/*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* Instances.java
* Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
*
*/
package weka.core;
import weka.core.converters.ArffLoader.ArffReader;
import weka.core.converters.ConverterUtils.DataSource;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.io.Serializable;
import java.util.Enumeration;
import java.util.Random;
/**
* Class for handling an ordered set of weighted instances. <p>
*
* Typical usage: <p>
* <pre>
* import weka.core.converters.ConverterUtils.DataSource;
* ...
*
* // Read all the instances in the file (ARFF, CSV, XRFF, ...)
* DataSource source = new DataSource(filename);
* Instances instances = source.getDataSet();
*
* // Make the last attribute be the class
* instances.setClassIndex(instances.numAttributes() - 1);
*
* // Print header and instances.
* System.out.println("\nDataset:\n");
* System.out.println(instances);
*
* ...
* </pre><p>
*
* All methods that change a set of instances are safe, ie. a change
* of a set of instances does not affect any other sets of
* instances. All methods that change a datasets's attribute
* information clone the dataset before it is changed.
*
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @author Len Trigg (trigg@cs.waikato.ac.nz)
* @author FracPete (fracpete at waikato dot ac dot nz)
* @version $Revision: 1.76 $
*/
public class Instances
implements Serializable, RevisionHandler {
/** for serialization */
static final long serialVersionUID = -19412345060742748L;
/** The filename extension that should be used for arff files */
public final static String FILE_EXTENSION = ".arff";
/** The filename extension that should be used for bin. serialized instances files */
public final static String SERIALIZED_OBJ_FILE_EXTENSION = ".bsi";
/** The keyword used to denote the start of an arff header */
public final static String ARFF_RELATION = "@relation";
/** The keyword used to denote the start of the arff data section */
public final static String ARFF_DATA = "@data";
/** The dataset's name. */
protected /*@spec_public non_null@*/ String m_RelationName;
/** The attribute information. */
protected /*@spec_public non_null@*/ FastVector m_Attributes;
/* public invariant (\forall int i; 0 <= i && i < m_Attributes.size();
m_Attributes.elementAt(i) != null);
*/
/** The instances. */
protected /*@spec_public non_null@*/ FastVector m_Instances;
/** The class attribute's index */
protected int m_ClassIndex;
//@ protected invariant classIndex() == m_ClassIndex;
/** The lines read so far in case of incremental loading. Since the
* StreamTokenizer will be re-initialized with every instance that is read,
* we have to keep track of the number of lines read so far.
* @see #readInstance(Reader) */
protected int m_Lines = 0;
/** used in randomizeAttribute and undoRandomizeAttribute to store/restore
* the index of attribute that was last shuffled, and it's original values
*/
private int attIdx4Randomization = -1;
private double[] attIdxOrigValues;
/**
* Reads an ARFF file from a reader, and assigns a weight of
* one to each instance. Lets the index of the class
* attribute be undefined (negative).
*
* @param reader the reader
* @throws IOException if the ARFF file is not read
* successfully
*/
public Instances(/*@non_null@*/Reader reader) throws IOException {
ArffReader arff = new ArffReader(reader);
Instances dataset = arff.getData();
initialize(dataset, dataset.numInstances());
dataset.copyInstances(0, this, dataset.numInstances());
compactify();
}
/**
* Reads the header of an ARFF file from a reader and
* reserves space for the given number of instances. Lets
* the class index be undefined (negative).
*
* @param reader the reader
* @param capacity the capacity
* @throws IllegalArgumentException if the header is not read successfully
* or the capacity is negative.
* @throws IOException if there is a problem with the reader.
* @deprecated instead of using this method in conjunction with the
* <code>readInstance(Reader)</code> method, one should use the
* <code>ArffLoader</code> or <code>DataSource</code> class instead.
* @see weka.core.converters.ArffLoader
* @see weka.core.converters.ConverterUtils.DataSource
*/
//@ requires capacity >= 0;
//@ ensures classIndex() == -1;
@Deprecated public Instances(/*@non_null@*/Reader reader, int capacity)
throws IOException {
ArffReader arff = new ArffReader(reader, 0);
Instances header = arff.getStructure();
initialize(header, capacity);
m_Lines = arff.getLineNo();
}
/**
* Constructor copying all instances and references to
* the header information from the given set of instances.
*
* @param dataset the set to be copied
*/
public Instances(/*@non_null@*/Instances dataset) {
this(dataset, dataset.numInstances());
dataset.copyInstances(0, this, dataset.numInstances());
}
/**
* Constructor creating an empty set of instances. Copies references
* to the header information from the given set of instances. Sets
* the capacity of the set of instances to 0 if its negative.
*
* @param dataset the instances from which the header
* information is to be taken
* @param capacity the capacity of the new dataset
*/
public Instances(/*@non_null@*/Instances dataset, int capacity) {
initialize(dataset, capacity);
}
/**
* initializes with the header information of the given dataset and sets
* the capacity of the set of instances.
*
* @param dataset the dataset to use as template
* @param capacity the number of rows to reserve
*/
protected void initialize(Instances dataset, int capacity) {
if (capacity < 0)
capacity = 0;
// Strings only have to be "shallow" copied because
// they can't be modified.
m_ClassIndex = dataset.m_ClassIndex;
m_RelationName = dataset.m_RelationName;
m_Attributes = dataset.m_Attributes;
m_Instances = new FastVector(capacity);
}
/**
* Creates a new set of instances by copying a
* subset of another set.
*
* @param source the set of instances from which a subset
* is to be created
* @param first the index of the first instance to be copied
* @param toCopy the number of instances to be copied
* @throws IllegalArgumentException if first and toCopy are out of range
*/
//@ requires 0 <= first;
//@ requires 0 <= toCopy;
//@ requires first + toCopy <= source.numInstances();
public Instances(/*@non_null@*/Instances source, int first, int toCopy) {
this(source, toCopy);
if ((first < 0) || ((first + toCopy) > source.numInstances())) {
throw new IllegalArgumentException("Parameters first and/or toCopy out "+
"of range");
}
source.copyInstances(first, this, toCopy);
}
/**
* Creates an empty set of instances. Uses the given
* attribute information. Sets the capacity of the set of
* instances to 0 if its negative. Given attribute information
* must not be changed after this constructor has been used.
*
* @param name the name of the relation
* @param attInfo the attribute information
* @param capacity the capacity of the set
*/
public Instances(/*@non_null@*/String name,
/*@non_null@*/FastVector attInfo, int capacity) {
m_RelationName = name;
m_ClassIndex = -1;
m_Attributes = attInfo;
for (int i = 0; i < numAttributes(); i++) {
attribute(i).setIndex(i);
}
m_Instances = new FastVector(capacity);
}
/**
* Create a copy of the structure if the data has string or
* relational attributes, "cleanses" string types (i.e. doesn't
* contain references to the strings seen in the past) and all
* relational attributes.
*
* @return a copy of the instance structure.
*/
public Instances stringFreeStructure() {
FastVector newAtts = new FastVector();
for (int i = 0 ; i < m_Attributes.size(); i++) {
Attribute att = (Attribute)m_Attributes.elementAt(i);
if (att.type() == Attribute.STRING) {
newAtts.addElement(new Attribute(att.name(), (FastVector)null, i));
} else if (att.type() == Attribute.RELATIONAL) {
newAtts.addElement(new Attribute(att.name(), new Instances(att.relation(), 0), i));
}
}
if (newAtts.size() == 0) {
return new Instances(this, 0);
}
FastVector atts = (FastVector)m_Attributes.copy();
for (int i = 0; i < newAtts.size(); i++) {
atts.setElementAt(newAtts.elementAt(i), ((Attribute)newAtts.elementAt(i)).index());
}
Instances result = new Instances(this, 0);
result.m_Attributes = atts;
return result;
}
/**
* Adds one instance to the end of the set.
* Shallow copies instance before it is added. Increases the
* size of the dataset if it is not large enough. Does not
* check if the instance is compatible with the dataset.
* Note: String or relational values are not transferred.
*
* @param instance the instance to be added
*/
public void add(/*@non_null@*/ Instance instance) {
Instance newInstance = (Instance)instance.copy();
newInstance.setDataset(this);
m_Instances.addElement(newInstance);
}
/**
* Returns an attribute.
*
* @param index the attribute's index (index starts with 0)
* @return the attribute at the given position
*/
//@ requires 0 <= index;
//@ requires index < m_Attributes.size();
//@ ensures \result != null;
public /*@pure@*/ Attribute attribute(int index) {
return (Attribute) m_Attributes.elementAt(index);
}
/**
* Returns an attribute given its name. If there is more than
* one attribute with the same name, it returns the first one.
* Returns null if the attribute can't be found.
*
* @param name the attribute's name
* @return the attribute with the given name, null if the
* attribute can't be found
*/
public /*@pure@*/ Attribute attribute(String name) {
for (int i = 0; i < numAttributes(); i++) {
if (attribute(i).name().equals(name)) {
return attribute(i);
}
}
return null;
}
/**
* Checks for attributes of the given type in the dataset
*
* @param attType the attribute type to look for
* @return true if attributes of the given type are present
*/
public boolean checkForAttributeType(int attType) {
int i = 0;
while (i < m_Attributes.size()) {
if (attribute(i++).type() == attType) {
return true;
}
}
return false;
}
/**
* Checks for string attributes in the dataset
*
* @return true if string attributes are present, false otherwise
*/
public /*@pure@*/ boolean checkForStringAttributes() {
return checkForAttributeType(Attribute.STRING);
}
/**
* Checks if the given instance is compatible
* with this dataset. Only looks at the size of
* the instance and the ranges of the values for
* nominal and string attributes.
*
* @param instance the instance to check
* @return true if the instance is compatible with the dataset
*/
public /*@pure@*/ boolean checkInstance(Instance instance) {
if (instance.numAttributes() != numAttributes()) {
return false;
}
for (int i = 0; i < numAttributes(); i++) {
if (instance.isMissing(i)) {
continue;
} else if (attribute(i).isNominal() ||
attribute(i).isString()) {
if (!(Utils.eq(instance.value(i),
(double)(int)instance.value(i)))) {
return false;
} else if (Utils.sm(instance.value(i), 0) ||
Utils.gr(instance.value(i),
attribute(i).numValues())) {
return false;
}
}
}
return true;
}
/**
* Returns the class attribute.
*
* @return the class attribute
* @throws UnassignedClassException if the class is not set
*/
//@ requires classIndex() >= 0;
public /*@pure@*/ Attribute classAttribute() {
if (m_ClassIndex < 0) {
throw new UnassignedClassException("Class index is negative (not set)!");
}
return attribute(m_ClassIndex);
}
/**
* Returns the class attribute's index. Returns negative number
* if it's undefined.
*
* @return the class index as an integer
*/
// ensures \result == m_ClassIndex;
public /*@pure@*/ int classIndex() {
return m_ClassIndex;
}
/**
* Compactifies the set of instances. Decreases the capacity of
* the set so that it matches the number of instances in the set.
*/
public void compactify() {
m_Instances.trimToSize();
}
/**
* Removes all instances from the set.
*/
public void delete() {
m_Instances = new FastVector();
}
/**
* Removes an instance at the given position from the set.
*
* @param index the instance's position (index starts with 0)
*/
//@ requires 0 <= index && index < numInstances();
public void delete(int index) {
m_Instances.removeElementAt(index);
}
/**
* Deletes an attribute at the given position
* (0 to numAttributes() - 1). A deep copy of the attribute
* information is performed before the attribute is deleted.
*
* @param position the attribute's position (position starts with 0)
* @throws IllegalArgumentException if the given index is out of range
* or the class attribute is being deleted
*/
//@ requires 0 <= position && position < numAttributes();
//@ requires position != classIndex();
public void deleteAttributeAt(int position) {
if ((position < 0) || (position >= m_Attributes.size())) {
throw new IllegalArgumentException("Index out of range");
}
if (position == m_ClassIndex) {
throw new IllegalArgumentException("Can't delete class attribute");
}
freshAttributeInfo();
if (m_ClassIndex > position) {
m_ClassIndex--;
}
m_Attributes.removeElementAt(position);
for (int i = position; i < m_Attributes.size(); i++) {
Attribute current = (Attribute)m_Attributes.elementAt(i);
current.setIndex(current.index() - 1);
}
for (int i = 0; i < numInstances(); i++) {
instance(i).forceDeleteAttributeAt(position);
}
}
/**
* Deletes all attributes of the given type in the dataset. A deep copy of
* the attribute information is performed before an attribute is deleted.
*
* @param attType the attribute type to delete
* @throws IllegalArgumentException if attribute couldn't be
* successfully deleted (probably because it is the class attribute).
*/
public void deleteAttributeType(int attType) {
int i = 0;
while (i < m_Attributes.size()) {
if (attribute(i).type() == attType) {
deleteAttributeAt(i);
} else {
i++;
}
}
}
/**
* Deletes all string attributes in the dataset. A deep copy of the attribute
* information is performed before an attribute is deleted.
*
* @throws IllegalArgumentException if string attribute couldn't be
* successfully deleted (probably because it is the class attribute).
* @see #deleteAttributeType(int)
*/
public void deleteStringAttributes() {
deleteAttributeType(Attribute.STRING);
}
/**
* Removes all instances with missing values for a particular
* attribute from the dataset.
*
* @param attIndex the attribute's index (index starts with 0)
*/
//@ requires 0 <= attIndex && attIndex < numAttributes();
public void deleteWithMissing(int attIndex) {
FastVector newInstances = new FastVector(numInstances());
for (int i = 0; i < numInstances(); i++) {
if (!instance(i).isMissing(attIndex)) {
newInstances.addElement(instance(i));
}
}
m_Instances = newInstances;
}
/**
* Removes all instances with missing values for a particular
* attribute from the dataset.
*
* @param att the attribute
*/
public void deleteWithMissing(/*@non_null@*/ Attribute att) {
deleteWithMissing(att.index());
}
/**
* Removes all instances with a missing class value
* from the dataset.
*
* @throws UnassignedClassException if class is not set
*/
public void deleteWithMissingClass() {
if (m_ClassIndex < 0) {
throw new UnassignedClassException("Class index is negative (not set)!");
}
deleteWithMissing(m_ClassIndex);
}
/**
* Returns an enumeration of all the attributes.
*
* @return enumeration of all the attributes.
*/
public /*@non_null pure@*/ Enumeration enumerateAttributes() {
return m_Attributes.elements(m_ClassIndex);
}
/**
* Returns an enumeration of all instances in the dataset.
*
* @return enumeration of all instances in the dataset
*/
public /*@non_null pure@*/ Enumeration enumerateInstances() {
return m_Instances.elements();
}
/**
* Checks if two headers are equivalent.
*
* @param dataset another dataset
* @return true if the header of the given dataset is equivalent
* to this header
*/
public /*@pure@*/ boolean equalHeaders(Instances dataset){
// Check class and all attributes
if (m_ClassIndex != dataset.m_ClassIndex) {
return false;
}
if (m_Attributes.size() != dataset.m_Attributes.size()) {
return false;
}
for (int i = 0; i < m_Attributes.size(); i++) {
if (!(attribute(i).equals(dataset.attribute(i)))) {
return false;
}
}
return true;
}
/**
* Returns the first instance in the set.
*
* @return the first instance in the set
*/
//@ requires numInstances() > 0;
public /*@non_null pure@*/ Instance firstInstance() {
return (Instance)m_Instances.firstElement();
}
/**
* Returns a random number generator. The initial seed of the random
* number generator depends on the given seed and the hash code of
* a string representation of a instances chosen based on the given
* seed.
*
* @param seed the given seed
* @return the random number generator
*/
public Random getRandomNumberGenerator(long seed) {
Random r = new Random(seed);
r.setSeed(instance(r.nextInt(numInstances())).toString().hashCode() + seed);
return r;
}
/**
* Inserts an attribute at the given position (0 to
* numAttributes()) and sets all values to be missing.
* Shallow copies the attribute before it is inserted, and performs
* a deep copy of the existing attribute information.
*
* @param att the attribute to be inserted
* @param position the attribute's position (position starts with 0)
* @throws IllegalArgumentException if the given index is out of range
*/
//@ requires 0 <= position;
//@ requires position <= numAttributes();
public void insertAttributeAt(/*@non_null@*/ Attribute att, int position) {
if ((position < 0) ||
(position > m_Attributes.size())) {
throw new IllegalArgumentException("Index out of range");
}
att = (Attribute)att.copy();
freshAttributeInfo();
att.setIndex(position);
m_Attributes.insertElementAt(att, position);
for (int i = position + 1; i < m_Attributes.size(); i++) {
Attribute current = (Attribute)m_Attributes.elementAt(i);
current.setIndex(current.index() + 1);
}
for (int i = 0; i < numInstances(); i++) {
instance(i).forceInsertAttributeAt(position);
}
if (m_ClassIndex >= position) {
m_ClassIndex++;
}
}
/**
* Returns the instance at the given position.
*
* @param index the instance's index (index starts with 0)
* @return the instance at the given position
*/
//@ requires 0 <= index;
//@ requires index < numInstances();
public /*@non_null pure@*/ Instance instance(int index) {
return (Instance)m_Instances.elementAt(index);
}
/**
* Returns the kth-smallest attribute value of a numeric attribute.
* Note that calling this method will change the order of the data!
*
* @param att the Attribute object
* @param k the value of k
* @return the kth-smallest value
*/
public double kthSmallestValue(Attribute att, int k) {
return kthSmallestValue(att.index(), k);
}
/**
* Returns the kth-smallest attribute value of a numeric attribute.
* Note that calling this method will change the order of the data!
* The number of non-missing values in the data must be as least
* as last as k for this to work.
*
* @param attIndex the attribute's index
* @param k the value of k
* @return the kth-smallest value
*/
public double kthSmallestValue(int attIndex, int k) {
if (!attribute(attIndex).isNumeric()) {
throw new IllegalArgumentException("Instances: attribute must be numeric to compute kth-smallest value.");
}
int i,j;
// move all instances with missing values to end
j = numInstances() - 1;
i = 0;
while (i <= j) {
if (instance(j).isMissing(attIndex)) {
j--;
} else {
if (instance(i).isMissing(attIndex)) {
swap(i,j);
j--;
}
i++;
}
}
if ((k < 1) || (k > j+1)) {
throw new IllegalArgumentException("Instances: value for k for computing kth-smallest value too large.");
}
return instance(select(attIndex, 0, j, k)).value(attIndex);
}
/**
* Returns the last instance in the set.
*
* @return the last instance in the set
*/
//@ requires numInstances() > 0;
public /*@non_null pure@*/ Instance lastInstance() {
return (Instance)m_Instances.lastElement();
}
/**
* Returns the mean (mode) for a numeric (nominal) attribute as
* a floating-point value. Returns 0 if the attribute is neither nominal nor
* numeric. If all values are missing it returns zero.
*
* @param attIndex the attribute's index (index starts with 0)
* @return the mean or the mode
*/
public /*@pure@*/ double meanOrMode(int attIndex) {
double result, found;
int [] counts;
if (attribute(attIndex).isNumeric()) {
result = found = 0;
for (int j = 0; j < numInstances(); j++) {
if (!instance(j).isMissing(attIndex)) {
found += instance(j).weight();
result += instance(j).weight()*instance(j).value(attIndex);
}
}
if (found <= 0) {
return 0;
} else {
return result / found;
}
} else if (attribute(attIndex).isNominal()) {
counts = new int[attribute(attIndex).numValues()];
for (int j = 0; j < numInstances(); j++) {
if (!instance(j).isMissing(attIndex)) {
counts[(int) instance(j).value(attIndex)] += instance(j).weight();
}
}
return (double)Utils.maxIndex(counts);
} else {
return 0;
}
}
/**
* Returns the mean (mode) for a numeric (nominal) attribute as a
* floating-point value. Returns 0 if the attribute is neither
* nominal nor numeric. If all values are missing it returns zero.
*
* @param att the attribute
* @return the mean or the mode
*/
public /*@pure@*/ double meanOrMode(Attribute att) {
return meanOrMode(att.index());
}
/**
* Returns the number of attributes.
*
* @return the number of attributes as an integer
*/
//@ ensures \result == m_Attributes.size();
public /*@pure@*/ int numAttributes() {
return m_Attributes.size();
}
/**
* Returns the number of class labels.
*
* @return the number of class labels as an integer if the class
* attribute is nominal, 1 otherwise.
* @throws UnassignedClassException if the class is not set
*/
//@ requires classIndex() >= 0;
public /*@pure@*/ int numClasses() {
if (m_ClassIndex < 0) {
throw new UnassignedClassException("Class index is negative (not set)!");
}
if (!classAttribute().isNominal()) {
return 1;
} else {
return classAttribute().numValues();
}
}
/**
* Returns the number of distinct values of a given attribute.
* Returns the number of instances if the attribute is a
* string attribute. The value 'missing' is not counted.
*
* @param attIndex the attribute (index starts with 0)
* @return the number of distinct values of a given attribute
*/
//@ requires 0 <= attIndex;
//@ requires attIndex < numAttributes();
public /*@pure@*/ int numDistinctValues(int attIndex) {
if (attribute(attIndex).isNumeric()) {
double [] attVals = attributeToDoubleArray(attIndex);
int [] sorted = Utils.sort(attVals);
double prev = 0;
int counter = 0;
for (int i = 0; i < sorted.length; i++) {
Instance current = instance(sorted[i]);
if (current.isMissing(attIndex)) {
break;
}
if ((i == 0) ||
(current.value(attIndex) > prev)) {
prev = current.value(attIndex);
counter++;
}
}
return counter;
} else {
return attribute(attIndex).numValues();
}
}
/**
* Returns the number of distinct values of a given attribute.
* Returns the number of instances if the attribute is a
* string attribute. The value 'missing' is not counted.
*
* @param att the attribute
* @return the number of distinct values of a given attribute
*/
public /*@pure@*/ int numDistinctValues(/*@non_null@*/Attribute att) {
return numDistinctValues(att.index());
}
/**
* Returns the number of instances in the dataset.
*
* @return the number of instances in the dataset as an integer
*/
//@ ensures \result == m_Instances.size();
public /*@pure@*/ int numInstances() {
return m_Instances.size();
}
/**
* Shuffles the instances in the set so that they are ordered
* randomly.
*
* @param random a random number generator
*/
public void randomize(Random random) {
for (int j = numInstances() - 1; j > 0; j--)
swap(j, random.nextInt(j+1));
}
/**
* Does an undo of a previous call to randomizeAttribute, so that the
* original values of the attribute are restored. Only the original values
* before the last call to randomizeAttribute can be restored. Note, the
* original Instances object is modified.
*
* @throws Exception if there was no call to randomizeAttribute or if
* attributes were added or removed since the last call to
* <code>randomizeAttribute</code>
* @see randomizeAttribute
* @author Arne Muller (arne.muller@gmail.com)
*/
public void undoRandomizeAttribute() throws Exception {
if ( attIdx4Randomization < 0 )
throw new Exception("no randomization to undo!");
if ( attIdxOrigValues.length != this.numInstances() )
throw new Exception(
"meanwhile number of attributes has changed, can't undo!");
for ( int i=0; i<attIdxOrigValues.length; i++ ) {
Instance instance = (Instance)(m_Instances.elementAt(i));
instance.modifyValue(attIdx4Randomization, attIdxOrigValues[i]);
}
return;
}
/**
* Shuffles the values of a given attribute in all instances. Note,
* the original Instances object is modified (i.e. no copying), and the
* method is not thread save. To avoid undefined behavior of an Instances
* object you should not perform other Instances modifying operations between
* a call to <code>randomizeAttribute</code> and
* <code>undoRandomizeAttribute</code>.
*
* @param attIdx the index of the attribute to shuffle
* @param random a random number generator
* @param rounds how many rounds of shuffling, minimum must be 1. As more
* rounds of shuffling the more random your attribute value distribution
* (e.g. choose 3, but note that the time needed for shuffling is proportional
* to the number of rounds).
* @see undoRandomizeAttribute
* @author Arne Muller (arne.muller@gmail.com)
*/
public void randomizeAttribute(int attIdx, Random random, int rounds) {
attIdx4Randomization = attIdx;
attIdxOrigValues = this.attributeToDoubleArray(attIdx);
int n = numInstances();
for ( int j=0; j<rounds; j++ ) {
for ( int i=0; i<n; i++ ) {
int r = random.nextInt(n);
Instance iOne = (Instance)(m_Instances.elementAt(i));
Instance iTwo = (Instance)(m_Instances.elementAt(r));
double helper = iOne.value(attIdx);
iOne.modifyValue(attIdx, iTwo.value(attIdx));
iTwo.modifyValue(attIdx, helper);
}
}
return;
}
/**
* Reads a single instance from the reader and appends it
* to the dataset. Automatically expands the dataset if it
* is not large enough to hold the instance. This method does
* not check for carriage return at the end of the line.
*
* @param reader the reader
* @return false if end of file has been reached
* @throws IOException if the information is not read
* successfully
* @deprecated instead of using this method in conjunction with the
* <code>readInstance(Reader)</code> method, one should use the
* <code>ArffLoader</code> or <code>DataSource</code> class instead.
* @see weka.core.converters.ArffLoader
* @see weka.core.converters.ConverterUtils.DataSource
*/
@Deprecated public boolean readInstance(Reader reader) throws IOException {
ArffReader arff = new ArffReader(reader, this, m_Lines, 1);
Instance inst = arff.readInstance(arff.getData(), false);
m_Lines = arff.getLineNo();
if (inst != null) {
add(inst);
return true;
}
else {
return false;
}
}
/**
* Returns the relation's name.
*
* @return the relation's name as a string
*/
//@ ensures \result == m_RelationName;
public /*@pure@*/ String relationName() {
return m_RelationName;
}
/**
* Renames an attribute. This change only affects this
* dataset.
*
* @param att the attribute's index (index starts with 0)
* @param name the new name
*/
public void renameAttribute(int att, String name) {
Attribute newAtt = attribute(att).copy(name);
FastVector newVec = new FastVector(numAttributes());
for (int i = 0; i < numAttributes(); i++) {
if (i == att) {
newVec.addElement(newAtt);
} else {
newVec.addElement(attribute(i));
}
}
m_Attributes = newVec;
}
/**
* Renames an attribute. This change only affects this
* dataset.
*
* @param att the attribute
* @param name the new name
*/
public void renameAttribute(Attribute att, String name) {
renameAttribute(att.index(), name);
}
/**
* Renames the value of a nominal (or string) attribute value. This
* change only affects this dataset.
*
* @param att the attribute's index (index starts with 0)
* @param val the value's index (index starts with 0)
* @param name the new name
*/
public void renameAttributeValue(int att, int val, String name) {
Attribute newAtt = (Attribute)attribute(att).copy();
FastVector newVec = new FastVector(numAttributes());
newAtt.setValue(val, name);
for (int i = 0; i < numAttributes(); i++) {
if (i == att) {
newVec.addElement(newAtt);
} else {
newVec.addElement(attribute(i));
}
}
m_Attributes = newVec;
}
/**
* Renames the value of a nominal (or string) attribute value. This
* change only affects this dataset.
*
* @param att the attribute
* @param val the value
* @param name the new name
*/
public void renameAttributeValue(Attribute att, String val,
String name) {
int v = att.indexOfValue(val);
if (v == -1) throw new IllegalArgumentException(val + " not found");
renameAttributeValue(att.index(), v, name);
}
/**
* Creates a new dataset of the same size using random sampling
* with replacement.
*
* @param random a random number generator
* @return the new dataset
*/
public Instances resample(Random random) {
Instances newData = new Instances(this, numInstances());
while (newData.numInstances() < numInstances()) {
newData.add(instance(random.nextInt(numInstances())));
}
return newData;
}
/**
* Creates a new dataset of the same size using random sampling
* with replacement according to the current instance weights. The
* weights of the instances in the new dataset are set to one.
*
* @param random a random number generator
* @return the new dataset
*/
public Instances resampleWithWeights(Random random) {
double [] weights = new double[numInstances()];
for (int i = 0; i < weights.length; i++) {
weights[i] = instance(i).weight();
}
return resampleWithWeights(random, weights);
}
/**
* Creates a new dataset of the same size using random sampling
* with replacement according to the given weight vector. The
* weights of the instances in the new dataset are set to one.
* The length of the weight vector has to be the same as the
* number of instances in the dataset, and all weights have to
* be positive.
*
* @param random a random number generator
* @param weights the weight vector
* @return the new dataset
* @throws IllegalArgumentException if the weights array is of the wrong
* length or contains negative weights.
*/
public Instances resampleWithWeights(Random random,
double[] weights) {
if (weights.length != numInstances()) {
throw new IllegalArgumentException("weights.length != numInstances.");
}
Instances newData = new Instances(this, numInstances());
if (numInstances() == 0) {
return newData;
}
double[] probabilities = new double[numInstances()];
double sumProbs = 0, sumOfWeights = Utils.sum(weights);
for (int i = 0; i < numInstances(); i++) {
sumProbs += random.nextDouble();
probabilities[i] = sumProbs;
}
Utils.normalize(probabilities, sumProbs / sumOfWeights);
// Make sure that rounding errors don't mess things up
probabilities[numInstances() - 1] = sumOfWeights;
int k = 0; int l = 0;
sumProbs = 0;
while ((k < numInstances() && (l < numInstances()))) {
if (weights[l] < 0) {
throw new IllegalArgumentException("Weights have to be positive.");
}
sumProbs += weights[l];
while ((k < numInstances()) &&
(probabilities[k] <= sumProbs)) {
newData.add(instance(l));
newData.instance(k).setWeight(1);
k++;
}
l++;
}
return newData;
}
/**
* Sets the class attribute.
*
* @param att attribute to be the class
*/
public void setClass(Attribute att) {
m_ClassIndex = att.index();
}
/**
* Sets the class index of the set.
* If the class index is negative there is assumed to be no class.
* (ie. it is undefined)
*
* @param classIndex the new class index (index starts with 0)
* @throws IllegalArgumentException if the class index is too big or < 0
*/
public void setClassIndex(int classIndex) {
if (classIndex >= numAttributes()) {
throw new IllegalArgumentException("Invalid class index: " + classIndex);
}
m_ClassIndex = classIndex;
}
/**
* Sets the relation's name.
*
* @param newName the new relation name.
*/
public void setRelationName(/*@non_null@*/String newName) {
m_RelationName = newName;
}
/**
* Sorts the instances based on an attribute. For numeric attributes,
* instances are sorted in ascending order. For nominal attributes,
* instances are sorted based on the attribute label ordering
* specified in the header. Instances with missing values for the
* attribute are placed at the end of the dataset.
*
* @param attIndex the attribute's index (index starts with 0)
*/
public void sort(int attIndex) {
int i,j;
// move all instances with missing values to end
j = numInstances() - 1;
i = 0;
while (i <= j) {
if (instance(j).isMissing(attIndex)) {
j--;
} else {
if (instance(i).isMissing(attIndex)) {
swap(i,j);
j--;
}
i++;
}
}
quickSort(attIndex, 0, j);
}
/**
* Sorts the instances based on an attribute. For numeric attributes,
* instances are sorted into ascending order. For nominal attributes,
* instances are sorted based on the attribute label ordering
* specified in the header. Instances with missing values for the
* attribute are placed at the end of the dataset.
*
* @param att the attribute
*/
public void sort(Attribute att) {
sort(att.index());
}
/**
* Stratifies a set of instances according to its class values
* if the class attribute is nominal (so that afterwards a
* stratified cross-validation can be performed).
*
* @param numFolds the number of folds in the cross-validation
* @throws UnassignedClassException if the class is not set
*/
public void stratify(int numFolds) {
if (numFolds <= 0) {
throw new IllegalArgumentException("Number of folds must be greater than 1");
}
if (m_ClassIndex < 0) {
throw new UnassignedClassException("Class index is negative (not set)!");
}
if (classAttribute().isNominal()) {
// sort by class
int index = 1;
while (index < numInstances()) {
Instance instance1 = instance(index - 1);
for (int j = index; j < numInstances(); j++) {
Instance instance2 = instance(j);
if ((instance1.classValue() == instance2.classValue()) ||
(instance1.classIsMissing() &&
instance2.classIsMissing())) {
swap(index,j);
index++;
}
}
index++;
}
stratStep(numFolds);
}
}
/**
* Computes the sum of all the instances' weights.
*
* @return the sum of all the instances' weights as a double
*/
public /*@pure@*/ double sumOfWeights() {
double sum = 0;
for (int i = 0; i < numInstances(); i++) {
sum += instance(i).weight();
}
return sum;
}
/**
* Creates the test set for one fold of a cross-validation on
* the dataset.
*
* @param numFolds the number of folds in the cross-validation. Must
* be greater than 1.
* @param numFold 0 for the first fold, 1 for the second, ...
* @return the test set as a set of weighted instances
* @throws IllegalArgumentException if the number of folds is less than 2
* or greater than the number of instances.
*/
//@ requires 2 <= numFolds && numFolds < numInstances();
//@ requires 0 <= numFold && numFold < numFolds;
public Instances testCV(int numFolds, int numFold) {
int numInstForFold, first, offset;
Instances test;
if (numFolds < 2) {
throw new IllegalArgumentException("Number of folds must be at least 2!");
}
if (numFolds > numInstances()) {
throw new IllegalArgumentException("Can't have more folds than instances!");
}
numInstForFold = numInstances() / numFolds;
if (numFold < numInstances() % numFolds){
numInstForFold++;
offset = numFold;
}else
offset = numInstances() % numFolds;
test = new Instances(this, numInstForFold);
first = numFold * (numInstances() / numFolds) + offset;
copyInstances(first, test, numInstForFold);
return test;
}
/**
* Returns the dataset as a string in ARFF format. Strings
* are quoted if they contain whitespace characters, or if they
* are a question mark.
*
* @return the dataset in ARFF format as a string
*/
public String toString() {
StringBuffer text = new StringBuffer();
text.append(ARFF_RELATION).append(" ").
append(Utils.quote(m_RelationName)).append("\n\n");
for (int i = 0; i < numAttributes(); i++) {
text.append(attribute(i)).append("\n");
}
text.append("\n").append(ARFF_DATA).append("\n");
text.append(stringWithoutHeader());
return text.toString();
}
/**
* Returns the instances in the dataset as a string in ARFF format. Strings
* are quoted if they contain whitespace characters, or if they
* are a question mark.
*
* @return the dataset in ARFF format as a string
*/
protected String stringWithoutHeader() {
StringBuffer text = new StringBuffer();
for (int i = 0; i < numInstances(); i++) {
text.append(instance(i));
if (i < numInstances() - 1) {
text.append('\n');
}
}
return text.toString();
}
/**
* Creates the training set for one fold of a cross-validation
* on the dataset.
*
* @param numFolds the number of folds in the cross-validation. Must
* be greater than 1.
* @param numFold 0 for the first fold, 1 for the second, ...
* @return the training set
* @throws IllegalArgumentException if the number of folds is less than 2
* or greater than the number of instances.
*/
//@ requires 2 <= numFolds && numFolds < numInstances();
//@ requires 0 <= numFold && numFold < numFolds;
public Instances trainCV(int numFolds, int numFold) {
int numInstForFold, first, offset;
Instances train;
if (numFolds < 2) {
throw new IllegalArgumentException("Number of folds must be at least 2!");
}
if (numFolds > numInstances()) {
throw new IllegalArgumentException("Can't have more folds than instances!");
}
numInstForFold = numInstances() / numFolds;
if (numFold < numInstances() % numFolds) {
numInstForFold++;
offset = numFold;
}else
offset = numInstances() % numFolds;
train = new Instances(this, numInstances() - numInstForFold);
first = numFold * (numInstances() / numFolds) + offset;
copyInstances(0, train, first);
copyInstances(first + numInstForFold, train,
numInstances() - first - numInstForFold);
return train;
}
/**
* Creates the training set for one fold of a cross-validation
* on the dataset. The data is subsequently randomized based
* on the given random number generator.
*
* @param numFolds the number of folds in the cross-validation. Must
* be greater than 1.
* @param numFold 0 for the first fold, 1 for the second, ...
* @param random the random number generator
* @return the training set
* @throws IllegalArgumentException if the number of folds is less than 2
* or greater than the number of instances.
*/
//@ requires 2 <= numFolds && numFolds < numInstances();
//@ requires 0 <= numFold && numFold < numFolds;
public Instances trainCV(int numFolds, int numFold, Random random) {
Instances train = trainCV(numFolds, numFold);
train.randomize(random);
return train;
}
/**
* Computes the variance for a numeric attribute.
*
* @param attIndex the numeric attribute (index starts with 0)
* @return the variance if the attribute is numeric
* @throws IllegalArgumentException if the attribute is not numeric
*/
public /*@pure@*/ double variance(int attIndex) {
double sum = 0, sumSquared = 0, sumOfWeights = 0;
if (!attribute(attIndex).isNumeric()) {
throw new IllegalArgumentException("Can't compute variance because attribute is " +
"not numeric!");
}
for (int i = 0; i < numInstances(); i++) {
if (!instance(i).isMissing(attIndex)) {
sum += instance(i).weight() *
instance(i).value(attIndex);
sumSquared += instance(i).weight() *
instance(i).value(attIndex) *
instance(i).value(attIndex);
sumOfWeights += instance(i).weight();
}
}
if (sumOfWeights <= 1) {
return 0;
}
double result = (sumSquared - (sum * sum / sumOfWeights)) /
(sumOfWeights - 1);
// We don't like negative variance
if (result < 0) {
return 0;
} else {
return result;
}
}
/**
* Computes the variance for a numeric attribute.
*
* @param att the numeric attribute
* @return the variance if the attribute is numeric
* @throws IllegalArgumentException if the attribute is not numeric
*/
public /*@pure@*/ double variance(Attribute att) {
return variance(att.index());
}
/**
* Calculates summary statistics on the values that appear in this
* set of instances for a specified attribute.
*
* @param index the index of the attribute to summarize (index starts with 0)
* @return an AttributeStats object with it's fields calculated.
*/
//@ requires 0 <= index && index < numAttributes();
public AttributeStats attributeStats(int index) {
AttributeStats result = new AttributeStats();
if (attribute(index).isNominal()) {
result.nominalCounts = new int [attribute(index).numValues()];
}
if (attribute(index).isNumeric()) {
result.numericStats = new weka.experiment.Stats();
}
result.totalCount = numInstances();
double [] attVals = attributeToDoubleArray(index);
int [] sorted = Utils.sort(attVals);
int currentCount = 0;
double prev = Instance.missingValue();
for (int j = 0; j < numInstances(); j++) {
Instance current = instance(sorted[j]);
if (current.isMissing(index)) {
result.missingCount = numInstances() - j;
break;
}
if (current.value(index) == prev) {
currentCount++;
} else {
result.addDistinct(prev, currentCount);
currentCount = 1;
prev = current.value(index);
}
}
result.addDistinct(prev, currentCount);
result.distinctCount--; // So we don't count "missing" as a value
return result;
}
/**
* Gets the value of all instances in this dataset for a particular
* attribute. Useful in conjunction with Utils.sort to allow iterating
* through the dataset in sorted order for some attribute.
*
* @param index the index of the attribute.
* @return an array containing the value of the desired attribute for
* each instance in the dataset.
*/
//@ requires 0 <= index && index < numAttributes();
public /*@pure@*/ double [] attributeToDoubleArray(int index) {
double [] result = new double[numInstances()];
for (int i = 0; i < result.length; i++) {
result[i] = instance(i).value(index);
}
return result;
}
/**
* Generates a string summarizing the set of instances. Gives a breakdown
* for each attribute indicating the number of missing/discrete/unique
* values and other information.
*
* @return a string summarizing the dataset
*/
public String toSummaryString() {
StringBuffer result = new StringBuffer();
result.append("Relation Name: ").append(relationName()).append('\n');
result.append("Num Instances: ").append(numInstances()).append('\n');
result.append("Num Attributes: ").append(numAttributes()).append('\n');
result.append('\n');
result.append(Utils.padLeft("", 5)).append(Utils.padRight("Name", 25));
result.append(Utils.padLeft("Type", 5)).append(Utils.padLeft("Nom", 5));
result.append(Utils.padLeft("Int", 5)).append(Utils.padLeft("Real", 5));
result.append(Utils.padLeft("Missing", 12));
result.append(Utils.padLeft("Unique", 12));
result.append(Utils.padLeft("Dist", 6)).append('\n');
for (int i = 0; i < numAttributes(); i++) {
Attribute a = attribute(i);
AttributeStats as = attributeStats(i);
result.append(Utils.padLeft("" + (i + 1), 4)).append(' ');
result.append(Utils.padRight(a.name(), 25)).append(' ');
long percent;
switch (a.type()) {
case Attribute.NOMINAL:
result.append(Utils.padLeft("Nom", 4)).append(' ');
percent = Math.round(100.0 * as.intCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
result.append(Utils.padLeft("" + 0, 3)).append("% ");
percent = Math.round(100.0 * as.realCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
break;
case Attribute.NUMERIC:
result.append(Utils.padLeft("Num", 4)).append(' ');
result.append(Utils.padLeft("" + 0, 3)).append("% ");
percent = Math.round(100.0 * as.intCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
percent = Math.round(100.0 * as.realCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
break;
case Attribute.DATE:
result.append(Utils.padLeft("Dat", 4)).append(' ');
result.append(Utils.padLeft("" + 0, 3)).append("% ");
percent = Math.round(100.0 * as.intCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
percent = Math.round(100.0 * as.realCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
break;
case Attribute.STRING:
result.append(Utils.padLeft("Str", 4)).append(' ');
percent = Math.round(100.0 * as.intCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
result.append(Utils.padLeft("" + 0, 3)).append("% ");
percent = Math.round(100.0 * as.realCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
break;
case Attribute.RELATIONAL:
result.append(Utils.padLeft("Rel", 4)).append(' ');
percent = Math.round(100.0 * as.intCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
result.append(Utils.padLeft("" + 0, 3)).append("% ");
percent = Math.round(100.0 * as.realCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
break;
default:
result.append(Utils.padLeft("???", 4)).append(' ');
result.append(Utils.padLeft("" + 0, 3)).append("% ");
percent = Math.round(100.0 * as.intCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
percent = Math.round(100.0 * as.realCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
break;
}
result.append(Utils.padLeft("" + as.missingCount, 5)).append(" /");
percent = Math.round(100.0 * as.missingCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
result.append(Utils.padLeft("" + as.uniqueCount, 5)).append(" /");
percent = Math.round(100.0 * as.uniqueCount / as.totalCount);
result.append(Utils.padLeft("" + percent, 3)).append("% ");
result.append(Utils.padLeft("" + as.distinctCount, 5)).append(' ');
result.append('\n');
}
return result.toString();
}
/**
* Copies instances from one set to the end of another
* one.
*
* @param from the position of the first instance to be copied
* @param dest the destination for the instances
* @param num the number of instances to be copied
*/
//@ requires 0 <= from && from <= numInstances() - num;
//@ requires 0 <= num;
protected void copyInstances(int from, /*@non_null@*/ Instances dest, int num) {
for (int i = 0; i < num; i++) {
dest.add(instance(from + i));
}
}
/**
* Replaces the attribute information by a clone of
* itself.
*/
protected void freshAttributeInfo() {
m_Attributes = (FastVector) m_Attributes.copyElements();
}
/**
* Returns string including all instances, their weights and
* their indices in the original dataset.
*
* @return description of instance and its weight as a string
*/
protected /*@pure@*/ String instancesAndWeights(){
StringBuffer text = new StringBuffer();
for (int i = 0; i < numInstances(); i++) {
text.append(instance(i) + " " + instance(i).weight());
if (i < numInstances() - 1) {
text.append("\n");
}
}
return text.toString();
}
/**
* Partitions the instances around a pivot. Used by quicksort and
* kthSmallestValue.
*
* @param attIndex the attribute's index (index starts with 0)
* @param l the first index of the subset (index starts with 0)
* @param r the last index of the subset (index starts with 0)
*
* @return the index of the middle element
*/
//@ requires 0 <= attIndex && attIndex < numAttributes();
//@ requires 0 <= left && left <= right && right < numInstances();
protected int partition(int attIndex, int l, int r) {
double pivot = instance((l + r) / 2).value(attIndex);
while (l < r) {
while ((instance(l).value(attIndex) < pivot) && (l < r)) {
l++;
}
while ((instance(r).value(attIndex) > pivot) && (l < r)) {
r--;
}
if (l < r) {
swap(l, r);
l++;
r--;
}
}
if ((l == r) && (instance(r).value(attIndex) > pivot)) {
r--;
}
return r;
}
/**
* Implements quicksort according to Manber's "Introduction to
* Algorithms".
*
* @param attIndex the attribute's index (index starts with 0)
* @param left the first index of the subset to be sorted (index starts with 0)
* @param right the last index of the subset to be sorted (index starts with 0)
*/
//@ requires 0 <= attIndex && attIndex < numAttributes();
//@ requires 0 <= first && first <= right && right < numInstances();
protected void quickSort(int attIndex, int left, int right) {
if (left < right) {
int middle = partition(attIndex, left, right);
quickSort(attIndex, left, middle);
quickSort(attIndex, middle + 1, right);
}
}
/**
* Implements computation of the kth-smallest element according
* to Manber's "Introduction to Algorithms".
*
* @param attIndex the attribute's index (index starts with 0)
* @param left the first index of the subset (index starts with 0)
* @param right the last index of the subset (index starts with 0)
* @param k the value of k
*
* @return the index of the kth-smallest element
*/
//@ requires 0 <= attIndex && attIndex < numAttributes();
//@ requires 0 <= first && first <= right && right < numInstances();
protected int select(int attIndex, int left, int right, int k) {
if (left == right) {
return left;
} else {
int middle = partition(attIndex, left, right);
if ((middle - left + 1) >= k) {
return select(attIndex, left, middle, k);
} else {
return select(attIndex, middle + 1, right, k - (middle - left + 1));
}
}
}
/**
* Help function needed for stratification of set.
*
* @param numFolds the number of folds for the stratification
*/
protected void stratStep (int numFolds){
FastVector newVec = new FastVector(m_Instances.capacity());
int start = 0, j;
// create stratified batch
while (newVec.size() < numInstances()) {
j = start;
while (j < numInstances()) {
newVec.addElement(instance(j));
j = j + numFolds;
}
start++;
}
m_Instances = newVec;
}
/**
* Swaps two instances in the set.
*
* @param i the first instance's index (index starts with 0)
* @param j the second instance's index (index starts with 0)
*/
//@ requires 0 <= i && i < numInstances();
//@ requires 0 <= j && j < numInstances();
public void swap(int i, int j){
m_Instances.swap(i, j);
}
/**
* Merges two sets of Instances together. The resulting set will have
* all the attributes of the first set plus all the attributes of the
* second set. The number of instances in both sets must be the same.
*
* @param first the first set of Instances
* @param second the second set of Instances
* @return the merged set of Instances
* @throws IllegalArgumentException if the datasets are not the same size
*/
public static Instances mergeInstances(Instances first, Instances second) {
if (first.numInstances() != second.numInstances()) {
throw new IllegalArgumentException("Instance sets must be of the same size");
}
// Create the vector of merged attributes
FastVector newAttributes = new FastVector();
for (int i = 0; i < first.numAttributes(); i++) {
newAttributes.addElement(first.attribute(i));
}
for (int i = 0; i < second.numAttributes(); i++) {
newAttributes.addElement(second.attribute(i));
}
// Create the set of Instances
Instances merged = new Instances(first.relationName() + '_'
+ second.relationName(),
newAttributes,
first.numInstances());
// Merge each instance
for (int i = 0; i < first.numInstances(); i++) {
merged.add(first.instance(i).mergeInstance(second.instance(i)));
}
return merged;
}
/**
* Method for testing this class.
*
* @param argv should contain one element: the name of an ARFF file
*/
//@ requires argv != null;
//@ requires argv.length == 1;
//@ requires argv[0] != null;
public static void test(String [] argv) {
Instances instances, secondInstances, train, test, empty;
Random random = new Random(2);
Reader reader;
int start, num;
FastVector testAtts, testVals;
int i,j;
try{
if (argv.length > 1) {
throw (new Exception("Usage: Instances [<filename>]"));
}
// Creating set of instances from scratch
testVals = new FastVector(2);
testVals.addElement("first_value");
testVals.addElement("second_value");
testAtts = new FastVector(2);
testAtts.addElement(new Attribute("nominal_attribute", testVals));
testAtts.addElement(new Attribute("numeric_attribute"));
instances = new Instances("test_set", testAtts, 10);
instances.add(new Instance(instances.numAttributes()));
instances.add(new Instance(instances.numAttributes()));
instances.add(new Instance(instances.numAttributes()));
instances.setClassIndex(0);
System.out.println("\nSet of instances created from scratch:\n");
System.out.println(instances);
if (argv.length == 1) {
String filename = argv[0];
reader = new FileReader(filename);
// Read first five instances and print them
System.out.println("\nFirst five instances from file:\n");
instances = new Instances(reader, 1);
instances.setClassIndex(instances.numAttributes() - 1);
i = 0;
while ((i < 5) && (instances.readInstance(reader))) {
i++;
}
System.out.println(instances);
// Read all the instances in the file
reader = new FileReader(filename);
instances = new Instances(reader);
// Make the last attribute be the class
instances.setClassIndex(instances.numAttributes() - 1);
// Print header and instances.
System.out.println("\nDataset:\n");
System.out.println(instances);
System.out.println("\nClass index: "+instances.classIndex());
}
// Test basic methods based on class index.
System.out.println("\nClass name: "+instances.classAttribute().name());
System.out.println("\nClass index: "+instances.classIndex());
System.out.println("\nClass is nominal: " +
instances.classAttribute().isNominal());
System.out.println("\nClass is numeric: " +
instances.classAttribute().isNumeric());
System.out.println("\nClasses:\n");
for (i = 0; i < instances.numClasses(); i++) {
System.out.println(instances.classAttribute().value(i));
}
System.out.println("\nClass values and labels of instances:\n");
for (i = 0; i < instances.numInstances(); i++) {
Instance inst = instances.instance(i);
System.out.print(inst.classValue() + "\t");
System.out.print(inst.toString(inst.classIndex()));
if (instances.instance(i).classIsMissing()) {
System.out.println("\tis missing");
} else {
System.out.println();
}
}
// Create random weights.
System.out.println("\nCreating random weights for instances.");
for (i = 0; i < instances.numInstances(); i++) {
instances.instance(i).setWeight(random.nextDouble());
}
// Print all instances and their weights (and the sum of weights).
System.out.println("\nInstances and their weights:\n");
System.out.println(instances.instancesAndWeights());
System.out.print("\nSum of weights: ");
System.out.println(instances.sumOfWeights());
// Insert an attribute
secondInstances = new Instances(instances);
Attribute testAtt = new Attribute("Inserted");
secondInstances.insertAttributeAt(testAtt, 0);
System.out.println("\nSet with inserted attribute:\n");
System.out.println(secondInstances);
System.out.println("\nClass name: "
+ secondInstances.classAttribute().name());
// Delete the attribute
secondInstances.deleteAttributeAt(0);
System.out.println("\nSet with attribute deleted:\n");
System.out.println(secondInstances);
System.out.println("\nClass name: "
+ secondInstances.classAttribute().name());
// Test if headers are equal
System.out.println("\nHeaders equal: "+
instances.equalHeaders(secondInstances) + "\n");
// Print data in internal format.
System.out.println("\nData (internal values):\n");
for (i = 0; i < instances.numInstances(); i++) {
for (j = 0; j < instances.numAttributes(); j++) {
if (instances.instance(i).isMissing(j)) {
System.out.print("? ");
} else {
System.out.print(instances.instance(i).value(j) + " ");
}
}
System.out.println();
}
// Just print header
System.out.println("\nEmpty dataset:\n");
empty = new Instances(instances, 0);
System.out.println(empty);
System.out.println("\nClass name: "+empty.classAttribute().name());
// Create copy and rename an attribute and a value (if possible)
if (empty.classAttribute().isNominal()) {
Instances copy = new Instances(empty, 0);
copy.renameAttribute(copy.classAttribute(), "new_name");
copy.renameAttributeValue(copy.classAttribute(),
copy.classAttribute().value(0),
"new_val_name");
System.out.println("\nDataset with names changed:\n" + copy);
System.out.println("\nOriginal dataset:\n" + empty);
}
// Create and prints subset of instances.
start = instances.numInstances() / 4;
num = instances.numInstances() / 2;
System.out.print("\nSubset of dataset: ");
System.out.println(num + " instances from " + (start + 1)
+ ". instance");
secondInstances = new Instances(instances, start, num);
System.out.println("\nClass name: "
+ secondInstances.classAttribute().name());
// Print all instances and their weights (and the sum of weights).
System.out.println("\nInstances and their weights:\n");
System.out.println(secondInstances.instancesAndWeights());
System.out.print("\nSum of weights: ");
System.out.println(secondInstances.sumOfWeights());
// Create and print training and test sets for 3-fold
// cross-validation.
System.out.println("\nTrain and test folds for 3-fold CV:");
if (instances.classAttribute().isNominal()) {
instances.stratify(3);
}
for (j = 0; j < 3; j++) {
train = instances.trainCV(3,j, new Random(1));
test = instances.testCV(3,j);
// Print all instances and their weights (and the sum of weights).
System.out.println("\nTrain: ");
System.out.println("\nInstances and their weights:\n");
System.out.println(train.instancesAndWeights());
System.out.print("\nSum of weights: ");
System.out.println(train.sumOfWeights());
System.out.println("\nClass name: "+train.classAttribute().name());
System.out.println("\nTest: ");
System.out.println("\nInstances and their weights:\n");
System.out.println(test.instancesAndWeights());
System.out.print("\nSum of weights: ");
System.out.println(test.sumOfWeights());
System.out.println("\nClass name: "+test.classAttribute().name());
}
// Randomize instances and print them.
System.out.println("\nRandomized dataset:");
instances.randomize(random);
// Print all instances and their weights (and the sum of weights).
System.out.println("\nInstances and their weights:\n");
System.out.println(instances.instancesAndWeights());
System.out.print("\nSum of weights: ");
System.out.println(instances.sumOfWeights());
// Sort instances according to first attribute and
// print them.
System.out.print("\nInstances sorted according to first attribute:\n ");
instances.sort(0);
// Print all instances and their weights (and the sum of weights).
System.out.println("\nInstances and their weights:\n");
System.out.println(instances.instancesAndWeights());
System.out.print("\nSum of weights: ");
System.out.println(instances.sumOfWeights());
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Main method for this class. The following calls are possible:
* <ul>
* <li>
* <code>weka.core.Instances</code> help<br/>
* prints a short list of possible commands.
* </li>
* <li>
* <code>weka.core.Instances</code> <filename><br/>
* prints a summary of a set of instances.
* </li>
* <li>
* <code>weka.core.Instances</code> merge <filename1> <filename2><br/>
* merges the two datasets (must have same number of instances) and
* outputs the results on stdout.
* </li>
* <li>
* <code>weka.core.Instances</code> append <filename1> <filename2><br/>
* appends the second dataset to the first one (must have same headers) and
* outputs the results on stdout.
* </li>
* <li>
* <code>weka.core.Instances</code> randomize <seed> <filename><br/>
* randomizes the dataset with the given seed and outputs the result on stdout.
* </li>
* </ul>
*
* @param args the commandline parameters
*/
public static void main(String[] args) {
try {
Instances i;
// read from stdin and print statistics
if (args.length == 0) {
DataSource source = new DataSource(System.in);
i = source.getDataSet();
System.out.println(i.toSummaryString());
}
// read file and print statistics
else if ((args.length == 1) && (!args[0].equals("-h")) && (!args[0].equals("help"))) {
DataSource source = new DataSource(args[0]);
i = source.getDataSet();
System.out.println(i.toSummaryString());
}
// read two files, merge them and print result to stdout
else if ((args.length == 3) && (args[0].toLowerCase().equals("merge"))) {
DataSource source1 = new DataSource(args[1]);
DataSource source2 = new DataSource(args[2]);
i = Instances.mergeInstances(source1.getDataSet(), source2.getDataSet());
System.out.println(i);
}
// read two files, append them and print result to stdout
else if ((args.length == 3) && (args[0].toLowerCase().equals("append"))) {
DataSource source1 = new DataSource(args[1]);
DataSource source2 = new DataSource(args[2]);
if (!source1.getStructure().equalHeaders(source2.getStructure()))
throw new Exception("The two datasets have different headers!");
Instances structure = source1.getStructure();
System.out.println(source1.getStructure());
while (source1.hasMoreElements(structure))
System.out.println(source1.nextElement(structure));
structure = source2.getStructure();
while (source2.hasMoreElements(structure))
System.out.println(source2.nextElement(structure));
}
// read file and seed value, randomize data and print result to stdout
else if ((args.length == 3) && (args[0].toLowerCase().equals("randomize"))) {
DataSource source = new DataSource(args[2]);
i = source.getDataSet();
i.randomize(new Random(Integer.parseInt(args[1])));
System.out.println(i);
}
// wrong parameters
else {
System.err.println(
"\nUsage:\n"
+ "\tweka.core.Instances help\n"
+ "\tweka.core.Instances <filename>\n"
+ "\tweka.core.Instances merge <filename1> <filename2>\n"
+ "\tweka.core.Instances append <filename1> <filename2>\n"
+ "\tweka.core.Instances randomize <seed> <filename>\n"
);
System.exit(1);
}
}
catch (Exception ex) {
ex.printStackTrace();
System.err.println(ex.getMessage());
}
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.76 $");
}
}