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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.vectorizer;
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.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.util.ToolRunner;
import org.apache.lucene.analysis.Analyzer;
import org.apache.lucene.analysis.standard.StandardAnalyzer;
import org.apache.mahout.common.AbstractJob;
import org.apache.mahout.common.CommandLineUtil;
import org.apache.mahout.common.HadoopUtil;
import org.apache.mahout.common.Pair;
import org.apache.mahout.common.commandline.DefaultOptionCreator;
import org.apache.mahout.common.lucene.AnalyzerUtils;
import org.apache.mahout.math.hadoop.stats.BasicStats;
import org.apache.mahout.vectorizer.collocations.llr.LLRReducer;
import org.apache.mahout.vectorizer.common.PartialVectorMerger;
import org.apache.mahout.vectorizer.tfidf.TFIDFConverter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.List;
/**
* Converts a given set of sequence files into SparseVectors
*/
public final class SparseVectorsFromSequenceFiles extends AbstractJob {
private static final Logger log = LoggerFactory.getLogger(SparseVectorsFromSequenceFiles.class);
public static void main(String[] args) throws Exception {
ToolRunner.run(new SparseVectorsFromSequenceFiles(), args);
}
@Override
public int run(String[] args) throws Exception {
DefaultOptionBuilder obuilder = new DefaultOptionBuilder();
ArgumentBuilder abuilder = new ArgumentBuilder();
GroupBuilder gbuilder = new GroupBuilder();
Option inputDirOpt = DefaultOptionCreator.inputOption().create();
Option outputDirOpt = DefaultOptionCreator.outputOption().create();
Option minSupportOpt = obuilder.withLongName("minSupport").withArgument(
abuilder.withName("minSupport").withMinimum(1).withMaximum(1).create()).withDescription(
"(Optional) Minimum Support. Default Value: 2").withShortName("s").create();
Option analyzerNameOpt = obuilder.withLongName("analyzerName").withArgument(
abuilder.withName("analyzerName").withMinimum(1).withMaximum(1).create()).withDescription(
"The class name of the analyzer").withShortName("a").create();
Option chunkSizeOpt = obuilder.withLongName("chunkSize").withArgument(
abuilder.withName("chunkSize").withMinimum(1).withMaximum(1).create()).withDescription(
"The chunkSize in MegaBytes. Default Value: 100MB").withShortName("chunk").create();
Option weightOpt = obuilder.withLongName("weight").withRequired(false).withArgument(
abuilder.withName("weight").withMinimum(1).withMaximum(1).create()).withDescription(
"The kind of weight to use. Currently TF or TFIDF. Default: TFIDF").withShortName("wt").create();
Option minDFOpt = obuilder.withLongName("minDF").withRequired(false).withArgument(
abuilder.withName("minDF").withMinimum(1).withMaximum(1).create()).withDescription(
"The minimum document frequency. Default is 1").withShortName("md").create();
Option maxDFPercentOpt = obuilder.withLongName("maxDFPercent").withRequired(false).withArgument(
abuilder.withName("maxDFPercent").withMinimum(1).withMaximum(1).create()).withDescription(
"The max percentage of docs for the DF. Can be used to remove really high frequency terms."
+ " Expressed as an integer between 0 and 100. Default is 99. If maxDFSigma is also set, "
+ "it will override this value.").withShortName("x").create();
Option maxDFSigmaOpt = obuilder.withLongName("maxDFSigma").withRequired(false).withArgument(
abuilder.withName("maxDFSigma").withMinimum(1).withMaximum(1).create()).withDescription(
"What portion of the tf (tf-idf) vectors to be used, expressed in times the standard deviation (sigma) "
+ "of the document frequencies of these vectors. Can be used to remove really high frequency terms."
+ " Expressed as a double value. Good value to be specified is 3.0. In case the value is less "
+ "than 0 no vectors will be filtered out. Default is -1.0. Overrides maxDFPercent")
.withShortName("xs").create();
Option minLLROpt = obuilder.withLongName("minLLR").withRequired(false).withArgument(
abuilder.withName("minLLR").withMinimum(1).withMaximum(1).create()).withDescription(
"(Optional)The minimum Log Likelihood Ratio(Float) Default is " + LLRReducer.DEFAULT_MIN_LLR)
.withShortName("ml").create();
Option numReduceTasksOpt = obuilder.withLongName("numReducers").withArgument(
abuilder.withName("numReducers").withMinimum(1).withMaximum(1).create()).withDescription(
"(Optional) Number of reduce tasks. Default Value: 1").withShortName("nr").create();
Option powerOpt = obuilder.withLongName("norm").withRequired(false).withArgument(
abuilder.withName("norm").withMinimum(1).withMaximum(1).create()).withDescription(
"The norm to use, expressed as either a float or \"INF\" if you want to use the Infinite norm. "
+ "Must be greater or equal to 0. The default is not to normalize").withShortName("n").create();
Option logNormalizeOpt = obuilder.withLongName("logNormalize").withRequired(false)
.withDescription(
"(Optional) Whether output vectors should be logNormalize. If set true else false")
.withShortName("lnorm").create();
Option maxNGramSizeOpt = obuilder.withLongName("maxNGramSize").withRequired(false).withArgument(
abuilder.withName("ngramSize").withMinimum(1).withMaximum(1).create())
.withDescription(
"(Optional) The maximum size of ngrams to create"
+ " (2 = bigrams, 3 = trigrams, etc) Default Value:1").withShortName("ng").create();
Option sequentialAccessVectorOpt = obuilder.withLongName("sequentialAccessVector").withRequired(false)
.withDescription(
"(Optional) Whether output vectors should be SequentialAccessVectors. If set true else false")
.withShortName("seq").create();
Option namedVectorOpt = obuilder.withLongName("namedVector").withRequired(false)
.withDescription(
"(Optional) Whether output vectors should be NamedVectors. If set true else false")
.withShortName("nv").create();
Option overwriteOutput = obuilder.withLongName("overwrite").withRequired(false).withDescription(
"If set, overwrite the output directory").withShortName("ow").create();
Option helpOpt = obuilder.withLongName("help").withDescription("Print out help").withShortName("h")
.create();
Group group = gbuilder.withName("Options").withOption(minSupportOpt).withOption(analyzerNameOpt)
.withOption(chunkSizeOpt).withOption(outputDirOpt).withOption(inputDirOpt).withOption(minDFOpt)
.withOption(maxDFSigmaOpt).withOption(maxDFPercentOpt).withOption(weightOpt).withOption(powerOpt)
.withOption(minLLROpt).withOption(numReduceTasksOpt).withOption(maxNGramSizeOpt).withOption(overwriteOutput)
.withOption(helpOpt).withOption(sequentialAccessVectorOpt).withOption(namedVectorOpt)
.withOption(logNormalizeOpt)
.create();
try {
Parser parser = new Parser();
parser.setGroup(group);
parser.setHelpOption(helpOpt);
CommandLine cmdLine = parser.parse(args);
if (cmdLine.hasOption(helpOpt)) {
CommandLineUtil.printHelp(group);
return -1;
}
Path inputDir = new Path((String) cmdLine.getValue(inputDirOpt));
Path outputDir = new Path((String) cmdLine.getValue(outputDirOpt));
int chunkSize = 100;
if (cmdLine.hasOption(chunkSizeOpt)) {
chunkSize = Integer.parseInt((String) cmdLine.getValue(chunkSizeOpt));
}
int minSupport = 2;
if (cmdLine.hasOption(minSupportOpt)) {
String minSupportString = (String) cmdLine.getValue(minSupportOpt);
minSupport = Integer.parseInt(minSupportString);
}
int maxNGramSize = 1;
if (cmdLine.hasOption(maxNGramSizeOpt)) {
try {
maxNGramSize = Integer.parseInt(cmdLine.getValue(maxNGramSizeOpt).toString());
} catch (NumberFormatException ex) {
log.warn("Could not parse ngram size option");
}
}
log.info("Maximum n-gram size is: {}", maxNGramSize);
if (cmdLine.hasOption(overwriteOutput)) {
HadoopUtil.delete(getConf(), outputDir);
}
float minLLRValue = LLRReducer.DEFAULT_MIN_LLR;
if (cmdLine.hasOption(minLLROpt)) {
minLLRValue = Float.parseFloat(cmdLine.getValue(minLLROpt).toString());
}
log.info("Minimum LLR value: {}", minLLRValue);
int reduceTasks = 1;
if (cmdLine.hasOption(numReduceTasksOpt)) {
reduceTasks = Integer.parseInt(cmdLine.getValue(numReduceTasksOpt).toString());
}
log.info("Number of reduce tasks: {}", reduceTasks);
Class analyzerClass = StandardAnalyzer.class;
if (cmdLine.hasOption(analyzerNameOpt)) {
String className = cmdLine.getValue(analyzerNameOpt).toString();
analyzerClass = Class.forName(className).asSubclass(Analyzer.class);
// try instantiating it, b/c there isn't any point in setting it if
// you can't instantiate it
AnalyzerUtils.createAnalyzer(analyzerClass);
}
boolean processIdf;
if (cmdLine.hasOption(weightOpt)) {
String wString = cmdLine.getValue(weightOpt).toString();
if ("tf".equalsIgnoreCase(wString)) {
processIdf = false;
} else if ("tfidf".equalsIgnoreCase(wString)) {
processIdf = true;
} else {
throw new OptionException(weightOpt);
}
} else {
processIdf = true;
}
int minDf = 1;
if (cmdLine.hasOption(minDFOpt)) {
minDf = Integer.parseInt(cmdLine.getValue(minDFOpt).toString());
}
int maxDFPercent = 99;
if (cmdLine.hasOption(maxDFPercentOpt)) {
maxDFPercent = Integer.parseInt(cmdLine.getValue(maxDFPercentOpt).toString());
}
double maxDFSigma = -1.0;
if (cmdLine.hasOption(maxDFSigmaOpt)) {
maxDFSigma = Double.parseDouble(cmdLine.getValue(maxDFSigmaOpt).toString());
}
float norm = PartialVectorMerger.NO_NORMALIZING;
if (cmdLine.hasOption(powerOpt)) {
String power = cmdLine.getValue(powerOpt).toString();
if ("INF".equals(power)) {
norm = Float.POSITIVE_INFINITY;
} else {
norm = Float.parseFloat(power);
}
}
boolean logNormalize = false;
if (cmdLine.hasOption(logNormalizeOpt)) {
logNormalize = true;
}
log.info("Tokenizing documents in {}", inputDir);
Configuration conf = getConf();
Path tokenizedPath = new Path(outputDir, DocumentProcessor.TOKENIZED_DOCUMENT_OUTPUT_FOLDER);
//TODO: move this into DictionaryVectorizer , and then fold SparseVectorsFrom with EncodedVectorsFrom
// to have one framework for all of this.
DocumentProcessor.tokenizeDocuments(inputDir, analyzerClass, tokenizedPath, conf);
boolean sequentialAccessOutput = false;
if (cmdLine.hasOption(sequentialAccessVectorOpt)) {
sequentialAccessOutput = true;
}
boolean namedVectors = false;
if (cmdLine.hasOption(namedVectorOpt)) {
namedVectors = true;
}
boolean shouldPrune = maxDFSigma >= 0.0 || maxDFPercent > 0.00;
String tfDirName = shouldPrune
? DictionaryVectorizer.DOCUMENT_VECTOR_OUTPUT_FOLDER + "-toprune"
: DictionaryVectorizer.DOCUMENT_VECTOR_OUTPUT_FOLDER;
log.info("Creating Term Frequency Vectors");
if (processIdf) {
DictionaryVectorizer.createTermFrequencyVectors(tokenizedPath,
outputDir,
tfDirName,
conf,
minSupport,
maxNGramSize,
minLLRValue,
-1.0f,
false,
reduceTasks,
chunkSize,
sequentialAccessOutput,
namedVectors);
} else {
DictionaryVectorizer.createTermFrequencyVectors(tokenizedPath,
outputDir,
tfDirName,
conf,
minSupport,
maxNGramSize,
minLLRValue,
norm,
logNormalize,
reduceTasks,
chunkSize,
sequentialAccessOutput,
namedVectors);
}
Pair> docFrequenciesFeatures = null;
// Should document frequency features be processed
if (shouldPrune || processIdf) {
log.info("Calculating IDF");
docFrequenciesFeatures =
TFIDFConverter.calculateDF(new Path(outputDir, tfDirName), outputDir, conf, chunkSize);
}
long maxDF = maxDFPercent; //if we are pruning by std dev, then this will get changed
if (shouldPrune) {
long vectorCount = docFrequenciesFeatures.getFirst()[1];
if (maxDFSigma >= 0.0) {
Path dfDir = new Path(outputDir, TFIDFConverter.WORDCOUNT_OUTPUT_FOLDER);
Path stdCalcDir = new Path(outputDir, HighDFWordsPruner.STD_CALC_DIR);
// Calculate the standard deviation
double stdDev = BasicStats.stdDevForGivenMean(dfDir, stdCalcDir, 0.0, conf);
maxDF = (int) (100.0 * maxDFSigma * stdDev / vectorCount);
}
long maxDFThreshold = (long) (vectorCount * (maxDF / 100.0f));
// Prune the term frequency vectors
Path tfDir = new Path(outputDir, tfDirName);
Path prunedTFDir = new Path(outputDir, DictionaryVectorizer.DOCUMENT_VECTOR_OUTPUT_FOLDER);
Path prunedPartialTFDir =
new Path(outputDir, DictionaryVectorizer.DOCUMENT_VECTOR_OUTPUT_FOLDER + "-partial");
log.info("Pruning");
if (processIdf) {
HighDFWordsPruner.pruneVectors(tfDir,
prunedTFDir,
prunedPartialTFDir,
maxDFThreshold,
minDf,
conf,
docFrequenciesFeatures,
-1.0f,
false,
reduceTasks);
} else {
HighDFWordsPruner.pruneVectors(tfDir,
prunedTFDir,
prunedPartialTFDir,
maxDFThreshold,
minDf,
conf,
docFrequenciesFeatures,
norm,
logNormalize,
reduceTasks);
}
HadoopUtil.delete(new Configuration(conf), tfDir);
}
if (processIdf) {
TFIDFConverter.processTfIdf(
new Path(outputDir, DictionaryVectorizer.DOCUMENT_VECTOR_OUTPUT_FOLDER),
outputDir, conf, docFrequenciesFeatures, minDf, maxDF, norm, logNormalize,
sequentialAccessOutput, namedVectors, reduceTasks);
}
} catch (OptionException e) {
log.error("Exception", e);
CommandLineUtil.printHelp(group);
}
return 0;
}
}
