edu.cmu.tetrad.data.MixedDataBox 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 java.io.Serial;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* Stores a 2D array of double continuousData. Note that the missing value marker for this box is -99.
*
* @author josephramsey
* @version $Id: $Id
*/
public class MixedDataBox implements DataBox {
@Serial
private static final long serialVersionUID = 23L;
/**
* The variables in the dataset.
*/
private final List variables;
/**
* The number of rows in the dataset.
*/
private final int numRows;
/**
* The continuous data.
*/
private double[][] continuousData;
/**
* The discrete data.
*/
private int[][] discreteData;
/**
* The variables here are used only to determine which columns are discrete and which are continuous; bounds
* checking is not done.
*
* @param variables a {@link java.util.List} object
* @param numRows a int
*/
public MixedDataBox(List variables, int numRows) {
this.variables = variables;
this.numRows = numRows;
this.continuousData = new double[variables.size()][];
this.discreteData = new int[variables.size()][];
for (int j = 0; j < variables.size(); j++) {
if (variables.get(j) instanceof ContinuousVariable) {
this.continuousData[j] = new double[numRows];
Arrays.fill(this.continuousData[j], Double.NaN);
} else if (variables.get(j) instanceof DiscreteVariable) {
this.discreteData[j] = new int[numRows];
Arrays.fill(this.discreteData[j], -99);
}
}
}
/**
* This constructor allows other data readers to populate the fields directly.
*
* @param variables list of discrete and continuous variables
* @param numRows number of cases in the dataset
* @param continuousData continuous data
* @param discreteData discrete data
*/
public MixedDataBox(List variables, int numRows, double[][] continuousData, int[][] discreteData) {
this.variables = variables;
this.numRows = numRows;
this.continuousData = continuousData;
this.discreteData = discreteData;
if (variables == null) {
throw new IllegalArgumentException("Parameter variables cannot be null.");
}
if (numRows < 0) {
throw new IllegalArgumentException("Parameter numRows cannot be negative.");
}
if (continuousData == null) {
throw new IllegalArgumentException("Parameter continuousData cannot be null.");
}
if (discreteData == null) {
throw new IllegalArgumentException("Parameter discreteData cannot be null.");
}
// ensure the number of variables for both datasets are the same
int numOfVars = variables.size();
if (continuousData.length != numOfVars) {
throw new IllegalArgumentException(String.format("Continuous Data: expect %d variables but found %d.", numOfVars, continuousData.length));
}
if (discreteData.length != numOfVars) {
throw new IllegalArgumentException(String.format("Discrete Data: expect %d variables but found %d.", numOfVars, discreteData.length));
}
for (int i = 0; i < numOfVars; i++) {
// ensure there is data for either dataset, not both
if ((continuousData[i] == null) == (discreteData[i] == null)) {
String errMsg = String.format("Variable at index %d either has data for both discrete and continuous or has no data for both.", i);
throw new IllegalArgumentException(errMsg);
}
// ensure the number of rows for both dataset is consistent
if (continuousData[i] != null && continuousData[i].length != numRows) {
String errMsg = String.format("Continuous Data: Inconsistent row number at index %d. Expect %d rows but found %d.", i, numRows, continuousData[i].length);
throw new IllegalArgumentException(errMsg);
}
if (discreteData[i] != null && discreteData[i].length != numRows) {
String errMsg = String.format("Discrete Data: Inconsistent row number at index %d. Expect %d rows but found %d.", i, numRows, discreteData[i].length);
throw new IllegalArgumentException(errMsg);
}
}
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetrad.data.BoxDataSet} object
*/
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);
}
/**
* {@inheritDoc}
*/
@Override
public int numRows() {
return this.numRows;
}
/**
* {@inheritDoc}
*/
@Override
public int numCols() {
return this.variables.size();
}
/**
* {@inheritDoc}
*
* Sets the value at the given row/column to the given Number value. The value used is number.doubleValue().
*/
@Override
public void set(int row, int col, Number value) {
if (value == null) {
if (this.continuousData[col] != null) {
this.continuousData[col][row] = Double.NaN;
} else if (this.discreteData[col] != null) {
this.discreteData[col][row] = -99;
} else {
throw new IllegalArgumentException("Indices out of bounds or null value.");
}
} else {
if (this.continuousData[col] != null) {
this.continuousData[col][row] = value.doubleValue();
} else if (this.discreteData[col] != null) {
this.discreteData[col][row] = value.intValue();
} else {
throw new IllegalArgumentException("Indices out of bounds or null value.");
}
}
}
/**
* {@inheritDoc}
*/
@Override
public Number get(int row, int col) {
if (col >= this.continuousData.length || row >= numRows()) {
return null;
}
if (this.continuousData[col] != null) {
double v = this.continuousData[col][row];
return Double.isNaN(v) ? null : v;
} else if (this.discreteData[col] != null) {
double v = this.discreteData[col][row];
return v == -99 ? null : v;
}
throw new IllegalArgumentException("Indices out of range.");
}
/**
* {@inheritDoc}
*/
@Override
public DataBox copy() {
MixedDataBox box = new MixedDataBox(this.variables, numRows());
for (int i = 0; i < numRows(); i++) {
for (int j = 0; j < numCols(); j++) {
box.set(i, j, get(i, j));
}
}
return box;
}
/**
* {@inheritDoc}
*/
@Override
public DataBox like() {
int[] rows = new int[numRows()];
int[] cols = new int[numCols()];
for (int i = 0; i < numRows(); i++) {
rows[i] = i;
}
for (int j = 0; j < numCols(); j++) {
cols[j] = j;
}
return viewSelection(rows, cols);
}
/**
*
addVariable.
*
* @param variable a {@link edu.cmu.tetrad.graph.Node} object
*/
public void addVariable(Node variable) {
this.variables.add(variable);
this.continuousData = Arrays.copyOf(this.continuousData, this.continuousData.length + 1);
this.discreteData = Arrays.copyOf(this.discreteData, this.discreteData.length + 1);
if (variable instanceof ContinuousVariable) {
this.continuousData[this.continuousData.length - 1] = new double[this.numRows];
} else if (variable instanceof DiscreteVariable) {
this.discreteData[this.discreteData.length - 1] = new int[this.numRows];
} else {
throw new IllegalStateException();
}
}
/**
* {@inheritDoc}
*/
@Override
public DataBox viewSelection(int[] rows, int[] cols) {
List newVars = new ArrayList<>();
for (int c : cols) {
newVars.add(this.variables.get(c));
}
int row_num = rows.length;
int col_num = cols.length;
DataBox _dataBox = new MixedDataBox(newVars, row_num);
for (int i = 0; i < row_num; i++) {
for (int j = 0; j < col_num; j++) {
_dataBox.set(i, j, get(rows[i], cols[j]));
}
}
return _dataBox;
}
/**
* Getter for the field continuousData.
*
* @return an array of {@link double} objects
*/
public double[][] getContinuousData() {
return this.continuousData;
}
/**
* Getter for the field discreteData.
*
* @return an array of {@link int} objects
*/
public int[][] getDiscreteData() {
return this.discreteData;
}
}