Author: [log in to unmask]
Date: Fri May 29 15:35:29 2015
New Revision: 3067
Log:
Add command line utility class for skimming EVIO events.
Added:
java/trunk/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java
Added: java/trunk/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java
=============================================================================
--- java/trunk/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java (added)
+++ java/trunk/record-util/src/main/java/org/hps/record/evio/EvioEventSkimmer.java Fri May 29 15:35:29 2015
@@ -0,0 +1,232 @@
+package org.hps.record.evio;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+import org.jlab.coda.jevio.EventWriter;
+import org.jlab.coda.jevio.EvioEvent;
+import org.jlab.coda.jevio.EvioReader;
+import org.lcsim.util.log.DefaultLogFormatter;
+import org.lcsim.util.log.LogUtil;
+
+/**
+ * Skim EVIO events into a new file based on a list of event numbers to include.
+ * <p>
+ * The EVIO event numbers come from the event ID bank, and not from calling
+ * <code>EvioEvent.getEventNumber()</code>. These never match, unfortunately!
+ *
+ * @author Jeremy McCormick
+ * @author Norman Graf
+ */
+public class EvioEventSkimmer {
+
+ /**
+ * Setup the logger.
+ */
+ private static Logger LOGGER = LogUtil.create(EvioEventSkimmer.class, new DefaultLogFormatter(), Level.CONFIG);
+
+ /**
+ * Define command line options.
+ */
+ private static Options OPTIONS = new Options();
+ static {
+ OPTIONS.addOption("s", "skim-file", true, "list of event numbers to include in skim (text file)");
+ OPTIONS.addOption("o", "output-file", true, "output EVIO file with skimmed events");
+ OPTIONS.addOption("e", "evio-list", true, "input EVIO files to process (text file)");
+ OPTIONS.addOption("L", "log-level", true, "set log level (Java conventions)");
+ OPTIONS.addOption("n", "max-events", true, "max number of events to read");
+ }
+
+ /**
+ * Run the skim from the command line.
+ *
+ * @param args the command line arguments (parsed using Apache CLI)
+ */
+ public static void main(String[] args) {
+
+ PosixParser parser = new PosixParser();
+
+ CommandLine commandLine = null;
+ try {
+ commandLine = parser.parse(OPTIONS, args);
+ } catch (ParseException e) {
+ throw new RuntimeException(e);
+ }
+
+ if (commandLine.hasOption("L")) {
+ Level newLevel = Level.parse(commandLine.getOptionValue("L"));
+ LOGGER.config("setting new log level to " + newLevel);
+ LOGGER.setLevel(newLevel);
+ }
+
+ // Get list of EVIO files to process.
+ String evioTxtFile = null;
+ if (commandLine.hasOption("e")) {
+ evioTxtFile = commandLine.getOptionValue("e");
+ } else {
+ throw new RuntimeException("missing -e argument");
+ }
+ List<String> evioFilePaths = getEvioFilePaths(evioTxtFile);
+
+ // Get the EVIO output file path.
+ String evioFileOutPath = null;
+ if (commandLine.hasOption("o")) {
+ evioFileOutPath = commandLine.getOptionValue("o");
+ if (new File(evioFileOutPath).exists()) {
+ throw new RuntimeException("output file already exists: " + evioFileOutPath);
+ }
+ } else {
+ throw new RuntimeException("misisng -o argument");
+ }
+ LOGGER.config("output will be written to " + evioFileOutPath);
+
+ // Get the max number of events to read.
+ int maxEvents = Integer.MAX_VALUE;
+ if (commandLine.hasOption("n")) {
+ maxEvents = Integer.parseInt(commandLine.getOptionValue("n"));
+ LOGGER.config("max events set to " + maxEvents);
+ }
+
+ // Get the list of events to include in the skim.
+ String skimFilePath = null;
+ if (commandLine.hasOption("s")) {
+ skimFilePath = commandLine.getOptionValue("s");
+ LOGGER.config("skim events will be read from " + skimFilePath);
+ } else {
+ throw new RuntimeException("missing -s argument with skim events");
+ }
+ Set<Integer> skimEvents = getSkimEvents(skimFilePath);
+ LOGGER.config("got " + skimEvents.size() + " event numbers for skim");
+
+ EventWriter writer = null;
+ EvioReader reader = null;
+ try {
+
+ // Open writer with EVIO output path.
+ writer = new EventWriter(evioFileOutPath, false);
+
+ int nEventsRead = 0;
+
+ // Loop over input files.
+ fileLoop: for (String evioFileInPath : evioFilePaths) {
+
+ LOGGER.info("opening " + evioFileInPath + " for reading");
+ reader = new EvioReader(evioFileInPath, false, true);
+
+ // Read all events and include in the skim if they are in the event list.
+ EvioEvent evioEvent = null;
+ while ((evioEvent = reader.parseNextEvent()) != null) {
+ LOGGER.finer("read EVIO event " + evioEvent.getEventNumber());
+
+ if (nEventsRead >= maxEvents) {
+ LOGGER.info("max events " + maxEvents + " was reached");
+ break fileLoop;
+ }
+
+ // Set event number from event ID bank.
+ EvioEventUtilities.setEventNumber(evioEvent);
+
+ LOGGER.finest("event number set to " + evioEvent.getEventNumber() + " from event ID");
+
+ if (skimEvents.contains(evioEvent.getEventNumber())) {
+ // Event is accepted.
+ LOGGER.info("including event " + evioEvent.getEventNumber() + " in skim");
+ writer.writeEvent(evioEvent);
+ LOGGER.finer("wrote " + writer.getEventsWritten() + " events so far");
+ } else {
+ // Event is rejected.
+ LOGGER.finer("event " + evioEvent.getEventNumber() + " rejected");
+ }
+ ++nEventsRead;
+ }
+
+ // Close reader.
+ LOGGER.info("closing reader");
+ reader.close();
+ }
+ } catch (Exception e) {
+ throw new RuntimeException(e);
+ } finally {
+ writer.close();
+ try {
+ reader.close();
+ } catch (IOException e) {
+ LOGGER.log(Level.SEVERE, e.getMessage(), e);
+ }
+ }
+
+ LOGGER.info("Done!");
+ }
+
+ /**
+ * Get the list of EVIO files to process from a text file list.
+ *
+ * @param txtFilePath the text file with EVIO file list
+ * @return a list of paths to EVIO files
+ */
+ static List<String> getEvioFilePaths(String txtFilePath) {
+ List<String> evioFilePaths = new ArrayList<String>();
+ BufferedReader br = null;
+ try {
+ br = new BufferedReader(new FileReader(txtFilePath));
+ String currentLine = null;
+ while ((currentLine = br.readLine()) != null) {
+ evioFilePaths.add(currentLine.trim());
+ }
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ } finally {
+ try {
+ br.close();
+ } catch (IOException e) {
+ LOGGER.log(Level.SEVERE, e.getMessage(), e);
+ }
+ }
+ return evioFilePaths;
+ }
+
+ /**
+ * Get a list of event numbers to include in the skim.
+ *
+ * @param txtFilePath text file with list of events to include (one per line)
+ * @return the list of event numbers to include
+ */
+ static Set<Integer> getSkimEvents(String txtFilePath) {
+ Set<Integer> skimEvents = new LinkedHashSet<Integer>();
+ BufferedReader br = null;
+ String currentLine = null;
+ try {
+ br = new BufferedReader(new FileReader(txtFilePath));
+ while ((currentLine = br.readLine()) != null) {
+ String fileName = currentLine.trim();
+ LOGGER.config("including " + fileName + " in EVIO input files");
+ Integer skimEvent = Integer.parseInt(fileName);
+ skimEvents.add(skimEvent);
+ }
+ } catch (IOException e) {
+ throw new RuntimeException(e);
+ } catch (NumberFormatException e) {
+ LOGGER.log(Level.SEVERE, "bad number format in skim list: " + currentLine);
+ throw new RuntimeException(e);
+ } finally {
+ try {
+ br.close();
+ } catch (IOException e) {
+ LOGGER.log(Level.SEVERE, e.getMessage(), e);
+ }
+ }
+ return skimEvents;
+ }
+}
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