[
https://issues.apache.org/jira/browse/HAMA-94?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Thomas Jungblut updated HAMA-94:
--------------------------------
Description:
We want to add the cholesky decomposition / factorization to our upcoming math
package.
This is Edward's old cholesky decomposition map/reduce code..
{noformat}
/**
* Copyright 2007 The Apache Software Foundation
*
* 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.hama.algebra;
import java.io.IOException;
import org.apache.hadoop.hbase.HBaseConfiguration;
import org.apache.hadoop.hbase.HStoreKey;
import org.apache.hadoop.io.MapWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hama.FeatureVector;
import org.apache.hama.Matrix;
import org.apache.hama.TriangularMatrix;
import org.apache.hama.mapred.MatrixMap;
import org.apache.hama.mapred.MatrixOutputFormat;
/**
* Cholesky Decomposition.
* <p>
* For a symmetric, positive definite matrix A, the Cholesky decomposition is an
* lower triangular matrix L so that A = L*L'.
* </p>
*/
public class CholeskyDecompositionMap extends MatrixMap<Text, MapWritable> {
protected Matrix matrix_a;
protected TriangularMatrix matrix_l;
public static final String MATRIX_A = "cholesky.decomposition.matrix.a";
public static final String MATRIX_L = "cholesky.decomposition.matrix.l";
public void configure(JobConf job) {
HBaseConfiguration conf = new HBaseConfiguration();
Text a_name = new Text(job.get(MATRIX_A, ""));
Text l_name = new Text(job.get(MATRIX_L, ""));
matrix_a = new Matrix(conf, a_name);
matrix_l = new TriangularMatrix(conf, l_name);
}
/**
* @param matrix_a
* @param matrix_l
* @param map
* @param jobConf
*/
public static void initJob(String matrix_a, String matrix_l,
Class<CholeskyDecompositionMap> map, JobConf jobConf) {
initJob(matrix_a, map, jobConf);
jobConf.set(MatrixOutputFormat.OUTPUT, matrix_l);
jobConf.set(MATRIX_A, matrix_a);
jobConf.set(MATRIX_L, matrix_l);
}
@Override
public void map(HStoreKey key, MapWritable value,
OutputCollector<Text, MapWritable> output, Reporter reporter)
throws IOException {
int i = Integer.parseInt(String.valueOf(key.getRow()));
double[] ithRowOfL = new double[matrix_a.getRowDimension()];
double[] jthRowOfL = new double[matrix_a.getRowDimension()];
// Vector was added. I don't figure out the result. -- edward
FeatureVector iOfV = matrix_l.getRowVector(i);
for(int x = 0; x < iOfV.size(); x++) {
ithRowOfL[x] = iOfV.getDimAt(x);
}
for (int j = i; j < value.size(); j++) {
FeatureVector jOfV = matrix_l.getRowVector(i);
for(int x = 0; x < jOfV.size(); x++) {
jthRowOfL[x] = jOfV.getDimAt(x);
}
double sum = matrix_a.get(i, j);
for (int k = i - 1; k >= 0; k--) {
sum -= ithRowOfL[k] * jthRowOfL[k];
}
if (i == j) {
matrix_l.setToLower(j, i, Math.sqrt(sum));
} else {
double c = matrix_l.get(i, i);
matrix_l.setToLower(j, i, (sum / c));
}
}
}
}
{noformat}
was:
This is my old cholesky decomposition map/reduce code..
----
/**
* Copyright 2007 The Apache Software Foundation
*
* 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.hama.algebra;
import java.io.IOException;
import org.apache.hadoop.hbase.HBaseConfiguration;
import org.apache.hadoop.hbase.HStoreKey;
import org.apache.hadoop.io.MapWritable;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hama.FeatureVector;
import org.apache.hama.Matrix;
import org.apache.hama.TriangularMatrix;
import org.apache.hama.mapred.MatrixMap;
import org.apache.hama.mapred.MatrixOutputFormat;
/**
* Cholesky Decomposition.
* <p>
* For a symmetric, positive definite matrix A, the Cholesky decomposition is an
* lower triangular matrix L so that A = L*L'.
* </p>
*/
public class CholeskyDecompositionMap extends MatrixMap<Text, MapWritable> {
protected Matrix matrix_a;
protected TriangularMatrix matrix_l;
public static final String MATRIX_A = "cholesky.decomposition.matrix.a";
public static final String MATRIX_L = "cholesky.decomposition.matrix.l";
public void configure(JobConf job) {
HBaseConfiguration conf = new HBaseConfiguration();
Text a_name = new Text(job.get(MATRIX_A, ""));
Text l_name = new Text(job.get(MATRIX_L, ""));
matrix_a = new Matrix(conf, a_name);
matrix_l = new TriangularMatrix(conf, l_name);
}
/**
* @param matrix_a
* @param matrix_l
* @param map
* @param jobConf
*/
public static void initJob(String matrix_a, String matrix_l,
Class<CholeskyDecompositionMap> map, JobConf jobConf) {
initJob(matrix_a, map, jobConf);
jobConf.set(MatrixOutputFormat.OUTPUT, matrix_l);
jobConf.set(MATRIX_A, matrix_a);
jobConf.set(MATRIX_L, matrix_l);
}
@Override
public void map(HStoreKey key, MapWritable value,
OutputCollector<Text, MapWritable> output, Reporter reporter)
throws IOException {
int i = Integer.parseInt(String.valueOf(key.getRow()));
double[] ithRowOfL = new double[matrix_a.getRowDimension()];
double[] jthRowOfL = new double[matrix_a.getRowDimension()];
// Vector was added. I don't figure out the result. -- edward
FeatureVector iOfV = matrix_l.getRowVector(i);
for(int x = 0; x < iOfV.size(); x++) {
ithRowOfL[x] = iOfV.getDimAt(x);
}
for (int j = i; j < value.size(); j++) {
FeatureVector jOfV = matrix_l.getRowVector(i);
for(int x = 0; x < jOfV.size(); x++) {
jthRowOfL[x] = jOfV.getDimAt(x);
}
double sum = matrix_a.get(i, j);
for (int k = i - 1; k >= 0; k--) {
sum -= ithRowOfL[k] * jthRowOfL[k];
}
if (i == j) {
matrix_l.setToLower(j, i, Math.sqrt(sum));
} else {
double c = matrix_l.get(i, i);
matrix_l.setToLower(j, i, (sum / c));
}
}
}
}
Priority: Minor (was: Major)
> Implementation of cholesky decomposition
> ----------------------------------------
>
> Key: HAMA-94
> URL: https://issues.apache.org/jira/browse/HAMA-94
> Project: Hama
> Issue Type: New Feature
> Components: examples
> Reporter: Edward J. Yoon
> Priority: Minor
>
> We want to add the cholesky decomposition / factorization to our upcoming
> math package.
> This is Edward's old cholesky decomposition map/reduce code..
> {noformat}
> /**
> * Copyright 2007 The Apache Software Foundation
> *
> * 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.hama.algebra;
> import java.io.IOException;
> import org.apache.hadoop.hbase.HBaseConfiguration;
> import org.apache.hadoop.hbase.HStoreKey;
> import org.apache.hadoop.io.MapWritable;
> import org.apache.hadoop.io.Text;
> import org.apache.hadoop.mapred.JobConf;
> import org.apache.hadoop.mapred.OutputCollector;
> import org.apache.hadoop.mapred.Reporter;
> import org.apache.hama.FeatureVector;
> import org.apache.hama.Matrix;
> import org.apache.hama.TriangularMatrix;
> import org.apache.hama.mapred.MatrixMap;
> import org.apache.hama.mapred.MatrixOutputFormat;
> /**
> * Cholesky Decomposition.
> * <p>
> * For a symmetric, positive definite matrix A, the Cholesky decomposition is
> an
> * lower triangular matrix L so that A = L*L'.
> * </p>
> */
> public class CholeskyDecompositionMap extends MatrixMap<Text, MapWritable> {
> protected Matrix matrix_a;
> protected TriangularMatrix matrix_l;
> public static final String MATRIX_A = "cholesky.decomposition.matrix.a";
> public static final String MATRIX_L = "cholesky.decomposition.matrix.l";
> public void configure(JobConf job) {
> HBaseConfiguration conf = new HBaseConfiguration();
> Text a_name = new Text(job.get(MATRIX_A, ""));
> Text l_name = new Text(job.get(MATRIX_L, ""));
> matrix_a = new Matrix(conf, a_name);
> matrix_l = new TriangularMatrix(conf, l_name);
> }
> /**
> * @param matrix_a
> * @param matrix_l
> * @param map
> * @param jobConf
> */
> public static void initJob(String matrix_a, String matrix_l,
> Class<CholeskyDecompositionMap> map, JobConf jobConf) {
> initJob(matrix_a, map, jobConf);
> jobConf.set(MatrixOutputFormat.OUTPUT, matrix_l);
> jobConf.set(MATRIX_A, matrix_a);
> jobConf.set(MATRIX_L, matrix_l);
> }
> @Override
> public void map(HStoreKey key, MapWritable value,
> OutputCollector<Text, MapWritable> output, Reporter reporter)
> throws IOException {
> int i = Integer.parseInt(String.valueOf(key.getRow()));
> double[] ithRowOfL = new double[matrix_a.getRowDimension()];
> double[] jthRowOfL = new double[matrix_a.getRowDimension()];
> // Vector was added. I don't figure out the result. -- edward
> FeatureVector iOfV = matrix_l.getRowVector(i);
> for(int x = 0; x < iOfV.size(); x++) {
> ithRowOfL[x] = iOfV.getDimAt(x);
> }
> for (int j = i; j < value.size(); j++) {
> FeatureVector jOfV = matrix_l.getRowVector(i);
> for(int x = 0; x < jOfV.size(); x++) {
> jthRowOfL[x] = jOfV.getDimAt(x);
> }
> double sum = matrix_a.get(i, j);
> for (int k = i - 1; k >= 0; k--) {
> sum -= ithRowOfL[k] * jthRowOfL[k];
> }
> if (i == j) {
> matrix_l.setToLower(j, i, Math.sqrt(sum));
> } else {
> double c = matrix_l.get(i, i);
> matrix_l.setToLower(j, i, (sum / c));
> }
> }
> }
> }
> {noformat}
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