org.apache.mahout.clustering.canopy.CanopyDriver Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of mahout-mr Show documentation
Show all versions of mahout-mr Show documentation
Scalable machine learning libraries
/**
* 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.clustering.canopy;
import java.io.IOException;
import java.util.Collection;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.hadoop.util.ToolRunner;
import org.apache.mahout.clustering.AbstractCluster;
import org.apache.mahout.clustering.Cluster;
import org.apache.mahout.clustering.classify.ClusterClassificationDriver;
import org.apache.mahout.clustering.classify.ClusterClassifier;
import org.apache.mahout.clustering.iterator.CanopyClusteringPolicy;
import org.apache.mahout.clustering.iterator.ClusterWritable;
import org.apache.mahout.clustering.topdown.PathDirectory;
import org.apache.mahout.common.AbstractJob;
import org.apache.mahout.common.ClassUtils;
import org.apache.mahout.common.HadoopUtil;
import org.apache.mahout.common.commandline.DefaultOptionCreator;
import org.apache.mahout.common.distance.DistanceMeasure;
import org.apache.mahout.common.iterator.sequencefile.PathFilters;
import org.apache.mahout.common.iterator.sequencefile.PathType;
import org.apache.mahout.common.iterator.sequencefile.SequenceFileDirValueIterable;
import org.apache.mahout.math.VectorWritable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.collect.Lists;
import com.google.common.io.Closeables;
@Deprecated
public class CanopyDriver extends AbstractJob {
public static final String DEFAULT_CLUSTERED_POINTS_DIRECTORY = "clusteredPoints";
private static final Logger log = LoggerFactory.getLogger(CanopyDriver.class);
public static void main(String[] args) throws Exception {
ToolRunner.run(new Configuration(), new CanopyDriver(), args);
}
@Override
public int run(String[] args) throws Exception {
addInputOption();
addOutputOption();
addOption(DefaultOptionCreator.distanceMeasureOption().create());
addOption(DefaultOptionCreator.t1Option().create());
addOption(DefaultOptionCreator.t2Option().create());
addOption(DefaultOptionCreator.t3Option().create());
addOption(DefaultOptionCreator.t4Option().create());
addOption(DefaultOptionCreator.clusterFilterOption().create());
addOption(DefaultOptionCreator.overwriteOption().create());
addOption(DefaultOptionCreator.clusteringOption().create());
addOption(DefaultOptionCreator.methodOption().create());
addOption(DefaultOptionCreator.outlierThresholdOption().create());
if (parseArguments(args) == null) {
return -1;
}
Path input = getInputPath();
Path output = getOutputPath();
Configuration conf = getConf();
if (hasOption(DefaultOptionCreator.OVERWRITE_OPTION)) {
HadoopUtil.delete(conf, output);
}
String measureClass = getOption(DefaultOptionCreator.DISTANCE_MEASURE_OPTION);
double t1 = Double.parseDouble(getOption(DefaultOptionCreator.T1_OPTION));
double t2 = Double.parseDouble(getOption(DefaultOptionCreator.T2_OPTION));
double t3 = t1;
if (hasOption(DefaultOptionCreator.T3_OPTION)) {
t3 = Double.parseDouble(getOption(DefaultOptionCreator.T3_OPTION));
}
double t4 = t2;
if (hasOption(DefaultOptionCreator.T4_OPTION)) {
t4 = Double.parseDouble(getOption(DefaultOptionCreator.T4_OPTION));
}
int clusterFilter = 0;
if (hasOption(DefaultOptionCreator.CLUSTER_FILTER_OPTION)) {
clusterFilter = Integer
.parseInt(getOption(DefaultOptionCreator.CLUSTER_FILTER_OPTION));
}
boolean runClustering = hasOption(DefaultOptionCreator.CLUSTERING_OPTION);
boolean runSequential = getOption(DefaultOptionCreator.METHOD_OPTION)
.equalsIgnoreCase(DefaultOptionCreator.SEQUENTIAL_METHOD);
DistanceMeasure measure = ClassUtils.instantiateAs(measureClass, DistanceMeasure.class);
double clusterClassificationThreshold = 0.0;
if (hasOption(DefaultOptionCreator.OUTLIER_THRESHOLD)) {
clusterClassificationThreshold = Double.parseDouble(getOption(DefaultOptionCreator.OUTLIER_THRESHOLD));
}
run(conf, input, output, measure, t1, t2, t3, t4, clusterFilter,
runClustering, clusterClassificationThreshold, runSequential);
return 0;
}
/**
* Build a directory of Canopy clusters from the input arguments and, if
* requested, cluster the input vectors using these clusters
*
* @param conf
* the Configuration
* @param input
* the Path to the directory containing input vectors
* @param output
* the Path for all output directories
* @param measure
* the DistanceMeasure
* @param t1
* the double T1 distance metric
* @param t2
* the double T2 distance metric
* @param t3
* the reducer's double T1 distance metric
* @param t4
* the reducer's double T2 distance metric
* @param clusterFilter
* the minimum canopy size output by the mappers
* @param runClustering
* cluster the input vectors if true
* @param clusterClassificationThreshold
* vectors having pdf below this value will not be clustered. Its value should be between 0 and 1.
* @param runSequential
* execute sequentially if true
*/
public static void run(Configuration conf, Path input, Path output,
DistanceMeasure measure, double t1, double t2, double t3, double t4,
int clusterFilter, boolean runClustering, double clusterClassificationThreshold, boolean runSequential)
throws IOException, InterruptedException, ClassNotFoundException {
Path clustersOut = buildClusters(conf, input, output, measure, t1, t2, t3,
t4, clusterFilter, runSequential);
if (runClustering) {
clusterData(conf, input, clustersOut, output, clusterClassificationThreshold, runSequential);
}
}
/**
* Convenience method to provide backward compatibility
*/
public static void run(Configuration conf, Path input, Path output,
DistanceMeasure measure, double t1, double t2, boolean runClustering,
double clusterClassificationThreshold, boolean runSequential) throws IOException, InterruptedException,
ClassNotFoundException {
run(conf, input, output, measure, t1, t2, t1, t2, 0, runClustering,
clusterClassificationThreshold, runSequential);
}
/**
* Convenience method creates new Configuration() Build a directory of Canopy
* clusters from the input arguments and, if requested, cluster the input
* vectors using these clusters
*
* @param input
* the Path to the directory containing input vectors
* @param output
* the Path for all output directories
* @param t1
* the double T1 distance metric
* @param t2
* the double T2 distance metric
* @param runClustering
* cluster the input vectors if true
* @param clusterClassificationThreshold
* vectors having pdf below this value will not be clustered. Its value should be between 0 and 1.
* @param runSequential
* execute sequentially if true
*/
public static void run(Path input, Path output, DistanceMeasure measure,
double t1, double t2, boolean runClustering, double clusterClassificationThreshold, boolean runSequential)
throws IOException, InterruptedException, ClassNotFoundException {
run(new Configuration(), input, output, measure, t1, t2, runClustering,
clusterClassificationThreshold, runSequential);
}
/**
* Convenience method for backwards compatibility
*
*/
public static Path buildClusters(Configuration conf, Path input, Path output,
DistanceMeasure measure, double t1, double t2, int clusterFilter,
boolean runSequential) throws IOException, InterruptedException,
ClassNotFoundException {
return buildClusters(conf, input, output, measure, t1, t2, t1, t2,
clusterFilter, runSequential);
}
/**
* Build a directory of Canopy clusters from the input vectors and other
* arguments. Run sequential or mapreduce execution as requested
*
* @param conf
* the Configuration to use
* @param input
* the Path to the directory containing input vectors
* @param output
* the Path for all output directories
* @param measure
* the DistanceMeasure
* @param t1
* the double T1 distance metric
* @param t2
* the double T2 distance metric
* @param t3
* the reducer's double T1 distance metric
* @param t4
* the reducer's double T2 distance metric
* @param clusterFilter
* the int minimum size of canopies produced
* @param runSequential
* a boolean indicates to run the sequential (reference) algorithm
* @return the canopy output directory Path
*/
public static Path buildClusters(Configuration conf, Path input, Path output,
DistanceMeasure measure, double t1, double t2, double t3, double t4,
int clusterFilter, boolean runSequential) throws IOException,
InterruptedException, ClassNotFoundException {
log.info("Build Clusters Input: {} Out: {} Measure: {} t1: {} t2: {}",
input, output, measure, t1, t2);
if (runSequential) {
return buildClustersSeq(input, output, measure, t1, t2, clusterFilter);
} else {
return buildClustersMR(conf, input, output, measure, t1, t2, t3, t4,
clusterFilter);
}
}
/**
* Build a directory of Canopy clusters from the input vectors and other
* arguments. Run sequential execution
*
* @param input
* the Path to the directory containing input vectors
* @param output
* the Path for all output directories
* @param measure
* the DistanceMeasure
* @param t1
* the double T1 distance metric
* @param t2
* the double T2 distance metric
* @param clusterFilter
* the int minimum size of canopies produced
* @return the canopy output directory Path
*/
private static Path buildClustersSeq(Path input, Path output,
DistanceMeasure measure, double t1, double t2, int clusterFilter)
throws IOException {
CanopyClusterer clusterer = new CanopyClusterer(measure, t1, t2);
Collection canopies = Lists.newArrayList();
Configuration conf = new Configuration();
FileSystem fs = FileSystem.get(input.toUri(), conf);
for (VectorWritable vw : new SequenceFileDirValueIterable(
input, PathType.LIST, PathFilters.logsCRCFilter(), conf)) {
clusterer.addPointToCanopies(vw.get(), canopies);
}
Path canopyOutputDir = new Path(output, Cluster.CLUSTERS_DIR + '0' + Cluster.FINAL_ITERATION_SUFFIX);
Path path = new Path(canopyOutputDir, "part-r-00000");
SequenceFile.Writer writer = new SequenceFile.Writer(fs, conf, path,
Text.class, ClusterWritable.class);
try {
ClusterWritable clusterWritable = new ClusterWritable();
for (Canopy canopy : canopies) {
canopy.computeParameters();
if (log.isDebugEnabled()) {
log.debug("Writing Canopy:{} center:{} numPoints:{} radius:{}",
canopy.getIdentifier(),
AbstractCluster.formatVector(canopy.getCenter(), null),
canopy.getNumObservations(),
AbstractCluster.formatVector(canopy.getRadius(), null));
}
if (canopy.getNumObservations() > clusterFilter) {
clusterWritable.setValue(canopy);
writer.append(new Text(canopy.getIdentifier()), clusterWritable);
}
}
} finally {
Closeables.close(writer, false);
}
return canopyOutputDir;
}
/**
* Build a directory of Canopy clusters from the input vectors and other
* arguments. Run mapreduce execution
*
* @param conf
* the Configuration
* @param input
* the Path to the directory containing input vectors
* @param output
* the Path for all output directories
* @param measure
* the DistanceMeasure
* @param t1
* the double T1 distance metric
* @param t2
* the double T2 distance metric
* @param t3
* the reducer's double T1 distance metric
* @param t4
* the reducer's double T2 distance metric
* @param clusterFilter
* the int minimum size of canopies produced
* @return the canopy output directory Path
*/
private static Path buildClustersMR(Configuration conf, Path input,
Path output, DistanceMeasure measure, double t1, double t2, double t3,
double t4, int clusterFilter) throws IOException, InterruptedException,
ClassNotFoundException {
conf.set(CanopyConfigKeys.DISTANCE_MEASURE_KEY, measure.getClass()
.getName());
conf.set(CanopyConfigKeys.T1_KEY, String.valueOf(t1));
conf.set(CanopyConfigKeys.T2_KEY, String.valueOf(t2));
conf.set(CanopyConfigKeys.T3_KEY, String.valueOf(t3));
conf.set(CanopyConfigKeys.T4_KEY, String.valueOf(t4));
conf.set(CanopyConfigKeys.CF_KEY, String.valueOf(clusterFilter));
Job job = new Job(conf, "Canopy Driver running buildClusters over input: "
+ input);
job.setInputFormatClass(SequenceFileInputFormat.class);
job.setOutputFormatClass(SequenceFileOutputFormat.class);
job.setMapperClass(CanopyMapper.class);
job.setMapOutputKeyClass(Text.class);
job.setMapOutputValueClass(VectorWritable.class);
job.setReducerClass(CanopyReducer.class);
job.setOutputKeyClass(Text.class);
job.setOutputValueClass(ClusterWritable.class);
job.setNumReduceTasks(1);
job.setJarByClass(CanopyDriver.class);
FileInputFormat.addInputPath(job, input);
Path canopyOutputDir = new Path(output, Cluster.CLUSTERS_DIR + '0' + Cluster.FINAL_ITERATION_SUFFIX);
FileOutputFormat.setOutputPath(job, canopyOutputDir);
if (!job.waitForCompletion(true)) {
throw new InterruptedException("Canopy Job failed processing " + input);
}
return canopyOutputDir;
}
private static void clusterData(Configuration conf,
Path points,
Path canopies,
Path output,
double clusterClassificationThreshold,
boolean runSequential)
throws IOException, InterruptedException, ClassNotFoundException {
ClusterClassifier.writePolicy(new CanopyClusteringPolicy(), canopies);
ClusterClassificationDriver.run(conf, points, output, new Path(output, PathDirectory.CLUSTERED_POINTS_DIRECTORY),
clusterClassificationThreshold, true, runSequential);
}
}
© 2015 - 2024 Weber Informatics LLC | Privacy Policy