Util (ImgLib2 Javadocs 0-SNAPSHOT API)

java.lang.Object
- net.imglib2.util.Util

```
public class Util
extends Object
```
A collection of general-purpose utility methods for working with ImgLib2 data structures.

Author:

Stephan Preibisch, Stephan Saalfeld, Curtis Rueden

Constructor Summary

Constructors
Constructor and Description

Util()

Constructors
Constructor and Description
`Util()`

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`static double[]`	`asDoubleArray(Img<? extends RealType<?>> image)` Returns the pixels of an image of RealType as array of doubles.
`static double[]`	`asDoubleArray(Iterable<? extends RealType<?>> iterable)` Returns the content of `Iterable<RealType>` as array of doubles.
`static double[]`	`asDoubleArray(RandomAccessibleInterval<? extends RealType<?>> rai)` Returns the pixels of an RandomAccessibleInterval of RealType as array of doubles.
`static double`	`average(double[] values)`
`static float`	`average(float[] values)`
`static double`	`averageDouble(List<Double> values)`
`static float`	`averageFloat(List<Float> values)`
`static int`	`combineHash(int hash1, int hash2)`
`static double[]`	`createGaussianKernel1DDouble(double sigma, boolean normalize)` This method creates a gaussian kernel
`static double`	`distance(long[] position1, long[] position2)`
`static double`	`distance(RealLocalizable position1, RealLocalizable position2)`
`static boolean`	`equalIterationOrder(IterableInterval<?>... intervals)` Checks whether n `IterableInterval` have the same iteration order.
`static <T> T[]`	`genericArray(int length)` Deprecated.
`static double[]`	`getArrayFromValue(double value, int numDimensions)`
`static float[]`	`getArrayFromValue(float value, int numDimensions)`
`static int[]`	`getArrayFromValue(int value, int numDimensions)`
`static long[]`	`getArrayFromValue(long value, int numDimensions)`
`static <T extends NativeType<T>> ImgFactory<T>`	`getArrayOrCellImgFactory(Dimensions targetSize, int targetCellSize, T type)` Create an `ArrayImgFactory` if an image of the requested `targetSize` could be held in an `ArrayImg`.
`static <T extends NativeType<T>> ImgFactory<T>`	`getArrayOrCellImgFactory(Dimensions targetSize, T type)` Create an `ArrayImgFactory` if an image of the requested `targetSize` could be held in an `ArrayImg`.
`static int`	`getSuggestedKernelDiameter(double sigma)`
`static <T> ImgFactory<T>`	`getSuitableImgFactory(Dimensions targetSize, T type)` Create an appropriate `ImgFactory` for the requested `targetSize` and `type`.
`static <T,F extends Interval & RandomAccessible<T>> T`	`getTypeFromInterval(F rai)` Gets an instance of T from the `RandomAccessibleInterval` by querying the value at the min coordinate
`static <T,F extends RealInterval & RealRandomAccessible<T>> T`	`getTypeFromRealInterval(F rai)` Gets an instance of T from the `RandomAccessibleInterval` by querying the value at the min coordinate
`static double`	`gLog(double z, double c)`
`static float`	`gLog(float z, float c)`
`static double`	`gLogInv(double w, double c)`
`static double`	`gLogInv(float w, float c)`
`static <T extends ValueEquals<U>,U> boolean`	`imagesEqual(RandomAccessibleInterval<? extends T> a, RandomAccessibleInterval<? extends U> b)` Checks if both images have equal intervals and content.
`static <T,U> boolean`	`imagesEqual(RandomAccessibleInterval<? extends T> a, RandomAccessibleInterval<? extends U> b, BiPredicate<T,U> pixelEquals)` Checks if both images have equal intervals and content.
`static long[]`	`int2long(int[] i)`
`static boolean`	`isApproxEqual(double a, double b, double threshold)`
`static boolean`	`isApproxEqual(float a, float b, float threshold)`
`static int`	`ldu(int v)` (Hopefully) fast floor log₂ of an unsigned(!) integer value.
`static boolean`	`locationsEqual(Localizable l1, Localizable l2)` Determines whether the two `Localizable` objects have the same position, with `long` precision.
`static boolean`	`locationsEqual(RealLocalizable l1, RealLocalizable l2)` Determines whether the two `RealLocalizable` objects have the same position, with `double` precision.
`static double`	`log2(double value)`
`static int[]`	`long2int(long[] a)`
`static double`	`max(double[] values)`
`static void`	`max(double[] a, double[] b)` Writes max(a,b) into a
`static float`	`max(List<Float> values)`
`static <T extends Type<T> & Comparable<T>> T`	`max(T value1, T value2)`
`static double`	`median(double[] values)`
`static float`	`median(float[] values)`
`static long`	`median(long[] values)`
`static double`	`min(double[] values)`
`static void`	`min(double[] a, double[] b)` Writes min(a,b) into a
`static float`	`min(List<Float> values)`
`static <T extends Type<T> & Comparable<T>> T`	`min(T value1, T value2)`
`static double`	`percentile(double[] values, double percentile)` Computes the percentile of a collection of doubles (percentile 0.5 roughly corresponds to median)
`static int`	`pow(int a, int b)`
`static String`	`printCoordinates(boolean[] value)`
`static String`	`printCoordinates(double[] value)`
`static String`	`printCoordinates(float[] value)`
`static String`	`printCoordinates(int[] value)`
`static String`	`printCoordinates(long[] value)`
`static String`	`printCoordinates(RealLocalizable localizable)`
`static String`	`printInterval(Interval interval)`
`static void`	`quicksort(double[] data)`
`static void`	`quicksort(double[] data, int[] sortAlso, int left, int right)`
`static void`	`quicksort(double[] data, int left, int right)`
`static void`	`quicksort(float[] data)`
`static void`	`quicksort(float[] data, int left, int right)`
`static void`	`quicksort(long[] data)`
`static void`	`quicksort(long[] data, int left, int right)`
`static long`	`round(double value)`
`static int`	`round(float value)`
`static int`	`roundToInt(double value)`
`static int`	`roundToInt(float value)`
`static long`	`roundToLong(double value)`
`static long`	`roundToLong(float value)`
`static <T extends ValueEquals<T>> boolean`	`valueEqualsObject(T a, Object b)` This method should be used in implementations of `ValueEquals`, to override `Object.equals(Object)`.

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

Constructor Detail
- Util
```
public Util()
```

Method Detail

genericArray
```
@Deprecated
public static <T> T[] genericArray(int length)
```
Deprecated.

This does only work when T is erased to Object at call site.
See https://github.com/imglib/imglib2/issues/253

log2

public static double log2(double value)

getArrayFromValue

public static double[] getArrayFromValue(double value,
                                         int numDimensions)

getArrayFromValue

public static float[] getArrayFromValue(float value,
                                        int numDimensions)

getArrayFromValue

public static int[] getArrayFromValue(int value,
                                      int numDimensions)

getArrayFromValue

public static long[] getArrayFromValue(long value,
                                       int numDimensions)

distance

public static final double distance(RealLocalizable position1,
                                    RealLocalizable position2)

distance

public static final double distance(long[] position1,
                                    long[] position2)

percentile
```
public static double percentile(double[] values,
                                double percentile)
```
Computes the percentile of a collection of doubles (percentile 0.5 roughly corresponds to median)

Parameters:

values - - the values

percentile - - the percentile [0...1]

Returns:

the corresponding value

averageDouble

public static double averageDouble(List<Double> values)

averageFloat

public static float averageFloat(List<Float> values)

min

public static float min(List<Float> values)

max

public static float max(List<Float> values)

average

public static float average(float[] values)

average

public static double average(double[] values)

min

public static double min(double[] values)

max

public static double max(double[] values)

median

public static long median(long[] values)

median

public static double median(double[] values)

median

public static float median(float[] values)

quicksort

public static void quicksort(long[] data)

quicksort

public static void quicksort(long[] data,
                             int left,
                             int right)

quicksort

public static void quicksort(double[] data)

quicksort

public static void quicksort(double[] data,
                             int left,
                             int right)

quicksort

public static void quicksort(float[] data)

quicksort

public static void quicksort(float[] data,
                             int left,
                             int right)

quicksort

public static void quicksort(double[] data,
                             int[] sortAlso,
                             int left,
                             int right)

gLog

public static double gLog(double z,
                          double c)

gLog

public static float gLog(float z,
                         float c)

gLogInv

public static double gLogInv(double w,
                             double c)

gLogInv

public static double gLogInv(float w,
                             float c)

isApproxEqual

public static boolean isApproxEqual(float a,
                                    float b,
                                    float threshold)

isApproxEqual

public static boolean isApproxEqual(double a,
                                    double b,
                                    double threshold)

round
```
public static int round(float value)
```

round

public static long round(double value)

roundToInt

public static int roundToInt(float value)

roundToInt

public static int roundToInt(double value)

roundToLong

public static long roundToLong(float value)

roundToLong

public static long roundToLong(double value)

createGaussianKernel1DDouble
```
public static double[] createGaussianKernel1DDouble(double sigma,
                                                    boolean normalize)
```
This method creates a gaussian kernel

Parameters:

sigma - Standard Derivation of the gaussian function

normalize - Normalize integral of gaussian function to 1 or not...

Returns:

double[] The gaussian kernel

getSuggestedKernelDiameter

public static int getSuggestedKernelDiameter(double sigma)

printCoordinates

public static String printCoordinates(float[] value)

printCoordinates

public static String printCoordinates(double[] value)

printCoordinates

public static String printCoordinates(RealLocalizable localizable)

printInterval

public static String printInterval(Interval interval)

printCoordinates

public static String printCoordinates(int[] value)

printCoordinates

public static String printCoordinates(long[] value)

printCoordinates

public static String printCoordinates(boolean[] value)

pow

public static int pow(int a,
                      int b)

max

public static <T extends Type<T> & Comparable<T>> T max(T value1,
                                                        T value2)

min

public static <T extends Type<T> & Comparable<T>> T min(T value1,
                                                        T value2)

long2int

public static final int[] long2int(long[] a)

int2long

public static final long[] int2long(int[] i)

getTypeFromInterval
```
public static final <T,F extends Interval & RandomAccessible<T>> T getTypeFromInterval(F rai)
```
Gets an instance of T from the RandomAccessibleInterval by querying the value at the min coordinate

Type Parameters:

T - - the T

Parameters:

rai - - the RandomAccessibleInterval

Returns:

- an instance of T

getTypeFromRealInterval
```
public static final <T,F extends RealInterval & RealRandomAccessible<T>> T getTypeFromRealInterval(F rai)
```
Gets an instance of T from the RandomAccessibleInterval by querying the value at the min coordinate

Type Parameters:

T - - the T

Parameters:

rai - - the RandomAccessibleInterval

Returns:

- an instance of T

getArrayOrCellImgFactory
```
public static <T extends NativeType<T>> ImgFactory<T> getArrayOrCellImgFactory(Dimensions targetSize,
                                                                               T type)
```
Create an ArrayImgFactory if an image of the requested targetSize could be held in an ArrayImg. Otherwise return a CellImgFactory with as large as possible cell size.

Parameters:

targetSize - size of image that the factory should be able to create.

type - type of the factory.

Returns:

an ArrayImgFactory or a CellImgFactory.

getArrayOrCellImgFactory
```
public static <T extends NativeType<T>> ImgFactory<T> getArrayOrCellImgFactory(Dimensions targetSize,
                                                                               int targetCellSize,
                                                                               T type)
```
Create an ArrayImgFactory if an image of the requested targetSize could be held in an ArrayImg. Otherwise return a CellImgFactory with cell size targetCellSize (or as large as possible if targetCellSize is too large).

Parameters:

targetSize - size of image that the factory should be able to create.

targetCellSize - if a CellImgFactory is created, what should be the cell size.

type - type of the factory.

Returns:

an ArrayImgFactory or a CellImgFactory.

getSuitableImgFactory
```
public static <T> ImgFactory<T> getSuitableImgFactory(Dimensions targetSize,
                                                      T type)
```
Create an appropriate ImgFactory for the requested targetSize and type. If the target size is a Img, return its ImgFactory. If the type is a NativeType, then getArrayOrCellImgFactory(Dimensions, NativeType) is used; if not, a ListImgFactory is returned.

Parameters:

targetSize - size of image that the factory should be able to create.

type - type of the factory.

Returns:

an ArrayImgFactory, CellImgFactory or ListImgFactory as appropriate.

ldu
```
public static final int ldu(int v)
```
(Hopefully) fast floor log₂ of an unsigned(!) integer value.

Parameters:

v - unsigned integer

Returns:

floor log₂

equalIterationOrder
```
public static boolean equalIterationOrder(IterableInterval<?>... intervals)
```
Checks whether n IterableInterval have the same iteration order.

locationsEqual
```
public static boolean locationsEqual(Localizable l1,
                                     Localizable l2)
```
Determines whether the two Localizable objects have the same position, with long precision.
At first glance, this method may appear to be unnecessary, since there is also locationsEqual(RealLocalizable, RealLocalizable), which is more general. The difference is that this method compares the positions using Localizable.getLongPosition(int), which has higher precision in integer space than RealLocalizable.getDoublePosition(int) does, which is what the locationsEqual(RealLocalizable, RealLocalizable) method uses.

Parameters:

l1 - The first Localizable.

l2 - The second Localizable.

Returns:

True iff the positions are the same, including dimensionality.

See Also:

Localizable.getLongPosition(int)

locationsEqual
```
public static boolean locationsEqual(RealLocalizable l1,
                                     RealLocalizable l2)
```
Determines whether the two RealLocalizable objects have the same position, with double precision.

Parameters:

l1 - The first RealLocalizable.

l2 - The second RealLocalizable.

Returns:

True iff the positions are the same, including dimensionality.

See Also:

RealLocalizable.getDoublePosition(int)

imagesEqual

public static <T extends ValueEquals<U>,U> boolean imagesEqual(RandomAccessibleInterval<? extends T> a,
                                                               RandomAccessibleInterval<? extends U> b)

Checks if both images have equal intervals and content.

imagesEqual

public static <T,U> boolean imagesEqual(RandomAccessibleInterval<? extends T> a,
                                        RandomAccessibleInterval<? extends U> b,
                                        BiPredicate<T,U> pixelEquals)

Checks if both images have equal intervals and content. A predicate must be given to check if two pixels are equal.

min

public static final void min(double[] a,
                             double[] b)

Writes min(a,b) into a

Parameters:: a -; b -

max

public static final void max(double[] a,
                             double[] b)

Writes max(a,b) into a

Parameters:: a -; b -

asDoubleArray

public static double[] asDoubleArray(Iterable<? extends RealType<?>> iterable)

Returns the content of Iterable<RealType> as array of doubles.

asDoubleArray
```
public static double[] asDoubleArray(RandomAccessibleInterval<? extends RealType<?>> rai)
```
Returns the pixels of an RandomAccessibleInterval of RealType as array of doubles. The pixels are sorted in flat iteration order.

asDoubleArray
```
public static double[] asDoubleArray(Img<? extends RealType<?>> image)
```
Returns the pixels of an image of RealType as array of doubles. The pixels are sorted in flat iteration order.

valueEqualsObject

public static <T extends ValueEquals<T>> boolean valueEqualsObject(T a,
                                                                   Object b)

This method should be used in implementations of ValueEquals, to override Object.equals(Object).

See Also:: Object.equals(Object)

combineHash

public static int combineHash(int hash1,
                              int hash2)

Class Util

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Util

Method Detail

genericArray

log2

getArrayFromValue

getArrayFromValue

getArrayFromValue

getArrayFromValue

distance

distance

percentile

averageDouble

averageFloat

min

max

average

average

min

max

median

median

median

quicksort

quicksort

quicksort

quicksort

quicksort

quicksort

quicksort

gLog

gLog

gLogInv

gLogInv

isApproxEqual

isApproxEqual

round

round

roundToInt

roundToInt

roundToLong

roundToLong

createGaussianKernel1DDouble

getSuggestedKernelDiameter

printCoordinates

printCoordinates

printCoordinates

printInterval

printCoordinates

printCoordinates

printCoordinates

pow

max

min

long2int

int2long

getTypeFromInterval

getTypeFromRealInterval

getArrayOrCellImgFactory

getArrayOrCellImgFactory

getSuitableImgFactory

ldu

equalIterationOrder

locationsEqual

locationsEqual

imagesEqual

imagesEqual

min

max

asDoubleArray

asDoubleArray

asDoubleArray

valueEqualsObject

combineHash