MATH-1416: Replaced usage of combinatorics code with equivalent calls to "Commons Numbers".
Project: http://git-wip-us.apache.org/repos/asf/commons-math/repo Commit: http://git-wip-us.apache.org/repos/asf/commons-math/commit/d442a770 Tree: http://git-wip-us.apache.org/repos/asf/commons-math/tree/d442a770 Diff: http://git-wip-us.apache.org/repos/asf/commons-math/diff/d442a770 Branch: refs/heads/master Commit: d442a770f2ea6b8c0b50a001b1ef1d92511e9832 Parents: 0510759 Author: Gilles <er...@apache.org> Authored: Mon May 22 00:54:01 2017 +0200 Committer: Gilles <er...@apache.org> Committed: Mon May 22 00:54:01 2017 +0200 ---------------------------------------------------------------------- .../commons/math4/analysis/differentiation/DSCompiler.java | 7 ++++--- .../math4/analysis/interpolation/HermiteInterpolator.java | 8 +++++--- .../commons/math4/analysis/polynomials/PolynomialsUtils.java | 4 ++-- .../commons/math4/distribution/PascalDistribution.java | 7 ++++--- .../commons/math4/stat/inference/KolmogorovSmirnovTest.java | 4 ++-- .../math4/analysis/differentiation/DSCompilerTest.java | 4 ++-- .../analysis/differentiation/DerivativeStructureTest.java | 6 +++--- .../math4/analysis/polynomials/PolynomialsUtilsTest.java | 4 ++-- .../apache/commons/math4/linear/InverseHilbertMatrix.java | 8 ++++---- .../math4/stat/inference/KolmogorovSmirnovTestTest.java | 4 ++-- 10 files changed, 30 insertions(+), 26 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/main/java/org/apache/commons/math4/analysis/differentiation/DSCompiler.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/analysis/differentiation/DSCompiler.java b/src/main/java/org/apache/commons/math4/analysis/differentiation/DSCompiler.java index 3c1838d..dd857de 100644 --- a/src/main/java/org/apache/commons/math4/analysis/differentiation/DSCompiler.java +++ b/src/main/java/org/apache/commons/math4/analysis/differentiation/DSCompiler.java @@ -26,7 +26,7 @@ import org.apache.commons.math4.exception.MathArithmeticException; import org.apache.commons.math4.exception.MathInternalError; import org.apache.commons.math4.exception.NotPositiveException; import org.apache.commons.math4.exception.NumberIsTooLargeException; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.FactorialDouble; import org.apache.commons.math4.util.FastMath; import org.apache.commons.math4.util.MathArrays; @@ -123,6 +123,8 @@ import org.apache.commons.math4.util.MathArrays; * @since 3.1 */ public class DSCompiler { + /** Cache for factorials. */ + private static FactorialDouble FACTORIAL = FactorialDouble.create().withCache(30); /** Array of all compilers created so far. */ private static AtomicReference<DSCompiler[][]> compilers = @@ -1803,8 +1805,7 @@ public class DSCompiler { for (int k = 0; k < orders.length; ++k) { if (orders[k] > 0) { try { - term *= FastMath.pow(delta[k], orders[k]) / - CombinatoricsUtils.factorial(orders[k]); + term *= FastMath.pow(delta[k], orders[k]) / FACTORIAL.value(orders[k]); } catch (NotPositiveException e) { // this cannot happen throw new MathInternalError(e); http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/main/java/org/apache/commons/math4/analysis/interpolation/HermiteInterpolator.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/analysis/interpolation/HermiteInterpolator.java b/src/main/java/org/apache/commons/math4/analysis/interpolation/HermiteInterpolator.java index 5a30815..439eb1c 100644 --- a/src/main/java/org/apache/commons/math4/analysis/interpolation/HermiteInterpolator.java +++ b/src/main/java/org/apache/commons/math4/analysis/interpolation/HermiteInterpolator.java @@ -27,7 +27,7 @@ import org.apache.commons.math4.exception.MathArithmeticException; import org.apache.commons.math4.exception.NoDataException; import org.apache.commons.math4.exception.ZeroException; import org.apache.commons.math4.exception.util.LocalizedFormats; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.Factorial; /** Polynomial interpolator using both sample values and sample derivatives. * <p> @@ -86,11 +86,13 @@ public class HermiteInterpolator implements UnivariateDifferentiableVectorFuncti public void addSamplePoint(final double x, final double[] ... value) throws ZeroException, MathArithmeticException { + if (value.length > 20) { + throw new MathArithmeticException(LocalizedFormats.NUMBER_TOO_LARGE, value.length, 20); + } for (int i = 0; i < value.length; ++i) { - final double[] y = value[i].clone(); if (i > 1) { - double inv = 1.0 / CombinatoricsUtils.factorial(i); + double inv = 1.0 / Factorial.value(i); for (int j = 0; j < y.length; ++j) { y[j] *= inv; } http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/main/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtils.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtils.java b/src/main/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtils.java index 92e9e6d..018df81 100644 --- a/src/main/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtils.java +++ b/src/main/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtils.java @@ -22,7 +22,7 @@ import java.util.List; import java.util.Map; import org.apache.commons.math4.fraction.BigFraction; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.BinomialCoefficient; import org.apache.commons.math4.util.FastMath; /** @@ -331,7 +331,7 @@ public class PolynomialsUtils { final int[][] coeff = new int[dp1][dp1]; for (int i = 0; i < dp1; i++){ for(int j = 0; j <= i; j++){ - coeff[i][j] = (int) CombinatoricsUtils.binomialCoefficient(i, j); + coeff[i][j] = (int) BinomialCoefficient.value(i, j); } } http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java b/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java index f176865..9a693d1 100644 --- a/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java +++ b/src/main/java/org/apache/commons/math4/distribution/PascalDistribution.java @@ -19,8 +19,9 @@ package org.apache.commons.math4.distribution; import org.apache.commons.math4.exception.NotStrictlyPositiveException; import org.apache.commons.math4.exception.OutOfRangeException; import org.apache.commons.math4.exception.util.LocalizedFormats; +import org.apache.commons.numbers.combinatorics.BinomialCoefficientDouble; +import org.apache.commons.numbers.combinatorics.LogBinomialCoefficient; import org.apache.commons.numbers.gamma.RegularizedBeta; -import org.apache.commons.math4.util.CombinatoricsUtils; import org.apache.commons.math4.util.FastMath; /** @@ -125,7 +126,7 @@ public class PascalDistribution extends AbstractIntegerDistribution { if (x < 0) { ret = 0.0; } else { - ret = CombinatoricsUtils.binomialCoefficientDouble(x + + ret = BinomialCoefficientDouble.value(x + numberOfSuccesses - 1, numberOfSuccesses - 1) * FastMath.pow(probabilityOfSuccess, numberOfSuccesses) * FastMath.pow(1.0 - probabilityOfSuccess, x); @@ -140,7 +141,7 @@ public class PascalDistribution extends AbstractIntegerDistribution { if (x < 0) { ret = Double.NEGATIVE_INFINITY; } else { - ret = CombinatoricsUtils.binomialCoefficientLog(x + + ret = LogBinomialCoefficient.value(x + numberOfSuccesses - 1, numberOfSuccesses - 1) + logProbabilityOfSuccess * numberOfSuccesses + log1mProbabilityOfSuccess * x; http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java b/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java index ef45917..40d9d91 100644 --- a/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java +++ b/src/main/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTest.java @@ -22,6 +22,7 @@ import java.util.Arrays; import org.apache.commons.rng.simple.RandomSource; import org.apache.commons.rng.UniformRandomProvider; +import org.apache.commons.numbers.combinatorics.BinomialCoefficientDouble; import org.apache.commons.math4.distribution.EnumeratedRealDistribution; import org.apache.commons.math4.distribution.RealDistribution; import org.apache.commons.math4.distribution.AbstractRealDistribution; @@ -41,7 +42,6 @@ import org.apache.commons.math4.linear.Array2DRowFieldMatrix; import org.apache.commons.math4.linear.FieldMatrix; import org.apache.commons.math4.linear.MatrixUtils; import org.apache.commons.math4.linear.RealMatrix; -import org.apache.commons.math4.util.CombinatoricsUtils; import org.apache.commons.math4.util.FastMath; import org.apache.commons.math4.util.MathArrays; import org.apache.commons.math4.util.MathUtils; @@ -959,7 +959,7 @@ public class KolmogorovSmirnovTest { */ public double exactP(double d, int n, int m, boolean strict) { return 1 - n(m, n, m, n, calculateIntegralD(d, m, n, strict), strict) / - CombinatoricsUtils.binomialCoefficientDouble(n + m, m); + BinomialCoefficientDouble.value(n + m, m); } /** http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/test/java/org/apache/commons/math4/analysis/differentiation/DSCompilerTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/analysis/differentiation/DSCompilerTest.java b/src/test/java/org/apache/commons/math4/analysis/differentiation/DSCompilerTest.java index 4284505..c466a5c 100644 --- a/src/test/java/org/apache/commons/math4/analysis/differentiation/DSCompilerTest.java +++ b/src/test/java/org/apache/commons/math4/analysis/differentiation/DSCompilerTest.java @@ -23,7 +23,7 @@ import java.util.Map; import org.apache.commons.math4.analysis.differentiation.DSCompiler; import org.apache.commons.math4.exception.DimensionMismatchException; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.BinomialCoefficient; import org.junit.Assert; import org.junit.Test; @@ -37,7 +37,7 @@ public class DSCompilerTest { public void testSize() { for (int i = 0; i < 6; ++i) { for (int j = 0; j < 6; ++j) { - long expected = CombinatoricsUtils.binomialCoefficient(i + j, i); + long expected = BinomialCoefficient.value(i + j, i); Assert.assertEquals(expected, DSCompiler.getCompiler(i, j).getSize()); Assert.assertEquals(expected, DSCompiler.getCompiler(j, i).getSize()); } http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/test/java/org/apache/commons/math4/analysis/differentiation/DerivativeStructureTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/analysis/differentiation/DerivativeStructureTest.java b/src/test/java/org/apache/commons/math4/analysis/differentiation/DerivativeStructureTest.java index 7d2a1be..824b3e4 100644 --- a/src/test/java/org/apache/commons/math4/analysis/differentiation/DerivativeStructureTest.java +++ b/src/test/java/org/apache/commons/math4/analysis/differentiation/DerivativeStructureTest.java @@ -29,7 +29,7 @@ import org.apache.commons.math4.exception.NumberIsTooLargeException; import org.apache.commons.rng.UniformRandomProvider; import org.apache.commons.rng.simple.RandomSource; import org.apache.commons.numbers.core.ArithmeticUtils; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.Factorial; import org.apache.commons.math4.util.FastMath; import org.apache.commons.numbers.core.Precision; import org.junit.Assert; @@ -188,7 +188,7 @@ public class DerivativeStructureTest extends ExtendedFieldElementAbstractTest<De DerivativeStructure r = new DerivativeStructure(1, 6, 0, x).reciprocal(); Assert.assertEquals(1 / x, r.getValue(), 1.0e-15); for (int i = 1; i < r.getOrder(); ++i) { - double expected = ArithmeticUtils.pow(-1, i) * CombinatoricsUtils.factorial(i) / + double expected = ArithmeticUtils.pow(-1, i) * Factorial.value(i) / FastMath.pow(x, i + 1); Assert.assertEquals(expected, r.getPartialDerivative(i), 1.0e-15 * FastMath.abs(expected)); } @@ -797,7 +797,7 @@ public class DerivativeStructureTest extends ExtendedFieldElementAbstractTest<De DerivativeStructure log = new DerivativeStructure(1, maxOrder, 0, x).log(); Assert.assertEquals(FastMath.log(x), log.getValue(), epsilon[0]); for (int n = 1; n <= maxOrder; ++n) { - double refDer = -CombinatoricsUtils.factorial(n - 1) / FastMath.pow(-x, n); + double refDer = -Factorial.value(n - 1) / FastMath.pow(-x, n); Assert.assertEquals(refDer, log.getPartialDerivative(n), epsilon[n]); } } http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/test/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtilsTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtilsTest.java b/src/test/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtilsTest.java index e9d2d09..9387e34 100644 --- a/src/test/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtilsTest.java +++ b/src/test/java/org/apache/commons/math4/analysis/polynomials/PolynomialsUtilsTest.java @@ -18,7 +18,7 @@ package org.apache.commons.math4.analysis.polynomials; import org.apache.commons.math4.analysis.UnivariateFunction; import org.apache.commons.math4.analysis.integration.IterativeLegendreGaussIntegrator; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.BinomialCoefficient; import org.apache.commons.math4.util.FastMath; import org.apache.commons.numbers.core.Precision; import org.junit.Assert; @@ -292,7 +292,7 @@ public class PolynomialsUtilsTest { for (int w = 0; w < 10; ++w) { for (int i = 0; i < 10; ++i) { PolynomialFunction jacobi = PolynomialsUtils.createJacobiPolynomial(i, v, w); - double binomial = CombinatoricsUtils.binomialCoefficient(v + i, i); + double binomial = BinomialCoefficient.value(v + i, i); Assert.assertTrue(Precision.equals(binomial, jacobi.value(1.0), 1)); } } http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/test/java/org/apache/commons/math4/linear/InverseHilbertMatrix.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/linear/InverseHilbertMatrix.java b/src/test/java/org/apache/commons/math4/linear/InverseHilbertMatrix.java index 141f34b..3a44e9d 100644 --- a/src/test/java/org/apache/commons/math4/linear/InverseHilbertMatrix.java +++ b/src/test/java/org/apache/commons/math4/linear/InverseHilbertMatrix.java @@ -21,7 +21,7 @@ import org.apache.commons.math4.linear.ArrayRealVector; import org.apache.commons.math4.linear.RealLinearOperator; import org.apache.commons.math4.linear.RealVector; import org.apache.commons.numbers.core.ArithmeticUtils; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.BinomialCoefficient; /** * This class implements inverses of Hilbert Matrices as @@ -58,11 +58,11 @@ public class InverseHilbertMatrix */ public long getEntry(final int i, final int j) { long val = i + j + 1; - long aux = CombinatoricsUtils.binomialCoefficient(n + i, n - j - 1); + long aux = BinomialCoefficient.value(n + i, n - j - 1); val = ArithmeticUtils.mulAndCheck(val, aux); - aux = CombinatoricsUtils.binomialCoefficient(n + j, n - i - 1); + aux = BinomialCoefficient.value(n + j, n - i - 1); val = ArithmeticUtils.mulAndCheck(val, aux); - aux = CombinatoricsUtils.binomialCoefficient(i + j, i); + aux = BinomialCoefficient.value(i + j, i); val = ArithmeticUtils.mulAndCheck(val, aux); val = ArithmeticUtils.mulAndCheck(val, aux); return ((i + j) & 1) == 0 ? val : -val; http://git-wip-us.apache.org/repos/asf/commons-math/blob/d442a770/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java ---------------------------------------------------------------------- diff --git a/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java b/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java index d663568..66cc387 100644 --- a/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java +++ b/src/test/java/org/apache/commons/math4/stat/inference/KolmogorovSmirnovTestTest.java @@ -25,7 +25,7 @@ import org.apache.commons.math4.distribution.NormalDistribution; import org.apache.commons.math4.distribution.UniformRealDistribution; import org.apache.commons.rng.simple.RandomSource; import org.apache.commons.rng.UniformRandomProvider; -import org.apache.commons.math4.util.CombinatoricsUtils; +import org.apache.commons.numbers.combinatorics.BinomialCoefficient; import org.apache.commons.math4.util.FastMath; import org.apache.commons.math4.util.MathArrays; import org.apache.commons.math4.exception.NotANumberException; @@ -644,7 +644,7 @@ public class KolmogorovSmirnovTestTest { counts[x] += 1; } - final int numCombinations = (int) CombinatoricsUtils.binomialCoefficient(arraySize, numberOfTrueValues); + final int numCombinations = (int) BinomialCoefficient.value(arraySize, numberOfTrueValues); final long[] observed = new long[numCombinations]; final double[] expected = new double[numCombinations];
