ArrayUtil

java.lang.Object
- mcib3d.utils.ArrayUtil

Direct Known Subclasses:

HistogramUtil
```
public class ArrayUtil
extends java.lang.Object
```
class allowing :
storage of arrays with util function such as statistics and sorting

Constructor Summary

Constructors
Constructor and Description
`ArrayUtil(java.util.ArrayList<java.lang.Double> list)`
`ArrayUtil(double[] data)` constructeur
`ArrayUtil(int size)` constructeur
`ArrayUtil(int[] data)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`boolean`	`addValue(int position, double value)` Addition a value at a index
`void`	`addValueArray(ArrayUtil tabToAdd)`
`void`	`concat(ArrayUtil tabToAdd)` concat an array to the end
`double`	`convolve(double[] kernel, double D)` Convolution with a kernel
`int`	`countValue(double val)`
`int`	`countValueAbove(double val)`
`ArrayUtil`	`distinctValues()` Array with only distinct values (sorted)
`void`	`divideAll(double value)`
`ImagePlus`	`drawBar(int scale)` drawing of the array as an image
`void`	`fillRange(int start, int end, int step)`
`void`	`fillValue(double val)`
`static double[]`	`fitGaussian(double[] values, double initSD, int maxR)` Fit a gaussian to the values (radial distribution)
`void`	`fromArrayListDouble(java.util.ArrayList<java.lang.Double> arr)`
`void`	`fromArrayListInt(java.util.ArrayList<java.lang.Integer> arr)`
`double[]`	`getArray()` Gets the array attribute of the ArrayUtil object
`int[]`	`getArrayInt()`
`java.util.ArrayList<java.lang.Double>`	`getArrayList()`
`ArrayUtil`	`getCopy()` Gets the copy of the ArrayUtil object
`ArrayUtil`	`getDifferenceNext()`
`ArrayUtil`	`getDifferenceNextAbs()`
`int`	`getFirstLocalExtrema(double thresholdMax, double thresholdMin)`
`int`	`getFirstLocalMaxima(int start, double threshold)`
`int`	`getFirstLocalMinima(double threshold)`
`ArrayUtil[]`	`getHistogram(int nBins)`
`ArrayUtil`	`getIntegerHistogram()`
`double`	`getKurtosis()` Kurtosis, order 4
`int`	`getLimitInf(int th)` First encoutered value not zero, starting from th
`int`	`getLimitSup()` Last index whose value is not zero
`double`	`getMaxAbsDifference(ArrayUtil hmean)`
`double`	`getMaximum()` The maximum value
`double[]`	`getMaximumAbove(double th)` The maximum value
`double`	`getMaximumBelow(double th)`
`int`	`getMaximumIndex()` The maximum value
`double[]`	`getMaximumStarting(int th)`
`double`	`getMean()` Average value
`double`	`getMinimum()` The minimum value
`double`	`getMinimumAbove(double th)` Gets the minimum value above a threshold
`int`	`getMinimumIndex()`
`double[]`	`getMinMax()`
`int`	`getMode()`
`int`	`getModeNonZero()`
`Plot`	`getPlot()`
`Plot`	`getPlot(java.lang.String title, java.lang.String xLabel, java.lang.String yLabel)`
`int`	`getSize()` Deprecated. see size() get the number of elements
`double`	`getSkewness()` skewness, order 3
`double`	`getStdDev()` standard deviation
`ArrayUtil`	`getSubTabUtil(int startIndex, int newSize)` extract a sub-array from this array
`double`	`getSum()` sum of all elements
`double`	`getValue(int pos)` get value at an index
`int`	`getValueInt(int pos)`
`double`	`getVariance()` Variance value (not biased)
`double`	`getVariance2()` Variance value (not biased) fast version
`boolean`	`hasOneValue(java.util.ArrayList vals)` One of the values are in the array ?
`boolean`	`hasOneValueInt(java.util.ArrayList vals)` One of the values are in the array ? For int values (does not work if ArrayList is int and values is double)
`boolean`	`hasOnlyValue(int val)` test if array has only one particular value
`boolean`	`hasOnlyValuesInt(java.util.ArrayList vals)` test if array has only particular values
`boolean`	`hasValue(int val)` The value is in the array ?
`int`	`indexOf(double value)`
`int`	`indexOfSumPercent(double percent)` Index to get x % of the values
`void`	`insertValues(int pos, ArrayUtil tmp)`
`boolean`	`isEmpty()`
`boolean`	`isEqual(ArrayUtil other)` test if two arrays are identical
`boolean`	`isEqual(ArrayUtil other, int begin, int end)` test if two arrays are identical between two indexes
`boolean`	`isMaximum(double val)`
`int`	`IsoData()` isodata algorithm (for histogram)
`boolean`	`isSorted()`
`static int[]`	`kMeans_Histogram1D(int[] histogram, int nbClasses, int thmin)` COPIED FROM ICY (A.
`ArrayUtil`	`localMean(int rad)` local mean filtering
`double`	`median()` Find median.
`double`	`medianSort()` The median (sorted array)
`boolean`	`putValue(int pos, double value)` put a value to a index
`void`	`removeValueAt(int index)` remove a value at a position
`int`	`removeValues(double val)`
`void`	`reverse()`
`void`	`saveArray(java.lang.String dir, java.lang.String file, java.lang.String header)`
`void`	`setSize(int size)` new size of the array (can incresase size of array)
`void`	`setValues(ArrayUtil tmp)` put values inside an array
`void`	`shuffle()` random mix of the values
`int`	`size()`
`void`	`sort()`
`int[]`	`sortIndexShellMeitzner()` Get the indexes of sorted array (Shell-Meitzner algorithm) do not sort the array
`void`	`sortJava()`
`void`	`sortMultithread()`
`void`	`sortShellMeitzner()` Sort the array (Shell-Meitzner algorithm) increasing
`java.lang.String`	`toString()` information to be displayed

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

- Constructor Detail
  - ArrayUtil
```
public ArrayUtil(int size)
```
    constructeur
    
    Parameters:
    
    size - number of elements
  - ArrayUtil
```
public ArrayUtil(double[] data)
```
    constructeur
    
    Parameters:
    
    data - double array
  - ArrayUtil
```
public ArrayUtil(int[] data)
```
  - ArrayUtil
```
public ArrayUtil(java.util.ArrayList<java.lang.Double> list)
```
- Method Detail
  - fitGaussian
```
public static double[] fitGaussian(double[] values,
                                   double initSD,
                                   int maxR)
```
    Fit a gaussian to the values (radial distribution)
    
    Parameters:
    
    values - to fit
    
    initSD -
    
    maxR - maximum interval
    
    Returns:
    
    the gaussian fitted values
  - kMeans_Histogram1D
```
public static int[] kMeans_Histogram1D(int[] histogram,
                                       int nbClasses,
                                       int thmin)
```
    COPIED FROM ICY (A. DUFOUR) KMeans classification algorithm, optimized for 1D histogram data. The algorithm is initialized by spacing the class centers equally
    
    Parameters:
    
    histogram - the histogram to classify
    
    nbClasses - the number of classes to extract
    
    Returns:
    
    the optimal class centers after convergence
  - fromArrayListInt
```
public void fromArrayListInt(java.util.ArrayList<java.lang.Integer> arr)
```
  - fromArrayListDouble
```
public void fromArrayListDouble(java.util.ArrayList<java.lang.Double> arr)
```
  - putValue
```
public boolean putValue(int pos,
                        double value)
```
    put a value to a index
    
    Parameters:
    
    pos - position in the array
    
    value - value to put
    
    Returns:
    
    false if position does not exist
  - getValue
```
public double getValue(int pos)
```
    get value at an index
    
    Parameters:
    
    pos - position in the array
    
    Returns:
    
    the value, or NaN if does not exist
  - getValueInt
```
public int getValueInt(int pos)
```
  - getSize
```
public int getSize()
```
    Deprecated. see size() get the number of elements
    
    Returns:
    
    number of elements
  - setSize
```
public void setSize(int size)
```
    new size of the array (can incresase size of array)
    
    Parameters:
    
    size - The new size value
  - size
```
public int size()
```
  - getArray
```
public double[] getArray()
```
    Gets the array attribute of the ArrayUtil object
    
    Returns:
    
    The array value
  - getArrayInt
```
public int[] getArrayInt()
```
  - getArrayList
```
public java.util.ArrayList<java.lang.Double> getArrayList()
```
  - fillValue
```
public void fillValue(double val)
```
    Parameters:
    
    val -
  - fillRange
```
public void fillRange(int start,
                      int end,
                      int step)
```
  - getMaximum
```
public double getMaximum()
```
    The maximum value
    
    Returns:
    
    max value
  - getMaximumAbove
```
public double[] getMaximumAbove(double th)
```
    The maximum value
    
    Returns:
    
    max value
  - getMaximumStarting
```
public double[] getMaximumStarting(int th)
```
  - getMaximumIndex
```
public int getMaximumIndex()
```
    The maximum value
    
    Returns:
    
    max value
  - getFirstLocalMaxima
```
public int getFirstLocalMaxima(int start,
                               double threshold)
```
  - getFirstLocalMinima
```
public int getFirstLocalMinima(double threshold)
```
  - getFirstLocalExtrema
```
public int getFirstLocalExtrema(double thresholdMax,
                                double thresholdMin)
```
  - isMaximum
```
public boolean isMaximum(double val)
```
    Parameters:
    
    val -
    
    Returns:
  - getMaximumBelow
```
public double getMaximumBelow(double th)
```
    Parameters:
    
    th -
    
    Returns:
  - getLimitSup
```
public int getLimitSup()
```
    Last index whose value is not zero
    
    Returns:
    
    The limitSup value
  - getLimitInf
```
public int getLimitInf(int th)
```
    First encoutered value not zero, starting from th
    
    Parameters:
    
    th - minimum index
    
    Returns:
    
    The limitInf value
  - getMinimum
```
public double getMinimum()
```
    The minimum value
    
    Returns:
    
    min value
  - getMinimumIndex
```
public int getMinimumIndex()
```
  - getMinMax
```
public double[] getMinMax()
```
  - getMinimumAbove
```
public double getMinimumAbove(double th)
```
    Gets the minimum value above a threshold
    
    Parameters:
    
    th - the threshold
    
    Returns:
    
    The minimumAbove value
  - getMean
```
public double getMean()
```
    Average value
    
    Returns:
    
    average value
  - getSum
```
public double getSum()
```
    sum of all elements
    
    Returns:
    
    sum
  - getStdDev
```
public double getStdDev()
```
    standard deviation
    
    Returns:
    
    std dev
  - getSkewness
```
public double getSkewness()
```
    skewness, order 3
    
    Returns:
    
    skewness value (- for right distribution, 0 symmetric, + left distribution)
  - getKurtosis
```
public double getKurtosis()
```
    Kurtosis, order 4
    
    Returns:
    
    kurtosis (peakiness)
  - getVariance
```
public double getVariance()
```
    Variance value (not biased)
    
    Returns:
    
    variance
  - getVariance2
```
public double getVariance2()
```
    Variance value (not biased) fast version
    
    Returns:
    
    variance
  - getMaxAbsDifference
```
public double getMaxAbsDifference(ArrayUtil hmean)
```
    Parameters:
    
    hmean -
    
    Returns:
  - countValue
```
public int countValue(double val)
```
  - countValueAbove
```
public int countValueAbove(double val)
```
  - distinctValues
```
public ArrayUtil distinctValues()
```
    Array with only distinct values (sorted)
    
    Returns:
  - localMean
```
public ArrayUtil localMean(int rad)
```
    local mean filtering
    
    Parameters:
    
    rad - radius for filtering
    
    Returns:
    
    filtered array
  - addValue
```
public boolean addValue(int position,
                        double value)
```
    Addition a value at a index
    
    Parameters:
    
    position - the position index
    
    value - the value to add
    
    Returns:
    
    true if position < size
  - divideAll
```
public void divideAll(double value)
```
    Parameters:
    
    value -
  - isSorted
```
public boolean isSorted()
```
    Returns:
  - sortJava
```
public void sortJava()
```
  - sort
```
public void sort()
```
  - sortMultithread
```
public void sortMultithread()
```
  - sortShellMeitzner
```
public void sortShellMeitzner()
```
    Sort the array (Shell-Meitzner algorithm) increasing
  - sortIndexShellMeitzner
```
public int[] sortIndexShellMeitzner()
```
    Get the indexes of sorted array (Shell-Meitzner algorithm) do not sort the array
    
    Returns:
    
    the sorted index
  - medianSort
```
public double medianSort()
```
    The median (sorted array)
    
    Returns:
    
    mediane
  - median
```
public double median()
```
    Find median. Modified algorithm according to http://www.geocities.com/zabrodskyvlada/3alg.html Contributed by HeinzKlar. (copied form ij.plugin.filter.rankfilters
    
    Returns:
    
    Median value
  - convolve
```
public double convolve(double[] kernel,
                       double D)
```
    Convolution with a kernel
    
    Parameters:
    
    kernel - the kernel
    
    D - the divisor
    
    Returns:
    
    the convolved value
  - indexOf
```
public int indexOf(double value)
```
    Parameters:
    
    value -
    
    Returns:
  - indexOfSumPercent
```
public int indexOfSumPercent(double percent)
```
    Index to get x % of the values
    
    Parameters:
    
    percent - percentage(1.0=100; 0.5=50% ...)
    
    Returns:
    
    index in the array
  - hasValue
```
public boolean hasValue(int val)
```
    The value is in the array ?
    
    Parameters:
    
    val - the value
    
    Returns:
    
    true if value in the array
  - hasOneValue
```
public boolean hasOneValue(java.util.ArrayList vals)
```
    One of the values are in the array ?
    
    Parameters:
    
    vals - the values
    
    Returns:
    
    true if one of the values is in the array
  - hasOneValueInt
```
public boolean hasOneValueInt(java.util.ArrayList vals)
```
    One of the values are in the array ? For int values (does not work if ArrayList is int and values is double)
    
    Parameters:
    
    vals - the values
    
    Returns:
    
    true if one of the values is in the array
  - hasOnlyValue
```
public boolean hasOnlyValue(int val)
```
    test if array has only one particular value
    
    Parameters:
    
    val - the value
    
    Returns:
    
    true if only this value is inside the array
  - hasOnlyValuesInt
```
public boolean hasOnlyValuesInt(java.util.ArrayList vals)
```
    test if array has only particular values
    
    Parameters:
    
    vals - the value
    
    Returns:
    
    true if only this value is inside the array
  - IsoData
```
public int IsoData()
```
    isodata algorithm (for histogram)
    
    Returns:
    
    the computed isodata value
  - drawBar
```
public ImagePlus drawBar(int scale)
```
    drawing of the array as an image
    
    Parameters:
    
    scale - scale value
  - shuffle
```
public void shuffle()
```
    random mix of the values
  - setValues
```
public void setValues(ArrayUtil tmp)
```
    put values inside an array
    
    Parameters:
    
    tmp - the array of values to put
  - insertValues
```
public void insertValues(int pos,
                         ArrayUtil tmp)
```
  - isEqual
```
public boolean isEqual(ArrayUtil other)
```
    test if two arrays are identical
    
    Parameters:
    
    other - the other array
    
    Returns:
    
    true if arrays are equal
  - isEmpty
```
public boolean isEmpty()
```
  - isEqual
```
public boolean isEqual(ArrayUtil other,
                       int begin,
                       int end)
```
    test if two arrays are identical between two indexes
    
    Parameters:
    
    other - the other array
    
    begin - start index
    
    end - end index
    
    Returns:
    
    The equal value
  - getCopy
```
public ArrayUtil getCopy()
```
    Gets the copy of the ArrayUtil object
    
    Returns:
    
    The copy array
  - toString
```
public java.lang.String toString()
```
    information to be displayed
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    text
  - removeValueAt
```
public void removeValueAt(int index)
```
    remove a value at a position
    
    Parameters:
    
    index - the position index
  - removeValues
```
public int removeValues(double val)
```
  - addValueArray
```
public void addValueArray(ArrayUtil tabToAdd)
```
    Parameters:
    
    tabToAdd -
  - getPlot
```
public Plot getPlot()
```
  - getPlot
```
public Plot getPlot(java.lang.String title,
                    java.lang.String xLabel,
                    java.lang.String yLabel)
```
  - concat
```
public void concat(ArrayUtil tabToAdd)
```
    concat an array to the end
    
    Parameters:
    
    tabToAdd - the array to concat
  - reverse
```
public void reverse()
```
  - getSubTabUtil
```
public ArrayUtil getSubTabUtil(int startIndex,
                               int newSize)
```
    extract a sub-array from this array
    
    Parameters:
    
    startIndex - start index
    
    newSize - new size
    
    Returns:
    
    The subTabUtil value
  - getDifferenceNext
```
public ArrayUtil getDifferenceNext()
```
  - getDifferenceNextAbs
```
public ArrayUtil getDifferenceNextAbs()
```
  - getHistogram
```
public ArrayUtil[] getHistogram(int nBins)
```
  - getIntegerHistogram
```
public ArrayUtil getIntegerHistogram()
```
    Returns:
  - getMode
```
public int getMode()
```
  - getModeNonZero
```
public int getModeNonZero()
```
  - saveArray
```
public void saveArray(java.lang.String dir,
                      java.lang.String file,
                      java.lang.String header)
```

Class ArrayUtil

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ArrayUtil

ArrayUtil

ArrayUtil

ArrayUtil

Method Detail

fitGaussian

kMeans_Histogram1D

fromArrayListInt

fromArrayListDouble

putValue

getValue

getValueInt

getSize

setSize

size

getArray

getArrayInt

getArrayList

fillValue

fillRange

getMaximum

getMaximumAbove

getMaximumStarting

getMaximumIndex

getFirstLocalMaxima

getFirstLocalMinima

getFirstLocalExtrema

isMaximum

getMaximumBelow

getLimitSup

getLimitInf

getMinimum

getMinimumIndex

getMinMax

getMinimumAbove

getMean

getSum

getStdDev

getSkewness

getKurtosis

getVariance

getVariance2

getMaxAbsDifference

countValue

countValueAbove

distinctValues

localMean

addValue

divideAll

isSorted

sortJava

sort

sortMultithread

sortShellMeitzner

sortIndexShellMeitzner

medianSort

median

convolve

indexOf

indexOfSumPercent

hasValue

hasOneValue

hasOneValueInt

hasOnlyValue

hasOnlyValuesInt

IsoData

drawBar

shuffle

setValues

insertValues

isEqual

isEmpty

isEqual

getCopy

toString