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history embeddings done

This commit is contained in:
David Shorten 2021-07-23 17:26:18 +10:00
parent deb9d97520
commit 0e530cdceb
2 changed files with 62 additions and 37 deletions
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95
java/source/infodynamics/measures/spiking/integration/TransferEntropyCalculatorSpikingIntegration.java
View File

@ -72,10 +72,10 @@ public class TransferEntropyCalculatorSpikingIntegration implements
* destination only
*/
Vector<double[][]> targetEmbeddingsFromSpikes = null;
Vector<double[][]> sourceEmbeddingsFromSpikes = null;
Vector<double[][]> targetEmbeddingsFromSamples = null;
Vector<double[][]> sourceEmbeddingsFromSamples = null;
Vector<double[]> targetEmbeddingsFromSpikes = null;
Vector<double[]> sourceEmbeddingsFromSpikes = null;
Vector<double[]> targetEmbeddingsFromSamples = null;
Vector<double[]> sourceEmbeddingsFromSamples = null;
Vector<double[][]> destPastAndNextTimings = null;
@ -298,10 +298,10 @@ public class TransferEntropyCalculatorSpikingIntegration implements
numEventsPerObservationSet = new Vector<Integer>();
// New
targetEmbeddingsFromSpikes = new Vector<double[][]>();
sourceEmbeddingsFromSpikes = new Vector<double[][]>();
targetEmbeddingsFromSamples = new Vector<double[][]>();
sourceEmbeddingsFromSamples = new Vector<double[][]>();
targetEmbeddingsFromSpikes = new Vector<double[]>();
sourceEmbeddingsFromSpikes = new Vector<double[]>();
targetEmbeddingsFromSamples = new Vector<double[]>();
sourceEmbeddingsFromSamples = new Vector<double[]>();
// Send all of the observations through:
Iterator<double[]> sourceIterator = vectorOfSourceSpikeTimes.iterator();
@ -316,6 +316,10 @@ public class TransferEntropyCalculatorSpikingIntegration implements
targetEmbeddingsFromSpikes, sourceEmbeddingsFromSpikes,
targetEmbeddingsFromSamples, sourceEmbeddingsFromSamples);
}
for (int i = 0; i < 5; i++) {
System.out.println(Arrays.toString(targetEmbeddingsFromSpikes.elementAt(i)));
}
// Now we have collected all the events.
// Load up the search structures:
@ -370,8 +374,10 @@ public class TransferEntropyCalculatorSpikingIntegration implements
}
protected void makeEmbeddingsAtPoints(double[] pointsAtWhichToMakeEmbeddings, double[] sourceSpikeTimes, double[] destSpikeTimes,
Vector<double[][]> targetEmbeddings, Vector<double[][]> sourceEmbeddings) {
System.out.println("foo");
Vector<double[]> targetEmbeddings, Vector<double[]> sourceEmbeddings) {
//System.out.println("foo");
Random random = new Random();
int embedding_point_index = 0;
int most_recent_dest_index = k;
@ -388,41 +394,58 @@ public class TransferEntropyCalculatorSpikingIntegration implements
for (;embedding_point_index < pointsAtWhichToMakeEmbeddings.length; embedding_point_index++) {
// Advance the tracker of the most recent dest index
while (most_recent_dest_index < destSpikeTimes.length) {
// Case where we will not be able to evaluate the following else if
if (most_recent_dest_index == destSpikeTimes.length - 2) {
// The final spike is still behind the current embedding point, so advance
if (destSpikeTimes[most_recent_dest_index + 1] <
pointsAtWhichToMakeEmbeddings[embedding_point_index]) {
most_recent_dest_index += 1;
}
break;
} else if (destSpikeTimes[most_recent_dest_index + 1] < pointsAtWhichToMakeEmbeddings[embedding_point_index]) {
while (most_recent_dest_index < (destSpikeTimes.length - 1)) {
if (destSpikeTimes[most_recent_dest_index + 1] < pointsAtWhichToMakeEmbeddings[embedding_point_index]) {
most_recent_dest_index++;
} else {
break;
}
}
// Do the same for the most recent source index
while (most_recent_source_index < sourceSpikeTimes.length) {
// Case where we will not be able to evaluate the following else if
if (most_recent_source_index == sourceSpikeTimes.length - 2) {
// The final spike is still behind the current embedding point, so advance
if (sourceSpikeTimes[most_recent_source_index + 1] <
pointsAtWhichToMakeEmbeddings[embedding_point_index]) {
most_recent_source_index += 1;
}
break;
} else if (sourceSpikeTimes[most_recent_source_index + 1] < pointsAtWhichToMakeEmbeddings[embedding_point_index]) {
while (most_recent_source_index < (sourceSpikeTimes.length - 1)) {
if (sourceSpikeTimes[most_recent_source_index + 1] < pointsAtWhichToMakeEmbeddings[embedding_point_index]) {
most_recent_source_index++;
} else {
break;
}
}
System.out.println(most_recent_dest_index + " " + most_recent_source_index + " " + embedding_point_index);
System.out.println(destSpikeTimes[most_recent_dest_index] + " " + sourceSpikeTimes[most_recent_source_index] + " " +
pointsAtWhichToMakeEmbeddings[embedding_point_index]);
//System.out.println(most_recent_dest_index + " " + most_recent_source_index + " " + embedding_point_index);
//System.out.println(destSpikeTimes[most_recent_dest_index] + " " + sourceSpikeTimes[most_recent_source_index] + " " +
// pointsAtWhichToMakeEmbeddings[embedding_point_index]);
//System.out.println(k + " " + l);
double[] destPast = new double[k];
double[] sourcePast = new double[l];
destPast[0] = pointsAtWhichToMakeEmbeddings[embedding_point_index] -
destSpikeTimes[most_recent_dest_index];
sourcePast[0] = pointsAtWhichToMakeEmbeddings[embedding_point_index] -
sourceSpikeTimes[most_recent_source_index];
if (addNoise) {
destPast[0] += random.nextGaussian()*noiseLevel;
sourcePast[0] += random.nextGaussian()*noiseLevel;
}
for (int i = 1; i < k; i++) {
destPast[i] = destSpikeTimes[most_recent_dest_index - i + 1] -
destSpikeTimes[most_recent_dest_index - i];
if (addNoise) {
destPast[i - 1] += random.nextGaussian()*noiseLevel;
}
}
for (int i = 1; i < l; i++) {
sourcePast[i] = sourceSpikeTimes[most_recent_source_index - i + 1] -
sourceSpikeTimes[most_recent_source_index - i];
if (addNoise) {
sourcePast[i - 1] += random.nextGaussian()*noiseLevel;
}
}
//System.out.println(Arrays.toString(destPast));
//System.out.println(Arrays.toString(sourcePast));
//System.out.println();
targetEmbeddings.add(destPast);
sourceEmbeddings.add(sourcePast);
}
}
@ -430,8 +453,8 @@ public class TransferEntropyCalculatorSpikingIntegration implements
int timeSeriesIndex, Vector<double[][]>[] eventTimings,
Vector<double[][]> destPastAndNextTimings, Vector<Integer> eventTypeLocator,
Vector<Integer> eventIndexLocator, Vector<Integer> numEventsPerObservationSet,
Vector<double[][]> targetEmbeddingsFromSpikes, Vector<double[][]> sourceEmbeddingsFromSpikes,
Vector<double[][]> targetEmbeddingsFromSamples, Vector<double[][]> sourceEmbeddingsFromSamples)
Vector<double[]> targetEmbeddingsFromSpikes, Vector<double[]> sourceEmbeddingsFromSpikes,
Vector<double[]> targetEmbeddingsFromSamples, Vector<double[]> sourceEmbeddingsFromSamples)
throws Exception {
// addObservationsAfterParamsDetermined(sourceSpikeTimes, destSpikeTimes);
@ -455,6 +478,8 @@ public class TransferEntropyCalculatorSpikingIntegration implements
makeEmbeddingsAtPoints(destSpikeTimes, sourceSpikeTimes, destSpikeTimes, targetEmbeddingsFromSpikes, sourceEmbeddingsFromSpikes);
makeEmbeddingsAtPoints(randomSampleTimes, sourceSpikeTimes, destSpikeTimes, targetEmbeddingsFromSamples, sourceEmbeddingsFromSamples);
// Scan to find the indices by which we have k and l spikes for dest and source
// respectively

4
tester.py
View File

@ -58,8 +58,8 @@ teCalcClass = JPackage("infodynamics.measures.spiking.integration").TransferEntr
teCalc = teCalcClass()
teCalc.setProperty("NORMALISE", "true") # Normalise the individual variables
teCalc.initialise(1) # Use history length 1 (Schreiber k=1)
teCalc.setProperty("k", "2")
teCalc.setProperty("l", "2")
teCalc.setProperty("k_HISTORY", "2")
teCalc.setProperty("l_HISTORY", "2")
teCalc.setProperty("knns", "4") # Use Kraskov parameter K=4 for 4 nearest points
# # Perform calculation with correlated source:
teCalc.setObservations(JArray(JDouble, 1)(sourceArray), JArray(JDouble, 1)(destArray))