add recon-mutil

.github/workflows/ci.yml

@@ -227,12 +227,12 @@ jobs:
           tar xzf clara.tar.gz
           tar xzf coatjava.tar.gz
       - run: ls
-      - name: run test
-        run: ./bin/run-clara -y ./etc/services/rgd-clarode.yml -t 4 -n 500 -c ./clara -o ./tmp ./clas_018779.evio.00001
+      - name: run clara
+        run: ./coatjava/bin/run-clara -y ./etc/services/rgd-clarode.yml -t 4 -n 100 -c ./clara -o ./tmp ./clas_018779.evio.00001
+      - name: run mutil
+        run: ./coatjava/bin/recon-mutil -y ./etc/services/rgd-clarode.yml -t 4 -n 30 -o rec.hipo ./clas_018779.evio.00001
       - name: ls tmp
-        run: ls -lhtr tmp
-      - name: rename
-        run: mv -v tmp/rec_clas_018779.evio.00001.hipo rec.hipo
+        run: ls -lhtr . tmp
       - uses: actions/upload-artifact@v7
         with:
           name: test_clara_result

.gitlab-ci.yml

@@ -175,6 +175,14 @@ clara:
     - run-clara -v -c $CLARA_HOME -t 4 -y ./etc/services/rgd-clarode.yml -n 30 -o out $EVIOFILE
     - mv out/rec_$EVIOFILE.hipo claroded.hipo
 
+recon-mutil:
+  stage: test
+  needs: [build,download]
+  dependencies: [build,download]
+  script:
+    - tar -xzf coatjava.tar.gz
+    - recon-mutil -t 4 -y ./etc/services/rgd-clarode.yml -n 30 -o rec_$EVIOFILE.hipo $EVIOFILE
+
 profile:
   extends: .clon
   allow_failure: true

bin/recon-mutil

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+. `dirname $0`/../libexec/env.sh
+
+split_cli $@
+
+export MALLOC_ARENA_MAX=1
+
+java ${JAVA_OPTS-} -Xms10240m -XX:+UseParallelGC ${jvm_options[@]} \
+    -cp ${COATJAVA_CLASSPATH:-''} \
+    org.jlab.clas.reco.ReconMutil \
+    ${class_options[@]}

common-tools/clara-io/pom.xml

@@ -36,12 +36,6 @@
       <artifactId>jnp-hipo4</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>org.jlab.clas</groupId>
-      <artifactId>clas-io</artifactId>
-      <version>14.2.0-SNAPSHOT</version>
-    </dependency>
-
     <dependency>
       <groupId>org.jlab.clas</groupId>
       <artifactId>clas-detector</artifactId>
@@ -50,7 +44,7 @@
 
     <dependency>
       <groupId>org.jlab.clas</groupId>
-      <artifactId>clas-utils</artifactId>
+      <artifactId>clas-io</artifactId>
       <version>14.2.0-SNAPSHOT</version>
     </dependency> 
 

common-tools/clara-io/src/main/java/org/jlab/io/clara/Clas12Writer.java

@@ -1,22 +1,11 @@
 package org.jlab.io.clara;
 
-import java.io.File;
 import java.nio.file.Path;
-import java.util.List;
-import java.util.TreeMap;
-import java.util.TreeSet;
 import org.jlab.clara.std.services.EventWriterException;
 import org.jlab.detector.calib.utils.ConstantsManager;
-import org.jlab.detector.decode.CLASDecoder4;
-import org.jlab.detector.helicity.HelicitySequence;
-import org.jlab.detector.helicity.HelicitySequenceDelayed;
-import org.jlab.detector.helicity.HelicityState;
-import org.jlab.detector.scalers.DaqScalersSequence;
-import org.jlab.detector.serial.PostProcessor;
-import org.jlab.jnp.hipo4.data.Bank;
+import org.jlab.detector.serial.SerialHoncho;
 import org.jlab.jnp.hipo4.data.Event;
 import org.jlab.jnp.hipo4.data.SchemaFactory;
-import org.jlab.jnp.hipo4.io.HipoReader;
 import org.jlab.jnp.hipo4.io.HipoWriterSorted;
 import org.jlab.jnp.utils.file.FileUtils;
 import org.json.JSONObject;
@@ -26,41 +15,24 @@
  * 1. Copies certain banks on-the-fly to new tag-1 events
  * 2. Caches helicity states, scaler readouts, and unix time
  * 3. Writes HEL::flip, RUN/HEL::scaler, and RUN::unix to new tag-1 events
- * 4. Runs post-processing, writing tag-1 information to all events 
  * 5. Adds .hipo to the output filename, if necessary
  *
  * @author baltzell
  */
 public class Clas12Writer extends HipoToHipoWriter {
 
-    static final String[] TAG1BANKS = {"RUN::scaler","HEL::scaler","RAW::scaler","RAW::epics","HEL::flip","COAT::config"};
-
-    Bank[] tag1banks;
-    Bank runConfig;
-    Bank helicityAdc;
+    SerialHoncho serial;
     ConstantsManager conman;
-    TreeMap<Integer,Integer> eventUnix;
-    TreeSet<HelicityState> helicities;
-    DaqScalersSequence scalers;
     SchemaFactory fullSchema;
-    boolean postprocess;
 
     private void init(JSONObject opts) {
         fullSchema = new SchemaFactory();
         fullSchema.initFromDirectory(FileUtils.getEnvironmentPath("CLAS12DIR","etc/bankdefs/hipo4"));
-        runConfig = new Bank(fullSchema.getSchema("RUN::config"));
-        helicityAdc = new Bank(fullSchema.getSchema("HEL::adc"));
-        helicities = new TreeSet<>();
-        scalers = new DaqScalersSequence(fullSchema);
+        serial = new SerialHoncho(fullSchema);
         conman = new ConstantsManager();
-        eventUnix = new TreeMap<>();
         conman.init("/runcontrol/hwp","/runcontrol/helicity");
-        postprocess = opts.optBoolean("postprocess", false);
         if (opts.has("variation")) conman.setVariation(opts.getString("variation"));
         if (opts.has("timestamp")) conman.setTimeStamp(opts.getString("timestamp"));
-        tag1banks = new Bank[TAG1BANKS.length];
-        for (int i=0; i<tag1banks.length; ++i)
-            tag1banks[i] = new Bank(fullSchema.getSchema(TAG1BANKS[i]));
     }
 
     @Override
@@ -78,89 +50,15 @@ protected HipoWriterSorted createWriter(Path file, JSONObject opts) throws Event
 
     @Override
     protected void writeEvent(Object event) throws EventWriterException {
-        scalers.add((Event)event);
-        ((Event)event).read(runConfig);
-        ((Event)event).read(helicityAdc);
-        if (runConfig.getRows() > 0) {
-            int unix = runConfig.getInt("unixtime",0);
-            int evno = runConfig.getInt("event",0);
-            if (unix > 0 && evno > 0) eventUnix.put(evno, unix);
-        }
-        helicities.add(HelicityState.createFromFadcBank(helicityAdc, runConfig, conman));
-        Event t = CLASDecoder4.createTaggedEvent((Event)event, runConfig, tag1banks);
+        Event t = serial.read((Event)event);
         if (!t.isEmpty()) writer.addEvent(t, 1);
         super.writeEvent(event);
     }
 
     @Override
     protected void closeWriter() {
-        HelicitySequence.writeFlips(fullSchema, writer, helicities);
-        writer.addEvent(getUnixEvent(runConfig),1);
+        serial.finish(writer);
         super.closeWriter();
-        if (postprocess) postprocess();
-        // keep the latest helicity/scaler reading for the next file:
-        while (helicities.size() > 60) helicities.pollFirst();
-        scalers.clear(10);
-    }
-
-    /**
-     * Get the first valid run number from a RUN::config bank.
-     * @return run
-     */
-    private int getRunNumber() {
-        Event e = new Event();
-        HipoReader r = new HipoReader();
-        r.open(filename);
-        while (r.hasNext()) {
-            r.nextEvent(e);
-            e.read(runConfig);
-            if (runConfig.getRows()>0 && runConfig.getInt("run",0)>0)
-                return runConfig.getInt("run",0);
-        }
-        return 0;
+        serial.clear();
     }
-
-    /**
-     * Get a new event with a RUN::unix bank containing event-timestamp mapping,
-     * and the latest RUN::config bank.
-     * @param config
-     * @return 
-     */
-    private Event getUnixEvent(Bank config) {
-        Bank unix = new Bank(fullSchema.getSchema("RUN::unix"));
-        unix.setRows(eventUnix.size());
-        int row = 0;
-        for (int evno : eventUnix.keySet()) {
-            unix.putInt("event", row, evno);
-            unix.putInt("unixtime",row, eventUnix.get(evno));
-            row++;
-        }
-        Event e = new Event();
-        e.write(config);
-        e.write(unix);
-        return e;
-    }
-
-    /**
-     * Copy helicity/charge tag-1 information to all events.
-     */
-    private void postprocess() {
-        int d = conman.getConstants(getRunNumber(), "/runcontrol/helicity").getIntValue("delay",0,0,0);
-        HelicitySequenceDelayed helicity = new HelicitySequenceDelayed(d);
-        helicity.addStream(helicities);
-        PostProcessor p = new PostProcessor(List.of(filename), fullSchema, helicity, scalers);
-        HipoReader r = new HipoReader();
-        r.open(filename);
-        Event e = new Event();
-        writer.open("pp_"+filename);
-        while (r.hasNext()) {
-            r.nextEvent(e);
-            p.processEvent(e);
-            HipoToHipoWriter.writeEvent(writer, e, schemaBankList);
-        }
-        writer.close();
-        new File(filename).delete();
-        new File("pp_"+filename).renameTo(new File(filename));
-    }
-
 }

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

@@ -34,11 +34,11 @@ public CLASDecoderPool(int size, String variation, String timestamp) {
         }
     }
 
-    public CLASDecoder take() throws InterruptedException {
+    public CLASDecoder take() {
         return pool.poll();
     }
 
-    public void put(CLASDecoder decoder) throws InterruptedException {
+    public void put(CLASDecoder decoder) {
         pool.offer(decoder);
     }
 

common-tools/clas-detector/src/main/java/org/jlab/detector/serial/PostProcessor.java

@@ -231,6 +231,22 @@ public void processEvent(Event event) {
         }
     }
 
+    public void processFile(String input, String output) {
+        Event event = new Event();
+        HipoReader r = new HipoReader();
+        r.open(input);
+        HipoWriterSorted w = new HipoWriterSorted();
+        w.getSchemaFactory().initFromDirectory(ClasUtilsFile.getResourceDir("CLAS12DIR", "etc/bankdefs/hipo4"));
+        w.setCompressionType(2);
+        w.open(output);
+        while (r.hasNext()) {
+            r.nextEvent(event);
+            processEvent(event);
+            if (w != null) w.addEvent(event);
+        }
+        r.close();
+    }
+
     /**
      * The "postprocess" program.
      * @param args