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This commit is contained in:
David Shorten 2018-12-19 17:15:47 +11:00
parent 504c6262f0
commit 8bcf41e572
1 changed files with 10 additions and 3 deletions
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13
java/source/infodynamics/measures/spiking/integration/TransferEntropyCalculatorSpikingIntegration.java
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@ -521,6 +521,9 @@ public class TransferEntropyCalculatorSpikingIntegration implements
int numberOfEvents = eventTypeLocator.size();
double contributionFromSpikes = 0;
double contributionRate_X = 0;
double contributionRate_XY = 0;
int numContributions = 0;
double totalTimeLength = 0;
// Create temporary storage for arrays used in the neighbour counting:
@ -855,11 +858,11 @@ public class TransferEntropyCalculatorSpikingIntegration implements
// This code section takes the counts of spikes and total intervals, and
// estimates the log rates.
// Inferred rates raw:
double rawRateGivenSourceAndDest = (double) countOfDestNextInWindow / timeInWindowWithMatchingJointHistories;
double rawRateGivenDest = (double) countOfDestNextMatched / timeInWindowWithMatchingDestHistory;
double rawRateGivenSourceAndDest = ((double) (Knns - 1)) / timeInWindowWithMatchingJointHistories;
double rawRateGivenDest = ((double) (countOfDestNextMatched - 1)) / timeInWindowWithMatchingDestHistory;
// Attempt at bias correction:
// Using digamma of neighbour_count - 1, since the neighbour count now includes our search point and it's really k waiting times
double logRateGivenSourceAndDestCorrected = MathsUtils.digamma(Knns) //- (1.0 / (double) Knns) // I don't think this correction is required
double logRateGivenSourceAndDestCorrected = MathsUtils.digamma(Knns) //`- (1.0 / (double) Knns) // I don't think this correction is required
- Math.log(timeInWindowWithMatchingJointHistories);
double logRateGivenDestCorrected = MathsUtils.digamma(countOfDestNextMatched) // - (1.0 / (double) countOfDestNextMatched) // I don't think this correction is required
- Math.log(timeInWindowWithMatchingDestHistory);
@ -890,6 +893,9 @@ public class TransferEntropyCalculatorSpikingIntegration implements
// Add the contribution in:
// a.If we were using digamma logs:
contributionFromSpikes += logRateGivenSourceAndDestCorrected - logRateGivenDestCorrected;
contributionRate_X += rawRateGivenDest;
contributionRate_XY += rawRateGivenSourceAndDest;
numContributions++;
// contributionFromSpikes += Math.log(rawRateGivenSourceAndDest / rawRateGivenDest);
@ -901,6 +907,7 @@ public class TransferEntropyCalculatorSpikingIntegration implements
// totalSearchTimeWindowCondDestPast));
}
System.out.println("All done!");
System.out.println(contributionRate_X/(float)numContributions + " " + contributionRate_XY/(float)numContributions);
contributionFromSpikes /= totalTimeLength;
return contributionFromSpikes;
}