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Refactoring discrete conditional TE calculator to take source as first argument before destination (to match continuous calculators)

This commit is contained in:
joseph.lizier 2014-08-06 00:32:54 +00:00
parent d3bb73bba0
commit 6c0d2f4e99
1 changed files with 30 additions and 32 deletions
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62
java/source/infodynamics/measures/discrete/ConditionalTransferEntropyCalculator.java
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@ -188,12 +188,11 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
/**
* Add observations for a single source-destination-conditionals set
* to our estimates of the pdfs.
*
* @param dest destination time series
* @param source source time series
* @param dest destination time series
* @param conditionals conditionals multivariate time series
*/
public void addObservations(int[] dest, int[] source, int[][] conditionals)
public void addObservations(int[] source, int[] dest, int[][] conditionals)
throws Exception {
int rows = dest.length;
@ -255,13 +254,12 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* {@link MatrixUtils#computeCombinedValues(int[][], int)}. This cannot be
* checked here however, so use at your own risk!
* </p>
*
* @param dest destination time series
* @param source source time series
* @param dest destination time series
* @param conditionals conditionals univariate time series - it is assumed
* that the user has combined the values of the multivariate conditionals time series
*/
public void addObservations(int[] dest, int[] source, int[] conditionals)
public void addObservations(int[] source, int[] dest, int[] conditionals)
throws Exception {
int rows = dest.length;
@ -383,17 +381,17 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
*
* @param states
*/
public void addObservations(int states[][], int destCol, int sourceCol, int[] othersAbsolute) {
addObservations(states, destCol, sourceCol, othersAbsolute, false);
public void addObservations(int states[][], int sourceCol, int destCol, int[] othersAbsolute) {
addObservations(states, sourceCol, destCol, othersAbsolute, false);
}
private void addObservations(int states[][], int destCol, int sourceCol, int[] othersAbsolute, boolean cleanedOthers) {
private void addObservations(int states[][], int sourceCol, int destCol, int[] othersAbsolute, boolean cleanedOthers) {
int[] cleanedOthersAbsolute;
if (cleanedOthers) {
cleanedOthersAbsolute = othersAbsolute;
} else {
cleanedOthersAbsolute = cleanAbsoluteOthers(othersAbsolute, destCol,
sourceCol, k > 0);
cleanedOthersAbsolute = cleanAbsoluteOthers(othersAbsolute, sourceCol,
destCol, k > 0);
// This call made redundant by cleanAbsoluteOthers:
// confirmEnoughAbsoluteOthers(othersAbsolute, destCol, sourceCol);
}
@ -685,19 +683,19 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* @return
*/
public double[] computeLocalFromPreviousObservations
(int states[][], int destCol, int sourceCol, int[] othersAbsolute){
(int states[][], int sourceCol, int destCol, int[] othersAbsolute){
return computeLocalFromPreviousObservations(states, destCol, sourceCol, othersAbsolute, false);
return computeLocalFromPreviousObservations(states, sourceCol, destCol, othersAbsolute, false);
}
private double[] computeLocalFromPreviousObservations
(int states[][], int destCol, int sourceCol, int[] othersAbsolute, boolean cleanedOthers){
(int states[][], int sourceCol, int destCol, int[] othersAbsolute, boolean cleanedOthers){
int[] cleanedOthersAbsolute;
if (cleanedOthers) {
cleanedOthersAbsolute = othersAbsolute;
} else {
cleanedOthersAbsolute = cleanAbsoluteOthers(othersAbsolute,
destCol, sourceCol, k > 0);
sourceCol, destCol, k > 0);
// This call made redundant by cleanOffsetOthers:
// confirmEnoughAbsoluteOthers(othersAbsolute, destCol, sourceCol);
}
@ -803,18 +801,18 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* This method suitable for heterogeneous agents
*
* @param states - 2D array of states
* @param destCol - column index for the destination agent
* @param sourceCol - column index for the source agent
* @param destCol - column index for the destination agent
* @param othersAbsolute - column indices for other causal info contributors
* @return
*/
public double[] computeLocal(int states[][], int destCol, int sourceCol, int[] othersAbsolute) {
public double[] computeLocal(int states[][], int sourceCol, int destCol, int[] othersAbsolute) {
initialise();
int[] cleanedOthers = cleanAbsoluteOthers(othersAbsolute, destCol,
sourceCol, k > 0);
addObservations(states, destCol, sourceCol, cleanedOthers, true);
return computeLocalFromPreviousObservations(states, destCol, sourceCol, cleanedOthers, true);
int[] cleanedOthers = cleanAbsoluteOthers(othersAbsolute, sourceCol,
destCol, k > 0);
addObservations(states, sourceCol, destCol, cleanedOthers, true);
return computeLocalFromPreviousObservations(states, sourceCol, destCol, cleanedOthers, true);
}
/**
@ -825,15 +823,15 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* This method suitable for heterogeneous agents
*
* @param states - 2D array of states
* @param destCol - column index for the destination agent
* @param sourceCol - column index for the source agent
* @param destCol - column index for the destination agent
* @param othersAbsolute - column indices for other causal info contributors
* @return
*/
public double computeAverageLocal(int states[][], int destCol, int sourceCol, int[] othersAbsolute) {
public double computeAverageLocal(int states[][], int sourceCol, int destCol, int[] othersAbsolute) {
initialise();
addObservations(states, destCol, sourceCol, othersAbsolute);
addObservations(states, sourceCol, destCol, othersAbsolute);
return computeAverageLocalOfObservations();
}
@ -866,13 +864,13 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* node itself not included only when removeDest is set to true)
*
* @param others
* @param dest
* @param src
* @param dest
* @param removeDest remove the destination itself from the count
* of absolute others.
* @return
*/
public static int countOfAbsoluteOthers(int[] others, int dest, int src,
public static int countOfAbsoluteOthers(int[] others, int src, int dest,
boolean removeDest) {
int countOfOthers = 0;
for (int index = 0; index < others.length; index++) {
@ -908,15 +906,15 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* contributors is long enough compared to our expectation
*
* @param othersAbsolute
* @param dest
* @param src
* @param dest
* @param removeDest remove the destination itself from the count
* of absolute others.
* @return
*/
public boolean confirmEnoughAbsoluteOthers(int[] othersAbsolute, int dest,
int src, boolean removeDest) {
if (countOfAbsoluteOthers(othersAbsolute, dest, src, removeDest) !=
public boolean confirmEnoughAbsoluteOthers(int[] othersAbsolute, int src,
int dest, boolean removeDest) {
if (countOfAbsoluteOthers(othersAbsolute, src, dest, removeDest) !=
numOtherInfoContributors) {
throw new RuntimeException("Incorrect number of others in absolutes");
}
@ -969,15 +967,15 @@ public class ConditionalTransferEntropyCalculator extends InfoMeasureCalculator
* Checks that there are enough other information contributors.
*
* @param others
* @param dest
* @param src
* @param dest
* @param removeDest Remove the destination itself from the cleaned
* other sources (if it is there). Should not be done
* if k == 0 (because then the destination is not included
* in the past history)
* @return
*/
public int[] cleanAbsoluteOthers(int[] others, int dest, int src,
public int[] cleanAbsoluteOthers(int[] others, int src, int dest,
boolean removeDest) {
int[] cleaned = new int[numOtherInfoContributors];
int countOfOthers = 0;