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Scalable machine learning libraries
/**
* 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.classifier.df.data;
import com.google.common.base.Preconditions;
import com.google.common.io.Closeables;
import org.apache.commons.lang3.ArrayUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.codehaus.jackson.map.ObjectMapper;
import org.codehaus.jackson.type.TypeReference;
import java.io.IOException;
import java.nio.charset.Charset;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
/**
* Contains information about the attributes.
*/
@Deprecated
public class Dataset {
/**
* Attributes type
*/
public enum Attribute {
IGNORED,
NUMERICAL,
CATEGORICAL,
LABEL;
public boolean isNumerical() {
return this == NUMERICAL;
}
public boolean isCategorical() {
return this == CATEGORICAL;
}
public boolean isLabel() {
return this == LABEL;
}
public boolean isIgnored() {
return this == IGNORED;
}
private static Attribute fromString(String from) {
Attribute toReturn = LABEL;
if (NUMERICAL.toString().equalsIgnoreCase(from)) {
toReturn = NUMERICAL;
} else if (CATEGORICAL.toString().equalsIgnoreCase(from)) {
toReturn = CATEGORICAL;
} else if (IGNORED.toString().equalsIgnoreCase(from)) {
toReturn = IGNORED;
}
return toReturn;
}
}
private Attribute[] attributes;
/**
* list of ignored attributes
*/
private int[] ignored;
/**
* distinct values (CATEGORIAL attributes only)
*/
private String[][] values;
/**
* index of the label attribute in the loaded data (without ignored attributed)
*/
private int labelId;
/**
* number of instances in the dataset
*/
private int nbInstances;
/** JSON serial/de-serial-izer */
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
// Some literals for JSON representation
static final String TYPE = "type";
static final String VALUES = "values";
static final String LABEL = "label";
protected Dataset() {}
/**
* Should only be called by a DataLoader
*
* @param attrs attributes description
* @param values distinct values for all CATEGORICAL attributes
*/
Dataset(Attribute[] attrs, List[] values, int nbInstances, boolean regression) {
validateValues(attrs, values);
int nbattrs = countAttributes(attrs);
// the label values are set apart
attributes = new Attribute[nbattrs];
this.values = new String[nbattrs][];
ignored = new int[attrs.length - nbattrs]; // nbignored = total - nbattrs
labelId = -1;
int ignoredId = 0;
int ind = 0;
for (int attr = 0; attr < attrs.length; attr++) {
if (attrs[attr].isIgnored()) {
ignored[ignoredId++] = attr;
continue;
}
if (attrs[attr].isLabel()) {
if (labelId != -1) {
throw new IllegalStateException("Label found more than once");
}
labelId = ind;
if (regression) {
attrs[attr] = Attribute.NUMERICAL;
} else {
attrs[attr] = Attribute.CATEGORICAL;
}
}
if (attrs[attr].isCategorical() || (!regression && attrs[attr].isLabel())) {
this.values[ind] = new String[values[attr].size()];
values[attr].toArray(this.values[ind]);
}
attributes[ind++] = attrs[attr];
}
if (labelId == -1) {
throw new IllegalStateException("Label not found");
}
this.nbInstances = nbInstances;
}
public int nbValues(int attr) {
return values[attr].length;
}
public String[] labels() {
return Arrays.copyOf(values[labelId], nblabels());
}
public int nblabels() {
return values[labelId].length;
}
public int getLabelId() {
return labelId;
}
public double getLabel(Instance instance) {
return instance.get(getLabelId());
}
public Attribute getAttribute(int attr) {
return attributes[attr];
}
/**
* Returns the code used to represent the label value in the data
*
* @param label label's value to code
* @return label's code
*/
public int labelCode(String label) {
return ArrayUtils.indexOf(values[labelId], label);
}
/**
* Returns the label value in the data
* This method can be used when the criterion variable is the categorical attribute.
*
* @param code label's code
* @return label's value
*/
public String getLabelString(double code) {
// handle the case (prediction is NaN)
if (Double.isNaN(code)) {
return "unknown";
}
return values[labelId][(int) code];
}
@Override
public String toString() {
return "attributes=" + Arrays.toString(attributes);
}
/**
* Converts a token to its corresponding integer code for a given attribute
*
* @param attr attribute index
*/
public int valueOf(int attr, String token) {
Preconditions.checkArgument(!isNumerical(attr), "Only for CATEGORICAL attributes");
Preconditions.checkArgument(values != null, "Values not found (equals null)");
return ArrayUtils.indexOf(values[attr], token);
}
public int[] getIgnored() {
return ignored;
}
/**
* @return number of attributes that are not IGNORED
*/
private static int countAttributes(Attribute[] attrs) {
int nbattrs = 0;
for (Attribute attr : attrs) {
if (!attr.isIgnored()) {
nbattrs++;
}
}
return nbattrs;
}
private static void validateValues(Attribute[] attrs, List[] values) {
Preconditions.checkArgument(attrs.length == values.length, "attrs.length != values.length");
for (int attr = 0; attr < attrs.length; attr++) {
Preconditions.checkArgument(!attrs[attr].isCategorical() || values[attr] != null,
"values not found for attribute " + attr);
}
}
/**
* @return number of attributes
*/
public int nbAttributes() {
return attributes.length;
}
/**
* Is this a numerical attribute ?
*
* @param attr index of the attribute to check
* @return true if the attribute is numerical
*/
public boolean isNumerical(int attr) {
return attributes[attr].isNumerical();
}
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (!(obj instanceof Dataset)) {
return false;
}
Dataset dataset = (Dataset) obj;
if (!Arrays.equals(attributes, dataset.attributes)) {
return false;
}
for (int attr = 0; attr < nbAttributes(); attr++) {
if (!Arrays.equals(values[attr], dataset.values[attr])) {
return false;
}
}
return labelId == dataset.labelId && nbInstances == dataset.nbInstances;
}
@Override
public int hashCode() {
int hashCode = labelId + 31 * nbInstances;
for (Attribute attr : attributes) {
hashCode = 31 * hashCode + attr.hashCode();
}
for (String[] valueRow : values) {
if (valueRow == null) {
continue;
}
for (String value : valueRow) {
hashCode = 31 * hashCode + value.hashCode();
}
}
return hashCode;
}
/**
* Loads the dataset from a file
*
* @throws java.io.IOException
*/
public static Dataset load(Configuration conf, Path path) throws IOException {
FileSystem fs = path.getFileSystem(conf);
long bytesToRead = fs.getFileStatus(path).getLen();
byte[] buff = new byte[Long.valueOf(bytesToRead).intValue()];
FSDataInputStream input = fs.open(path);
try {
input.readFully(buff);
} finally {
Closeables.close(input, true);
}
String json = new String(buff, Charset.defaultCharset());
return fromJSON(json);
}
/**
* Serialize this instance to JSON
* @return some JSON
*/
public String toJSON() {
List> toWrite = new LinkedList<>();
// attributes does not include ignored columns and it does include the class label
int ignoredCount = 0;
for (int i = 0; i < attributes.length + ignored.length; i++) {
Map attribute;
int attributesIndex = i - ignoredCount;
if (ignoredCount < ignored.length && i == ignored[ignoredCount]) {
// fill in ignored atttribute
attribute = getMap(Attribute.IGNORED, null, false);
ignoredCount++;
} else if (attributesIndex == labelId) {
// fill in the label
attribute = getMap(attributes[attributesIndex], values[attributesIndex], true);
} else {
// normal attribute
attribute = getMap(attributes[attributesIndex], values[attributesIndex], false);
}
toWrite.add(attribute);
}
try {
return OBJECT_MAPPER.writeValueAsString(toWrite);
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
/**
* De-serialize an instance from a string
* @param json From which an instance is created
* @return A shiny new Dataset
*/
public static Dataset fromJSON(String json) {
List> fromJSON;
try {
fromJSON = OBJECT_MAPPER.readValue(json, new TypeReference>>() {});
} catch (Exception ex) {
throw new RuntimeException(ex);
}
List attributes = new LinkedList<>();
List ignored = new LinkedList<>();
String[][] nominalValues = new String[fromJSON.size()][];
Dataset dataset = new Dataset();
for (int i = 0; i < fromJSON.size(); i++) {
Map attribute = fromJSON.get(i);
if (Attribute.fromString((String) attribute.get(TYPE)) == Attribute.IGNORED) {
ignored.add(i);
} else {
Attribute asAttribute = Attribute.fromString((String) attribute.get(TYPE));
attributes.add(asAttribute);
if ((Boolean) attribute.get(LABEL)) {
dataset.labelId = i - ignored.size();
}
if (attribute.get(VALUES) != null) {
List get = (List) attribute.get(VALUES);
String[] array = get.toArray(new String[get.size()]);
nominalValues[i - ignored.size()] = array;
}
}
}
dataset.attributes = attributes.toArray(new Attribute[attributes.size()]);
dataset.ignored = new int[ignored.size()];
dataset.values = nominalValues;
for (int i = 0; i < dataset.ignored.length; i++) {
dataset.ignored[i] = ignored.get(i);
}
return dataset;
}
/**
* Generate a map to describe an attribute
* @param type The type
* @param values - values
* @param isLabel - is a label
* @return map of (AttributeTypes, Values)
*/
private Map getMap(Attribute type, String[] values, boolean isLabel) {
Map attribute = new HashMap<>();
attribute.put(TYPE, type.toString().toLowerCase(Locale.getDefault()));
attribute.put(VALUES, values);
attribute.put(LABEL, isLabel);
return attribute;
}
}
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