jidt/java/source/infodynamics/measures/continuous/ChannelCalculator.java

/*
 *  Java Information Dynamics Toolkit (JIDT)
 *  Copyright (C) 2012, Joseph T. Lizier
 *  
 *  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/>.
 */

package infodynamics.measures.continuous;

/**
 * An interface for calculators computing measures from a source to a destination
 * for single variables in each (specific examples intended here
 * are the mutual information and transfer entropy)
 * 
 * 
 * @author Joseph Lizier, <a href="joseph.lizier at gmail.com">email</a>,
 * <a href="http://lizier.me/joseph/">www</a>
 *
 */
public interface ChannelCalculator extends ChannelCalculatorCommon {

	/**
	 * <p>Sets the single set of observations to compute the PDFs from.
	 * Cannot be called in conjunction with 
	 * {@link #startAddObservations()}/{@link #addObservations(double[], double[])} /
	 * {@link #finaliseAddObservations()}.</p>
	 * 
	 * @param source observations for the source variable
	 * @param destination observations for the destination variable
	 * @throws Exception
	 */
	public void setObservations(double source[], double destination[]) throws Exception;
	
	/**
	 * <p>Adds a new set of observations to update the PDFs with - is
	 * intended to be called multiple times.
	 * Must be called after {@link #startAddObservations()}; call
	 * {@link #finaliseAddObservations()} once all observations have
	 * been supplied.</p>
	 * 
	 * <p><b>Important:</b> this does not append these observations to the previously
	 *  supplied observations, but treats them independently - i.e. measurements
	 *  such as the transfer entropy will not join them up to examine k
	 *  consecutive values in time.</p>
	 *  
	 * <p>Note that the arrays source and destination must not be over-written by the user
	 *  until after finaliseAddObservations() has been called
	 *  (they are not copied by this method necessarily, but the method
	 *  may simply hold a pointer to them).</p>
	 * 
	 * @param source observations for the source variable
	 * @param destination observations for the destination variable
	 * @throws Exception
	 */
	public void addObservations(double[] source, double[] destination) throws Exception;

	/**
	 * <p>Adds a new set of observations to update the PDFs with - is
	 * intended to be called multiple times.
	 * Must be called after {@link #startAddObservations()}; call
	 * {@link #finaliseAddObservations()} once all observations have
	 * been supplied.</p>
	 * 
	 * <p><b>Important:</b> this does not append these observations to the previously
	 *  supplied observations, but treats them independently - i.e. measurements
	 *  such as the transfer entropy will not join them up to examine k
	 *  consecutive values in time.</p>
	 *  
	 * <p>Note that the arrays source and destination must not be over-written by the user
	 *  until after finaliseAddObservations() has been called
	 *  (they are not copied by this method necessarily, but the method
	 *  may simply hold a pointer to them).</p>
	 * 
	 * @param source observations for the source variable
	 * @param destination observations for the destination variable
	 * @param startTime first time index to take observations on
	 * @param numTimeSteps number of time steps to use
	 * @throws Exception
	 */
	public void addObservations(double[] source, double[] destination,
			int startTime, int numTimeSteps) throws Exception ;

	/**
	 * <p>Sets the single set of observations to compute the PDFs from.
	 * Cannot be called in conjunction with 
	 * {@link #startAddObservations()}/{@link #addObservations(double[], double[])} /
	 * {@link #finaliseAddObservations()}.</p>
	 * 
	 * @param source observations for the source variable
	 * @param destination observations for the destination variable
	 * @param sourceValid time series (with time indices the same as source)
	 *  indicating whether the source at that point is valid.
	 * @param destValid time series (with time indices the same as destination)
	 *  indicating whether the destination at that point is valid.
	 * @throws Exception
	 */
	public void setObservations(double[] source, double[] destination,
			boolean[] sourceValid, boolean[] destValid) throws Exception;

}