ArrayMath (Stanford JavaNLP API)

java.lang.Object
- edu.stanford.nlp.math.ArrayMath

```
public class ArrayMath
extends java.lang.Object
```
Methods for operating on numerical arrays as vectors and matrices.

Author:

Teg Grenager

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class ArrayMath.InvalidElementException

Nested Classes
Modifier and Type	Class and Description
`static class`	`ArrayMath.InvalidElementException`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static double[]`	`add(double[] a, double c)`
`static float[]`	`add(float[] a, double c)`
`static void`	`addInPlace(double[][] m1, double[][] m2)` Add the two 2d arrays and write the answer in place of `m1`.
`static void`	`addInPlace(double[] a, double b)` Increases the values in the first array a by b.
`static void`	`addInPlace(float[] a, double b)` Increases the values in this array by b.
`static void`	`addMultInPlace(double[] a, double[] b, double c)` Add c times the array b to array a.
`static void`	`addMultInto(double[] a, double[] b, double[] c, double d)`
`static int`	`argmax_tieLast(double[] a)`
`static int`	`argmax(double[] a)`
`static int`	`argmax(float[] a)`
`static int`	`argmax(int[] a)`
`static int`	`argmin(double[] a)`
`static int`	`argmin(float[] a)`
`static int`	`argmin(int[] a)`
`static void`	`assertFinite(double[] vector, java.lang.String vectorName)`
`static double`	`average(double[] a)`
`static java.lang.Double[]`	`box(double[] assignment)`
`static java.lang.Integer[]`	`box(int[] assignment)`
`static int[][]`	`castToInt(double[][] doubleCounts)`
`static boolean`	`contains(int[] a, int i)`
`static boolean`	`containsInSubarray(int[] a, int begin, int end, int i)`
`static int`	`countCloseToZero(double[] v, double epsilon)`
`static int`	`countInfinite(double[] v)`
`static int`	`countNaN(double[] v)`
`static int`	`countNegative(double[] v)`
`static int`	`countNonZero(double[] v)`
`static int`	`countPositive(double[] v)`
`static int[][]`	`deepCopy(int[][] counts)`
`static int[]`	`diag(int[][] a)` Returns diagonal elements of the given (square) matrix.
`static void`	`divideInPlace(double[] a, double b)` Divides the values in this array by b.
`static double`	`dotProduct(double[] a, double[] b)` Assumes that both arrays have same length.
`static double`	`dotProduct(double[] a, float[] b)` Dot product of a and b.
`static float`	`dotProduct(float[] a, float[] b)` Dot product of a and b.
`static float[]`	`doubleArrayToFloatArray(double[] a)`
`static float[][]`	`doubleArrayToFloatArray(double[][] a)`
`static double`	`entropy(double[] probs)`
`static double[]`	`exp(double[] a)`
`static void`	`expInPlace(double[] a)`
`static double[]`	`filterInfinite(double[] v)`
`static double[]`	`filterNaN(double[] v)`
`static double[]`	`filterNaNAndInfinite(double[] v)`
`static double[]`	`floatArrayToDoubleArray(float[] a)`
`static double[][]`	`floatArrayToDoubleArray(float[][] a)`
`static boolean`	`hasInfinite(double[] a)`
`static boolean`	`hasNaN(double[] a)`
`static boolean`	`hasNaN(float[] a)`
`static int`	`indexOf(int n, int[] a)`
`static double`	`innerProduct(double[] a, double[] b)`
`static double`	`innerProduct(float[] a, float[] b)`
`static double`	`iterativeAverage(double[] a)` This version avoids certain types of overflow.
`static double`	`jensenShannonDivergence(double[] a, double[] b)` Returns the Jensen Shannon divergence (information radius) between a and b, defined as the average of the kl divergences from a to b and from b to a.
`static double`	`klDivergence(double[] from, double[] to)`
`static double`	`L1Norm(double[] a)`
`static void`	`L1normalize(double[] a)`
`static double`	`L2Norm(double[] a)`
`static float`	`L2Norm(float[] a)`
`static void`	`L2normalize(double[] a)`
`static void`	`L2normalize(float[] a)`
`static double[][]`	`load2DMatrixFromFile(java.lang.String filename)`
`static double[]`	`log(double[] a)`
`static void`	`logInPlace(double[] a)`
`static void`	`logNormalize(double[] a)` Makes the values in this array sum to 1.0.
`static double`	`logSum(double... logInputs)` Returns the log of the sum of an array of numbers, which are themselves input in log form.
`static double`	`logSum(double[] logInputs, int fromIndex, int toIndex)` Returns the log of the portion between `fromIndex`, inclusive, and `toIndex`, exclusive, of an array of numbers, which are themselves input in log form.
`static double`	`logSum(double[] logInputs, int fromIndex, int afterIndex, int stride)` Returns the log of the portion between `fromIndex`, inclusive, and `toIndex`, exclusive, of an array of numbers, which are themselves input in log form.
`static float`	`logSum(float[] logInputs)` Returns the log of the sum of an array of numbers, which are themselves input in log form.
`static double`	`logSum(java.util.List<java.lang.Double> logInputs)`
`static double`	`logSum(java.util.List<java.lang.Double> logInputs, int fromIndex, int toIndex)`
`static void`	`main(java.lang.String[] args)` For testing only.
`static double`	`max(java.util.Collection<java.lang.Double> a)`
`static double`	`max(double[] a)`
`static float`	`max(float[] a)`
`static int`	`max(int... vector)`
`static int`	`max(int[][] matrix)` Returns the smallest element of the matrix
`static double`	`mean(double[] a)`
`static double`	`mean(int[] a)` Return the mean of an array of int.
`static double`	`median(double[] a)`
`static double`	`min(double... vector)`
`static float`	`min(float[] a)`
`static int`	`min(int... vector)`
`static int`	`min(int[][] matrix)` Returns the smallest element of the matrix
`static double[]`	`multiply(double[] a, double c)` Scales the values in this array by c.
`static float[]`	`multiply(float[] a, float c)` Scales the values in this array by c.
`static void`	`multiplyInPlace(double[] a, double b)` Scales the values in this array by b.
`static void`	`multiplyInPlace(float[] a, double b)` Scales the values in this array by b.
`static void`	`multiplyInto(double[] a, double[] b, double c)`
`static double`	`norm_1(double[] a)` Computes 1-norm of vector.
`static double`	`norm_1(float[] a)` Computes 1-norm of vector.
`static double`	`norm_inf(double[] a)` Computes inf-norm of vector.
`static double`	`norm_inf(float[] a)` Computes inf-norm of vector.
`static double`	`norm(double[] a)` Computes 2-norm of vector.
`static double`	`norm(float[] a)` Computes 2-norm of vector.
`static void`	`normalize(double[] a)` Makes the values in this array sum to 1.0.
`static void`	`normalize(float[] a)` Makes the values in this array sum to 1.0.
`static int`	`numRows(double[] v)`
`static double[]`	`pairwiseAdd(double[] a, double[] b)`
`static float[]`	`pairwiseAdd(float[] a, float[] b)`
`static int[]`	`pairwiseAdd(int[] a, int[] b)`
`static void`	`pairwiseAddInPlace(double[] to, double[] from)` Add the two 1d arrays in place of `to`.
`static void`	`pairwiseAddInPlace(double[] to, float[] from)` Add the two 1d arrays in place of `to`.
`static void`	`pairwiseAddInPlace(double[] to, int[] from)`
`static void`	`pairwiseAddInPlace(double[] to, short[] from)`
`static void`	`pairwiseAddInPlace(float[] to, float[] from)`
`static void`	`pairwiseDivideInPlace(double[] a, double[] b)` Divide the first array by the second elementwise, and store results in place.
`static double[]`	`pairwiseMultiply(double[] a, double[] b)` Assumes that both arrays have same length.
`static void`	`pairwiseMultiply(double[] a, double[] b, double[] result)` Puts the result in the result array.
`static float[]`	`pairwiseMultiply(float[] a, float[] b)` Assumes that both arrays have same length.
`static void`	`pairwiseMultiply(float[] a, float[] b, float[] result)` Puts the result in the result array.
`static double[]`	`pairwiseScaleAdd(double[] a, double[] b, double bScale)`
`static void`	`pairwiseScaleAddInPlace(double[] to, double[] from, double fromScale)`
`static double[]`	`pairwiseSubtract(double[] a, double[] b)`
`static float[]`	`pairwiseSubtract(float[] a, float[] b)`
`static void`	`pairwiseSubtractInPlace(double[] to, double[] from)`
`static double`	`pearsonCorrelation(double[] x, double[] y)` Direct computation of Pearson product-moment correlation coefficient.
`static double[]`	`pow(double[] a, double c)` raises each entry in array a by power c
`static float[]`	`pow(float[] a, float c)` raises each entry in array a by power c
`static void`	`powInPlace(double[] a, double c)` Scales the values in this array by c.
`static void`	`powInPlace(float[] a, float c)` Sets the values in this array by to their value taken to cth power.
`static int[]`	`range(int end)` Generate a range of integers from start (inclusive) to end (exclusive).
`static int[]`	`range(int start, int end)` Generate a range of integers from start (inclusive) to end (exclusive).
`static void`	`reverse(int[] a)`
`static double`	`safeMax(double[] v)` Returns the largest value in a vector of doubles.
`static double`	`safeMean(double[] v)` Returns the mean of a vector of doubles.
`static double`	`safeMin(double[] v)` Returns the smallest value in a vector of doubles.
`static double`	`safeStdev(double[] v)` Returns the standard deviation of a vector of doubles.
`static int`	`sampleFromDistribution(double[] d)` Samples from the distribution over values 0 through d.length given by d.
`static int`	`sampleFromDistribution(double[] d, java.util.Random random)` Samples from the distribution over values 0 through d.length given by d.
`static int`	`sampleFromDistribution(float[] d, java.util.Random random)` Samples from the distribution over values 0 through d.length given by d.
`static void`	`sampleWithoutReplacement(int[] array, int numArgClasses)` Fills the array with sample from 0 to numArgClasses-1 without replacement.
`static void`	`sampleWithoutReplacement(int[] array, int numArgClasses, java.util.Random rand)` Fills the array with sample from 0 to numArgClasses-1 without replacement.
`static void`	`setToLogDeterministic(double[] a, int i)`
`static void`	`setToLogDeterministic(float[] a, int i)`
`static void`	`shuffle(int[] a)`
`static void`	`shuffle(int[] a, java.util.Random rand)`
`static double`	`sigLevelByApproxRand(boolean[] A, boolean[] B)`
`static double`	`sigLevelByApproxRand(boolean[] A, boolean[] B, int iterations)`
`static double`	`sigLevelByApproxRand(double[] A, double[] B)` Computes the significance level by approximate randomization, using a default value of 1000 iterations.
`static double`	`sigLevelByApproxRand(double[] A, double[] B, int iterations)` Takes a pair of arrays, A and B, which represent corresponding outcomes of a pair of random variables: say, results for two different classifiers on a sequence of inputs.
`static double`	`sigLevelByApproxRand(int[] A, int[] B)`
`static double`	`sigLevelByApproxRand(int[] A, int[] B, int iterations)`
`static double[]`	`softmax(double[] scales)`
`static double`	`standardErrorOfMean(double[] a)`
`static void`	`standardize(double[] a)` Standardize values in this array, i.e., subtract the mean and divide by the standard deviation.
`static double`	`stdev(double[] a)`
`static double`	`sum(double[] a)` Returns the sum of an array of doubles.
`static double`	`sum(double[] a, int fromIndex, int toIndex)` Returns the sum of the portion of an array of numbers between `fromIndex`, inclusive, and `toIndex`, exclusive.
`static float`	`sum(float[] a)`
`static int`	`sum(int[] a)`
`static int`	`sum(int[][] a)`
`static double`	`sumSquared(double[] a)`
`static double`	`sumSquaredError(double[] a)`
`static java.lang.String`	`toBinaryString(byte[] b)`
`static java.lang.String`	`toString(byte[] a)`
`static java.lang.String`	`toString(byte[] a, java.text.NumberFormat nf)`
`static java.lang.String`	`toString(double[] a)`
`static java.lang.String`	`toString(double[][] counts)`
`static java.lang.String`	`toString(double[][] counts, int cellSize, java.lang.Object[] rowLabels, java.lang.Object[] colLabels, int rowLabelSize, java.text.NumberFormat nf, boolean printRowTotals, boolean printColumnTotals, java.lang.Object topLeft)`
`static java.lang.String`	`toString(double[][] counts, int cellSize, java.lang.Object[] rowLabels, java.lang.Object[] colLabels, java.text.NumberFormat nf, boolean printTotals)`
`static java.lang.String`	`toString(double[] a, java.text.NumberFormat nf)`
`static java.lang.String`	`toString(float[] a)`
`static java.lang.String`	`toString(float[][] counts)`
`static java.lang.String`	`toString(float[][] counts, int cellSize, java.lang.Object[] rowLabels, java.lang.Object[] colLabels, java.text.NumberFormat nf, boolean printTotals)`
`static java.lang.String`	`toString(float[] a, java.text.NumberFormat nf)`
`static java.lang.String`	`toString(int[] a)`
`static java.lang.String`	`toString(int[][] counts)`
`static java.lang.String`	`toString(int[][] counts, java.lang.Object[] rowLabels, java.lang.Object[] colLabels, int labelSize, int cellSize, java.text.NumberFormat nf, boolean printTotals)`
`static java.lang.String`	`toString(int[] a, java.text.NumberFormat nf)`
`static double[]`	`unbox(java.util.Collection<java.lang.Double> list)`
`static int[]`	`unboxToInt(java.util.Collection<java.lang.Integer> list)`
`static double`	`variance(double[] a)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

numRows

public static int numRows(double[] v)

range
```
public static int[] range(int end)
```
Generate a range of integers from start (inclusive) to end (exclusive). Similar to the Python range() builtin function.

Parameters:

end - Ending number (exclusive)

Returns:

integers from [0...end)

range
```
public static int[] range(int start,
                          int end)
```
Generate a range of integers from start (inclusive) to end (exclusive). Similar to the Python range() builtin function.

Parameters:

start - Beginning number (inclusive)

end - Ending number (exclusive)

Returns:

integers from [start...end)

doubleArrayToFloatArray

public static float[] doubleArrayToFloatArray(double[] a)

floatArrayToDoubleArray

public static double[] floatArrayToDoubleArray(float[] a)

floatArrayToDoubleArray

public static double[][] floatArrayToDoubleArray(float[][] a)

doubleArrayToFloatArray

public static float[][] doubleArrayToFloatArray(double[][] a)

exp

public static double[] exp(double[] a)

log

public static double[] log(double[] a)

expInPlace

public static void expInPlace(double[] a)

logInPlace

public static void logInPlace(double[] a)

softmax

public static double[] softmax(double[] scales)

addInPlace
```
public static void addInPlace(double[] a,
                              double b)
```
Increases the values in the first array a by b. Does it in place.

Parameters:

a - The array

b - The amount by which to increase each item

addInPlace
```
public static void addInPlace(float[] a,
                              double b)
```
Increases the values in this array by b. Does it in place.

Parameters:

a - The array

b - The amount by which to increase each item

addMultInPlace

public static void addMultInPlace(double[] a,
                                  double[] b,
                                  double c)

Add c times the array b to array a. Does it in place.

multiplyInPlace

public static void multiplyInPlace(double[] a,
                                   double b)

Scales the values in this array by b. Does it in place.

multiplyInPlace

public static void multiplyInPlace(float[] a,
                                   double b)

Scales the values in this array by b. Does it in place.

divideInPlace

public static void divideInPlace(double[] a,
                                 double b)

Divides the values in this array by b. Does it in place.

powInPlace

public static void powInPlace(double[] a,
                              double c)

Scales the values in this array by c.

powInPlace

public static void powInPlace(float[] a,
                              float c)

Sets the values in this array by to their value taken to cth power.

add

public static double[] add(double[] a,
                           double c)

add

public static float[] add(float[] a,
                          double c)

multiply

public static double[] multiply(double[] a,
                                double c)

Scales the values in this array by c.

multiply

public static float[] multiply(float[] a,
                               float c)

Scales the values in this array by c.

pow

public static double[] pow(double[] a,
                           double c)

raises each entry in array a by power c

pow

public static float[] pow(float[] a,
                          float c)

raises each entry in array a by power c

pairwiseAddInPlace

public static void pairwiseAddInPlace(float[] to,
                                      float[] from)

pairwiseAddInPlace
```
public static void pairwiseAddInPlace(double[] to,
                                      double[] from)
```
Add the two 1d arrays in place of to.

Throws:

java.lang.IllegalArgumentException - If to and from are not of the same dimensions

pairwiseAddInPlace
```
public static void pairwiseAddInPlace(double[] to,
                                      float[] from)
```
Add the two 1d arrays in place of to.

Throws:

java.lang.IllegalArgumentException - If to and from are not of the same dimensions

pairwiseAddInPlace

public static void pairwiseAddInPlace(double[] to,
                                      int[] from)

pairwiseAddInPlace

public static void pairwiseAddInPlace(double[] to,
                                      short[] from)

addInPlace
```
public static void addInPlace(double[][] m1,
                              double[][] m2)
```
Add the two 2d arrays and write the answer in place of m1.

Throws:

java.lang.IllegalArgumentException - If m1 and m2 are not of the same dimensions

pairwiseSubtractInPlace

public static void pairwiseSubtractInPlace(double[] to,
                                           double[] from)

pairwiseScaleAddInPlace

public static void pairwiseScaleAddInPlace(double[] to,
                                           double[] from,
                                           double fromScale)

pairwiseAdd

public static int[] pairwiseAdd(int[] a,
                                int[] b)

pairwiseAdd

public static double[] pairwiseAdd(double[] a,
                                   double[] b)

pairwiseAdd

public static float[] pairwiseAdd(float[] a,
                                  float[] b)

pairwiseScaleAdd

public static double[] pairwiseScaleAdd(double[] a,
                                        double[] b,
                                        double bScale)

pairwiseSubtract

public static double[] pairwiseSubtract(double[] a,
                                        double[] b)

pairwiseSubtract

public static float[] pairwiseSubtract(float[] a,
                                       float[] b)

dotProduct

public static double dotProduct(double[] a,
                                double[] b)

Assumes that both arrays have same length.

dotProduct
```
public static float dotProduct(float[] a,
                               float[] b)
```
Dot product of a and b.
Assumes that both arrays have same length. Sum is done using a double.

Parameters:

a - float vector

b - float vector

Returns:

a dot b

dotProduct
```
public static double dotProduct(double[] a,
                                float[] b)
```
Dot product of a and b.
Assumes that both arrays have same length. Sum is done using a double.

Parameters:

a - double vector

b - float vector

Returns:

a dot b

pairwiseMultiply

public static double[] pairwiseMultiply(double[] a,
                                        double[] b)

Assumes that both arrays have same length.

pairwiseMultiply

public static float[] pairwiseMultiply(float[] a,
                                       float[] b)

Assumes that both arrays have same length.

pairwiseMultiply

public static void pairwiseMultiply(double[] a,
                                    double[] b,
                                    double[] result)

Puts the result in the result array. Assumes that all arrays have same length.

pairwiseMultiply

public static void pairwiseMultiply(float[] a,
                                    float[] b,
                                    float[] result)

Puts the result in the result array. Assumes that all arrays have same length.

pairwiseDivideInPlace
```
public static void pairwiseDivideInPlace(double[] a,
                                         double[] b)
```
Divide the first array by the second elementwise, and store results in place. Assume arrays have the same length

hasNaN

public static boolean hasNaN(double[] a)

hasInfinite

public static boolean hasInfinite(double[] a)

hasNaN

public static boolean hasNaN(float[] a)

countNaN

public static int countNaN(double[] v)

filterNaN

public static double[] filterNaN(double[] v)

countInfinite

public static int countInfinite(double[] v)

countNonZero

public static int countNonZero(double[] v)

countCloseToZero

public static int countCloseToZero(double[] v,
                                   double epsilon)

countPositive

public static int countPositive(double[] v)

countNegative

public static int countNegative(double[] v)

filterInfinite

public static double[] filterInfinite(double[] v)

filterNaNAndInfinite

public static double[] filterNaNAndInfinite(double[] v)

sum
```
public static double sum(double[] a)
```
Returns the sum of an array of doubles.

sum
```
public static double sum(double[] a,
                         int fromIndex,
                         int toIndex)
```
Returns the sum of the portion of an array of numbers between fromIndex, inclusive, and toIndex, exclusive. Returns 0 if fromIndex >= toIndex.

sum
```
public static int sum(int[] a)
```

sum
```
public static float sum(float[] a)
```

sum
```
public static int sum(int[][] a)
```

diag
```
public static int[] diag(int[][] a)
```
Returns diagonal elements of the given (square) matrix.

average

public static double average(double[] a)

iterativeAverage
```
public static double iterativeAverage(double[] a)
```
This version avoids certain types of overflow.

norm_inf
```
public static double norm_inf(double[] a)
```
Computes inf-norm of vector. This is just the largest absolute value of an element.

Parameters:

a - Array of double

Returns:

inf-norm of a

norm_inf
```
public static double norm_inf(float[] a)
```
Computes inf-norm of vector.

Returns:

inf-norm of a

norm_1
```
public static double norm_1(double[] a)
```
Computes 1-norm of vector.

Parameters:

a - A vector of double

Returns:

1-norm of a

norm_1
```
public static double norm_1(float[] a)
```
Computes 1-norm of vector.

Parameters:

a - A vector of floats

Returns:

1-norm of a

norm
```
public static double norm(double[] a)
```
Computes 2-norm of vector.

Parameters:

a - A vector of double

Returns:

Euclidean norm of a

norm
```
public static double norm(float[] a)
```
Computes 2-norm of vector.

Parameters:

a - A vector of floats

Returns:

Euclidean norm of a

argmax
```
public static int argmax(double[] a)
```
Returns:

the index of the max value; if max is a tie, returns the first one.

argmax_tieLast
```
public static int argmax_tieLast(double[] a)
```
Returns:

the index of the max value; if max is a tie, returns the last one.

max
```
public static double max(double[] a)
```

max

public static double max(java.util.Collection<java.lang.Double> a)

argmax
```
public static int argmax(float[] a)
```
Returns:

the index of the max value; if max is a tie, returns the first one.

max
```
public static float max(float[] a)
```

argmin
```
public static int argmin(double[] a)
```
Returns:

the index of the min value; if min is a tie, returns the lowest index one.

min

public static double min(double... vector)

Returns:: The minimum value in an array.

safeMin
```
public static double safeMin(double[] v)
```
Returns the smallest value in a vector of doubles. Any values which are NaN or infinite are ignored. If the vector is empty, 0.0 is returned.

argmin
```
public static int argmin(float[] a)
```
Returns:

the index of the min value; if min is a tie, returns the first one.

min
```
public static float min(float[] a)
```

argmin
```
public static int argmin(int[] a)
```
Returns:

the index of the min value; if min is a tie, returns the first one.

min
```
public static int min(int... vector)
```
Returns:

the min value.

argmax
```
public static int argmax(int[] a)
```
Returns:

the index of the max value; if max is a tie, returns the first one.

max
```
public static int max(int... vector)
```
Returns:

the index of the max value; if max is a tie, returns the first one.

min
```
public static int min(int[][] matrix)
```
Returns the smallest element of the matrix

max
```
public static int max(int[][] matrix)
```
Returns the smallest element of the matrix

safeMax
```
public static double safeMax(double[] v)
```
Returns the largest value in a vector of doubles. Any values which are NaN or infinite are ignored. If the vector is empty, 0.0 is returned.

logSum
```
public static double logSum(double... logInputs)
```
Returns the log of the sum of an array of numbers, which are themselves input in log form. This is all natural logarithms. Reasonable care is taken to do this as efficiently as possible (under the assumption that the numbers might differ greatly in magnitude), with high accuracy, and without numerical overflow.

Parameters:

logInputs - An array of numbers [log(x1), ..., log(xn)]

Returns:

log(x1 + ... + xn)

logSum
```
public static double logSum(double[] logInputs,
                            int fromIndex,
                            int toIndex)
```
Returns the log of the portion between fromIndex, inclusive, and toIndex, exclusive, of an array of numbers, which are themselves input in log form. This is all natural logarithms. Reasonable care is taken to do this as efficiently as possible (under the assumption that the numbers might differ greatly in magnitude), with high accuracy, and without numerical overflow. Throws an IllegalArgumentException if logInputs is of length zero. Otherwise, returns Double.NEGATIVE_INFINITY if fromIndex >= toIndex.

Parameters:

logInputs - An array of numbers [log(x1), ..., log(xn)]

fromIndex - The array index to start the sum from

toIndex - The array index after the last element to be summed

Returns:

log(x1 + ... + xn)

logSum
```
public static double logSum(double[] logInputs,
                            int fromIndex,
                            int afterIndex,
                            int stride)
```
Returns the log of the portion between fromIndex, inclusive, and toIndex, exclusive, of an array of numbers, which are themselves input in log form. This is all natural logarithms. This version incorporates a stride, so you can sum only select numbers. Reasonable care is taken to do this as efficiently as possible (under the assumption that the numbers might differ greatly in magnitude), with high accuracy, and without numerical overflow. Throws an IllegalArgumentException if logInputs is of length zero. Otherwise, returns Double.NEGATIVE_INFINITY if fromIndex >= toIndex.

Parameters:

logInputs - An array of numbers [log(x1), ..., log(xn)]

fromIndex - The array index to start the sum from

afterIndex - The array index after the last element to be summed

Returns:

log(x1 + ... + xn)

logSum

public static double logSum(java.util.List<java.lang.Double> logInputs)

logSum

public static double logSum(java.util.List<java.lang.Double> logInputs,
                            int fromIndex,
                            int toIndex)

logSum
```
public static float logSum(float[] logInputs)
```
Returns the log of the sum of an array of numbers, which are themselves input in log form. This is all natural logarithms. Reasonable care is taken to do this as efficiently as possible (under the assumption that the numbers might differ greatly in magnitude), with high accuracy, and without numerical overflow.

Parameters:

logInputs - An array of numbers [log(x1), ..., log(xn)]

Returns:

log(x1 + ... + xn)

innerProduct

public static double innerProduct(double[] a,
                                  double[] b)

innerProduct

public static double innerProduct(float[] a,
                                  float[] b)

load2DMatrixFromFile

public static double[][] load2DMatrixFromFile(java.lang.String filename)
                                       throws java.io.IOException

Throws:: java.io.IOException

box

public static java.lang.Integer[] box(int[] assignment)

unboxToInt

public static int[] unboxToInt(java.util.Collection<java.lang.Integer> list)

box

public static java.lang.Double[] box(double[] assignment)

unbox

public static double[] unbox(java.util.Collection<java.lang.Double> list)

indexOf

public static int indexOf(int n,
                          int[] a)

castToInt

public static int[][] castToInt(double[][] doubleCounts)

normalize
```
public static void normalize(double[] a)
```
Makes the values in this array sum to 1.0. Does it in place. If the total is 0.0 or NaN, throws an RuntimeException.

L1normalize

public static void L1normalize(double[] a)

L2normalize

public static void L2normalize(double[] a)

normalize
```
public static void normalize(float[] a)
```
Makes the values in this array sum to 1.0. Does it in place. If the total is 0.0 or NaN, throws an RuntimeException.

L2normalize

public static void L2normalize(float[] a)

standardize
```
public static void standardize(double[] a)
```
Standardize values in this array, i.e., subtract the mean and divide by the standard deviation. If standard deviation is 0.0, throws a RuntimeException.

L2Norm

public static double L2Norm(double[] a)

L2Norm

public static float L2Norm(float[] a)

L1Norm

public static double L1Norm(double[] a)

logNormalize
```
public static void logNormalize(double[] a)
```
Makes the values in this array sum to 1.0. Does it in place. If the total is 0.0, throws a RuntimeException. If the total is Double.NEGATIVE_INFINITY, then it replaces the array with a normalized uniform distribution. CDM: This last bit is weird! Do we really want that?

sampleFromDistribution
```
public static int sampleFromDistribution(double[] d)
```
Samples from the distribution over values 0 through d.length given by d. Assumes that the distribution sums to 1.0.

Parameters:

d - the distribution to sample from

Returns:

a value from 0 to d.length

sampleFromDistribution
```
public static int sampleFromDistribution(double[] d,
                                         java.util.Random random)
```
Samples from the distribution over values 0 through d.length given by d. Assumes that the distribution sums to 1.0.

Parameters:

d - the distribution to sample from

Returns:

a value from 0 to d.length

sampleFromDistribution
```
public static int sampleFromDistribution(float[] d,
                                         java.util.Random random)
```
Samples from the distribution over values 0 through d.length given by d. Assumes that the distribution sums to 1.0.

Parameters:

d - the distribution to sample from

Returns:

a value from 0 to d.length

klDivergence

public static double klDivergence(double[] from,
                                  double[] to)

jensenShannonDivergence
```
public static double jensenShannonDivergence(double[] a,
                                             double[] b)
```
Returns the Jensen Shannon divergence (information radius) between a and b, defined as the average of the kl divergences from a to b and from b to a.

setToLogDeterministic

public static void setToLogDeterministic(float[] a,
                                         int i)

setToLogDeterministic

public static void setToLogDeterministic(double[] a,
                                         int i)

mean

public static double mean(double[] a)

mean
```
public static double mean(int[] a)
```
Return the mean of an array of int.

median

public static double median(double[] a)

safeMean
```
public static double safeMean(double[] v)
```
Returns the mean of a vector of doubles. Any values which are NaN or infinite are ignored. If the vector is empty, 0.0 is returned.

sumSquaredError

public static double sumSquaredError(double[] a)

sumSquared

public static double sumSquared(double[] a)

variance

public static double variance(double[] a)

stdev

public static double stdev(double[] a)

safeStdev
```
public static double safeStdev(double[] v)
```
Returns the standard deviation of a vector of doubles. Any values which are NaN or infinite are ignored. If the vector contains fewer than two values, 1.0 is returned.

standardErrorOfMean

public static double standardErrorOfMean(double[] a)

sampleWithoutReplacement

public static void sampleWithoutReplacement(int[] array,
                                            int numArgClasses)

Fills the array with sample from 0 to numArgClasses-1 without replacement.

sampleWithoutReplacement

public static void sampleWithoutReplacement(int[] array,
                                            int numArgClasses,
                                            java.util.Random rand)

Fills the array with sample from 0 to numArgClasses-1 without replacement.

shuffle
```
public static void shuffle(int[] a)
```

shuffle

public static void shuffle(int[] a,
                           java.util.Random rand)

reverse
```
public static void reverse(int[] a)
```

contains

public static boolean contains(int[] a,
                               int i)

containsInSubarray

public static boolean containsInSubarray(int[] a,
                                         int begin,
                                         int end,
                                         int i)

pearsonCorrelation
```
public static double pearsonCorrelation(double[] x,
                                        double[] y)
```
Direct computation of Pearson product-moment correlation coefficient. Note that if x and y are involved in several computations of pearsonCorrelation, it is perhaps more advisable to first standardize x and y, then compute innerProduct(x,y)/(x.length-1).

sigLevelByApproxRand
```
public static double sigLevelByApproxRand(double[] A,
                                          double[] B)
```
Computes the significance level by approximate randomization, using a default value of 1000 iterations. See documentation for other version of method.

sigLevelByApproxRand
```
public static double sigLevelByApproxRand(double[] A,
                                          double[] B,
                                          int iterations)
```
Takes a pair of arrays, A and B, which represent corresponding outcomes of a pair of random variables: say, results for two different classifiers on a sequence of inputs. Returns the estimated probability that the difference between the means of A and B is not significant, that is, the significance level. This is computed by "approximate randomization". The test statistic is the absolute difference between the means of the two arrays. A randomized test statistic is computed the same way after initially randomizing the arrays by swapping each pair of elements with 50% probability. For the given number of iterations, we generate a randomized test statistic and compare it to the actual test statistic. The return value is the proportion of iterations in which a randomized test statistic was found to exceed the actual test statistic.

Parameters:

A - Outcome of one r.v.

B - Outcome of another r.v.

Returns:

Significance level by randomization

sigLevelByApproxRand

public static double sigLevelByApproxRand(int[] A,
                                          int[] B)

sigLevelByApproxRand

public static double sigLevelByApproxRand(int[] A,
                                          int[] B,
                                          int iterations)

sigLevelByApproxRand

public static double sigLevelByApproxRand(boolean[] A,
                                          boolean[] B)

sigLevelByApproxRand

public static double sigLevelByApproxRand(boolean[] A,
                                          boolean[] B,
                                          int iterations)

toBinaryString

public static java.lang.String toBinaryString(byte[] b)

toString

public static java.lang.String toString(double[] a)

toString

public static java.lang.String toString(double[] a,
                                        java.text.NumberFormat nf)

toString

public static java.lang.String toString(float[] a)

toString

public static java.lang.String toString(float[] a,
                                        java.text.NumberFormat nf)

toString

public static java.lang.String toString(int[] a)

toString

public static java.lang.String toString(int[] a,
                                        java.text.NumberFormat nf)

toString

public static java.lang.String toString(byte[] a)

toString

public static java.lang.String toString(byte[] a,
                                        java.text.NumberFormat nf)

toString

public static java.lang.String toString(int[][] counts)

toString

public static java.lang.String toString(int[][] counts,
                                        java.lang.Object[] rowLabels,
                                        java.lang.Object[] colLabels,
                                        int labelSize,
                                        int cellSize,
                                        java.text.NumberFormat nf,
                                        boolean printTotals)

toString

public static java.lang.String toString(double[][] counts)

toString

public static java.lang.String toString(double[][] counts,
                                        int cellSize,
                                        java.lang.Object[] rowLabels,
                                        java.lang.Object[] colLabels,
                                        java.text.NumberFormat nf,
                                        boolean printTotals)

toString

public static java.lang.String toString(double[][] counts,
                                        int cellSize,
                                        java.lang.Object[] rowLabels,
                                        java.lang.Object[] colLabels,
                                        int rowLabelSize,
                                        java.text.NumberFormat nf,
                                        boolean printRowTotals,
                                        boolean printColumnTotals,
                                        java.lang.Object topLeft)

toString

public static java.lang.String toString(float[][] counts)

toString

public static java.lang.String toString(float[][] counts,
                                        int cellSize,
                                        java.lang.Object[] rowLabels,
                                        java.lang.Object[] colLabels,
                                        java.text.NumberFormat nf,
                                        boolean printTotals)

main

public static void main(java.lang.String[] args)

For testing only.

Parameters:: args - Ignored

deepCopy

public static int[][] deepCopy(int[][] counts)

addMultInto

public static void addMultInto(double[] a,
                               double[] b,
                               double[] c,
                               double d)

multiplyInto

public static void multiplyInto(double[] a,
                                double[] b,
                                double c)

entropy

public static double entropy(double[] probs)

assertFinite

public static void assertFinite(double[] vector,
                                java.lang.String vectorName)
                         throws ArrayMath.InvalidElementException

Throws:: ArrayMath.InvalidElementException

Class ArrayMath

Nested Class Summary

Method Summary

Methods inherited from class java.lang.Object

Method Detail

numRows

range

range

doubleArrayToFloatArray

floatArrayToDoubleArray

floatArrayToDoubleArray

doubleArrayToFloatArray

exp

log

expInPlace

logInPlace

softmax

addInPlace

addInPlace

addMultInPlace

multiplyInPlace

multiplyInPlace

divideInPlace

powInPlace

powInPlace

add

add

multiply

multiply

pow

pow

pairwiseAddInPlace

pairwiseAddInPlace

pairwiseAddInPlace

pairwiseAddInPlace

pairwiseAddInPlace

addInPlace

pairwiseSubtractInPlace

pairwiseScaleAddInPlace

pairwiseAdd

pairwiseAdd

pairwiseAdd

pairwiseScaleAdd

pairwiseSubtract

pairwiseSubtract

dotProduct

dotProduct

dotProduct

pairwiseMultiply

pairwiseMultiply

pairwiseMultiply

pairwiseMultiply

pairwiseDivideInPlace

hasNaN

hasInfinite

hasNaN

countNaN

filterNaN

countInfinite

countNonZero

countCloseToZero

countPositive

countNegative

filterInfinite

filterNaNAndInfinite

sum

sum

sum

sum

sum

diag

average

iterativeAverage

norm_inf

norm_inf

norm_1

norm_1

norm

norm

argmax