getGaussian(0, sigma);
+            }
 
+            // Get the pedestal for the channel.
+            int pedestal = (int) Math.round(getPedestalConditions(cellID));   
+
             // An ADC value is not allowed to exceed 4095. If a
             // larger value is observed, 4096 (overflow) is given
             // instead. (This corresponds to >2 Volts.)
@@ -847,16 +850,16 @@ private static final void addDaughtersToSet(MCParticle particle, Set<MCParticle>
     /**
      * Gets the gain for the indicated subdetector channel.
      * @param channelID - The channel ID.
-     * @return Returns the value of the gain in units of ADC/MeV as a
+     * @return Returns the value of the gain in units of MeV/ADC as a
      * <code>double</code>.
      */
     protected abstract double getGainConditions(long channelID);
 
     /**
      * Gets the noise sigma for the indicated subdetector channel.
      * @param channelID - The channel ID.
-     * @return Returns the value of the noise sigma as a
-     * <code>double</code>.
+     * @return Returns the value of the noise sigma in units of ADC for one
+     * 4-ns sample as a <code>double</code>.
      */
     protected abstract double getNoiseConditions(long channelID);
 
@@ -866,7 +869,17 @@ private static final void addDaughtersToSet(MCParticle particle, Set<MCParticle>
      * @return Returns the timestamp flag as an <code>int</code>.
      */
     protected abstract int getTimestampFlag();
-
+
+    /**
+     * Generate photoelectron/amplification noise for a pulse's amplitude.
+     * @param hit - The hit for which to generate a fluctuation.
+     * @return Returns a fluctuation in units GeV. 
+     */
+    protected double getAmplitudeFluctuation(CalorimeterHit hit) {
+        double sigma = Math.sqrt(hit.getRawEnergy() * EcalUtils.MeV / pePerMeV);
+        return RandomGaussian.getGaussian(0, sigma);
+    }
+
     @Override
     protected Collection<TriggeredLCIOData<?>> getOnTriggerData(double triggerTime) {
         // Create a list to store the extra collections.

ecal-readout-sim/src/main/java/org/hps/readout/ecal/FADCEcalReadoutDriver.java

@@ -73,7 +73,7 @@ public class FADCEcalReadoutDriver extends EcalReadoutDriver<RawCalorimeterHit>
     private double fixedGain = -1;
     private boolean constantTriggerWindow = true;
     private boolean addNoise = true;
-    private double pePerMeV = 32.8;
+    private double pePerMeV = EcalUtils.photoelectronsPerMeV;
     private boolean use2014Gain = false;
     private PulseShape pulseShape = PulseShape.ThreePole;