org.apache.mahout.math.hadoop.stochasticsvd.SSVDHelper Maven / Gradle / Ivy
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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.math.hadoop.stochasticsvd;
import com.google.common.base.Function;
import com.google.common.collect.Iterators;
import com.google.common.io.Closeables;
import java.io.Closeable;
import java.io.IOException;
import java.util.ArrayDeque;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.Deque;
import java.util.Iterator;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
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.common.IOUtils;
import org.apache.mahout.common.Pair;
import org.apache.mahout.common.iterator.sequencefile.PathFilters;
import org.apache.mahout.common.iterator.sequencefile.PathType;
import org.apache.mahout.common.iterator.sequencefile.SequenceFileDirIterator;
import org.apache.mahout.common.iterator.sequencefile.SequenceFileDirValueIterator;
import org.apache.mahout.math.DenseMatrix;
import org.apache.mahout.math.DenseSymmetricMatrix;
import org.apache.mahout.math.DenseVector;
import org.apache.mahout.math.Matrix;
import org.apache.mahout.math.UpperTriangular;
import org.apache.mahout.math.Vector;
import org.apache.mahout.math.VectorWritable;
import org.apache.mahout.math.function.Functions;
/**
* set of small file manipulation helpers.
*/
public final class SSVDHelper {
private static final Pattern OUTPUT_FILE_PATTERN = Pattern.compile("(\\w+)-(m|r)-(\\d+)(\\.\\w+)?");
private SSVDHelper() {
}
/**
* load single vector from an hdfs file (possibly presented as glob).
*/
static Vector loadVector(Path glob, Configuration conf) throws IOException {
SequenceFileDirValueIterator iter =
new SequenceFileDirValueIterator<>(glob,
PathType.GLOB,
null,
null,
true,
conf);
try {
if (!iter.hasNext()) {
throw new IOException("Empty input while reading vector");
}
VectorWritable vw = iter.next();
if (iter.hasNext()) {
throw new IOException("Unexpected data after the end of vector file");
}
return vw.get();
} finally {
Closeables.close(iter, true);
}
}
/**
* save single vector into hdfs file.
*
* @param v vector to save
*/
public static void saveVector(Vector v,
Path vectorFilePath,
Configuration conf) throws IOException {
VectorWritable vw = new VectorWritable(v);
FileSystem fs = FileSystem.get(conf);
try (SequenceFile.Writer w = new SequenceFile.Writer(fs,
conf,
vectorFilePath,
IntWritable.class,
VectorWritable.class)) {
w.append(new IntWritable(), vw);
}
/*
* this is a writer, no quiet close please. we must bail out on incomplete
* close.
*/
}
/**
* sniff label type in the input files
*/
static Class sniffInputLabelType(Path[] inputPath,
Configuration conf)
throws IOException {
FileSystem fs = FileSystem.get(conf);
for (Path p : inputPath) {
FileStatus[] fstats = fs.globStatus(p);
if (fstats == null || fstats.length == 0) {
continue;
}
FileStatus firstSeqFile;
if (fstats[0].isDir()) {
firstSeqFile = fs.listStatus(fstats[0].getPath(), PathFilters.logsCRCFilter())[0];
} else {
firstSeqFile = fstats[0];
}
SequenceFile.Reader r = null;
try {
r = new SequenceFile.Reader(fs, firstSeqFile.getPath(), conf);
return r.getKeyClass().asSubclass(Writable.class);
} finally {
Closeables.close(r, true);
}
}
throw new IOException("Unable to open input files to determine input label type.");
}
static final Comparator PARTITION_COMPARATOR =
new Comparator() {
private final Matcher matcher = OUTPUT_FILE_PATTERN.matcher("");
@Override
public int compare(FileStatus o1, FileStatus o2) {
matcher.reset(o1.getPath().getName());
if (!matcher.matches()) {
throw new IllegalArgumentException("Unexpected file name, unable to deduce partition #:"
+ o1.getPath());
}
int p1 = Integer.parseInt(matcher.group(3));
matcher.reset(o2.getPath().getName());
if (!matcher.matches()) {
throw new IllegalArgumentException("Unexpected file name, unable to deduce partition #:"
+ o2.getPath());
}
int p2 = Integer.parseInt(matcher.group(3));
return p1 - p2;
}
};
public static Iterator> drmIterator(FileSystem fs, Path glob, Configuration conf,
Deque closeables)
throws IOException {
SequenceFileDirIterator ret =
new SequenceFileDirIterator<>(glob,
PathType.GLOB,
PathFilters.logsCRCFilter(),
PARTITION_COMPARATOR,
true,
conf);
closeables.addFirst(ret);
return Iterators.transform(ret, new Function, Pair>() {
@Override
public Pair apply(Pair p) {
return new Pair(p.getFirst(), p.getSecond().get());
}
});
}
/**
* helper capabiltiy to load distributed row matrices into dense matrix (to
* support tests mainly).
*
* @param fs filesystem
* @param glob FS glob
* @param conf configuration
* @return Dense matrix array
*/
public static DenseMatrix drmLoadAsDense(FileSystem fs, Path glob, Configuration conf) throws IOException {
Deque closeables = new ArrayDeque<>();
try {
List denseData = new ArrayList<>();
for (Iterator> iter = drmIterator(fs, glob, conf, closeables);
iter.hasNext(); ) {
Pair p = iter.next();
Vector v = p.getSecond();
double[] dd = new double[v.size()];
if (v.isDense()) {
for (int i = 0; i < v.size(); i++) {
dd[i] = v.getQuick(i);
}
} else {
for (Vector.Element el : v.nonZeroes()) {
dd[el.index()] = el.get();
}
}
denseData.add(dd);
}
if (denseData.size() == 0) {
return null;
} else {
return new DenseMatrix(denseData.toArray(new double[denseData.size()][]));
}
} finally {
IOUtils.close(closeables);
}
}
/**
* Load multiple upper triangular matrices and sum them up.
*
* @return the sum of upper triangular inputs.
*/
public static DenseSymmetricMatrix loadAndSumUpperTriangularMatricesAsSymmetric(Path glob, Configuration conf) throws IOException {
Vector v = loadAndSumUpVectors(glob, conf);
return v == null ? null : new DenseSymmetricMatrix(v);
}
/**
* @return sum of all vectors in different files specified by glob
*/
public static Vector loadAndSumUpVectors(Path glob, Configuration conf)
throws IOException {
SequenceFileDirValueIterator iter =
new SequenceFileDirValueIterator<>(glob,
PathType.GLOB,
null,
PARTITION_COMPARATOR,
true,
conf);
try {
Vector v = null;
while (iter.hasNext()) {
if (v == null) {
v = new DenseVector(iter.next().get());
} else {
v.assign(iter.next().get(), Functions.PLUS);
}
}
return v;
} finally {
Closeables.close(iter, true);
}
}
/**
* Load only one upper triangular matrix and issue error if mroe than one is
* found.
*/
public static UpperTriangular loadUpperTriangularMatrix(Path glob, Configuration conf) throws IOException {
/*
* there still may be more than one file in glob and only one of them must
* contain the matrix.
*/
try (SequenceFileDirValueIterator iter = new SequenceFileDirValueIterator<>(glob,
PathType.GLOB,
null,
null,
true,
conf)) {
if (!iter.hasNext()) {
throw new IOException("No triangular matrices found");
}
Vector v = iter.next().get();
UpperTriangular result = new UpperTriangular(v);
if (iter.hasNext()) {
throw new IOException("Unexpected overrun in upper triangular matrix files");
}
return result;
}
}
/**
* extracts row-wise raw data from a Mahout matrix for 3rd party solvers.
* Unfortunately values member is 100% encapsulated in {@link org.apache.mahout.math.DenseMatrix} at
* this point, so we have to resort to abstract element-wise copying.
*/
public static double[][] extractRawData(Matrix m) {
int rows = m.numRows();
int cols = m.numCols();
double[][] result = new double[rows][];
for (int i = 0; i < rows; i++) {
result[i] = new double[cols];
for (int j = 0; j < cols; j++) {
result[i][j] = m.getQuick(i, j);
}
}
return result;
}
}
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