keel.Algorithms.Statistical_Classifiers.Logistic.core

Class Utils

java.lang.Object

keel.Algorithms.Statistical_Classifiers.Logistic.core.Utils

public final class Utils
extends java.lang.Object

Class implementing some simple utility methods.

Version:

$Revision: 1.1 $

Author:

Eibe Frank, Yong Wang, Len Trigg, Julien Prados

Field Summary

Fields

Modifier and Type	Field and Description
static double	log2 The natural logarithm of 2.
static double	SMALL The small deviation allowed in double comparisons

Constructor Summary

Constructors

Constructor and Description
Utils()

Method Summary

Modifier and Type	Method and Description
static java.lang.String	arrayToString(java.lang.Object array) Returns the given Array in a string representation.
static java.lang.String	backQuoteChars(java.lang.String string) Converts carriage returns and new lines in a string into \r and \n.
static void	checkForRemainingOptions(java.lang.String[] options) Checks if the given array contains any non-empty options.
static java.lang.String	convertNewLines(java.lang.String string) Converts carriage returns and new lines in a string into \r and \n.
static double	correlation(double[] y1, double[] y2, int n) Returns the correlation coefficient of two double vectors.
static java.lang.String	doubleToString(double value, int afterDecimalPoint) Rounds a double and converts it into String.
static java.lang.String	doubleToString(double value, int width, int afterDecimalPoint) Rounds a double and converts it into a formatted decimal-justified String.
static boolean	eq(double a, double b) Tests if a is equal to b.
static java.lang.Object	forName(java.lang.Class classType, java.lang.String className, java.lang.String[] options) Creates a new instance of an object given it's class name and (optional) arguments to pass to it's setOptions method.
static java.lang.Class	getArrayClass(java.lang.Class c) Returns the basic class of an array class (handles multi-dimensional arrays).
static int	getArrayDimensions(java.lang.Class array) Returns the dimensions of the given array.
static int	getArrayDimensions(java.lang.Object array) Returns the dimensions of the given array.
static boolean	getFlag(char flag, java.lang.String[] options) Checks if the given array contains the flag "-Char".
static boolean	getFlag(java.lang.String flag, java.lang.String[] options) Checks if the given array contains the flag "-String".
static java.lang.String	getOption(char flag, java.lang.String[] options) Gets an option indicated by a flag "-Char" from the given array of strings.
static java.lang.String	getOption(java.lang.String flag, java.lang.String[] options) Gets an option indicated by a flag "-String" from the given array of strings.
static int	getOptionPos(char flag, java.lang.String[] options) Gets the index of an option or flag indicated by a flag "-Char" from the given array of strings.
static int	getOptionPos(java.lang.String flag, java.lang.String[] options) Gets the index of an option or flag indicated by a flag "-String" from the given array of strings.
static boolean	gr(double a, double b) Tests if a is greater than b.
static boolean	grOrEq(double a, double b) Tests if a is greater or equal to b.
static double	info(int[] counts) Computes entropy for an array of integers.
static java.lang.String	joinOptions(java.lang.String[] optionArray) Joins all the options in an option array into a single string, as might be used on the command line.
static double	kthSmallestValue(double[] array, int k) Returns the kth-smallest value in the array
static double	kthSmallestValue(int[] array, int k) Returns the kth-smallest value in the array.
static double	log2(double a) Returns the logarithm of a for base 2.
static double[]	logs2probs(double[] a) Converts an array containing the natural logarithms of probabilities stored in a vector back into probabilities.
static void	main(java.lang.String[] ops) Main method for testing this class.
static int	maxIndex(double[] doubles) Returns index of maximum element in a given array of doubles.
static int	maxIndex(int[] ints) Returns index of maximum element in a given array of integers.
static double	mean(double[] vector) Computes the mean for an array of doubles.
static int	minIndex(double[] doubles) Returns index of minimum element in a given array of doubles.
static int	minIndex(int[] ints) Returns index of minimum element in a given array of integers.
static void	normalize(double[] doubles) Normalizes the doubles in the array by their sum.
static void	normalize(double[] doubles, double sum) Normalizes the doubles in the array using the given value.
static java.lang.String	padLeft(java.lang.String inString, int length) Pads a string to a specified length, inserting spaces on the left as required.
static java.lang.String	padRight(java.lang.String inString, int length) Pads a string to a specified length, inserting spaces on the right as required.
static java.lang.String[]	partitionOptions(java.lang.String[] options) Returns the secondary set of options (if any) contained in the supplied options array.
static int	probRound(double value, java.util.Random rand) Rounds a double to the next nearest integer value in a probabilistic fashion (e.g. 0.8 has a 20% chance of being rounded down to 0 and a 80% chance of being rounded up to 1).
static double	probToLogOdds(double prob) Returns the log-odds for a given probabilitiy.
static java.lang.String	quote(java.lang.String string) Quotes a string if it contains special characters.
static java.util.Properties	readProperties(java.lang.String resourceName) Reads properties that inherit from three locations.
static java.lang.String	removeSubstring(java.lang.String inString, java.lang.String substring) Removes all occurrences of a string from another string.
static java.lang.String	replaceSubstring(java.lang.String inString, java.lang.String subString, java.lang.String replaceString) Replaces with a new string, all occurrences of a string from another string.
static java.lang.String	revertNewLines(java.lang.String string) Reverts \r and \n in a string into carriage returns and new lines.
static int	round(double value) Rounds a double to the next nearest integer value.
static double	roundDouble(double value, int afterDecimalPoint) Rounds a double to the given number of decimal places.
static boolean	sm(double a, double b) Tests if a is smaller than b.
static boolean	smOrEq(double a, double b) Tests if a is smaller or equal to b.
static int[]	sort(double[] array) Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
static int[]	sort(int[] array) Sorts a given array of integers in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
static java.lang.String[]	splitOptions(java.lang.String quotedOptionString) Split up a string containing options into an array of strings, one for each option.
static int[]	stableSort(double[] array) Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array.
static double	sum(double[] doubles) Computes the sum of the elements of an array of doubles.
static int	sum(int[] ints) Computes the sum of the elements of an array of integers.
static java.lang.String	unbackQuoteChars(java.lang.String string) The inverse operation of backQuoteChars().
static java.lang.String	unquote(java.lang.String string) unquotes are previously quoted string (but only if necessary), i.e., it removes the single quotes around it.
static double	variance(double[] vector) Computes the variance for an array of doubles.
static double	xlogx(int c) Returns c*log2(c) for a given integer value c.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log2

public static double log2

The natural logarithm of 2.

SMALL

public static double SMALL

The small deviation allowed in double comparisons

Constructor Detail

Utils

public Utils()

Method Detail

readProperties

public static java.util.Properties readProperties(java.lang.String resourceName)
                                           throws java.lang.Exception

Reads properties that inherit from three locations. Properties are first defined in the system resource location (i.e. in the CLASSPATH). These default properties must exist. Properties defined in the users home directory (optional) override default settings. Properties defined in the current directory (optional) override all these settings.

Parameters:

resourceName - the location of the resource that should be loaded. e.g.: "keel.Algorithms.Statistical_Classifiers.Logistic.core/Utils.props". (The use of hardcoded forward slashes here is OK - see jdk1.1/docs/guide/misc/resources.html) This routine will also look for the file (in this case) "Utils.props" in the users home directory and the current directory.

Returns:

the Properties

Throws:

java.lang.Exception - if no default properties are defined, or if an error occurs reading the properties files.

correlation

public static final double correlation(double[] y1,
                                       double[] y2,
                                       int n)

Returns the correlation coefficient of two double vectors.

Parameters:

y1 - double vector 1

y2 - double vector 2

n - the length of two double vectors

Returns:

the correlation coefficient

removeSubstring

public static java.lang.String removeSubstring(java.lang.String inString,
                                               java.lang.String substring)

Removes all occurrences of a string from another string.

Parameters:

inString - the string to remove substrings from.

substring - the substring to remove.

Returns:

the input string with occurrences of substring removed.

replaceSubstring

public static java.lang.String replaceSubstring(java.lang.String inString,
                                                java.lang.String subString,
                                                java.lang.String replaceString)

Replaces with a new string, all occurrences of a string from another string.

Parameters:

inString - the string to replace substrings in.

subString - the substring to replace.

replaceString - the replacement substring

Returns:

the input string with occurrences of substring replaced.

padLeft

public static java.lang.String padLeft(java.lang.String inString,
                                       int length)

Pads a string to a specified length, inserting spaces on the left as required. If the string is too long, characters are removed (from the right).

Parameters:

inString - the input string

length - the desired length of the output string

Returns:

the output string

padRight

public static java.lang.String padRight(java.lang.String inString,
                                        int length)

Pads a string to a specified length, inserting spaces on the right as required. If the string is too long, characters are removed (from the right).

Parameters:

inString - the input string

length - the desired length of the output string

Returns:

the output string

doubleToString

public static java.lang.String doubleToString(double value,
                                              int afterDecimalPoint)

Rounds a double and converts it into String.

Parameters:

value - the double value

afterDecimalPoint - the (maximum) number of digits permitted after the decimal point

Returns:

the double as a formatted string

doubleToString

public static java.lang.String doubleToString(double value,
                                              int width,
                                              int afterDecimalPoint)

Rounds a double and converts it into a formatted decimal-justified String. Trailing 0's are replaced with spaces.

Parameters:

value - the double value

width - the width of the string

afterDecimalPoint - the number of digits after the decimal point

Returns:

the double as a formatted string

getArrayClass

public static java.lang.Class getArrayClass(java.lang.Class c)

Returns the basic class of an array class (handles multi-dimensional arrays).

Parameters:

c - the array to inspect

Returns:

the class of the innermost elements

getArrayDimensions

public static int getArrayDimensions(java.lang.Class array)

Returns the dimensions of the given array. Even though the parameter is of type "Object" one can hand over primitve arrays, e.g. int[3] or double[2][4].

Parameters:

array - the array to determine the dimensions for

Returns:

the dimensions of the array

getArrayDimensions

public static int getArrayDimensions(java.lang.Object array)

Returns the dimensions of the given array. Even though the parameter is of type "Object" one can hand over primitve arrays, e.g. int[3] or double[2][4].

Parameters:

array - the array to determine the dimensions for

Returns:

the dimensions of the array

arrayToString

public static java.lang.String arrayToString(java.lang.Object array)

Returns the given Array in a string representation. Even though the parameter is of type "Object" one can hand over primitve arrays, e.g. int[3] or double[2][4].

Parameters:

array - the array to return in a string representation

Returns:

the array as string

eq

public static boolean eq(double a,
                         double b)

Tests if a is equal to b.

Parameters:

a - a double

b - a double

Returns:

True if a is equal to b.

checkForRemainingOptions

public static void checkForRemainingOptions(java.lang.String[] options)
                                     throws java.lang.Exception

Checks if the given array contains any non-empty options.

Parameters:

options - an array of strings

Throws:

java.lang.Exception - if there are any non-empty options

getFlag

public static boolean getFlag(char flag,
                              java.lang.String[] options)
                       throws java.lang.Exception

Checks if the given array contains the flag "-Char". Stops searching at the first marker "--". If the flag is found, it is replaced with the empty string.

Parameters:

flag - the character indicating the flag.

options - the array of strings containing all the options.

Returns:

true if the flag was found

Throws:

java.lang.Exception - if an illegal option was found

getFlag

public static boolean getFlag(java.lang.String flag,
                              java.lang.String[] options)
                       throws java.lang.Exception

Checks if the given array contains the flag "-String". Stops searching at the first marker "--". If the flag is found, it is replaced with the empty string.

Parameters:

flag - the String indicating the flag.

options - the array of strings containing all the options.

Returns:

true if the flag was found

Throws:

java.lang.Exception - if an illegal option was found

getOption

public static java.lang.String getOption(char flag,
                                         java.lang.String[] options)
                                  throws java.lang.Exception

Gets an option indicated by a flag "-Char" from the given array of strings. Stops searching at the first marker "--". Replaces flag and option with empty strings.

Parameters:

flag - the character indicating the option.

options - the array of strings containing all the options.

Returns:

the indicated option or an empty string

Throws:

java.lang.Exception - if the option indicated by the flag can't be found

getOption

public static java.lang.String getOption(java.lang.String flag,
                                         java.lang.String[] options)
                                  throws java.lang.Exception

Gets an option indicated by a flag "-String" from the given array of strings. Stops searching at the first marker "--". Replaces flag and option with empty strings.

Parameters:

flag - the String indicating the option.

options - the array of strings containing all the options.

Returns:

the indicated option or an empty string

Throws:

java.lang.Exception - if the option indicated by the flag can't be found

getOptionPos

public static int getOptionPos(char flag,
                               java.lang.String[] options)

Gets the index of an option or flag indicated by a flag "-Char" from the given array of strings. Stops searching at the first marker "--".

Parameters:

flag - the character indicating the option.

options - the array of strings containing all the options.

Returns:

the position if found, or -1 otherwise

getOptionPos

public static int getOptionPos(java.lang.String flag,
                               java.lang.String[] options)

Gets the index of an option or flag indicated by a flag "-String" from the given array of strings. Stops searching at the first marker "--".

Parameters:

flag - the String indicating the option.

options - the array of strings containing all the options.

Returns:

the position if found, or -1 otherwise

quote

public static java.lang.String quote(java.lang.String string)

Quotes a string if it contains special characters. The following rules are applied: A character is backquoted version of it is one of " ' % \ \n \r \t. A string is enclosed within single quotes if a character has been backquoted using the previous rule above or contains { } or is exactly equal to the strings , ? space or "" (empty string). A quoted question mark distinguishes it from the missing value which is represented as an unquoted question mark in arff files.

Parameters:

string - the string to be quoted

Returns:

the string (possibly quoted)

See Also:

unquote(String)

unquote

public static java.lang.String unquote(java.lang.String string)

unquotes are previously quoted string (but only if necessary), i.e., it removes the single quotes around it. Inverse to quote(String).

Parameters:

string - the string to process

Returns:

the unquoted string

See Also:

quote(String)

backQuoteChars

public static java.lang.String backQuoteChars(java.lang.String string)

Converts carriage returns and new lines in a string into \r and \n. Backquotes the following characters: ` " \ \t and %

Parameters:

string - the string

Returns:

the converted string

See Also:

unbackQuoteChars(String)

convertNewLines

public static java.lang.String convertNewLines(java.lang.String string)

Converts carriage returns and new lines in a string into \r and \n.

Parameters:

string - the string

Returns:

the converted string

revertNewLines

public static java.lang.String revertNewLines(java.lang.String string)

Reverts \r and \n in a string into carriage returns and new lines.

Parameters:

string - the string

Returns:

the converted string

partitionOptions

public static java.lang.String[] partitionOptions(java.lang.String[] options)

Returns the secondary set of options (if any) contained in the supplied options array. The secondary set is defined to be any options after the first "--". These options are removed from the original options array.

Parameters:

options - the input array of options

Returns:

the array of secondary options

unbackQuoteChars

public static java.lang.String unbackQuoteChars(java.lang.String string)

The inverse operation of backQuoteChars(). Converts back-quoted carriage returns and new lines in a string to the corresponding character ('\r' and '\n'). Also "un"-back-quotes the following characters: ` " \ \t and %

Parameters:

string - the string

Returns:

the converted string

See Also:

backQuoteChars(String)

splitOptions

public static java.lang.String[] splitOptions(java.lang.String quotedOptionString)
                                       throws java.lang.Exception

Split up a string containing options into an array of strings, one for each option.

Parameters:

quotedOptionString - the string containing the options

Returns:

the array of options

Throws:

java.lang.Exception - in case of an unterminated string, unknown character or a parse error

joinOptions

public static java.lang.String joinOptions(java.lang.String[] optionArray)

Joins all the options in an option array into a single string, as might be used on the command line.

Parameters:

optionArray - the array of options

Returns:

the string containing all options.

forName

public static java.lang.Object forName(java.lang.Class classType,
                                       java.lang.String className,
                                       java.lang.String[] options)
                                throws java.lang.Exception

Creates a new instance of an object given it's class name and (optional) arguments to pass to it's setOptions method. If the object implements OptionHandler and the options parameter is non-null, the object will have it's options set. Example use:

 String classifierName = Utils.getOption('W', options);
 Classifier c = (Classifier)Utils.forName(Classifier.class,
                                          classifierName,
                                          options);
 setClassifier(c);
 

Parameters:

classType - the class that the instantiated object should be assignable to -- an exception is thrown if this is not the case

className - the fully qualified class name of the object

options - an array of options suitable for passing to setOptions. May be null. Any options accepted by the object will be removed from the array.

Returns:

the newly created object, ready for use.

Throws:

java.lang.Exception - if the class name is invalid, or if the class is not assignable to the desired class type, or the options supplied are not acceptable to the object

info

public static double info(int[] counts)

Computes entropy for an array of integers.

Parameters:

counts - array of counts

Returns:

- a log2 a - b log2 b - c log2 c + (a+b+c) log2 (a+b+c) when given array [a b c]

smOrEq

public static boolean smOrEq(double a,
                             double b)

Tests if a is smaller or equal to b.

Parameters:

a - a double

b - a double

Returns:

True if a is smaller or equal to b.

grOrEq

public static boolean grOrEq(double a,
                             double b)

Tests if a is greater or equal to b.

Parameters:

a - a double

b - a double

Returns:

True if a is greater or equal to b.

sm

public static boolean sm(double a,
                         double b)

Tests if a is smaller than b.

Parameters:

a - a double

b - a double

Returns:

True if a is smaller than b.

gr

public static boolean gr(double a,
                         double b)

Tests if a is greater than b.

Parameters:

a - a double

b - a double

Returns:

True if a is greater than b.

kthSmallestValue

public static double kthSmallestValue(int[] array,
                                      int k)

Returns the kth-smallest value in the array.

Parameters:

array - the array of integers

k - the value of k

Returns:

the kth-smallest value

kthSmallestValue

public static double kthSmallestValue(double[] array,
                                      int k)

Returns the kth-smallest value in the array

Parameters:

array - the array of double

k - the value of k

Returns:

the kth-smallest value

log2

public static double log2(double a)

Returns the logarithm of a for base 2.

Parameters:

a - a double

Returns:

the logarithm for base 2

maxIndex

public static int maxIndex(double[] doubles)

Returns index of maximum element in a given array of doubles. First maximum is returned.

Parameters:

doubles - the array of doubles

Returns:

the index of the maximum element

maxIndex

public static int maxIndex(int[] ints)

Returns index of maximum element in a given array of integers. First maximum is returned.

Parameters:

ints - the array of integers

Returns:

the index of the maximum element

mean

public static double mean(double[] vector)

Computes the mean for an array of doubles.

Parameters:

vector - the array

Returns:

the mean

minIndex

public static int minIndex(int[] ints)

Returns index of minimum element in a given array of integers. First minimum is returned.

Parameters:

ints - the array of integers

Returns:

the index of the minimum element

minIndex

public static int minIndex(double[] doubles)

Returns index of minimum element in a given array of doubles. First minimum is returned.

Parameters:

doubles - the array of doubles

Returns:

the index of the minimum element

normalize

public static void normalize(double[] doubles)

Normalizes the doubles in the array by their sum.

Parameters:

doubles - the array of double

Throws:

java.lang.IllegalArgumentException - if sum is Zero or NaN

normalize

public static void normalize(double[] doubles,
                             double sum)

Normalizes the doubles in the array using the given value.

Parameters:

doubles - the array of double

sum - the value by which the doubles are to be normalized

Throws:

java.lang.IllegalArgumentException - if sum is zero or NaN

logs2probs

public static double[] logs2probs(double[] a)

Converts an array containing the natural logarithms of probabilities stored in a vector back into probabilities. The probabilities are assumed to sum to one.

Parameters:

a - an array holding the natural logarithms of the probabilities

Returns:

the converted array

probToLogOdds

public static double probToLogOdds(double prob)

Returns the log-odds for a given probabilitiy.

Parameters:

prob - the probabilitiy

Returns:

the log-odds after the probability has been mapped to [Utils.SMALL, 1-Utils.SMALL]

round

public static int round(double value)

Rounds a double to the next nearest integer value. The JDK version of it doesn't work properly.

Parameters:

value - the double value

Returns:

the resulting integer value

probRound

public static int probRound(double value,
                            java.util.Random rand)

Rounds a double to the next nearest integer value in a probabilistic fashion (e.g. 0.8 has a 20% chance of being rounded down to 0 and a 80% chance of being rounded up to 1). In the limit, the average of the rounded numbers generated by this procedure should converge to the original double.

Parameters:

value - the double value

rand - the random number generator

Returns:

the resulting integer value

roundDouble

public static double roundDouble(double value,
                                 int afterDecimalPoint)

Rounds a double to the given number of decimal places.

Parameters:

value - the double value

afterDecimalPoint - the number of digits after the decimal point

Returns:

the double rounded to the given precision

sort

public static int[] sort(int[] array)

Sorts a given array of integers in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. The sort is stable. (Equal elements remain in their original order.)

Parameters:

array - this array is not changed by the method!

Returns:

an array of integers with the positions in the sorted array.

sort

public static int[] sort(double[] array)

Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. NOTE THESE CHANGES: the sort is no longer stable and it doesn't use safe floating-point comparisons anymore. Occurrences of Double.NaN are treated as Double.MAX_VALUE

Parameters:

array - this array is not changed by the method!

Returns:

an array of integers with the positions in the sorted array.

stableSort

public static int[] stableSort(double[] array)

Sorts a given array of doubles in ascending order and returns an array of integers with the positions of the elements of the original array in the sorted array. The sort is stable (Equal elements remain in their original order.) Occurrences of Double.NaN are treated as Double.MAX_VALUE

Parameters:

array - this array is not changed by the method!

Returns:

an array of integers with the positions in the sorted array.

variance

public static double variance(double[] vector)

Computes the variance for an array of doubles.

Parameters:

vector - the array

Returns:

the variance

sum

public static double sum(double[] doubles)

Computes the sum of the elements of an array of doubles.

Parameters:

doubles - the array of double

Returns:

the sum of the elements

sum

public static int sum(int[] ints)

Computes the sum of the elements of an array of integers.

Parameters:

ints - the array of integers

Returns:

the sum of the elements

xlogx

public static double xlogx(int c)

Returns c*log2(c) for a given integer value c.

Parameters:

c - an integer value

Returns:

c*log2(c) (but is careful to return 0 if c is 0)

main

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

Main method for testing this class.

Parameters:

ops - some dummy options