simple truth efficiency calculator

bin/trutheff

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+. `dirname $0`/../libexec/env.sh
+
+export MALLOC_ARENA_MAX=1
+
+java -Xmx1536m -Xms1024m -XX:+UseSerialGC \
+    -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/services/*:$CLAS12DIR/lib/utils/*" \
+    org.jlab.analysis.efficiency.Truth \
+    $*

common-tools/clas-analysis/src/main/java/org/jlab/analysis/efficiency/Truth.java

@@ -0,0 +1,183 @@
+package org.jlab.analysis.efficiency;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.TreeMap;
+import org.jlab.jnp.hipo4.data.Bank;
+import org.jlab.jnp.hipo4.data.Event;
+import org.jlab.jnp.hipo4.data.Schema;
+import org.jlab.jnp.hipo4.data.SchemaFactory;
+import org.jlab.jnp.hipo4.io.HipoReader;
+import org.jlab.jnp.utils.json.JsonArray;
+import org.jlab.jnp.utils.json.JsonObject;
+import org.jlab.utils.options.OptionParser;
+
+/**
+ * Efficiency matrix calculator based solely on the MC::GenMatch truth-matching
+ * bank (which is purely hit-based), and a pid assignment match in MC::Particle
+ * and REC::Particle.
+ * 
+ * @author baltzell
+ */
+public class Truth {
+
+    static final int UDF = 0;
+    static final List<Integer> NEGATIVES = Arrays.asList(11, -211, -321, -2212);
+    static final List<Integer> POSITIVES = Arrays.asList(-11, 211, 321, 2212, 45);
+    static final List<Integer> NEUTRALS = Arrays.asList(22, 2112);
+    static List<Integer> PIDS;
+
+    Schema mcGenMatch;
+    Schema mcParticle;
+    Schema recParticle;
+    long[][] recTallies;
+    long[] mcTallies;
+
+    public static void main(String[] args) {
+        OptionParser o = new OptionParser("trutheff");
+        o.setRequiresInputList(true);
+        o.parse(args);
+        System.out.println(o.getInputList());
+        Truth t = new Truth(o.getInputList().get(0));
+        t.add(o.getInputList());
+        System.out.println(t.toTable());
+        System.out.println(t.toJson());
+    }
+
+    public Truth(SchemaFactory s) {
+        init(s);
+    }
+
+    public Truth(HipoReader r) {
+        init(r.getSchemaFactory());
+    }
+
+    public Truth(String filename) {
+        HipoReader r = new HipoReader();
+        r.open(filename);
+        init(r.getSchemaFactory());
+    }
+
+    private void init(SchemaFactory schema) {
+        PIDS = new ArrayList(NEGATIVES);
+        PIDS.addAll(POSITIVES);
+        PIDS.addAll(NEUTRALS);
+        PIDS.add(UDF);
+        mcTallies = new long[PIDS.size()];
+        recTallies = new long[PIDS.size()][PIDS.size()];
+        mcGenMatch = schema.getSchema("MC::GenMatch");
+        mcParticle = schema.getSchema("MC::Particle");
+        recParticle = schema.getSchema("REC::Particle");
+    }
+
+    /**
+     * Get one element of the efficiency matrix.
+     * @param truth true PID
+     * @param rec reconstructed PID
+     * @return probability
+     */
+    public float get(int truth, int rec) {
+        long sum = mcTallies[PIDS.indexOf(truth)];
+        return sum>0 ? ((float)recTallies[PIDS.indexOf(truth)][PIDS.indexOf(rec)])/sum : 0;
+    }
+
+    /**
+     * Add an event in the form of truth and reconstructed particle species.
+     * @param truth truth PID
+     * @param rec reconstructed PID
+     */
+    public void add(int truth, int rec) {
+        if (PIDS.contains(truth)) {
+            mcTallies[PIDS.indexOf(truth)]++;
+            if (!PIDS.contains(rec)) recTallies[PIDS.indexOf(truth)][UDF]++;
+            else recTallies[PIDS.indexOf(truth)][PIDS.indexOf(rec)]++;
+        }
+    }
+
+    /**
+     * Add a HIPO event.
+     * @param e 
+     */
+    public void add(Event e) {
+        Bank bm = new Bank(mcParticle);
+        Bank br = new Bank(recParticle);
+        e.read(bm);
+        e.read(br);
+        TreeMap<Short,Short> good = getMapping(e);
+        for (short row=0; row<bm.getRows(); ++row) {
+            if (!good.containsKey(row)) add(bm.getInt("pid",row), UDF);
+            else add(bm.getInt("pid",row), br.getInt("pid",good.get(row)));
+        }
+    }
+
+    /**
+     * Add input HIPO files by path.
+     * @param filenames
+     */
+    public void add(List<String> filenames) {
+        Event e = new Event();
+        for (String f : filenames) {
+            HipoReader r = new HipoReader();
+            r.open(f);
+            while (r.hasNext()) {
+                r.nextEvent(e);
+                add(e);
+            }
+        }
+    }
+
+    /**
+     * Truth-matching banks contain pointers to MC::Particle and REC::Particle,
+     * and here we cache that mapping to avoid nested loops.
+     */
+    private TreeMap getMapping(Event e) {
+        Bank b = new Bank(mcGenMatch);
+        e.read(b);
+        TreeMap<Short,Short> m = new TreeMap<>();
+        for (int row=0; row<b.getRows(); ++row)
+            m.put(b.getShort("mcindex", row), b.getShort("pindex",row));
+        return m;
+    }
+
+    /**
+     * Get efficiencies as a human-readable table.
+     * @return 
+     */
+    public String toTable() {
+        StringBuilder s = new StringBuilder();
+        s.append("      ");
+        for (int i=0; i<PIDS.size(); ++i) {
+            s.append(String.format("%7d",PIDS.get(i)));
+            if (PIDS.size()==i+1) s.append("\n");
+        }
+        for (int i=0; i<PIDS.size(); ++i) {
+            s.append(String.format("%6d",PIDS.get(i)));
+            for (int j=0; j<PIDS.size(); ++j) {
+                s.append(String.format("%7.4f",get(PIDS.get(i),PIDS.get(j))));
+                if (PIDS.size()==j+1) s.append("\n");
+            }
+        }
+        return s.toString();
+    }
+
+    /**
+     * Get efficiencies as a JSON object.
+     * @return 
+     */
+    public JsonObject toJson() {
+        JsonObject ret = new JsonObject();
+        JsonArray pids = new JsonArray();
+        JsonArray effs = new JsonArray();
+        for (int i=0; i<PIDS.size(); ++i) {
+            pids.add(PIDS.get(i));
+            JsonArray a = new JsonArray();
+            for (int j=0; j<PIDS.size(); ++j)
+                a.add(get(PIDS.get(i),PIDS.get(j)));
+            effs.add(a);
+        }
+        ret.add("pids", pids);
+        ret.add("effs", effs);
+        return ret;
+    }
+}

common-tools/clas-utils/src/main/java/org/jlab/utils/options/OptionParser.java

@@ -1,8 +1,3 @@
-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.jlab.utils.options;
 
 import java.util.ArrayList;
@@ -16,17 +11,15 @@
  */
 public class OptionParser {
 
-    private Map<String,OptionValue> optionsDescriptors = new TreeMap<String,OptionValue>();    
-    private Map<String,OptionValue>    requiredOptions = new TreeMap<String,OptionValue>();
-    private Map<String,OptionValue>      parsedOptions = new TreeMap<String,OptionValue>();
-    private List<String>               parsedInputList = new ArrayList<String>();
+    private Map<String,OptionValue> optionsDescriptors = new TreeMap<>();    
+    private Map<String,OptionValue>    requiredOptions = new TreeMap<>();
+    private Map<String,OptionValue>      parsedOptions = new TreeMap<>();
+    private List<String>               parsedInputList = new ArrayList<>();
     private String                             program = "undefined";
     private boolean                  requiresInputList = true;
     private String                  programDescription = "";
 
-    public OptionParser(){
-
-    }
+    public OptionParser(){}
 
     public OptionParser(String pname){
         this.program = pname;
@@ -130,7 +123,6 @@ public void parse(String[] args){
             System.exit(0);
         }
 
-//this.show(arguments);
         for(Map.Entry<String,OptionValue> entry : this.requiredOptions.entrySet()){
             boolean status = entry.getValue().parse(arguments);
             if(status==false) { 
@@ -153,7 +145,11 @@ public void parse(String[] args){
                 this.parsedInputList.add(item);
             }
         }
-        //this.show(arguments);
+
+        // FIXME:  seems like we should really be throwing a RuntimeException ...
+        if (this.requiresInputList && this.parsedInputList.isEmpty()) {
+            System.err.println(" \n*** ERROR *** Empty Input List.");
+        }
     }
 
     public List<String> getInputList(){
@@ -167,9 +163,7 @@ public static void main(String[] args){
         parser.addOption("-r", "10");
         parser.addOption("-t", "25.0");
         parser.addOption("-d", "35");
-
         parser.parse(options);
-
         parser.show();        
     }
 }

install-clara

@@ -59,7 +59,7 @@ function cleanup() {
 
 function build_clara {
     export CLARA_HOME=$1
-    git clone https://github.com/baltzell/clara-java
+    git clone https://code.jlab.org/hallb/clas12/clara-java
     cd clara-java
     git checkout java21
     ./gradlew && ./gradlew deploy

validation/advanced-tests/run-eb-tests.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 webDir=http://clasweb.jlab.org/clas12offline/distribution/coatjava/validation_files/eb
-webVersion=5.10-fid-r11
+webVersion=5.10-fid-tm-r11
 webDir=$webDir/$webVersion
 
 # coatjava must already be built at ../../coatjava/
@@ -40,11 +40,11 @@ do
 done
 
 # last argument is input file stub:
-webFileStub="${@: -1}"
+stub="${@: -1}"
 
 # sanity check on filestub name,
 # just to error with reasonable message before proceeding:
-case $webFileStub in
+case $stub in
     # electron in forward, hadron in forward:
     electronproton)
         ;;
@@ -79,7 +79,7 @@ case $webFileStub in
     electrondeuteronC)
         ;;
     *)
-      echo Invalid input evio file:  $webFileStub
+      echo Invalid input evio file:  $stub
       exit 1
 esac
 
@@ -122,28 +122,28 @@ then
     fi
 
     # download test files, if necessary:
-    wget -N --no-check-certificate $webDir/${webFileStub}.hipo
+    wget -N --no-check-certificate $webDir/${stub}.hipo
     if [ $? != 0 ] ; then echo "wget validation files failure" ; exit 1 ; fi
 
     # update the schema dictionary:  (no longer necessary now that recon-util does it)
-    #rm -f up_${webFileStub}.hipo
-    #../../coatjava/bin/hipo-utils -update -d ../../coatjava/etc/bankdefs/hipo4/ -o up_${webFileStub}.hipo ${webFileStub}.hipo
+    #rm -f up_${stub}.hipo
+    #../../coatjava/bin/hipo-utils -update -d ../../coatjava/etc/bankdefs/hipo4/ -o up_${stub}.hipo ${stub}.hipo
 
     # run reconstruction:
-    rm -f out_${webFileStub}.hipo
+    rm -f out_${stub}.hipo
     if [ $useClara -eq 0 ]
     then
         GEOMDBVAR=$geoDbVariation
         export GEOMDBVAR
-        ../../coatjava/bin/recon-util -i ${webFileStub}.hipo -o out_${webFileStub}.hipo -c 2
+        ../../coatjava/bin/recon-util -i ${stub}.hipo -o out_${stub}.hipo -c 2
     else
         echo "set inputDir $PWD/" > cook.clara
         echo "set outputDir $PWD/" >> cook.clara
         echo "set threads 7" >> cook.clara
         echo "set javaMemory 2" >> cook.clara
         echo "set session s_cook" >> cook.clara
         echo "set description d_cook" >> cook.clara
-        ls ${webFileStub}.hipo > files.list
+        ls ${stub}.hipo > files.list
         echo "set fileList $PWD/files.list" >> cook.clara
         echo "run local" >> cook.clara
         echo "exit" >> cook.clara
@@ -152,8 +152,10 @@ then
 fi
 
 # run Event Builder tests:
-java -DCLAS12DIR="$COAT" -Xmx1536m -Xms1024m -cp $classPath2 -DINPUTFILE=out_${webFileStub}.hipo org.junit.runner.JUnitCore eb.EBTwoTrackTest
+java -DCLAS12DIR="$COAT" -Xmx1536m -Xms1024m -cp $classPath2 -DINPUTFILE=out_${stub}.hipo org.junit.runner.JUnitCore eb.EBTwoTrackTest
 if [ $? != 0 ] ; then echo "EBTwoTrackTest unit test failure" ; exit 1 ; else echo "EBTwoTrackTest passed unit tests" ; fi
 
+$COAT/bin/trutheff ./out_${stub}.hipo
+
 exit 0