Merge pull request #599 from JeffersonLab/development

Go to master for new production release

build-coatjava.sh

@@ -73,6 +73,7 @@ mkdir -p coatjava/lib/services
 ### clean up any cache copies ###
 rm -rf ~/.m2/repository/org/hep/hipo
 rm -rf ~/.m2/repository/org/jlab
+cd common-tools/coat-lib; $mvn clean; cd -
 
 unset CLAS12DIR
 if [ $runUnitTests == "yes" ]; then

common-tools/clas-analysis/pom.xml

@@ -3,14 +3,14 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-analysis</artifactId>
-  <version>6.5.9-SNAPSHOT</version>
+  <version>6.5.11-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>6.5.9-SNAPSHOT</version>
+    <version>6.5.11-SNAPSHOT</version>
   </parent>
 
   <build>
@@ -30,31 +30,31 @@
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-physics</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency>
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-detector</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency>
 
     <dependency>

common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterFcup.java

@@ -1,7 +1,7 @@
 package org.jlab.analysis.eventmerger;
 import java.util.LinkedHashMap;
 import java.util.Map;
-import org.jlab.detector.decode.DaqScalersSequence;
+import org.jlab.detector.scalers.DaqScalersSequence;
 import org.jlab.jnp.hipo4.data.*;
 import org.jlab.jnp.hipo4.io.HipoReader;
 import org.jlab.jnp.utils.data.TextHistogram;

common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/FilterTrigger.java

@@ -1,5 +1,5 @@
 package org.jlab.analysis.eventmerger;
-import org.jlab.detector.decode.DaqScalersSequence;
+import org.jlab.detector.scalers.DaqScalersSequence;
 import org.jlab.jnp.hipo4.data.*;
 import org.jlab.jnp.hipo4.io.HipoReader;
 import org.jlab.jnp.utils.data.*;

common-tools/clas-analysis/src/main/java/org/jlab/analysis/eventmerger/RandomTriggerFilter.java

@@ -1,6 +1,6 @@
 package org.jlab.analysis.eventmerger;
 import java.util.List;
-import org.jlab.detector.decode.DaqScalersSequence;
+import org.jlab.detector.scalers.DaqScalersSequence;
 import org.jlab.jnp.hipo4.data.*;
 import org.jlab.jnp.hipo4.io.HipoReader;
 import org.jlab.jnp.hipo4.io.HipoWriterSorted;

common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/RebuildScalers.java

@@ -6,7 +6,8 @@
 import java.util.List;
 import org.jlab.detector.calib.utils.ConstantsManager;
 import org.jlab.detector.calib.utils.RCDBConstants;
-import org.jlab.detector.decode.DaqScalers;
+import org.jlab.detector.scalers.DaqScalers;
+import org.jlab.detector.helicity.HelicitySequenceManager;
 import org.jlab.jnp.hipo4.data.Bank;
 import org.jlab.jnp.hipo4.data.Event;
 import org.jlab.jnp.hipo4.io.HipoReader;
@@ -23,6 +24,7 @@
 public class RebuildScalers {
 
     static final String CCDB_FCUP_TABLE="/runcontrol/fcup";
+    static final String CCDB_SLM_TABLE="/runcontrol/slm";
 
     public static void main(String[] args) {
 
@@ -36,6 +38,8 @@ public static void main(String[] args) {
             System.exit(1);
         }
 
+        HelicitySequenceManager helSeq = new HelicitySequenceManager(8,inputList);
+
         HipoWriterSorted writer = new HipoWriterSorted();
         writer.getSchemaFactory().initFromDirectory(ClasUtilsFile.getResourceDir("COATJAVA", "etc/bankdefs/hipo4"));
         writer.setCompressionType(1);
@@ -44,54 +48,64 @@ public static void main(String[] args) {
         Event event = new Event();
         Bank rawScalerBank = new Bank(writer.getSchemaFactory().getSchema("RAW::scaler"));
         Bank runScalerBank = new Bank(writer.getSchemaFactory().getSchema("RUN::scaler"));
+        Bank helScalerBank = new Bank(writer.getSchemaFactory().getSchema("HEL::scaler"));
         Bank runConfigBank = new Bank(writer.getSchemaFactory().getSchema("RUN::config"));
 
         ConstantsManager conman = new ConstantsManager();
-        conman.init(Arrays.asList(new String[]{CCDB_FCUP_TABLE}));
+        conman.init(Arrays.asList(new String[]{CCDB_FCUP_TABLE,CCDB_SLM_TABLE}));
 
         for (String filename : inputList) {
 
             HipoReader reader = new HipoReader();
             reader.open(filename);
 
             RCDBConstants rcdb = null;
-            IndexedTable ccdb = null;
+            IndexedTable ccdb_fcup = null;
+            IndexedTable ccdb_slm = null;
 
             while (reader.hasNext()) {
 
                 // read the event and necessary banks:
                 reader.nextEvent(event);
                 event.read(runConfigBank);
                 event.read(runScalerBank);
+                event.read(helScalerBank);
                 event.read(rawScalerBank);
 
                 // this is the bank we're here to rebuild:
                 event.remove(runScalerBank.getSchema());
+                event.remove(helScalerBank.getSchema());
 
                 // get CCDB/RCDB constants:
                 if (runConfigBank.getInt("run",0) >= 100) {
-                    ccdb = conman.getConstants(runConfigBank.getInt("run",0),CCDB_FCUP_TABLE);
+                    ccdb_fcup = conman.getConstants(runConfigBank.getInt("run",0),CCDB_FCUP_TABLE);
+                    ccdb_slm = conman.getConstants(runConfigBank.getInt("run",0),CCDB_SLM_TABLE);
                     rcdb = conman.getRcdbConstants(runConfigBank.getInt("run",0));
                 }
 
                 // now rebuild the RUN::scaler bank: 
-                if (rcdb!=null && ccdb !=null && rawScalerBank.getRows()>0) {
+                if (rcdb!=null && ccdb_fcup !=null && rawScalerBank.getRows()>0) {
 
-                    // Run duration in seconds.  Nasty but works, until RCDB (uses java.sql.Time)
-                    // is changed to support full date and not just HH:MM:SS.  Meanwhile just
-                    // requires that runs last less than 24 hours.
-                    Date uet = new Date(runConfigBank.getInt("unixtime",0)*1000L);
+                    // Inputs for calculation run duration in seconds, since for
+                    // some run periods the DSC2 clock rolls over during a run.
                     Time rst = rcdb.getTime("run_start_time");
-                    final double s1 = rst.getSeconds()+60*rst.getMinutes()+60*60*rst.getHours();
-                    final double s2 = uet.getSeconds()+60*uet.getMinutes()+60*60*uet.getHours();
-                    final double seconds = s2<s1 ? s2+60*60*24-s1 : s2-s1;
-
-                    // modify RUN::scaler and put it back in the event:
-                    DaqScalers ds = DaqScalers.create(rawScalerBank, ccdb, seconds);
-                    runScalerBank.putFloat("fcupgated",0,ds.getBeamChargeGated());
-                    runScalerBank.putFloat("fcup",0,ds.getBeamCharge());
-                    runScalerBank.putFloat("livetime",0,ds.getLivetime());
+                    Date uet = new Date(runConfigBank.getInt("unixtime",0)*1000L);
+
+                    DaqScalers ds = DaqScalers.create(rawScalerBank, ccdb_fcup, ccdb_slm, rst, uet);
+                    runScalerBank = ds.createRunBank(writer.getSchemaFactory());
+                    helScalerBank = ds.createHelicityBank(writer.getSchemaFactory());
+
+                    // the scaler banks always are slightly after the helicity changes, so
+                    // assign the previous (delay-corrected) helicity state to this scaler reading:
+                    helScalerBank.putByte("helicity",0,helSeq.search(event,-1).value());
+                    if (helSeq.getHalfWavePlate(event))
+                        helScalerBank.putByte("helicityRaw",0,(byte)(-1*helSeq.search(event,-1).value()));
+                    else
+                        helScalerBank.putByte("helicityRaw",0,helSeq.search(event,-1).value());
+
+                    // put modified HEL/RUN::scaler back in the event:
                     event.write(runScalerBank);
+                    event.write(helScalerBank);
                 }
 
                 writer.addEvent(event, event.getEventTag());

common-tools/clas-analysis/src/main/java/org/jlab/analysis/postprocess/Tag1ToEvent.java

@@ -11,8 +11,8 @@
 
 import org.jlab.utils.system.ClasUtilsFile;
 
-import org.jlab.detector.decode.DaqScalers;
-import org.jlab.detector.decode.DaqScalersSequence;
+import org.jlab.detector.scalers.DaqScalers;
+import org.jlab.detector.scalers.DaqScalersSequence;
 
 import org.jlab.detector.helicity.HelicityBit;
 import org.jlab.detector.helicity.HelicitySequenceManager;
@@ -40,6 +40,7 @@ public static void main(String[] args) {
         OptionParser parser = new OptionParser("postprocess");
         parser.addOption("-q","0","do beam charge and livetime (0/1=false/true)");
         parser.addOption("-d","0","do delayed helicity (0/1=false/true)");
+        parser.addOption("-f","0","do global offline helicity flip (0/1=false/true)");
         parser.addRequired("-o","output.hipo");
         parser.parse(args);
 
@@ -57,13 +58,14 @@ public static void main(String[] args) {
         // helicity / beamcharge options:
         final boolean doHelicity = parser.getOption("-d").intValue() != 0;
         final boolean doBeamCharge = parser.getOption("-q").intValue() != 0;
+        final boolean doHelicityFlip = parser.getOption("-f").intValue() != 0;
         if (!doHelicity && !doBeamCharge) {
             parser.printUsage();
             System.err.println("\n >>>>> error : at least one of -q/-d must be specified\n");
             System.exit(1);
         }
 
-        HelicitySequenceManager helSeq = new HelicitySequenceManager(8,inputList);
+        HelicitySequenceManager helSeq = new HelicitySequenceManager(8,inputList,doHelicityFlip);
         DaqScalersSequence chargeSeq = DaqScalersSequence.readSequence(inputList);
 
         HipoWriterSorted writer = new HipoWriterSorted();
@@ -75,9 +77,9 @@ public static void main(String[] args) {
 
         // we're going to modify this bank:
         Bank recEventBank = new Bank(writer.getSchemaFactory().getSchema("REC::Event"));
-
-        // FIXME: we shouldn't need this bank, but just the event:
-        Bank runConfigBank = new Bank(writer.getSchemaFactory().getSchema("RUN::config"));
+        
+        // we're going to modify this bank if doHelicityFlip is set:
+        Bank helFlipBank = new Bank(writer.getSchemaFactory().getSchema("HEL::flip"));
 
         long badCharge = 0;
         long goodCharge = 0;
@@ -93,19 +95,26 @@ public static void main(String[] args) {
 
                 reader.nextEvent(event);
                 event.read(recEventBank);
+                event.read(helFlipBank);
+
                 event.remove(recEventBank.getSchema());
 
-                // FIXME:  we shouldn't need this bank, but just the event:
-                event.read(runConfigBank);
-                final long timestamp = runConfigBank.getLong("timestamp", 0);
+                if (doHelicityFlip && helFlipBank.getRows()>0) {
+                    event.remove(helFlipBank.getSchema());
+                    helFlipBank.setByte("helicity", 0, (byte)-helFlipBank.getByte("helicity",0));
+                    helFlipBank.setByte("helicityRaw", 0, (byte)-helFlipBank.getByte("helicityRaw",0));
+                    event.write(helFlipBank);
+                }
 
                 // do the lookups:
                 HelicityBit hb = helSeq.search(event);
-                DaqScalers ds = chargeSeq.get(timestamp);
+                DaqScalers ds = chargeSeq.get(event);
 
-                // write heliicty to REC::Event:
+                // count helicity good/bad;
                 if (Math.abs(hb.value())==1) goodHelicity++;
                 else badHelicity++;
+
+                // write heliicty to REC::Event:
                 if (doHelicity) {
                     recEventBank.putByte("helicity",0,hb.value());
                 }
@@ -115,8 +124,8 @@ public static void main(String[] args) {
                 else {
                     goodCharge++;
                     if (doBeamCharge) {
-                        recEventBank.putFloat("beamCharge",0,ds.getBeamChargeGated());
-                        recEventBank.putDouble("liveTime",0,ds.getLivetime());
+                        recEventBank.putFloat("beamCharge",0, (float) ds.dsc2.getBeamChargeGated());
+                        recEventBank.putDouble("liveTime",0,ds.dsc2.getLivetime());
                     }
                 }
 

common-tools/clas-detector/pom.xml

@@ -3,14 +3,14 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>org.jlab.clas</groupId>
   <artifactId>clas-detector</artifactId>
-  <version>6.5.9-SNAPSHOT</version>
+  <version>6.5.11-SNAPSHOT</version>
   <packaging>jar</packaging>
 
   <parent>
     <groupId>org.jlab.clas</groupId>
     <artifactId>clas12rec</artifactId>
     <relativePath>../../parent/pom.xml</relativePath>
-    <version>6.5.9-SNAPSHOT</version>
+    <version>6.5.11-SNAPSHOT</version>
   </parent>
 
   <build>
@@ -30,7 +30,7 @@
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-utils</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency>
 
     <dependency>
@@ -42,13 +42,13 @@
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-io</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency> 
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-geometry</artifactId>
-      <version>6.5.9-SNAPSHOT</version>
+      <version>6.5.11-SNAPSHOT</version>
     </dependency>
 
     <dependency>