Merge branch 'development' into iss72-uRwell-newGeo

bin/hipo-json

@@ -0,0 +1,8 @@
+#!/bin/sh
+
+. `dirname $0`/env.sh 
+
+java -Xms1024m \
+    -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/plugins/*" \
+    org.jlab.utils.JsonUtils \
+    $*

bin/run-groovy

@@ -50,4 +50,4 @@ echo "*****************************************"
 echo " "
 echo " "
 export JAVA_OPTS="-Dsun.java2d.pmoffscreen=false -Djava.util.logging.config.file=$CLAS12DIR/etc/logging/debug.properties -Xms1024m -Xmx2048m -XX:+UseSerialGC"
-groovy -cp "$JYPATH" $*
+groovy -cp "$JYPATH" "$@"

bin/run-jshell

@@ -0,0 +1,50 @@
+#!/bin/sh
+
+. `dirname $0`/env.sh 
+
+export CLAS12DIR=`dirname $0`/..
+
+#--------------------------------------------------------------
+# Adding supporting COAT jar files
+for i in `ls -a $CLAS12DIR/lib/clas/*.jar`
+do  
+#echo "$i"
+if [ -z "${JYPATH}" ] ; then
+JYPATH="$i"
+else
+JYPATH=${JYPATH}:"$i"
+fi
+done 
+#--------------------------------------------------------------
+# Adding supporting plugins directory
+for i in `ls -a $CLAS12DIR/lib/services/*.jar`
+do
+if [ -z "${JYPATH}" ] ; then
+JYPATH="$i"
+else
+JYPATH=${JYPATH}:"$i"
+fi
+done
+#--------------------------------------------------------------
+# Adding supporting plugins directory
+#--------------------------------------------------------------
+# Done loading plugins
+#--------------------------------------------------------------
+# Adding supporting plugins directory 
+for i in `ls -a $CLAS12DIR/lib/utils/*.jar`
+do
+if [ -z "${JYPATH}" ] ; then
+JYPATH="$i"
+else
+JYPATH=${JYPATH}:"$i"
+fi
+done
+#-------------------------------------------------------------
+echo " "
+echo " "
+echo "*****************************************"
+echo "*    Running COAT-JAVA JShell Scripts   *" 
+echo "*****************************************"
+echo " "
+echo " "
+jshell --class-path "$JYPATH" "$@"

build-coatjava.sh

@@ -92,8 +92,8 @@ cp -r etc coatjava/
 which python3 >& /dev/null && python=python3 || python=python
 $python etc/bankdefs/util/bankSplit.py coatjava/etc/bankdefs/hipo4 || exit 1
 mkdir -p coatjava/lib/clas
-cp external-dependencies/JEventViewer-1.1.jar coatjava/lib/clas/
-cp external-dependencies/vecmath-1.3.1-2.jar coatjava/lib/clas/
+#cp external-dependencies/JEventViewer-1.1.jar coatjava/lib/clas/
+#cp external-dependencies/vecmath-1.3.1-2.jar coatjava/lib/clas/
 mkdir -p coatjava/lib/utils
 cp external-dependencies/jclara-4.3-SNAPSHOT.jar coatjava/lib/utils
 #cp external-dependencies/jaw-1.0.jar coatjava/lib/utils

common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/Dictionary.java

@@ -39,11 +39,18 @@ public void printDictionary() {
     }
 
     public void readDictionary(String fileName, TestMode mode, int wireBinning, int stripBinning, int sectorDependence) {
+        this.readDictionary(fileName, mode, wireBinning, stripBinning, sectorDependence, -1);
+    }
+
+    public void readDictionary(String fileName, TestMode mode, int wireBinning, int stripBinning, int sectorDependence, int maxRoads) {
 
         System.out.println("\nReading dictionary from file " + fileName);
+        System.out.println("\nMaximum number of roads set to: " + maxRoads);
         int nFull  = 0;
         int nDupli = 0;
 
+        if(maxRoads<0) maxRoads = Integer.MAX_VALUE;
+
         File fileDict = new File(fileName);
 
         try {
@@ -52,7 +59,7 @@ public void readDictionary(String fileName, TestMode mode, int wireBinning, int
             ProgressPrintout progress = new ProgressPrintout();
 
             String line = null;
-            while ((line = txtreader.readLine()) != null) {
+            while ((line = txtreader.readLine()) != null && maxRoads>nFull) {
 
                 Road road = new Road(line);
                 road.setBinning(wireBinning, stripBinning, sectorDependence);

common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/DictionaryValidator.java

@@ -183,9 +183,9 @@ public EmbeddedCanvasTabbed getCanvas() {
         return canvas;
     }
 
-    public void init(String filename, TestMode mode, int wireBin, int stripBin, int sectorDependence) {
+    public void init(String filename, TestMode mode, int wireBin, int stripBin, int sectorDependence, int maxRoads) {
         this.dictionary = new Dictionary();
-        this.dictionary.readDictionary(filename, mode, wireBin, stripBin, sectorDependence);
+        this.dictionary.readDictionary(filename, mode, wireBin, stripBin, sectorDependence, maxRoads);
         this.createHistos(mode, wireBin, stripBin, sectorDependence);
         this.plotRoads();
     }
@@ -313,14 +313,15 @@ public static void main(String[] args) {
         parser.addOption("-pid"      , "0", "select particle PID for new dictionary, 0: no selection,");
         parser.addOption("-charge"   , "0", "select particle charge for new dictionary, 0: no selection");
         parser.addOption("-wire"     , "1", "dc wire bin size in road finding");
-        parser.addOption("-strip"    , "2", "pcal strip bin size in road finding");
+        parser.addOption("-strip"    , "1", "pcal strip bin size in road finding");
         parser.addOption("-sector"   , "0", "sector dependent roads, 0=false, 1=true)");
         parser.addOption("-smear"    , "1", "smearing in wire/paddle/strip matching");
         parser.addOption("-mode"     , "0", "select test mode, " + TestMode.getOptionsString());
         parser.addOption("-threshold", "1", "select roads momentum threshold in GeV");
         parser.addOption("-vzmin"  , "-10", "minimum vz (cm)");
         parser.addOption("-vzmax"  ,  "10", "maximum vz (cm)");
         parser.addOption("-n"        ,"-1", "maximum number of events to process for validation");
+        parser.addOption("-r"        ,"-1", "maximum number of roads to use for validation");
         parser.parse(args);
 
         String dictionaryFileName = null;
@@ -362,6 +363,7 @@ public static void main(String[] args) {
             System.exit(1);
         }
         int maxEvents  = parser.getOption("-n").intValue();
+        int maxRoads   = parser.getOption("-r").intValue();
 
         double thrs    = parser.getOption("-threshold").doubleValue();
         double vzmin   = parser.getOption("-vzmin").doubleValue();
@@ -381,9 +383,10 @@ public static void main(String[] args) {
         System.out.println("Smearing for wire/paddle/strip matching set to: " + smear);
         System.out.println("Test mode set to:                               " + mode);
         System.out.println("Maximum number of events to process set to:     " + maxEvents);
+        System.out.println("Maximum number of roads to use set to:          " + maxRoads);
 
         DictionaryValidator validator = new DictionaryValidator();
-        validator.init(dictionaryFileName, mode, wireBin, stripBin, sector);                
+        validator.init(dictionaryFileName, mode, wireBin, stripBin, sector, maxRoads);                
     //        tm.printDictionary();
         validator.processFile(testFileName,wireBin,stripBin,sector,smear,mode,maxEvents,pid,charge,thrs, vzmin, vzmax);
         validator.plotHistos();

common-tools/clas-analysis/src/main/java/org/jlab/analysis/roads/Road.java

@@ -161,7 +161,7 @@ public static ArrayList<Road> getRoads(DataEvent event, int chargeSelect, int pi
                         }
                     }
                     road.setSector((byte) trackSector);
-                    if(road.getLayerHits(3)<3 || road.getSuperLayers()!=6) continue;
+    //                if(road.getSuperLayerHits(3)<3 || road.getSuperLayers()!=6) continue;
                     // now check other detectors
                      // check FTOF
                     if(recScintillator!=null) {
@@ -578,11 +578,11 @@ public byte getSector() {
         return (byte) sec;
     }
 
-    public int getLayerHits(int layer) {
+    public int getSuperLayerHits(int superlayer) {
         int n=0;
-        if(layer>0  && layer<=6) {
-            for(int isl=0; isl<6; isl++) {
-                if(this.dcWires[layer-1+isl*6]>0) n++;
+        if(superlayer>0  && superlayer<=6) {
+            for(int il=0; il<6; il++) {
+                if(this.dcWires[(superlayer-1)*6+il]>0) n++;
             }
         }
         return n;
@@ -606,7 +606,7 @@ public Particle getParticle() {
 
     public double getPhi() {
         double phi = Math.toDegrees(particle.phi());
-        if(sector==0)
+        if(this.getSector()==0)
             return (phi+360+30)%60-30;
         else
             return phi;
@@ -618,18 +618,20 @@ public ArrayList<Byte> getKey() {
 
     public ArrayList<Byte> getKey(TestMode mode) {
         ArrayList<Byte> road = new ArrayList<>();
+        for(int i=0; i<13; i++) {
+            road.add((byte) 0);
+        }
+
         for(int isl=0; isl<6; isl++) {
             for(int il=0; il<6; il++) {
                 int layer = isl*6+il+1;
                 if(this.dcWires[layer-1] != 0) {
-                    road.add(this.getWire(layer));
+                    road.set(isl, this.getWire(layer));
                     break;
                 }
             }
         }
-        for(int i=6; i<13; i++) {
-            road.add((byte) 0);
-        }
+
         if(mode.contains(TestMode.DCPCALU)) {
             road.set(8, this.getStrip(1));
             if(mode.contains(TestMode.DCFTOFPCALU)) {
@@ -684,12 +686,13 @@ public List<ArrayList<Byte>> getKeys(TestMode mode, int width) {
         }}}}}}}}}}}
         return keys;
     }
+
     public final boolean isValid() {
         return this.isValid(TestMode.DC);
     }
 
     public boolean isValid(TestMode mode) {
-        boolean value = this.getLayerHits(3)>=3 && this.getSuperLayers()==6;
+        boolean value = this.getSuperLayerHits(3)>=3 && this.getSuperLayers()==6;
         if(mode.contains(TestMode.DCPCALU)) {
             value = value && this.ecalStrips[0]>0;
             if(mode.contains(TestMode.DCFTOFPCALU)) {

common-tools/clas-io/src/main/java/org/jlab/utils/JsonUtils.java

@@ -6,10 +6,14 @@
 import java.io.OutputStreamWriter;
 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.io.HipoReader;
 import org.jlab.jnp.utils.json.JsonArray;
 import org.jlab.jnp.utils.json.JsonObject;
 import org.jlab.jnp.utils.json.JsonValue;
 import org.jlab.jnp.utils.json.PrettyPrint;
+import org.jlab.utils.options.OptionParser;
 import org.json.JSONObject;
 
 /**
@@ -49,6 +53,15 @@ public static void show(DataBank bank, String varName) {
         show(read(bank,varName));
     }
 
+    /**
+     *  Just print it to the screen, nicely.
+     * @param bank
+     * @param varName 
+     */
+    public static void show(Bank bank, String varName) {
+        show(read(bank,varName));
+    }
+
     /**
      * Convenience method to get a JsonObject from a bank.
      * @param bank bank to read
@@ -58,6 +71,14 @@ public static void show(DataBank bank, String varName) {
     public static JsonObject read(DataBank bank, String varName) {
         return JsonObject.readFrom(new String(bank.getByte(varName)));
     }
+
+    public static JsonObject read(Bank bank, String varName) {
+        byte[] x = new byte[bank.getRows()];
+        for (int i=0; i<bank.getRows(); ++i) {
+            x[i] = bank.getByte(varName,i);
+        }
+        return JsonObject.readFrom(new String(x));
+    }
 
     /**
      * This won't be useful once DataBank.setByte(String,byte[]) is implemented
@@ -239,5 +260,47 @@ public static DataBank extend(DataEvent event, String bankName, String varName,
         return extend(event, bankName, varName, Map2Json(extension));
     }
 
+    public static void main(String args[]) {
+        OptionParser parser = new OptionParser("hipo-json");
+        parser.addRequired("-b","bank name");
+        parser.addOption("-v", "json", "variable name");
+        parser.addOption("-i", "1", "ignore parsing errors");
+        parser.setRequiresInputList(true);
+        parser.parse(args);
+        final String bankName = parser.getOption("-b").stringValue();
+        final String varName = parser.getOption("-v").stringValue();
+        int nerrors = 0;
+        for (String filename : parser.getInputList()) {
+            Event event = new Event();     
+            HipoReader reader = new HipoReader();
+            reader.open(filename);
+            if (!reader.getSchemaFactory().hasSchema(bankName)) {
+                System.err.println("\nERROR:  Bank does not exist in file's schema:  "+bankName);
+                System.exit(1);
+            }
+            if (!reader.getSchemaFactory().getSchema(bankName).hasEntry(varName)) {
+                System.err.println("\nERROR:  Variable does not exist in file's schema:  "+bankName+"."+varName);
+                System.exit(1);
+            }
+            System.err.println(reader.getSchemaFactory().getSchema(bankName).getSchemaString());
+            Bank bank = reader.getSchemaFactory().getBank(bankName);
+            while (reader.hasNext()) {
+                reader.nextEvent(event);
+                if (event.hasBank(reader.getSchemaFactory().getSchema(bankName))) {
+                    event.read(bank);
+                    try {
+                        JsonUtils.show(bank,varName);
+                    }
+                    catch (org.jlab.jnp.utils.json.ParseException e) {
+                        if (++nerrors > 3 && parser.getOption("-i").intValue()!=0) {
+                            System.err.println("\nERROR:  Too many parsing errors.\nAre you sure your variable "+bankName+"."+varName+" is a byte array representing a JSON string?");
+                            System.exit(1);
+                        }    
+                    }
+                }
+            }
+            reader.close();
+        }
+    }
 
 }

reconstruction/cvt/src/main/java/org/jlab/rec/cvt/track/StraightTrack.java

@@ -191,6 +191,7 @@ public void findTrajectory() {
                     stVec.setTrkThetaAtSurface(ThetaTrackIntersPlane);
                     stVec.setTrkToModuleAngle(trkToMPlnAngl);
                     stVec.setCalcCentroidStrip(CalcCentroidStrip);
+                    stVec.setSurfaceDetector(DetectorType.BST.getDetectorId()); 
                     if(stateVecs.size()>0 
                             && stateVecs.get(stateVecs.size()-1).x()==stVec.x()
                             && stateVecs.get(stateVecs.size()-1).y()==stVec.y()
@@ -230,7 +231,8 @@ public void findTrajectory() {
                     stVec.setTrkThetaAtSurface(ThetaTrackIntersSurf);
                     stVec.setTrkToModuleAngle(trkToMPlnAngl);
                     stVec.setCalcCentroidStrip(CalcCentroidStrip); 
-                     if(stateVecs.size()>0 
+                    stVec.setSurfaceDetector(DetectorType.BMT.getDetectorId()); 
+                    if(stateVecs.size()>0 
                             && stateVecs.get(stateVecs.size()-1).x()==stVec.x()
                             && stateVecs.get(stateVecs.size()-1).y()==stVec.y()
                             && stateVecs.get(stateVecs.size()-1).z()==stVec.z()) {

reconstruction/cvt/src/main/java/org/jlab/rec/cvt/trajectory/TrajectoryFinder.java

@@ -120,6 +120,7 @@ public Trajectory findTrajectory(int id, Ray ray, ArrayList<Cross> candCrossList
                             continue;
                         }
 
+                        stVec.setSurfaceDetector(DetectorType.BST.getDetectorId());
                         Cluster clsOnTrk = null;
                         if (l % 2 == 0) {
                             clsOnTrk = c.getCluster1(); 
@@ -195,6 +196,7 @@ public Trajectory findTrajectory(int id, Ray ray, ArrayList<Cross> candCrossList
                             continue;
                         } 
 
+                        stVec.setSurfaceDetector(DetectorType.BMT.getDetectorId());
                         if (c.getType()==BMTType.C) { //C-detector measuring Z
                             //if(traj.isFinal) { // reset the cross only for final trajectory
 
@@ -226,9 +228,9 @@ public Trajectory findTrajectory(int id, Ray ray, ArrayList<Cross> candCrossList
         }
 
         //Collections.sort(stateVecs);
-
         stateVecs.sort(Comparator.comparing(StateVec::y));
-        for (int l = 0; l < stateVecs.size(); l++) {
+        for (int l = 0; l < stateVecs.size(); l++) { 
+            stateVecs.get(l).setSurfaceDetector(DetectorType.CVT.getDetectorId());
             stateVecs.get(l).setPlaneIdx(l);
         }
         traj.setTrajectory(stateVecs);