/*
* avenir: Predictive analytic based on Hadoop Map Reduce
* Author: Pranab Ghosh
*
* Licensed 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.avenir.explore;
import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.NullWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.Mapper;
import org.apache.hadoop.mapreduce.Reducer;
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.chombo.util.GenericAttributeSchema;
import org.chombo.util.NumericalAttrStatsManager;
import org.chombo.util.Pair;
import org.chombo.util.Tuple;
import org.chombo.util.Utility;
/**
* @author pranab
*
*/
public class NumericalCorrelation extends Configured implements Tool {
/* (non-Javadoc)
* @see org.apache.hadoop.util.Tool#run(java.lang.String[])
*/
@Override
public int run(String[] args) throws Exception {
Job job = new Job(getConf());
String jobName = "Cross correlation between numerical attributes";
job.setJobName(jobName);
job.setJarByClass(NumericalCorrelation.class);
FileInputFormat.addInputPath(job, new Path(args[0]));
FileOutputFormat.setOutputPath(job, new Path(args[1]));
Utility.setConfiguration(job.getConfiguration(), "chombo");
job.setMapperClass(NumericalCorrelation.CorrelationMapper.class);
job.setReducerClass(NumericalCorrelation.CorrelationReducer.class);
job.setCombinerClass(NumericalCorrelation.CorrelationCombiner.class);
job.setMapOutputKeyClass(Tuple.class);
job.setMapOutputValueClass(Tuple.class);
job.setOutputKeyClass(NullWritable.class);
job.setOutputValueClass(Text.class);
int numReducer = job.getConfiguration().getInt("nuc.num.reducer", -1);
numReducer = -1 == numReducer ? job.getConfiguration().getInt("num.reducer", 1) : numReducer;
job.setNumReduceTasks(numReducer);
int status = job.waitForCompletion(true) ? 0 : 1;
return status;
}
/**
* @author pranab
*
*/
public static class CorrelationMapper extends Mapper<LongWritable, Text, Tuple, Tuple> {
private Tuple outKey = new Tuple();
private Tuple outVal = new Tuple();
private String fieldDelimRegex;
private int count = 1;
private String[] items;
private GenericAttributeSchema schema;
private List<Pair<Integer, Integer>> attrPairs;
private Map<Integer, Double> attrMean = new HashMap<Integer, Double>();
private int firstAttr;
private int secondAttr;
private double first;
private double second;
private double sum;
protected void setup(Context context) throws IOException, InterruptedException {
Configuration config = context.getConfiguration();
fieldDelimRegex = config.get("field.delim.regex", ",");
attrPairs = Utility. assertIntPairListConfigParam(config, "nuc.attr.pairs", Utility.configDelim, Utility.configSubFieldDelim, "");
schema = Utility.getGenericAttributeSchema(config, "nuc.schema.file.path");
if (null != schema) {
//validate
int[] attrs = new int[attrPairs.size() * 2];
int i = 0;
for (Pair<Integer, Integer> pair : attrPairs) {
attrs[i++] = pair.getLeft();
attrs[i++] = pair.getRight();
}
if (!schema.areNumericalAttributes(attrs)) {
throw new IllegalArgumentException("attributes should be numerical");
}
}
//get mean values
NumericalAttrStatsManager statsManager = new NumericalAttrStatsManager( config, "nuc.stats.file.path", fieldDelimRegex);
for (Pair<Integer, Integer> pair : attrPairs) {
attrMean.put(pair.getLeft(), statsManager.getMean(pair.getLeft()));
attrMean.put(pair.getRight(), statsManager.getMean(pair.getRight()));
}
}
@Override
protected void map(LongWritable key, Text value, Context context)
throws IOException, InterruptedException {
items = value.toString().split(fieldDelimRegex);
for (Pair<Integer, Integer> pair : attrPairs) {
outKey.initialize();
outVal.initialize();
firstAttr = pair.getLeft();
first = Double.parseDouble(items[firstAttr]);
secondAttr = pair.getRight();
second = Double.parseDouble(items[secondAttr]);
sum = (first - attrMean.get(firstAttr)) * (second - attrMean.get(secondAttr));
outKey.add(firstAttr, secondAttr);
outVal.add(sum, count);
context.write(outKey, outVal);
}
}
}
/**
* @author pranab
*
*/
public static class CorrelationCombiner extends Reducer<Tuple, Tuple, Tuple, Tuple> {
private Tuple outVal = new Tuple();
private double sum;
private int totalCount;
protected void reduce(Tuple key, Iterable<Tuple> values, Context context)
throws IOException, InterruptedException {
sum = 0;
totalCount = 0;
int i = 0;
for (Tuple val : values) {
sum += val.getDouble(0);
totalCount += val.getInt(1);
}
outVal.initialize();
outVal.add(sum, totalCount);
context.write(key, outVal);
}
}
/**
* @author pranab
*
*/
public static class CorrelationReducer extends Reducer<Tuple, Tuple, NullWritable, Text> {
protected Text outVal = new Text();
protected StringBuilder stBld = new StringBuilder();;
protected String fieldDelim;
private double sum;
private int totalCount;
private Map<Integer, Double> attrStdDev = new HashMap<Integer, Double>();
private double corr;
private List<Pair<Integer, Integer>> attrPairs;
/* (non-Javadoc)
* @see org.apache.hadoop.mapreduce.Reducer#setup(org.apache.hadoop.mapreduce.Reducer.Context)
*/
protected void setup(Context context) throws IOException, InterruptedException {
Configuration config = context.getConfiguration();
fieldDelim = config.get("field.delim.out", ",");
NumericalAttrStatsManager statsManager = new NumericalAttrStatsManager(config, "nuc.stats.file.path", fieldDelim);
attrPairs = Utility. assertIntPairListConfigParam(config, "nuc.attr.pairs", Utility.configDelim, Utility.configSubFieldDelim, "");
for (Pair<Integer, Integer> pair : attrPairs) {
attrStdDev.put(pair.getLeft(), statsManager.getStdDev(pair.getLeft()));
attrStdDev.put(pair.getRight(), statsManager.getStdDev(pair.getRight()));
}
}
/* (non-Javadoc)
* @see org.apache.hadoop.mapreduce.Reducer#reduce(KEYIN, java.lang.Iterable, org.apache.hadoop.mapreduce.Reducer.Context)
*/
protected void reduce(Tuple key, Iterable<Tuple> values, Context context)
throws IOException, InterruptedException {
sum = 0;
totalCount = 0;
int i = 0;
for (Tuple val : values) {
sum += val.getDouble(0);
totalCount += val.getInt(1);
}
sum /= totalCount;
corr = sum / (attrStdDev.get(key.getInt(0)) * attrStdDev.get(key.getInt(1)));
outVal.set("" + key.getInt(0) + fieldDelim +key.getInt(1) + fieldDelim + corr );
context.write(NullWritable.get(), outVal);
}
}
/**
* @param args
*/
public static void main(String[] args) throws Exception {
int exitCode = ToolRunner.run(new NumericalCorrelation(), args);
System.exit(exitCode);
}
}