edu.cmu.tetrad.data.BoxDataSet Maven / Gradle / Ivy
///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA //
///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetrad.data;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.util.*;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.text.NumberFormat;
import java.util.*;
/**
* Wraps a DataBox in such a way that mixed data sets can be stored. The type of each column must be specified by a
* Variable object, which must be either a
* ContinuousVariable or a DiscreteVariable. This
* class violates object orientation in that the underlying data matrix is retrievable using the getDoubleData() method.
* This is allowed so that external calculations may be performed on large datasets without having to allocate extra
* memory. If this matrix needs to be modified externally, please consider making a copy of it first, using the
* TetradMatrix copy() method.
*
* The data set may be given a name; this name is not used internally.
*
* The data set has a list of variables associated with it, as described above. This list is coordinated with the stored
* data, in that data for the i'th variable will be in the i'th column.
*
* A subset of variables in the data set may be designated as selected. This selection set is stored with the data set
* and may be manipulated using the
* select and deselect methods.
*
* A multiplicity m_i may be associated with each case c_i in the dataset, which is interpreted to mean that that c_i
* occurs m_i times in the dataset.
*
* Knowledge may be associated with the data set, using the
* setKnowledge method. This knowledge is not used internally to
* the data set, but it may be retrieved by algorithms and used.
*
*
* @author josephramsey
* @version $Id: $Id
* @see edu.cmu.tetrad.data.Variable
* @see Knowledge
*/
public final class BoxDataSet implements DataSet {
@Serial
private static final long serialVersionUID = 23L;
/**
* Case ID's. These are strings associated with some or all of the cases of the dataset.
*/
private final Map caseIds = new HashMap<>();
/**
* The name of the data model. This is not used internally; it is only here in case an external class wants this
* dataset to have a name.
*
* @serial
*/
private Map columnToTooltip;
/**
* The name of the data model. This is not used internally; it is only here in case an external class wants this
* dataset to have a name.
*/
private String name = "";
/**
* The list of variables. These correspond columnwise to the columns of
* data.
*/
private List variables;
/**
* The container storing the data. Rows are cases; columns are variables. The order of columns is coordinated with
* the order of variables in getVariables().
*
* @serial
*/
private DataBox dataBox;
/**
* The set of selected variables.
*
* @serial
*/
private Set selection = new HashSet<>();
/**
* A map from cases to case multipliers. If a case is not in the domain of this map, its case multiplier is by
* default 1. This is the number of repetitions of the case in the dataset. The sample size is obtained by summing
* over these multipliers.
*
* @serial
*/
private Map multipliers = new HashMap<>();
/**
* The knowledge associated with this data.
*
* @serial
*/
private Knowledge knowledge = new Knowledge();
/**
* The number formatter used for printing out continuous values.
*/
private transient NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
/**
* The character used as a delimiter when the dataset is printed.
*/
private char outputDelimiter = '\t';
/**
* Constructs a new data set with the given number of rows and columns, with all values set to missing.
*
* @param dataBox The data box.
* @param variables The variables.
*/
public BoxDataSet(DataBox dataBox, List variables) {
this.dataBox = dataBox;
this.variables = new ArrayList<>(variables);
if (dataBox.numCols() != variables.size()) {
throw new IllegalArgumentException("Number of columns must match the number of variables.");
}
}
/**
* Makes of copy of the given data set.
*
* @param dataSet The data set to copy.
*/
public BoxDataSet(BoxDataSet dataSet) {
this.name = dataSet.name;
this.variables = new LinkedList<>(dataSet.variables);
this.dataBox = dataSet.dataBox.copy();
this.selection = new HashSet<>(dataSet.selection);
this.multipliers = new HashMap<>(dataSet.multipliers);
this.knowledge = dataSet.knowledge.copy();
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return A simple exemplar of this class.
*/
public static BoxDataSet serializableInstance() {
List vars = new ArrayList<>();
for (int i = 0; i < 4; i++) {
vars.add(new ContinuousVariable("X" + i));
}
return new BoxDataSet(new ShortDataBox(4, 4), vars);
}
/**
* Writes the object to the specified ObjectOutputStream.
*
* @param out The ObjectOutputStream to write the object to.
* @throws IOException If an I/O error occurs.
*/
@Serial
private void writeObject(ObjectOutputStream out) throws IOException {
try {
out.defaultWriteObject();
} catch (IOException e) {
TetradLogger.getInstance().log("Failed to serialize object: " + getClass().getCanonicalName()
+ ", " + e.getMessage());
throw e;
}
}
/**
* Reads the object from the specified ObjectInputStream. This method is used during deserialization
* to restore the state of the object.
*
* @param in The ObjectInputStream to read the object from.
* @throws IOException If an I/O error occurs.
* @throws ClassNotFoundException If the class of the serialized object cannot be found.
*/
@Serial
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
try {
in.defaultReadObject();
} catch (IOException e) {
TetradLogger.getInstance().log("Failed to deserialize object: " + getClass().getCanonicalName()
+ ", " + e.getMessage());
throw e;
}
}
/**
* Attempts to translate element into a double value, returning it if successful, otherwise throwing an
* exception. To be successful, the object must be either a Number or a String.
*
* @throws IllegalArgumentException if the translation cannot be made. The reason is in the message.
*/
private static double getValueFromObjectContinuous(Object element) {
if ("*".equals(element) || "".equals(element)) {
return ContinuousVariable.getDoubleMissingValue();
} else if (element instanceof Number) {
return ((Number) element).doubleValue();
} else if (element instanceof String) {
try {
return Double.parseDouble((String) element);
} catch (NumberFormatException e) {
return ContinuousVariable.getDoubleMissingValue();
}
} else {
throw new IllegalArgumentException(
"The argument 'element' must be "
+ "either a Number or a String.");
}
}
/**
* Getter for the field columnToTooltip.
*
* @return a {@link java.util.Map} object
*/
public Map getColumnToTooltip() {
return this.columnToTooltip;
}
/**
* Gets the name of the data set.
*
* @return a {@link java.lang.String} object
*/
public String getName() {
return this.name;
}
/**
* {@inheritDoc}
*
* Sets the name of the data set.
*/
public void setName(String name) {
if (name == null) {
return;
// throw new NullPointerException("Name must not be null.");
}
this.name = name;
}
/**
*
getNumColumns.
*
* @return the number of variables in the data set.
*/
public int getNumColumns() {
return this.variables.size();
}
/**
* getNumRows.
*
* @return the number of rows in the rectangular data set, which is the maximum of the number of rows in the list of
* wrapped columns.
*/
public int getNumRows() {
return this.dataBox.numRows();
}
/**
* {@inheritDoc}
*
* Sets the value at the given (row, column) to the given int value, assuming the variable for the column is
* discrete.
*/
public void setInt(int row, int column, int value) {
ensureRows(row + 1);
Node variable = getVariable(column);
if (!(variable instanceof DiscreteVariable _variable)) {
throw new IllegalArgumentException(
"Can only set ints for discrete columns.");
}
if (value < 0 && value != -99) {
throw new IllegalArgumentException(
"Value must be a positive integer: " + value);
}
if (value >= _variable.getNumCategories()) {
if (_variable.isAccommodateNewCategories()) {
accomodateIndex(_variable, value);
} else {
throw new IllegalArgumentException(
"Not a value for that variable: " + value);
}
}
try {
setIntPrivate(row, column, value);
} catch (Exception e) {
if (row < 0 || column < 0 || row >= getNumRows() || column >= getNumColumns()) {
throw new IllegalArgumentException(
"Row or columns out of range.");
}
}
}
/**
* {@inheritDoc}
*
* Sets the value at the given (row, column) to the given double value, assuming the variable for the column is
* continuous.
*/
public void setDouble(int row, int column, double value) {
ensureRows(row + 1);
try {
this.dataBox.set(row, column, value);
} catch (Exception e) {
if (row < 0 || column < 0 || row >= getNumRows() || column >= getNumColumns()) {
throw new IllegalArgumentException(
"Row or columns out of range.");
}
}
}
/**
* {@inheritDoc}
*/
public Object getObject(int row, int col) {
Object variable = getVariable(col);
if (variable instanceof ContinuousVariable) {
return getDouble(row, col);
} else if (variable instanceof DiscreteVariable _variable) {
if (_variable.isCategoryNamesDisplayed()) {
return _variable.getCategory(getInt(row, col));
} else {
return getInt(row, col);
}
}
throw new IllegalArgumentException("Not a row/col in this data set: " + row + ", " + col);
}
/**
* {@inheritDoc}
*/
public void setObject(int row, int col, Object value) {
Object variable = getVariable(col);
if (variable instanceof ContinuousVariable) {
setDouble(row, col, BoxDataSet.getValueFromObjectContinuous(value));
} else if (variable instanceof DiscreteVariable) {
setInt(row, col, getValueFromObjectDiscrete(value,
(DiscreteVariable) variable));
} else {
throw new IllegalArgumentException(
"Expecting either a continuous "
+ "or a discrete variable.");
}
}
/**
*
getSelectedIndices.
*
* @return the indices of the currently selected variables.
*/
public int[] getSelectedIndices() {
List variables = getVariables();
Set selection = getSelection();
int[] indices = new int[selection.size()];
int j = -1;
for (int i = 0; i < variables.size(); i++) {
if (selection.contains(variables.get(i))) {
indices[++j] = i;
}
}
return indices;
}
/**
* {@inheritDoc}
*
* Adds the given variable to the data set, increasing the number of columns by one, moving columns i >=
* index to column i + 1, and inserting a column of missing values at column i.
*/
public void addVariable(Node variable) {
if (this.variables.contains(variable)) {
throw new IllegalArgumentException("Expecting a new variable: " + variable);
}
try {
this.variables.add(variable);
} catch (Exception e) {
e.printStackTrace();
}
resize(this.dataBox.numRows(), this.variables.size());
int col = this.dataBox.numCols() - 1;
for (int i = 0; i < this.dataBox.numRows(); i++) {
this.dataBox.set(i, col, null);
}
}
/**
* {@inheritDoc}
*
* Adds the given variable to the dataset, increasing the number of columns by one, moving columns i >=
* index to column i + 1, and inserting a column of missing values at column i.
*/
public void addVariable(int index, Node variable) {
if (this.variables.contains(variable)) {
throw new IllegalArgumentException("Expecting a new variable.");
}
if (index < 0 || index > this.variables.size()) {
throw new IndexOutOfBoundsException("Index must in (0, #vars).");
}
this.variables.add(index, variable);
resize(this.dataBox.numRows(), this.variables.size());
Number[][] _data = new Number[this.dataBox.numRows()][this.dataBox.numCols()];
for (int j = 0; j < this.dataBox.numCols(); j++) {
if (j < index) {
for (int i = 0; i < this.dataBox.numRows(); i++) {
_data[i][j] = this.dataBox.get(i, j);
}
} else if (j == index) {
for (int i = 0; i < this.dataBox.numRows(); i++) {
_data[i][j] = null;
}
} else {
for (int i = 0; i < this.dataBox.numRows(); i++) {
_data[i][j] = this.dataBox.get(i, j - 1);
}
}
}
}
/**
* {@inheritDoc}
*
*
getVariable.
*/
public Node getVariable(int col) {
return this.variables.get(col);
}
/**
* {@inheritDoc}
*/
public int getColumn(Node variable) {
return this.variables.indexOf(variable);
}
/**
* {@inheritDoc}
*
* Changes the variable for the given column from from to
* to. Supported currently only for discrete variables.
*/
public void changeVariable(Node from, Node to) {
if (!(from instanceof DiscreteVariable _from
&& to instanceof DiscreteVariable _to)) {
throw new IllegalArgumentException(
"Only discrete variables supported.");
}
int col = this.variables.indexOf(_from);
List oldCategories = _from.getCategories();
List newCategories = _to.getCategories();
int[] indexArray = new int[oldCategories.size()];
for (int i = 0; i < oldCategories.size(); i++) {
indexArray[i] = newCategories.indexOf(oldCategories.get(i));
}
for (int i = 0; i < getNumRows(); i++) {
if (this.dataBox.get(i, col) == null) {
break;
}
int value = getInt(i, col);
int newIndex = 0;
try {
newIndex = indexArray[value];
} catch (Exception e) {
e.printStackTrace();
}
if (newIndex == -1) {
this.dataBox.set(i, col, null);
} else {
setInt(i, col, newIndex);
}
}
this.variables.set(col, _to);
}
/**
* {@inheritDoc}
*/
public Node getVariable(String varName) {
for (Node variable1 : this.variables) {
if (variable1.getName().equals(varName)) {
return variable1;
}
}
return null;
}
/**
* Getter for the field variables.
*
* @return (a copy of) the List of Variables for the data set, in the order of their columns.
*/
public List getVariables() {
return new LinkedList<>(this.variables);
}
/**
* Getter for the field knowledge.
*
* @return a copy of the knowledge associated with this data set. (Cannot be null.)
*/
public Knowledge getKnowledge() {
return this.knowledge.copy();
}
/**
* {@inheritDoc}
*
* Sets knowledge to be associated with this data set. May not be null.
*/
public void setKnowledge(Knowledge knowledge) {
if (knowledge == null) {
throw new NullPointerException();
}
this.knowledge = knowledge.copy();
}
/**
*
getVariableNames.
*
* @return (a copy of) the List of Variables for the data set, in the order of their columns.
*/
public List getVariableNames() {
List vars = getVariables();
List names = new ArrayList<>();
for (Node variable : vars) {
String name = variable.getName();
names.add(name);
}
return names;
}
/**
* {@inheritDoc}
*
* Marks the given column as selected if 'selected' is true or deselected if 'selected' is false.
*/
public void setSelected(Node variable, boolean selected) {
if (selected) {
if (this.variables.contains(variable)) {
getSelection().add(variable);
}
} else if (this.variables.contains(variable)) {
getSelection().remove(variable);
}
}
/**
* Marks all variables as deselected.
*/
public void clearSelection() {
getSelection().clear();
}
/**
* {@inheritDoc}
*
* Ensures that the dataset has at least the number of rows, adding rows if necessary to make that the case. The new
* rows will be filled with missing values.
*/
public void ensureRows(int rows) {
if (rows > getNumRows()) {
resize(rows, getNumColumns());
}
}
/**
* {@inheritDoc}
*
* Ensures that the dataset has at least the given number of columns, adding continuous variables with unique names
* until that is true. The new columns will be filled with missing values.
*/
public void ensureColumns(int columns, List excludedVariableNames) {
for (int col = getNumColumns(); col < columns; col++) {
int i = 0;
String _name;
while (true) {
_name = "X" + (++i);
if (getVariable(_name) == null
&& !excludedVariableNames.contains(_name)) {
ContinuousVariable variable = new ContinuousVariable(_name);
addVariable(variable);
resize(getNumRows(), getNumColumns());
break;
}
}
}
}
/**
* {@inheritDoc}
*/
@Override
public boolean existsMissingValue() {
for (int i = 0; i < getNumRows(); i++) {
for (int j = 0; j < getNumColumns(); j++) {
if (this.variables.get(j) instanceof ContinuousVariable) {
if (Double.isNaN(getDouble(i, j))) return true;
}
if (this.variables.get(j) instanceof DiscreteVariable) {
if (getInt(i, j) == -99) return true;
}
}
}
return false;
}
/**
* {@inheritDoc}
*/
public boolean isSelected(Node variable) {
return getSelection().contains(variable);
}
/**
* {@inheritDoc}
*
* Removes the column for the variable at the given index, reducing the number of columns by one.
*/
public void removeColumn(int index) {
if (index < 0 || index >= this.variables.size()) {
throw new IllegalArgumentException("Not a column in this data set: " + index);
}
this.variables.remove(index);
int[] rows = new int[this.dataBox.numRows()];
for (int i = 0; i < this.dataBox.numRows(); i++) {
rows[i] = i;
}
int[] cols = new int[this.dataBox.numCols() - 1];
int m = -1;
for (int i = 0; i < this.dataBox.numCols(); i++) {
if (i != index) {
cols[++m] = i;
}
}
this.dataBox = viewSelection(rows, cols);
}
private DataBox viewSelection(int[] rows, int[] cols) {
return this.dataBox.viewSelection(rows, cols);
}
/**
* {@inheritDoc}
*
* Removes the columns for the given variable from the dataset, reducing the number of columns by one.
*/
@Override
public void removeColumn(Node variable) {
int index = this.variables.indexOf(variable);
if (index != -1) {
removeColumn(index);
}
}
/**
* {@inheritDoc}
*
* Creates and returns a dataset consisting of those variables in the list vars. Vars must be a subset of the
* variables of this DataSet. The ordering of the elements of vars will be the same as in the list of variables in
* this DataSet.
*/
public DataSet subsetColumns(List vars) {
if (!(getVariables().containsAll(vars))) {
List missingVars = new ArrayList<>(vars);
missingVars.removeAll(getVariables());
throw new IllegalArgumentException(
"All vars must be original vars: " + missingVars);
}
int[] rows = new int[this.dataBox.numRows()];
for (int i = 0; i < rows.length; i++) {
rows[i] = i;
}
int[] cols = new int[vars.size()];
for (int j = 0; j < cols.length; j++) {
cols[j] = getVariables().indexOf(vars.get(j));
}
DataBox _dataBox = viewSelection(rows, cols);
BoxDataSet _dataSet = new BoxDataSet(_dataBox, vars);
// _dataSet.name = name + "_copy";
_dataSet.variables = vars;
_dataSet.selection = new HashSet<>();
_dataSet.multipliers = new HashMap<>(this.multipliers);
// Might have to delete some knowledge.
_dataSet.knowledge = this.knowledge.copy();
return _dataSet;
}
/**
* isContinuous.
*
* @return true iff this is a continuous data set--that is, if every column in it is continuous. (By implication,
* empty datasets are both discrete and continuous.)
*/
public boolean isContinuous() {
for (int i = 0; i < getNumColumns(); i++) {
Node variable = this.variables.get(i);
if (!(variable instanceof ContinuousVariable)) {
return false;
}
}
return true;
}
/**
* isDiscrete.
*
* @return true iff this is a discrete data set--that is, if every column in it is discrete. (By implication, empty
* datasets are both discrete and continuous.)
*/
public boolean isDiscrete() {
for (int i = 0; i < getNumColumns(); i++) {
Node column = this.variables.get(i);
if (!(column instanceof DiscreteVariable)) {
return false;
}
}
return true;
}
/**
* isMixed.
*
* @return true if this is a mixed data set--that is, if it contains at least one continuous column and one discrete
* columnn.
*/
public boolean isMixed() {
int numContinuous = 0;
int numDiscrete = 0;
for (int i = 0; i < getNumColumns(); i++) {
Node column = this.variables.get(i);
if (column instanceof ContinuousVariable) {
numContinuous++;
} else if (column instanceof DiscreteVariable) {
numDiscrete++;
} else {
throw new IllegalArgumentException(
"Column not of type continuous"
+ "or of type discrete; can't classify this data set.");
}
}
return numContinuous > 0 && numDiscrete > 0;
}
/**
* getCorrelationMatrix.
*
* @return the correlation matrix for this dataset. Defers to
* Statistic.covariance() in the COLT matrix library, so it
* inherits the handling of missing values from that library--that is, any off-diagonal correlation involving a
* column with a missing value is Double.NaN, although all of the on-diagonal elements are 1.0. If that's not the
* desired behavior, missing values can be removed or imputed first.
*/
public Matrix getCorrelationMatrix() {
if (!isContinuous()) {
throw new IllegalStateException("Not a continuous data set.");
}
return MatrixUtils.convertCovToCorr(getCovarianceMatrix());
}
/**
* getCovarianceMatrix.
*
* @return the covariance matrix for this dataset. Defers to
* Statistic.covariance() in the COLT matrix library, so it
* inherits the handling of missing values from that library--that is, any covariance involving a column with a
* missing value is Double.NaN. If that's not the desired behavior, missing values can be removed or imputed first.
*/
public Matrix getCovarianceMatrix() {
if (!isContinuous()) {
throw new IllegalStateException("Not a continuous data set.");
}
if (getNumColumns() == 0) return new Matrix(0, 0);
return new CovarianceMatrix(this).getMatrix();
}
/**
* {@inheritDoc}
*/
public int getInt(int row, int column) {
Number value = this.dataBox.get(row, column);
if (value == null) {
return DiscreteVariable.MISSING_VALUE;
} else {
return value.intValue();
}
}
/**
* {@inheritDoc}
*/
public double getDouble(int row, int column) {
Number value = this.dataBox.get(row, column);
if (value == null) {
return ContinuousVariable.getDoubleMissingValue();
} else {
return value.doubleValue();
}
}
/**
* toString.
*
* @return a string, suitable for printing, of the dataset. Lines are separated by '\n', tokens in the line by
* whatever character is set in the
* setOutputDelimiter() method. The list of variables is printed
* first, followed by one line for each case. This method should probably not be used for saving to files. If that's
* your goal, use the DataSavers class instead.
* @see #setOutputDelimiter(Character)
* @see DataWriter
*/
public String toString() {
StringBuilder buf = new StringBuilder();
List variables = getVariables();
buf.append("\n");
for (int i = 0; i < getNumColumns(); i++) {
buf.append(variables.get(i));
if (i < getNumColumns() - 1) {
buf.append(this.outputDelimiter);
}
}
buf.append("\n");
for (int i = 0; i < getNumRows(); i++) {
for (int j = 0; j < getNumColumns(); j++) {
Node variable = getVariable(j);
if (variable instanceof ContinuousVariable) {
if (Double.isNaN(getDouble(i, j))) {
buf.append("*");
} else {
buf.append(getNumberFormat().format(getDouble(i, j)));
}
if (j < getNumColumns() - 1) {
buf.append(this.outputDelimiter);
}
} else if (variable instanceof DiscreteVariable _variable) {
int value = getInt(i, j);
if (value == -99) {
buf.append("*");
} else {
String category = _variable.getCategory(value);
if (category.indexOf(this.outputDelimiter) == -1) {
buf.append(category);
} else {
buf.append("\"").append(category).append("\"");
}
}
if (j < getNumColumns() - 1) {
buf.append(this.outputDelimiter);
}
} else {
throw new IllegalStateException(
"Expecting either a continuous "
+ "variable or a discrete variable: variable = " + variable
+ " type = " + variable.getClass());
}
}
buf.append("\n");
}
buf.append("\n");
if (this.knowledge != null && !this.knowledge.isEmpty()) {
buf.append(this.knowledge);
}
return buf.toString();
}
/**
* getDoubleData.
*
* @return a copy of the underlying COLT TetradMatrix matrix, containing all of the data in this dataset, discrete
* data included. Discrete data will be represented by ints cast to doubles. Rows in this matrix are cases, and
* columns are variables. The list of variable, in the order in which they occur in the matrix, is given by
* getVariables().
*
* If isMultipliersCollapsed() returns false, multipliers in the dataset are first expanded before returning the
* matrix, so the number of rows in the returned matrix may not be the same as the number of rows in this dataset.
* @throws java.lang.IllegalStateException if this is not a continuous data set.
* @see #getVariables
*/
public Matrix getDoubleData() {
Matrix copy = new Matrix(this.dataBox.numRows(), this.dataBox.numCols());
for (int i = 0; i < this.dataBox.numRows(); i++) {
for (int j = 0; j < this.dataBox.numCols(); j++) {
Number number = this.dataBox.get(i, j);
if (number == null) {
copy.set(i, j, Double.NaN);
} else {
copy.set(i, j, number.doubleValue());
}
}
}
return copy;
}
/**
*
subsetColumns.
*
* @param indices an array of {@link int} objects
* @return a new data set in which the the column at indices[i] is placed at index i, for i = 0 to indices.length -
* 1. (Moved over from Purify.)
*/
public DataSet subsetColumns(int[] indices) {
List variables = getVariables();
List _variables = new LinkedList<>();
for (int index : indices) {
_variables.add(variables.get(index));
}
int[] rows = new int[this.dataBox.numRows()];
for (int i = 0; i < rows.length; i++) {
rows[i] = i;
}
DataBox _data = viewSelection(rows, indices);
BoxDataSet _dataSet = new BoxDataSet(_data, _variables);
// _dataSet.name = name + "_copy";
_dataSet.name = this.name;
_dataSet.variables = _variables;
_dataSet.selection = new HashSet<>();
_dataSet.multipliers = new HashMap<>(this.multipliers);
// Might have to delete some knowledge.
_dataSet.knowledge = this.knowledge.copy();
return _dataSet;
}
/**
* subsetRows.
*
* @param rows an array of {@link int} objects
* @return a {@link edu.cmu.tetrad.data.DataSet} object
*/
public DataSet subsetRows(int[] rows) {
int[] cols = new int[this.dataBox.numCols()];
for (int i = 0; i < cols.length; i++) {
cols[i] = i;
}
DataBox newBox = this.dataBox.viewSelection(rows, cols);
BoxDataSet _data = new BoxDataSet(this);
_data.dataBox = newBox;
return _data;
}
/**
* {@inheritDoc}
*/
@Override
public DataSet subsetRowsColumns(int[] rows, int[] columns) {
List variables = getVariables();
List _variables = new LinkedList<>();
for (int index : columns) {
_variables.add(variables.get(index));
}
DataBox _data = viewSelection(rows, columns);
BoxDataSet _dataSet = new BoxDataSet(_data, _variables);
// _dataSet.name = name + "_copy";
_dataSet.name = this.name;
_dataSet.variables = _variables;
_dataSet.selection = new HashSet<>();
_dataSet.multipliers = new HashMap<>(this.multipliers);
// Might have to delete some knowledge.
_dataSet.knowledge = this.knowledge.copy();
return _dataSet;
}
/**
* {@inheritDoc}
*
* Removes the given columns from the data set.
*/
@Override
public void removeCols(int[] cols) {
int[] rows = new int[this.dataBox.numRows()];
for (int i = 0; i < this.dataBox.numRows(); i++) {
rows[i] = i;
}
int[] retainedCols = new int[this.variables.size() - cols.length];
int i = -1;
for (int j = 0; j < this.variables.size(); j++) {
if (Arrays.binarySearch(cols, j) < 0) {
retainedCols[++i] = j;
}
}
List retainedVars = new LinkedList<>();
for (int retainedCol : retainedCols) {
retainedVars.add(this.variables.get(retainedCol));
}
this.dataBox = viewSelection(rows, retainedCols);
this.variables = retainedVars;
this.selection = new HashSet<>();
this.multipliers = new HashMap<>(this.multipliers);
this.knowledge = this.knowledge.copy(); // Might have to delete some knowledge.
}
/**
* Removes the given rows from the data set.
*
* @param selectedRows an array of {@link int} objects
*/
public void removeRows(int[] selectedRows) {
int[] cols = new int[this.dataBox.numCols()];
for (int i = 0; i < this.dataBox.numCols(); i++) {
cols[i] = i;
}
int[] retainedRows = new int[this.dataBox.numRows() - selectedRows.length];
int i = -1;
for (int j = 0; j < this.dataBox.numRows(); j++) {
if (Arrays.binarySearch(selectedRows, j) < 0) {
retainedRows[++i] = j;
}
}
this.dataBox = viewSelection(retainedRows, cols);
this.selection = new HashSet<>();
this.multipliers = new HashMap<>(this.multipliers);
this.knowledge = this.knowledge.copy(); // Might have to delete some knowledge.
}
/**
* {@inheritDoc}
*/
@Override
public boolean equals(Object obj) {
if (obj == null) {
return false;
} else if (this == obj) {
return true;
} else if (!(obj instanceof BoxDataSet)) {
return false;
}
BoxDataSet otherDataSet = (BoxDataSet) obj;
// compare number of columns
if (getNumColumns() != otherDataSet.getNumColumns()) {
return false;
}
// compare number of rows
if (getNumRows() != otherDataSet.getNumRows()) {
return false;
}
// compare nodes
if (!getVariables().equals(otherDataSet.getVariables())) {
return false;
}
Node[] nodes = getVariables().toArray(new Node[0]);
for (int i = 0; i < getNumRows(); i++) {
for (int j = 0; j < getNumColumns(); j++) {
Node variable = nodes[j];
double val = getDouble(i, j);
double otherVal = otherDataSet.getDouble(i, j);
if (variable instanceof ContinuousVariable) {
if (Double.isNaN(val) ^ Double.isNaN(otherVal)) {
return false;
} else if (!(Double.isNaN(val) && Double.isNaN(otherVal))) {
if (Double.compare(Double.parseDouble(this.nf.format(val)), Double.parseDouble(this.nf.format(otherVal))) != 0) {
return false;
}
}
} else {
if (!(val == otherVal)) {
return false;
}
}
}
}
return true;
}
/**
* {@inheritDoc}
*/
@Override
public DataSet copy() {
return new BoxDataSet(this);
}
/**
* {@inheritDoc}
*/
@Override
public DataSet like() {
return new BoxDataSet(this.dataBox.like(), this.variables);
}
/**
* {@inheritDoc}
*
* Sets the character ('\t', ' ', ',', for instance) that is used to delimit tokens when the data set is printed out
* using the toString() method.
*
* @see #toString
*/
public void setOutputDelimiter(Character character) {
this.outputDelimiter = character;
}
/**
* Randomly permutes the rows of the dataset.
*/
public void permuteRows() {
List permutation = new ArrayList<>();
for (int i = 0; i < getNumRows(); i++) {
permutation.add(i);
}
RandomUtil.shuffle(permutation);
DataBox data2 = this.dataBox.like();
for (int i = 0; i < getNumRows(); i++) {
for (int j = 0; j < getNumColumns(); j++) {
data2.set(i, j, this.dataBox.get(permutation.get(i), j));
}
}
this.dataBox = data2;
}
private void setIntPrivate(int row, int col, int value) {
this.dataBox.set(row, col, value);
}
/**
* Resizes the data to the given dimensions. Data that does not fall within the new dimensions is lost, and
* positions in the redimensioned data that have no correlates in the old data are set to missing (that is,
* Double.NaN).
*
* @param rows The number of rows in the redimensioned data.
* @param cols The number of columns in the redimensioned data.
*/
private void resize(int rows, int cols) {
MixedDataBox newBox = new MixedDataBox(this.variables, rows);
for (int j = 0; j < cols; j++) {
for (int i = 0; i < rows; i++) {
if (i < this.dataBox.numRows() && j < this.dataBox.numCols()) {
newBox.set(i, j, this.dataBox.get(i, j));
}
}
}
this.dataBox = newBox;
}
/**
* @return the set of selected nodes, creating a new set if necessary.
*/
private Set getSelection() {
if (this.selection == null) {
this.selection = new HashSet<>();
}
return this.selection;
}
/**
* Attempts to translate element into an int value, returning it if successful, otherwise throwing an
* exception. To be successful, the object must be either a Number or a String.
*
* @throws IllegalArgumentException if the translation cannot be made. The reason is in the message.
*/
private int getValueFromObjectDiscrete(Object element,
DiscreteVariable variable) {
if ("*".equals(element) || "".equals(element)) {
return DiscreteVariable.MISSING_VALUE;
}
if (variable.isAccommodateNewCategories()) {
if (element instanceof Number) {
int index = ((Number) element).intValue();
if (!variable.checkValue(index)) {
if (index >= variable.getNumCategories()) {
accomodateIndex(variable, index);
} else {
throw new IllegalArgumentException("Variable " + variable
+ " is not accepting "
+ "new categories. Problem category is " + ".");
}
}
return index;
} else if (element instanceof String label) {
variable = accomodateCategory(variable, label);
int index = variable.getIndex(label);
if (index == -1) {
throw new IllegalArgumentException(
"Not a category for this variable: " + -1);
}
return index;
} else {
throw new IllegalArgumentException(
"The argument 'element' must be "
+ "either a Number or a String.");
}
} else if (element instanceof Number) {
int index = ((Number) element).intValue();
if (!variable.checkValue(index)) {
return DiscreteVariable.MISSING_VALUE;
}
return index;
} else if (element instanceof String label) {
int index = variable.getIndex(label);
if (index == -1) {
return DiscreteVariable.MISSING_VALUE;
}
return index;
} else {
throw new IllegalArgumentException(
"The argument 'element' must be "
+ "either a Number or a String.");
}
}
/**
* If the given category is not already a category for a cagetory, augments the range of category by one and sets
* the category of the new value to the given category.
*/
private DiscreteVariable accomodateCategory(DiscreteVariable variable,
String category) {
if (category == null) {
throw new NullPointerException();
}
List categories = variable.getCategories();
if (!categories.contains(category)) {
List newCategories = new LinkedList<>(categories);
newCategories.add(category);
DiscreteVariable newVariable
= new DiscreteVariable(variable.getName(), newCategories);
changeVariable(variable, newVariable);
return newVariable;
}
return variable;
}
/**
* Increases the number of categories if necessary to make sure that this variable has the given index.
*/
private void accomodateIndex(DiscreteVariable variable, int index) {
if (!variable.isAccommodateNewCategories()) {
throw new IllegalArgumentException("This variable is not set "
+ "to accomodate new categories.");
}
if (index >= variable.getNumCategories()) {
adjustCategories(variable, index + 1);
}
}
/**
* Adjusts the size of the categories list to match the getModel number of categories. If the list is too short, it
* is padded with default categories. If it is too long, the extra categories are removed.
*/
private void adjustCategories(DiscreteVariable variable,
int numCategories) {
List categories
= new LinkedList<>(variable.getCategories());
List newCategories = new LinkedList<>(categories);
if (categories.size() > numCategories) {
if (variable.getCategories().size() > 0) {
newCategories.subList(0, variable.getCategories().size()).clear();
}
} else if (categories.size() < numCategories) {
for (int i = categories.size(); i < numCategories; i++) {
String category = DataUtils.defaultCategory(i);
if (categories.contains(category)) {
continue;
}
newCategories.add(category);
}
}
DiscreteVariable to
= new DiscreteVariable(variable.getName(), newCategories);
changeVariable(variable, to);
}
/**
* getNumberFormat.
*
* @return the number format, which by default is the one at
* NumberFormatUtil.getInstance().getNumberFormat(), but can be
* set by the user if desired.
* @see #setNumberFormat(java.text.NumberFormat)
*/
public NumberFormat getNumberFormat() {
if (this.nf == null) {
this.nf = NumberFormatUtil.getInstance().getNumberFormat();
}
return this.nf;
}
/**
* {@inheritDoc}
*
* Sets the number format to be used when printing out the data set. The default is the one at
*/
public void setNumberFormat(NumberFormat nf) {
if (nf == null) {
throw new NullPointerException();
}
this.nf = nf;
}
/**
*
Getter for the field dataBox.
*
* @return the data box that holds the data for this data set.
*/
public DataBox getDataBox() {
return this.dataBox;
}
}