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simple truth efficiency calculator (#396)
* update URL * truth efficiency matrix calculator * cleanup, add warning printout * rename, cleanup, add json * merge scripts * use an array * parallelize * cleanup * actually loop * now it works * use gemc files with truth-matching enabled * cleanup, run truth efficiency * bugfix * cleanup and bugfix * bugfix, now it works * avoid unnecessary lookups * more convenient JSON structure * cleanup for thread safety * make adding threadsafe
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‎bin/trutheff‎

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

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

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

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

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

‎install-clara‎

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function build_clara {
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export CLARA_HOME=$1
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git clone https://github.com/baltzell/clara-java
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git clone https://code.jlab.org/hallb/clas12/clara-java
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cd clara-java
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git checkout java21
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./gradlew && ./gradlew deploy

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

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#!/bin/bash
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webDir=http://clasweb.jlab.org/clas12offline/distribution/coatjava/validation_files/eb
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webVersion=5.10-fid-r11
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webVersion=5.10-fid-tm-r11
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webDir=$webDir/$webVersion
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# coatjava must already be built at ../../coatjava/
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done
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# last argument is input file stub:
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webFileStub="${@: -1}"
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stub="${@: -1}"
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# sanity check on filestub name,
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# just to error with reasonable message before proceeding:
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case $webFileStub in
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case $stub in
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# electron in forward, hadron in forward:
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electronproton)
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;;
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electrondeuteronC)
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;;
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*)
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echo Invalid input evio file: $webFileStub
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echo Invalid input evio file: $stub
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exit 1
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esac
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fi
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# download test files, if necessary:
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wget -N --no-check-certificate $webDir/${webFileStub}.hipo
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wget -N --no-check-certificate $webDir/${stub}.hipo
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if [ $? != 0 ] ; then echo "wget validation files failure" ; exit 1 ; fi
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# update the schema dictionary: (no longer necessary now that recon-util does it)
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#rm -f up_${webFileStub}.hipo
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#../../coatjava/bin/hipo-utils -update -d ../../coatjava/etc/bankdefs/hipo4/ -o up_${webFileStub}.hipo ${webFileStub}.hipo
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#rm -f up_${stub}.hipo
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#../../coatjava/bin/hipo-utils -update -d ../../coatjava/etc/bankdefs/hipo4/ -o up_${stub}.hipo ${stub}.hipo
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# run reconstruction:
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rm -f out_${webFileStub}.hipo
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rm -f out_${stub}.hipo
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if [ $useClara -eq 0 ]
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then
136136
GEOMDBVAR=$geoDbVariation
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export GEOMDBVAR
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../../coatjava/bin/recon-util -i ${webFileStub}.hipo -o out_${webFileStub}.hipo -c 2
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../../coatjava/bin/recon-util -i ${stub}.hipo -o out_${stub}.hipo -c 2
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else
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echo "set inputDir $PWD/" > cook.clara
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echo "set outputDir $PWD/" >> cook.clara
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echo "set threads 7" >> cook.clara
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echo "set javaMemory 2" >> cook.clara
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echo "set session s_cook" >> cook.clara
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echo "set description d_cook" >> cook.clara
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ls ${webFileStub}.hipo > files.list
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ls ${stub}.hipo > files.list
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echo "set fileList $PWD/files.list" >> cook.clara
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echo "run local" >> cook.clara
149149
echo "exit" >> cook.clara
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fi
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# run Event Builder tests:
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java -DCLAS12DIR="$COAT" -Xmx1536m -Xms1024m -cp $classPath2 -DINPUTFILE=out_${webFileStub}.hipo org.junit.runner.JUnitCore eb.EBTwoTrackTest
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java -DCLAS12DIR="$COAT" -Xmx1536m -Xms1024m -cp $classPath2 -DINPUTFILE=out_${stub}.hipo org.junit.runner.JUnitCore eb.EBTwoTrackTest
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if [ $? != 0 ] ; then echo "EBTwoTrackTest unit test failure" ; exit 1 ; else echo "EBTwoTrackTest passed unit tests" ; fi
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158+
$COAT/bin/trutheff ./out_${stub}.hipo
159+
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exit 0
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‎validation/advanced-tests/src/eb/scripts/gemc-all.sh‎

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