/*
* 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 3 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, see <http://www.gnu.org/licenses/>.
*/
/*
* SparseInstance.java
* Copyright (C) 2000-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.core;
import java.util.ArrayList;
import java.util.Enumeration;
/**
* Class for storing an instance as a sparse vector. A sparse instance only
* requires storage for those attribute values that are non-zero. Since the
* objective is to reduce storage requirements for datasets with large numbers
* of default values, this also includes nominal attributes -- the first nominal
* value (i.e. that which has index 0) will not require explicit storage, so
* rearrange your nominal attribute value orderings if necessary. Missing values
* will be stored explicitly.
*
* @author Eibe Frank
* @version $Revision: 9028 $
*/
public class SparseInstance extends AbstractInstance {
/** for serialization */
private static final long serialVersionUID = -3579051291332630149L;
/** The index of the attribute associated with each stored value. */
protected int[] m_Indices;
/** The maximum number of values that can be stored. */
protected int m_NumAttributes;
/**
* Constructor that generates a sparse instance from the given instance.
* Reference to the dataset is set to null. (ie. the instance doesn't have
* access to information about the attribute types)
*
* @param instance the instance from which the attribute values and the weight
* are to be copied
*/
public SparseInstance(Instance instance) {
m_Weight = instance.weight();
m_Dataset = null;
m_NumAttributes = instance.numAttributes();
if (instance instanceof SparseInstance) {
m_AttValues = ((SparseInstance) instance).m_AttValues;
m_Indices = ((SparseInstance) instance).m_Indices;
} else {
double[] tempValues = new double[instance.numAttributes()];
int[] tempIndices = new int[instance.numAttributes()];
int vals = 0;
for (int i = 0; i < instance.numAttributes(); i++) {
if (instance.value(i) != 0) {
tempValues[vals] = instance.value(i);
tempIndices[vals] = i;
vals++;
}
}
m_AttValues = new double[vals];
m_Indices = new int[vals];
System.arraycopy(tempValues, 0, m_AttValues, 0, vals);
System.arraycopy(tempIndices, 0, m_Indices, 0, vals);
}
}
/**
* Constructor that copies the info from the given instance. Reference to the
* dataset is set to null. (ie. the instance doesn't have access to
* information about the attribute types)
*
* @param instance the instance from which the attribute info is to be copied
*/
public SparseInstance(SparseInstance instance) {
m_AttValues = instance.m_AttValues;
m_Indices = instance.m_Indices;
m_Weight = instance.m_Weight;
m_NumAttributes = instance.m_NumAttributes;
m_Dataset = null;
}
/**
* Constructor that generates a sparse instance from the given parameters.
* Reference to the dataset is set to null. (ie. the instance doesn't have
* access to information about the attribute types)
*
* @param weight the instance's weight
* @param attValues a vector of attribute values
*/
public SparseInstance(double weight, double[] attValues) {
m_Weight = weight;
m_Dataset = null;
m_NumAttributes = attValues.length;
double[] tempValues = new double[m_NumAttributes];
int[] tempIndices = new int[m_NumAttributes];
int vals = 0;
for (int i = 0; i < m_NumAttributes; i++) {
if (attValues[i] != 0) {
tempValues[vals] = attValues[i];
tempIndices[vals] = i;
vals++;
}
}
m_AttValues = new double[vals];
m_Indices = new int[vals];
System.arraycopy(tempValues, 0, m_AttValues, 0, vals);
System.arraycopy(tempIndices, 0, m_Indices, 0, vals);
}
/**
* Constructor that inititalizes instance variable with given values.
* Reference to the dataset is set to null. (ie. the instance doesn't have
* access to information about the attribute types) Note that the indices need
* to be sorted in ascending order. Otherwise things won't work properly.
*
* @param weight the instance's weight
* @param attValues a vector of attribute values (just the ones to be stored)
* @param indices the indices of the given values in the full vector (need to
* be sorted in ascending order)
* @param maxNumValues the maximium number of values that can be stored
*/
public SparseInstance(double weight, double[] attValues, int[] indices,
int maxNumValues) {
int vals = 0;
m_AttValues = new double[attValues.length];
m_Indices = new int[indices.length];
for (int i = 0; i < attValues.length; i++) {
if (attValues[i] != 0) {
m_AttValues[vals] = attValues[i];
m_Indices[vals] = indices[i];
vals++;
}
}
if (vals != attValues.length) {
// Need to truncate.
double[] newVals = new double[vals];
System.arraycopy(m_AttValues, 0, newVals, 0, vals);
m_AttValues = newVals;
int[] newIndices = new int[vals];
System.arraycopy(m_Indices, 0, newIndices, 0, vals);
m_Indices = newIndices;
}
m_Weight = weight;
m_NumAttributes = maxNumValues;
m_Dataset = null;
}
/**
* Constructor of an instance that sets weight to one, all values to be
* missing, and the reference to the dataset to null. (ie. the instance
* doesn't have access to information about the attribute types)
*
* @param numAttributes the size of the instance
*/
public SparseInstance(int numAttributes) {
m_AttValues = new double[numAttributes];
m_NumAttributes = numAttributes;
m_Indices = new int[numAttributes];
for (int i = 0; i < m_AttValues.length; i++) {
m_AttValues[i] = Utils.missingValue();
m_Indices[i] = i;
}
m_Weight = 1;
m_Dataset = null;
}
/**
* Produces a shallow copy of this instance. The copy has access to the same
* dataset. (if you want to make a copy that doesn't have access to the
* dataset, use <code>new SparseInstance(instance)</code>
*
* @return the shallow copy
*/
@Override
public Object copy() {
SparseInstance result = new SparseInstance(this);
result.m_Dataset = m_Dataset;
return result;
}
/**
* Returns the index of the attribute stored at the given position.
*
* @param position the position
* @return the index of the attribute stored at the given position
*/
@Override
public int index(int position) {
return m_Indices[position];
}
/**
* Locates the greatest index that is not greater than the given index.
*
* @return the internal index of the attribute index. Returns -1 if no index
* with this property could be found
*/
public int locateIndex(int index) {
int min = 0, max = m_Indices.length - 1;
if (max == -1) {
return -1;
}
// Binary search
while ((m_Indices[min] <= index) && (m_Indices[max] >= index)) {
int current = (max + min) / 2;
if (m_Indices[current] > index) {
max = current - 1;
} else if (m_Indices[current] < index) {
min = current + 1;
} else {
return current;
}
}
if (m_Indices[max] < index) {
return max;
} else {
return min - 1;
}
}
/**
* Merges this instance with the given instance and returns the result.
* Dataset is set to null.
*
* @param inst the instance to be merged with this one
* @return the merged instances
*/
@Override
public Instance mergeInstance(Instance inst) {
double[] values = new double[numValues() + inst.numValues()];
int[] indices = new int[numValues() + inst.numValues()];
int m = 0;
for (int j = 0; j < numValues(); j++, m++) {
values[m] = valueSparse(j);
indices[m] = index(j);
}
for (int j = 0; j < inst.numValues(); j++, m++) {
values[m] = inst.valueSparse(j);
indices[m] = numAttributes() + inst.index(j);
}
return new SparseInstance(1.0, values, indices, numAttributes()
+ inst.numAttributes());
}
/**
* Returns the number of attributes.
*
* @return the number of attributes as an integer
*/
@Override
public int numAttributes() {
return m_NumAttributes;
}
/**
* Returns the number of values in the sparse vector.
*
* @return the number of values
*/
@Override
public int numValues() {
return m_Indices.length;
}
/**
* Replaces all missing values in the instance with the values contained in
* the given array. A deep copy of the vector of attribute values is performed
* before the values are replaced.
*
* @param array containing the means and modes
* @exception IllegalArgumentException if numbers of attributes are unequal
*/
@Override
public void replaceMissingValues(double[] array) {
if ((array == null) || (array.length != m_NumAttributes)) {
throw new IllegalArgumentException("Unequal number of attributes!");
}
double[] tempValues = new double[m_AttValues.length];
int[] tempIndices = new int[m_AttValues.length];
int vals = 0;
for (int i = 0; i < m_AttValues.length; i++) {
if (isMissingSparse(i)) {
if (array[m_Indices[i]] != 0) {
tempValues[vals] = array[m_Indices[i]];
tempIndices[vals] = m_Indices[i];
vals++;
}
} else {
tempValues[vals] = m_AttValues[i];
tempIndices[vals] = m_Indices[i];
vals++;
}
}
m_AttValues = new double[vals];
m_Indices = new int[vals];
System.arraycopy(tempValues, 0, m_AttValues, 0, vals);
System.arraycopy(tempIndices, 0, m_Indices, 0, vals);
}
/**
* Sets a specific value in the instance to the given value (internal
* floating-point format). Performs a deep copy of the vector of attribute
* values before the value is set.
*
* @param attIndex the attribute's index
* @param value the new attribute value (If the corresponding attribute is
* nominal (or a string) then this is the new value's index as a
* double).
*/
@Override
public void setValue(int attIndex, double value) {
int index = locateIndex(attIndex);
if ((index >= 0) && (m_Indices[index] == attIndex)) {
if (value != 0) {
double[] tempValues = new double[m_AttValues.length];
System.arraycopy(m_AttValues, 0, tempValues, 0, m_AttValues.length);
tempValues[index] = value;
m_AttValues = tempValues;
} else {
double[] tempValues = new double[m_AttValues.length - 1];
int[] tempIndices = new int[m_Indices.length - 1];
System.arraycopy(m_AttValues, 0, tempValues, 0, index);
System.arraycopy(m_Indices, 0, tempIndices, 0, index);
System.arraycopy(m_AttValues, index + 1, tempValues, index,
m_AttValues.length - index - 1);
System.arraycopy(m_Indices, index + 1, tempIndices, index,
m_Indices.length - index - 1);
m_AttValues = tempValues;
m_Indices = tempIndices;
}
} else {
if (value != 0) {
double[] tempValues = new double[m_AttValues.length + 1];
int[] tempIndices = new int[m_Indices.length + 1];
System.arraycopy(m_AttValues, 0, tempValues, 0, index + 1);
System.arraycopy(m_Indices, 0, tempIndices, 0, index + 1);
tempIndices[index + 1] = attIndex;
tempValues[index + 1] = value;
System.arraycopy(m_AttValues, index + 1, tempValues, index + 2,
m_AttValues.length - index - 1);
System.arraycopy(m_Indices, index + 1, tempIndices, index + 2,
m_Indices.length - index - 1);
m_AttValues = tempValues;
m_Indices = tempIndices;
}
}
}
/**
* Sets a specific value in the instance to the given value (internal
* floating-point format). Performs a deep copy of the vector of attribute
* values before the value is set.
*
* @param indexOfIndex the index of the attribute's index
* @param value the new attribute value (If the corresponding attribute is
* nominal (or a string) then this is the new value's index as a
* double).
*/
@Override
public void setValueSparse(int indexOfIndex, double value) {
if (value != 0) {
double[] tempValues = new double[m_AttValues.length];
System.arraycopy(m_AttValues, 0, tempValues, 0, m_AttValues.length);
m_AttValues = tempValues;
m_AttValues[indexOfIndex] = value;
} else {
double[] tempValues = new double[m_AttValues.length - 1];
int[] tempIndices = new int[m_Indices.length - 1];
System.arraycopy(m_AttValues, 0, tempValues, 0, indexOfIndex);
System.arraycopy(m_Indices, 0, tempIndices, 0, indexOfIndex);
System.arraycopy(m_AttValues, indexOfIndex + 1, tempValues, indexOfIndex,
m_AttValues.length - indexOfIndex - 1);
System.arraycopy(m_Indices, indexOfIndex + 1, tempIndices, indexOfIndex,
m_Indices.length - indexOfIndex - 1);
m_AttValues = tempValues;
m_Indices = tempIndices;
}
}
/**
* Returns the values of each attribute as an array of doubles.
*
* @return an array containing all the instance attribute values
*/
@Override
public double[] toDoubleArray() {
double[] newValues = new double[m_NumAttributes];
for (int i = 0; i < m_AttValues.length; i++) {
newValues[m_Indices[i]] = m_AttValues[i];
}
return newValues;
}
/**
* Returns the description of one instance in sparse format. If the instance
* doesn't have access to a dataset, it returns the internal floating-point
* values. Quotes string values that contain whitespace characters.
*
* @return the instance's description as a string
*/
@Override
public String toStringNoWeight() {
return toStringNoWeight(AbstractInstance.s_numericAfterDecimalPoint);
}
/**
* Returns the description of one instance in sparse format. If the instance
* doesn't have access to a dataset, it returns the internal floating-point
* values. Quotes string values that contain whitespace characters.
*
* @param afterDecimalPoint maximum number of digits permitted after the
* decimal point for numeric values
*
* @return the instance's description as a string
*/
public String toStringNoWeight(int afterDecimalPoint) {
StringBuffer text = new StringBuffer();
text.append('{');
for (int i = 0; i < m_Indices.length; i++) {
if (i > 0)
text.append(",");
if (isMissingSparse(i)) {
text.append(m_Indices[i] + " ?");
} else {
if (m_Dataset == null) {
text.append(m_Indices[i] + " "
+ Utils.doubleToString(m_AttValues[i], afterDecimalPoint));
} else {
if (m_Dataset.attribute(m_Indices[i]).isNominal()
|| m_Dataset.attribute(m_Indices[i]).isString()
|| m_Dataset.attribute(m_Indices[i]).isDate()) {
try {
text.append(m_Indices[i] + " "
+ Utils.quote(stringValue(m_Indices[i])));
} catch (Exception e) {
e.printStackTrace();
System.err.println(new Instances(m_Dataset, 0));
System.err.println("Att:" + m_Indices[i] + " Val:"
+ valueSparse(i));
throw new Error("This should never happen!");
}
} else if (m_Dataset.attribute(m_Indices[i]).isRelationValued()) {
try {
text.append(m_Indices[i]
+ " "
+ Utils.quote(m_Dataset.attribute(m_Indices[i])
.relation((int) valueSparse(i)).stringWithoutHeader()));
} catch (Exception e) {
e.printStackTrace();
System.err.println(new Instances(m_Dataset, 0));
System.err.println("Att:" + m_Indices[i] + " Val:"
+ valueSparse(i));
throw new Error("This should never happen!");
}
} else {
text.append(m_Indices[i] + " "
+ Utils.doubleToString(m_AttValues[i], afterDecimalPoint));
}
}
}
}
text.append('}');
return text.toString();
}
/**
* Returns an instance's attribute value in internal format.
*
* @param attIndex the attribute's index
* @return the specified value as a double (If the corresponding attribute is
* nominal (or a string) then it returns the value's index as a
* double).
*/
@Override
public double value(int attIndex) {
int index = locateIndex(attIndex);
if ((index >= 0) && (m_Indices[index] == attIndex)) {
return m_AttValues[index];
} else {
return 0.0;
}
}
/**
* Deletes an attribute at the given position (0 to numAttributes() - 1).
*
* @param pos the attribute's position
*/
@Override
protected void forceDeleteAttributeAt(int position) {
int index = locateIndex(position);
m_NumAttributes--;
if ((index >= 0) && (m_Indices[index] == position)) {
int[] tempIndices = new int[m_Indices.length - 1];
double[] tempValues = new double[m_AttValues.length - 1];
System.arraycopy(m_Indices, 0, tempIndices, 0, index);
System.arraycopy(m_AttValues, 0, tempValues, 0, index);
for (int i = index; i < m_Indices.length - 1; i++) {
tempIndices[i] = m_Indices[i + 1] - 1;
tempValues[i] = m_AttValues[i + 1];
}
m_Indices = tempIndices;
m_AttValues = tempValues;
} else {
int[] tempIndices = new int[m_Indices.length];
double[] tempValues = new double[m_AttValues.length];
System.arraycopy(m_Indices, 0, tempIndices, 0, index + 1);
System.arraycopy(m_AttValues, 0, tempValues, 0, index + 1);
for (int i = index + 1; i < m_Indices.length; i++) {
tempIndices[i] = m_Indices[i] - 1;
tempValues[i] = m_AttValues[i];
}
m_Indices = tempIndices;
m_AttValues = tempValues;
}
}
/**
* Inserts an attribute at the given position (0 to numAttributes()) and sets
* its value to be missing.
*
* @param pos the attribute's position
*/
@Override
protected void forceInsertAttributeAt(int position) {
int index = locateIndex(position);
m_NumAttributes++;
if ((index >= 0) && (m_Indices[index] == position)) {
int[] tempIndices = new int[m_Indices.length + 1];
double[] tempValues = new double[m_AttValues.length + 1];
System.arraycopy(m_Indices, 0, tempIndices, 0, index);
System.arraycopy(m_AttValues, 0, tempValues, 0, index);
tempIndices[index] = position;
tempValues[index] = Utils.missingValue();
for (int i = index; i < m_Indices.length; i++) {
tempIndices[i + 1] = m_Indices[i] + 1;
tempValues[i + 1] = m_AttValues[i];
}
m_Indices = tempIndices;
m_AttValues = tempValues;
} else {
int[] tempIndices = new int[m_Indices.length + 1];
double[] tempValues = new double[m_AttValues.length + 1];
System.arraycopy(m_Indices, 0, tempIndices, 0, index + 1);
System.arraycopy(m_AttValues, 0, tempValues, 0, index + 1);
tempIndices[index + 1] = position;
tempValues[index + 1] = Utils.missingValue();
for (int i = index + 1; i < m_Indices.length; i++) {
tempIndices[i + 1] = m_Indices[i] + 1;
tempValues[i + 1] = m_AttValues[i];
}
m_Indices = tempIndices;
m_AttValues = tempValues;
}
}
/**
* Constructor for sub classes.
*/
protected SparseInstance() {
};
/**
* Main method for testing this class.
*/
public static void main(String[] options) {
try {
// Create numeric attributes "length" and "weight"
Attribute length = new Attribute("length");
Attribute weight = new Attribute("weight");
// Create vector to hold nominal values "first", "second", "third"
ArrayList<String> my_nominal_values = new ArrayList<String>(3);
my_nominal_values.add("first");
my_nominal_values.add("second");
my_nominal_values.add("third");
// Create nominal attribute "position"
Attribute position = new Attribute("position", my_nominal_values);
// Create vector of the above attributes
ArrayList<Attribute> attributes = new ArrayList<Attribute>(3);
attributes.add(length);
attributes.add(weight);
attributes.add(position);
// Create the empty dataset "race" with above attributes
Instances race = new Instances("race", attributes, 0);
// Make position the class attribute
race.setClassIndex(position.index());
// Create empty instance with three attribute values
SparseInstance inst = new SparseInstance(3);
// Set instance's values for the attributes "length", "weight", and
// "position"
inst.setValue(length, 5.3);
inst.setValue(weight, 300);
inst.setValue(position, "first");
// Set instance's dataset to be the dataset "race"
inst.setDataset(race);
// Print the instance
System.out.println("The instance: " + inst);
// Print the first attribute
System.out.println("First attribute: " + inst.attribute(0));
// Print the class attribute
System.out.println("Class attribute: " + inst.classAttribute());
// Print the class index
System.out.println("Class index: " + inst.classIndex());
// Say if class is missing
System.out.println("Class is missing: " + inst.classIsMissing());
// Print the instance's class value in internal format
System.out.println("Class value (internal format): " + inst.classValue());
// Print a shallow copy of this instance
SparseInstance copy = (SparseInstance) inst.copy();
System.out.println("Shallow copy: " + copy);
// Set dataset for shallow copy
copy.setDataset(inst.dataset());
System.out.println("Shallow copy with dataset set: " + copy);
// Print out all values in internal format
System.out.print("All stored values in internal format: ");
for (int i = 0; i < inst.numValues(); i++) {
if (i > 0) {
System.out.print(",");
}
System.out.print(inst.valueSparse(i));
}
System.out.println();
// Set all values to zero
System.out.print("All values set to zero: ");
while (inst.numValues() > 0) {
inst.setValueSparse(0, 0);
}
for (int i = 0; i < inst.numValues(); i++) {
if (i > 0) {
System.out.print(",");
}
System.out.print(inst.valueSparse(i));
}
System.out.println();
// Set all values to one
System.out.print("All values set to one: ");
for (int i = 0; i < inst.numAttributes(); i++) {
inst.setValue(i, 1);
}
for (int i = 0; i < inst.numValues(); i++) {
if (i > 0) {
System.out.print(",");
}
System.out.print(inst.valueSparse(i));
}
System.out.println();
// Unset dataset for copy, delete first attribute, and insert it again
copy.setDataset(null);
copy.deleteAttributeAt(0);
copy.insertAttributeAt(0);
copy.setDataset(inst.dataset());
System.out.println("Copy with first attribute deleted and inserted: "
+ copy);
// Same for second attribute
copy.setDataset(null);
copy.deleteAttributeAt(1);
copy.insertAttributeAt(1);
copy.setDataset(inst.dataset());
System.out.println("Copy with second attribute deleted and inserted: "
+ copy);
// Same for last attribute
copy.setDataset(null);
copy.deleteAttributeAt(2);
copy.insertAttributeAt(2);
copy.setDataset(inst.dataset());
System.out.println("Copy with third attribute deleted and inserted: "
+ copy);
// Enumerate attributes (leaving out the class attribute)
System.out.println("Enumerating attributes (leaving out class):");
Enumeration enu = inst.enumerateAttributes();
while (enu.hasMoreElements()) {
Attribute att = (Attribute) enu.nextElement();
System.out.println(att);
}
// Headers are equivalent?
System.out.println("Header of original and copy equivalent: "
+ inst.equalHeaders(copy));
// Test for missing values
System.out.println("Length of copy missing: " + copy.isMissing(length));
System.out.println("Weight of copy missing: "
+ copy.isMissing(weight.index()));
System.out.println("Length of copy missing: "
+ Utils.isMissingValue(copy.value(length)));
// Prints number of attributes and classes
System.out.println("Number of attributes: " + copy.numAttributes());
System.out.println("Number of classes: " + copy.numClasses());
// Replace missing values
double[] meansAndModes = { 2, 3, 0 };
copy.replaceMissingValues(meansAndModes);
System.out.println("Copy with missing value replaced: " + copy);
// Setting and getting values and weights
copy.setClassMissing();
System.out.println("Copy with missing class: " + copy);
copy.setClassValue(0);
System.out.println("Copy with class value set to first value: " + copy);
copy.setClassValue("third");
System.out.println("Copy with class value set to \"third\": " + copy);
copy.setMissing(1);
System.out.println("Copy with second attribute set to be missing: "
+ copy);
copy.setMissing(length);
System.out.println("Copy with length set to be missing: " + copy);
copy.setValue(0, 0);
System.out.println("Copy with first attribute set to 0: " + copy);
copy.setValue(weight, 1);
System.out.println("Copy with weight attribute set to 1: " + copy);
copy.setValue(position, "second");
System.out.println("Copy with position set to \"second\": " + copy);
copy.setValue(2, "first");
System.out.println("Copy with last attribute set to \"first\": " + copy);
System.out.println("Current weight of instance copy: " + copy.weight());
copy.setWeight(2);
System.out.println("Current weight of instance copy (set to 2): "
+ copy.weight());
System.out.println("Last value of copy: " + copy.toString(2));
System.out.println("Value of position for copy: "
+ copy.toString(position));
System.out.println("Last value of copy (internal format): "
+ copy.value(2));
System.out.println("Value of position for copy (internal format): "
+ copy.value(position));
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Returns the revision string.
*
* @return the revision
*/
@Override
public String getRevision() {
return RevisionUtils.extract("$Revision: 9028 $");
}
}