org.apache.mahout.classifier.sequencelearning.hmm.ViterbiEvaluator.java Source code

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Here is the source code for org.apache.mahout.classifier.sequencelearning.hmm.ViterbiEvaluator.java

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/**
 * Licensed to the Apache Software Foundation (ASF) under one or more
 * contributor license agreements.  See the NOTICE file distributed with
 * this work for additional information regarding copyright ownership.
 * The ASF licenses this file to You under the Apache License, Version 2.0
 * (the "License"); you may not use this file except in compliance with
 * the License.  You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.apache.mahout.classifier.sequencelearning.hmm;

import java.io.DataInputStream;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.List;
import java.util.Scanner;

import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import com.google.common.io.Closeables;
import org.apache.commons.cli2.CommandLine;
import org.apache.commons.cli2.Group;
import org.apache.commons.cli2.Option;
import org.apache.commons.cli2.OptionException;
import org.apache.commons.cli2.builder.ArgumentBuilder;
import org.apache.commons.cli2.builder.DefaultOptionBuilder;
import org.apache.commons.cli2.builder.GroupBuilder;
import org.apache.commons.cli2.commandline.Parser;
import org.apache.mahout.common.CommandLineUtil;
import org.apache.mahout.common.commandline.DefaultOptionCreator;

/**
 * Command-line tool for Viterbi evaluating
 */
public final class ViterbiEvaluator {

    private ViterbiEvaluator() {
    }

    public static void main(String[] args) throws IOException {
        DefaultOptionBuilder optionBuilder = new DefaultOptionBuilder();
        ArgumentBuilder argumentBuilder = new ArgumentBuilder();

        Option inputOption = DefaultOptionCreator.inputOption().create();

        Option outputOption = DefaultOptionCreator.outputOption().create();

        Option modelOption = optionBuilder.withLongName("model").withDescription("Path to serialized HMM model")
                .withShortName("m")
                .withArgument(argumentBuilder.withMaximum(1).withMinimum(1).withName("path").create())
                .withRequired(true).create();

        Option likelihoodOption = optionBuilder.withLongName("likelihood")
                .withDescription("Compute likelihood of observed sequence").withShortName("l").withRequired(false)
                .create();

        Group optionGroup = new GroupBuilder().withOption(inputOption).withOption(outputOption)
                .withOption(modelOption).withOption(likelihoodOption).withName("Options").create();

        try {
            Parser parser = new Parser();
            parser.setGroup(optionGroup);
            CommandLine commandLine = parser.parse(args);

            String input = (String) commandLine.getValue(inputOption);
            String output = (String) commandLine.getValue(outputOption);

            String modelPath = (String) commandLine.getValue(modelOption);

            boolean computeLikelihood = commandLine.hasOption(likelihoodOption);

            //reading serialized HMM
            DataInputStream modelStream = new DataInputStream(new FileInputStream(modelPath));
            HmmModel model;
            try {
                model = LossyHmmSerializer.deserialize(modelStream);
            } finally {
                Closeables.close(modelStream, true);
            }

            //reading observations
            List<Integer> observations = Lists.newArrayList();
            Scanner scanner = new Scanner(new FileInputStream(input), "UTF-8");
            try {
                while (scanner.hasNextInt()) {
                    observations.add(scanner.nextInt());
                }
            } finally {
                scanner.close();
            }

            int[] observationsArray = new int[observations.size()];
            for (int i = 0; i < observations.size(); ++i) {
                observationsArray[i] = observations.get(i);
            }

            //decoding
            int[] hiddenStates = HmmEvaluator.decode(model, observationsArray, true);

            //writing output
            PrintWriter writer = new PrintWriter(
                    new OutputStreamWriter(new FileOutputStream(output), Charsets.UTF_8), true);
            try {
                for (int hiddenState : hiddenStates) {
                    writer.print(hiddenState);
                    writer.print(' ');
                }
            } finally {
                Closeables.close(writer, false);
            }

            if (computeLikelihood) {
                System.out.println("Likelihood: " + HmmEvaluator.modelLikelihood(model, observationsArray, true));
            }
        } catch (OptionException e) {
            CommandLineUtil.printHelp(optionGroup);
        }
    }
}