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Added Java support for GPU surrogate calculation.

This commit is contained in:
Pedro Martinez Mediano 2017-05-22 15:03:32 +10:00
parent 118e32d9ad
commit 001227c730
1 changed files with 12 additions and 4 deletions
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16
java/source/infodynamics/measures/continuous/kraskov/MutualInfoCalculatorMultiVariateKraskov.java
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@ -600,8 +600,8 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
* and implement a GPU routine to calculate all values in a single call
* to the GPU code.
*/
protected double[] gpuComputeFromObservations(
int startTimePoint, int numTimePoints, boolean returnLocals) throws Exception {
protected double[] gpuComputeFromObservations(int startTimePoint,
int numTimePoints, boolean returnLocals, int nb_surrogates) throws Exception {
ensureCudaLibraryLoaded();
@ -619,7 +619,7 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
try {
res = MIKraskov(totalObservations, sourceObservations, dimensionsSource,
destObservations, dimensionsDest, k, returnLocals, useMaxNorm, isAlgorithm1, 0);
destObservations, dimensionsDest, k, returnLocals, useMaxNorm, isAlgorithm1, nb_surrogates);
} catch (Throwable e) {
System.out.println("WARNING. Error in GPU code. Reverting back to CPU.");
e.printStackTrace();
@ -630,6 +630,14 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
}
/**
* FIXME
*/
protected double[] gpuComputeFromObservations(int startTimePoint,
int numTimePoints, boolean returnLocals) throws Exception {
return gpuComputeFromObservations(startTimePoint, numTimePoints, returnLocals, 0);
}
/**
* Native method to calculate MI in GPU.
*/
@ -723,7 +731,7 @@ public abstract class MutualInfoCalculatorMultiVariateKraskov
public EmpiricalMeasurementDistribution computeSignificance(int numPermutationsToCheck)
throws Exception {
if (useGPU) {
double[] res = gpuComputeFromObservations(0, totalObservations, false); // TODO FIXME
double[] res = gpuComputeFromObservations(0, totalObservations, false, numPermutationsToCheck);
return new EmpiricalMeasurementDistribution(
MatrixUtils.select(res, 1, res.length - 1), res[0]);
} else {