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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/bash | ||
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| . `dirname $0`/../libexec/env.sh | ||
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| export MALLOC_ARENA_MAX=1 | ||
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| java -Xmx1536m -Xms1024m -XX:+UseSerialGC \ | ||
| -cp "$CLAS12DIR/lib/clas/*:$CLAS12DIR/lib/services/*:$CLAS12DIR/lib/utils/*" \ | ||
| 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; | ||
| 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; | ||
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| /** | ||
| * 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 { | ||
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| 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); | ||
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| List<Integer> validPids; | ||
| Schema mcGenMatch; | ||
| Schema mcParticle; | ||
| Schema recParticle; | ||
| long[][] recTallies; | ||
| long[] mcTallies; | ||
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| public static void main(String[] args) { | ||
| OptionParser o = new OptionParser("trutheff"); | ||
| o.setRequiresInputList(true); | ||
| o.parse(args); | ||
| Truth t = new Truth(o.getInputList().get(0)); | ||
| t.add(o.getInputList()); | ||
| System.out.println(t.toTable()); | ||
| System.out.println(t.toJson()); | ||
| } | ||
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| public Truth(SchemaFactory s) { | ||
| init(s); | ||
| } | ||
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| public Truth(HipoReader r) { | ||
| init(r.getSchemaFactory()); | ||
| } | ||
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| public Truth(String filename) { | ||
| HipoReader r = new HipoReader(); | ||
| r.open(filename); | ||
| init(r.getSchemaFactory()); | ||
| } | ||
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| private void init(SchemaFactory schema) { | ||
| validPids = new ArrayList(NEGATIVES); | ||
| validPids.addAll(POSITIVES); | ||
| validPids.addAll(NEUTRALS); | ||
| validPids.add(UDF); | ||
| mcTallies = new long[validPids.size()]; | ||
| recTallies = new long[validPids.size()][validPids.size()]; | ||
| mcGenMatch = schema.getSchema("MC::GenMatch"); | ||
| mcParticle = schema.getSchema("MC::Particle"); | ||
| recParticle = schema.getSchema("REC::Particle"); | ||
| } | ||
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| /** | ||
| * 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[validPids.indexOf(truth)]; | ||
| return sum>0 ? ((float)recTallies[validPids.indexOf(truth)][validPids.indexOf(rec)])/sum : 0; | ||
| } | ||
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| /** | ||
| * Add an event in the form of truth and reconstructed particle species. | ||
| * @param truth truth PID | ||
| * @param rec reconstructed PID | ||
| */ | ||
| public synchronized void add(int truth, int rec) { | ||
| final int t = validPids.indexOf(truth); | ||
| if (t < 0) return; | ||
| final int r = validPids.indexOf(rec); | ||
| mcTallies[t]++; | ||
| if (r < 0) recTallies[t][UDF]++; | ||
| else recTallies[t][r]++; | ||
| } | ||
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| /** | ||
| * 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))); | ||
| } | ||
| } | ||
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| /** | ||
| * 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); | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * 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; | ||
| } | ||
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| /** | ||
| * Get efficiencies as a human-readable table. | ||
| * @return | ||
| */ | ||
| public String toTable() { | ||
| StringBuilder s = new StringBuilder(); | ||
| s.append(" "); | ||
| for (int i=0; i<validPids.size(); ++i) { | ||
| s.append(String.format("%7d",validPids.get(i))); | ||
| if (validPids.size()==i+1) s.append("\n"); | ||
| } | ||
| for (int i=0; i<validPids.size(); ++i) { | ||
| s.append(String.format("%6d",validPids.get(i))); | ||
| for (int j=0; j<validPids.size(); ++j) { | ||
| s.append(String.format("%7.4f",get(validPids.get(i),validPids.get(j)))); | ||
| if (validPids.size()==j+1) s.append("\n"); | ||
| } | ||
| } | ||
| return s.toString(); | ||
| } | ||
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| /** | ||
| * Get efficiencies as a JSON object. | ||
| * @return | ||
| */ | ||
| public JsonObject toJson() { | ||
| JsonObject effs = new JsonObject(); | ||
| JsonArray pids = new JsonArray(); | ||
| for (int i=0; i<validPids.size(); ++i) { | ||
| pids.add(validPids.get(i)); | ||
| JsonArray a = new JsonArray(); | ||
| for (int j=0; j<validPids.size(); ++j) | ||
| a.add(get(validPids.get(i),validPids.get(j))); | ||
| effs.add(Integer.toString(validPids.get(i)),a); | ||
| } | ||
| JsonObject ret = new JsonObject(); | ||
| ret.add("pids", pids); | ||
| ret.add("effs", effs); | ||
| return ret; | ||
| } | ||
| } |
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