Examples with SMC dr.inference.smc.SMC used on opensource projects

Example 1 with SMC

use of dr.inference.smc.SMC in project beast-mcmc by beast-dev.

the class MCMCParser method parseSMC.

/**
 * Parse the SMC variant of MCMC.
 * @param xo the XML object
 * @return the SMC object
 * @throws XMLParseException an exception of there is an XML parse error
 */
private SMC parseSMC(String id, XMLObject xo) throws XMLParseException {
    List<StateLoaderSaver> particleStates = new ArrayList<StateLoaderSaver>();
    String particleFolder = System.getProperty("smc.particle_folder");
    File folder = new File(particleFolder);
    if (!folder.isDirectory()) {
        throw new XMLParseException("Specified particle folder is not a folder");
    }
    File[] particleFiles = folder.listFiles();
    if (particleFiles == null || particleFiles.length == 0) {
        throw new XMLParseException("Specified particle folder is empty");
    }
    for (final File particleFile : particleFiles) {
        if (particleFile.isFile() && particleFile.getName().endsWith(".part")) {
            final File saveFile = new File(particleFile.getAbsolutePath() + ".out");
            particleStates.add(Factory.INSTANCE.getStateLoaderSaver(particleFile, saveFile));
        }
    }
    if (particleStates.size() == 0) {
        throw new XMLParseException("No particle files were found in the folder");
    }
    SMC smc = new SMC(id, particleStates);
    long chainLength = xo.getLongIntegerAttribute(CHAIN_LENGTH);
    SMCOptions options = new SMCOptions(chainLength);
    OperatorSchedule opsched = (OperatorSchedule) xo.getChild(OperatorSchedule.class);
    Likelihood likelihood = (Likelihood) xo.getChild(Likelihood.class);
    likelihood.setUsed();
    ArrayList<Logger> loggers = new ArrayList<Logger>();
    for (int i = 0; i < xo.getChildCount(); i++) {
        Object child = xo.getChild(i);
        if (child instanceof Logger) {
            loggers.add((Logger) child);
        }
    }
    Logger[] loggerArray = new Logger[loggers.size()];
    loggers.toArray(loggerArray);
    java.util.logging.Logger.getLogger("dr.inference").info("\nCreating the SMC chain set:" + "\n  particles = " + particleStates.size() + "\n  chain length = " + options.getChainLength());
    smc.init(options, likelihood, opsched, loggerArray);
    return smc;
}