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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.clustering.cdbw;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Writable;
import org.apache.mahout.clustering.AbstractCluster;
import org.apache.mahout.clustering.Cluster;
import org.apache.mahout.clustering.ClusteringTestUtils;
import org.apache.mahout.clustering.ModelDistribution;
import org.apache.mahout.clustering.canopy.Canopy;
import org.apache.mahout.clustering.canopy.CanopyDriver;
import org.apache.mahout.clustering.dirichlet.DirichletDriver;
import org.apache.mahout.clustering.dirichlet.models.GaussianClusterDistribution;
import org.apache.mahout.clustering.fuzzykmeans.FuzzyKMeansDriver;
import org.apache.mahout.clustering.kmeans.KMeansDriver;
import org.apache.mahout.clustering.kmeans.TestKmeansClustering;
import org.apache.mahout.clustering.meanshift.MeanShiftCanopyDriver;
import org.apache.mahout.common.distance.DistanceMeasure;
import org.apache.mahout.common.distance.EuclideanDistanceMeasure;
import org.apache.mahout.math.DenseVector;
import org.apache.mahout.math.VectorWritable;
import org.apache.mahout.utils.MahoutTestCase;
import org.junit.Before;
import org.junit.Test;
public final class TestCDbwEvaluator extends MahoutTestCase {
private static final double[][] REFERENCE = {
{ 1, 1 }, { 2, 1 }, { 1, 2 }, { 2, 2 }, { 3, 3 }, { 4, 4 }, { 5, 4 }, { 4, 5 }, { 5, 5 } };
private Map> representativePoints;
private Map clusters;
@Override
@Before
public void setUp() throws Exception {
super.setUp();
Configuration conf = new Configuration();
FileSystem fs = FileSystem.get(conf);
// Create test data
List sampleData = TestKmeansClustering.getPointsWritable(REFERENCE);
ClusteringTestUtils.writePointsToFile(sampleData, getTestTempFilePath("testdata/file1"), fs, conf);
}
private void checkRefPoints(int numIterations) throws IOException {
for (int i = 0; i <= numIterations; i++) {
Path out = new Path(getTestTempDirPath("output"), "representativePoints-" + i);
Configuration conf = new Configuration();
FileSystem fs = FileSystem.get(conf);
for (FileStatus file : fs.listStatus(out)) {
if (!file.getPath().getName().startsWith(".")) {
SequenceFile.Reader reader = new SequenceFile.Reader(fs, file.getPath(), conf);
try {
Writable clusterId = new IntWritable(0);
VectorWritable point = new VectorWritable();
while (reader.next(clusterId, point)) {
System.out.println("\tC-" + clusterId + ": " + AbstractCluster.formatVector(point.get(), null));
}
} finally {
reader.close();
}
}
}
}
}
/**
* Initialize synthetic data using 4 clusters dC units from origin having 4 representative points dP from each center
* @param dC a double cluster center offset
* @param dP a double representative point offset
* @param measure the DistanceMeasure
*/
private void initData(double dC, double dP, DistanceMeasure measure) {
clusters = new HashMap();
clusters.put(1, new Canopy(new DenseVector(new double[] { -dC, -dC }), 1, measure));
clusters.put(3, new Canopy(new DenseVector(new double[] { -dC, dC }), 3, measure));
clusters.put(5, new Canopy(new DenseVector(new double[] { dC, dC }), 5, measure));
clusters.put(7, new Canopy(new DenseVector(new double[] { dC, -dC }), 7, measure));
representativePoints = new HashMap>();
for (Cluster cluster : clusters.values()) {
List points = new ArrayList();
representativePoints.put(cluster.getId(), points);
points.add(new VectorWritable(cluster.getCenter().clone()));
points.add(new VectorWritable(cluster.getCenter().plus(new DenseVector(new double[] { dP, dP }))));
points.add(new VectorWritable(cluster.getCenter().plus(new DenseVector(new double[] { dP, -dP }))));
points.add(new VectorWritable(cluster.getCenter().plus(new DenseVector(new double[] { -dP, -dP }))));
points.add(new VectorWritable(cluster.getCenter().plus(new DenseVector(new double[] { -dP, dP }))));
}
}
@Test
public void testCDbw0() {
DistanceMeasure measure = new EuclideanDistanceMeasure();
initData(1, 0.25, measure);
CDbwEvaluator evaluator = new CDbwEvaluator(representativePoints, clusters, measure);
assertEquals("inter cluster density", 0.0, evaluator.interClusterDensity(), EPSILON);
assertEquals("separation", 1.5, evaluator.separation(), EPSILON);
assertEquals("intra cluster density", 0.8944271909999157, evaluator.intraClusterDensity(), EPSILON);
assertEquals("CDbw", 1.3416407864998736, evaluator.getCDbw(), EPSILON);
}
@Test
public void testCDbw1() {
DistanceMeasure measure = new EuclideanDistanceMeasure();
initData(1, 0.5, measure);
CDbwEvaluator evaluator = new CDbwEvaluator(representativePoints, clusters, measure);
assertEquals("inter cluster density", 0.0, evaluator.interClusterDensity(), EPSILON);
assertEquals("separation", 1.0, evaluator.separation(), EPSILON);
assertEquals("intra cluster density", 0.44721359549995787, evaluator.intraClusterDensity(), EPSILON);
assertEquals("CDbw", 0.44721359549995787, evaluator.getCDbw(), EPSILON);
}
@Test
public void testCDbw2() {
DistanceMeasure measure = new EuclideanDistanceMeasure();
initData(1, 0.75, measure);
CDbwEvaluator evaluator = new CDbwEvaluator(representativePoints, clusters, measure);
assertEquals("inter cluster density", 1.017921815355728, evaluator.interClusterDensity(), EPSILON);
assertEquals("separation", 0.24777966925931558, evaluator.separation(), EPSILON);
assertEquals("intra cluster density", 0.29814239699997197, evaluator.intraClusterDensity(), EPSILON);
assertEquals("CDbw", 0.07387362452083261, evaluator.getCDbw(), EPSILON);
}
@Test
public void testCanopy() throws Exception { // now run the Job
DistanceMeasure measure = new EuclideanDistanceMeasure();
CanopyDriver.runJob(getTestTempDirPath("testdata"), getTestTempDirPath("output"), measure, 3.1, 2.1, true, false);
int numIterations = 2;
Path output = getTestTempDirPath("output");
CDbwDriver.runJob(new Path(output, "clusters-0"), new Path(output, "clusteredPoints"), output, measure, numIterations, 1);
checkRefPoints(numIterations);
}
@Test
public void testKmeans() throws Exception {
DistanceMeasure measure = new EuclideanDistanceMeasure();
// now run the Canopy job to prime kMeans canopies
CanopyDriver.runJob(getTestTempDirPath("testdata"), getTestTempDirPath("output"), measure, 3.1, 2.1, false, false);
// now run the KMeans job
Path output = getTestTempDirPath("output");
KMeansDriver.runJob(getTestTempDirPath("testdata"), new Path(output, "clusters-0"), output, measure, 0.001, 10, 1, true, false);
int numIterations = 2;
CDbwDriver.runJob(new Path(output, "clusters-2"), new Path(output, "clusteredPoints"), output, measure, numIterations, 1);
checkRefPoints(numIterations);
}
@Test
public void testFuzzyKmeans() throws Exception {
DistanceMeasure measure = new EuclideanDistanceMeasure();
// now run the Canopy job to prime kMeans canopies
CanopyDriver.runJob(getTestTempDirPath("testdata"), getTestTempDirPath("output"), measure, 3.1, 2.1, false, false);
// now run the KMeans job
Path output = getTestTempDirPath("output");
FuzzyKMeansDriver.runJob(getTestTempDirPath("testdata"),
new Path(output, "clusters-0"),
output,
measure,
0.001,
10,
1,
2,
true,
true,
0,
false);
int numIterations = 2;
CDbwDriver.runJob(new Path(output, "clusters-4"), new Path(output, "clusteredPoints"), output, measure, numIterations, 1);
checkRefPoints(numIterations);
}
@Test
public void testMeanShift() throws Exception {
DistanceMeasure measure = new EuclideanDistanceMeasure();
MeanShiftCanopyDriver.runJob(getTestTempDirPath("testdata"),
getTestTempDirPath("output"),
measure,
2.1,
1.0,
0.001,
10,
false,
true,
false);
int numIterations = 2;
Path output = getTestTempDirPath("output");
CDbwDriver.runJob(new Path(output, "clusters-2"), new Path(output, "clusteredPoints"), output, measure, numIterations, 1);
checkRefPoints(numIterations);
}
@Test
public void testDirichlet() throws Exception {
ModelDistribution modelDistribution =
new GaussianClusterDistribution(new VectorWritable(new DenseVector(2)));
DirichletDriver.runJob(getTestTempDirPath("testdata"),
getTestTempDirPath("output"),
modelDistribution,
15,
5,
1.0,
1,
true,
true,
0,
true);
int numIterations = 2;
Path output = getTestTempDirPath("output");
CDbwDriver.runJob(new Path(output, "clusters-5"),
new Path(output, "clusteredPoints"),
output,
new EuclideanDistanceMeasure(),
numIterations,
1);
checkRefPoints(numIterations);
}
@Test
public void testEmptyCluster() {
DistanceMeasure measure = new EuclideanDistanceMeasure();
initData(1, 0.25, measure);
Canopy cluster = new Canopy(new DenseVector(new double[] { 10, 10 }), 19, measure);
clusters.put(cluster.getId(), cluster);
List points = new ArrayList();
representativePoints.put(cluster.getId(), points);
CDbwEvaluator evaluator = new CDbwEvaluator(representativePoints, clusters, measure);
assertEquals("inter cluster density", 0.0, evaluator.interClusterDensity(), EPSILON);
assertEquals("separation", 1.5, evaluator.separation(), EPSILON);
assertEquals("intra cluster density", 0.7155417527999326, evaluator.intraClusterDensity(), EPSILON);
assertEquals("CDbw", 1.073312629199899, evaluator.getCDbw(), EPSILON);
}
@Test
public void testSingleValueCluster() {
DistanceMeasure measure = new EuclideanDistanceMeasure();
initData(1, 0.25, measure);
Canopy cluster = new Canopy(new DenseVector(new double[] { 0, 0 }), 19, measure);
clusters.put(cluster.getId(), cluster);
List points = new ArrayList();
points.add(new VectorWritable(cluster.getCenter().plus(new DenseVector(new double[] { 1, 1 }))));
representativePoints.put(cluster.getId(), points);
CDbwEvaluator evaluator = new CDbwEvaluator(representativePoints, clusters, measure);
assertEquals("inter cluster density", 0.0, evaluator.interClusterDensity(), EPSILON);
assertEquals("separation", 0.0, evaluator.separation(), EPSILON);
assertEquals("intra cluster density", 0.7155417527999326, evaluator.intraClusterDensity(), EPSILON);
assertEquals("CDbw", 0.0, evaluator.getCDbw(), EPSILON);
}
}
