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Minor optimization to function to calculate the log of exponentials. 

* Avoids calling Math.Pow whenever possible (skips -Inf and 0 values),
leads to better performance.
This commit is contained in:
Nigel Delaney 2014-06-11 16:18:32 -04:00
parent 3079755b4c
commit 5e258bfeff
1 changed files with 29 additions and 17 deletions
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46
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/MathUtils.java
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@ -265,21 +265,28 @@ public class MathUtils {
return log10sumLog10(log10p, start, log10p.length);
}
public static double log10sumLog10(final double[] log10p,final int start,final int finish) {
double sum = 0.0;
public static double log10sumLog10(final double[] log10p, final int start, final int finish) {
double maxValue = arrayMax(log10p, finish);
if(maxValue == Double.NEGATIVE_INFINITY)
final int maxElementIndex = MathUtils.maxElementIndex(log10p, start, finish);
double maxValue = log10p[maxElementIndex];
if(maxValue == Double.NEGATIVE_INFINITY) {
return maxValue;
for (int i = start; i < finish; i++) {
if ( Double.isNaN(log10p[i]) || log10p[i] == Double.POSITIVE_INFINITY ) {
throw new IllegalArgumentException("log10p: Values must be non-infinite and non-NAN");
}
sum += Math.pow(10.0, log10p[i] - maxValue);
}
return Math.log10(sum) + maxValue;
double sum = 1.0;
for (int i = start; i < finish; i++) {
double curVal = log10p[i];
double scaled_val = curVal - maxValue;
if (i == maxElementIndex || curVal == Double.NEGATIVE_INFINITY) {
continue;
}
else {
sum += Math.pow(10.0, scaled_val);
}
}
if ( Double.isNaN(sum) || sum == Double.POSITIVE_INFINITY ) {
throw new IllegalArgumentException("log10p: Values must be non-infinite and non-NAN");
}
return maxValue + (sum != 1.0 ? Math.log10(sum) : 0.0);
}
public static double sumLog10(final double[] log10values) {
@ -848,19 +855,25 @@ public class MathUtils {
return maxElementIndex(array, array.length);
}
public static int maxElementIndex(final double[] array, final int endIndex) {
public static int maxElementIndex(final double[] array, final int start, final int endIndex) {
if (array == null || array.length == 0)
throw new IllegalArgumentException("Array cannot be null!");
int maxI = 0;
for (int i = 1; i < endIndex; i++) {
if (start > endIndex) {
throw new IllegalArgumentException("Start cannot be after end.");
}
int maxI = start;
for (int i = (start+1); i < endIndex; i++) {
if (array[i] > array[maxI])
maxI = i;
}
return maxI;
}
public static int maxElementIndex(final double[] array, final int endIndex) {
return maxElementIndex(array, 0, endIndex);
}
public static int maxElementIndex(final int[] array) {
return maxElementIndex(array, array.length);
}
@ -878,7 +891,6 @@ public class MathUtils {
if (array[i] > array[maxI])
maxI = i;
}
return maxI;
}