edu.stanford.rsl.conrad.utils

Class FloatArrayUtil

java.lang.Object

edu.stanford.rsl.conrad.utils.FloatArrayUtil

public abstract class FloatArrayUtil
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
FloatArrayUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static float[]	add(float[] sum, float toAdd) Adds a constant to the first array
static void	add(float[] sum, float[] toAdd) Adds one array to the first array
static float	computeAverageIncrement(float[] array) Computes the average increment of the array
static float	computeMean(float[] array) Computes the mean value of a given array
static float	computeMean(float[] values, int start, int end) computes the mean of the array "values" on the interval [start, end].
static float	computeMeanSquareError(float[] x, float[] y) computes the mean square error of array x to array y
static float	computeRootMeanSquareError(float[] x, float[] y) computes the root mean square error of array x to array y
static float	computeSSIMArrays(float[] x, float[] y) computes the correlation coefficient between two arrays after Pearson
static float	computeStddev(float[] array, float mean) Computes the standard deviation given an array and its mean value
static float	computeStddev(float[] array, float mean, int start, int end)
static float	concordanceCorrelateArrays(float[] x, float[] y) computes the concordance correlation coefficient between two arrays
static float[]	convolve(float[] input, float[] kernel) Performs a 1-D convolution of the input array with the kernel array. New array will be only of size
static float	correlateArrays(float[] x, float[] y) computes the correlation coefficient between two arrays after Pearson
static float	covarianceOfArrays(float[] x, float[] y) computes the covariance between two arrays
static float[]	divide(float[] array, float divident) Divides all entries of array by divident.
static float[]	divide(float[] array, float[] divident) Divides all entries of the two arrays element by element. Works in place and overwrites array.
static void	exp(float[] array) Uses Math.exp() on all elements of the array Works in place and overwrites array.
static int	findClosestIndex(float x, float[] array) returns the closest index in the array to the given value
static void	forceSymmetryComplexDoubleArray(float[] array) Forces an complex float array to be symmetric.
static void	forceSymmetryRealArray(float[] array) Forces a real float array to be symmetric.
static float[]	gaussianFilter(float[] weights, float sigma) Gaussian smoothing of the elements of the array "weights"
static boolean	isNaN(float[] array) tests if any of the values in the given array is NaN
static void	log(float[] array) Uses Math.log() on all elements of the array Works in place and overwrites array.
static float[]	meanFilter(float[] weights, int context) Performs mean filtering of the array.
static float[]	min(float[] array, float min)
static float[]	minAndMaxOfArray(float[] array) Returns the minimal and the maximal value in a given array
static float	minOfArray(float[] array) Returns the minimal value in a given array
static float[]	multiply(float[] array, float factor) Multiplies all entries of array by factor.
static void	multiply(float[] array, float[] array2) Multiplies all entries of the two arrays element by element. Works in place and overwrites array.
static float[]	pow(float[] array, float exp) calls Math.pow for each element of the array
static void	print(float[] array) Prints the array on standard out.
static void	print(float[] array, java.text.NumberFormat nf) Prints the contents of the float array on standard out.
static void	print(java.lang.String name, float[] array) Prints the array on standard out.
static void	print(java.lang.String name, float[] array, java.text.NumberFormat nf) Prints the array on standard out and denotes the arrays name.
static void	removeOutliers(float[] weights, float threshold) Removes outliers from the array which differ more than threshold from the last value.
static void	saveForVisualization(int imageNumber, float[] array) Stores an array for later visualization at index imageNumber
static void	suppressCenter(float[] weights, int threshold)
static java.lang.String	toString(float[] array) Converts the array to a String representation.
static java.lang.String	toString(float[] array, java.lang.String delimiter) Converts the array to a String representation.
static ij.ImagePlus	visualizeBufferedArrays(java.lang.String title) Displays the arrays stored with "saveForVisualization" as ImagePlus.

Methods inherited from class java.lang.Object

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

Constructor Detail

FloatArrayUtil

public FloatArrayUtil()

Method Detail

saveForVisualization

public static void saveForVisualization(int imageNumber,
                        float[] array)

Stores an array for later visualization at index imageNumber

Parameters:

imageNumber - the number

array - the array

convolve

public static float[] convolve(float[] input,
               float[] kernel)

Performs a 1-D convolution of the input array with the kernel array.
New array will be only of size

 output.lenght = input.length - (2 * (kernel.length/2));
 

(Note that integer arithmetic is used here)

Parameters:

input - the array to be convolved

kernel - the kernel

Returns:

the output array.

visualizeBufferedArrays

public static ij.ImagePlus visualizeBufferedArrays(java.lang.String title)

Displays the arrays stored with "saveForVisualization" as ImagePlus.

Parameters:

title - the title of the ImagePlus

Returns:

the reference to the ImagePlus

See Also:

saveForVisualization(int imageNumber, float [] array)

forceSymmetryComplexDoubleArray

public static void forceSymmetryComplexDoubleArray(float[] array)

Forces an complex float array to be symmetric. Left / first half of the array is mirrored to the right / second half

Parameters:

array - the complex array

isNaN

public static boolean isNaN(float[] array)

tests if any of the values in the given array is NaN

Parameters:

array -

Returns:

true if the array contains at least one entry with NaN

forceSymmetryRealArray

public static void forceSymmetryRealArray(float[] array)

Forces a real float array to be symmetric. Left / first half of the array is mirrored to the right / second half

Parameters:

array - the real array

findClosestIndex

public static int findClosestIndex(float x,
                   float[] array)

returns the closest index in the array to the given value

Parameters:

x - the value

array - the array

Returns:

the desired index in the array

covarianceOfArrays

public static float covarianceOfArrays(float[] x,
                       float[] y)

computes the covariance between two arrays

Parameters:

x - the one array

y - the other array

Returns:

the correlation

correlateArrays

public static float correlateArrays(float[] x,
                    float[] y)

computes the correlation coefficient between two arrays after Pearson

Parameters:

x - the one array

y - the other array

Returns:

the correlation

computeSSIMArrays

public static float computeSSIMArrays(float[] x,
                      float[] y)

computes the correlation coefficient between two arrays after Pearson

Parameters:

x - the one array

y - the other array

Returns:

the correlation

concordanceCorrelateArrays

public static float concordanceCorrelateArrays(float[] x,
                               float[] y)

computes the concordance correlation coefficient between two arrays

Parameters:

x - the one array

y - the other array

Returns:

the correlation

computeMeanSquareError

public static float computeMeanSquareError(float[] x,
                           float[] y)

computes the mean square error of array x to array y

Parameters:

x - the one array

y - the other array

Returns:

the mean square error

computeRootMeanSquareError

public static float computeRootMeanSquareError(float[] x,
                               float[] y)

computes the root mean square error of array x to array y

Parameters:

x - the one array

y - the other array

Returns:

the root mean square error.

suppressCenter

public static void suppressCenter(float[] weights,
                  int threshold)

removeOutliers

public static void removeOutliers(float[] weights,
                  float threshold)

Removes outliers from the array which differ more than threshold from the last value.

Parameters:

weights - the weight

threshold - the threshold

computeMean

public static float computeMean(float[] values,
                int start,
                int end)

computes the mean of the array "values" on the interval [start, end].

Parameters:

values - the array

start - the start index

end - the end index

Returns:

the mean value

computeAverageIncrement

public static float computeAverageIncrement(float[] array)

Computes the average increment of the array

Parameters:

array - the array

Returns:

the average increment

meanFilter

public static float[] meanFilter(float[] weights,
                 int context)

Performs mean filtering of the array.

Parameters:

weights - the array

context - the context to be used for smoothing (from -context/2 to context/2)

Returns:

the smoothed array

gaussianFilter

public static float[] gaussianFilter(float[] weights,
                     float sigma)

Gaussian smoothing of the elements of the array "weights"

Parameters:

weights - the array

sigma - the standard deviation

Returns:

the smoothed array

computeStddev

public static float computeStddev(float[] array,
                  float mean)

Computes the standard deviation given an array and its mean value

Parameters:

array - the array

mean - the mean value of the array

Returns:

the standard deviation

computeStddev

public static float computeStddev(float[] array,
                  float mean,
                  int start,
                  int end)

computeMean

public static float computeMean(float[] array)

Computes the mean value of a given array

Parameters:

array - the array

Returns:

the mean value as float

minAndMaxOfArray

public static float[] minAndMaxOfArray(float[] array)

Returns the minimal and the maximal value in a given array

Parameters:

array - the array

Returns:

an array with minimal and maximal value

minOfArray

public static float minOfArray(float[] array)

Returns the minimal value in a given array

Parameters:

array - the array

Returns:

the minimal value

add

public static void add(float[] sum,
       float[] toAdd)

Adds one array to the first array

Parameters:

sum - the first array

toAdd - the array to add

add

public static float[] add(float[] sum,
          float toAdd)

Adds a constant to the first array

Parameters:

sum - the first array

toAdd - the constant to add

divide

public static float[] divide(float[] array,
             float divident)

Divides all entries of array by divident.

Parameters:

array - the array

divident - the number used for division.

multiply

public static float[] multiply(float[] array,
               float factor)

Multiplies all entries of array by factor.

Parameters:

array - the array

factor - the number used for multiplication.

multiply

public static void multiply(float[] array,
            float[] array2)

Multiplies all entries of the two arrays element by element.
Works in place and overwrites array.

Parameters:

array - the array

array2 - the other array.

exp

public static void exp(float[] array)

Uses Math.exp() on all elements of the array Works in place and overwrites array.

Parameters:

array - the array

divide

public static float[] divide(float[] array,
             float[] divident)

Divides all entries of the two arrays element by element.
Works in place and overwrites array.

Parameters:

array - the array

divident - the other array.

log

public static void log(float[] array)

Uses Math.log() on all elements of the array Works in place and overwrites array.

Parameters:

array - the array

print

public static void print(float[] array,
         java.text.NumberFormat nf)

Prints the contents of the float array on standard out.

Parameters:

array -

nf - the NumberFormat

print

public static void print(java.lang.String name,
         float[] array,
         java.text.NumberFormat nf)

Prints the array on standard out and denotes the arrays name.

Parameters:

name - the name

array - the array

nf - the number format

print

public static void print(java.lang.String name,
         float[] array)

Prints the array on standard out. Uses NumberFormat.getInstance() for number formatting

Parameters:

name - the name

array - the array

print

public static void print(float[] array)

Prints the array on standard out. Uses NumberFormat.getInstance() for number formatting

Parameters:

array - the array

pow

public static float[] pow(float[] array,
          float exp)

calls Math.pow for each element of the array

Parameters:

array -

exp - the exponent.

Returns:

reference to the input array

min

public static float[] min(float[] array,
          float min)

toString

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

Converts the array to a String representation. Calls toString(array, " ").

Parameters:

array - the array

Returns:

the String representation

See Also:

toString(float[],String)

toString

public static java.lang.String toString(float[] array,
                        java.lang.String delimiter)

Converts the array to a String representation. delimiter is used to connect the elements of the array.

Parameters:

array - the array

delimiter - the delimiter

Returns:

the String representation