Merge branch 'development' into development

Author: mathieuouillon

etc/bankdefs/util/dumpBankIDs.rb .github/make_banks_readme.rbetc/bankdefs/util/dumpBankIDs.rb renamed to .github/make_banks_readme.rb

@@ -51,13 +51,8 @@
 # dump a table
 puts """# Bank Group and Item IDs
 
-This file was generated by
-```bash
-#{$0} #{ARGV.join ' '}
-```
-
-> [!IMPORTANT]
-> Please re-run this script if you modify any of the bank definitions.
+> [!NOTE]
+> Iguana banks, which are defined in the Iguana repository, use group number 30000.
 
 """
 

.github/make_banks_readme_precommit.sh

@@ -0,0 +1,2 @@
+#!/usr/bin/env sh
+.github/make_banks_readme.rb etc/bankdefs/hipo4 > etc/bankdefs/hipo4/README.md

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+repos:
+- repo: local
+  hooks:
+    - id: make_banks_readme
+      name: make banks readme
+      entry: .github/make_banks_readme_precommit.sh
+      language: script
+      pass_filenames: false

common-tools/clas-detector/src/main/java/org/jlab/detector/decode/CLASDecoder4.java

@@ -260,6 +260,7 @@ public Bank getDataBankWF(String name, DetectorType type) {
             b.putShort("component", i, (short) a.get(i).getDescriptor().getComponent());
             b.putByte("order", i, (byte) a.get(i).getDescriptor().getOrder());
             b.putLong("timestamp", i, a.get(i).getADCData(0).getTimeStamp());
+            b.putInt("time", i, (int)a.get(i).getADCData(0).getTime());
             DetectorDataDgtz.ADCData xxx = a.get(i).getADCData(0);
             for (int j=0; j<xxx.getPulseSize(); ++j)
                 b.putShort(String.format("s%d",j+1), i, xxx.getPulseValue(j));

common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/HipoExtractor.java

@@ -129,8 +129,10 @@ protected List<Pulse> getPulses(int n, IndexedTable it, DataBank wfBank) {
         for (int i=0; i<wfBank.rows(); ++i) {
             for (int j=0; j<n; ++j)
                 samples[j] = wfBank.getShort(String.format("s%d",j+1), i);
-            List<Pulse> p = it==null ? extract(null, i, samples) :
-                extract(it.getNamedEntry(getIndices(wfBank,i)), i, samples);
+	    long timestamp = wfBank.getLong("timestamp",i);
+	    int time = wfBank.getInt("time",i);
+            List<Pulse> p = it==null ? extract(null, i, timestamp, time, samples) :
+                extract(it.getNamedEntry(getIndices(wfBank,i)), i, timestamp, time, samples);
             if (p!=null && !p.isEmpty()) {
                 if (pulses == null) pulses = new ArrayList<>();
                 pulses.addAll(p);
@@ -147,8 +149,10 @@ protected List<Pulse> getPulses(int n, IndexedTable it, Bank wfBank) {
                 samples[j] = wfBank.getShort(String.format("s%d",j+1), i);
                 // FIXME:  Can speed this up (but looks like not for DataBank?):
                 //samples[j] = wfBank.getShort(String.format(5+j,j+1), i);
-            List p = it==null ? extract(null, i, samples) :
-                extract(it.getNamedEntry(getIndices(wfBank,i)), i, samples);
+	    int time = wfBank.getInt("time",i);
+	    long timestamp = wfBank.getLong("timestamp",i);
+            List p = it==null ? extract(null, i, timestamp, time, samples) :
+                extract(it.getNamedEntry(getIndices(wfBank,i)), i, timestamp, time, samples);
             if (p!=null && !p.isEmpty()) {
                 if (pulses == null) pulses = new ArrayList<>();
                 pulses.addAll(p);

common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/IExtractor.java

@@ -5,6 +5,6 @@
 
 public interface IExtractor <T> {
 
-    public List<T> extract(NamedEntry pars, int id, short... samples);
+    public List<T> extract(NamedEntry pars, int id, long par1, long par2, short... samples);
 
 }

common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode3.java

@@ -20,11 +20,13 @@ public class Mode3 extends HipoExtractor {
     /**
      * @param pars CCDB row
      * @param id link to row in source bank
+     * @param par1
+     * @param par2
      * @param samples ADC samples
      * @return extracted pulses 
      */
     @Override
-    public List<Pulse> extract(NamedEntry pars, int id, short... samples) {
+    public List<Pulse> extract(NamedEntry pars, int id, long par1, long par2, short... samples) {
 
         List<Pulse> pulses = null;
 

common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/Mode7.java

@@ -29,8 +29,8 @@ private static float calculateTime(int t0, float ped, short... samples) {
     }
 
     @Override
-    public List<Pulse> extract(NamedEntry pars, int id, short... samples) {
-        List<Pulse> pulses = super.extract(pars, id, samples);
+    public List<Pulse> extract(NamedEntry pars, int id, long par1, long par2, short... samples) {
+        List<Pulse> pulses = super.extract(pars, id, par1, par2, samples);
         for (Pulse p : pulses)
             p.time = calculateTime((int)p.time, p.pedestal, samples);
         return pulses;

common-tools/clas-detector/src/main/java/org/jlab/detector/pulse/ModeAHDC.java

@@ -5,11 +5,7 @@
 import org.jlab.io.base.DataBank;
 import org.jlab.io.base.DataEvent;
 import org.jlab.jnp.hipo4.data.Bank;
-import org.jlab.jnp.hipo4.data.Event;
-import org.jlab.jnp.hipo4.data.SchemaFactory;
 import org.jlab.utils.groups.IndexedTable;
-
-import net.jcip.annotations.GuardedBy;
 import org.jlab.utils.groups.NamedEntry;
 
 
@@ -32,7 +28,7 @@ public class ModeAHDC extends HipoExtractor  {
 	 * @param samples ADC samples
 	 */
 	@Override
-	public List<Pulse> extract(NamedEntry pars, int id, short... samples){
+	public List<Pulse> extract(NamedEntry pars, int id, long par1, long par2, short... samples){
 		// Settings parameters (they can be initialised by a CCDB)
 		float samplingTime = 44;
 		int sparseSample = 0;

common-tools/clas-tracking/src/main/java/org/jlab/clas/tracking/kalmanfilter/zReference/KFitter.java

@@ -708,7 +708,9 @@ private boolean filter(int k, boolean forward, double annealingFactor) {
             return false;
         }
     }
-
+    
+    // Since no vertex inforamtion, the starting point for path length is the final point at the last layer.
+    // After vertex information is obtained, transition for the starting point from the final point to vertex will be taken.
     private boolean filter(int k, boolean forward) {
         StateVec sVec = sv.transported(forward).get(k);
         org.jlab.clas.tracking.kalmanfilter.AMeasVecs.MeasVec mVec = mv.measurements.get(k);
@@ -857,7 +859,9 @@ public Matrix filterCovMat(double[] H, Matrix Ci, double V) {
     private void calcFinalChisq(int sector) {
         calcFinalChisq(sector, false);
     }
-    
+        
+    // Since no vertex inforamtion, the starting point for path length is the final point at the last layer.
+    // After vertex information is obtained, transition for the starting point from the final point to vertex will be taken.
     private void calcFinalChisq(int sector, boolean nofilter) {
         int k = svzLength - 1;
         this.chi2 = 0;
@@ -880,9 +884,9 @@ private void calcFinalChisq(int sector, boolean nofilter) {
             sv.transport(sector, k, 0, sVec, mv, this.getSwimmer(), forward);
 
             StateVec svc = sv.transported(forward).get(0);
-            path += svc.deltaPath;
+            path += (forward ? 1 : -1) * svc.deltaPath;
             svc.setPathLength(path);
-
+            
             double V0 = mv.measurements.get(0).surface.unc[0];
 
             Point3D point = new Point3D(svc.x, svc.y, mv.measurements.get(0).surface.measPoint.z());
@@ -922,7 +926,7 @@ private void calcFinalChisq(int sector, boolean nofilter) {
 
                 double h = mv.hDoca(point, mv.measurements.get(k1 + 1).surface.wireLine[0]);
                 svc = sv.transported(forward).get(k1 + 1);
-                path += svc.deltaPath;
+                path += (forward ? 1 : -1) * svc.deltaPath;
                 svc.setPathLength(path);
                 svc.setProjector(mv.measurements.get(k1 + 1).surface.wireLine[0].origin().x());
                 svc.setProjectorDoca(h);
@@ -975,7 +979,7 @@ private void calcFinalChisqDAF(int sector, boolean nofilter) {
             sv.transport(sector, k, 0, sVec, mv, this.getSwimmer(), forward);
 
             StateVec svc = sv.transported(forward).get(0);
-            path += svc.deltaPath;
+            path += (forward ? 1 : -1) * svc.deltaPath;
             svc.setPathLength(path);
 
             Point3D point = new Point3D(svc.x, svc.y, mv.measurements.get(0).surface.measPoint.z());
@@ -1047,7 +1051,7 @@ private void calcFinalChisqDAF(int sector, boolean nofilter) {
                 }
 
                 svc = sv.transported(forward).get(k1 + 1);
-                path += svc.deltaPath;
+                path += (forward ? 1 : -1) * svc.deltaPath;
                 svc.setPathLength(path);
 
                 point = new Point3D(sv.transported(forward).get(k1 + 1).x, sv.transported(forward).get(k1 + 1).y, mv.measurements.get(k1 + 1).surface.measPoint.z());
@@ -1116,6 +1120,10 @@ private void calcFinalChisqDAF(int sector, boolean nofilter) {
     public Matrix propagateToVtx(int sector, double Zf) {
         return sv.transport(sector, finalStateVec.k, Zf, finalStateVec, mv, this.getSwimmer());
     }
+    
+    public double getDeltaPathToVtx(int sector, double Zf) {
+        return sv.getDeltaPath(sector, finalStateVec.k, Zf, finalStateVec, mv, this.getSwimmer());
+    }
 
     //Todo: apply the common funciton to replace current function above
     @Override