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Posted to user@mahout.apache.org by Aleksander Sadecki <al...@pi.esisar.grenoble-inp.fr> on 2014/05/20 15:44:29 UTC
How to print data after canopy clustering
Hi Experts,
Here you can find simple piece of code which I wrote:
/****************************************************************************/
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.mahout.clustering.Cluster;
import org.apache.mahout.clustering.canopy.CanopyDriver;
import org.apache.mahout.clustering.classify.WeightedPropertyVectorWritable;
import org.apache.mahout.common.distance.EuclideanDistanceMeasure;
import org.apache.mahout.math.RandomAccessSparseVector;
import org.apache.mahout.math.Vector;
import org.apache.mahout.math.VectorWritable;
public class Clustering {
private final static String root = "C:\\root\\BI\\";
private final static String dataDir = root + "synthetic_control.data";
private final static String seqDir = root + "synthetic_control.seq";
private final static String outputDir = root + "output";
private final static String partMDir = outputDir + "\\"
+ Cluster.CLUSTERED_POINTS_DIR + "\\part-m-0";
private final static String SEPARATOR = " ";
private final static int NUMBER_OF_ELEMENTS = 2;
private Configuration conf;
private FileSystem fs;
public Clustering() throws IOException {
conf = new Configuration();
fs = FileSystem.get(conf);
}
public void convertToVectorFile() throws IOException {
BufferedReader reader = new BufferedReader(new FileReader(dataDir));
SequenceFile.Writer writer = new SequenceFile.Writer(fs, conf,
new Path(seqDir), LongWritable.class, VectorWritable.class);
String line;
long counter = 0;
while ((line = reader.readLine()) != null) {
String[] c;
c = line.split(SEPARATOR);
double[] d = new double[c.length];
for (int i = 0; i < NUMBER_OF_ELEMENTS; i++) {
try {
d[i] = Double.parseDouble(c[i]);
} catch (Exception ex) {
d[i] = 0;
}
}
Vector vec = new RandomAccessSparseVector(c.length);
vec.assign(d);
VectorWritable writable = new VectorWritable();
writable.set(vec);
writer.append(new LongWritable(counter++), writable);
}
writer.close();
}
public void createClusters(double t1, double t2,
double clusterClassificationThreshold, boolean runSequential)
throws ClassNotFoundException, IOException, InterruptedException {
EuclideanDistanceMeasure measure = new EuclideanDistanceMeasure();
Path inputPath = new Path(seqDir);
Path outputPath = new Path(outputDir);
CanopyDriver.run(inputPath, outputPath, measure, t1, t2, runSequential,
clusterClassificationThreshold, runSequential);
}
public void printClusters() throws IOException {
SequenceFile.Reader readerSequence = new SequenceFile.Reader(fs,
new Path(partMDir), conf);
IntWritable key = new IntWritable();
WeightedPropertyVectorWritable value = new WeightedPropertyVectorWritable();
while (readerSequence.next(key, value)) {
System.out.println(value.toString() + " belongs to cluster "
+ key.toString());
}
readerSequence.close();
}
}
/****************************************************************************/
Here we have got 3 different methods.
A. convertToVectorFile()
This function takes a file C:\root\BI\synthetic_control.data and converts it into another file (I was following book Mahout in Action ).
For file:
0.01 1.0
0.1 0.9
0.1 0.95
12.0 13.0
12.5 12.8
it generated for me the following structure:
>tree /F
C:.
.synthetic_control.seq.crc
synthetic_control.data
synthetic_control.seq
with log in Eclipse:
DEBUG Groups - Creating new Groups object
DEBUG Groups - Group mapping impl=org.apache.hadoop.security.ShellBasedUnixGroupsMapping; cacheTimeout=300000
DEBUG UserGroupInformation - hadoop login
DEBUG UserGroupInformation - hadoop login commit
DEBUG UserGroupInformation - using local user:NTUserPrincipal : xxxxxxxx
DEBUG UserGroupInformation - UGI loginUser:xxxxxxxx
DEBUG FileSystem - Creating filesystem for file:///
DEBUG NativeCodeLoader - Trying to load the custom-built native-hadoop library...
DEBUG NativeCodeLoader - Failed to load native-hadoop with error: java.lang.UnsatisfiedLinkError: no hadoop in java.library.path
DEBUG NativeCodeLoader - java.library.path=C:\Program Files\Java\jre7\bin;C:\Windows\Sun\Java\bin;C:\Windows\system32;C:\Windows;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x86;C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x64;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\MATLAB\R2009b\runtime\win64;C:\Program Files\MATLAB\R2009b\bin;C:\Program Files\TortoiseSVN\bin;C:\Users\xxxxxxxx\Documents\apache-maven-3.1.1\bin;.
WARN NativeCodeLoader - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
B. createClusters()
Next method generates clusters. When I run it it gives me a log:
INFO CanopyDriver - Build Clusters Input: C:/Users/xxxxxxxx/Desktop/BI/synthetic_control.seq Out: C:/Users/xxxxxxxx/Desktop/BI/output Measure: org.apache.mahout.common.distance.EuclideanDistanceMeasure@2224ece4 t1: 2.0 t2: 3.0
DEBUG CanopyClusterer - Created new Canopy:0 at center:[0.010, 1.000]
DEBUG CanopyClusterer - Added point: [0.100, 0.900] to canopy: C-0
DEBUG CanopyClusterer - Added point: [0.100, 0.950] to canopy: C-0
DEBUG CanopyClusterer - Created new Canopy:1 at center:[12.000, 13.000]
DEBUG CanopyClusterer - Added point: [12.500, 12.800] to canopy: C-1
DEBUG CanopyDriver - Writing Canopy:C-0 center:[0.070, 0.950] numPoints:3 radius:[0.042, 0.041]
DEBUG CanopyDriver - Writing Canopy:C-1 center:[12.250, 12.900] numPoints:2 radius:[0.250, 0.100]
DEBUG FileSystem - Starting clear of FileSystem cache with 1 elements.
DEBUG FileSystem - Removing filesystem for file:///
DEBUG FileSystem - Removing filesystem for file:///
DEBUG FileSystem - Done clearing cache
and I can see more files in my directory:
>tree /F
C:.
│ .synthetic_control.seq.crc
│ synthetic_control.data
│ synthetic_control.seq
│
└───output
├───clusteredPoints
│ .part-m-0.crc
│ part-m-0
│
└───clusters-0-final
.part-r-00000.crc
._policy.crc
part-r-00000
_policy
Reading the log we can see that everything worked well. We have got 2 clusters with proper points.
C. printClusters()
Here is my problem.
I have no erros but I cannot see any results in console screen. My code never goes in while loop.
Thank you for any help